Origin of Species: new online variorum

Yesterday, the world celebrated the sesquicentennial of the publication of The Origin of Species. But it is worth stressing that there was not one "Origin of Species", but six different editions produced in Britain alone during Darwin's lifetime. Fifty years ago, in time for the hundredth anniversary of the first publication, Morse Peckham produced a variorum text, which showed the variant readings between the six editions. However, Peckham's variorum has always been difficult to follow and is decidedly old-fashioned with its literal use of cut and paste.

To celebrate the 150th anniversary, my colleague at the University of Birmingham, Barbara Bordalejo, working with John van Wyhe at Darwin Online, has produced a fantastic new digital online variorum, which is much more flexible and user-friendly than Peckham's. Take a look at it here: http://darwin-online.org.uk/Variorum/index.html

For more details, see the editor's introduction: http://darwin-online.org.uk/Variorum/Introduction.html

At last, all of us can follow the evolution of The Origin!

First thoughts on "Creation"

Yesterday afternoon, I went to see "Creation", the new film out centred on Charles Darwin's relationships with his wife and his daughter, Annie. I guess I am in a unique position in writing this as I am sitting about two hundred yards from Montreal House in Malvern, where Annie died in 1851 and I live on land that was once part of the estate of the Lodge, the house in which Darwin and his family (including Annie) stayed for a few months in 1849.

But geographical proximity is not the real issue here--I have been far too close psychologically and intellectually to Darwin and his life, and Annie's role in it, for far too long to ever approach the movie as most viewers will. With that in mind, I was preparing to be disappointed, but in fact for the most part I enjoyed the movie, as did my children, because I remembered to tell myself that it was a work of imagination not historical biography.

There are lots of minor historical inaccuracies in the film, but as Eugenie Scott has pointed out, "Creation" will bring many aspects of Darwin's life, particularly his family life, to a wider audience, including the tragic loss of his daughter here in Malvern and the misery of his chronic illness. The acting is great, particularly Martha West as Annie and real husband and wife team Paul Bettany and Jennifer Connelly as Charles and Emma. And the lavish cinematography is a treat.

There were two things in the film I did not like. One was the way in which it flitted from one part of Darwin's life to another, back and forth across the decades. I would have preferred a simpler narrative. But more problematic was the way in which the film inter-linked Darwin's various struggles, intellectual and emotional, when as far as I am aware they were never linked. For example, there is no evidence that the death of Annie Darwin had any effect whatsoever on Darwin's work on the Origin of Species. And it is unclear to me whether differences in attitude to religion between Charles and Emma Darwin, which were clearly raised as an issue around the time of their marriage, persisted as a problem in their relationship as late as the film suggests, i.e. into the late 1850s. I may be wrong and will have to look into this, but the level of emotional intensity on Darwin's part in the film on this issue strikes me as off-kilter.

But all-in-all, a good film which I advise you to go and see! At the very least, it will banish the tired icon of Darwin as merely an old man with a bushy beard!

The evolution of the Origin revisualised

A few years back, Peter Robinson and Barbara Bordalejo, both textual scholars, came to work here in Birmingham. They, along with local New Testament scholar David Parker, have been at the forefront of efforts to exploit computers in textual scholarship and use the kind of phylogenetic approaches used on biological sequences to unravel the patterns of evolutionary branching among manuscripts. Peter and Barbara had worked extensively on Chaucer's Canterbury Tales, but shortly after her arrival here, Barbara was searching for a fresh project. David Parker, perhaps rather provocatively for a Reverend Professor, suggested that Barbara, Peter and I work together on the evolution of Darwin's Origin of Species, treating Darwin's publications as "textual genomes". We did some preliminary work on this and submitted a proposal to the Arts and Humanities Research Council, but alas it was not funded...

But the best proof that one is working on something worthwhile is when someone else comes up with the same idea quite independently (cf Wallace on Ternate!). So it is gratifying to see two examples of people doing the kind of analyses and developing the same kind of visualisation tools that we envisaged:

• The (En)tangled Word Bank is the work of computer scientist Greg McInerny and London-based visual artist Stefanie Posavec (see Science Blog Post) and is certainly pretty, although whether it can be used by scholars to unravel Darwin's thinking is unclear.
• Ben Fry's The Preservation of Favoured Traces looks more useful and provides a more intuitive view of changes, but sadly appears to lack a zoom tool, so that one can only gain a "God's eye" view of the whole text, without been able to look closely at individual sections.

But both projects provide a fascinating proof of concept and it would be great to see them integrated more fully into a project like Darwin Online, where they could make a real contribution to Darwin scholarship!

