The New Yorker has an interesting and well written blog article by Gareth Cook that reviews the new Discotute tome Darwin’s Doubt - Doubting Darwin’s Doubt. Cook places the book and Meyer’s argument in the context of the history of Intelligent Design creationism as a cynical rebranding exercise aimed at inveigling creationism back into American schools after a series of legal setbacks for creationists. Well worth reading. Cook notes the odd approach of ID creationists – that scientific understanding of the world and universe has reached its limits, and that what is left can only be explained by the interventions of God a supernatural designer:

Most absurd of all is the book’s stance on knowledge: if something cannot be fully explained by today’s science—and there is plenty about the Cambrian, and the universe, that cannot—then we should assume it is fundamentally beyond explanation, and therefore the work of a supreme deity.

Darwin’s Doubt may well have entered the New York Times hardback bestseller list (oddly, I think this is in the non-fiction section), but amongst those who know an understand science, and particularly those disciplines related to evolutionary biology, it’s very unlikely to gain any traction.

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Stephen Meyer’s latest creationist book, Darwin’s Doubt, was launched a week or so ago, so it was only a matter of time before Glasgow’s Discotute wannabees C4ID joined the fun. And so it proves, with the latest missive from chemist Dr Alastair Noble reaching my inbox.

Unfortunately for Meyer (who is not a biologist) his latest tome, published by the religious imprint HarperOne, has already been reviewed and dissected (Meyer’s Hopeless Monster, Part IILuskin’s Hopeless Monster) by people more competent than he in matters to do with evolution, palaeontology  phylogenetics and phylogeny. The email from C4ID seems to consider scientific understanding of the world (and indeed the Universe) around us to be some kind of popularity contest, in which determined attempts to dupe the public into believing that Intelligent Design creationism is in any way a credible explanation of life’s diversity will in some way make the existence of a supernatural ‘designer’ into a reality. Apparently believing that evolutionary biology, palaeontology and geology have all stood still since the middle of the 19th century, Alastair Noble provides the following quotations from The Origin of Species, and in so doing resorts to the traditional creationist trick of selective quoting, aka ‘quote mining‘. As is usual in creationist circles, Darwin’s the victim (see the Talk Origins Quote Mine Project).

‘The number of intermediate varieties, which have formerly existed on earth, must be truly enormous.  Why then is not every geological formation and every stratum full of such intermediate links?  Geology assuredly does not reveal any such finely graduated organic chain.’

On looking at The Origin of Species, we find this passage. Note however the final sentence – which I’ve underlined, a sentence in which Darwin gives an explanation.

‘In the sixth chapter I enumerated the chief objections which might be justly urged against the views maintained in this volume. Most of them have now been discussed. One, namely the distinctness of specific forms, and their not being blended together by innumerable transitional links, is a very obvious difficulty. I assigned reasons why such links do not commonly occur at the present day, under the circumstances apparently most favourable for their presence, namely on an extensive and continuous area with graduated physical conditions. I endeavoured to show, that the life of each species depends in a more important manner on the presence of other already defined organic forms, than on climate; and, therefore, that the really governing conditions of life do not graduate away quite insensibly like heat or moisture. I endeavoured, also, to show that intermediate varieties, from existing in lesser numbers than the forms which they connect, will generally be beaten out and exterminated during the course of further modification and improvement. The main cause, however, of innumerable intermediate links not now occurring everywhere throughout nature depends on the very process of natural selection, through which new varieties continually take the places of and exterminate their parent-forms. But just in proportion as this process of extermination has acted on an enormous scale, so must the number of intermediate varieties, which have formerly existed on the earth, be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.’

Here’s another interesting mangling of Darwin by C4ID:

‘The difficulty of understanding the absence of vast piles of fossiliferous strata, which on my theory were no doubt somewhere accumulated before the Silurian (ie Cambrian) epoch is very great. I allude to the manner in which numbers of species of the same group suddenly appear in the lowest known fossiliferous rocks.’

