International E.coli Alliance conference

I promised I would give some publicity to this poorly advertised meeting of the International E. coli Alliance, which is still open to applicants. 

The International E.coli Alliance conference will be held at the Wellcome Trust Conference Centre at Hinxton, near Cambridge, England from 24^th- 27^th September 2008. This is a 4 day meeting which will cover the impact of the genomics and post-genomics revolution in microbiology, with special focus on bacterial regulatory strategies and pathogenic mechanisms.

Non-experts keen to know more about E. coli should take a look at Carl Zimmer's latest book: Microcosm.

A few comments from van Wyhe on the Dawkins show

I managed to make contact with John van Wyhe today and he is even less tolerant of the errors in the Dawkins show than I am!

Here is what he said, with my own hypertext links and comments added in:

Thanks Mark - your blog is great- though I made a longer list of blunders while watching! (You can use this if you want) 

I was very disappointed with the Darwin documentary. There are a lot of people who spend their lives studying the man and yet here we get Dawkins' second-hand gloss with only one expert, Randal Keynes, briefly on screen.

First of all, the major theme was not "Who was Charles Darwin and how did he figure out how life works"? Instead, it was “Darwin is better than religious explanations”.

Dawkins Claim: Darwin wanted to be a priest instead of his family's desire he be a physician.

In fact, it was his family's idea he become a clergyman.

Dawkins Claim: His family connections got him the Beagle voyage offer.

It was his Cambridge connections, not his family connections.

 [specifically Henslow]

Dawkins Claim: Darwin was one of the first to recognized that fossils were the remains of extinct organisms!

Wrong by centuries!

[centuries is a bit strong: my understanding is that Cuvier was the first to establish this in the 1790s, more than forty years before Darwin's Beagle voyage, but the recognition that fossils were the remains of once-living but not necessarily extinct, organisms goes back to Steno, over a century and a half before Darwin, so Darwin is far from the first]

Dawkins Claim: Darwin was one of the first to see that the world was older than 6000 years! 

Again, wrong by centuries. In fact many discoveries are attributed to Darwin rather than to Richard Owen, Lyell and the entire scientific community of his day and the preceding generations. This Darwin lives in a vacuum!

Dawkins Claim: He thought his theory would be ‘upsetting’ so he therefore hesitated in publishing it.

Nonsense!

The people on your blog who think they disagree with me and say 'it was lots of factors' have obviously not read my article! If you cite this copy people can read it for free:

http://darwin-online.org.uk/people/van_Wyhe_2007_Mind_the_gap_did_Darwin_avoid_publishing_his_theory.pdf

 All best, John -- Dr John van Wyhe

Director The Complete Work of Charles Darwin Online University of Cambridge CRASSH, 17 Mill Lane, Cambridge, CB2 1RX http://darwin-online.org.uk/ Fax: 01223 (7)65276

Bye-Fellow Christ's College, Cambridge

 

Audiobooks: Beagle, Origin, Dawkins and Darwin

Given the current interest in Dawkins' latest series on Darwin, it is worth noting that Dawkins had recorded a five-hour-long abridged version of the Origin of the Species, which is now available in iTunes

Click on the link to load it up in your version of iTunes:

http://phobos.apple.com/WebObjects/MZStore.woa/wa/viewAudiobook?id=269853133&s=143444

(but my version of iTunes isn't working after upgrading to 7.7.1 grrr!! When is Apple gonna get it right?)

It is by far the best audio version of the book and provides an easy introduction for those intimidated by the prospect of reading the whole volume. 

For the completist, a full 19-hour audio  version of the Origin is available from Darwin Online, but as it is computer- generated it is hard work to listen to.

Another hidden, and free, audiobook treasure is a series of readings from Darwin's Beagle Diary, performed by a professional British actor, Jo Stone-Fewings, which were originally broadcast on the BBC and are now available via Darwin Online.

Darwinian myths and Cartesian doubt

Ryan Gregory left this comment on my earlier post about Dawkins and Darwin's delay:

I enjoyed the post, and in general I agree. The point of my earlier post was simply that 1) people had been citing the essay without mentioning the fact that some other Darwin scholars do not agree with van Wyhe (the reason I cited Odling Smee is not the supposed search for a single keyword, but rather because it mentions other scholars who disagree and was the only source I knew of that made the point), and 2) that sometimes the fear of reaction leads to delay in a more complicated manner. As I concluded,

I think "yes or no" to the question of whether Darwin delayed publication out of fear is very simplistic. Anyone who has written anything of substance knows that sometimes the effect of fear of reaction is procrastination and/or excessive desire to include every piece of information available. Both can cause writing to take longer than it otherwise would. Was Darwin thorough? Yes. Is that one reason it took so long? Undoubtedly. Was he so thorough because of a fear of reaction? Probably at least in part.

