Of figs and fusions: Darwin's great tree of life rehabilitated?

In one of his notebooks, Darwin sketched an iconic figure of the tree of life, prefaced by a pregnant "I Think" (see adjacent image). Darwin also wrote some of his finest prose about the tree of life in the Origin of Species:

"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."

But in recent years there has been a great deal of fuss about whether it is still acceptable to talk about a tree of life and whether we should instead be talking about a ring of life or net of life, because there appear to have been many fusions between different lineages, particularly early in life's history, in addition to the lineage splittings that underlie a traditional branching phylogeny.

And, yeah, I get the point, if your idea of a tree is similar to the  tree drawn by Darwin's associate Haeckel, a boring old deciduous tree from northern Europe or North America, with a single trunk and no fusions between trunks or branches.

But for me the tree simile still "largely speaks the truth"--you just have to broaden your idea of what a tree looks like! 

Here are some images of a fig tree that I snapped while on a recent holiday in Sicily. Here you can see what appear to be rampant fusions between trunks and branches*. To me this suggests that Darwin's simile is fine, so long as you think fig tree, not oak tree!

*OK, I realise that in fact these apparent fusions between branches are the result of aerial roots arising from branches that then grow downloads, but for a simile to work, it doesn't need to be accurate in every detail!

Even Koonin nods

Classicists have a turn of phrase, "Even Homer Nods". The phrase originates from the Roman poet Horace (et idem indignor quandoque bonus dormitat Homerus) and has become a proverbial phrase not just for Homer's numerous continuity errors, but more generally to allow for slip-ups by someone of such high stature that the idea that they can make mistakes seems unthinkable. 

Eugene Koonin is a colossus in the application of bioinformatics to the study of evolution, with over 500 papers to his name. But I am afraid in a paper just published he suffers from his very own Homeric nod.

An abstract and link to the paper in question can be found here:

Koonin EV (2008). Evolution of genome architecture. Int J Biochem Cell Biol.

The offending phrase is the very first sentence of the abstract:

"Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection."

which elicits a roar in response: NO, HE DIDN'T!!

Eugene appears to have overlooked a whole section of Chapter XIII of the Origin of Species, entitled Rudimentary, atrophied, or aborted organs and starting off with:

Organs or parts in this strange condition, bearing the stamp of inutility, are extremely common throughout nature. For instance, rudimentary mammæ are very general in the males of mammals: I presume that the "bastard-wing" in birds may be safely considered as a digit in a rudimentary state: in very many snakes one lobe of the lungs is rudimentary; in other snakes there are rudiments of the pelvis and hind limbs. Some of the cases of rudimentary organs are extremely curious; for instance, the presence of teeth in fœtal whales, which when grown up have not a tooth in their heads; and the presence of teeth, which never cut through the gums, in the upper jaws of our unborn calves. It has even been stated on good authority that rudiments of teeth can be detected in the beaks of certain embryonic birds. Nothing can be plainer than that wings are formed for flight, yet in how many insects do we see wings so reduced in size as to be utterly incapable of flight, and not rarely lying under wing-cases, firmly soldered together!

And as Darwin himself recognised, such rudimentary features are not some throwaway feature under the Theory of Evolution, but a crucial pillar of support for it!

On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the ordinary doctrine of creation, might even have been anticipated, and can be accounted for by the laws of inheritance.

And of course similar arguments apply at the level of genomes. No intelligent designer would ever leave such a mess of junk behind in the genomes of mammals like ourselves. And why would such a creator deliberately break the gene that allows us humans to make vitamin C?! Is scurvy a message from God telling us not to undertake long sea voyages of exploration? (here is an exercise for students on this issue)

But back to the offending paper. So, here we have a "Kooninian nod" equal to the resurrection of Pylaimenes. Even the "well-born" sometimes slip up!

PS. I am afraid that Eugene's outline of natural selection in the paper itself also strikes me as rather shaky, but as I am about to disappear off on vacation, I will leave it to the reader to work out why.

Is America ready for a creationist president?

That's a rhetorical question, as it looks like the answer is going to be no!

But anyone comforted by the fact that neither presidential candidate is a creationist, should think again. The Lancet has just published this letter by John Alam in which he calculates the risk of McCain dying during each year of his four-year term of office from a recurrence of his melanoma as 6%, i.e. 24% overall. The figure has been contested--see this posting on Wired Science (which oddly seems to have the figure as 22%, even from Alam). But then the Wired author Brandon Keim points out that a man of McCain's age stands around a 11% chance of dying within four years even without melanoma.

So what all this means is that a McCain victory would bring a 11-24% chance of a creationist president (i.e. Sarah Palin), a risk that is too high for any sane person*. So, let's just hope the polls are right and we are looking forward to an Obama landslide!

*some will argue that America already has a creationist president, but my understanding is that Bush's official position is teach the controversy fence-sitting.

2009, Tom Paine's Remains and Darwin

Prompted by Carl Zimmer's recent posting on Paine and Washington's experiment with marsh gas, I have finally gotten around to dealing with a topic on my mind for quite a while....

As a Darwin fan, I named my first two children Charles and Emma. And so a friend groaned when he heard that I called my second son Thomas--he presumed after Thomas Huxley.

But he presumed wrong! In fact, Tom was after my other hero (besides Darwin), Thomas Paine. 

Paine was a remarkable character. Born in Thetford, Norfolk, he played a role in both the American and French revolutions. Paine can be said to be the father of the United States of America, not only in naming the country, but in stirring up the revolution with his pamphlet Common Sense. But crucially, he went beyond just trading British national identity for an American one--he recast the colonies' disagreement with the British government and crown as an argument about the very nature of government and society. Not just, should we not have this king, but no one should have any kings anywhere!

