Thursday, July 28, 2011

Survival of the aptest: evolutionary turns of phrase

The terms adaptation and evolution pre-date Darwin. The term “adapt” comes from the Latin adaptare, to make fit. William Paley used the terms “adapted” and “adaptation” repeatedly in Natural Theology (1809):

“The eyes of fishes also, compared with those of terrestrial animals, exhibit certain distinctions of structure, adapted to their state and elements.”

The word “evolution” stems from the Latin evolutio meaning “unfolding”, particularly “the unrolling and reading of a scroll, the reading of a book”. The term has acquired a general meaning covering any process of formation or growth or development; in biology it was first used as a term to describe embryological development. The word “evolution” was first used in connection with the development of species in 1762 by Swiss naturalist Charles Bonnet, who developed a theory of pre-formation (females carry within them all future generations in a miniature form) and catastrophism.

Curiously, Darwin, in the first edition of The Origin, never used the term “evolution”; instead his preferred phrase for the idea was “descent with modification”. He did use the term “evolved”, however, as the very last word of his text.

The term “natural selection” originates with Darwin, but was criticized as being too anthropomorphic, breathing agency into an inanimate process – selection implies a selector. Darwin in a letter to his geologist friend Lyell, a year or so after completing The Origin, states that if he were starting afresh he would have used the term “natural preservation”.

However, the phrase that caught the public’s imagination, then and now, is survival of the fittest, which originates not with Darwin, but with his contemporary Herbert Spencer. Alfred Russel Wallace regularly urged Darwin to dump the term natural selection and replace it with Spencer’s phrase. Darwin went half way – in the fifth edition of The Origin he added “or Survival of the Fittest” to “Natural Selection” in the title of Chapter 4 and used the phrase several times in the text.

Despite its popularity with the public, the phrase “survival of the fittest” is now seldom if ever used by professional biologists and has been eliminated from any serious presentation of Darwin’s ideas. There are several problems with it. A modern reading misunderstands Darwin’s meaning: in Darwin’s time, the word “fittest” primarily meant “best suited” or “most appropriate” rather than, as now, “in best physical shape”.

But more troublesome, the phrase has helped fuel the excesses of Social Darwinism, erroneously suggesting that evolution provides moral justification for “might makes right” and for the mistreatment and even murder of those designated “unfit”. In addition, if the fittest are defined as those best equipped to survive, the phrase becomes an uninformative tautology that obscures the essential features of natural selection.

Instead, when it comes to the survival of the aptest, “natural selection” has emerged as clear winner!

Darwin’s captain: Robert FitzRoy

Robert FitzRoy (1805–65) entered the Royal Navy at age thirteen and, after passing exams with full marks, moved quickly up the ranks. In 1828, he became temporary captain of the Beagle, returning the ship to England in October 1830. The following May, FitzRoy stood unsuccessfully as Tory candidate for Ipswich. A few weeks later, the Beagle and her captain were commissioned for a second South American Survey.

Fitzroy knew that he was prone to bouts of morbid depression and was haunted by two recent suicides. The first was that of his uncle Viscount Castlereagh, a brilliant but controversial politician who, as Foreign Secretary, had helped bring peace to Europe in the wake of the Napoleonic Wars (Shelley damns him in his brilliant Masque of Anarchy). In 1822, Castlereagh fell victim to a real or imagined gay sex scandal, claiming to the king that he was being blackmailed. His mind unhinged, three days later he slit his own throat with a letter opener.

The second incident occurred a few years later, during the Beagle’s first survey of the southern hemisphere under the command of Captain Pringle Stokes. In August 1828, during the gloomy southern winter, Stokes locked the door to his cabin, shot himself in the head, and then took an agonizing twelve days to die.

Mindful of these dangerous precedents, FitzRoy took Darwin along as his gentleman companion and changed the course of history. Nonetheless, FitzRoy did succumb to despair part way through the second Beagle journey, resigning his captaincy for a short while before being persuaded to resume command.

But FitzRoy was more than just a bit player in Darwin’s story. In the 1840s, he served as the Tory MP for Durham before serving disastrously as the second Governor of New Zealand – during his term, the colony almost became bankrupt and a new war broke out.

