Monday, December 23, 2013

University of Washington DNA "Duons" Press Release Overshadows Science Paper

In what's ending up as a abject lesson against using hype to publicize scientific papers, a WashU University of Washington Science paper entitled "Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution" by Stergachis et al. was accompanied by a press release that's been pretty much hung up to dry at Forbes by Emily Willingham:
The hype began with the way hype often begins: an institutional news release offering us the holy grail/huge breakthrough/game-changing finding of the day. This kind of exaggeration is the big reason any science consumer should look well beyond the news release in considering new findings. A news release is a marketing tool. You’re reading an advertisement when you read a news release. In this case, the advertisement/news release not only goes off the rails with the hype, it’s also scientifically garbled and open to all kinds of misinterpretation, as the comments at the link to the release make clear.
The whole news release is found here isn't actually that much more hyped up than a lot of scientific releases coming from the usual biased sources.  Here, a UW press release was written by a media consultant engaged by (and I presume paid by) UW to promote work that - you guessed it - a team of UW scientists just published.  Apart from awkwardly referring to codons as a "64-letter alphabet", I don't think you can fault them for joining the scientific hype arms race that's ongoing if you want to get a publication noticed.

As far as claims for "discovering double meaning in the genetic code", here's the actual abstract from the Stergachis et al. paper:
Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution.
Let's paraphrase and simplify:
DNA encodes protein and transcription factor (TF) binding sites. We mapped TF binding sites within protein coding regions, and found that 1 out of 6 codons also encode TF binding sites.  For convenience, we call these "Duons".  Duons are evolutionarily conserved, probably because they code for both amino acids and TF binding sites.  We also found TFs tend to not recognize stop codons, and that about 1 in 5 SNPs within duons alter TF binding.
And that's it. The abstract itself doesn't claim that this team was the first to find duons, or to find a second genetic code, or anything shocking like arsenic based life forms.  They simply used a term to conveniently refer to known a feature of codons; in other words, they made up some jargon, and others ran with it.

The actual paper is actually pretty good, and helps to explain how evolution/mutation of silent SNPs can change gene transcription patterns without changing (usually damaging) the protein encoded at the site.  Most importantly, there's nothing about a second genetic code, in the classical sense of the term.  There didn't find any secret tRNAs in the study, nor did they find rogue ribosomes that no one noticed over the past 60 years.

I'm going to assume that the team at UW didn't proofread the press release before it went out.  If they did, maybe they brushed it off as 'just another release' that will fall into obscurity on the UW site.  That might have been their mistake, but I'm just speculating here.

In either case, this is a perfect lesson that scientific experts need to be engaged in all parts of the science communications process.  It also shows how even a great Science paper can be overshadowed by what many assume to be a simple press release.