Not content with stirring things up in America, Paine a few years later became an enthusiastic supporter of the French Revolution, for which he gained honorary French citizenship. His book supporting the French Revolutionaries, the Rights of Man got him into trouble with the British authorities, so he hot-footed it over to France. But then he fell out of favour with the ruling faction and missed execution only by chance (a mark indicating that he should be guillotined was placed on the wrong side of a door). However, the fear of death brought out arguably his best work, The Age of Reason, which I am currently reading on my iPhone (is just chance that two works by Paine and two by Darwin feature along the few dozen ebooks available as iPhone apps--I sense a freethinkers' conspiracy at work!).

Paine is not remembered only for his remarkable biography, but also because of the remarkable clarity of his prose, which over two centuries on remains a model of plain truth plainly spoken. A read through Common Sense reveals not only a persistent outrageous rudeness towards the British Crown and monarchy in general but a series of memorable one-liners:

• "...a long habit of not thinking a thing WRONG, gives it a superficial appearance of being RIGHT"
• "Time makes more converts than reason."
• "The cause of America is in a great measure the cause of all mankind."
• "Society is produced by our wants, and government by wickedness"
• "How impious is the title of sacred majesty applied to a worm, who in the midst of his splendor is crumbling into dust!"
• "One of the strongest NATURAL proofs of the folly of hereditary right in kings, is, that nature disapproves it, otherwise, she would not so frequently turn it into ridicule by giving mankind an ASS FOR A LION."
• "The present state of America is truly alarming to every man who is capable of reflexion."
• "When my country, into which I had just set my foot, was set on fire about my ears, it was time to stir. It was time for every man to stir."
• [of a monarchist] "one, who hath, not only given up the proper dignity of a man, but sunk himself beneath the rank of animals, and contemptibly crawls through the world like a worm."

The Rights of Man is similarly laced with plain-speaking vitriol against the British establishment, generalising the anti-monarchist argument against the entire hereditary aristocracy. But I am particularly fond of the up-lifting finale, predicting the spread of freedom across the world, which would make fine reading for any joint Darwin-Lincoln bicentenary celebration next year:

"It is now towards the middle of February. Were I to take a turn into the country, the trees would present a leafless, wintery appearance. As people are apt to pluck twigs as they walk along, I perhaps might do the same, and by chance might observe, that a single bud on that twig had begun to swell. I should reason very unnaturally, or rather not reason at all, to suppose this was the only bud in England which had this appearance. Instead of deciding thus, I should instantly conclude, that the same appearance was beginning, or about to begin, every where; and though the vegetable sleep will continue longer on some trees and plants than on others, and though some of them may not blossom for two or three years, all will be in leaf in the summer, except those which are rotten. What pace the political summer may keep with the natural, no human foresight can determine. It is, however, not difficult to perceive that the spring is begun."

But with The Age of Reason Paine scandalized not just the British establishment, but most Americans too. Over 200 years before Dawkins and his God Delusion, Paine laid out the common-sense arguments against Christianity, although Paine retained a belief in a noble creator-deity. As in the previous two works, here Paine often pulls no punches nor makes any effort at politeness towards those he is attacking:

• "All national institutions of churches, whether Jewish, Christian or Turkish, appear to me no other than human inventions, set up to terrify and enslave mankind, and monopolize power and profit."
• "Whenever we read the obscene stories, the voluptuous debaucheries, the cruel and torturous executions, the unrelenting vindictiveness, with which more than half the Bible is filled, it would be more consistent that we called it the word of a demon, than the Word of God. It is a history of wickedness, that has served to corrupt and brutalize mankind; and, for my own part, I sincerely detest it, as I detest everything that is cruel."

But perhaps more destructive is his gently mocking tone:

"The Christian mythologists tell us that Christ died for the sins of the world, and that he came on Purpose to die. Would it not then have been the same if he had died of a fever or of the small pox, of old age, or of anything else?"

or the utter common sense of his arguments--here for example on whether Christ could have died for our sins:

"If I owe a person money, and cannot pay him, and he threatens to put me in prison, another person can take the debt upon himself, and pay it for me. But if I have committed a crime, every circumstance of the case is changed. Moral justice cannot take the innocent for the guilty even if the innocent would offer itself. To suppose justice to do this, is to destroy the principle of its existence, which is the thingitself. It is then no longer justice. It is indiscriminate revenge."

or his Carl-Sagan-esque rejoicing in the immensity of the universe and scorn at the parochialism of Christianity:

"Since, then, no part of our earth is left unoccupied, why is it to be supposed that the immensity of space is a naked void, lying in eternal waste? There is room for millions of worlds as large or larger than ours, and each of them millions of miles apart from each other."

"Those fixed stars continue always at the same distance from each other, and always in the same place, as the Sun does in the center of our system. The probability, therefore, is that each of those fixed stars is also a Sun, round which another system of worlds or planets, though too remote for us to discover, performs its revolutions, as our system of worlds does round our central Sun. By this easy progression of ideas, the immensity of space will appear to us to be filled with systems of worlds; and that no part of space lies at waste, any more than any part of our globe of earth and water is left unoccupied..."

"From whence then could arise the solitary and strange conceit that the Almighty, who had millions of worlds equally dependent on his protection, should quit the care of all the rest, and come to die in our world, because, they say, one man and one woman had eaten an apple! And, on the other hand, are we to suppose that every world in the boundless creation had an Eve, an apple, a serpent, and a redeemer? In this case, the person who is irreverently called the Son of God, and sometimes God himself, would have nothing else to do than to travel from world to world, in an endless succession of death, with scarcely a momentary interval of life."

It is hard to imagine the effect if all Americans were made to study all of Paine's work in school, including the Age of Reason! But I guess that would be disallowed under the First Amendment. 

And I digress...