However, FitzRoy is justly celebrated for his pioneering contributions to meteorology: he invented the storm glass (a device for predicting the weather), developed new and improved barometers and invented weather forecasts and gale warnings for fisherman.

FitzRoy retired in 1863 with the rank of Vice-Admiral. But, at the age of sixty, the depression he had so feared aboard the Beagle finally caught up with him – one morning, FitzRoy got out of bed, went to his washroom and, echoing his uncle’s demise, slit his own throat with a razor.

Friday, July 22, 2011

Don't let Rough Guides let The Rough Guide to Evolution go out of print!

Is it possible to be very happy and very disappointed at the same time? That is about how I am feeling right now!!

Why am I happy?
Well, as I pointed out a few posts back, my university, the University of Birmingham, has taken the bold step of buying 6000 copies of my book The Rough Guide to Evolution and will be giving a copy to every new undergraduate student at the start of the next academic year in September.

This is a wonderful initiative--just imagine students, studying every subject we teach (and all their lecturers), all reading about evolution and its impact on every aspect of human thought at the very same time in the very same week!! Has there ever been anything like it?!! Other universities have had student books, but these have always been novels or memoirs. This is the first time, a whole cohort of students has been simultaneously reading one factual book and, Darwin and evolution fans, rejoice in the fact that it is on evolution!!

And to cap it all, we are having a series of events at the University allied to the launch of this "Great Read" initiative, including a talk from the award-winning Ken Miller, subject of so many positive tweets for his recent talk at the Evolution 2011 conference in Norman, Oklahoma and Darwin descendant and novelist Emma Darwin talking about the evolution of a novel!

So, why am I disappointed?
Because the University has now emptied the warehouse at Rough Guides of copies of the book and so this initiative will drive the book out of print, unless Rough Guides agree to a reprint. The minimum reprint is 3000 copies and I shouldn't imagine Rough Guides are paying more than a couple of quid per copy to be printed, so we are talking only a few thousand pounds of investment here.

So how have Rough Guides responded?
They have said that it is too risky for them to print another 3000 copies, because they cannot be certain of the demand! :-(

And why does it matter if the Rough Guide to Evolution is now out of print?
It seems very sad to me that the Rough Guide to Evolution will soon be out of print, when ideally you the public should be at least be getting a reprint and at best a new edition. All those five star reviews and for nothing!

And then there is the fact that the Great Read initiative will soon be communicated to hundreds of thousands of our alumni, many of whom are likely to want to buy their own copies of The Rough Guide to Evolution.

And some of the parents of students coming here are going to want their own copies.

And so will some of our university staff who are not teaching first years, and so don't get a copy of the Rough Guide to Evolution for free!

And what about all those who hear of the initiative via media reports?

And finally there is all you evolution fans out there in the blogosphere and twittersphere and on Facebook.

If you don't have one already, wouldn't you still like to be able to buy a copy for yourself?

And if you do have your own copy, wouldn't you recommend The Rough Guide to Evolution to friends and family?

And if you work for an organisation that defends evolution and science (e.g. the NCSE), wouldn't you want to continue to be able to recommend it--or even buy it for use in--your outreach programme?

An experiment
So, dear reader, why don't we do an experiment to see how much support and demand their is for a reprint, just from you people reading this, let alone all those alumni and parents?

If you are on twitter, please tweet or retweet "@roughguides please don't let #roughguidetoevolution go out of print; I want a copy; please reprint now!" with a link to this page. I will retweet the message each day for a week!

If you are not on twitter, please add a comment to this blog (and follow the link to get here if reading on Facebook) confirming that you don't want the Rough Guide to Evolution to go out of print and why.

If you feel particularly strongly about this, please e-mail Rough Guides editor Andrew Lockett ( politely expressing your dismay and providing evidence for the value of keeping The Rough Guide to Evolution in print.

So, let's see how it goes. If we get only a few dozen statements of support, then Rough Guides are right not to do a reprint. If we get hundreds, that will give them pause for thought, but probably won't be enough. But if we get thousands, then they will have to take notice.

