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.

C4ID still doesn’t understand science.

Dr Alastair Noble has penned a rather defensive article at the C4ID website, in response to James Williams’ recent blog concerning some radio discussions he had had with Noble (Intelligent Design Creationism is not Science). Unlike Williams’ blog (and this one), the C4ID website does not brook any comment, preferring to push their line of reasoning unchallenged.

I have a number of comments and observations relating to the latest Noble epistle and in particular in relation to Intelligent Design creationism as an alternative to an evolutionary explanation of life’s diversity.  For my rebuttal of many of C4ID’s claims about ID as an alternative to evolutionary biology, see my article “C4ID’s Introduction to Intelligent Design: A critique”.

Firstly, is Intelligent Design creationism actually a scientific enterprise? Well, the origins of ID as a front for biblical creationism are well-established (the ‘Wedge Strategy‘). ID was devised as a way of adding an apparently scientific veneer to creationism as a way of inveigling creationism back into American public schools. Unlike the UK, where we are plagued by a high proportion of church schools, the American consitutional separation of church and state essentially forbids the teaching of religious doctrine (most notably theologically aberrant doctrines such as Young Earth Creationism). We mustn’t get diverted into a supposition that YEC is the only form of creationism: there are a variety of creationist stances, including those of a more theistic evolutionary bent. And that is to only consider christian creationism.

So, it’s clear that ID was devised as a front for creationist infiltration of the American school system, and that it does this by using words and arguments lifted from science. But is it science? The answer to that has to be a resounding ‘no’. ID creationism merely takes the stance that a complex living system seems to be to complex to have evolved, and that a designer must somehow have put that system in place. This is a profoundly un-intellectual approach, and is essentially saying “I cannot understand how this has come into being, I will not investigate and I will assume a Designer”. And what supernatural entity would have had the capacity to design the bacterial flagellum (in all its varieties), bacteria (in all their varieties), plants, animals, fungi etc? Who else but the god of Alastair Noble. If this is not creationism, I don’t know what is.

Does ID creationism advance credible, testable hypotheses? No. ID creationism merely takes the observation of biological complexity and advances the claim that it must have been designed. There is no proof of design other than the observer’s ignorance. Does ID creationism have any truly explanatory power? No.

Williams’ contention that I don’t know the definition of Intelligent Design used by the Discovery Institute is just fatuous. The primary definition of ID, widely used by Discovery, is that ‘certain features of the universe and of living things are best explained by an intelligent cause, not by an undirected process such as natural selection’.

Well this may be attractive to someone who, as a chemist, may well have received little or no biological education. But for those of us who have, and who are both active researchers and teachers in the biological sciences, this is trivial fluff. Natural selection is the process that ultimately gives the illusion of design, using as raw material the genetic variation that continually arises.

What that means is that there is hard evidence in nature which suggests design. The starting point is the evidence. No-one is imposing design on nature and then looking for evidence. It’s the other way round. What James Williams seems to find difficult is the difference between a scientific conclusion and its implications. Of course ID has profound religious and philosophical implications, but those are consequent to the interpretation of the evidence. [my emphasis]

The key here is that design is suggested. Not that it is a reality. One really cannot conclude that something is designed just because it looks that way. In my opinion, Noble is disengenuous here here when he claims that the religious and philosophical implications are consequent to interpretation of evidence – I cannot believe he is unaware of the evidence that ID creationism was devised for the purpose of infiltrating religious views into American schools. Much of this evidence comes from the Discovery Institute and was famously examined in Kitzmiller v. Dover Area School District.

And as to whether Williams’ position on the claim that ID creationism is truly science, I refer the reader to the very article to which Noble takes exception (Intelligent Design Creationism is not Science) – it would be unreasonable to cut and paste so much text.

