Jonathan M who seems to have become a regular blogger for the Discovery Institute has noticed this blog once again (From the Darwinist Blogosphere, Stephen Meyer’s Trip to London Elicits a Typical Reaction) in a posting at the bizarrely named Evolution News website – no comments permitted there, it would seem. The BCSE believes Jonathan M to be Jonathan MacLatchie (sometimes his name is given as McLatchie), an undergraduate student in forensic science [UPDATE: Jonathan is now taking a Masters degree in Evolutionary Biology & Systematics at the University of Glasgow (!) ] who appears to have absorbed a typical strategy beloved of Intelligent Design creationists: of devising neologisms that don’t correspond to normally used science terminology, and combined this with ignorance of biology. P. Z. Myers was exposed to some of his ‘thinking’ while visiting Glasgow.

Jonathan begins with a quite mind-bending outline of DNA structure in regard to its genetic role.

For one thing, the point that Meyer makes about the bonding in DNA is that “there are no chemical bonds between the bases along the longitudinal axis in the center of the helix. Yet it is precisely along this axis of the DNA molecule that the genetic information is stored” (SITC, p. 242). It is this fundamental property of DNA that allows DNA to carry the information it does. The bases of DNA do not align in the sequential arrangement they do because of physical necessity or chemical affinity. The arrangement, on the contrary, is arbitrary — any arrangement is possible, but only some arrangements convey functional specificity.

This paragraph just baffles me. I presume this quotation is referring to adjacent bases along each DNA strand, rather that the base pairs themselves. I’m not clear why this ‘fundamental property’ bothers Jonathan M – he seems to have a major comprehension failure at this point.

Meyer’s argument also does not say that “x is complex; therefore, x is designed,” nor does Meyer commit the “god-of-the-gaps” fallacy. On the contrary, Meyer argues — based on the standard historical (abductive) scientific method — that there is only one known cause, one category of explanation, that is known by virtue of our uniform and repeated experience to be able to produce large volumes of highly complex (improbable) and functionally specific information. Thus, in the absence of viable competing explanations, it follows that the most likely explanation for this phenomenon is that it too arose by virtue of an intelligent cause.

Oh, for goodness’ sake, this ( “x is complex; therefore, x is designed,”) is exactly what Meyer is saying. He cannot envisage a mechanism giving rise to the genetic code, so he invokes a supernatural entity. And, yes, we have clearly demonstrable mechanisms by which genetic information can grow in both quantity and complexity. I even see this happening in the lab in experimental timescales.  Jonathan is ignorantly regurgitating ID creationist neologisms, to invoke a supernatural entity.

Jonathan takes a contributor to the CIS forum, Simon, to task, accusing him of not reading the ID creationist literature (I suspect that Simon, or “Simon” as Jonathan rather disparagingly refers to him, is somewhat better qualified to understand the science than he is, judging from his profile at the CIS forum):

“Simon” also cites polyploidy as a means by which specified complexity can arise. But Signature in the Cell is concerned with the origin of such specified complexity in the first life, and polyploidy concerns genome duplication in eukaryotes. Moreover, even in eukaryotes, polyploidy only appears to have a major effect within plants — so its relevance to the origin of the first life is dubious.

This is Jonathan wiffly-waffling around a subject he doesn’t seem to have a strong grasp of. It’s often stated in ID creationist circles (such as the C4ID) that there is no known source of ‘information’ other than from an intelligent mind. This is clearly nonsense, as Simon knows: gene and genome duplication provides the raw material for whole families of diverged genes to arise. What is ‘specified complexity”? Is it the genetic code itself? The mere existence of heritable material? Is this the same as Meyer’s undefined “specified information”?

Jonathan – your statement on polyploidy is naive. Genes duplicate. Sections of chromosome duplicate. Chromosomes can fuse and duplicate, genomes can duplicate. It’s not all about polyploidy. But once there is genetic redundancy due to duplication, novel gene functions can evolve. There are good examples of this in the scientific literature.

