Saturday, August 30, 2008

Life imitating art in museum bungle--not quite

When I first heard that a British museum had to cover up a reference to evolution after a complaint, I thought we were in for a re-run of the hilarious Simpsons episode on evolution, which you can view here on OneGoodMove.

But in fact on further reading, this seems more cock-up rather than conspiracy. The complaint was over some text that read
He used the same layers of fossils that had supported the Genesis view of evolution to show the slow changes that are taking place over the millennia of earth history.

The complaint was that there is no Genesis view of evolution, which I guess is a fairly reasonable one, and the museum's position is that this is just an opportunity to correct some badly written text, rather than an opportunity for secular activism, which I also think is probably a reasonable stance (although the complainant was supposedly a Christian fundamentalist).

But whatever the real reason, it gave me an excuse to point out the excellent and hilarious Simpson's episode!

Evolutionary poetry, art, drama and music from the cutting room floor

Yesterday I received the proofs from the last chapter of narrative text from the Rough Guide to Evolution, on evolution's influence on Philosophy and the Arts. Because of a re-jig it won't actually be the last chapter in the book but third to last (the books ends with a consideration of creationism and religion). 

But I am pleased with the latest chapter, as is Joe Staines, the editor at Rough Guides who has been working on it, who commented yesterday 
"Think chapter works well as a mixture of the serious and the lighthearted (probably not often that Matthew Arnold and Suzy Quatro get mentioned in the same context)." 
Today have been rather bone-headedly forcing the Resources material that was initally appended to each chapter into a final coherent section. Nearly done! 

An inevitable consequence of trimming the Philosophy and the Arts chapter on grounds of space and coherence is that some of the material on evolutionary poetry and music that I compiled won't be appearing in print... 

So, let me share it with you here! 

I don’t have time to mark everything up with links to poems or MP3s, but you should be able to find most things via Google or iTunes. But remember these are just the offcuts—for the very best stuff, you will have to wait until you can get hold of the book in print!  

In recent times, many poets have woven evolutionary themes into their poems; examples include  
  • Neil Rollinson’s My Father Shaving Charles Darwin
  • Rita Dove’s The Fish in the Stone
  • Christopher Reid’s Amphibiology
  • John Updike’s The Naked Ape
  • Michael Donaghy’s Touch
  • Richard Wilbur’s Lamarck Elaborated 
  • Amy Clampitt’s The Sun Underfoot among the Shadows

In The Evolutionary Tales (1993) Ron Ecker echoes Chaucer’s Canterbury Tales, presenting commentaries on evolutionary themes in rhyming iambic pentameter. 

Several poems in The Human Genome: Poems on The Book of Life (, by Scottish poet Gillian Ferguson, deal with evolutionary themes—examples include All Life is One, Comparative Genomics, Shall I dare to believe the mouse is my brother

Recently, Robby Cleiren, Frank Vercruyssen and the Belgian theater company Tg STAN ( used  transcripts from the Scopes trial to recreate the court case on stage as The Monkey Trial, while Americans Frank Megna and Bob Ladendorf provide a fresh treatment of the Scopes trial, together with the Dover trial, in their one-act piece Darwin's Nightmare.

In his 2007 play, Trumpery, American writer Peter Parnell explores Darwin’ life before and after publication of The Origin, highlighting the trials of Darwin’s home life and Wallace’s contribution to the conception of evolution, with a climax focused on Darwin’s attitude to spiritualism. The title comes from a phrase in the letter Darwin wrote to Lyell asking what to do with Wallace’s letter: “This is a trumpery affair to trouble you with.” 

In Darwin's Wings, first broadcast on Australian radio in 2006, Danish-born playwright Mette Jakobsen places Darwin in a dialogue with the mythical character Orpheus, as he tries to come to terms with the loss of his daughter. 

Floyd Sandford wrote, and acts in Darwin Remembers, a one-actor living-history piece, first performed in Iowa in 2000. 

British dramatist Craig Baxter worked with the Darwin Correspondence Project to create a theatrical piece Re:Design ( from a nearly 40-year series of letters between Darwin and his American friend Asa Gray. Baxter’s piece re-creates on stage the two men’s intimate discussions of the impact of their scientific discoveries on their personal and religious beliefs. 

Many more pieces of Darwinian drama are likely to surface during the bicentenary year—watch out in particular for Darwin’s Worms (, a piece focused on Darwin’s relationship with the smallest of creatures, currently under development in Manchester, England. 

Evolutionary Art and Music 
For the past two decades, evolution and aesthetics have collided in the production of art and music, exploiting computer programs and human choices to evolve pleasing auditory or visual artefacts. Drawing on evolutionary computing, these approaches rely on repeated rounds of reproduction, variation (recombination and/or mutation) and selection to improve on a starting population of images or sounds. The fitness function usually depends on the viewer or listener making an explicit choice as to which variants they prefer, although attempts have been made to use unconscious cues (e.g. time spent looking) or to take humans out of the loop entirely (The Black Shoals Stock Market Planetarium evolves images from financial data). 

John "Al" Biles is a pioneer of evolutionary music, entering the field in 1993 with his GenJam program, which evolves improvised jazz music. Biles plays alongside GenJam to human audiences as the Al Biles Virtual Quintet. In a recent evolutionary art study, American computer scientist David Oranchak extracted colours and textures from popular photos from the photo-sharing site Flickr and then used these to breed abstract images that would appeal to humans. Flickr is even home to its own Generative & Evolutionary Art group. 

In the Electric Sheep project (, fractal images, together with the software that drives their evolution, are distributed to networked computers, which display them as screensavers. Viewers vote for their favorite “sheep”, which live longer and breed more successfully, allow the global “flock” to evolve more pleasing animations for its worldwide audience. 

Readers can also try their hand at evolutionary art with Jerry Huxtable’s Genetic Art applet (  

Evolution-inspired music 

Prog-rock’s homage to evolutionary traditions continues with Evolution, a five-piece, female-fronted band from Devon; Staten Island-based band Simple Evolution and Darwin's Radio, based in southern England.   