And now a request please! Can either or both projects now incorporate the two forerunners of the Origin: Darwin's 1842 Pencil Sketch and his 1844 essay (both transcribed here), so we can see quite how much of the Origin was written over ten years before Darwin started on his "big book"  Natural Selection (which should also be included). It always amazes me how much of the structure of Darwin's argument was laid out in those two manuscripts from the 1840s, but it would be nice to see visually how many of the words are in common too.

I have outsold my advance!

Just a brief note to report the good news that I have outsold the advance against royalties that I was given for my book, The Rough Guide to Evolution and have just had an additional payment. I think only about half of Rough Guides do this at all and I was quietly hoping to do so within the first year of publication. But the fact that I have done so in the first six months is good news indeed (as is the fact that a French translation courtesy of Edition Tournon is in the offing!). 

Thanks to all of you who bought the book and/or recommended it!

The Darwin Song Project

I have to confess that there is not much folk music in my iTunes library, but last week my copy of the Darwin Song Project CD arrived. And I am impressed!

The Darwin Song Project is the fruit of a frenetic collaboration between eight of the world's top folk artists, who composed the 17 songs of the album during a week-long retreat in a Shropshire farmhouse and then performed them in the new Theatre Severn in Darwin's home town Shrewsbury in March this year.

Even though it incorporates the Annie hypothesis, my favourite song on the album is the Dylanesque "Kingdom Come", which investigates how differences in religious belief divided Charles from his wife Emma. It opens with what must be a unique first line--an account of the life cycle of ichneumonid wasps, parasitic wasps that lay their eggs in the flesh of living caterpillars and which troubled Darwin!

Another delight is this mock-Country number, "We'll him down". I dedicate this YouTube link to all my friends from Dover, Pennsylvania (Lauri, Cyndi, Tammy and Nick)! Let's hope their Creationist compatriots realise that the song is ironic!

Videos for three other songs from the project are also available on YouTube. You can find out more about the project from its website and from this BBC Radio 4 show. And you can place your order for the CD here.

[Review of the album from The Guardian.]

Lamarck, Darwin and the Tree of Life

There has been some interesting discussion in the blogosphere as to whether Lamarck beat Darwin to the Tree of Life metaphor:

• http://scienceblogs.com/geneticfuture/2009/08/lamarck_beat_darwin_to_the_tre.php
  
• http://www.genetic-inference.co.uk/blog/?p=505
  

I am due to speak on this subject at the upcoming Society for General Microbiology meeting in Edinburgh, so I was intrigued to read these posts.

Here is my own quick-fire rather disorganised contribution to the argument, quickly cribbed off my Powerpoint slides, with a shameless inattention to sources:

It seems that Pallas did indeed come up with this metaphor in words before Lamarck and Darwin, even though he didn't draw a tree. This is what he wrote in 

Elenchus Zoophytorum (1766):

At omnium optime Arboris imagine adumbraretur Corporum organicorum Systema, quae a radice statim, e simplicissimis plantis atque ani- malibus duplicem, varie contiguum proferat truncum, Animalem & Vegetabilem; Quorum prior, per Mollusca pergat ad Pisces, emisso magno inter haec Insectorum laterali ramo, hinc ad Amphibia; & extremo cacumine Quadrupedia sustineret, Aves vero pro laterali pariter magno ramo infra Quadrupedia exsereret.

“But the system of organic bodies is best of all represented by an image of a tree which immediately from the root would lead forth out of the most simple plants and animals a double, variously contiguous animal and vegetable trunk; the first of which would proceed from molluscs to fishes, with a large side branch of insects sent out between these, hence to amphibians and at the farthest tip it would sustain the quadrupeds, but below the quadrupeds it would put forth birds as an equally large side branch.”

Augustin Augier in 1801 deserves credit for this description of a phylogenetic tree:

‘‘A figure like a genealogical tree appears to be the most proper to grasp the order and gradation of the series or branches which form classes or families. This figure, which I call a botanical tree, shows the agreements which the different series of plants maintain amongst each other, although detaching themselves from the trunk; just as a genealogical tree shows the order in which different branches of the same family came from the stem to which they owe their origin.’

see http://www.bio.sdsu.edu/faculty/archibald/Archibald08JHBonline.pdf for a depiction of Augier's tree. In fact, this article in general is an excellent source of information on the whole issue of evolutionary trees and in particular draws attention to a paleontological chart from 1840 that looks a lot like an evolutionary tree.