And if all my twitter followers retweet the message that and then all their followers retweet it, we could have thousands of tweets in days!

The game's afoot--get tweeting!

Thursday, July 21, 2011

Another five star review

5.0 out of 5 stars A Grand and Glorious Guide to Evolution,
By John Kwok (New York, NY USA)

Why is evolution one of the most important ideas of science? Who was Charles Darwin, and why should he be seen as one of the greatest scientists of all time? How has evolutionary thought influenced sciences other than biology? What impact has evolutionary thought made on the humanities and arts? Why is evolution controversial? These are the principal questions addressed by British microbiologist Mark Pallen in "The Rough Guide to Evolution". It is a relatively terse masterpiece of scientific writing and content, which tells the story of evolution and its fundamental importance to human society and culture in barely more than three hundred twenty pages. "The Rough Guide to Evolution" deserves a place on the bookshelves of everyone, both the scientifically literate, and especially, those who are not, simply for the compelling story it tells about the origins, history and current thinking with regards to evolution.

The largest, most important, section is entitled "Part 1: Ideas and Evidence", tracing the history of evolutionary thought, from antiquity to the very present. The first three chapters summarize early thinking on evolution and, of course, Darwin's life and career. Pallen's biographical chapters on Darwin (2 and 3) are especially noteworthy for dispelling myths about Darwin's life and work, and for succinctly presenting the main concepts of his theory of evolution via natural selection (which was discovered independently by Wallace). Chapter 4 is a most admirable summary of the major lines of evidence for evolution, covering everything from biogeography to missing links in the fossil record, vestigial organs in humans, and the significance of homology. In Chapter 5 ("Evolutionary Biology"), Pallen offers among the best written accounts I have read on the nature of speciation (accompanied by simple, well-executed diagrams illustrating the major types) and of phylogenetic systematics (more popularly known as "cladistics"), emphasizing how much modern evolutionary biology has advanced considerably since the joint publication of Darwin and Wallace's ideas on natural selection in 1858 (The only glaring omissions appear to be extensive discussions of coevolution and of ecology, especially of the important species area effect, noted first by one of Darwin's heroes, Baron Alexander von Humboldt.).

A relatively brief section on the history of life (Part 2) is subtitled, "The Greatest Story Ever Told". Much to my surprise, in one long chapter (6), Pallen discusses not only the origin of life on Earth, but also a surprisingly thorough summary of the entire Phanerozoic Eon (the history of life since the dawn of the Cambrian Period, approximately 550 million years ago), which notes not just the major innovations in that history (evolution of the earliest metazoans and the successive invasions of the land by plants and animals), but such, quite literally, Earth-shattering, events as the terminal Permian and Cretaceous mass extinctions, which, respectively, wiped out approximately 96 and 50 percent of Earth's biota (There's an extensive discussion too on the probable causes of mass extinctions, which, amazingly, refers to the important 1982 paper by American invertebrate paleontologists J. John Sepkoski and David M. Raup.). Human evolution is covered extensively in the following chapter (7), and this may be as noteworthy for both the socio-political aspects of paleoanthropology and, of course, its fossil evidence.

Part 3 ("Impact") emphasizes evolution's influence on other sciences, humanities and the arts, and its still controversial relationship to certain religions. For these reasons alone, readers may find this the most interesting, most compelling, section of this Rough Guide. In Chapter 8, Pallen truly covers a vast terrain, emphasizing how natural selection is influencing modern cosmology, computer science, and even, economics (which, I suppose, isn't surprising, given how early modern economics - in the form of Adam Smith's thinking - influenced Darwin's own conception of the "economy of nature"). He also devotes much attention to the still controversial evolutionary psychology and its intellectual ancestor, sociobiology (Incidentally Pallen neglects to mention American entomologist E. O. Wilson's seminal contribution to ecology; the MacArthur - Wilson model of equilibrium island biogeography. One might argue persuasively that this very concept has had as much importance in modern biology - especially in the realm of conservation biology - as has sociobiology.). Chapter 9, devoted to evolution's impact on philosophy and the arts, covers everything from late 19th Century Victorian fiction to science fiction, and even, rock and roll and reggae. Chapter 10, on evolution's uneasy relationship with politics, not only discusses at length, Herbert Spencer's Social Darwinism (It was he, not Darwin, who coined the phrase "survival of the fittest".), but also lays to rest the ridiculous canard that, somehow, Darwinian thought inspired Hitler and his fellow Nazis towards committing the Holocaust. Chapter 11 traces evolution's peculiar history with Western religions, including Islam, and provides a most concise overview of the American creationist movement, from the 1925 Scopes Trial to the 2005 Dover Trial, refuting every major argument made by creationists against evolution, especially those by Intelligent Design creationists.