Soul and pop: American soul band Earth Wind & Fire included the track Evolution Orange on their 1981 album Raise!, while British soul singer Des'Ree released her Darwin Star on the album Supernatural in 1998. 

More rcent examples of entertaining evolutionary pop music include the bouncy Ape Man from Liverpool-based “horror rock” band Zombina & The Skeletones and Evolution from West Coast Jewish hippy Hyim.   

Hip-Hop meets eugenics in Darwin’s Folly, a track by Los Angeles rapper Avatar, with a chorus line “some people shouldn’t procreate, if they have to put paper bags over their faces to fornicate.” By contrast, East-coast Hip-Hop troupe Raw Produce stress the minus side of social Darwinism in Negative Darwinism.   

Classical, Sound Tracks and Electronic: In 1989, American composer Wendy Chambers created a large-scale music event, Symphony of the Universe, which included a movement devoted to evolution. 

English composer Martin Simpkin explored evolutionary themes in his album Birth Part 1

In his 2006 album Piano, American rockster Dexter Romweber turned his hand to classical music with Evolutionary Etude (an allusion to Chopin’s Revolutionary Etude). That same year, legendary American composer Philip Glass provided the music for a multimedia exploration of evolution Life, a journey through time, created by Dutch photographer Frans Lanting ( 

The classical-music soundtrack to the 2001 movie Evolution is worth a listen, as it the soundtrack to the cult TV show Heroes (particularly the show’s haunting melody Natural Selection).

Evolutionary themes also pervade electronic and dance music. In 1992, Scottish electronic music group The Shamen released Re: Evolution, in which they mix evolution with shamanism and Tipler’s Omega point. 

A few years later English techno band Opus III released the dance track Evolution Rush. 

A range of artists have released dance tracks entitled Evolution (e.g. Miro, Remote & Roger Eno, Beautiful World and Ram Trilogy) or Human Evolution (e.g. Blank & Jones or Cosmosis). 

If you want something a bit trippier try anything by Darwin Chamber (stage name of Mark Greenfield, who was such a fan of Charles he adopted his name) or the album The Genome Project by Swedish psychedelic trance band Chromosome.   

Thursday, August 28, 2008

Teaching evolution to American school kids

Just read through this interesting article from the New York Times on the trials and tribulations of teaching evolution in a US classroom. 

Let's have a round of applause for David Campbell's efforts!

Blast! An ORF is not a coding sequence!

Now that The Rough Guide to Evolution is very nearly finished and the summer holidays are nearly over, my thoughts are returning to my "day job" as a bacteriologist with an interest in bioinformatics, genomics and pathogenesis (how bacteria cause disease). In particular, I am struggling with a backlog of papers and grant proposals that I have agreed to peer-review, which I will have to clear before starting work on a grant proposal on bacterial flagellar function (of which more later).

Having a blog of my own gives me a chance to highlight to a wider audience some of the problems that crop up time and again in papers submitted for review. These are technical points, so the non-specialist reader should ignore these posts. But conversely, I would ask the specialist reader to bring these points to as the attention of all their colleagues and to as wide an audience as possible!

Problems commonly arise when lab-based scientists include some bioinformatics in their work. Such scientists are typically extremely careful in describing their laboratory work, taking care to ensure that methods are described in enough detail for anyone competent in the field can reproduce them, even to the extent of saying which supplier they used for any given chemical or growth medium.
BUT when it comes to bioinformatics, they are often very imprecise and even cavalier in their use of language and in the assumptions they make! 

Simply stating "we did a BLAST search" is equivalent to saying "we grew some bacteria under undefined conditions, for an undefined length of time in an undefined growth medium"! The outcome of bioinformatics analyses often depends critically on the conditions used, just as in lab-based work, so it is crucial to specify which particular version of a program was used under what settings (e.g. was the filter on or off in BLASTP, which matrix was used, were composition-based statistics employed, what word size was used?). Better still, one should repeat the search under a variety of settings and show that the results are or are not the same whatever the settings.

Another common problem, which I encountered again today, is a confusion between "ORFs" and "coding sequences"(or CDSs) in bacterial genomes. An ORF is an open reading frame, i.e. a stretch of nucleotide sequence in a given reading frame that does not contain a stop codon, or in other words, a stretch of sequence within a reading frame bounded by two stop codons. It is NOT the same as a coding sequence (or CDS), which can be defined as a stretch of nucleotide sequence that directly encodes a protein product. CDSs are a feature of protein-coding genes, but simply identifying CDSs does not guarantee that you have found all the genes, as CDSs are not a feature of tRNA, rRNA and small regulatory RNA genes.

Identifying ORFs in a given stretch of bacterial DNA is a computationally trivial problem--it can be done even with a pencil and paper. Any given stretch of sequence typically contains many ORFs but very few if any of them will encode real proteins, i.e. represent CDSs.  

For example, here is a diagrammatic representation of stretch of DNA from  the E. coli K-12 MG1655 genome highlighting the recognised annotated CDSs:

And here is the same stretch of sequence, showing the far more numerous ORFs >100 codons.

As you can see ORFs are not the same as coding sequences!!

A rule of thumb is that the longer an ORF is, the more likely it is to encode a protein and for many genomes, simply choosing long ORFs is a good way of identifying *some* of the protein-coding genes. However, there a many problems with relying on ORF-finding alone to identify CDSs:

  1. In some cases, particularly in GC-rich genomes, long ORFs are common even though most do not encode proteins. It is not uncommon to see multiple long overlapping ORFs in such genomes and antisense ORFs, which run in the opposite direction to CDSs are often seen.
  2. Because short ORFS are so common, relying on ORF-finding alone to identify short CDSs is prone to massive over-prediction.
  3. Even when an ORF contains a CDS, it will often contain additional sequence upstream of the real start codon. Remember--an ORF is simply a stretch of sequence bounded by two stop codons. Typically, there will be dozens of codons in the ORF upstream of the CDS.