But when I tried to respond with a comment, I found myself hamstrung by Blogger's inability to tolerate any complex HTML in a comment, so I am posting my response here.

---

Thanks for the comment. I agree there is no simple answer to this. I am sure I am the same as most scientists in that I have several projects on the go or planned out at any one time, and why I get on with some of them and procrastinate on others is a complex question. I guess the same was true for Darwin.

But in writing the Rough Guide to Evolution one thing that struck me was that, time and again, ideas that start off as suggestions or suppositions soon harden into dogma, without any new evidence.

Before I started the book I was certain that Darwin's insights relied on his studies on Galapagos finches, that Darwin became an atheist when his daughter died, that Huxley trounced Wilberforce in Oxford and that was some kind of plausible link between Darwin and the Nazis…

...and that Darwin delayed publication through fear of the consequences vis a vis religion. 

I even quoted the line about confessing a murder a few years back when we created the Origin of Species in Dub. 

But now I feel much more skeptical about all these claims—even to the point of Cartesian doubt! As John points out in his paper, some of the most recent additions to the story (e.g. the story that Darwin was so fearful he dreamt about being hung) melt away when one bothers to look at what Darwin actually wrote. In a sense, John, by putting all of Darwin’s writings on line for all to see amounts to a reformation in Darwin studies, where the rest of us no longer need an intermediate between ourselves and Darwin scholars to work out what he meant.

 Take a look at the absurd scene at 8.43 mins into this snippet from the PBS documentary series, where Darwin is led to the gallows!

And look at what Darwin actually wrote about the man being hung (in 1838, over twenty years before the Origin) and judge for yourself whether this justifies the interpretation depicted in the scene!

Sept. 21st Was witty in a dream in a confused manner. Thought that a person was hung & came to life, & then made many jokes about not having run away & having faced death like, a hero, & then I had some confused idea of showing scar behind (instead of front) (having changed hanging into his head cut off) as kind of wit showing he had | honourable wounds. all this was kind of wit.—I changed I believe from hanging to head cut off /there was the feeling of banter and joking/ because the whole train of Dr. Monro111 experiment about hanging came before me showing impossibility of person recovering from hanging on account of blood, but all these ideas came one after other, without ever comparing them. I neither doubted them or believed them.—Believing consists in the comparison of ideas, connected with judgment.

You can even look at Darwin’s handwritten original here:

http://darwin-online.org.uk/content/frameset?itemID=CUL-DAR125.-&viewtype=image&pageseq=137

Another key point is that although John might be seen as a new kid on the block in Darwin studies, none of the senior scholars in the field have attempted to counter his claims in writing, which is surely a key requirement of scholarship. I guess we have to watch this space. Maybe in another ten or twenty years, everyone will be laughing at the “Darwin’s delay” myth just like we laugh at the inheritance of acquired characteristics today?

Did Dawkins get it wrong on Darwin’s delay?

Last night I watched Dawkins on Darwin on Channel 4, in the first of his three part series The Genius of Charles Darwin. It strikes me as odd that they are airing it now, when it would make more sense to do so during the bicentenary year, but then I guess it will help build the sense of anticipation for Darwin200.

In general I thought it was an accomplished entry-level piece on Darwin and evolution that will go down well with non-expert viewers (as judged from a sample of my wife and two children) and meets Dawkins’ usual high standards of linguistic craftsmanship—I particularly liked the one sentence summary of natural selection: “The race is survival, the finishing line reproduction!”

I note that Peter of The HMS Beagle Project liveblogged the show while it was actually being broadcast, which makes for fun reading and must have been hard work!

So, was there anything wrong with the programme? 

A general complaint was that it came across rather too much as Darwin hagiography (and I am a Darwin fan!) After watching the show, the naïve viewer might come away with the idea that Darwin discovered everything, from fossils to forelimb homologies, when the work of many other scientists fed into Darwin’s theorising. Also, introducing Craig Venter as the man who sequenced the human genome is likely to rile those involved in the publicly funded human genome project (but that is not detract from Venter’s sequencing efforts in general, which, through TIGR and JCVI, have shed more light on the diversity/common ancestry of life than any other comparable effort).

Moving on to specific points, alarm bells rang in my head on two occasions.

