Wednesday, May 27, 2009

From the Origin of Species to the origin of infection

This article has just appeared in a special Darwin 200 issue of Microbiology Today, where you can obtain a PDF of this piece and much more besides. But they have given me permission to post it here too, where it benefits from hypertext links for the interested reader.

From the Origin of Species to the origin of infection
2009 marks the bicentenary of the birth of Charles Darwin and the 150th anniversary of the publication of On the Origin of Species by Means of Natural Selection. The impact of Darwin’s theory of evolution by natural selection is felt throughout biology and even beyond it — in disciplines as diverse as computer science and cosmology. Darwin’s theory is widely touted as ‘the best idea anyone ever had’ and arguably ranks as the most influential change in human thought in modern times (although as microbiologists, we may wish to claim that the germ theory of infection is of more practical significance).

What about Darwin and microbiology? Antibiotic resistance is widely cited as a tangible example of Darwinian evolution. But Darwin himself lived through the birth of our discipline, so it is not surprising to learn that there are links between Darwin and the founding fathers of microbiology.

Darwin and natural selection

Charles Darwin was born and schooled in Shrewsbury, an English market town close to the Welsh border. He tried, and ducked out of, a medical education in Edinburgh, then studied at Cambridge with a view to joining the clergy. But his reputation as a naturalist earned him a place on a round- the-world trip on HMS Beagle, which primed him for his revolutionary ideas on evolution. He started to formulate his thoughts on evolution shortly after his return from the Beagle voyage, recording a riot of ideas, sometimes earthy or even vulgar, in a series of notebooks. For inspiration on his ideas of the struggle for existence and natural selection, he drew on the work of Robert Malthus, who had suggested that human populations always eventually out-run the means to sustain them. Darwin outlined his theory in a ‘pencil sketch’ of 1842 and an essay of 1844, but, preoccupied with other work, delayed publication until the late 1850s, when he was spurred into action by the rival work of Alfred Russel Wallace.

In On the Origin of Species by Means of Natural Selection, first published in 1859, Darwin eloquently (and presciently, given its subsequent influence on antibiotic resistance) emphasizes the remarkable power of natural selection:
‘We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.’ [link]
Later, in Variation Under Domestication [note: not The Descent of Man as stated in PDF], despite his ignorance of the nature of inheritance, Darwin points out that the variation that is a prerequisite of natural selection originates independently of the selection itself.

In the decades after his death, while Darwin’s ideas of evolutionary change and common ancestry were widely accepted, his principal mechanism for change, natural selection, was not. However, in the mid-20th century, Darwin’s intellectual legacy was reconciled with Mendelian genetics in what is often called ‘The Modern Synthesis’. As part of this reconciliation, bacteria were brought into the broader evolutionary genetic framework, principally through the experiments on the genetics of phage susceptibility published by Salvador Luria and Max Delbrück in 1941. In their famous fluctuation test, Luria and Delbrück confirmed Darwin’s hunch that variation precedes selection, rather than arising in response to it, and thrust bacteria centre stage as biological entities with fully-fledged genetics. A few years later, in 1945, Milislav Demerec repeated the fluctuation test on penicillin resistance in Staphylococcus aureus, showing for the first time the awesome power of natural selection to curtail our biochemical victories over micro-organisms.

Darwin and Pasteur

Shortly after Darwin published The Origin, in Paris, Louis Pasteur performed a series of experiments that demolished the theory of spontaneous generation. Darwin was well aware of the on-going controversy. In 1860, in a letter to his friend Lyell, he refers to the work of Pasteur’s rival Pouchet:
‘I have seen something about the infusorial experiments in Paris: Quatrefage objected to their accuracy. Some old experiments were several years ago tried in Germany with astonishing precautions (air all passed through sulphuric acid & caustic potash) and infusoria never appeared.’
A few years later in 1863, he wrote to the English botanist George Bentham:
‘I am very glad that you are going to allude to Pasteur; I was struck with infinite admiration at his work.’
In disproving spontaneous generation, Pasteur might be seen as undercutting Darwin’s theory of evolution by removing a mechanism for the generation of the first life forms. However, Darwin was sharp enough to realize that the conditions under which life first originated were likely to be quite different from those around today. In 1871, he wrote to his botanist friend Joseph Hooker:
‘It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a proteine [sic] compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.’
As far as I am aware, Pasteur never made any direct reference to Darwin, although he opened his 1864 address to the Sorbonne on spontaneous generation with these expressive lines:
‘Great problems are in question today, keeping every thinking man in suspense: the unity or multiplicity of human races, the creation of man 1,000 years or 1,000 centuries ago; the fixity of species, or the slow and progressive transformation of one species into another…’
Half a century later, an essay in Science magazine concluded:
‘Darwin, master of the organic world sleeps near Newton, master of the inorganic, in the great [Westminster] Abbey, among the most famous of his race. Pasteur rests alone in the chapel of his laboratory … Both rest forever among the immortals. the last half of the nineteenth century may well be called their age “the Age of Darwin and Pasteur”.’