The text from darwin is as follows:

On the sudden appearance of groups of Allied Species in the lowest known fossiliferous strata.
There is another and allied difficulty, which is much graver. I allude to the manner in which numbers of species of the same group, suddenly appear in the lowest known fossiliferous rocks. Most of the arguments which have convinced me that all the existing species of the same group have descended from one progenitor, apply with nearly equal force to the earliest known species. For instance, I cannot doubt that all the Silurian trilobites have descended from some one crustacean, which must have lived long before the Silurian age, and which probably differed greatly from any known animal. Some of the most ancient Silurian animals, as the Nautilus, Lingula, &c., do not differ much from living species; and it cannot on my theory be supposed, that these old species were the progenitors of all the species of the orders to which they belong, for they do not present characters in any degree intermediate between them. If, moreover, they had been the progenitors of these orders, they would almost certainly have been long ago supplanted and exterminated by their numerous and improved descendants.
Consequently, if my theory be true, it is indisputable that before the lowest Silurian stratum was deposited, long periods elapsed, as long as, or probably far longer than, the whole interval from the Silurian age to the present day; and that during these vast, yet quite unknown, periods of time, the world swarmed with living creatures.

To the question why we do not find records of these vast primordial periods, I can give no satisfactory answer. Several of the most eminent geologists, with Sir R. Murchison at their head, are convinced that we see in the organic remains of the lowest Silurian stratum the dawn of life on this planet. Other highly competent judges, as Lyell and the late E. Forbes, dispute this conclusion. We should not forget that only a small portion of the world is known with accuracy. M. Barrande has lately added another and lower stage to the Silurian system, abounding with new and peculiar species. Traces of life have been detected in the Longmynd beds beneath Barrande’s so-called primordial zone. The presence of phosphatic nodules and bituminous matter in some of the lowest azoic rocks, probably indicates the former existence of life at these periods. But the difficulty of understanding the absence of vast piles of fossiliferous strata, which on my theory no doubt were somewhere accumulated before the Silurian epoch, is very great. If these most ancient beds had been wholly worn away by denudation, or obliterated by metamorphic action, we ought to find only small remnants of the formations next succeeding them in age, and these ought to be very generally in a metamorphosed condition. But the descriptions which we now possess of the Silurian deposits over immense territories in Russia and in North America, do not support the view, that the older a formation is, the more it has suffered the extremity of denudation and metamorphism.’

Note the splitting and reordering of Darwin’s text. Note also that this selective quoting is identified at the Talk Origins Quote Mine Project (quote #2.4), where the section of text is set correctly in context.

What’s really peculiar about the Discotute’s publicity drive for Darwin’s Doubt isn’t so much related to the content of the book (see Matzke’s review for a deconstruction of that), but this tendency of creationists (and I include Intelligent Design creationists here) to hang all their angst about natural explanations of life’s diversity on Darwin – labelling those of us who see the vast quantity of evidence supporting evolution as outweighing the absence of evidence for the existence of supernatural entities as Darwinists (see Paul Braterman’s blog for more on this – Don’t say Darwin unless you mean it – for more on this).

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A couple of years ago, I took the effort to read and review Stephen Meyer’s book Signature in the Cell, a risible romp through misrepresentations of molecular biology, origins of life research and information theory (No Signature in the Cell). My heart sank when I saw that Meyer was to publish another book, entitled Darwin’s Doubt, this time seeking to expose supposed problems with the fossil record, particularly around the so-called Cambrian Explosion. The Discovery Institute have trailed this book mercilessly over the past couple of months, even appealing for donations to support the publicity drive.

This morning Nick Matzke’s review of the book was posted at Panda’s Thumb (Meyer’s Hopeless Monster, Part 2), and frankly, it’s a devastating critique. The review points out serious deficiencies in Meyer’s understanding of Phylogenetics, Phylogenetic Taxonomy, or current understanding of the Cambrian and pre-Cambrian fauna.  And as an added bonus, I don’t need to read it.

The book is published by HarperOne (as was Signature in the Cell). HarperOne describes itself as follows:

For 30 years we have published the books that have changed people’s lives, influenced culture, built bridges between faiths, and withstood the test of time. View this video for more about HarperOne and our authors and readers.

The most important books across the full spectrum of religion, spirituality, and personal growth, adding to the wealth of the world’s wisdom by stirring the waters of reflection on the primary questions of life while respecting all traditions.