Firstly, around 9 minutes into the programme, Dawkins visits the Galapagos, where he says of Darwin:

Here he began to wonder why God would have created distinctive kinds of tortoise, finch or iguana on more or less identical small islands. Were iguanas like these related, rather than separately created. Were they cousins of the similar but different iguanas on nearby islands?

Although it is true that in the popular imagination, the Galápagos Islands are the one place on Darwin’s Beagle voyage that looms larger than anywhere else, you won’t find any evidence in Darwin’s writings for any 'eureka moment' during his visit there. His notes reveal that it was only months later, during his journey home in summer of 1836, that the Galápagos mocking birds raised his first suspicions as to the fixity of species: 

When I see these Islands in sight of each other… tenanted by these birds, but slightly differing in structure & filling the same place in nature, I must suspect they are only varieties . . . If there is the slightest foundation for these remarks the zoology of Archipelagoes will be well worth examining; for such facts would undermine the stability of Species

In fact, Darwin was more struck by how odd the inhabitants of the Galapagos were compared to the rest of the world than by the subtle differences between the inhabitants of individual islands:

The natural history of this archipelago is very remarkable: it seems to be a little world within itself; the greater number of its inhabitants, both vegetable and animal, being found nowhere else.

Plus, Dawkins’ choice of iguanas to illustrate this point struck me as a bit odd (although he avoided the obvious trap of using Darwin’s finches: see Sulloway’s dismissal of this old myth). 

The most obvious distinction among the Galapagos iguanas is between the marine and terrestrial iguanas, which are separate species, each peculiar to the archipelago. But Darwin was again struck by the restricted distribution of the iguanas

It is very interesting thus to find a well-characterized genus, having its aquatic and terrestrial species, belonging to so confined a portion of the world

I wasn’t aware that Darwin noted, within each species, any differences specific to different islands. But on checking, he does make passing references to some such differences. In the first edition of the Journal of Researches (1839), Darwin notes of the marine iguana:

On the island of Albemarle they seem to grow to a greater size than on any other.

And of the land iguana, he writes:

We will now turn to the terrestrial species (Amb. subcristatus of Gray).* This species, differently from the last, is confined to the central islands of the Archipelago, namely to Albemarle, James, Barrington, and Indefatigable. To the southward, in Charles, Hood, and Chatham islands, and to the northward, in Towers, Bindloes, and Abington, I neither saw nor heard of any. It would appear as if this species had been created in the centre of the Archipelago, and thence had been dispersed only to a certain distance. (my italics)

So, I guess one could make an argument that inter-island differences between iguanas might have has a minor influence on Darwin’s views on the origin of species, but there is no evidence that Darwin’s speculations actually occurred on the islands, rather than on the way home or even in England.

A second more troublesome point occurs much later on, at 44 mins into the film, when Dawkins states:

But he was strangely reluctant to go public with his idea… But he was acutely aware of how upsetting this flat contradiction of the religious story would be. He hesitated to publish.

Here Dawkins jumps in with both feet with his uncritical acceptance of the myth of Darwin’s delay. It is true that many recent accounts of Darwin’s life suggest that he delayed publication of his theory of evolution and that, fearful of its reception, he kept it secret for many years…

But none of this is mentioned in Darwin’s autobiography, in his obituaries or in the early accounts of his life. Only in the mid-twentieth century did these myths of “Darwin’s delay” begin to gain currency. I direct readers to a recent tightly argued paper by Darwin scholar John van Wyhe

Mind the gap: did Darwin avoid publishing his theory for many years? John van Wyhe (2007) http://journals.royalsociety.org/content/gk6840u115705166/

Here, van Wyhe highlights the many distortions and fabrications that have crept into the Darwin story over the years and shown how these are derived from biased readings of a handful of passages plucked from Darwin’s enormous written output. Darwin’s apparent delay was not down to any fears about the consequences of publishing on evolution. Instead, it was simply the accumulation of facts, ideas and arguments outrunning his ability to investigate, analyse and write about them, particularly when slowed down by illness.

Of course, not everyone agrees with van Wyhe: see this posting from a few weeks back on Genomicron. But the article by Nature journalist Lucy Odling-Smee that is refered to in the blog is hardly a match for van Wyhe’s tightly argued prose and van Wyhe himself has told me that the rules of fair play were suspended here, in that he was never granted a right to reply in Nature to the Odling-Smee piece. One particular problem is that Odling-Smee mis represents what van Wyhe did:

To carry out his study, Van Wyhe searched for the word "delay" in primary and secondary sources covering the period in which Darwin was working on Origin of Species.