Darwin, Cohn and the origin of infection

Darwin maintained an extensive network of correspondents. Among them was the German Jewish botanist and bacteriologist, Ferdinand Cohn (1828–1898), who is widely recognized as the father of bacterial taxonomy. Cohn was the first to classify bacteria according to their microscopic appearance and the first to describe sporulation in Bacillus. He was instrumental in publishing Robert Koch’s work on Bacillus anthracis.

From 1874 until 1882, Darwin and Cohn maintained a lively correspondence, principally on botany. On 26 September 1876 Darwin writes to invite Cohn and his wife to visit him at Down House. And then, the very next day, Darwin writes to his son Frank, saying that he hopes they will not come! Apparently the subsequent visit was a success. However, for microbiologists, one particular exchange of letters stands out. In January 1878, Cohn writes to Darwin, discussing Koch’s recent discovery of the anthrax bacillus. Darwin’s response is a triumphant celebration of the birth of medical microbiology:
‘I thank you sincerely for your most kind letter and I return your wishes for the New Year with all my heart. Your letter has interested me greatly. Dr Sanderson showed me some admirable photographs on glass by Dr Koch of the Organisms which cause Splenic Fever. But your letter and the valuable work which you have given me make the case much clearer to me. I well remember saying to myself between 20 and 30 years ago, that if ever the origin of any infectious disease could be proved, it would be the greatest triumph to Science; and now I rejoice to have seen the triumph.’ 
Further reading

Darwin, C. (1859). On The Origin of Species By Means of Natural Selection. London: John Murray.

Pallen, M. (2009). The Rough Guide to Evolution. London: Rough Guides.

Creager, A.N.H. (2007). Adaptation or selection? Old issues and new stakes in the postwar debates over bacterial drug resistance. Stud Hist Phil Biol Biomed Sci 38, 159–190.

Sedgwick, W.T. (1923). Darwin and Pasteur: an essay in comparative biography. Science 52, 286. – The complete works of Charles Darwin online. – Darwin Correspondence Project

Sunday, May 24, 2009

The Origin of Species as an organism: census, taxonomy and evolution

Last Friday, John van Wyhe, creator of Darwin Online, visited me in Birmingham. He gave a nice seminar on Darwin's Delay (or lack of it: see John's paper on this topic), which covered familiar ground for me. But one interesting topic that cropped up in our discussions, which I was unaware of, was a census of all first editions of The Origin, due to culminate in November in time for the book's 150th anniversary

Following John's advice, I tracked down this description of the census on Darwin Online. The census reminds me of a similar effort to track down all extant copies of Copernicus's masterwork De Revolutionibus, which I read about a copies of years ago in The Book Nobody Read, by Owen Gingerich.

This new census of The Origin falls into a line of thinking that has been rattling around for quite a while. Just as Darwin placed variation between organisms within a species centre stage in biology as the very seed corn of evolution by natural selection, it is also important to recognise that documents also evolve by descent with modification—and The Origin of Species is no exception! 

In Darwin's lifetime, there were six different editions authored by him, with numerous small and large differences from one edition to the next. These differences were collated in a printed variorum by Morse Peckham around fifty years ago (now available online via Google books). My colleagues at the University of Birmingham Barbara Bordalejo and Peter Robinson are working on a digital variorum.