For these reasons, ORF finding alone is never used to identify bacterial protein-coding genes. Instead, two other more sophisticated approaches are used: detection of homology at the protein level and use of Markov models to identify sequences that look like CDSs (the industry standard program for this is Glimmer).

So, please can I never again be sent a paper to review that discusses "the difficulties in identifying ORFs" or talks of "predicted ORFs" or "putative ORFs" or "hypothetical ORFs", when the authors mean "the difficulties in identifying CDSs" or predicted or putative or hypothetical CDSs!!

Some of you out there may wish to protest that I am being too prescriptive and that the (mis)use of ORF to mean CDS is so common that we should treat the two terms as synonymous. In response, I would argue that maintenance of the distinction is essential to the clarity of thought and precise use of language that should be the hall marks of all scientific discourse! 

Wednesday, August 27, 2008

The inter-species kiss we weren't allowed to use...

While we are on the subject of copyright, let me highlight another absurdity. When the first round of mockups were created for the cover for The Rough Guide to Evolution,  Rough Guides included a design based on the image shown here, which was produced to accompany the 1968 movie Planet of the Apes. I thought it was a perfect image for the cover, with just the right amount of shock value (especially as Charlton Heston had also played Moses!). The image is in the Corbis database, which Rough Guides uses and which, I assumed, meant that it was available for use on payment of a fee. 

A little while later, after I had enthusiastically endorsed the picture, it turned out that things are a lot more complicated when it comes to movie images. It seems that it is not enough to pay Corbis for the image. To use a movie image on a book cover,  all the various stakeholders in the film have to agree or have died. But by late-2007,  most of them were already dead, and then when Heston died in April, I thought we were in with a chance. But, alas, even after his death, it seems that there are too many complex dependencies for the image to be used. 

We do now have an excellent cover image for The Rough Guide to Evolution (of a quizzical chimp looking the reader in the eye), so I am not too upset. But the silliness, or least unworkability, of copyright law in the Internet age is illustrated by the results of a Google image search, which turns up numerous copies of the inter-species kiss on the web.

Although the latter-day Heston is often viewed as right-wing NRA nutcase, it is worth remembering the earlier feisty civil rights version. 

I wonder what he would have made of Obama? Or of McCain's misappropriation of his Moses to attack Obama, which surely exceeds any problem we could have caused enlisting Heston to the cause of evolution?!

Wikipedia and the question of who owns Darwin

We live in age where "information wants to be free" and steadily ever more information that one used to have to pay for is now available online free of charge, from maps to bibliographic databases such as Medline to scientific articles themselves. But "free to look at" does not mean "free to use for whatever purpose one likes", and what happens when two online giants of the information age (Wikipedia and Darwin Online) collide?

The Wikipedia must surely rate as one of the seven wonders of the Internet. But although simple in concept--an encyclopedia in which anyone can create and edit material--in fact, it has grown to be a highly complex  trans-national organisation, with its own culture and customs. Beneath the simple exterior of the wiki article lies a complex machinery of rules, edits, discussions and guidelines...

A couple of times when I have tried to contribute myself, I have come away somewhat disgruntled--once over the neutering suffered by the no-bacteria-on-the-moon article mentioned in an earlier post and on another occasion, when I tried to create an entry for Charles Darwin 1st (1758-1778), the uncle of the more famous CD and the son of Erasmus Darwin. Before I had even finished the article, a notice was slapped on, saying that the article was likely to be deleted very soon on grounds of lack of notability--a decision made by someone whose credentials one could only guess at!

But although my own experiences have led me to have mixed feelings about the Wikipedia, I marvel at the effort put in behind the scenes in terms of arguments for or against a given position on what should be included. There is something magical here with the Wikipedia, as I know from experience that attempts to get research communities to engage in community annotation or maintenance of subject-specific wikis (e.g. the E. coli wiki) usually collapse in apathy, as academics say they are just too busy to contribute. How is it that the Wikipedia manages to enlist so much support from so many unpaid volunteers! And how do these people find the time for all this, when academics are so busy?

A couple of examples suffice to illustrate the remarkable internal machinations of the Wikipedia:

1. In one of the Wikipedia's lamest edit wars, the issue of whether the fact that Darwin and Lincoln were born on the very same day is notable enough for inclusion in their respective Wikipedia entries has generated the equivalent of a short novel's worth of words of discussion! See further discussion on the I'm-from-Missouri blog.

2. Just this morning I came across this protracted and fascinating discussion as to whether John van Wyhe at Darwin Online is able to assert copyright on the images scanned from out-of-copyright printed works. This issue has a particular interest for me, as we explored whether we could afford to use some of John's images in The Rough Guide to Evolution in the light of the tight budget we had been allotted for pictures. In a nutshell, the argument is whether the Wikipedia and its sister resource, Wikimedia Commons, has the right to appropriate these images from John's Darwin Online site without his permission and without payment on the grounds that the images are in the public domain. 

John argues that the act of scanning creates copyright, at least in English law. Various wikipedians argue that mechanical processes that do not add originality do not create copyright where none exists to start with; that English copyright law does or does not allow for "sweat of the brow" efforts; that the Wikipedia should or should not ignore English law and so on! 

John, perhaps wisely, has refused to take part in the discussions--he is busily writing or editing several books on Darwin (working on one book has been exhaustive enough for me!). In the end, the wikipedians seem to have side-stepped the issue by starting to scan in their own images, and so I am left unclear what the precise legal position is. One elephant-in-the-room argument that they haven't addressed is whether changing an image from a paper format to a digital format creates copyright. Or does this not make any difference?

The question of who owns Darwin goes deeper than these arguments over copyright of images. Cambridge University claims to own the copyright on all Darwin's letters, whether held by the University or in private hands. This seems a bit odd to me, as when Darwin sent someone a letter, one would have thought that the recipient gained ownership of the letter and perhaps even copyright of what was in it. I wonder what case law exists on this.

One thing is clear, in the Internet age, who owns Darwin remains a highly contentious point!