Last, but not least, Part 4 ("Resources") is an all too brief coda to this splendid book, outlining the extensive print, other media, and online resources available to those interested in exploring further, both evolution and its intellectual and cultural impact on contemporary societies. Chapter 12 is written especially for the diehard Darwin fan, describing most of the buildings in London and elsewhere associated with Darwin. Chapter 13 discusses primarily the commemorative events associated each year with his birthday (February 12), especially this bicentennial year. Chapter 14 summarizes the extensive literature on Darwin - and should be invaluable as a bibliographic guide alone, even if it's not nearly as complete as I would have wished - and other media references. Finally, at the very end, Chapter 15 is a superb glossary of key evolutionary biology scientific terms and concepts.

If one is seeking a one-stop, all inclusive, guide to evolution and its intellectual and cultural impact on contemporary society, then buy this book. Trust me. Without a doubt, Mark Pallen has demonstrated most persuasively, and most brilliantly, how and why evolution is so important.

Wednesday, July 20, 2011

Charles Darwin senior: cause of death and place of burial

Following up from on my previous post, a picture is now available of Charles Darwin senior's last resting place, thanks to Kim Traynor

And has been incorporated into the Wikipedia entry, which has also been greatly expanded by Dave Souza.

Dave asked me to explain why I thought that it was almost certain that CD Senior died from meningococcal disease. The clues stem from the passage I mentioned earlier:
"About the end of April, Mr. Darwin had employed the greatest part of a day in accurately dissecting the brain of a child which had died of hydrocephalus, and which he had attended during its life. That very evening he was seized with severe head-ach. This, however, did not prevent him from being present in the Medical Society, where he mentioned to Dr. Duncan the dissection he had made, and promised the next day to furnish him with an account of all the circumstances in writing. But the next day, to his headach there supervened other febrile symptoms. And, in a short time, from the hemorrhagies, petechial eruption, and foetid loose stools which occurred,his disease manifested a very putrescent tendency."
The clues are two-fold:

1. meningococcal disease is commonest in childhood and adolescence, so it is one of the likeliest causes of a fatal infection of the brain in a child
2. The petechial haemorrhages are a give-away: as recent clinical guidelines state: "fever plus a petechial rash is meningococcaemia until proven otherwise"

Curiously, I cannot find any other case reports of meningooccal infection acquired from a postmortem examination. This 1995 guidance from the Communicable Disease Report places cadavers with meningococcal disease in an intermediate risk category, whereas this more recent guidance from the HPA is rather more dismissive: "No cases have been reported following post-mortem contact with a case of meningococcal

But all in all, I still conclude that meningococcal disease is by far and away the most likely cause of death here.

Sunday, July 17, 2011

Last resting place of Charles Darwin rediscovered

OK, so you are wondering what I am going on about with that title, as we all know that Charles Darwin (1809-1882), the famous naturalist and father of evolution is buried in Westminster Abbey!?!