Alastair Noble, who holds a PhD in Chemistry, frequently writes about DNA. From his writing, he appears to be rather ignorant, misguided or just ill-informed on the subject. This PhD of his is much-touted as some kind of qualification as a scientist – presumably it’s hoped (with some justification) that the public won’t grasp the distinction between chemistry and biology. Unfortunately a PhD awarded about 40 years ago in a non-biological discipline (albeit followed by a brief research career in chemistry) does not really qualify him to make many of his public statements on biology. What may be more of a guide to his attempts to further ID creationism is his religious background (Noble is an elder of the Cartsbridge Evangelical Church in Glasgow and a lay preacher). Indeed very, very few supporters of ID creationism are biologists (and those that are, such as Michael Behe, hold strong religious views).

Scientists of course don’t know how DNA came to be the near-universal genetic material, though many hypotheses have been forwarded, among them that the forerunner may have been RNA. Aspects of these hypotheses frame testable questions, though how good an explanation of life’s origins we can reach is debatable. From the point of view of evolutionary biology, this is moot: evolutionary biology deals with the processes by which the diversity of life around us arose, not the origins of life. It is interesting to note the congruence in strategy between ID creationisms and young earth creationists as they all consider the origins of life to be a big problem for evolutionary biology.

Noble recommends that:

[…] Williams reads ‘God’s Undertaker – Has Science buried God’ (Lion 2009) by Prof John Lennox, a world-class mathematician at Oxford, who certainly knows what he is talking about when he deals with types of information.

Yes, Lennox, who is I believe a creationist and holds strong religious views is a mathematician, not a biologist.

It may be hard for someone with a 40 year old qualification in Chemistry to grasp this, but decades of biological research involving genetics and molecular biology has not only demonstrated that genetic information can and does increase (and decrease) during the diversification of life, but has clearly shown how these changes can and do occur. Alastair Noble exhorts us to read more on the subject:

For biological life, it matters a great deal whether the information is functional or not, and Shallit simply fails to deal with this. Stephen Meyer in his book ‘Signature in the Cell’ (HarperOne 2009) certainly does.

Well, Meyer is the founder of the Discovery Institute. His biography at the Wikipedia page is informative: several of his qualifications derive from religious institutions, and none are in biology.

What, then, of the vast scientific enterprise, particularly in the biological sciences, for whom evolutionary biology is key to interpreting experimatal data? Are all these investigators really denying the truth of the existence of a Designer? Is this a conspiracy against the lone intellectuals in the ID creationist movement? Is this, as Alastair Noble contends, ‘Intellectual Fascism’?

Or is this really the paranoia of a small band of energetic people pushing a religious agenda?

Melanie Phillips displays scientific ignorance…twice

Melanie Phillips has in my opinion dug herself into a bit of a hole over the last few days, writing an opinion piece in The Spectator (Creating an insult to intelligence) concerning Intelligent Design (a subject she does seem ill-equipped to comment on), and after it got rather rubbished (by people who are better qualified), a lengthy follow-up also published in the Spectator (The secular inquisition). In the first article, Phillips is somewhat exercised by those who claim that ID is merely creationism in disguise – in particular a Radio 4 interview with Ken Miller, in which:

Miller referred to a landmark US court case in 2005, Kitzmiller v Dover Area School District, which did indeed uphold the argument that Intelligent Design was a form of Creationism in its ruling that teaching Intelligent Design violated the constitutional ban against teaching religion in public schools. But the court was simply wrong, doubtless because it had heard muddled testimony from the likes of Prof Miller.

Phillips goes on to define creationism as follows:

Creationism, whose proponents are Bible literalists, is a specific doctrine which holds that the earth was literally created in six days.

Of course, those of us used to dealing with fundie dimwits are aware that this merely described Young Earth Creationism. There’s a whole spectrum of creationist belief, including Francis Collins’  BioLogos, which is a rehashed theistic evolution. But what of ID? Of ID, Phillips says:

Intelligent Design, whose proponents are mainly scientists, holds that the complexity of science suggests that there must have been a governing intelligence behind the origin of matter, which could not have developed spontaneously from nothing.

So, here we have a definition that really describes a creation event. Indeed Phillips goes on to write:

The confusion arises partly out of ignorance, with people lazily confusing belief in a Creator with Creationism.

