In reponse to the latest crawling from a Student Union over the recent Jesus and Mo fracas, and indeed the recent example of intimidation at an event featuring a dicussion of sharia law and women’s rights:

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The blog’s been a bit quiet lately, because I have been busy.  Partly with work, but also because I embarked on reading one of the major works in the Intelligent Design canon.

I am halfway through Stephen Meyer’s opus ‘Signature in the Cell’. (I bought this as a Kindle edition, which hasn’t been well put together by the publisher).  So far he’s been alternating between schoolbook level molecular biology, and a history of theories of the origin of life (his treatment of origin of life is rather more detailed, and presumably reflects elements of his PhD thesis).  Intermingled with this are strange bids for sympathy (for example over the Dover trial and the fiasco of the improperly refereed paper) and odd anecdotes, which resemble parables and which are claimed to be examples of how he teaches students, via bizarre straw man arguments. Oh, and a credulous treatment of Dembski’s version information theory (specified functional information is frequently mentioned but never defined adequately). It’s all very odd, and so far seems to be building up to the proposition that because science hasn’t explained the origin of life satisfactorily (to Meyer’s satisfaction, I mean), that a supernatural entity must have done it. Stylistically, the book’s a mixture of clarity and obfuscation, which may well reflect the subject areas that Meyer is most and least comfortable with.

I’m looking forward to a detailed description of how Meyer thinks an intelligent designer may have brought all this to pass.  Hopefully I’ll have finished the book reasonably soon, when I’ll put together a review.

Update: I note that Jack Scanlon (So, Discovery Institute, do I win an award or what?) has been flagged at another post at the ridiculously named Evolution News and Views ‘blog’ (One of These Days, Alice, One of These Days. Pow! Right in the Kisser!).  Well, I began trudging through the 550-odd pages of text as soon as the book was delivered to my Kindle.  I am still manfully ploughing through it.

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Today

A nice response to the ongoing fracas at the UCL student’s union over the use of a Jesus and Mo cartoon in an atheist group’s publicity. Read more about this at The New Humanist (Student atheist society in censorship row with student union over Muhammad cartoon)

The Atheist, Secularist and Humanist Society (ASHS) at University College London has become embroiled in a censorship row with the university’s student union over the use of a Muhammad-related cartoon on a Facebook page advertising its weekly drinks social.

An interesting situation, particularly given UCL’s origin as the first University in England to be established on an entirely secular basis. My irony meter is flickering in the red zone.

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According to the BHA website, Government changes Free School model funding agreement to ban creationist schools. From that article:

The British Humanist Association (BHA) has welcomed a new revision of the model funding agreement for Free Schools by the Government in order to preclude ‘the teaching, as an evidence-based view or theory, of any view or theory that is contrary to established scientific and/or historical evidence and explanations.’ This highly significant change has been made in order to ban creationism from being taught in Free Schools, and prevent creationist groups from opening schools. The change follows the BHA coordinating the ‘Teach evolution, not creationism!’ campaign, which called for this precise change.

Good news indeed. More information at the BHA website, with further onward links.

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One of the recurring modes adopted by Intelligent Design creationists is to adopt the strategy whereby an example of a complex biological system is looked at and it is decided that evolution cannot explain its origin. We see this enshrined in bogus concepts such as ‘irreducible complexity’, ‘specified functional information’ and the like. By claiming a process of inference, ID creationists seek to declare that an intelligent designer must have been involved in the appearance of such complex systems.

Of course, the problem with this strategy is that one by one, these examples are likely to fall to genuine scientific advance (examples include Behe’s favourites such as the bacterial flagellum and the vertebrate immune system spring to mind).  A neat example of  an approach to better understanding the evolution of protein complexes has just appeared as an Advance Online Publication at Nature (Finnigan et al (2012) Nature “Evolution of increased complexity in a molecular machine” doi:10.1038/nature10724). There’s also an accompanying News and Views article (Doolittle (2012) Nature “Evolutionary biology: A ratchet for protein complexity” doi:10.1038/nature10816).

Schematic diagram of V-ATPase

V-ATPases are membrane bound protein complexes that serve to translocate protons across membranes, and important cellular function that maintain the pH within membrane bound organelles.  The diagram shows a representation of the V-ATPase.  The pink ring of subunits is the Vo subcomplex, a membrane bound assembly of six proteins, each with several membrane spanning domains.  In the majority of eukaryotes, there are two distinct related proteins in the Vo-ATPase subcomplex, while in fungi there are three, known as Vma3, Vma11 and Vma16.  The different subunits do not randomly associate: of the six proteins in the yeast Vo-ATPase, for example, there are four molecules of Vma3 and one each of Vma11 and Vma16. Vma11 always lies between Vma3 and Vma16, and and Vma3 cannot interact with the same surface of Vma16 that Vma11 can.

