One of science’s saving graces is that a fair number of scientists will publicly admit that they are wrong (and then there’s Marc Hauser*…). Last week, at the Human Microbiome Project meeting, Jonathan Eisen gave a talk about the GEBA project which is an effort to sequence the genomes of a diverse group of bacteria to create a bacterial genomic encyclopedia. At one point during his talk, Eisen mentioned that originally all of the genomes in the project were to be finished, although that standard has been relaxed. Eisen then noted that with the new sequencing technologies, it’s feasible to sequence 1,000 genomes.
So that led to some guy named Mike asking a question about this.
Before I get to the question, it’s important to explain what finishing means. When we sequence a genome–and a bacterial genome can be thought of as a circle of DNA (A, T, C, G, etc.)–we don’t actually sequence the entire circle. We sequence most of it, and have large chunks known as scaffolds. For technically reasons, we can’t sequence across these gaps–these ‘fragmented’ genomes are known as draft genomes. Closing these gaps is known as finishing (i.e., there is one scaffold for the entire genome). Unlike producing draft genomes, it is not a ‘production’ process. If you want to know how long it takes to finish a genome, well, we’ll know when it’s finished. Sometimes it takes only a few days, but other times, it can take weeks, or months. It’s expensive, and requires lots of people and resources.
So back to that guy named Mike. That asshole asked Eisen (and I’m paraphrasing here), if you plan on sequencing thousands of genomes, finishing doesn’t seem feasible for most of them. How important is a closed, finished genome for much of what GEBA is trying to do (e.g., discover new genes)? Eisen responded (paraphrasing again) that finishing wasn’t really essential**, even though he, in older papers, argued that it was needed.
Then Eisen said, “I was wrong.”
That’s rarely spoken in public.
Kudos to Eisen for being honest.
*Admitting you’re wrong after you get caught doesn’t count.
**If you have a crappy draft with lots of scaffolds, some finishing can help to ensure that you don’t have contaminant scaffolds (i.e., scaffolds that are from a different organism).