C4ID: Digital cameras based on compound eyes, therefore Intelligent Design creationism. Eh?

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.

Discotute mask slips

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.

A March miscellany

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]).

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.

The ‘Logic’ of Sherlock Holmes

It’s always struck me that Intelligent Design creationists always seem to fall into a hole of illogic. Essentially, they will argue that a particular biological feature, (examples such as bacterial flagella, the vertebrate immune system, and the origin of life spring to mind) are complex, have a cursory investigation of what is known about those case…then pronounce they cannot have come about by natural causes hence an intelligent designer (aka god) must have done it.

This in many ways reflects one of the classic quotes of the fictional (let us remember) detective Sherlock Holmes.

“When you dismiss the impossible, whatever you have left, however improbable, is the answer.”

There’s a rather nice discussion of this piece of ‘logic’ over by Dave Gamble at the Skeptical Science blog: Beware The Logic of Sherlock Holmes. Essentially, it’s all very well applying such reasoning to a murder within a room with locked windows and doors, but in the real world of scientific research (as opposed to the fantasy world of Intelligent Design), it’s very difficult to rule that, for example, further detailed hypotheses concerning the origins of life may surface through conventional scientific approaches. Dave observes that one should always apply the following:

Are all the other options truly “impossible”?

Perhaps the very premise itself is wrong

In fact have you truly eliminated all other possibilities, is it not more possible that there is a simpler alternative that you have not yet considered?

To invoke an invisible magic designer to explain a bit of biology while denying that science may ultimately identify a plausible (or, dare I say it, demonstrable) explanation is nothing more than an elaborated ‘God of the Gaps’ argument (Intelligent Design creationism’s much vaunted “inference to the best explanation”). We saw this strategy shot down in flames at the Dover trial. And for ID creationists to claim an intelligent magic designer is the best explanation for the origin of life is just the same: scientific investigation has led to several hypotheses for origins of life. Based on evidence from chemistry and physics, and on what is know of prebiotic conditions on Earth, surely there is more going for those scientific hypotheses than a religiously motivated cop-out?

Happy Kitzmas 2012

It’s the seventh anniversary of the judgement in Kitzmiller v. Dover Area School District, the American court case that definitively rulled that Intelligent Design creationism was indeed religious and was therefore forbidden from publicly funded schools in the USA. I posted a more detailed overview this time last year (Happy Kitzmas!), making observations on the implications of the verdict.

In the last year, the C4ID has merely flailed around holding ‘conferences’ to preach to the already converted but not managing to insert Intelligent Design creationism into schools (Centre for Intelligent Design 2012). Indeed the biggest worry regarding schools and creationism has been the approval of a number Free Schools with the kind of religious ethos that is likely to bring with it the baggage of creationism – this remains a concern despite public pronouncements from the Government.

What will 2013 bring?

The not so irreducible complexity of the mousetrap

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.

Thursday linkage

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.

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.