What has all this to do with Darwin?, I hear you ask. Well, I discovered the answer in a book entitled The Trouble with Tom by Paul Collins. 

As Collins points out, the publication of Paine's Age of Reason in America turned him from national hero to villain very quickly. He died in June 1809 (his life thus overlapping with Charles Darwin's by just a few months) and as the ever-eloquent Ingersoll (another American hero who all Americans should read) puts it:

Thomas Paine had passed the legendary limit of life. One by one most of his old friends and acquaintances had deserted him. Maligned on every side, execrated, shunned and abhorred -- his virtues denounced as vices -- his services forgotten -- his character blackened, he preserved the poise and balance of his soul. He was a victim of the people, but his convictions remained unshaken. He was still a soldier in the army of freedom, and still tried to enlighten and civilize those who were impatiently waiting for his death. Even those who loved their enemies hated him, their friend -- the friend of the whole world -- with all their hearts. On the 8th of June, 1809, death came -- Death, almost his only friend.

At his funeral no pomp, no pageantry, no civic procession, no military display. In a carriage, a woman and her son who had lived on the bounty of the dead -- on horseback, a Quaker, the humanity of whose heart dominated the creed of his head -- and, following on foot, two negroes filled with gratitude -- constituted the funeral cortege of Thomas Paine.

No minister of religion would allow Paine to be buried on consecrated ground and so he was interred on his own farmland in upstate New York, neglected hero of the American Revolution... 

But then Tom Paine's remains took on a strange afterlife, when an English radical William Cobbett adopted Paine as an English hero and in 1819 dug up his bones and returned them to England, in the hope of building a fittingly grand tomb for them. Instead, they mouldered away in a trunk in Cobbett's attic and then became separated from one another, with the skull and a right hand going their own way...

And, guess where, in Paine's vast universe of millions of worlds, they ended up...?

...in the Kent village of Downe, in a house called Tro[w]mer Lodge, owned by Charles Darwin's daughter Elizabeth and situated a few hundred yards from the more famous Down House. As Collins recounts, Paine's skull was for a few years in the mid-19th Century in the possession of a country parson, Reverend Robert Ainslie, who rented Trowmer Lodge from Elizabeth Darwin. The skull is no longer there, but the building is.

Of course, none of this counts as anything other than coincidence. I can find no evidence that Darwin ever read Paine (although the Darwin Correspondence project shows two of his correspondents did: Joseph Hooker and Matthew Patrick), let alone knew that Paine's skull was just up the road as he wrote The Descent of Man. But, just as Stephen Jay Gould used to delight in the happy coincidence that two of his heroes, Darwin and Lincoln, were born on the very same day, I relish this slightly ghoulish connection between two of my heroes! 

So, next year in the midst of all the celebrations of Darwin200, of the joint bicentenary of Darwin's and Lincoln's births, spare a thought for Thomas Paine, citizen of the world and father of the USA and do something to commemorate this great man on the bicentennary of his death, June 8th 2009. And American readers, as you elect a new president, spare a thought for us poor Brits, who two hundred years after Paine's death, still have to live under the yoke of the British crown and the weight of an established church!

For details of UK Paine200 celebrations, see http://www.tompaine200.org.uk/.

Dodgy Darwinian analogies involving hedge funds

And now evolution even features in the Financial Times, although the analogies between the Galapagos and hedge funds strike me as rather contrived:

Hedge funds poised for harsh phase of evolution

Another snippet about the Darwin biog film Creation

See "My Week" by Toby Jones writing in the Independent on his role as Huxley in the forthcoming film Creation. Looks like it is going to be an exciting film! The screenplay is by John Collee, whose early work Paper Mask I still remember from when I was a junior doctor. And as a stray factoid, when I used to work as a trainee medical microbiologist in the late 1980s, I met John's brother, George Collee, who is an anaesthetist at the Royal Free Hospital.

Darwin's Second Life

During the completion of The Rough Guide to Evolution, the editor waggishly added his own title to the section on Artificial Life: "Getting Alife".  On similar note, I have just seen this post 

http://darwinevolving.blogspot.com/2008/10/second-life-for-darwin.html

from the Darwin Evolving blog (feed here). It appears that Darwin and his Beagle journey will be re-born in the multi-player simulation game Second Life. I have avoided the game up till now, but perhaps I now need to get an account and create an avatar (would be nice to lose the grey hair, beer belly and double-chin!).

Icons of evolution: McCain as missing link

My first thought when I saw the image at the top of this entry, which is in all the papers and all over the Internet is just how reminiscent it is of the "March of Progress", the famous drawing that shows a sequence of primates walking from left to right, starting with a small knuckle-walking ape on the left, progressing through a series of apemen, and finishing with a modern human male on the right (which according to the conventions of our racist culture inevitably has to be a full-bloodied white European male).

The original version was drawn by Rudy Zallinger and published in the Time-Life book Early Man in 1970. Carl Zimmer and others have gone looking for it on the web, but apparently it is nowhere to be found. However given that has spawned many humorous variants and even a tattoo.

Plus it was misused by Jonathan Wells in his book Icons of Evolution (see discussion here on Talk.Origins) 

Well, here is another humorous variant to add to the list, and for a change, this time the white European male does not feature as the pinnacle of evolution, but as a decidedly dodgy missing link!

Silly but fun KNTV song and show on Darwin

As I write, the UK TV Channel 4 is broadcasting an amusing programme on Charles Darwin as part of a 10-part series for children, KNTV Philosophy, presented by virtual hosts Kierky and Nietzsche, two teenage science-obsessed rock thrash musicians from the fictitious communist country of Slabovia. 