Triumph and disaster

Returned from holiday on Friday to face a hard drive failure on my MacBook Pro! Unfortunately I didn't have a recent back up of the whole drive--tried using Time Machine a few months back but the backup drive (a Freecom Tough Drive Pro 260) kept failing. Fortunately, recent versions of most work-related files are still going to be accessible from my e-mail server (good thing I don't clear it out too often) and from my desktop Mac G5. But I have lost a few month's worth of snapshots and the video of a recent trip to London. 

I guess I assumed that hard drive failures are rare and only ever happened to other people. In future, I will engage in a proper back up schedule! For now will have to squat on my wife's laptop until a new drive has been fitted in my own machine (am I the only one who feels as if I have lost an arm when unable to use my own machine?)

Now in the closing straights with the book The Rough Guide to Evolution. Have just finalised the text of the final chapter (on Philosophy and the Arts) and now have just the edits on the Resources section and the compiling of an Index to deal with. 

I submitted the proposal for the book nearly thirteen months ago, on August 1st 2007. With luck, I should have it finished, more by accident than by design, within the span of thirteen months and ten day's hard labour that Darwin expended on the first edition of The Origin!

I abstracted the MS. begun on a much larger scale in 1856, and completed the volume on the same reduced scale. It cost me thirteen months and ten days' hard labour. It was published under the title of the 'Origin of Species,' in November 1859. Though considerably added to and corrected in the later editions, it has remained substantially the same book.

Judge John E. Jones' concluding words at the Dover trial provide a similar amusing coincidence:

MR. GILLEN: Your Honor, I have one question, and that's this: By my reckoning, this is the 40th day since the trial began and tonight will be the 40th night, and I would like to know if you did that on purpose.

THE COURT: Mr. Gillen, that is an interesting coincidence, but it was not by design.

(Laughter and applause.)

Friday, August 15, 2008

Birmingham, England now relocated to the Bible belt

One last short post before I go on holiday...

Hot on the heels of the news from Effect Measure and the BBC that Birmingham City Council has banned access to atheism and wicca, comes new evidence that Birmingham, England has been relocated to the Bible belt...

Perhaps time for a re-run of the Scopes trial in Smethwick or Dudley?

Dawkins on Darwin, economics and Hitler

Dawkins Episode 2

I am just about to disappear off on holiday for a week, but last night my wife pointed out that the blog was getting a lot of traffic from a comment I posted on Sneer Review saying that I would blog on Dawkins, Darwin and Hitler, so I thought I would deliver on my promise and squeeze in one last quick post before a week off.

This week saw the second episode of Dawkins’ series The Genius of Charles Darwin. It seems that copyright counts for nothing these days, as the episode is already available on YouTube and even for download (the same site makes Dawkins reading The Origin available, but it looks like it takes a long time to download; buy from iTunes instead). Plus the show was live-blogged on the Beagle blog.

The response to the second episode has been a bit more muted than it was to the first episode. The one clear opinion from Laelaps dovetails with my own, which is that it was all rather so-so. My children came away confused as to what point was being made and there was certainly a lot of sloppy use of language. Laelaps has already pointed out the teleology in Dawkins description of hominin evolution. Plus for me Dawkins' use of the value-laden word “misfiring” to describe the neural/evolutionary basis of our moral instinct goes against the very point that he is trying to make towards the end of the show: that civilised values can and should be uncoupled from natural selection.

Also the use of the term “fifth ape” confused me. Initially I thought he was being clever and remembering to count the two species of chimpanzee (common chimp and bonobo) in his reckoning of the great apes (hominidae), but then it turned out he was adopting an idiosyncratic anthropocentric view of ape taxonomy, evaluating the great apes at genus level but lumping all four genera/thirteen species of gibbon together as just one of his "five" apes!

I was also somewhat taken aback by Dawkins very superficial treatment of social Darwinism and eugenics-and-the-Nazis. I appreciate that one can only say so much in a one hour show, but why bother at all if it can only be done so superficially?


Starting with social Darwinism, Dawkins dismissed the use of evolutionary thinking in economics with two put-downs: use of a ruthlessly selectionist regime at Enron led to its downfall and in any case applying evolution to economics is only an exercise in metaphor or analogy. I don’t know whether the point about Enron was well made, but the latter point seems rather feeble, as there is nothing wrong with the use of metaphor and analogy, when appropriately applied. After all, Darwin’s conception of natural selection was a metaphor drawn from the artificial selection employed by animal and plant breeders. In fact, it seems rather odd to dismiss all the influences of evolution on economics and cross-fertilisation between the two fields in quite such an offhand manner.

For example, just as Darwin is seen as the father of modern biology, the Scottish economist Adam Smith (1723–90) is credited with laying the foundations of economics with his 1776 masterpiece The Wealth of Nations. In this highly influential book, Smith analysed and defended free market economics, arguing that, although a free market appears chaotic and free of restraints, with each man acting for himself, the market is in fact steered by an “invisible hand” to a rational outcome, producing just the right amount and variety of goods at the right price. 

There is a clear analogy between the undirected effects of Smith’s invisible hand in the creation of wealth and the designer-free biological adaptations forged by Darwin’s natural selection and I think the argument has even been made that Smith’s arguments directly fed into Darwin’s thinking . Similarly, competition can still be seen as a driving force in both economics and evolution, even if one dismisses the crudities of social Darwinism. And it seems to me that the division of labour and diversification in an economic setting are highly analogous to adaptive radiations seen during biological evolution. 

For more information on the influence of evolutionary thinking on economics, see the wikipedia article on Evolutionary Economics or take a look at  the work of Richard Nelson/Sidney Winter in the US and Geoffrey Hodgson in the UK or at Howard Aldrich’s Organizations and Environments (1979) and Organizations Evolving (1999). Or ask an expert in game theory or agent-based modeling—approaches which amply straddle the divide between economics and evolution.

So instead of, like Dawkins, dismissing the influence of evolution on economics as just so much analogizing, we should be celebrating the fecundity of Darwin’s thought and influence in this field!