Chambers in his Vestiges of the Natural History of Creation has something that looks a bit like an evolutionary tree, although it is probably best described as a developmental tree. Follow this link: http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=A2&pageseq=215

Note that Darwin's first depiction of an evolutionary tree is arguably not the oft-quoted "I think" figure, but these "coral of life" depiction that appears a few pages earlier in his notebook.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=CUL-DAR121.-&pageseq=27

And finally, Wallace hit on the metaphor independently. One can dispute whether his tree-like diagrams on the classification of birds really count as evolutionary trees, but his verbal description in the article he published in 1855 clearly pre-date Darwin's published descriptions of the tree of life and add the appealing analogy of the human vascular system:

On the law which has regulated the Introduction of New Species. Annals and Magazine of Natural History, including Zoology, Botany, and Geology 16: (September): 184-196.
“We are also made aware of the difficulty of arriving at a true classification, even in a small and perfect group;—in the actual state of nature it is almost impossible, the species being so numerous and the modifications of form and structure so varied, arising probably from the immense number of species which have served as antitypes for the existing species, and thus produced a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak or the vascular system of the human body. Again, if we consider that we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others, the whole difficulty of the true Natural System of classification becomes apparent to us.”

Interestingly, Wallace is now buried under a huge fossilised tree:

 [NB we all know it is really a huge fossil phallus ;-) ]

But the last word goes to Darwin, with his melodic prose:

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications. 

And for those of you who like reggae, try those "beautifiul ramifactions" Jamaican-styleee...

Happy Birthday to this Blog! And hello to a new blog on bacterial pathogenomics

Last week, while I was away on vacation in France, this blog had its first birthday. During this last year, the blog has plotted the completion, publication and reception of my book The Rough Guide to Evolution, but has covered much more besides in its 193 postings—from evolutionary tourism to flagellar biology. According to Google Analytics, the blog has received over 23,000 visits from 137 countries! 

It is unclear quite how well the book is selling, as I am still awaiting accurate figures for the first half of the year, but I have been told that worldwide sales so far are likely to be around 10,000-10,500, which means that there is a good chance I will have just outsold my advance against royalties in the first six months of the book's life!

But now I must confess that a change is at hand. I have to re-focus my efforts on my "day job" as a microbiologist, so, although I won't be closing this blog, I will be posting less often here. Instead, I will be using the insights into blogging that I have gained from this blog to drive forward a new blog Pathogens: Genes and Genomes, which will convey the excitement generated by the collision of high-throughput sequencing and clinical and environmental bacteriology. Feel free to join us there and to raise a glass to The Rough Guide to Evolution, book and blog!

Rough Guide to Evolution in Nature again this week

The Rough Guide to Evolution features again in the prestigious scientific journal Nature this week, thanks to Eugenie Scott (executive director of the US National Center for Science Education), who recommends it as Summer reading:

"The 200th anniversary of Charles Darwin's birth, plus the 150th anniversary of the publication of his best-known book, On the Origin of Species, make 2009 the year to learn about evolution. Mark Pallen's The Rough Guide to Evolution provides a concise summary of what you need to know: a brief history of the idea that all living things share common ancestry, a complete survey of the mechanisms of evolution and a solid summary of how life originated and then adapted through time to a changing planet. He livens up the story with literary, musical and cultural references so that you never feel you are being told to eat your vegetables. Alas, it is not only non-specialists who don't have a firm grasp of the strength of theory and data supporting the modern understanding of evolution — many scientists outside the field of evolutionary biology struggle too. This entertaining handbook will bring anyone up to date."

Thanks Genie!

Baba Brinkman's Rap Guide to Evolution now available in MP3

Canadian Lit Hop artist Baba Brinkman has just released his new album, The Rap Guide to Evolution, and as a special promotion, the album can be downloaded for free during the month of August in MP3 format. Follow the links from Baba's web page to get your copy: http://www.babasword.com/

Although Baba is not charging for downloads, he would appreciate donations to cover production costs.

The Rap Guide to Evolution is a hip-hop exploration of modern Evolutionary Biology. The album is based on the stage show of the same name, which appears at the Edinburgh Fringe Festival this August. Follow Baba's progress at the Fringe via his own blog for the event (Darwin on the Fringe) and be sure to go see the show if you are visiting the Fringe.

From Digbeth watesland to darwin-inspired arts space

Just picked this up from the Behind Closer Doors project website:

Two artists from Birmingham are part of an unusual project which has transformed a Digbeth waste-ground into a darwin-inspired exhibition space.