You can find out more about the series here:
http://www.4learning.co.uk/support/programmenotes/micro/kntv/
and about the Darwin episode here:
http://www.4learning.co.uk/support/programmenotes/micro/kntv/prog2.html

Curiously, the show has not yet appeared on YouTube but UK viewers who use Windows should be able to watch it on 4oD (but when oh when are these muppets going to get this service working for Macs??!).

Also, you can see a clip of a Darwin song from the show from the AniBoom website:

KNTV has its own website: http://www.slabovia.tv complete with its own video player, but as yet the Darwin material isn't there. But it's worth a visit to see the silly songs on Karl Marx and Adam Smith!

Evolution and Poverty: Great is our Sin

Wednesday 15th October is Blog Action Day 2008, with the theme of POVERTY. Although I have missed the boat according to Greenwich Mean Time, as far as my Hawaiian readers go it is still a little after 9pm on the 15th (and Google analytics shows that there have been visits to the Blog from the fiftieth state), so here goes...

In the Rough Guide to Evolution, there is a whole chapter on evolution and politics. Here are a few pertinent excerpts:

The earliest and most notorious extension of evolutionary thinking to politics was social Darwinism – the view that competition between individuals and between nations could, and should, drive social and economic progress in human societies. Inherent to social Darwinism was the suggestion that the richest and most “socially developed” should be allowed to flourish in society, while the poor and the weak should be left to fend for themselves, even if this meant suffering and death...

One key influence was the Essay on the Principle of Population (1798) by Thomas Malthus... [but] even stronger influence on social Darwinism was English philosopher Herbert Spencer who, as early as 1851, had attacked what he called the “spurious philanthropists”, who “[b]lind to the fact that, under the natural order of things, society is constantly excreting its unhealthy, imbecile, slow, vacillating, faithless members, …advocate an interference which not only stops the purifying process, but even increases the vitiation – absolutely encouraging the multiplication of the reckless and incompetent by offering them an unfailing provision and discourages the multiplication of the competent and provident.”

Social Darwinism is generally linked to laissez faire economics and non-interventionist politics. American industrialists readily adopted evolutionary language. John D. Rockefeller said, “The growth of a large business is merely a survival of the fittest”, while Andrew Carnegie claimed that the law of competition “is best for the race, because it insures the survival of the fittest in every department. We accept and welcome, therefore… great inequality of environment, the concentration of wealth, business, industrial and commercial, in the hands of a few, and the law of competition between these, as being not only beneficial, but essential for the future progress of the race..."

Social Darwinism fails both as hypothesis and policy for a number of reasons. Firstly, it equates evolution solely with competition, when co-operation and altruism are also the products of evolution... A second problem with social Darwinism is that it confuses economic and social success with biological success and what is natural with what is desirable... In fact, a more palatable interpretation of evolution sees natural selection as an enemy of the values of a civilized society. As Thomas Huxley stated in his 1893 lecture Evolution and Ethics: “Let us understand, once and for all, that the ethical progress of society depends, not on imitating the cosmic process, still less in running away from it, but in combating it."

A third problem with social Darwinism is that it implies a rigid biological determinism in which one’s station in life is set by one’s innate unimprovable abilities. However, even at the height of social Darwinism, evolutionists like Huxley expressed a more enlightened view of the improvability of humans and human societies. 

Huxley wrote in his 1888 essay, The Struggle for Existence:

“…the endeavor to improve the condition under which our industrial population live, to amend the drainage of densely peopled streets, to provide baths, washhouses, and gymnasia … to furnish some provision for instruction and amusement in public libraries … is not only desirable from a philanthropic point of view, but an essential condition of safe industrial development....”  

and he closes the essay with:

 “There is, perhaps, no more hopeful sign of progress among us, in the last half-century, than the steadily increasing devotion which has been and is directed to measures for promoting physical and moral welfare among the poorer classes…” 

The descendants of those that Spencer counted as the “excrement of society” nowadays enjoy levels of health and wealth, education and intellectual achievement far beyond his imagination. However, these improvements have come about not through the effects of natural selection, but because of deliberate efforts to improve the lot of the poorest and most vulnerable in society through the kind of measures Huxley advocated, twinned with modern innovations such as vaccination and contraception.

Of course what I have written above applies to Western societies, where we have seen an astonishing rise in the standard of living since Darwin and Huxley's time. It should not be seen as a Panglossian smugness that all is now right with the world. In developing countries, poverty is just as bad if not worse than it was 150 years ago and the Third World poor are engaged in a relentless "struggle for existence", particularly in the face of infectious diseases such as AIDS, malaria and tuberculosis. But the point here is that change is possible--as Barack Obama puts it: "yes we can to opportunity and prosperity". Poverty is not inevitable and biology does not equal destiny. I leave the last word to Darwin, who, in the Voyage of the Beagle, compared poverty to slavery and dismissed the inevitability of both conditions (my emphasis):

It is often attempted to palliate slavery by comparing the state of slaves with our poorer countrymen: if the misery of our poor be caused not by the laws of nature, but by our institutions, great is our sin; but how this bears on slavery, I cannot see; as well might the use of the thumb-screw be defended in one land, by showing that men in another land suffered from some dreadful disease. Those who look tenderly at the slave-owner, and with a cold heart at the slave, never seem to put themselves into the position of the latter;—what a cheerless prospect, with not even a hope of change! picture to yourself the chance, ever hanging over you, of your wife and your little children—those objects which nature urges even the slave to call his own—being torn from you and sold like beasts to the first bidder! And these deeds are done and palliated by men, who profess to love their neighbours as themselves, who believe in God, and pray that his Will be done on earth! It makes one's blood boil, yet heart tremble, to think that we Englishmen and our American descendants, with their boastful cry of liberty, have been and are so guilty: but it is a consolation to reflect, that we at least have made a greater sacrifice, than ever made by any nation, to expiate our sin.