But another key facet of The Origin's evolution that intrigues me is just how much of it was written over fifteen years before 1859 in two short documents, Darwin's 1842 Pencil Sketch and 1844 Essay. It is interesting to take favourite passages from the Origin and see their ancestors in those earlier drafts. Here are is the most obvious example, the closing words:
"There is a simple grandeur in the view of life with its powers of growth, assimilation and reproduction, being originally breathed into matter under one or a few forms, and that whilst this our planet has gone circling on according to fixed laws, and land and water, in a cycle of change, have gone on replacing each other, that from so simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved." 1842 Pencil Sketch. 
"There is a [simple] grandeur in this view of life with its several powers of growth, reproduction and of sensation, having been originally breathed into matter under a few forms, perhaps into only one, and that whilst this planet has gone cycling onwards according to the fixed laws of gravity and whilst land and water have gone on replacing each other—that from so simple an origin, through the selection of infinitesimal varieties, endless forms most beautiful and most wonderful have been evolved." 1844 Essay
"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." The Origin of Species, First Edition. NB: in the 2nd edition "by the Creator" is introduced after "originally breathed."
But the new census of the first edition hammers home the differences not just between editions, but also between copies of the very same edition. Start off by taking a look at the census guide for a panoply of features that can be used to classify a copy of The Origin as a First Edition. A key hallmark is the misspelling of species on p. 20:
There can be no doubt that a race may be modified by occasional crosses, if aided by the careful selection of those individual mongrels, which present any desired character; but that a race could be obtained nearly intermediate between two extremely different races or speceies, I can hardly believe. The Origin, First Edition, Page 20
But look at all the other minute differences, for example in the binding:
  1. If there is a full stop after MURRAY at the bottom of the spine, it is a 2nd or 3rd edition binding. 
  2. If the letters at the bottom of the spine are short and square (as opposed to tall and thin), it is a 2nd edition binding. 
  3. If the second N in LONDON is slightly lower than the other letters, it is a 3rd edition binding. 

And there are differences even within the first edition!
For original bindings there are two variants, the difference being the width of LONDON. In the first variant, LONDON at the bottom of the spine is 16mm wide; in the second variant, it is 18mm.
I will leave it to the train-spotters among you to look at the guide for all the minutiae;-) 

But those who prefer more human stories behind the history of the copies of the first edition take a look at this article from the New York Times: Digging for Darwin.

And perhaps I should close with a new variant of the ending of the Origin:
"There is grandeur in this view of The Origin of Species, with its several powers, having been originally breathed by Darwin into a few forms or into one; and that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless editions and variants most beautiful and most wonderful have been, and are being, evolved!"

Very gradual change we can believe in

I just came across this fantastic poster/T-shirt image, created by Mike Rosulek at the University of Illinois. Lyell's gradualism meets Shepard Fairey's Obama poster! (hat tip: Nick Loman)

There are several more variations on a theme on Mike's blog, one of them let down by a misquote (a Darrow quote, often erroneously attributed to Darwin). And why is Darwin always an old man in any iconography?! We should learn to appreciate the young frisky Darwin epitomised by Anthony Smith's recent sculpture!

Anyhow, here is my selection of Darwin "change" quotes that Mike might like to try on later versions of poster:
  • "Over all these causes of Change I am convinced that the accumulative action of Selection, whether applied methodically and more quickly, or unconsciously and more slowly, but more efficiently, is by far the predominant Power." Origin p. 43
  • "We see nothing of these slow changes in progress, until the hand of time has marked the long lapse of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were." Origin p.84
  • "I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection." Origin p. 109
  • "I doubt whether species under nature ever undergo abrupt changes." Origin p. 454
  • "geology plainly declares that all species have changed; and they have changed in the manner which my theory requires, for they have changed slowly and in a graduated manner." Origin p. 465
  • "species have changed, and are still slowly changing by the preservation and accumulation of successive slight favourable variations." Origin p. 480

And if you prefer to draw on the alternative Obama Hope poster for an analogous Darwin image, how about this quote:
"We shall never, probably, disentangle the inextricable web of affinities between the members of any one class; but when we have a distinct object in view, and do not look to some unknown plan of creation, we may hope to make sure but slow progress." Origin p. 434

Friday, May 15, 2009

Rough Guide to Evolution in the Malvern Gazette

My local newspaper, the Malvern Gazette are running a story this week on The Rough Guide to Evolution, complete with my ugly mug. You can pick up the story online here. But for the mugshot, you will have to buy a  print copy!

Friday, May 8, 2009

The Wire, the Darwins, re-ups and the N word

OK, confession time! After the Darwin bicentenary, even as a hardened Darwin fan, I had had my fill of darwinizing*, at least for a while. And after writing, editing and launching The Rough Guide to Evolution, I was a little maxed out on evolution. 

So, what did I do to purge my mind of Darwin and evolution (as a necessary prerequisite for renewing my interest)? Since February, I have watched four series of the excellent cult TV series, The Wire. In fact, this evening I started the first episode of the final fifth series.

But why am I telling you this? Surely, there is no connection between Darwin, evolution and The Wire? Well, according to its originator, David Simon, The Wire draws inspiration from the epic poetry and tragic drama of Ancient Greece (with some not-so-hidden clues: "The Greek" is a main character and in Series Four, Prez reads out test questions in class on Greek myths). 

And as Jonathan Gotschall, and other proponents of literary Darwinism have shown, you need evolution to explain the world of Homer (see Gotschall's book: The Rape of Troy: Evolution, Violence, and the World of Homer). So, how long, I wonder, before the literary Darwinists start deconstructing The Wire?!