On Intelligent Design creationism’s testable predictions, as presented by Jonathan:

For example, it predicts the presence of complex and functionally specific information in the cell; it predicts the already-alluded-to rarity of functional protein folds in amino acid sequence space; it predicts certain patterns in the history of life (e.g., the saltationist nature of the fossil record; morphological disparity preceding diversity, etc.); it predicts that design purposes will be discovered for systems that are currently thought to be functionless (such as the discoveries of the past decade or two which have uncovered a myriad of functions for so-called “junk DNA”). In astronomy, it predicts that, as science progresses, the number of instances of fine tuning in the laws and constants of physics will increase and not decrease over time. And it makes many other predictions as well.

OK, here is why I think this is just so much nonsense:

“it predicts the presence of complex and functionally specific information in the cell” – This is a quite bizarre claim. The Intelligent Design variant of creationism arose in the 1990s. At that time, the presence of large amounts of genetic ‘information’ in cells was well-known. In what way is the presence of information a sensible prediction? And as far as I can tell, this whole ‘complex and functionally specific information’ remains remarkably ill-defined (see for example this demolition by Myers), and in particular is inconsistent with conventional information theory. If we’re now going to think of the origins of life and the genetic systems we see around us today, all ID creationists are saying is that they cannot understand how it happened, and in their religiously motivated world-view prefer to fall back on supernatural intervention rather than taking a genuinely scientific approach to the problem. How is complex and functionally specific information defined?

“it predicts the already-alluded-to rarity of functional protein folds in amino acid sequence space”. This is quite interesting, particularly given Axe’s background as a post-doc in Alan Fersht’s lab in Cambridge. But as far as I can see, this boils down to the usual incredulity argument. For Axe, with a pedigree of working in a prestigious lab in Cambridge, I would have thought a more prestigious outlet for this review might have been possible. As it is, he’s reduced to publishing in the Biologic Institute house journal, with the not-so-impressive archive of 7 papers over its two years of existence, all authored by members of the editorial board (all of whom appear to be creationists of one variety or another).

“it predicts certain patterns in the history of life (e.g., the saltationist nature of the fossil record”; morphological disparity preceding diversity, etc.). This sounds almost as though Jonathan is proposing a rather more interventionist kind of creationism than I normally understand is represented by Intelligent Design creationism: that intervention by a Designer (who, let’s face it, for the Discovery Institute is really the Judeo-Christian god, not Zeus, or Odin, or any other mythological entity) has been repeatedly intervening in the appearance of life-forms on Earth.  Of course, the links between Intelligent Design creationism (which publicly denies that the designer/creator is God) and other forms of creationism, notably those of the Young Earth persuasion have been pretty clearly documented.  Indeed the main figures in C4ID have clear links to biblical literalism and young earth creationism.

“it predicts that design purposes will be discovered for systems that are currently thought to be functionless (such as the discoveries of the past decade or two which have uncovered a myriad of functions for so-called “junk DNA”)” OK, so here Jonathan says that a prediction from Intelligent Design creationism is that design purposes will be found. This is frankly astonishing. How can purpose be ascribed to an unidentified ‘Designer’? How can we divine purpose? What purpose would Jonathan ascribe to his Designer/god’s intent to create the so-called Junk DNA? Where in his Bible does he see the culturally primitive scribes mention DNA when they are transcribing the word of the Designer/god?. This supposed prediction also invokes visions of the stultifying effect of dogma. It may well be that at church/temple/mosque/synagogue pronouncements can be made in the expectation that the word of the deity (as relayed by the priesthood) will be unchanging, but in a world of science, evidence counts. Not the ID creationist kind of negative evidence (“it seems improbable to me; I can’t understand why this is so”), but real, experimentally derived, evidence. Accordingly, the collective understanding of genome structure and function changes as evidence accumulates. As an undergraduate in genetics, one of the great mysteries was the so-called ‘c-value paradox’ – why did genomes vary so greatly in size, even between apparently closely related species?  As techniques and technologies advanced, a clearer and clearer picture of genome composition has been revealed. And, yes, some DNA has been referred to as ‘junk’. But as evidence is uncovered, some of this stuff does have a function. Not always a genetic function. And a lot of this is semantics. DNA sequences could have a ‘function’ related to their propagation (I’m thinking here of P-elements in Drosophila), but not a function that has a role in the biology of the organism.