The Beagles: Voyages, Death and Re-Birth

Here is a modified early draft of a box that appears, much shortened, in the Rough Guide to Evolution...

The Beagles: Voyages, Death and Re-Birth
HMS Beagle, the ship that took Darwin around the world in the 1830s, must rate as one of the most famous naval vessels of all time. Darwin wrote up his experiences in a work commonly called “The Voyage of the Beagle” (although he never used that title; he called it the Journal of Researches, but there are several other alternative names). However, in fact there were several voyages and there have been several Beagles.

Darwin’s Beagle was launched in May 1820 as a ten-gun brig (a vessel with two square-rigged masts). A few months later, she took part in the coronation celebrations for George VI, before being taken out of service for five years. In September 1825, in preparation for her use as a survey vessel, she was fitted out with an extra mast (thus becoming a barque) and lost four of her guns. Her first voyage took place from 1825-1830, when she surveyed the southern regions of South America. She set sail under the command of Captain Pringle Stokes. However, in 1828, when faced with the desolate Straits of Magellan, Stokes became suicidal and shot himself in the head. By a sad twist of fate, it took him twelve days to die, alone in his cabin. He was replaced first by a Lieutenant Skyring, but then a few months later by Robert Fitzroy, who captained the Beagle on its second and most famous voyage from 1831-1836.

The Beagle made a third voyage as a survey vessel from 1837 to 1843, mapping the coastline of Australia. During that trip, surveyor John Lort Stokes (no relation to Pringle), who had accompanied Darwin on the second voyage, named an Australian harbour “Port Darwin” (now the City of Darwin, capital of the Northern Territory), after his former shipmate.

In 1845, the Beagle took on a new life as a coastguard vessel, guarding the Essex marshes while deployed in the River Roach, near the village of Paglesham. She served as home to coastguards and their families for many years, but then disappeared from the historical record. However, recent investigations by Robert Prescott of the University of St. Andrews, have confirmed that the Beagle survived intact until 1870, when parts of her timbers were sold to two local men, William Murray and Thomas Rainer. It is thought that the timbers were used to build a new farmhouse and boat house. However, the hull probably just sank into the mire, where in 2003, Prescott found traces matching the expected profile of the hull using an approach known as atomic dielectric resonance. All that remains of one of the most important vessels in history lies “full fathom five” below the Essex mud!

But Darwin’s ship was actually just the third of nine Royal Navy vessels to bear the name HMS Beagle. The first was constructed around 1766 by the Bombay Marine, the navy of the East India Company, while the last, a survey ship equipped with motorboats called FitzRoy and Darwin, was sold off, re-named and re-fitted in 2002. Several of the Beagle ships saw combat: the second (1804-14) in the Napoleonic wars, the fourth (1854-62) in the Crimean War, the seventh (1909-21) at Gallipoli and the eighth (1930-45) in the Second World War. The fifth Beagle (1872-83) is remembered as the site of the controversial extra-judicial hanging of a South Sea islander.

Beagle 2, named by British scientist Colin Pillinger after Darwin’s vessel, was an ill-fated British spacecraft that formed part of the 2003 Mars Express mission, but was unfortunately lost on Christmas Day 2003. Plans are now afoot for a successor, tentatively named Beagle 2 Evolution, that could fly in 2009.

Also in or shortly after 2009, Darwin’s ship is scheduled to rise again, in the form of a £3.5 million replica of HMS Beagle, built in the Welsh port of Milford Haven. The Beagle Project was initiated by David Lort-Phillips, a Welsh farmer and distant relative of John Lort Stokes, and Peter McGrath, a writer and yachtsman. The re-built Beagle will celebrate the Darwin bicentenary by visiting sites of significance to the original ship and subsequently be used in cutting-edge molecular and metagenomics surveys of plant animal and bacterial biodiversity. Sign up to the Beagle Project Blog to learn more.

Further reading

• http://www.aboutdarwin.com/literature/Beagles.html
  
• Voyage of the Beagle at Darwin Online
  
• http://en.wikipedia.org/wiki/HMS_Beagle_(disambiguation)
  
• HMS Beagle. The Story of Darwin's Ship by Keith Thomson
  
• HMS "Beagle": Survey Ship Extraordinary (Anatomy of the Ship)--build your own model of the Beagle!
• Beagle: From Darwin's Epic Voyage to the British Mission to Mars by Colin Pillinger 

Human evolution over or speeding up?

"Compare and contrast..." goes the start of many an exam question. Well, in catching up on my reading of blogs and news media, I have just come across an interesting pair of articles, ripe for the compare-and contrast-treatment:

• How We Evolve by BENJAMIN PHELAN from Seed magazine, which claims that human evolution has sped up recently.
  
• Evolution is complete: so where do we go from here? by STEVE JONES in the Daily Telegraph, which claims that human evolution has stopped!
  

I will leave it to you the reader to work through the two articles and do your own "compare-and-contrast" assessment, but my own inclination is to side with Phelan rather than Jones on this. 

In fact, it seems odd that Jones is still publishing articles like this, because he has been making this point for a decade or more and this is nothing new in the Telegraph article. When  Jones first started saying human evolution is over, we were still in the history-is-over epoch, before 9/11, the Afghanistan and Iraq wars and the reassertion of Russian military and political power. 

Even back then, I found several problems Jones' argument:

• It reeks of first-world complacency, when infant mortality is still so high in the Third World and populations are still being decimated by HIV, TB and malaria.
  
• Even if the vast majority of people survive to reproductive age, the fact that even a small number do not is still enough to drive evolution. As Darwin said: "A grain in the balance will determine which individual shall live and which shall die, -- which variety or species shall increase in number, and which shall decrease, or finally become extinct."
  