That doesn’t seem to me to be a lazy confusion. ID proponents do invoke a creator in the world-view. Indeed the Kitzmiller v Dover case clearly blew apart the claims of ID proponents that ID was indeed a scientific approach. In fact ID cannot make testable scientific proposals, because in the end, a supernatural entity is responsible. Phillips winds up with this:

On Today, Humphrys perfectly reasonably pressed Miller further. If ID was merely a disguised form of Creationism, he asked, why were so many intelligent people prepared to accept ID but not Creationism? Miller replied:

Intelligent people can sometimes be wrong.

Indeed; and it is Prof Miller who is wrong. Creationism and Intelligent Design are two completely different ways of looking at the world; and you don’t have to subscribe to either to realise the untruth that is being propagated — and the wrong that is being done to people’s reputations — by the pretence that they are connected.

Actually, intelligent people can be wrong. Phillips may well be intelligent, but it would seem that on scientific issues she is woefully undereducated. A quick squizz at Wikipedia reveals not only that her higher education was in English at St Anne’s College, Oxford, but that she’s been involved in other scientific controversies. She apparently perpetuates the MMR-autism myth (earning the wrath of Dr Ben Goldacre, who is said to have called her “the MMR sceptic who just doesn’t understand science”) and is a global warming denialist.  So, should we take her views as to the scientific nature of ID seriously? I suggest not.

A number of bloggers have taken her to task over this article, notably Jerry Coyne, author of the excellent “Why Evolution is True” (a book, incidentally, that Phillips should read, if she’s not done so already), who blogged (UK columnist defends intelligent design) a brief but heavy criticism. In response to that article and others, Phillips came out fighting, with the second Spectator article, and one that’s even longer than the first, but even less convincing. It’s this article that really reveals the depths of Phillips ignorance. Classic misapprehensions abound:

So what’s the big hullabaloo about? ID proponents are said by the Charles Johnsons of this world to deny evolution. But this is not so. Creationists deny evolution. But ID proponents say over and over again they are not Creationists and accept many aspects of evolution, in particular that organisms develop and change over time.

What they don’t accept is that random, blind-chance evolution accounts for the origin of all species and the origin of life, the universe and everything. ID proponents say the idea that science can account for everything – the doctrine known variously as materialism or scientism – flies in the face of reason and evidence and seeks to commandeer the space previously reserved for the unknowable, or religion, which can sit very comfortably alongside science, as it does for so many. [my emphasis]

Well, actually, evolution isn’t “random blind-chance”, as any biology student would know, and evolution does not concern “the origin of life, the universe and everything”. Phillips later writes:

ID is thus a paradox. The whole point is that it states that the ‘intelligent designer’ it posits as the only logical inference from scientifically verifiable complexity cannot be known through scientific means. This is because the essence of the ID idea is that there is a limit to science beyond which it cannot go, since science cannot prove nor disprove the existence of God nor any kind of ‘ultimate designer’ of the universe which thus stands outside that universe and its laws. That is where science stops and faith begins.

OK, so there we have it, clearly stated by Melanie Phillips – Intelligent Design is not science. Can she now accept that she has been pontificating about something she doesn’t know about or understand? Well, sort of:

To repeat – I have no particular brief for ID. I am not in a position to judge whether its arguments about ‘irreducible complexity’ and the logic of intelligent design are soundly based or not. But I do know that the attempt to shut down this debate runs against every principle of rationality and scientific freedom; and that the claim that it is rooted not in science but in religious fundamentalism is a falsehood designed to smear and intimidate people into silence.

Phillips clearly isn’t in a position to judge ID on its scientific merits. She shouldn’t have written the first article, let alone dig herself deeper with the second.  Jerry Coyne’s latest response can be found at his blog (Poor beleaguered Melanie Phillips!). He finishes with this line “On the other head, maybe she’s just ignorant and biased, like the Inquisitors themselves.” On the evidence of these two articles, I’m inclined to agree.