In the wake of the revered scientist’s bicentenary, Helen Grundy and Anne Guest are set to launch Unnatural Selection on 30th July at the Rea garden in Floodgate Street. The project is supported by Arts Council funding and the artists’ collective Behind Closed Doors.

Unnatural Selection aims to replicate Darwin’s methods of using his garden as a laboratory to observe nature, collect samples and carry out experiments.

There is a related workshop on saturday 1st August from 12-3pm.

Hat tip: Lewis Bingle.

PCR in song and video!

The polymerase chain reaction revolutionised molecular biology twenty years ago, opened up the study of ancient DNA from extinct organisms, and similar DNA amplification methods underpin the current revolution in high-throughput sequencing, so it is great to see molecular biology company BioRad celebrating this wonderful technique with a couple of hilarious catchy tongue-in-cheek songs.

Baba Brinkman at the Cambridge Darwin festival

I ducked out of the Cambridge Darwin festival for a variety of reasons, including severe cash flow problems after renovating my house. But Baba Brinkman went and from various sources I hear he had a great time there.

Here he is rapping to David Attenborough in King's College.

Another stray link between Darwin and the Wire...

Perhaps my earlier attempts to draw up links between the Darwins and the cult TV show The Wire were rather fanciful... 

But how about this for a more tangible link (left): Darwin's daughter Annie in the forthcoming film Creation is played by 10-year-old Martha West, daughter of Dominic West, who played Jimmy McNulty in The Wire! 

Everything connects...

I was suckered too...

In case anyone is thinking I have been too rough in publicising quite how many people have fallen for the Annie myth, let me confess, I was suckered by this story too and that is why I am quite so cross to see reality not match up to mythos. 

Here am I, in that piece of whimsy, the Origin of Species in Dub, falling for the myth that Annie's death influenced Darwin's evolutionary writings: 

http://www.infection.bham.ac.uk/BPAG/Dub/Videos/Track8.html

The spread of the Annie myth: it's worse than I thought

My posting on the spread of the Annie hypothesis has elicited this interesting posting on "the Angry Bitter Atheist myth"--the idea that a dismissal of religion purely on intellectual grounds isn't enough; instead atheists must also be angry at God for some tragedy or other. In fact, I have tried to avoid calling the "Annie hypothesis" (the claim that Annie's death triggered Darwin's final loss of faith in Christianity), the "Annie myth", for fear of drawing legal action (c.f. the bogus legal action against Simon Singh's use of the term "bogus"). 

But it is hard to avoid the conclusion that this story has been propagated so widely because it appeals to some human need for an emotional narrative, and so in that sense the term "myth" is appropriate. Plus, those who want to persuade Christians and other religious believers that Darwin was a thoroughly good chap for his work on evolution will wish to avoid the idea that his ideas on evolution had anything to do with his own loss of faith (even though they didn't have much to do with it)--far safer to blame it on a personal tragedy! 

Anyhow, on further investigation, I have found a few more examples of the uncritical acceptance of the Annie myth:

• Larry Moran and Niles Eldredge netted as uncritical devotees of the Annie myth in a single posting! Eldredge may be good on science, but he swallows both the "removed what little was left of his religious faith" myth and states as fact rather than wild guess that Annie died from tuberculosis.
• This article and podcast on Annie Darwin from the Oxford Dictionary of National Biography: "Darwin's experience of his daughter's life and his bereavement had a double significance for his thinking. Recent scholarship (Moore) has shown that it was probably the final factor in his gradual rejection of Christian faith"
• Plus this article from the same source on Darwin himself: "Moore reassessed Darwin's religious faith, showing that while he remained a pillar of his rural parish, the deaths of his father in 1848 and daughter Annie in 1851 finally led him to give up Christianity."
• Evolution 101 by Randy Moore
• More proof that even Carl Zimmer isn't infallible.
• The Mini Oxford Handbook of Clinical Medicine, which ascribes Annie's death to typhoid fever rather than the usual tuberculosis.
• Dinesh D'Souza's blog entry linking Annie's death and Darwin's loss of faith with the problem of evil
• Telegraph columnist George Pitcher in his article "Charles Darwin was not the father of atheism" 
• David Livingstone in a chapter in Where Science and Christianity meet lends credence to Moore's account of the Annie myth, but with more balance than most commentators, and he also goes for "typhoid fever" as cause of death.
• Even creationists are suckered in! http://www.evolutionthelie.com/history-of-science/evolutions-fatal-fruit-nurturing-charles-darwin/

It seems I really do need to get this paper finished and published to prevent this nonsense spreading further!