So I imagine that’s a reasonable home for Meyer’s book, given the Discovery Institute’s Wedge Strategy.

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Paraphyly

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Another week, another silly article at the C4ID website! Antony Latham, a GP in the Outer Hebrides, has penned a peculiarly illogical article (The compound eye of arthropods is a model for designing specialised digital cameras) leading from a paper which outlines how the arthropod compound eye has been used as a model for designing digital cameras. Ultimately, of course, he takes the usual creationist tack of claiming (i) that the evolution of visual systems has not been explained, and that (ii) this means that supernatural creation is the only alternative answer. Since Latham believes (I think) in only one more divine entity than I do, I guess that means the biblical god.

Dickinsonia costata, of the Ediacaran biota. (via Wikipedia)

But what’s the basis for this claim that we don’t know how eyes (in this case compound eyes of arthropods) evolved? His claim is that we have no direct physical evidence (i.e. fossils) – and dismisses the paucity of soft-bodied fossils as an explanation because we have the Ediacaran fauna. The Ediacaran fauna are somewhat enigmatic (see the image to the right) – we don’t really know what kind of organisms these were, or whether they had light-sensitive structures (let alone structures capable of forming or perceiving images). Fossils of soft-bodies Pre-Cambrian organisms are still rare, and it seems likely that primitive eye-spots might be hard to recognise in such fossils.

Fossils are of course not the only evidence that may be used to study the evolutionary origins of eyes – biologists look at biochemical, molecular, genetic and of course morphological evidence within extant taxa. We also have functional studies, such as those concerning the transcription factor Pax6, which appears to be involved in the early stages of forming eye structures in diverse taxa.

But what is striking about the creationist approach – and let’s face it, Intelligent Design creationism is no exception – is that creationists cannot even be bothered to look at the depth of scientific investigation into questions around the origins and evolution of eyes. Instead they revel in their ignorance and proudly proclaim (generally erroneously) that evolutionary biology can’t explain <something>, therefore a god/creator/designer must have done <something>. Latham cites Gould’s Wonderful Life – a 24 year old popular science account of the rediscovery of the Burgess Shale fauna. I scratched my head a bit at this: while it is well over 20 years since I read it, I didn’t recall any attempt to describe the evolution of compound eyes. Sure enough, the three mentions of eyes found in the index merely point to descriptions of Burgess Shale arthropods which have compound eyes. [Latham also cites his own work, The Naked Emperor: Darwinism Exposed, portions of which can be read via Google Books. On the basis of those samples, I am unlikely to cough up for the book.]

Creationists, whose view of the world is seemingly blinkered by the closed and literalist view of a ‘holy book’, appear to believe that scientific investigation has similarly reached its limits and what is not yet understood will never be understood. Just a quick Google search reveals numerous publications in which biologists have applied, and are evidently continuing to apply, a wide variety of approaches to address the question of the origin and evolution of eyes (I’ve listed a couple below). As usual, the Intelligent Design creationist approach is found seriously wanting.

Oakley (2003) On Homology of Arthropod Compound Eyes Integr. Comp. Biol. 43 (4): 522-530. doi: 10.1093/icb/43.4.522 – addresses the issue of whether the compound eyes of arthropods are monophyletic or not: that is, whether they arose more than once in the arthropods.

Gehring (2011) Chance and Necessity in Eye Evolution Genome Biol Evol 3 1053-1066.doi: 10.1093/gbe/evr061 – Gehring’s lab discovered that the transcription factor Pax6 seems to play a universal role in the initiation of eye development during development. Gehring proposes (on the basis of conserved function between vertebrate and insect Pax6) that eyes are derived from a single evolutionary origin. This review is worth reading for the overview it provides of the conserved genetic pathways in eye development.

Postscript

Just as I was about to publish this, an article by Rosa Rubicondior popped into my feed: Dunning-Kruger Creationists. It seems rather relevant.

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P Z Myers amuses me with his latest Pharyngula posting on Intelligent Design creationism: The Discovery Institute’s mask just slipped a bit more. The post includes a video from the Discovery Institute’s Stephen Meyer, who pontificates away about the existence of his god/creator. Meyer repeats once more the silly misrepresentations of Signature in the Cell, and really comes of the fence. Once more the Discotute claims that Intelligent Design creationism is science slip further away. As Myers says:

It’s been settled for a long time, but this is one more nail in the coffin: Intelligent Design is simply a front for religious pitchmen. And not just any religion, but far right Christianity.