But I am talking about the first Charles Darwin, the naturalist's uncle, who lived from 1758 to 1778. This Charles Darwin was the eldest son of Erasmus Darwin and Mary Pole (who incidentally died from an overdose of morphine). Here is what the younger Charles Darwin wrote about his uncle:
"His [Erasmus's] eldest son, Charles (born September 3, 1758), was a young man of extraordinary promise, but died (May 15, 1778) before he was twenty-one years old from the effects of a wound received whilst dissecting the brain of a child. He inherited from his father a strong taste for various branches of science, for writing verses, and for mechanics. "Tools were his playthings," and making machines was one of the first efforts of his ingenuity, and one of the first sources of his amusement." *

He also inherited stammering. With the hope of curing him, his father sent him to France when about eight years old (1766-67), with a private tutor, thinking that if he was not allowed to speak English for a time, the habit of stammering might be lost; and it is a curious fact that in after years when speaking French he never stammered. At a very early age he collected specimens of all kinds. When sixteen years old he was sent for a year to Oxford, but he did not like the place, and "thought (in the words of his father) that the vigour of the mind languished in the pursuit of classical elegance, like Hercules at the distaff, and sighed to be removed to the robuster exercise of the medical school of Edinburgh."

He stayed three years at Edinburgh, working hard at his medical studies, and attending "with diligence all the sick poor of the parish of Waterleith, and supplying them with the necessary medicines." The Esculapian Society awarded him its first gold medal for an experimental enquiry on pus and mucus. Notices of him appeared in various journals; and all the writers agree about his uncommon energy and abilities. He seems, like his father, to have excited the warm affection of his friends. Professor Andrew Duncan, in whose family vault Charles was buried, cut a lock of hair from the corpse, and took it to a jeweller, whose apprentice, afterwards the famous Sir H. Raeburn, set it in a locket for a memorial.* The venerable professor spoke to me about him with the warmest affection forty-seven years after his death, when I was a young medical student in Edinburgh. The inscription on his tomb, written by his father, says, with more truth than is usual on such occasions: "Possessed of uncommon abilities and activity, he had acquired knowledge in every department of medical and philosophical science, much beyond his years." 'Harveian Discourse,' by Professor A. Duncan, 1824.

Dr. [Erasmus] Darwin was able to reach Edinburgh before Charles died, and had at first hopes of his recovery; but these hopes, as he informed my father, "with anguish, soon disappeared. Two days afterwards he wrote to Wedgwood to the same effect, ending his letter with the words, God bless you, my dear friend, may your children succeed better." Two and a half years afterwards he again wrote to Wedgwood, I am rather in a situation to demand than to administer consolation."
A more detailed description of CD the elder's death strongly supports a diagnosis of meningococcal disease:
"About the end of April, Mr. Darwin had employed the greatest part of a day in accurately dissecting the brain of a child which had died of hydrocephalus, and which he had attended during its life. That very evening he was seized with severe head-ach. This, however, did not prevent him from being present in the Medical Society, where he mentioned to Dr. Duncan the dissection he had made, and promised the next day to furnish him with an account of all the circumstances in writing. But the next day, to his headach there supervened other febrile symptoms. And, in a short time, from the hemorrhagies, petechial eruption, and foetid loose stools which occurred,his disease manifested a very putrescent tendency."
Charles Darwin the elder is also notable because Erasmus Darwin claimed, after his son's death, that Charles had discovered the usefulness of digitalis/foxglove before William Withering, who is usually credited with this discovery (and who used to work here in Birmingham). This led to a longstanding feud between these two members of the Lunar Society of Birmingham.

And now to title of this post.

In a previous post (The evolutionary tourist in Edinburgh), I claimed that Charles Darwin senior was buried in St. Cuthbert’s Church, located in Lothian Road, at the eastern end of Princes Street. Now I have just received an email from veteran Wikipedian Dave Souza, who writes:
"Today an anon editor helpfully pointed out that we'd both got the wrong kirk, the Duncan family vault was in the graveyard of the Chapel of Ease built for St Cuthbert's Church on the South side of Edinburgh, and later renamed the Buccleuch Parish Church Burying Ground. It's sited at 33 Chapel Street, not far from the Old College of the University of Edinburgh."
Click on the two links above to see quite how far apart the two sites are.

So all we need now is for an enthusiastic Darwin fan in Edinburgh to visit the graveyard and capture a photo of CD the elder's tomb and I will post it here!