“In astronomy, it predicts that, as science progresses, the number of instances of fine tuning in the laws and constants of physics will increase and not decrease over time. And it makes many other predictions as well.” The fine-tuning argument has always seemed to me to be somewhat tautologous. Had the constants been different, we would not be here to look at the Universe and its physical constants. We have a sample size of 1. Exactly 1. Who knows if physical constants could have been different. I certainly don’t (I’m not a physicist). I doubt that Jonathan does either, except it’s another of those claims that creationists parrot.

I would have thought the stand-out prediction of Intelligent Design creationism would be the unequivocal demonstration of the existence of that Designer/creator.

On the subject of Meyer’s book, I am at least displaying honesty when, as Jonathan observes, I say I didn’t read his book. Which is why I didn’t review the book, and I didn’t review the talk. Actually, one reason for thinking of attending the lecture would have been to get a copy of Signature in the Cell. But balancing the cost (not value) of the book (£8.99 at Amazon) with the travel costs to and from the venue (several times more than the cost of the book) I decided that wasn’t a good deal. I suppose the cost of travel may explain why Jonathan didn’t attend Meyer’s lecture either, and has chosen as I have done to make comment on Meyer’s other outputs. Besides, science isn’t usually advanced through popular science publications (which for example tend not to appear in University libraries). Usually, the popsci books follow genuine scientific advances published in bona fide science journals. Peer-reviewed journals. Genuinely peer-reviewed publications from Meyer are quite thin on the ground.

Jonathan refers to a list of supposedly peer-reviewed ID publications. I note the prominence of BIO-Complexity, the Biologic Institute’s house journal. With its seven papers in two years, it is hardly prolific and might be best regarded as vanity publishing. I have looked at two sevenths of its published output, and neither is a research paper.

Finally, I’m not a Professor, at least in the British sense of academia.

And finally, finally, I expressly did not review Meyer’s book, even though Alastair Noble claims I did in a comment in this blog.

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Back in September, I received a plain envelope at my work address.  In it was an invitation to attend an event in Whitehall, London.  This invitation from Lord Mackay of Clashfern, was for an’”Evening lecture and supper with Dr Stephen Meyer”, which would feature a “careful presentation of the ‘fiendishly difficult’ problem of the origin of life and the evidence for intelligent design”, and was held on 17th November.  I’ve obscured my name from the image below (click the image for a larger version).

Interestingly, the front of the invitation was a little coy about the organisers.  It did surprise me that Lord Mackay, one of the more outstanding lawyers of the 20th Century (according to Wikipedia) would take an interest in intelligent design creationism.  But Lord Mackay was a member of the Free Presbyterian Church of Scotland until a rumpus developed following his attendance at a Roman Catholic colleague’s funeral.  From Wikipedia:

Lord Mackay of Clashfern is also remembered for an incident when he, an elder of the Free Presbyterian Church of Scotland, attended the funeral Masses of two close Roman Catholic friends. On one of these occasions, Lord Mackay attended in his role as Lord Advocate as the deceased was a member of the judiciary. This was considered a grave offence by the Free Presbyterian Church authorities and he was suspended from church office, bringing about a split and the formation of Associated Presbyterian Church in 1989, which supported greater “liberty of conscience”.

Notably, the triumvirate  behind C4ID hold strongly religious views, and at least one is a lay preacher.

All is made clear on the reverse of the invitation, where the Centre for Intelligent Design logo is prominently displayed.  And indeed the accompanying letter is headed with the C4ID logo.  All attendees are to be blessed with a copy of Meyer’s book ‘Signature in the Cell’.

Bizarrely (as you can see), the reverse of the invitation uses a piece of puffery from  Thomas Nagel, Professor of Law and Professor of Philosophy at New York University.  This, rather than being derived from an actual review of the book (which, it might be suggested, a Professor of Law and of Philosophy might not be best equipped to deliver) was actually Nagel’s submission to the Times Literary Supplement 2009 Books of the Year.

I haven’t read Meyer’s book, so receiving a copy would have been interesting.  I have, however, read a number of articles about the book, both supportive and dismissive (particularly those who take issue with Meyer’s (mis)use of information theory), together with a number of Meyer’s articles.  Most of these are un-refereed book chapters, though a recent review paper has appeared in the Biologic Institute house ‘journal’ BIO-Complexity (of which, more later in this article).  As an aside, the Discovery Institute has released a brief publication entitled ‘Signature of Controversy‘, which is a response to the many criticisms of Signature in the Cell and very largely figures the rather abusive and puerile writing of one David Klinghoffer.

It would seem that the topic of the lecture (entitled “Is there a signature in the cell?”) principally relates to the origins of life, and in particular, it would seem to relate to the difficulty Meyer has in understanding how the genetic code was able to arise in the first place.  Of course, once organisms with heritable genetic material were present on Earth, normal and well understood evolutionary processes would have given rise to the diversity of life on the planet.  I don’t suppose that is something Meyer subscribes to, since he is one of the principal architects (and an author) of the Wedge Strategy- the duplicitous strategy that aimed to supplant evolution with creationism by an extensive rebranding exercise.  The scheme came a little unstuck when the Dover school board in Pennsylvania, which was at the time influenced by creationists, attempted to force Intelligent Design into science classrooms.  The subsequent trial (Kitzmiller v. Dover Area School District) ruled that Intelligent Design was a rebranding of creationism, that it was not a scientific approach and that teaching it in American schools was unconstitutiomal.  This judgement forced the Discovery Institute onto the back foot.  More recently, the Centre for Intelligent Design was established in the UK, based in Glasgow, apparently to regurgitate the DI line.

The Centre for Intelligent Design makes much of the supposition that only intelligence can bring about ‘information’.  Unfortunately from their point of view, increase (and decrease) in gene number and genome size are clearly observable, not only by comparative genomics studies of a wide variety of taxa, but by direct observation of within species genome variation. What’s more, those of us engaged in laboratory genetics are well aware of the kinds of genome changes that can occur even within the timescale of laboratory work.

In contrast to the ongoing efforts of science, one of the hallmarks of Intelligent Design creationism is that they don’t conduct novel research aimed at proving the existence of design.  How can they? – ID isn’t science and makes no testable predictions. What ID creationists do is to focus on individual cases where they assert evolutionary biology cannot explain how some feature arose (usually by claiming “irreducible complexity” or some such tosh) and claim that if evolution wasn’t responsible, intelligent design is the only alternative – a pretty dubious way of claiming evidence for ID.  Unfortunately for the likes of Michael Behe, each time one of these assertions is made, those pesky scientists come along and knock it down.  Examples include the bacterial flagellum and the vertebrate immune system.  The rather wonderful Nova TV documentary about Kitzmiller v. Dover Area School District I linked to the other day (US TV Documentary – Judgment Day: Intelligent Design On Trial) demolishes those two canards of intelligent design creationism in a very accessible fashion.

From what I’d read of Meyer’s written output, it seemed likely that Meyer’s tack would be to claim that the probability of the appearance of a genetic code that enabled life to begin is so vanishingly small that it must have been designed.  What I have noted is a paper by Meyer (with his colleage  Paul A. Nelson) in the Biologic Institute house ‘journal’ BIO-Complexity.  The Biologic Institute is funded by the Discovery Institute and really fits the Wedge Strategy as an attempt to portray ID as a scientific discipline, largely by playing at science.  BIO-Complexity is an example: an apparently above-board journal website with quite specific aims:

BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal’s scope.