• Even if the vast majority of people survive to reproductive age, in an era of contraception and family planning, not all will have the same number of children. Any genetic difference that underlies this differential in reproductive success will still be the subject of natural selection. It’s a matter of speculation what affect fertility control will have on the human gene pool. When procreation is a matter of choice, rather than an inevitable consequence of passion, perhaps there will be a selective pressure for children to become steadily more manageable: if your first child is a terror, you might choose not to have any more! And conversely, whatever genes make people like children will be selected for!
  
• If evolution is defined as any change in the frequency of alleles in the human gene pool, then lifting the selective pressure against what would, before modern society and medicine, have been deleterious genes or combinations of genes, then we are clearly in an era of massive evolutionary change. For example, is it really plausible that the rise in Caesarian sections is not having some effect on the distribution of genes underlying pelvic anatomy or determining the likelihood of other complications during labour?

Add to that the arguments in the Seed article and in the articles cited therein, and I see little or no cogency in Jones' arguments. I will leave the last word to Darwin:

“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.”

Additional reading:

Recent acceleration of human adaptive evolution, Hawks et al, PNAS
Not the end of evolution again! by John Wilkins on the Evolving Thoughts blog

Not a lot happens in Cornwall...

Why else would the fact that the actors working on a film about Darwin had to "to cover up against the elements during a break from filming in Cornwall" prove newsworthy? :-)

Darwin stars shelter from elements from thisiscornwall.co.uk

Now the film itself: that is newsworthy!

Which science book should the next US president read?

Nature magazine (which was founded with help from Darwin's associates Huxley and Hooker and celebrates its 139th birthday on US election day, November 4th) posed this question in its 24 September issue:

Which science book should the next US president read?

In response, Jerry Coyne,  Professor of Ecology and Evolution at the University of Chicago wrote

"Anyone aspiring to be president should have a basic acquaintance with evolution and with the masses of evidence that it's not just a theory, but a fact. Charles Darwin's On the Origin of Species comes to mind, but it is outdated and written in turgid Victorian prose that is uncongenial to modern readers. Future US leaders should read a short, popular work that lays out the evidence for evolution and dispels the spectres of creationism and intelligent design without dwelling on religion. Sadly, no book fills this niche. My attempt, Why Evolution is True (Viking, 2009), will be published only after the election...

Sorry, Jerry, the correct answer to the question is The Rough Guide to Evolution, which will be available just a few weeks after the election. In fact, I'll make sure Barack Obama gets a signed copy and just for devilment make sure that creationist Sarah Palin gets one too, to enjoy after her lapse back into obscurity!

جميع الرجال الاخوة כל הגברים הם אחים

Just picked up this poignant piece from Wired News on the recovery and display of pages from the diary of Israeli astronaut Ilan Ramon, who died on the Space Shuttle Columbia. Thirty seven pages from the Ramon's diary were recovered and have been painstakingly reconstructed. 

The diaries are in Hebrew, a language which in Darwin's time was considered extinct, a linguistic dodo, having fallen out of use as anything other than a liturgical language for well over two millenia.  As Darwin noted in The Descent of Man: 

“Dominant languages and dialects spread widely, and lead to the gradual extinction of other tongues. A language, like a species, when once extinct, never, as Sir C. Lyell remarks, reappears”.

But Hebrew provides the most telling counter-example to Darwin's and Lyell's dictum, with a revival which, I thought until recently,  began a few months after Darwin's death with the birth of Itamar Ben-Avi. In particular, legend has it that Hebrew was re-born through the single-handed efforts of Itamar's father Eliezer Ben-Yehuda, who had settled in Palestine in the early 1880s and insisted in speaking to Itamar solely in Hebrew.

However, it turns out to be not so simple as that. Although Itamar was the first native speaker of the language in modern times, the language's revival as a literary language had been underway for over a century, through the Haskalah, a Jewish version of the Enlightenment that brought European Jews into contact with the wider intellectual life of the continent. 

In fact, one of the early responses to Darwin's Origin of Species was written in Hebrew. On reading The Origin, Polish-born Naphtali Halevi (1840–94) sought to reconcile evolution with the Torah. In 1876, six years before Itamar Ben-Avi was born, Halevi sent Darwin a long essay in Hebrew, Toldot Adam, which Darwin mentioned in his autobiography: “an essay in Hebrew … showing that the theory is contained in the Old Testament”. 

Both essay and covering letter were in Hebrew, and as Darwin could not read the language, he asked Henry Bradshaw, librarian at Cambridge University, to have the letter translated. In the covering letter, Halevi addresses Darwin: 

“To the Lord, the Prince, who ‘stands for an ensign of the people’ (Isa. xi. 10), the Investigator of the generation, the ‘bright son of the morning’ (Isa. xiv. 12), Charles Darwin, may he live long!” 

In the essay, Halevi makes an argument, drawn from a rather idiosyncratic analysis of word use in the Torah, that there were no irreconcilable contradictions between Darwin’s evolution and the Genesis account of creation. For more information, see this paper by Edward Dodson.

Aside from extinction, Darwin makes other comparisons between biological and linguistic evolution. In The Origin he writes:

“It may be worthwhile to illustrate this view of classification, by taking the case of languages. If we possessed a perfect pedigree of mankind, a genealogical arrangement of the races of man would afford the best classification of the various languages now spoken throughout the world … The various degrees of difference in the languages from the same stock, would have to be expressed by groups subordinate to groups; but the proper or even only possible arrangement would still be genealogical…”

While in the Descent of Man he writes:

“We find in distinct languages striking homologies due to community of descent, and analogies due to a similar process of formation."

The enduring conflict between Hebrew-speaking Israelis and Arabic-speaking Palestinians is never far from the news, but ironically Hebrew and Arabic provide a telling example of Darwin's principle of descent with modification, with obvious similarities even between the everyday greetings Shalom/Salaam. 