But there is a more shocking link between The Wire and Charles and Emma Darwin... 

Before I reveal it, we have to be clear that some words are so offensive that they can never be used in polite company (nor written here!). For example, after a visit to Darwin's home town Shrewsbury, I dried up, while trying explain the etymological origins of "Grope Lane" to a young lady, and said she would just have to Google it

But the cast of The Wire are not "polite company", and one word that is thrown around repeatedly on the show is the N word (particularly in its Rap reincarnation with an "a" at the end). This is a word that remains not just highly offensive, but highly controversial (there has even been a documentary discussing whether it should be used even among African Americans).

Now, it is well known that Darwins were on the side of the angels in the debate over slavery, but they lived long before the birth of political correctness. So, take a guess as to what nickname Emma Darwin used for Charles?...

But while the very word is now seen as so offensive as to be unrepeatable, the Darwins' use is a back-handed compliment to people of colour, as it is meant to highlight the fact that Charles was very hard-working. I can find no instances in which the Darwins used it as a racist term of abuse (although Darwin did use it to describe slave ants).

Of course, there is another link between the Darwin-Wedgwood family and The Wire: (ab)use of drugs. Charles Darwin's excesses were limited to alcohol, cigarettes and snuff, but his elder brother Erasmus Alvey Darwin suffered the misery of long-term opium addiction. CD's grandfather, the physician-poet Erasmus Darwin, was a liberal prescriber and user of the drug—in fact his wife (and CD's grandmother) Mary Howard may well have died from overuse of alcohol and opium. Erasmus Darwin also prescribed it for CD's uncle, Thomas Wedgwood (an associate of that well-known opium eater, Coleridge).

So, maybe I have a distorted sense of humour, but a smile crosses my face when, in an act of creative anachronism, I imagine a Baltimorean Emma Darwin discussing her brother-in-law's drug use with her husband: "N-, that man cannot do without his re-up, yo!"**


*a term in fact coined by Coleridge to disparage the speculations of Erasmus Darwin, CD's grandfather.

**And if you think I have an over-active imagination, in her novel "Charles Darwin in Cyberspace", Claire Burch has an ergot-intoxicated Emma Darwin slipping between 19th Century England and 20th Century New York!

Thursday, May 7, 2009

Humpty dumpty judge sides with BCA in Singh hearing

Bad news, I am afraid, from the courtroom in the BCA versus Simon Singh case (see yesterday's post). The Judge, emulating Humpty Dumpty in Through the Looking Glass, has decided that he is the master of Singh's words and can decide that they mean what he wants them to mean. He has ruled that Singh's words:
"The British Chiropractic Association claims that their members can help treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying, even though there is not a jot of evidence. This organisation is the respectable face of the chiropractic profession and yet it happily promotes bogus treatments."

should be interpreted as meaning that Singh is claiming that the BCA knew the treatments were bogus and dishonestly promoted them anyway. Singh is likely to appeal!

More news here:

I am hoping for a more lawyerly commentary on the hearing from Jack-of-Kent in the next day or two.

Interesting post on protein folding and evolution

A few months back, John Farrell, a Catholic writer and producer working in Boston, approached me, concerned over a creationist argument about the evolution of protein folding. I answered him best I could, but also put him touch with several people far more expert in this field than I am. It is pleasing to see the fruits of his enquiries laid on his own blog here:

The Evolution of Protein Folding: Is a Crisis Brewing for Darwin?

Interested readers should take a look!

Wednesday, May 6, 2009

It's not just creationists who are nutty: Simon Singh versus non-evidence-based nonsense from the British Chiropractic Association

I would like to think that readers of this blog, and anyone who has read my book, are happy to agree that creationism is, in the words of Baba Brinkman, "dead wrong". But sadly there are many other forms of non-evidence-based nonsense out there, from conspiracy theories to the use of chiropractic to treat asthma or bed-wetting.

Simon Singh is a well-known writer, who first came to prominence with his documentary and subsequent book on Fermat's Last Theroem. When a few years ago, with Dominic White, I released The Origin of Species in Dub, I was delighted to see a comment from Simon, saying that he had enjoyed it and I gave him a DVD of the videos from the work when he visited the University of Birmingham a few years back.

Today, Simon is going to court in London for a preliminary hearing in a libel case brought against him by the British Chiropractic Association for a piece he wrote in the Guardian. The following links provide some of the background:

I wish Simon luck today in his struggle against this legal idiocy! You can e-mail him your support on and join the relevant Facebook group here.