(I note that Kluwer, a respectable scientific publisher, originally planned a journal called Biocomplexity: its launch issue was cancelled due to a lack of submissions.  I don’t think this should be confused with the Biologic Institute creation.)  BIO-Complexity’s editorial board comprises a disparate collection of people who support Intelligent Design creationism or, it would seem in some cases, a more conventional young earth creationism.  To date, and through two years of publishing, only a handful of publications have been made.  And these are derived from members of the editorial board, and largely include members of the Discovery and Biologic Institutes (vanity publishing?).

Meyer and Nelson’s recent publication in BIO-complexity is really an objection to the work of Yarus and colleagues modelling how an RNA world could have come into being.  It’s not really a research paper, and kind of fits the ID strategy of knocking down science with the intention of allowing an ID ‘explanation’ to fill the gap.  This would be in keeping with Meyer and Nelson’s expertise (Meyer qualified as an earth scientist and has a PhD in Philosophy of science, while Nelson similarly has a PhD in Philosophy): Nelson appears in the past to have held young earth creationist views.

My particular scientific field is not related to the origins of life, and it’s always seemed to me that figuring out how life began on Earth is particularly challenging, especially as our understanding of likely pre-biotic conditions changes periodically. Nevertheless, the scientific approach is to try and figure out plausible hypotheses: if Meyer and Nelson have bona fide concerns about Yarus’ hypotheses, I’d be the last to censor them.  I’d be even happier if Meyer and Nelson had the science background sufficient to set up their own experimental programme.

An email communication from C4ID a week or so before the lecture said in part (the comment is mine):

At the request of some guests and to encourage open discussion, we wish to conduct the evening with a modification of the Chatham House Rule as follows:  Guests are free to report, formally or informally, on the content of the lecture, the nature of the issues raised at question time, and the identities of the host, lecturer and representatives of the Centre for Intelligent Design.  However the identities of all the other guests who attend and who may contribute to the debate should not be revealed unless specific permission is given by them to do so. [ It's hard to see how the planned release of video recording of the event could avoid identifying attendees if they questioned the speaker] We thank you for respecting our wishes in this matter.

Quite what significance (if any) this holds I don’t know.  But one interpretation might be that attendance from individuals outside the obvious ID creationism circles was looking low, and the organisers felt this statement might encourage them to come along.  In the end, I chose not to attend, not because I have scientific objections to hearing Meyer’s message, but because I object to the Discovery Institute’s working methods, its deceptive Wedge strategy (of which Meyer is an author), and that attendance might be taken as offering support to ID creationism (despite C4ID’s intention that attendee identity be kept secret). I did not want to add apparent legitimacy to ID creationism my my attendance, even though my attendance would have been as a private individual rather than as a representative of my employer. Finally, I don’t believe that lectures delivered to lay audiences are the most effective way of communicating science (or, in the case of ID creationism, pseudoscience): I would much rather read the technical literature. Unfortunately, Intelligent Design creationists are unable to generate research of the kind that would find its way into the science literature.

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This blog is entitled “Wonderful Life” mostly because I find the world around me wonderful, in part because of what we do know of its origins, but also because of what we don’t (yet) know.  I don’t need to have any invisible creator to have instigated, directed or interfered in any way in the origins of life.  I noticed that PZ Myers of Pharyngula has posted this diagram (God’s timeline) of the history of the Universe (seen from a human perspective), comparing the scientific and creationist explanations:

I think the diagram originated over at Petros Goes On And On A Bit.  The diagram’s cool because it shows the enormity of big time, and how long the development of our planet and the life on it has taken to arise – and contrasts it with the truly less-than-wonderful biblical explanation.

Now, I know which I find more wonderful…

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This week’s Nature includes a brief paper that concludes that multicellular life originated about 100 million years earlier that previously known. The work places sponges in the Cryogenian period, >635 million years ago, prior to the Ediacaran period. See Flies & Bikes for more on this paper.  Formally, of course the paper suggests that either demosponges were there, or an ancestor – but still, more evidence of the antiquity of life on Earth!

Love et al (2009) Fossil steroids record the appearance of Demospongidae dueing the Cryogenian period. Nature 457; 718-723. doi:10.1038/nature07673 (subscription required)

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