Junk DNA and Media science literacy.
How on earth the two subjects could be related is not immediately clear though the poor quality of some of today’s news publications might suggest otherwise. First let’s get a handle on what the most recent kerfuffle in biological science is about and how it reflects deeply on the often limited science literacy found in our publications.
It starts with Junk DNA. The phrase alone seems to be disparaging as if ‘nature’ somehow carelessly left us with a baggage train of useless material in our genes. Which apparently it did and as such has been used as the flagship of empirical evidence for the sometimes messy process of evolution in living biology.
Modern Geneticists consider the genes that regularly write to or regulate proteins (less than 10%) the main functional sequence of human DNA. The remaining 90 % is largely inactive or ‘junk’ DNA.
It is reflective of an attitude increasingly popularized through the last century of rapid scientific advance. One that says that evolution, much like some utilitarian toymaker, jury-rigs species over the eons to get the job done, but nothing more. According to conventional science most life on Earth is unknowingly left to carry an enormous load of genetic detritus.
But when you look at the astonishing complexity and mathematical elegance of DNA, fractal knots and super molecular structures, it’s understandable that you might wonder if there was perhaps a hidden genetic El Dorado secreted in the Junk DNA wilderness. Well in that case, you wouldn’t be the only one to consider this.
Late in 2012 Scientists with the international ENCODE (the Encyclopedia Of DNA Elements) consortium, launched by the National Genome Research Institute in 2003, announced what the authors said was a breakthrough in identifying all the functional elements in the human genome sequence. The claimed breakthrough in analysis of DNA functionality was published across 30 papers in Nature with the consortium claiming that vast lengths of DNA, previously dismissed as “junk”, were in fact vital to the way the genome works.
IE. Not Junk.
Dr. Ewan Birney, of the European Bioinformatics Institute near Cambridge, one of the project’s principal investigators was particularly effusive in support for ENCODE’s series of papers and their startling conclusions.
“We always knew that protein-coding genes were not the whole story,”
It was claimed the majority of the geneticists were wrong about all that useless Junk DNA and that NGR, made famous when it published the completed human genome in 2003, had in fact trumped other institutes with yet another piece of groundbreaking work in human genetics.
The response from NGR’s peers in biological science was scathing, critical and at times near vitriolic. In the meantime controversy built as religious authorities and Creationists waxed lyrical about this being evidence of Gods design in nature and proof that evolution was a flawed theory.
Confused? Not sure who to believe?
Well it seems most of the mainstream media weren’t.
Of course it started with the prestigious journal, Nature, marketing the story in true entrepreneurial fashion, with a number of firsts – cross-publication topic threads, a dedicated iPad/eBook App and web site and a virtual machine.
But the slavish uncritical merchandising of NGR’s claims by journalists, who for the most part were enchanted with the apparent breakthrough, made an already precipitous situation worse.
Journalists got very busy designing elaborate models, pages of articles and online tutorials to explain this apparent breakthrough.
“Far From ‘Junk’,” headlined Gina Kolata of The New York Times, credulously, with not a hint of doubt about the paradigm shaking conclusions. Robin McKie, The Guardian (UK)’s top-flight science editor raved that last September’s announcement was the scientific surprise of 2012.
Perhaps not surprisingly the response by NGR’s peers in the biological sciences community was far from an endorsement of their claims.
“Everything that Encode claims is wrong,” charged the lead author of the paper caustically titled “On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE.”
Dr. Graur and his co-authors are among the leading geneticists in the world today. They claim that the Encore group made a ‘noob’ Genetics mistake in confusing biological activity with actual functional importance in the cell. Graur said,
“They completely exaggerated the amount of human DNA that has a role to play inside our cells. Most of the human genome is devoid of function and these people are wrong to say otherwise.”
“This is not the work of scientists,”
He added, scathingly and perhaps a little savagely.
“This is the work of a group of badly trained technicians.”
Another well known biologist and now journalist, John Timmer, wrote a similarly provocative piece for ‘Arstechnica’ lambasting how press releases were co-opting science and scientific history titled “Most of What You Read was Wrong: How Press Releases Rewrote Scientific History”
Timmer went on to say how “activity” measured by the ENCODE tests doesn’t necessarily imply this DNA is doing anything for us.