The Nazis

Moving on to the eugenics/Nazi issue, one wonders whether Dawkins is right to give the oxygen of publicity to this attempt to discredit evolution though guilt by association, as seen in the 2004 book From Darwin to Hitler, by Discovery Institute historian Richard Weikart and in the recent film Expelled: No Intelligence Allowed. But having raised the issue, is Dawkins right to dismiss it in just a few words, along the lines of the Nazis, like Darwin, drew inspiration from animal and plant breeders, but didn’t get their ideas directly from Darwin. This strikes me a rather simplistic response (and where did Dawkins get it from?) to the equally simplistic claim that Darwin led to the Nazis and can be blamed for the Holocaust.

In fact this claim can be dismissed on a number of grounds...

Firstly, it is clear that there is no direct link between Darwin and Hitler, as Darwin died before Hitler was even born—a fact parodied in this recent spoof letter from Darwin to Hitler’s mother. 

And one looks in vain in anything Darwin ever wrote or did for any direct support for anti-Semitism. In fact, Darwin had Jewish friends and admirers. In discussing The Origin in his autobiography, Darwin seemed pleased that “Even an essay in Hebrew has appeared on it…!” For eight years, Darwin corresponded with the German Jewish bacteriologist Ferdinand Cohn (1828-1898) and he received a visit from Cohn at Down House in 1876. And just once in all the millions of words that he wrote does Darwin slip into the language of cultural stereotyping—in one letter in which he writes “we are as rich as Jews”.

But what about an indirect link? Well, here one is on very shaky ground

Is it ever fair to hold a historical figure personally responsible for all the future unbidden and unforeseeable consequences of all that he or she has said or done? Was Jesus responsible for the Inquisition or Muhammad for 9/11? Can we blame Newton and his laws of motion for the damage caused by cruise missiles? And even where one can establish a chain of causal links between scientific discoveries and their subsequent abuses, does this mean that we must belittle the discovery or close down future research?

Protestant Christians are on the shakiest ground when using this argument, as it allows us to indict Martin Luther for the Holocaust, with his On The Jews and their Lies (1543), which was avidly quoted by Hitler. Chillingly, the first of ten recommendations from Luther was “First to set fire to their synagogues or schools...” Should we really blame Luther for Kristallnacht?

In fact, Nazi ideology was derived from a range of ideas and beliefs, which included anti-Semitism, militaristic Nationalism, anti-Capitalism and anti-Communism. The Nazis also blended a distorted German Christian tradition with Nordic mythology and derived their zest for eugenics as much from ancient Sparta as from any modern sources. The influence of evolutionary thinking on Hitler was, if anything, very minor: nowhere in Mein Kampf does he mention Darwin, natural selection or biological evolution. In fact, in the first edition of the book, Hitler comes across as a young Earth creationist, claiming at one point that “this planet will, as it did thousands of years ago, move through the ether devoid of men”.

As Stephen Jay Gould pointed out in his essay The most unkindest cut of all, the Nazis did cite an evolutionary principle at one important point, at the Wannsee conference in 1942, where they chose mass murder of remaining Jews on the grounds that

 “[t]he possible final remnant will… have to be treated accordingly, because it is the product of natural selection and would, if released, act as a the seed of a new Jewish revival.” 

But here the argument seems to be that the Nazis should be wary of the effects of natural selection, rather than try to emulate it. And in any case, is this one fleeting reference – which some might see as a unnerving prophecy of the subsequent re-birth of a Jewish homeland in Israel – really enough to damn Darwin for Dachau?

I leave the last word to the Jewish Anti-defamation League, who issued this press release in response to Expelled:

The film Expelled: No Intelligence Allowed misappropriates the Holocaust and its imagery as a part of its political effort to discredit the scientific community which rejects so-called intelligent design theory.

Hitler did not need Darwin to devise his heinous plan to exterminate the Jewish people and Darwin and evolutionary theory cannot explain Hitler's genocidal madness.

Using the Holocaust in order to tarnish those who promote the theory of evolution is outrageous and trivializes the complex factors that led to the mass extermination of European Jewry.


Thursday, August 14, 2008

In search of the ultimate evolutionary concept album part 2...

I had hoped to finish up on my earlier post in the search for the ultimate Darwinian concept album, but am not going to have time to do this thread justice before I disappear for a week’s holiday in sunny (?) Somerset. Instead, let me take the discussion forward but leaving you waiting for more…

In the earlier post, I considered the concept album “Darwin!” by Italian progrock band Banco Del Muto Soccorso. Of similar vintage and another contender for the title of ultimate evolutionary theme album is Rick Wakeman's second solo album, Journey to the Centre of the Earth, recorded live at the Royal Festival Hall in London in 1974. Loosely based on the Jules Verne book of the same name, it weaves in many evolutionary themes, as the album’s protagonists encounter among other things:

  • “impressions of rock weeds and mosses from the Silurian epoch,” 
  • a terrifying battle between two sea monsters (an ichthyosaur and a plesiosaur) 
  •  a herd of mastodon, marshalled by a primitive human. 

But the album, like the book, is tainted by its association with the long discredited hollow Earth theory, an idea even more absurd than creationism, so it will never satisfy today’s hard-headed evolutionist.

Perhaps worth mentioning in passing are my own efforts in the Origin of Species in Dub, a reggae version of Darwin’s masterpiece, which was created in collaboration with Jamaican scientist Dominic White. I’d like to think we kept as true to what Darwin actually wrote as is possible in an album of this kind. But we have to fall out of this race because we are, at best, strictly amateur musicians (the term “loop monkey” springs to mind).   