An attractive proposal for the evolutionary origin of the three Vo-ATPase subunits would be via a process of gene duplication and subsequent divergence of the resulting paralogues. In the case of the fungi, at least two such gene duplication events would be inferred to give rise  to the three Vo-ATPase subunit proteins.  Finnigan et al took a very interesting approach to looking at the evolution of the yeast (budding yeast, Saccharomyces cerevisiae) Vo-ATPase proteins in which a bioinformatic approach to inferring the sequence of last common ancestors was married to a more conventional approach of expressing protein sequences in yeast of a variety of genotypes.  Yeast is particularly well-suited to these sorts of analyses, as targetted mutagenesis of specific genes is very simple and rapid, and the technology of gene expression is well developed.

A candidate ancestral protein to Vma3 and Vma11 (referred to as Anc.3-11) was predicted from the bioinformatic analysis, a corresponding gene synthesised in vitro and expressed in yeast, and its ability to complement deletion mutants of Vma3 and Vma11 assessed by testing viability of the complemented yeast mutant to grow on a selective medium.  Further experiments used gene fusions to evaluate the ability of proteins to interact with different sides of the V-ATPase subunits. Anc.3-11 protein successfully complements mutations in Vma3 and Vma11.  The proposed scheme is that gene duplication gave rise to two paralogues.  These paralogues ultimately gave rise to Vma3 and Vma11, Vma3 losing the ability to interacte with the  ’anticlockwise’ side of Vma16 and Vma11 losing the ability to interact with the ‘clockwise’ face of Vma16 and probably one face of Vma3.

The authors went on to investigate specific sequence changes which arose during the evolution of the Vo-ATPase subunits with the intention of narrowing down the individual amino acid changes that are responsible for the interaction changes.  Single amino acid changes were identified which altered the interaction behaviour of Anc.3-11 such that it lost the ability to behave as both Vma3 and Vma11 but instead acquired the binding properties of Vma3 or Vma11. The paper concludes by noting that

This view of the evolution of molecular machines is related to recent models that explain other biological phenomena—such as the retention of large numbers of duplicate genes and mobile genetic elements within genomes—as the product of degenerative processes acting on modular biological systems. Although mutations that enhanced the functions of individual ring components may have occurred during evolution, our data indicate that simple degenerative mutations are sufficient to explain the historical increase in complexity of a crucial molecular machine. There is no need to invoke the acquisition of ‘novel’ functions caused by low-probability mutational combinations.

Apart from observing that this paper presents a really neat approach to investigating evolutionary origins of protein complexes, it seems to me that the findings make a serious inroad into the understanding of how mutations that may be neutral or ‘degenerative’ can bring about the increase in complexity of a multiprotein subunit.  And from the perspective of Science versus Intelligent Design creationism, it clearly illustrates the gulf between Intelligent Design creationism (where one throws up one’s hands and capitulates to state of ignorance and then to the acceptance of a supernatural entity) and a truly scientific approach in which a sensible investigative approach is undertaken to solve a biological problem. Furthermore, I think the findings in this paper are relevant to asking whether concepts such as ‘irreducible complexity’ have any validity.

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The British Humanist association reports that the Everyday Champions Church is returning to the Free Scool fray (Creationist Everyday Champions Church re-launch Free School bid as ‘Exemplar Academy’). Sort of, anyway.  It turns out it’s the same people, without overt Church involvement.  According to the BHA:

Everyday Champions Academy was proposed and sponsored by Everyday Champions Church, a creationist church based in Newark. Following having their bid rejected, the team met with the Department for Education in an attempt to get the decision overturned, and their local MP, Patrick Mercer, met with Secretary of State for Education Michael Gove to attempt the same thing.

What the heck their MP is doing trying to go against Government policy on not teaching creation?  Anyway, the people behind the bid are trying again.

The new Exemplar Academy is proposed by the same group of individuals from Everyday Champions Church as proposed the previous Free School, however the Church is no longer sponsoring the school, and the school will no longer be formally designated with a religious character. Instead, it will have a Christian ‘faith ethos’. 

Sounds ominous to me.  It’s worth visiting the BHA site for the full low-down.  Of course this is just the tip of the iceberg when it comes to attempts by evangelicals and fundamentalists to drum their ridiculous creationist notions into children’s minds.

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The latest newsletter from the British Centre for Science Education (BCSE) is now available on the BCSE Blog.

