Takedown of ENCODE’s claims that 80% of the human genome is functional

Those of us who are biologists with interests in genetics and genome biology were somewhat taken aback by ENCODE’s claim last year that around 80% of the human genome was functional, a claim that flew in the face of evidence that a very large proportion had no known function, and was regarded as ‘junk’. That this assertion essentially seemed to depend wholly on a novel definition of usage of the word ‘function’ seemed to escape those who jumped on the ‘death of junk DNA’ bandwagon.

What was completely obvious was that creationists, particularly those of the Intelligent Design variety would seize on such reports with alacrity. And so it proved. Indeed, in a recent C4ID mailing Alastair Noble (who’s doctorate is in Chemistry, not Biology) continued to trumpet the death of junk DNA – but only following a bizarre reference to a recent detective TV show, seemingly asserting that the show’s writers know science better than Brian Cox.

Now a group of scientists have published a paper that represents something of a takedown of ENCODE’s bizarre PR focussed claims (On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE). I’ll write more about this paper when I’ve finished reading it fully, but the abstract concludes:

The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

Crikey. It’ll be interesting to see what ENCODE’s response will be, if any. My own view is that a substantial and valuable body of genome annotation was conducted by ENCODE, and it’s a shame it’s overshadowed by this one bizarre claim.

Will the Intelligent Design creationists take note? I doubt it.

Update/Postscript: I note this reference to Intelligent Design creationists near the end of the paper:

We urge biologists not be afraid of junk DNA. The only people that should be afraid are those claiming that natural processes are insufficient to explain life and that evolutionary theory should be supplemented or supplanted by an intelligent designer (e.g., Dembski 1998; Wells 2004). ENCODE’s take-home message that everything has a function implies purpose, and purpose is the only thing that evolution cannot provide. Needless to say, in light of our investigation of the ENCODE publication, it is safe to state that the news concerning the death of “junk DNA” have been greatly exaggerated.

Review: From Stars to Stalagmites – How everything connects

From Stars to Stalagmites – How everything connects
World Scientific 2012 ISBN 13 978 981 4324 97 7
Paul S. Braterman*

I am a pretty avid reader of popular science books, but generally speaking I’ve mostly read books with a general emphasis on biology, particularly evolutionary biology. From Stars to Stalagmites is therefore a bit different from my usual reading fare, taking a chemist’s view on the world. In essence, the book spends 16 chapters explaining how we know stuff. Stuff ranging from the age of the Earth to how CFCs were incriminated as the cause of the ozone holes. Many of these accounts are told with specific reference to the people who shaped the theories and the science. I don’t mean just the scientists – policy-makers and polticians also feature highly – a good example being the chapters on figuring out the cause of the ozone hole and on global warming.

I could summarise this book as “a collection of stories about stuff”, but that would ignore the central theme that comes across as one read through the book: how we know how natural processes work, and how we can use this understanding to probe the deep history of our planet, figure out how to rescue our planet from anthropogenic destruction and so forth.

On reflection some, if not all, of the chapters come across as excellent material for presentations. Whether such has been the origins of the work or not, I do believe that the book itself would have benefited from a bit more in the way of illustration…

For me, stand out chapters include the opening chapter on the age of the Earth (Chapter 1), that on Fritz Haber, the First World War and explosives (Chapter 6), and the 14th Chapter on why water is weird. But I guess those preferences reflect my interests; the book is consistently interesting and clearly written.

In dealing with the evolution of ideas about the Earth’s antiquity, Braterman effectively sets the stage for all the controversies manufactured by the biblical literalists who insist in (mis)interpreting the bible to deduce that the Earth is a mere 6000 years (give or take a little). The chapter takes the reader on a journey in the changing scientific understanding of earth science, which neatly encapsulates the nature of scientific discovery. I think this example illustrates the value of this book. It’s not necessarily in its factual content, but in the way rational and thoughtful investigation of the world and its material phenomena can lead to clearer understanding of the world around us. And more than this, several chapters describe how current understanding can and does change as science advances, both in terms of techniques and in the application of knowledge from disparate areas of investigation.

To conclude, From Stars to Stalagmites is a valued addition to my bookshelf and a fine example of popular science writing.

*Disclosure: Paul Braterman is a BCSE committee member, as am I.

Sean Eddy on Junk DNA

This link arrived via the HHMI Twitter feed – Sean R. Eddy’s FAQ on Junk DNA: The C-value paradox, junk DNA, and ENCODE.