Instead, what we really need is a concept album about Darwin, that encompasses a range of genres, is produced by professionals with an international reputation and is performed by established rock stars. And to find what has to be front-runner for the ultimate evolutionary concept album, one has to fast-forward nearly two decades from Banco’s and Wakeman’s efforts to the early 1990s…

I will tell you more when I return from holiday, but for now will leave you with a taster from the album: the late great Austrian white Rap artist Falco rapping about Darwin in a curious mixture of English and German…


Original lyrics


Hey, hey yah know what I am talking about

Er hieß Charles Darwin, und sie nannten ihn'nen Freak

Keine Bibel, Keine Offenbarung bremsten ihn ein

Denn seine Haltung hielt


Nachts - nachts - des Nachts war er aktiv

Aktiver, als man es sich nur vorstellen kann

But tags - tagsüber vermied er Sonnenlicht

And that's the reason daß ich euch sag'


Er war der Mann - he was a man

Genie und Partisan - a fascinating man

Sie sah ihn an - he was a man

Sie wußte, daß er - kann

A fascinating man


Science and fiction griffen nach dem Universe

Denn da ist more space in it

Darwin dachte dazu nur

Wir gehen auf-recht

And push it to the limit


Nachts - nachts - des Nachts war er aktiv

Aktiver, als man es sich nur vorstellen kann

Und tags - tagsüber vermied er Sonnenlicht

And that's the reason daß ich euch sag'


Er war der Mann - he was a man

Genie und Partisan - a fascinating man

Sie sah ihn an - he was a man

Sie wußte, daß er - kann

A fascinating man


Er war der Mann - he was a man

Genie und Partisan - a fascinating man

Sie sah ihn an - he was a man

Und wußte aufrecht geht der - Mann

A fascinating man


Can you hear me, Charles?



English Translation


Hey, hey yah know what I am talking about

He was Charles Darwin, and they called him a freak

No Bible, No revelation to hold him back

That was his attitude


At night - at night - by night he was active

More active than you can imagine

But by day - by day he avoided the sunlight

And that's the reason that I tell you…


He was the man - he was a man

Genius and partisan - a fascinating man

She looked at him - he was a man

She knew that he - can

A fascinating man


Science and fiction grappled with the Universe

Because there is more space in it

Darwin thought only about this

We go to law

And push it to the limit


At night - at night - by night he was active

More active than you can imagine

And by day - by day he avoided the sunlight

And that's the reason that I tell you…


He was the man - he was a man

Genius and partisan - a fascinating man

She looked at him - he was a man

She knew that he - can

A fascinating man


He was the man - he was a man

Genius and partisan - a fascinating man

She looked at him - he was a man

And, knew that upright stood the man

A fascinating man


Can you hear me, Charles?



Tuesday, August 12, 2008

Dawkins stitched up by Ofcom?!

My wife just alerted me to this statement from Dawkins, buried away on his web site:,2956,Richard-Dawkins-the-naive-professor,Libby-Purves,page2#225904

57. Comment #225904 by Richard Dawkins on August 7, 2008 at 1:44 pm

It is honest and direct for RD to state in his TV program that it was because of evolution that made him an atheist.

Thank you, but I have to admit that this, and other honest statements of atheism, were thrust upon me, against my will (especially right at the beginning of Episode 1), not by the Director or the television company, but by the LAWYER! That sounds weird. It isn't strictly a legal worry, but a worry about satisfying Ofcom, the regulatory body that controls British television. I don't fully understand it, but I THINK it has something to do with the need to 'respect' creationists. The lawyer thought that Ofcom would have preferred me to present 'both sides'. Because I obviously wasn't going to do that, he thought the next best thing was to be completely up front and announce, in advance, that the reason I took the line I did was that I was an atheist.

Of course, I don't like the sound of that at all. I'd prefer to say I'm an evolutionist because the evidence is so convincing. It is as though the lawyer has been infected by the 'all opinions are equally valid' viewpoint. So it's OK to promote evolution rather than creation, so long as I announce, IN ADVANCE that I am an atheist. 

Does anyone understand that? I'm far from sure that I do.


Ofcom is the independent regulator and competition authority for the communication industries in the United Kingdom, one of a series of such quangos. And so it seems that Dawkins is forced to be more in-yer-face about his atheism than he might otherwise be because of a defensive legal position. But I guess it is fruitless to try to complain to Ofcom on this issue, as it is a defensive lawyer who has set this in motion rather than Ofcom per se!

Here is an earlier piece from Dawkins about the absurd perceived need for fair treatment of all positions!

Neanderthal jigsaw puzzles

In August 1856, more than three years before Darwin published The Origin of Species, the top of a skull and fifteen other bones were recovered from a cave (the Kleine Feldhof grotto) in the Neander valley near Düsseldorf in Germany. A local teacher Johann Carl Fuhlrott soon identified them as human, and along with local anatomy professor Hermann Schaaffhausen, described the bones in a paper in 1857, suggesting that they represented the remains of an ancient extinct race of humans. Now known as Neanderthal 1, Fuhlrott’s fossil bones became the type specimen for a new species, Homo neanderthalensis (although in retrospect earlier finds from Belgium and Gibraltar belong to the same species).

In 1997, pioneering Swedish molecular archaeologist Svante Pääbo (b. 1955) obtained the first mitochondrial DNA sequence from the original Neanderthal specimen and confirmed that Neanderthals lay outside the range of variation seen in modern humans. Less than two years ago, Neanderthal genetics was transformed into stone-age genomics, when powerful new sequencing approaches were applied to a 38,000-year old leg bone from the Vindija cave in Croatia. Two papers appeared in November 2006 revealing analyses of up to a million base pairs of Neanderthal genome sequence. More recent analyses have established that the Neanderthal FOXP2 gene (potentially involved in speech) was identical to that in modern humans, that at least some Neanderthals had pale skin and red hair, but that Neanderthal Y chromosomes differed from those of modern humans. 

This week Pääbo and his team have delivered the next breakthrough in Neanderthal genomics with the publication in the journal Cell of the complete sequence (35-fold coverage) of a mitochondrial genome from the Vindija Neanderthal sample. The newly assembled sequence has allowed Pääbo’s team to estimate how much contamination from modern human DNA has affected their analyses (very little), how DNA gets degraded with time and to evaluate the prospects for a full nuclear Neanderthal genome (good). For a fuller discussion, see the posting by John Hawks in his own blog.