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Happy Kitzmas. This is the sixth anniversary of the famous decision in Kitzmiller vs Dover School Board, which really exposed the duplicity of those in the Intelligent Design creationist movement. Judge Jones, who many did not see as a particular ally to those fighting this incursion of religion into American schools, actually provided a exceptional smack-down of the devious and dishonest strategy taken by those wishing to push Intelligent Design creationism as science. This has led to many US-based bloggers to conclude that Intelligent Design creationism is something of a ‘busted flush’. But in reality, this is only true in the USA, where publicly funded schools are prohibited by the Constitution from teaching or promoting religion. In contrast, here in the UK we have a government that actively encourages the development of faith schools, and via its ideologically driven Free Schools raises the spectre of increasing the presence of creationism in our nation’s schools.

I have been re-reading much of the Dover trial transcripts and associated material available on the web, and quite frankly the hopelessness of the Intelligent Design creationists’ position should have been evident from the start.  In fact it was obvious to the Discovery Institute, who with drew their ‘big guns’ from the case.  Crucial to the case was the testimony of Barbara Forrest, who’s book Creationism’s Trojan Horse: The Wedge of Intelligent Design (written in collaboration with Paul Gross) clearly demolishes any pretence that Intelligent Design is in any way different from any other religious ideology.  Indeed, the underlying history of the ID creationist movement is littered with creationist and religious outpourings by ID creationist principals, all of whom I suspect clearly recognise where their support (particularly financial) was to be sourced.

The Discovery Institute did their best to prevent Forrest’s testimony.  In an article written a few months after Jones handed down his verdict, Forrest makes some interesting points, including the appearance of a faked interview (later flagged as a ‘parody’) – unfortunately this appears to have been ‘disappeared’ from the web. Interestingly, one reads that William Dembski attended Forrest’s deposition – and withdrew from the case four days later.

So, why do I not recognise this as the end of Intelligent Design creationism?  Because in the UK, we are seeing an upsurge of interest in religiously motivated schools, using the government’s Free School programme.  This of course is seen by some as pushing at the open door labelled ‘Faith Schools’.  If the Catholics and Church of England can run so many schools, why can’t the more aggressive evangelical arm of creationism do the same? (There are some other kinds of faith school, but this article is concerned mostly with those of a christian focus.) The British Humanist Association is most concerned (More creationist Free Schools planned for 2013 opening), as is the BCSE.

One possible source for creationist material is the Centre for Intelligent Design (C4ID). C4ID is based in Glasgow, is run by a triumvirate of evangelical christians (at least one of whom preached the literal truth of the creation as described in Genesis), and funded by unclear means.  It seems to be largely a conduit for pushing the kind of material produced by the Discovery Institute. Recent events organised by C4ID have included an especially secret Intelligent Design conference, a lecture tour (mostly of churches) by American ID proponent Michael Behe, and last month a lecture by the senior Discovery Institute figure Stephen Meyer. I was invited to the latter event, and blogged about the reasons I didn’t go - also see this follow-up article.  On the ground, we have a young man, Jonathan McLatchie, with a strange internet presence. I don’t think he’s officially part of C4ID, but he is clearly part of the ID creationist machine, frequently posting his garbled and distorted accounts of biology in attempts to make evolution look unfounded.  Amusingly, McLatchie often cross-posts his material over at a christian website, where his other postings make interesting reading.  His latest biology related drivel can be seen at the (bizarrely named) Evolution News and Views blog: Treasure in the Genetic Goldmine: PZ Myers Fails on “Junk DNA” (in which McLatchie has another go at PZ Myers – see Moran and Myers’ take at Sandwalk) and Animation Reveals Engineering Elegance of RNA Interference (in which McLatchie seems somewhat overawed by an animation of molecules in action).  I do worry that all this blogging activity will jeopardise his progress towards gaining his Masters in Evolutionary Biology.  Yes, Jonathan McLatchie, a person who choses to believe that evolution is wrong and that life is due to the efforts of a supernatural entity, appears to be studying for a Masters in Evolutionary Biology.  When my irony meter subsides, two thoughts cross my mind – firstly, whether McLatchie seeks to emulate Jonathan Wells (who’s misapprehensions of Junk DNA he frequently parrots), and secondly, how he presents his belief system while at university.

So, Merry Kitzmas to my American colleagues.  Not such a Merry Kitzmas over the pond in Blighty, where an entrenched faith school system coupled with ideologically driven educational policies leave British kids vulnerable to being taught bullshit as an alternative to evolution.  With any luck, the C4ID crew will botch things as badly as did the defendants back in 2005.

