ENCODE, junk DNA and creationists

I see the ignorant, stupid, devious and downright dishonest within the creationist cohorts have been joined by the Centre For Intelligent Design, which is delighted by the junk DNA misinformation circulating in the media. I received an email from C4ID’s Dr Alastair Noble:

Who would have thought it? ‘Junk’ DNA, the widely-promoted ‘killer’ argument for Neo-Darwinian evolution, bites the dust.

No less an authority than the Cambridge-based European Bioinformatics Institute tells us that ‘junk’ DNA is no longer an accurate representation of the situation and that very much more of DNA than was thought contains active genetic information. But Intelligent Design theorists have been suggesting for some time that 98% or so of junk in DNA seemed unlikely. Maybe ID can make accurate scientific predictions after all!

You must hear Dr Doug Axe (Seattle) and Prof John Lennox (Oxford) discuss these and related matters at the Centre for Intelligent Design’s conference at Malvern on September 28/29th.

Unfortunately, being a chemist with a brief research career several decades ago (and with the distinct need to demonstrate a creator) has not left Alastair Noble’s abilities to comprehend science in good stead, and he’s had to rely on various media sources regurgitating a simplistic rewrite of molecular biology history coupled with an equally uncritical definition of the word ‘function’, as used by ENCODE. I suppose another factor has been the woeful public relations train wreck that the ENCODE mass publication has become. Regarding this whole debacle, there’s been quite a bit of discussion around the blogosphere. ( My own genome science background relates to the fruit fly Drosophila melanogaster – while this shares many of the “junk” features of the human genome, they are less marked.)

Probably leading the charge against the ENCODE PR has been Larry Moran (Sandwalk), who has seen it as inadvertently shoring up Intelligent Design creationism. Sandwalk has featured problems with the reporting of ENCODE on a almost daily basis. As Larry Moran observes

Is this what science is going to be like in the future—the person with the biggest advertising budget wins the scientific debate?

Several blogs have touched on the ‘junk DNA’ matter. T. Ryan Gregory has made several postings at Genomicron explaining exactly what is wrong with ENCODE’s public statements of “80% Functional” – see for example ENCODE (2012) vs. Comings (1972). He also has a list of major news outlets who’ve uncritically regurgitated stories about the death of junk DNA (The ENCODE media hype machine).  Over at Cryptogenomicon, Sean Eddy has ENCODE says what? outlining in considerable detail exactly what’s wrong with the claims that 80%  (or even more) of the human genome has an identified function.

Ars Technica have an extremely well written overview of the ENCODE PR debacle, Most of what you read was wrong: how press releases rewrote scientific history.

It is a great shame that commentators such as Alastair Noble don’t know enough of the history of molecular biology, or indeed enough of the complexity of the typical eukaryotic genome to take a more critical view of the mass media’s simplistic take-home message of ENCODE, merely repeating the inaccuracy in the delighted but mistaken belief that it shores up their creationist (ID or otherwise) beliefs.

If you have an iPad, I can recommend the Nature ENCODE app, which makes it clear that the 30 or so papers simultaneously published last week don’t exist merely to back up the bizarre and inaccurate (both scientifically and historically) claim to have overturned some junk DNA paradigm, but rather represent a detailed characterisation of human genome structure, mapping out a wide variety of genome modifications often associated with gene activity. Projects such as ENCODE yield huge data sets that aren’t themselves necessarily interesting to individual scientists, but which provide the basis for considerable future investigations.

Alastair Noble referred to Intelligent Design theorists. Well that’ll be because Intelligent Design creationists don’t actually do experiments. And were they to honestly interpret the literature, they’d see that junk DNA is very real in the human genome. What’s God the designer got against salamanders and amoebae? Why favour puffer fish with a particularly economical genome?

Information Input Theory – A Trademarked “Research Field”?

Here’s an odd website that popped up in my news feed. It proclaims itself the “International Laboratory of ID Science“. Apparently it’s all about something called Information Input Theory. A phrase which apparently has been trade marked. And with supreme irony, given the text on the home page, the website is subtitled Evidence and Reason! According to the site,

IIT is a field of Intelligent Design science which predicts intelligent inputs, specified complexity and adaptation value in biological systems. IIT is a study of information, it overlaps studies in computer science, information theory, bioinformatics and biomechanics.
IIt is a recognised tool, a respected and trusted science.

I had a quick Google search of the phrase Information Input Theory. Nothing other than the site and its facebook page comes up, so I suspect it’s scarcely a recognised tool, or a respected and trusted science. Other hallmarks of a, shall we say, oddball site are the oddly written prose often using neologisms and words that are just plain wrong. Oh, and over-interpretations and misinterpretations of science.

On the off chance that this really is some kind of offshoot of Intelligent Design creationism, I Googled “Information Input Theory” + “Discovery Institute” since the Discotute have a bit of a track record in abusing information theory, but I only hit one page, an individual’s Facebook page. I didn’t fare much better replacing the Discotute with its UK equivalent, the centre for Intelligent Design. I presume therefore that whoever (or what) is behind this website is not overtly connected with either outfit.

So this looks to be a off-piste oddball site. Of course, it appears to be a website that’s still being built (it has lots non-functional links), but top of the list of “Reference Links” is a link to The Bible. Which probably explains a lot.

There’s not much content. On the front page are brief discussions of the famous Cairns paper of 1988 (Cairns J, Overbaugh J, Miller S. The origin of mutants. Nature. 1988;335:142-145. Link), neglecting to mention work that’s been done since (such as Hendrickson et al. Amplification-mutagenesis: evidence that “directed” adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proceedings of the National Academy of Sciences of the United States of America. 2002;99(4):2164-9. Link). Oh and a lot of poorly drafted verbiage that doesn’t make sense to me. Also on the front page is a brief discussion of a preprint paper by Gregory Chaitin on some sort of mathematical modelling of evolution, which I haven’t read, but about which this brief burst of gibberish is completely unilluminating.

There are a few pages of text, for example objecting to evolution (names here as Darwinism) which begins with a bonkers assertion:

The theory of evolution is not one theory but, a collection of theories, e.g. Natural Selection – DNA sequencing, coordination of sexual selection etc.
Darwinism or (Neo-Darwinism) is a subject of philosophy and in particular, a want, rather than actual science, which hinders the public from adopting the actuality of design in science.

And it gets worse! I’ve rarely read such inarticulate writings, even from creationists. Peculiarly, the link entitled ‘Science behind ITT’ take one to a page with the tab heading Jesus Loves You, with a ludicrous collection of gibberish the like of which I’ve only really seen on true nut-job alt-med sites.