C4ID, ‘Expelled’ and dishonesty

December 16, 2012 in Centre for Intelligent Design by admin | No comments

A few years ago, a bizarrely deceitful film was released: Expelled: No Intelligence Allowed. This pro-Intelligent Design creationism production made a variety of assertions, and did feature some interviews with the likes of Richard Dawkins – obtained by misrepresentation and edited to significantly alter the interviewees’ opinions. See for example what they did to Dawkins.

The website Expelled Exposed gives a detailed analysis of this film. Many websites exposed the deceitful strategies taken by the produced of the film, and the company behind it eventually went belly up and its assets sold off – including the film itself.

So, what do I find at the C4ID website, but a transcript of the interview segment with Richard Dawkins, together with a commentary from Alastair Noble.

Dr Alastair Noble: you should be ashamed of yourself for repeating this dishonesty.

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Centre for Intelligent Design 2012

December 15, 2012 in Centre for Intelligent Design by admin | 4 comments

No sooner had I noted that the jolly old Discotute wannabees C4ID had been rather quiet of late than I received an email update, representing something of a review of 2012. Apparently

We’ve had a very productive year and it has been an exciting 12 months for the advance of Intelligent Design (ID) more generally.

So what have Alastair Noble and Co been up to in 2012?

Junk DNA a myth?

Well, first off, C4ID trumpet the death of junk DNA. This of course reveals their ineptitude as regards biology. I would refer readers to this article which contains links debunking this idea that 80% of the human genome is ‘functional’: ENCODE, junk DNA and creationists. Oh, and this too: Sean Eddy on Junk DNA. Essentially the ENCODE project redefined the word ‘functional’ to include DNA sequences with no biological function. Of course creationists (especially ID creationists) bought that line as it suited their brand of science denialism to the hilt. How else could they explain their magical designer/creator’s ineptitude in saddling us (and pretty much all other eukaryotes) with so much apparently meaningless DNA?

Nagel’s book and Meyer’s book

Next up is the story that philosopher Thomas Nagel wrote a book addressing the ‘Darwinian Conception of Nature’. Readers might check out Jerry Coyne’s blog Why Evolution is True for more on Nagel on evolution. I’m not sure why this merits mention in C4ID’s review of 2012, as the book doesn’t seem to be connected to C4ID. Of course Nagel nominated Signature in the Cell as one of his books of 2009 (rather old news). But readers might refer to the Wikipedia page on Nagel as regards Intelligent Design: it seems odd to me that Alastair Noble brings Nagel up in the context of ID creationism. I reviewed Meyer’s Signature in the Cell and found it a poor effort. Meyer is one of the authors of the Wedge Strategy, the smoking gun that reveals the creationist roots of Intelligent Design.

The Tyndale Philosophy Conference

Alastair Noble seems quite pleased at the success of this meeting where ID creationists spoke to other ID creationists and presumably reinforced their opinions. This is the same strategy used for the Malvern ID conference.

And finally

C4ID welcomes Dr Emma Carter to their ranks, as Academic Liaison Consultant. Dunno exactly what that role would be, but we’re to expect a website refresh.

Who’s Emma Carter? C4ID don’t say. A quick google for Dr Emma Carter (“emma carter” + “intelligent design”) brings up one candidate, an engineer, (but no direct evidence that these two Carters are the same).

I think 2012 has been business as usual for C4ID. Which means they continue to fail to overturn a century and a half of research which has built upon Darwin’s theory, and which ultimately explains very effectively the diversity of life on this planet.

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Review: From Stars to Stalagmites – How everything connects

December 11, 2012 in review, science by admin | 5 comments

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.

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Free schools must teach evolution

November 30, 2012 in creationism by admin | 5 comments

There’s an article in today’s Guardian which indicates that all these free schools which form part of Michael Gove’s misguided concept of state centralisation of education must teach evolution (Free schools must teach evolution, ministers announce).

All free schools will be forced to present evolution as a comprehensive and central tenet of scientific theory, ministers have announced, following lobbying by senior scientists concerned that Christian-run institutions could exploit loopholes in the rules to present creationism as a credible theory.

The significance here is clear – for all the free schools founded by the more extreme sectors of evangelical christianity (and, I guess, schools run with any other religious ethos) evolution must be taught as part of the science curriculum. The worry had been that such Free schools such as the Grindon Hall Christian School (see The Grindon Hall Creation Policy document) would teach their (ir)relevant creation myths under the guise of Religious Studies, and then just omit evolutionary biology from their science classes.

Still, worries must arise around just how these religiously motivated Free schools will be inspected – both in terms of how effective this can be and who actually does the inspection.

Wouldn’t it just be easier not to allow these kinds of people to run schools in the first place?

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The not so irreducible complexity of the mousetrap

October 23, 2012 in intelligent design by admin | No comments

The rather nice Bioimplement blog, which alas is updated somewhat infrequently has a particularly detailed overview of the history of the mousetrap. The mousetrap is often cited to illustrate the concept of irreducible complexity: a device  which could not function with one of its parts missing. Irreducible complexity is one of those important concepts of Intelligent Design creationism, helping ID creationists posit the existence of a god designer because the ID creationist cannot conceive how complexity can arise through non-supernatural means.