The HHMI tweet refers to this as an upcoming Current Biology article. It’s a spectacularly clear and lucid exposition in a historical context of what junk DNA is. It clearly explains why ENCODE’s message that 80% of the human genome is functional is so off-base.

I don’t suppose it will deflect the inane claims of the Intelligent Design creationists. But one can only hope.

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?

Evolution of protein complexes

One of the recurring modes adopted by Intelligent Design creationists is to adopt the strategy whereby an example of a complex biological system is looked at and it is decided that evolution cannot explain its origin. We see this enshrined in bogus concepts such as ‘irreducible complexity’, ‘specified functional information’ and the like. By claiming a process of inference, ID creationists seek to declare that an intelligent designer must have been involved in the appearance of such complex systems.

Of course, the problem with this strategy is that one by one, these examples are likely to fall to genuine scientific advance (examples include Behe’s favourites such as the bacterial flagellum and the vertebrate immune system spring to mind).  A neat example of  an approach to better understanding the evolution of protein complexes has just appeared as an Advance Online Publication at Nature (Finnigan et al (2012) Nature “Evolution of increased complexity in a molecular machine” doi:10.1038/nature10724). There’s also an accompanying News and Views article (Doolittle (2012) Nature “Evolutionary biology: A ratchet for protein complexity” doi:10.1038/nature10816). Continue reading “Evolution of protein complexes”

Why the Everyday Champions Church’s Free School bid was rejected.

The British Humanist Association reveals why the Everyday Champions Church’s bid for a Free School was rejected (Everyday Champions Church Free School bid rejected due to creationism).  As the title of that blog article indicates, it was pretty much down to the ECC’s stance on creationism.  The Church’s leader, Pastor Gareth Morgan, made it pretty clear how the school planned to present creationism:

“Creationism will be taught as the belief of the leadership of the school,” Pastor Morgan said. “It will not be taught exclusively in the sciences, for example. At the same time, evolution will be taught as a theory.”

According to the BHA’s report:

The school’s bid was rejected on Monday, and the reason is now known. In having their bid rejected, the Church was told by the Department for Education that ‘The Secretary of State carefully considered your application, the views and beliefs of your organisation as set out in your application, your responses at interview and information about your organisation available in the public domain. He was unable to accept that an organisation with creationist beliefs could prevent these views being reflected in the teaching in the school and in its other activities. It is his firm view that the teaching of creationist views as a potentially valid alternative theory is not acceptable in a 21st century state funded school.’ The Church is now planning to re-apply for 2013, and is adamant that they would only teach the story of creation in RE.

It’s a little disheartening to hear that this bunch who clearly read the much (mis-) translated writings of a gang of bronze-age nomads as the literal truth of a supernatural entity are going to make a second bid to be allowed to interfere with the education of children.  Hopefully the next attempt won’t gain much more traction in the DfE.

Of course the wider issue here is that too many schools are faith schools of one kind or another.  I strongly support the BHA’s campaign against faith schools, though I fear in the current reactionary and socially conservative political scene it’s going to be an uphill battle.  See also the campaign to strengthen the prohibition of the teaching of creationism in science classes (Teach Evolution not Creationism).  In my view, the place for creationism  has its place in the curriculum: in Religious Education classes along with all the other creation myths that have been claimed over the millennia.

And as a postscript, the so-called Intelligent Design form of creationism is also not science.  It can propose no hypotheses, makes no testable predictions, and merely claims to infer the existence of an unproven supernatural entity.

Moran takes apart “The Myth of Junk DNA”

Recently Larry Moran (Sandwalk) has been working his way through Jonathan Wells’ latest literary effort, The Myth of Junk DNA. The latest installment is Sandwalk: Junk & Jonathan: Part 8—Chapter 5.

Dr Dr Wells, of course, is the Discovery Institute Fellow who is one of the speakers at C4ID’s secret summer school this year (actually the existence of the summer school’s not a secret, but they’re keeping the identities of the participants secret).

Anyway, Moran’s deconstruction of The Myth of Junk DNA is rooted in a detailed look at what all that DNA is, how one defines “junk”, how perceptions of the apparently non-functional DNA has changed as genome science has moved forward (in a way that the non-science of Intelligent Design creationism can not), and mis-citation of sources.  The latest installment deals with pseudogenes.  It’s worth catching up with the whole set of articles.