“Many press reports that resulted painted an entirely fictitious history of biology’s past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can’t entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work—and, in some cases, the scientists themselves.”
Timmer still thinks, despite the heavy critique inferred in his articles title, that NGR are doing important work and that not everything in the ENCODE papers was wrong.
ENCODE biologist John Stamatoyannopoulos (made popular by his quotes in initial press releases) claims that the skeptics hadn’t fully understood the papers, and that some of the activity measured in their tests does involve human genes and contributes something to our human physiology. But he did admit that the press conference was misleading by claiming that 80% of our genome was essential and useful. He puts that number at closer to 40%. And as an ENCODE stalwart otherwise he stands by all the ENCODE claims: Speaking to Faye Flam at Knight Science Journalism he said –
“What the ENCODE papers (not the main paper in Nature, but the other length papers that accompanied it) have to say about transposons is incredibly interesting. Essentially, large numbers of these elements come alive in an incredibly cell-specific fashion, and this activity is closely synchronized with cohorts of nearby regulatory DNA regions that are not in transposons, and with the activity of the genes that those regulatory elements control. All of which points squarely to the conclusion that such transposons have been co-opted for the regulation of human genes — that they have become regulatory DNA. This is the rule, not the exception….”
So if its Junk DNA, until we know what it does (if anything) we still have ENCODE concluding that 60% of our DNA is junk, and their majority of scientist critics holding that at the very least, 9% is functional, even though we still don’t know what most of that 9% actually does.
In summary it does seems that Encode had said that 40% of the genome is ‘functional’ in that 40% of the genome has genes that are capable of coding for proteins or do regularly code for proteins. The major dispute is over the fact that Encode initially claimed that this was synonymous with 40% of the genome being ‘vital for life’ as referenced in the article. Something which is at best a highly dubious claim if not just plain false.
So the evidence so far seems to indicate that ENCODE is not the silver bullet to a new DNA treasure trove, but its future utility and scope has not yet been fully explored. In the meantime, one of the prime virtues in science is in order, patience.
A quality that both NGR and the resulting media scramble might well have paid heed to; raising what I believe to be an equally important issue. That the need for rigorous integrity in the reporting of scientific breakthroughs and the relentless competition to release sensational headlines may not always be in sync. The trend of press popularization of new scientific discoveries has a dark side that makes it increasingly possible for misinformation to be released as fact. Particularly when the nature of such discoveries are increasingly highly technical and cannot be easily reduced to simple sound bites and news clips. The media requires an increasing sophistication in its understanding of the science behind such discoveries to keep up with the science itself. Otherwise they risk continuing to ‘drop the ball’ in relation to ENCODE-like discoveries.
The Commercial pressures are not only an extant factor with the media but with the developers themselves. NGR ran with the ball and released the ENCODE with claims that seem well beyond the parameters of the actual data they had collected. NGR was no doubt seeking to be yet again the first in another breakthrough and that is understandable. Ground floor developments lead to patents and future funding opportunities that trailing laboratories and research institutes can only dream of. But this practice in the long run hurts science and adds to the misunderstandings of public perception about science itself.
The inevitable backflips that result can damage public confidence in the scientific community and in turn harm future funding from both the public and private sector. Worse still, such gaffs by the media and hasty developers may also contribute to a consumerist perception of science where belief and subjective standards cloud what should be an evidentiary led empirical process.
After all science is the most rigorous of humanity’s exploratory and experimental systems and needs to remain so to continue to deliver real world results. Results which are vital in driving human progress encompassing both economic and social evolution.
When media and commercially competitive pressures prioritize market share and early commercial exploitation over adherence to the actual data and the quality of its dissemination – then that is when the rot sets in.
As the rapidly evolving science of the near future radically reshapes our world, it may well be vital for better public clarity and understanding that both the developers of new technology’s and our media do not race ahead of the data or their understanding of it in a precipitous race for fiscal and intellectual success.