Although assembly of this molecular mitochondrial jigsaw is a remarkable achievement, for me the most jaw-dropping moment in recent studies on Neanderthals comes from the solution of a more tangible puzzle. The cave where Neanderthal 1 was discovered was destroyed in the 19th century, as the area was excavated and flattened to provide the local steel industry with limestone. It was thus generally assumed that the first, and most important, Neanderthal site was lost to science. But in the late 1990s, German archaeologists Ralf Schmitz and Jurgen Thissenset set about finding it. Poring over 19th-century paintings and old maps, they recognized a rock that still stood in the valley. They dug nearby and found cave debris. After careful examination, a team of archaeologists found over sixty Neanderthal skeletal fragments, from at least three individuals. Their efforts culminated in a triumphant solution to a skeletal jigsaw puzzle: three of the newfound bony fragments fitted perfectly on to the original specimen, excavated near a century and a half before (read more here)!

Oh and one final point! Palaeoanthropologists (or should that be “paleoathropologists”) cannot decide on how Neanderthal should be spelt. All agree that the original spelling Neanderthal is preserved forever in the species name Homo neanderthalensis, but in recent years a number of them, including Pääbo, have taking to using the modern German spelling for the Neander valley (Neandertal) to describe members of this species. In PubMed, at the time of writing, “Neanderthal” beats “Neandertal” by 209 to 183 citations. Someone somewhere should make a definitive ruling on this!

Saturday, August 9, 2008

Ever wondered what it is like to experience the visual aura of a migraine attack?

As I write I am experiencing what medics call a scintillating scotoma, which is something that happens to me every once in a while. Usually these are associated with migraine, but I get what is called a "forme fruste" of migraine or acephalgic migraine, where I don't get the headache, but do get the visual effects. So, I am not sure whether I should count myself lucky not to get the headache, or unlucky in that I get this problem at all!

Anyhow, trying to explain what it is like is often frustrating, but recently I came across this YouTube video which captures it perfectly (although running at over ten times normal speed: attacks usually take 15-20 minutes):

Who needs fireworks with all this going on in one's visual cortex!

Friday, August 8, 2008

Is there life on Mars: yes, probably...

Now that the Rough Guide to Evolution is nearly finished and a couple of grant proposals are off the desk, I have been able to grab a bit of time to catch on my backlog of reading. The first article that caught my eye was a piece in Microbiology Today by Charles Cockell entitled Is Microbial Life on Mars possible? I was expecting the usual "maybe, maybe not", but instead Cockell starts the article with a tangential answer, which equates to a "probably yes":

"It is not often apparent to microbiologists or members of the public that we know for certain that there has been life on Mars. Since the crash of the Soviet’s Mars 2 lander on the surface of the planet in 1971 (Fig. 1), a diversity of landed and crashed probes of various kinds, many of them not sterilized, have been delivered to the surface of Mars by the world’s space-faring nations. Only the Viking spacecraft (Fig. 2), which landed in 1976, were completely heat sterilized to kill spores. Many of these spacecraft have delivered an inventory of spores found in spacecraft assembly facilities, including Bacillus species. A fascinating scientific question is whether there is, on the surface of Mars today, a viable spore hidden and shielded from Mars’ intense UV radiation in one of these various contraptions. There seems to no reason why a spore, cooled to Mars’ average temperature of –60 °C should not have survived since the 1970s. So on the face of it the answer to the question I was asked to address is likely to be ‘yes’."
Elsewhere in the same issue, Lewis Dartnell describes the microbial flora of spacecraft and discusses the idea of planetary protection

Neither Cockell nor Dartnell mention the widespread urban myth that bacteria survived on the Moon for three years on board Surveyor 3. Here are a few examples of it being cited:

A few years ago at a meeting on Astrobiology in Loughborough, I raised this claim with NASA astrobiologist Lynn Rothschild, who stated quite clearly that NASA no longer believed it. I was thus surprised to hear the claim repeated in a BBC Horizon programme broadcast a few years later, in November 2006. I contacted Lynn by e-mail, who put me in touch with NASA's Planetary Protection Officer, John Rummel, who had actually appeared in the show. He told me that he had discussed the claim with the producer of the show and made it clear that NASA no longer supported it:

If the BBC program (BBC Horizon?) stated that the microbe survived on the Moon, and didn’t also have me on saying that it was likely contamination, then I have a bone to pick with the producer!

I never did get to hear whether they picked over that bone, but I did discuss with John how one could squash such an urban myth. I hit on the idea of writing a Wikipedia article entitled The Myth of Streptococcus mitis on the Moon and linking to it from the Apollo 12 and Surveyor 3 pages. 

I haven't look at the page lately, but it survives to this day, but to comply with the Wikipedia neutral point of view, it is now entitled Reports of Streptococcus mitis on the Moon. In fact, much of what I wrote has been stripped out but the Wikipedia lets you compare today's version with my original. Interesting to see how the Wikipedia's neutralism neuters an article (maybe Knols will prove more reliable, or maybe not). BUT worse still, someone has added in the counter-claim that NASA's official view is to accept the myth (will be e-mailing Lynn and John again on this one!)

Returning to Cockell's claim, one day humans will visit Mars and retrieve those probes, so we can see test Cockell's hypothesis and see how well terrestrial bacteria survive on Mars. But let us hope that next time, they take care not to contaminate them on the way home!

Coming soon: Fossil Detectives on BBC4

Have just noticed this post on the NatureWatch blog about Fossil Detectives, a new eight part series from the BBC Natural History Unit showcasing British fossils, fronted by geologist-cum-presenter Hermione Cockburn. The first episode will be on Thursday 21 Aug at 7.30pm on BBC 4, so if you are going on holiday, don't forget to set the video recorder. 