Anyway, a new article at Bioimplement traces the patent history of the modern day mousetrap (The mouse trap, redux), and finds it has a rather neat evolutionary history, which can be traced back to a fish hook.

The article itself is splendidly detailed, and is an entertaining read. Well worth reading.

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Sean Eddy on Junk DNA

October 21, 2012 in science by admin | 1 comment

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.

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Thursday linkage

October 11, 2012 in creationism, intelligent design by admin | No comments

Since my time available for blogging has somewhat disappeared at the moment, I’m merely going to briefly link to postings generally relevant to creationism.

Peer reviewed Intelligent Design creationism?

Claims of Peer Review for Intelligent Design examined … and debunked – Dave Gamble reviews the supposedly peer reviewed publications of intelligent design creationism, focussing on the output of the Discovery Institute. His initial filter weeds out papers in BIO-Complexity, the house journal of the Biologic Insitute (the research arm of the DI). Similarly, other classes of output are cast aside. Dave’s conclusion?

The complete lack of any credible scientific evidence tells you all you really need to know. Is there any scientific foundation for Intelligent Design? The quick one word summary is “No“.
With no credible evidence on the table, any and all creationist claims need not be addressed, but instead should simply be dismissed. If they wish to ever assert a claim that is not dismissed, then they need to first go do some science that backs it up.

But you really should read the article.

ENCODE and the reality of junk DNA

Of course, the big news in the last few weeks has been the bizarre claims of the ENCODE project that they have identified a ‘function’ for 80% of the human genome…and they expect that proportion to increase. This was eagerly set upon by ID creationists as some kind of demolition of the existence of junk DNA, along with erroneous claims that junk DNA was originally defined or equated with non-coding DNA. Of course, the latter is incorrect, and anyway, the ENCODE project had to redefine ‘function’ to get the 80% figure. It’s worth reading ENCODE says what? at the Cryptogenomicon blog – written by labs who really know what they are talking about.

Similarly T. Ryan Gregory at Genomicron has weighed in: ENCODE spokesperson: 40%, not 80%; Student ENCODE authors show the way; Good reads about ENCODE; ENCODE (2012) vs. Comings (1972). Many of these articles present a clear historical perspective.

Sites like Genomicron and Cryptogenomicron have articles that really ought to put to rest this new fable that Junk DNA is a myth, but it has spread like wildfire round the internet at the hands of those who are too ignorant or deceitful to understand the reality of the data.

The Salem hypothesis revisited

Here’s a blog article that popped up in my Trapit app the other day: Intelligent Design, Evolution, & Molecular Machines. The author, Orrin Woodward, would appear to be an engineer. That an engineer might sign up to ID creationism shouldn’t really be a surprise (see The Salem Hypothesis).

Almost unbelievably, Woodward homes in on that most discredited example of irreducible complexity, the bacterial flagellum. Reading this made it seem I was in a time warp and had ended up pre-Dover! What gives the game away are a series of quotations from the bible. Woodward closes with an exhortation “Indeed, it’s not as important that we all think the same, but it is desperately important today that we all start to think.” Unfortunately, his blog article clearly demonstrates the author’s unwillingness to think beyond outdated and discredited creationist misrepresentation of biology and his own religion’s sacred texts.

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ENCODE, junk DNA and creationists

September 11, 2012 in Centre for Intelligent Design, science by admin | 2 comments

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?

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Information Input Theory – A Trademarked “Research Field”?

September 4, 2012 in intelligent design by admin | 6 comments

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.

 

 

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The Grindon Hall Creation Policy document

July 25, 2012 in atheism by admin | 1 comment

In a rather incoherent* article in the Sunderland Echo, the Principal of Grindon Hall Christian School has made interesting claims about the much-discussed ‘Creation Policy’ document (Headteacher blasts claims his city school teaches creationism – All News – Sunderland Echo)

Chris Gray, principal of Grindon Hall Christian School, slammed a report that claimed the Pennywell school was run by a group with creationist views. The report, which appeared in a national newspaper, also claimed there was a document on the school’s website stating they taught creationism as a scientific theory. However, Mr Gray said the document was removed years ago and was originally written to distance the school from those views.

It’s interesting to note that the document really was present on their web server last week, when I blogged about it. I guess, strictly speaking, since there wasn’t a link from a web page, it could be argued that it wasn’t on their website…I suppose. But Mr Gray goes on to claim

“When we applied to the Government to become a free school they made sure of that and what The Guardian has done is find a very old document that we took off the website in 2005.”

Well, that doesn’t compute, since according to the Word file’s properties the document was created by Rachel Nurse (who appears to be a school administrator) in 2007. Mr Gray also claims

“And it was first written to distance ourselves from the issue of creationism. “I don’t believe in creationism, none of my staff believe in it and so I’m hoping this will blow over.

I don’t really understand how this document could be seen as having been written to distance the school from creationism. The document has now been deleted from the School’s webserver, but I imagine I’m not alone in having a copy.

* I’m not accusing the Principal of incoherence, merely that the printed article is incoherent.

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