In fact, recent population genetics study of the evolution of Jews and Palestinians, like this one:

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews.

suggest a deeper truth: not just are the languages related, but so are their speakers: Arabs and Jews are, biologically speaking, brothers!

Ron Numbers on humans, dinosaurs, and Sarah Palin

There is a whole chapter in the Rough Guide to Evolution on the religious opposition to the theory of evolution by natural selection. I was very fortunate to have the chapter looked over by Ron Numbers, who probably ranks as number one world expert on creationism and by Lauri Lebo, a journalist who covered the Dover trial. Both provided helpful feedback and reassurance that I had my facts straight (but usual caveat: any mistakes remain my responsibility, not theirs). 

I was thus interested to see Ron Numbers' take on the Sarah Palin's creationism. Read more on the Harvard University Press Publicity Blog.

Dispatches from the cutting edge... part 2 and a half

In my earlier posts on the research by Keiichi Namba, Tohru Minamino and their colleagues on the bacterial flagellum:

• Dispatches from the cutting edge of flagellar biology, part 1
  
• Dispatches from the cutting edge of flagellar biology, part 2

I promised to upload the latest movie from the team. Keiichi gave me permission to upload it on to YouTube, but at 30 minutes it is too long to go there, so I have placed it on Google Video. Ignore the rather cheesy opening and revel in the fantastic animations:

And note, although Namba et al talk of the flagellum as a machine, they just laugh at the notion of intelligent design!

While on the subject of flagellar biology and evolution, Nick Matzke recently drew my attention to these two papers:

• A channel connecting the mother cell and forespore during bacterial endospore formation PNAS September 30, 2008 vol. 105 no. 39 15100-15105
  
• A novel pathway of intercellular signalling in Bacillus subtilis involves a protein with similarity to a component of type III secretion channels. Mol Microbiol. 2008 Jul;69(2):402-17.

which both claim to have identified homology between a flagellar protein FliF, that forms the M-ring in the bacterial inner membrane and SpoIIIAH a protein involved in spore formation from the Gram-positive bacterium Bacillus subtilis. If true, this would be another step forward in undermining the argument made by intelligent design advocate Scott Minnich that lack of homology for flagellar proteins provides support for the ID position. 

However, as both sets of authors used a similar rather risky method for assigning homology, which covers only part of the protein, I am not entirely convinced by their claims. Full proof will come only from comparisons of the structures of the proteins. In the mean time, we should keep an open mind and it would be worrying if tentative claims of homology turn into dogmatic statements of fact before conclusive evidence is in. But the claims of homology do at least provide a framework for future research. Watch these proteins!

Colloquium on Darwin in Europe

Although I did cover some of the reverberations of Darwin's work in the UK and USA in the Rough Guide to Evolution, I didn't get much chance to cover its European reception (although Tolstoy's character Levin grappling with evolution in Anna Karenina does get a mention). So, I was interested to hear of this colloquium:

A one-day colloquium on Charles Darwin in Europe will be held at Darwin's alma mater Christ's College, Cambridge, on Thursday 26 February 2009 to celebrate the bicentenary of his birth as well as the launch of *The Reception of Charles Darwin in Europe*, edited by Eve-Marie Engels and Thomas F. Glick. The colloquium will continue the discussions begun in its pages.

*The Reception of Charles Darwin in Europe* will be published in late 2008 in two volumes by Continuum (London and New York). It forms part of the Athlone Critical Traditions Series: The Reception of British and Irish Authors in Europe, edited by Elinor Shaffer.

All are welcome to attend.

Registration costs £35 (£40 on the day); concessions £20.

Because of limited capacity early registration is advised.

Registration forms and further details are available from the Reception of British and Irish Authors in Europe Project Office: RBAE@clarehall.cam.ac.uk.

-------

Programme

9.30-10.00: Registration & morning coffee

10.00-10.15: Welcome and introduction:
Prof. Frank Kelly FRS, Master of Christ's College
Dr Elinor Shaffer FBA, Series Editor & Project Director

10.15-10.45: Prof. Eve-Marie Engels (Eberhard Karls Universität Tübingen)
'Varieties of the Early Reception of Charles Darwin in Germany'

10.45-11.15: Dr Paul White (Darwin Correspondence Project, Cambridge)
'The Character of Correspondence'

11.15-11.45: Dr Jonathan Hodge (University of Leeds)
'Natural Selection and Pangenesis in Europe: Weismann and De Vries'

11.45-12.00: Break

12.00-12.30: Prof. Helmut Pulte (Ruhr-Universität Bochum)
'Darwin and the "Exact Sciences"'

12.30-13.00: Prof. Thomas F. Glick (Boston University)
'Reception of Darwin: Protestants and Catholics'

13.00-14.00: Lunch (not included in registration fee)
A list of places to eat nearby will be provided for participants.


14.00-14.30: Prof. Peter C. Kjærgaard (Aarhus Universitet)
'One of us: How Danes appropriated Darwin'

14.30-15.00: Dr Daniel Schümann (Otto-Friedrich-Universität Bamberg)
'The Reception of Darwin's Ideas in Nineteenth-century Poland'

15.00-15.15: Break

15.15-15.45: A. S. Byatt, 'Darwin, Swedenborg, Angels and Insects: A Novelist's Encounters with Darwin'

15.45-16.15: Dr Philip Bullock (Worcester College, Oxford)
'"Gripped in a Vice': Russian Responses to Darwin from Musorgsky to Tolstoy'

16.15-16.30: Break

16.30-17.00: Prof. Robert Rehder (Université de Fribourg)
'Poems about Darwin'

17.00-17.30: Dr T. E. Bell (University of Warwick)
'Benito Pérez Galdós and Darwin's Reception in Spain'

17.30-18.00 Questions and discussion

18.00-19.00: Wine reception and reading by Emily Ballou from her Darwin poems

Poet, screenwriter and novelist Emily Ballou was awarded a Tyrone Guthrie Centre fellowship in Ireland through the Australia Council for the Arts for her verse portrait of Darwin. Her second novel, Aphelion, was published by Picador, Australia, in 2007. Her collection entitled The Darwin Poems will be published by the University of Western Australia Press in April 2009.

