Why do scientists—and many science aficionados—cringe when people use the term dark matter in genomics? For one, it’s an imprecise analogy borrowed from physics. In that field, dark matter refers to inscrutable matter that can’t be seen—except in terms of the gravitational effects it exerts upon other matter. As astrophysicist Summer Ash, director of outreach for the department of astronomy at Columbia University, has explained: “It’s hypothetical. Physicists made it up to explain why we see what we see.”

In contrast, noncoding DNA is very real and we can “see” it in the same way we can “see” protein-coding DNA—by sequencing a gene’s individual bases, or letters, that spell out the instructions for a protein, explains Leonid Kruglyak, a geneticist at UCLA. “The only reason noncoding DNA tends to get called dark matter is that it’s big compared with the coding regions of the genome, and we don’t fully understand it.”

Observes geneticist Daniel MacArthur at Massachusetts General Hospital and the Broad Institute: “An analogy only works if it’s a concept that the public already understands, but how well does the public understand dark matter in physics?” As the Wikipedia entry for dark matter warns: Not to be confused with antimatter, dark energy, dark fluid or dark flow. “When you explain a poorly understood concept with another poorly understood concept,” MacArthur adds, “it’s kind of dangerous.”

That poor understanding leads to another problem. Any analogy is useful only in a specific context; for example, the way the “book of life” is sometimes used to refer to the way that the human genome contains all the instructions for a single cell to develop into a fully mature human being. But the phrase dark matter in genomics is used in too many different contexts. Some scientists (and some journalists explaining their work) use it as a blanket term for all of the vast expanses of the genome that do not encode proteins. Others use it just for the noncoding genome that is transcribed into RNA. Still others use it to mean “missing heritability,” referring to the unexplained genetic risks associated with diseases such as type 2 diabetes—only about 10% of such predispositions can be traced to known locations in the genome. Then again, dark matter sometimes refers to DNA from organisms unknown to science, notes Kruglyak. “As a result, when someone says dark matter in genomics, it’s impossible to know what they actually mean.”

That said, some genomics researchers do use the words dark matter even in the titles of their papers. When asked for a better, more apt analogy to use in genomics, the scientists who object to this imprecision go, well, dark.