Hypocrite? Moi?

Things move fast these days for us science writers.

I’m writing this just after returning home from a radio studio in New Haven, where I was interviewed on NPR’s The Takeaway about my article in today’s New York Times on the gene’s identity crisis. (Speaking of fast, the segment is already archived for your listening pleasure here.)

And now I sit down to find that my next order of business is to respond to a pretty harsh judgment of the article that appeared overnight, from a scientist I respect.

Time for the fourth cup of coffee of the morning!

So: The scientist in question is Michael Eisen, a biologist at the Univiersity of California at Berkeley. Among the many interesting things Eisen studies are transcription factors, proteins that grab onto DNA to switch on and off the production of RNA and proteins. The sites where transcription factors bind to DNA lie outside the conventional boundaries of genes, realms that have sometimes been erroneously referred to with the blanket term of “junk DNA.”

A few weeks ago I took some journalists and press release writers to task about their description of a newly discovered site (known as an enhancer) that may have played a key role in the evolution of the distinctly human hand. They erroneously claimed that the enhancer had been previously considered useless junk DNA, and so the news was that it actually had a function. I pointed out that people have known about enhancers for about 30 years, and other important sites outside conventional genes for 50. I argued that the news about this hand enhancer was interesting enough without the messed-up history.

Eisen liked that post, but he thinks I’ve failed to follow my own advice in my new article, where I describe a lot of features of our DNA that don’t fit the classical concept of the gene, such as alternative splicing, noncoding RNA, and epigenetics:

Well, he needs to apply the same standard to himself. Alternative splicing was discovered in the late 1970’s. Non-coding RNAs in the 1980’s. And epigenetic effects were described over 50 years ago, with molecular mechanisms first worked out over 25 years ago…Science writers play a very important role as honest interpreters of science for the public. But if they don’t present science history accurately, they can’t be taken seriously as authorities on science present.

With all due respect, I would like to propose a hypothesis: Dr. Eisen blogged about my article without actually reading it all the way through.

I base this hypothesis on the fact that in my article I repeatedly pointed out that scientists knew of examples of alternative splicing and the rest long ago. So why write an article now? Because–as I said in the article–what were once considered exceptions to the rule have become the rule. What could be set aside when scientists reflected on the concept of the gene can no longer be ignored. This is a story not about one particular experiment that yielded one particular result, but the story of a large-scale change in the way scientists think. I like the way a scientist named Mark Gerstein put it during an interview:

 “The way biology works is different from mathematics,” said Mark Gerstein, a bioinformatician at Yale. “If you find one counterexample in mathematics, you go back and rethink the definitions. Biology is not like that. One or two counterexamples — people are willing to deal with that.”

I am not claiming that I’ve looked at the raw data from recent experiments and am telling scientists something they don’t already know. Just the reverse: I only wrote the story after talking to a number of scientists, some quoted in the article and some not, who all expressed a similar feeling that the weight of evidence today is leading to a remarkable change in how they think about genes. Nor did these scientists keep this feeling secret until I pried it from them–take a look, for example, at a new review in American Scientist co-authored by Gerstein that offers a new and improved definition of the gene, based on the research I describe in my article. I am also not claiming that all scientists feel the same way about the new results–for example, there’s a pretty spirited debate over how much of the noncoding RNA rolling off of our genomes does anything at all. And so I tried to squeeze a few quotes into the story to convey that disagreement.

Am I trying to have my cake and eat it too, as Eisen implies? I don’t think so, for the reasons I’ve laid out here. But maybe I’m wrong. I’m open to further criticism, but I still feel like these kinds of stories are worth writing. Some of the most interesting stories in science are move slowly on many fronts, rather than being one quick hit.