Then I checked your site link.

Then I realized…

Clearly, there is a massive intelligence at work.

“Genomes from yeast to man are almost totally transcribed. More than half of this transcription is composed of non-protein coding (nc)RNA. The organization of transcribed regions found in each cell is highly individualized and consists of overlapping RNAs in which the same genomic sequences encoded in both protein coding and non-coding transcripts. We have developed genome-wide transcription maps in several cell types belonging to multiple organisms. Our biochemical characterization of the mapped transcripts has revealed several common features found in eukaryotic transcriptomes. These include: 1) the number of RNA isoforms for protein coding genes is significantly underestimated relative to what most databases indicate, 2) more than 70% of all protein coding genes have at least one antisense transcript overlapping the coding transcript, 3) the 5’ and 3’ boundaries of most protein coding genes can be positioned hundreds of thousands to millions of base pairs away from the annotated ends of a gene, 4) chimeric RNAs are made by eukaryotic cells encoding portions of a genome mapping at great distances from each chimeric section, 5) the fate of many nc-transcripts is to be processed into short RNAs and 6) the 5’ and 3’ ends of protein coding genes are sites at which collections or short RNAs can be found. Many questions have emerged concerning this pervasive transcription. These questions focus on the nature of the regulatory regions and enzymatic processing pathways that control the expression and maturation of non-protein coding RNAs, respectively as well as the functions of these long and short ncRNAs. Answers to these questions will provide a new view of what a gene is and how genomes are organized and regulated.”

Carl: ‘Sup with no Genomicron on the blogroll?

What frustrates me - and you too I think, judging from your post on junk DNA - is that the need/desire to frame complex and inherently inherently science stories as revolutionary. Your nut graf clearly bases its pitch for people to keep reading on the idea that new research is overturning long-held beliefs about the structure of genes.

But, with all due respect to Mark Gerstein and other scientists who make similar points, I don’t think science viewed alternative splicing, non-coding transcription or epigenetics as oddities until these new studies came along (trans-splicing is another story). Rather, they were accepted as general phenomena whose scale and role in biology were poorly understood. What the new genomic studies have done is give us a detailed picture of precisely which alternative splice forms are made, which regions of non-coding DNA are transcribed, and what types of epigenetic marks are found in different regions of the genome. For all of our acceptance that these existed, we had little idea about what role they play in biology, or how they are generated and regulated.

Or, said more simply. We already knew that the genome was a dizzyingly complex place. The new data gives us the means to actually understand this complexity, and I don’t see why your story couldn’t have been framed around that idea.

This is more than just a minor pet peeve. The portrayal of science in the popular press is always around the idea that new experiments are showing that everything we’ve believed for decades was wrong, rather than showing it as a continuous process of discovery and elucidation. Yes, our initial models of genes were overly simplistic. But they weren’t really wrong either. They were useful abstractions of reality that allowed us to uncover the true complexity that exists in biology.

And let me just end by placing blame where blame is due. The stories on junk DNA that both you and I have criticized originate primarily with the authors of the studies in question and their press offices - who write press releases that pitch every new observation as novel and every new ideas as revolutionary. They do it because they think it’s the only way to get reporters to bite at their stories. We - scientists and science journalists - should work together to make sure this is unnecessary.