This month’s cover of Nature Genetics features a modified Venn diagram by Anthony Edwards¹ which illustrates the space of possible base combinations.

An article describing the layout is available on Nature Precedings. Myles Axton has also written a brief note which includes a quote from Dr. Edwards explaining the color codes used in the diagram: “Codons in contiguous areas always differ by just one base. Coloring the areas according to their corresponding amino acids leads to the final diagram. We have selected colors that help to classify the amino acids as basic, acidic, polar and nonpolar. Gray is used for the three stop codons.” I think this is a great way to use color to signify similarity—the same color represents the same amino acid.

The space of codons is frequently described in a 3-dimensional chart, like the one found here. While the 3d table is useful for looking up the corresponding amino acid, Dr. Edwards’s representation makes it easier to see the changes due to a single point mutation (e.g. a point mutation would be represented by moving from the space of the original codon to any one of the adjacent spaces).

Venn diagrams, invented by John Venn in 1881, were a response in part to the Euler’s circles invented in 1786. Traditional Venn diagrams, which only use circles, are limited in their ability to scale to higher dimensions (see this AMS article) and, when used to represent logical statements, cannot represent all possible logical statements (see the article on Diagrams in the Stanford Encyclopedia of Philosophy. Pierce followed up with a proposed technique for representing statements that were inexpressible in Venn diagrams (such as disjunctive statements—A or B—and existential statements—there exists an A that is also a B) by replacing Venn’s shading with a system of X’s and O’s connected by lines. However, Pierce’s system was unintuitive and difficult to follow. in 1994, Shin proposed a new technique that makes Pierce’s proposed modifications easier to use. Shin and Pierce both use a connecting line between x’s to express disjunctive information (e.g. A or B).

Instead of using color to express codons that code for the same amino acid (such as UCU and UCC), Edwards could have used connecting lines to express what is effectively a disjunctive relation. I tried overlaying this information on the black and white Edwards-Venn diagram and ended up with what looked like a bit of a cobweb. I also think I probably looked a bit like Russell Crowe’s character in A Beautiful Mind while sitting at my desk with a ruler and pen, connecting letters on a diagram.

¹ Edwards, A.W.F.. Picturing the genetic code. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.682.1 (2007)