I note that the video is linked with (produced by) Focus on the Family, and its “The Truth Project”. I somehow doubt their definition of Truth accords with mine.

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T. Ryan Gregory has posted a transcript of a BBC Radio 4 programme featuring ENCODE’s Ewan Birney – he discusses the 80% functional genome flap (BBC interview with Ewan Birney | Genomicron). You can hear the original broadcast. It’s just a shame they puffed up the 80% claim in the first place.

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Here’s a miscellany of stories from around the web. Apologies for the inaction at this blog of late.

C4ID peddle paranoia in Shetland.

The BCSE blog occasionally features items under the banner Creation Watch. A recent report () details an event organised in Shetland by Glasgow’s very own Discotute wannabees, the Centre for Intelligent Design (C4ID). The event appears to have emphasised the bizarre blend of paranoia, religious fervour and bad science that characterises the Intelligent Design brand of creationism. Fortunately, a rational and scientifically educated BCSE member was able to attend and report back on the event. His/her concluding remarks are interesting:

The Q & A session finished with the elderly man thanking Noble for joining us [massive round of applause] and he encouraged us to visit the local Christian bookstore and express our own interest in having Dr. Noble return for another talk to answer our many questions. This explains why The Centre for Intelligent Design was in Shetland, they were invited by the church-goers!

I don’t feel Dr. Noble really answered anyone’s questions. He talked, a lot, and very loudly, but there was no real substance to his words. Surprisingly no one asked “Who or what is responsible for this intelligent designing?”. I wanted to but I did not feel comfortable enough to ask and Noble’s previous lack of really answering anyone else’s questions led me to believe he would not answer mine either. His loud confrontational tone of voice and his obvious contempt for real science really put me off.

Not once was a god mentioned, although there was a large display of Christian books available to buy.

I left with the same unanswered question. There was no ‘unlocking of the mysteries of life’ unless I was willing to believe some yet unnamed intelligent mind designed it based on inference. I felt the topic was shifted from the realms of science to another department entirely, the realms of religion.

There doesn’t appear to have been much new here from C4ID, they are just peddling the tired old canards of ID creationism. Apparently they are trying to get the BBC to broadcast the dodgy creationist video Unlocking the Mystery of Life. I don’t think replacing rational investigation with supernatural ‘explanation’ unlocks any mysteries whatsoever. Good luck with that, Dr Noble.

Stephen Meyer writes again

It appears from an article at Panda’s Thumb that Stephen Meyer, one of the architects of the Wedge Strategy, has penned another book. This time Meyer tackles the so-called Cambrian Explosion. Having ploughed through his Signature in the Cell (see No Signature in the Cell), I’m in no hurry to read more of Meyer’s religiously-inspired writing. Apparently it’s going to be entitled Darwin’s Doubt, though I suspect that Stephen Meyer’s Doubt may be a better title. The Wedge Strategy, of course, outlines the Discovery Institute’s game plan for replacing science with religion and gives the lie to the Discotute’s assertion that Intelligent Design isn’t merely a rebranding of creationism.

I suppose this book is why the Discotute was soliciting pictures of the Burgess Shale (An amusing exchange between a Discotute employee and a Geology professor).

ENCODE and Junk DNA

I posted recently about a takedown of ENCODE’s claims regarding junk DNA (Takedown of ENCODE’s claims that 80% of the human genome is functional). Further publications have now emerged – see Larry Moran’s summary at Sandwalk (Ford Doolittle’s Critique of ENCODE) which hangs on a recent paper by Doolittle in PNAS (Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) an advance online publication on March 11, 2013. [doi: 10.1073/pnas.1221376110]).

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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.

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In this rather splendid blog article (The Discovery Institute feels sorry for my students – Mountain Beltway – AGU Blogosphere), Callan Bentley reveals a brief email correspondence between a Discotute ‘media relations specialist’, and writes an excellent takedown of Intelligent Design creationism.

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