Lot's more information, including a free guide (if in UK) from the Open University Website:

Thursday, August 7, 2008

In search of the ultimate evolutionary concept album part 1: "Darwin!" by Banco del Mutuo Soccorso

In the Rough Guide to Evolution, I was keen at the outset to have a section that documented popular music that had been influenced by, or that celebrated, Darwin and his theory of evolution. Even before my proposal had been accepted I found what I though must be the ultimate concept album on evolution—a little known progressive rock album called “Darwin!” 

I was encouraged by the commissioning editor’s assurance that this would definitely earn me brownie points with the founder of Rough Guides, Mark Ellingham, who is a great fan of progrock. But unfortunately, this all counted for naught, as Ellingham left the company just as I signed up.

So, let’s start with the caveat: progrock is an acquired taste, not for the faint-hearted. Although my musical tastes have veered off towards reggae, dub and world music, I still hold a nostalgic affection for progrock, which was the music to listen to when I was a teenager in the early 1970s.


“Darwin!” was released in 1972 as the second album by Italian progrock band Banco del Mutuo Soccorso. The album cover features the lead singer of the band in a psychedelic landscape within the face of a watch (presumably a reference to Paley’s watchmaker?).  The album is held in high regard among progrock fans. See, for example, these reviews:

Over the years, Banco, or BMS as they are called, have re-recorded and re-released various tracks from the album. You can listen to a medium-quality mono version of a more recent and shorter version of the opening track here on youtube:


However, purists still cling to the vintage 1970s feel of the original, which UK readers can buy from iTunes here.

NB: for some reason, Darwin! is not available in the US iTunes store, but US readers can buy an overpriced CD of the original album from or try their luck with a DVD of a live performance (but this will be regionalised). I will e-mail the band to complain about lack of availability in the US!

BUT, all is not lost: BMS are performing live next month in North America, here in Montreal!

The original album opens with a long track, L’evoluzione (“Evolution”), which lasts for fourteen minutes and encompasses a range of musical styles, from mellow to frenetic as it re-tells the origin of life on Earth.

The lyrics are, unsurprisingly, in Italian, which makes the track less accessible for an English-speaking audience. But I append a translation, which is a joint effort between myself and my colleague Barbara Bordalejo. Anyone with better translation skills, feel free to submit your own version!

Later tracks in the album include

  • "La conquista della posizione eretta" Conquest of the upright stance
  • “Danza dei grandi rettili”: Dance of the great reptiles
  • "Cento mani e cento occhi"  A hundred hands and a hundred eyes
  • "750,000 anni fa ... L'amore?" 750.000 years ago ... Love?"
  • "Miserere alla storia" The psalm of history
  • "Ed ora io domando tempo al tempo ed egli mi risponde ... Non ne ho!" And Now I wonder time to time and he answered me ... I have not!

Last year I contacted BMS letting them know that the Darwin bicentenary year was coming. Iaia de Capitani, Banco’s manager e-mailed me back to say that

Actually Banco is working on a new Darwin project looking forward to the Darwin Bicentennial. The new work is "L'evoluzione" of the evolution.

I tried to get the organizer of the Shresbury Darwin Festival interested in having BMS play l’evoluzione in Darwin’s home town on Darwin’s 200th birthday, but he thought there wouldn’t be enough interest among English festival goers :-(

So, in conclusion, there is no doubt that Darwin! is a strong contender for greatest concept albums yet created on the theme of Darwin and evolution—some progrock fans see it as the best progrock album ever! But, as we shall see in a subsequent post, there is at least one other serious contender...

 L'evoluzione: Evolution

Prova, prova a pensare un po' diverso

niente da grandi dei fu fabbricato

ma il creato s'è creato da sé

cellule fibre energia e calore.


Try, try to think a little differently

Nothing was made by great Gods

But creation has created itself

Cells, fibres, energy and heat.

Ruota dentro una nube la terra

gonfia al caldo tende le membra.

Ah la madre è pronta partorirà

già inarca il grembo

vuole un figlio e lo avrà

figlio di terra e di elettricità.

Strati grigi di lava e di corallo

cieli umidi e senza colori


The earth rotates within a cloud,

Heat inflates the organs

Oh, the mother will soon give birth

Now the womb contracts

Wants a child and will soon have one

Son of earth and electricity

Grey layers of lava and coral

Humid skies without colours


ecco il mondo sta respirando

muschi e licheni verdi spugne di terra

fanno da serra al germoglio che verrà.

Informi esseri il mare vomita

sospinti a cumuli su spiagge putride

i branchi torbidi la terra ospita

strisciando salgono sui loro simili

e il tempo cambierà i corpi flaccidi

in forme utili a sopravvivere.


Here the world is breathing.

Green moss and lichen, sponges of earth

Act as greenhouse for the buds that will come.

The sea vomits beings without form,

Damp heaps on putrid beaches.

The welcoming soil is home to turbid branches;

They emerge, crawling over their fellows

And time will mould the flaccid bodies

Into forms fit for survival.


Un sole misero il verde stempera

tra felci giovani di spore cariche

e suoni liberi in cerchio muovono

spirali acustiche nell'aria vergine.

Ed io che stupido ancora a credere

a chi mi dice che la carne è polvere.


A miserable sun nurses the vegetation

Through young ferns charged with spores

And free sounds circle round

Acoustic spirals in the virgin air.

And am I so stupid still to believe

Him who tells me that flesh is dust?



E se nel fossile di un cranio atavico

riscopro forme che a me somigliano

allora Adamo non può più esistere

e sette giorni soli son pochi per creare

e ora ditemi se la mia genesi

fu d'altri uomini o di quadrumani.


And if in the fossil of an atavistic skull

I rediscover forms that are similar to me

Then Adam can no longer exist

And seven days alone are too few for creation

And now tell me if my own genesis

Is not of men but of apes.


Adamo è morto ormai e la mia genesi

non è di uomini ma di quadrumani.


Now Adam is dead and my genesis

Is not of men but of apes.


Alto, arabescando un alcione

stride sulle ginestre e sul mare

ora il sole sa chi riscaldare


High up, circling in arabesques, a halcyon bird

Squeals over the sea and shrubs of broom and

Now the sun knows whom  to warm