Stephen Green, Christian Voice and vaccinations

Stephen Green, the batty bloke behind Christian Voice, resurfaced this week (after a glorious period of silence) as one of the complainants over the Corrie-creationism brouhaha.  Coincidentally, I notice that The Lay Scientist, who’s been blogging lately about The Daily Mail and its bizarre campaign against vaccination (oddly this appears to be restricted to it’s UK operation – its Irish output takes the opposite view) has posted an amusing article about the ASA’s comprehensive slapdown of Christian Voice (Christian Voice, the HPV Vaccine and Freedom of Speech).  The final paragraph is:

This of course is the same Stephen Green who sued the BBC for blasphemy, who upon the abolition of blasphemy laws in 2008 threatened that Christians would have to “take matters into their own hands” if people said anything that might offend God or Christ. In other words this odious little creature, a man who believes that husbands should have the right to rape their wives at will believes in freedom of speech only when it applies to him. He is a disgrace, to fellow Christians and to human beings in general.

Some of the commenters follow those links and are pretty appalled by what they find.

Confused response to Texan science education guidelines

Responses to the new guidelines for science education in Texas seem divided. The Freethinker blog takes the optimistic view (Evolution trumps creationism in Texas), saying:

The State Board of Education stripped two provisions from proposed science standards that would have raised questions about key principles of the theory of evolution.

The sections, according to this report, were written by board Chairman and creationist Don McLeroy. They would have required students in high school biology classes to study the “sufficiency or insufficiency” of common ancestry and natural selection of species. Both are key principles of Charles Darwin’s theory of evolution.

In identical 8-7 votes, board members – Five Democrats and three Republicans – joined to outvote the seven Republicans on the board aligned with fundie groups.

The vote means that students will now have to:

Analyze, evaluate, and critique scientific explanations by using empirical evidence, logical reasoning and experimental and observational testing.

For many onlookers, however, the new wording still leaves a lot to desire.  The Discovery Institute (who are of course pro-creationism/ID) seem quite pleased in their blog (Darwinists Trick Themselves in Texas).  Unfortunately they don’t appear to welcome critical thought or comment, so commenting is not possible there (I suppose that’s appropriate with that kind of blinkered religious world-view).

Science now weighs in with its view (New Texas Standards Question Evolution, Fossil Record – may require subscription):

New science standards for Texas schools strike a major blow to the teaching of evolution, say scientists and educators who last week tried unsuccessfully to block the adoption of last-minute amendments aimed at providing an opening for the teaching of creationism. The standards incorporate talking points from the intelligent design literature, including doubt that the fossil record provides convincing evidence of evolution. Supporters of the new standards, who prevailed on 27 March by a vote of 13 to 2, say the next step will be to press publishers to modify biology textbooks.

Science quotes Don McLeroy (the dim creationist dentist, who for some bizarre political reason chairs the relevant education board) as saying

“I think the new standards are wonderful,” says Don McLeroy, chair of the Texas Board of Education and a dentist who claims that “dogmatism about evolution” has sapped “America’s scientific soul.” McLeroy believes that biology texts, to meet the new standards, should include “an evaluation of the sudden appearance of fossils” and “an explanation of stasis or how certain organisms stay the same over time.” He also wants the textbooks to declare there is no “scientific explanation for the origin of life” and that “unguided natural processes cannot account for the complexity of the cell.”

The dim dentist is looking forward to the adoption of new textbooks in the next two years.  Recent amendments that students must learn the “strengths and weaknesses” of evolutionary theory were struck off, leading to (probably premature) jubilation in the science camp.  However the second day of the meeting saw the creationist lobby prevail with the addition of phrases such that teachers must “analyze, evaluate, and critique scientific explanations in all fields of science by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of scientific evidence of those scientific explanations so as to encourage critical thinking by the student.”  Further requirements to “analyze and evaluate scientific explanations concerning the complexity of the cell”;  “analyze and evaluate the evidence regarding formation of simple organic molecules and their organization into long complex molecules having information such as the DNA molecule for self-replicating life”;  “analyze and evaluate a variety of fossil types such as transitional fossils, proposed transitional fossils, significant fossil deposits with regard to their appearance, completeness, and alignments with scientific explanations in light of this fossil data” leave considerable room for mischief, particularly from those of the Intelligent Design side of the creationist spectrum, who frequently try to make claims that their views are scientific (which they plainly are not).