Update: I forgot to include this link to an article in the New York Times revealing how the Thomas More Law Center sought a case like this.  The article (In Intelligent Design Case, a Cause in Search of a Lawsuit) begins…

For years, a lawyer for the Thomas More Law Center in Michigan visited school boards around the country searching for one willing to challenge evolution by teaching intelligent design, and to face a risky, high-profile trial.

It’s worth a read.

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In a article today, the British Humanist Association  reports More creationist Free Schools planned for 2013 opening.  It’s clear that Michael Gove’s Free Schools programme is likely to continue to attract those of the devious and deceitful religious type.  If I take as an example the awful sounding Destiny Christian School proposed for opening in 2013.  The school’s website covers up mention of creationism, saying under the FAQs:

Destiny Christian School will provide a curriculum that is broad, rich, inclusive and based and in line with the National Curriculum.

The BHA article, however, clarifies their position:

In Bedford, Destiny Christian School is being proposed by the Miracle Church of God in Christ, and if approved to open, will be a member school of the Christian Schools’ Trust (CST). At an open meeting attended by a BHA supporter, the group were asked about their policy on creationism and responded that they believe creationism is science and intend to teach it as such.

The affiliation to the Christian Schools Trust is something of a giveaway. Incidentally, any school adhering to the CST Statement of Faith has to be considered suspect in the modern United Kingdom, in which religious belief is generally declining. It’s not actually terribly clear whether the horribly named Destiny Christian School actually does, but it has all the common evangelical hallmarks (including a request for prayers to deliver skilled people to the project team).

Clearly the Free School scheme is seen by those adhering to creationist wingnuttery as an open invitation to pollute impressionable young minds with an inadequate science education.  

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I see that Jonathan McLatchie has crossed Larry Moran’s radar (Fishing for Creationists).  Jonathan published one of his verbose articles taking issue with Jeffrey Shallit’s takedown of a video featuring Phillip Johnson, the grand-daddy of Intelligent Design creationism  (This Video Should be Shown to all Biology Students - see also A Discovery Institute Flack Responds) – it’s a video dating to the early days of the Intelligent Design variant of creationism, and reveals Johnson’s ignorance of biology and evolution.  The whole thing’s blown up to include another example of ID creationism misquoting, selectively quoting, and just plain failing to comprehend the scientific literature, this time on homology (both morphological and molecular).

Paul Nelson, in particular has weighed in at Sandwalk.  In case you’re wondering about Nelson’s background in biology, it is the usual extensive education seen in ID creationism.  According to his Wikipedia page,  ”In 1998, Nelson gained a PhD in philosophy from the University of Chicago”.  Anyway, the discussion has spilled out into a new post, Homology, where I expect the discussion to continue, amid the accusations that he’s selectively mis-quoting and misrepresenting the literature.  Worth following.

And on the ‘further incomprehension by McLatchie’ front, we have this blog article cross-posted to crossexamined*: An Eye-Opening Discovery: The Remarkable Vision of Anomalocaris. This is a ‘teaser’ paragraph from the full article at the very silly and mis-named Evolution News and Views, to which I don’t link, due to its ‘no comments’ policy).  For the rational-minded, the new discovery is really very interesting: that the ‘top predator’ in Cambrian seas was equipped with an effective visual system comprising a high resolution compound eye.  The proposal has elicited quite a bit of discussion, not least around whether or not the eyes are really part of Anomalocaris (which, interestingly, McLatchie doesn’t refer to), but also that it suggests that Anomalocaris had arthropod affinities.  Anomalocaris itself has had an interesting history in palaeontology, having over the years had body parts identified as three different species.  While I cannot fault McLatchie when he says “This beast poses mysteries both small and large”, he then ruins it by charging off into his usual nonsense.  Apparently the new discoveries make it another “tough day to be a Darwinian”, though it’s not clear quite why he says this, other than senior ID creationists say so (Meyer, Nelson and Chien** – the latter being one of the few biologists in the ranks of ID creationists), and that it’s the hoary old story of ‘sudden appearance’ of complex structures (such as a very high resolution compound eye) in the fossil record that exceeds his capacity to grasp the science.

For my part, I am fascinated by Anomalocaris, and look forward to further discoveries about the Cambrian seas. Not so much the ID creationist mangling of those discoveries!

*Jonathan McLatchie seems to be the sole blogger at crossexamined.  Many of his posts there are ‘interesting’.

** Chien apparently leads the Discovery Institute Paleontology Research Program, according to his Wikipedia page, though that page suggests he’s a biochemist rather than a palaeontologist.

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