19.00: Colloquium concludes

Darwinian Penguins

In a twist of art-will-eat-itself irony, I have just heard  the marketing approach of the publisher of the Rough Guide to Evolution described as "Darwinian"!

Rough Guides was founded by Mark Ellingham and started out in the early 1980s as an independent company. However, by 2002 the company had been sold to Penguin Books (which by then had been an imprint of Pearson for over thirty years), so in effect my publisher is Penguin.

And here is how Marketing Week opened one of its articles at the beginning of last month:

"Book publisher Penguin's Darwinian approach to developing its business in a sector steadfastly regarded as traditional has put it at the forefront of digital innovation."

The article continued with two major new items: Penguin's partnership with a dating agency, Match.com, with the aim of putting books back into courtship and Penguin's exploration of "crowdsourcing", i.e. massive collaborative Wikipedia-like authorship in the creation of  a novel in the Million Penguins project. Follow this link to read the full article from Marketing Week.

Ironic that Penguin Books should be at the forefront of Darwinian publishing, when their avian namesakes in the March of the Penguins have been taken by some as a revelation from God on how we should behave (or maybe that was just a story stirred up by the BBC?).

Darwin at Home!

Under a banner that proclaims that "evolution is natural as gravity!", Darwin@Home is an open source software project that aims to bring the process of evolution to your home computer. From the initial efforts to evolve locomotion, the project now encompasses a broader framework for evolution in general.

Darwin@Home is the latest in a series of initiatives within the field of Artificial Life that have produced compelling videos of in silico "lifeforms" that have evolved complex behaviours through natural selection. You just have to take a look at the project's eye-catching and though-provoking video:



And if you like that, you will also enjoy these other celebrations/illustrations of computer-based evolution in action that I found on YouTube:

Darwin Day 2009: the Origin of Species in Rap to bounce into Birmingham!

For the last four years, I have been organising a local Darwin Day event at the University of Birmingham, taking a lead from the Darwin Day movement that started in the USA. And now fast approaching is the biggest Darwin Day of them all (at least in my lifetime), with the bicentenary of Darwin's birth on February 12th 2009. 

What with writing the Rough Guide to Evolution and various other duties, I am only now starting to finalise arrangements for the big day. So far I have a couple of academics from outside our university agreeing to come and talk about their work (Fred Spoor from UCL on palaeoanthropology and Richard Emes from Keele University on the molecular evolution of the mammalian brain), plus Lauri Lebo has agreed to come from the US. Lauri is a journalist who covered the Dover Pennsylvania trial and has written a poignant personal account of the people involved (The Devil in Dover). So, we have already started to assemble a superb lineup for Darwin's 200th birthday bash!

But now I have just heard that we have acquired another headline act--Canadian Lit-Hop Rap artist Baba Brinkman has agreed to participate with a celebration of Darwin's life and legacy in Rap music! 

Baba visited Birmingham last year when he put on a performance of his best-known work, the Rap Canterbury Tales (website here; sample some videos here). But especially for us, Baba also wrote and performed a new rap poem Natural Selection, an excerpt from which appears below.

 

Baba has now agreed to produce a much more extensive celebration of Darwin and evolution for the bicentenary, which I am provisionally entitling The Origin of Species in Rap. I am hoping we can also arrange performances in other sites around the UK (e.g. Warwick, Shrewsbury, Cambridge, NHM--if you are interested in hosting a performance let us know).

Aside from Lit-Hop, Baba (son of Vancouver Quadra Liberal MP Joyce Murray) is also currently active in Canadian politics, especially as there is less than a fortnight to the Canadian election. He has produced a catchy track called Bounce that targets two of the contenders for post of 23rd Canadian PM, Conservative Stephen Harper and the New Democratic Party's Jack Layton. You can listen to the track by clicking on the arrow below, or download it for free from Baba’s MySpace page



The song envisions a future where both Stéphane Dion and Barack Obama win their respective elections, “so the whole continent goes progressive and conscientious.” Let's hope Baba's dream comes true before Darwin's 200th birthday!

The Effector Detector and a Common Love of Science

I have a new name: the effector detector!

This has just appeared in The Scientist: Effector Detector, which is a kind of follow up on a paper that I my team and my collaborators published a couple of years ago in PNAS. 

I had a little advance warning that this commentary was going to appear, but didn't get the chance to see it or comment on it in advance. The coverage seems rather superficial, and it neglects the important role that our Japanese collaborator Toru Tobe (from the University of Osaka) played in the work, which was just as important as mine (if not more so). But it is nice to be noticed!

Another nice thing about our original PNAS paper, aside from the science, was the international character of the team, which included scientists born in the UK, New Zealand, Israel, Iraq, France and Japan drawn from Christian, Jewish, Muslim and Shinto or Buddhist backgrounds. As local Birmingham scientist Joseph Priestley (discoverer of oxygen and religious and political radical; statue in Birmingham shown left) said in 1793 of the Lunar Society of Birmingham:

"We were united by a common love of Science, which we thought sufficient to bring together persons of all distinctions, Christians, Jews, Muslims* and Heathens, Monarchists and Republicans."

*Priestley used the old-fashioned term "Mohammetans", but I have translated his sentence into modern English.