A five-star review

This from Howard Kornberg via the site:

5.0 out of 5 stars Everything Evolutionary, 6 May 2009
This review is from: The Rough Guide to Evolution (Rough Guide Science/Phenomena) (Paperback)
If you're only going to purchase and read one book about Evolution, this has GOT to be the book. Pallen's great achievement is that he's been able to create a virtual encyclopaedia of information about Darwinian science, history and influence in a mere 340 pages. This does not mean that the treatment of any part of the subject is at all superficial; Pallen's great talent (aside from producing such clear and readable text) is his ability to get to the heart of the matter in such a direct and concise way. For the non-scientifically inclined reader this means that he/she can come to grips with these not so obvious concepts without what seems a long, confusing and tedious uphill grind. Nor is the excellent treatment of how the mechanisms of Evolution work done at the cost of less focus on the implications of Evolution on Philosophy, Politics, Religion, the Arts and even modern hip culture. Pallen brings to life the histories and character profiles of the great evolutionary scientists - Darwin himself, Mendel, Bill Hamilton, John Maynard Smith and many others, making the subject all the more human.

Pallen's treatment of the subject of the "science wars" of Creationism vs. Evolution and Religion vs. Science, where such an understanding is so necessary these days for a well-informed reader, is unparalleled in both clarity and conciseness. Pallen also provides many light-hearted Evolutionary diversions, e.g. a "top-10" evolutionary iPod playlist, evolution based games, entertainments, and one of the best reference reading guides around.

The book can be read "cover to cover" or even by just skipping about, without losing any understanding of the topic; indeed the book is an entirely enticing and tasty smorgasbord of information about this important and fascinating subject. The book is not just an excellent introductory read for the newcomer to the subject, even someone who have done some quite a lot of serious reading on the subject of Evolution is still certain to broaden, clarify or update his/her subject knowledge by reading Rough Guide. All-in-all a wonderful read by someone who not only writes well, but also an author who really knows and loves his entire subject.

Tuesday, July 5, 2011

The phoenix rises from the ashes, the coelacanth from the ocean!

Apologies, dear reader. This blog has been dormant for over a year...

There were a couple of reasons for this
  1. I felt the need to re-focus my efforts on my "day job" in bacterial pathogenomics rather than devote myself to things Darwinian and evolutionary
  2. I also did somewhat max out on Darwin and evolution during the Darwin bicentenary year.
However, in the last eighteen months, I have had some success in getting grants in and papers out (although papers still lagging behind grants), what with an MRC grant on Acinetobacter genomics, a BBSRC grant on the chicken gut microbiome and a major stake in an NIHR research centre for surgical reconstruction and microbiology. Plus the blog and twitter feeds associated with my research group (@pathogenomenick and @mjpallen) are now well established. So, there is now enough slack in the system for me to return to this blog!

But another more pressing reason presents itself—in fact, a new highly positive development. My University, the University of Birmingham, has adopted my book The Rough Guide to Evolution as the "Birmingham book", which will be given out to all new undergraduates starting this October (>5000 students!).

The book was selected after a due process involving judges from all over the University. I am very flattered that the selection panel agreed that the book covers the influence of evolutionary thinking across all disciplines and human endeavours, so it can form a talking point for tutorials and teaching in all sorts of courses. Its adoption by the University is a bold move, but our Vice-Chancellor has said that whether students agree with or disagree with, like or dislike the subject, they have to confront the big ideas of time and evolution is one of them. It is going to one huge evolution fest, with so many students and staff thinking about evolution all in the same place and at the same time. Does anyone know of any similar venture elsewhere in the world!?

Anyhow, with this new development, I am more conscious than ever of how events have moved on in the last couple of years since I wrote the book and how much needs updating. I have discussed the possibility of a second edition with the publishers, but it seems that the book trade is down on its luck at the moment and they won't commit to that just now.

So, I intend to fill in the gaps here, on this blog, reviewing all the exciting new publications and productions that stemmed from the bicentenary year, plus highlighting new discoveries that augment what is in the book, so that when students start in October they will have an online supplement to bring them right up to date. Please send me your suggestions for what I should review or discuss as the big discoveries or best publications/productions in evolution 2009-11!

I thank anyone who has kept me in your blogroll and ask all those who deleted it to restore it!

And to jump-start the renaissance of the blog, let me post my favourite top ten posts from the 180+ that I posted in 2008-9: