Sonic hedgehog and Beethoven: an oral history of how some genes got their names

Scientists are systematic and meticulous when it comes to naming genes.

They use computer programs to identify new ones and follow standardized guidelines to give them names like TP53, APOE, BRCA1.

That, however, has not always been the case. During the late 1970s to 1990s, the heyday for newly identified genes, scientists selected names based on emotion and free association. The results were public displays of scientific wit, whimsy, and irreverence.

STAT interviewed a handful of researchers about that Wild-West era and how they came up with some of the more memorable gene names.

Here’s what they had to say in their own words — though with responses condensed and lightly edited for clarity.

Ken and Barbie (1993)

Steven A. Wasserman, professor of biology at the University of California, San Diego

In 1993, after months of experimentation, Wasserman and his team identified 83 new genes in flies that affected male fertility. But before publishing, the researchers had to name each of them.

Wasserman: The genetics tradition is to sit down and have a naming party. Some of the genes [caused] mutant phenotypes that were similar to ones that other people had described.

For example, one way you can get male sterility is that you do a lousy job making sperm heads and you get these things that look like balls under the microscope. There was another lab that had named things “cannonball” and “cueball” and a few others. So we named some of our genes “bocce” and “pelota,” sort of following that tradition.

But then we had a few mutants that were just quite different. When we looked to see why these flies were sterile, it wasn’t that they didn’t make sperm — they made perfectly good sperm but they didn’t transfer to females. When we looked … it was because they didn’t have external genitals and neither did the females.

So thinking about a good name for adults that don’t have external genitals, we came to “Ken and Barbie.”

Pray for Elves (2002)

Suzanna Lewis, scientist and principal investigator at the Berkeley Bioinformatics Open-source Project

Lewis was hard at work annotating the fruit fly genome —a herculean task that involved using computer programs to map genes and identify specific characteristics of their DNA. As a consolation prize, she was able to name a gene.

Lewis: There were so many new genes, a few thousand that hadn’t been characterized in the lab. So we were just giving them unique identifier numbers. We were working late nights on this … there was such a deadline and so much pressure to get Drosophila finished and make all this information available.

I have to give Mark Yandell credit for the idea. … [The name] was an expression he liked to use, “When are the elves going to appear?”… When it was 3 a.m. in the morning, he really wanted the fairy tale, the shoemaker and the elves. He wanted the elves to come out and help finish the work magically.

I’ve been surprised that so many people have noticed [the name]. People remembered it. I guess a lot of people have that feeling when you’re really tired and working hard. We all would like to have the magic elves help us sometimes.

Sonic hedgehog (1993)

Cliff Tabin, professor and chairman of the department of genetics at Harvard Medical School

Robert Riddle, neurogenetics program director for the National Institute of Neurological Disorders and Stroke

When three collaborating laboratories — led by Cliff Tabin, Andrew McMahon, and Philip Ingham — discovered a family of genes critical for embryonic development, they made a deal. Each of the three genes, vertebrate versions of the “hedgehog” gene originally identified in fruit flies, would be named after species of real hedgehogs. But before publication, Robert Riddle, a postdoctoral fellow working in the Tabin lab, proposed another idea.

Tabin: It was the precomputer days. I got a mammalogy book and just looked up the names of different hedgehogs. I used three names. The original names that we used were desert hedgehogs that lived in Algeria, long-eared hedgehog, and common European hedgehog.

Riddle: I saw the ad for Sonic the Hedgehog in the back of a games magazine that my wife had brought home. I had never heard of that game … it sounded like the band Sonic Youth. I was into Sonic Youth among other bands. I thought [naming the gene Sonic hedgehog] would be a bit of a sly way for me to smile because it was somewhat of a reference to a band. … It started out as kind of a fun thing but people latched onto it.

Tabin: So I went to this meeting with Andy and Philip. We’re now going to write the papers. What are we going to call the names? They were not actually all that happy with the name [Sonic hedgehog] originally.

Andy was one of the founding people who discovered the vertebrate Wnt genes and they were basically naming them Wnt1, Wnt 2, Wnt3a, Wnt3b, etc., and he really didn’t like cutesy names. Phil, coming from the fly field originally, did like the idea of having more interesting names than just numbers. But he wanted names to reflect phenotypes or at least something about the gene. There’s nothing conveyed in the name Sonic hedgehog.

Each lab really contributed [to the research] in a major way … but we were the first ones who discovered a piece of Sonic. I sort of used that as leverage and said, “Well we were the first to do it, so my postdoc should have the right to name it.” And they begrudgingly said OK, they would go along with it. I think that they expected the name to disappear. They thought it would be called Shh. And that no one would ever call it Sonic.

Riddle: I think most people kind of smiled and thought it was another interesting developmental biology name. It was only a few years later that people started saying, “Well, no, maybe that name is too frivolous.” Initially I didn’t sense that was a concern. I still like the name.

Tabin: Even if we have fun saying gene names, there is very serious, rigorous science going on around it. It is not like we’re playing lighthearted games in the lab. We’re trying to understand very profound aspects of how the world works and predicting how biological systems work. … Naming genes is just a way of injecting a little light heartedness along the path.

Beethoven (2002)

Karen Avraham, professor at Tel Aviv University and vice dean of the Sackler Faculty of Medicine

A variation on naming genes is naming mutant alleles — versions of a “normal” gene that, due to changes in DNA, affect how an animal looks or behaves. One such allele, which is associated with hearing loss, is named after the famous composer. 

Avraham: There were a number of mouse mutants that our colleagues had discovered. … Every once in a while they would say, “You can pick the name. Would you like to pick it?”… Beethoven was deaf so the graduate students said let’s give the mice the name Beethoven.

We had to look through the database and make sure that Beethoven hadn’t been used for a mouse mutant before. It had not so we got permission to use the name; there was a committee of geneticists that had to approve it.

Initially when we found the Beethoven mouse … we didn’t know which gene the mutation was affecting to cause hearing loss. Later, we discovered that the mutation was in the gene TMC1 (transmembrane channel-like protein 1). So when we refer to Beethoven, we should be writing Tmc1 and then superscript Bth for Beethoven.

There are many geneticists who have named human diseases after themselves. Scientists like to name things. It gives them a feeling of ownership. I think once you have the freedom to do it, scientists are people and just would like to come up with something creative.