In spite of the possibility that the world may not need another -omics word, we (relentlessly) coined “lexomics” and defined it as follows:
Lexomics [leks-ohm-iks]: The study of the TEXTS of genomes with the goal of integrating all of the information coded within (the genes, the regulatory sequences, the topology, the dynamic changes in relationships) ANALOGOUS to a LITERATE READING of genomes with comprehension and appreciation for the COMPLEX, COMBINATORIC, SYNERGIES required to build whole organisms.
The framework or “working metaphor” for our research is Linguistics. We are developing our software tools as though they were modules in a comprehensive lexicon or concordance to genomic sequences. We have found this metaphor to be productive in several respects:
- A linguistic metaphor allows us to quickly explain our research to undergraduates either in a classroom setting or in our research laboratory where undergraduates write most of our software.
- e.g. The genes may be considered as simple imperative statements: “Do this” “Make that”
- However, the subtle grammar-by which we get exactly two eyes, positioned correctly on our faces–is in the regulatory sequences: “Do this” TWICE “Do this” on the face only “Do this” during the embryo stage
- e.g. The genes may be considered as “words” in a dictionary. If you gave ten different people a dictionary (or word list) and asked them to write an essay (or even a sentence) on the same specific topic–You would get ten different essays (or even ten different sentences) The DIFFERENCES are in the grammar and syntax. The cat sat in the sun. In the sunshine, sat a cat. A feline sat in the sun beam. e.g. Simple languages are error-prone “Fire!” can be easily mutated to “Hire!”
- Complex grammars and syntax make parsing and analysis more difficult but also solve some of the error proneness as in: “There is _ire flaming in the corner.” and provides useful information. “The house is on fire.” “The wastebasket is on fire.”
- The metaphor is readily understood by our non-scientist colleagues on our liberal arts campus. They often send students our way, help us with internal funding and even offer advice on linguistic analyses from a humanities point-of-view.
- The metaphor appeals to both of us-Mark LeBlanc (PhD thesis work with parsing children’s word problems) and Betsey Dyer (an amateur linguist).
- And finally, and perhaps most importantly the metaphor continues to produce good results for ourselves and others. Many researchers, such as Eric Davidson (with sea urchins) are finding laboratory evidence suggesting that there is indeed a grammar and syntax to gene regulation. Regulatory motifs do appear to have certain properties of “natural languages”-namely combinatoric modularity, context sensitivity, redundancy and a certain sloppiness that comes of having evolved. That is, the “grammar” by which a decision is made to either transcribe a gene or not, only has to be good enough for an organism to reproduce in a particular place and time. The grammar does not have to be perfectly streamlined and logical (and thus, ironically error-prone) (as in a computer language) but merely sufficient to make a transition into the next generation.