In fact, this is a parody of what van Wyhe did. Rather than pursue such a simplistic approach, van Wyhe’s conclusions were built on over a year’s careful in-depth scholarship! And so far, no expert critique of van Wyhe’s paper has appeared in the academic literature, suggesting that his critics are short on counter-arguments.

So, I let me nail my colours to the mast and say that I think Dawkins has got it wrong here: there was no delay, no fear, no secrecy – nothing but perspiration racing to keep up with inspiration!

 

We come from monkeys!!

A week or so ago, before I had my own blog, I tried to comment on this interesting post from John Wilkins on his blog Evolving Thoughts: Why are there still monkeys?

For some reason, the comment never made it through, but what I said was:

The best words on this topic are sung rather than written: http://www.emeraldrose.com/monkeys.htm

Lyrics here: http://www.emeraldrose.com/archivesages/wecomefrommonkeys.htm

Even the caveat is perfect:

For you science purists, yes, we considered the title "We Come From Genetic Precursors To Monkeys" but it was rejected on artistic grounds.

And you can even get the MP3 for free!

The Beagle's puzzling wiggle

I see that Karen James over on the Beagle Project Blog has been drawing up a new map of Darwin's Beagle voyage.

We have a map of the voyage in the Rough Guide to Evolution, but the map has to be taken as approximate, given how difficult it is to catch all the to-ing and fro-ing that the Beagle did along the coastline of South America on a map that shows the whole world. However, there was one feature that caught my eye when the map returned from the cartographers: a wiggle, as the Beagle sailed away from the coastline between Santiago and Concepcion to encircle the Juan Fernández Islands. When I checked other maps of the voyage, some have the wiggle...

For example, this one from the Darwin Day website:

...and the original map from The Beagle Diary publication that Karen referenced.

But some do not, including Karen's and the one from Darwin's Journal of Researches (aka Voyage of the Beagle).

From a quick look around, I have not been able to find any reference to this trip around the Juan Fernández islands in the text of the Beagle Diary or Journal of Researches.

Karen, or anyone else, can you shed light on this puzzling wiggle?!

Rough Guide to Videogames: an evolutionary perspective

Another Rough Guide is out this week: The Rough Guide to Videogames. And, as you might expect, a few weeks ago one of the authors, Kate Berens, launched a companion blog: Atypicalgamer.

For me, Kate's blog provides proof of the "it's-a-small-world" maxim, in that listed among her favourite links is Eurogamer, a company set up by the Loman brothers, Rupert and Nick. Nick is a medic/bioinformatician who runs xBASE, is doing a PhD with me and helped me find some videogames with an evolutionary theme when writing The Rough Guide to Evolution.

In fact, within the world of videogames, life simulation games with an evolutionary flavour have a noble pedigree stretching back to Sim-Life and beyond—although, as so-called God games, these usually incorporate a heavy dose of teleology or intelligent design to give the game a sense of purpose!

Nick's recommendations include Darwinia (www.darwinia.co.uk) and Creatures (www.gamewaredevelopment.co.uk). Off my own bat, I also tried out the Playstation game Darwin on my children, but they got bored of it before working it how it all worked.

But for those at the cutting edge of cool, there is only one evolutionary game worth talking about: Spore (wikipedia article; official web site: www.spore.com; preview here), even though it hasn't been released yet—it's not due out till next month! Despite this, Spore has its own YouTube channel with plenty of promotional videos—here's one:

The developers have wound anticipation to fever pitch with the release of the Spore Creature Creator (review on Eurogamer), which is available for free download. Spore's creator Will Wright recently boasted that the number of player-created species in Spore already exceeds the number of real biological species on planet Earth! There is even a Charles Darwin Spore creature (although I have to boast the Pallen family already has a CD mii on our Wii):

Oh, and the music for Spore is being developed by Brian Eno.

I look forward to hearing more on Spore from Kate's blog in a few short weeks' time!

Ginger genetics

On Friday my attention was drawn to this short film on the advantages and disadvantages of being ginger, made by Helen Cooper (one of my colleagues at the University of Birmingham) and Nick Rutter.

My reactions to the film are mixed. It certainly kept one’s attention and was entertaining throughout. I worry that in re-hashing prejudices against redheads, it might help fuel them—but in that case English comedian Katherine Tate could be held guilty of the same crime:

The film certainly stimulated my interest in the question “why ginger hair?” And in broad terms the science seems OK, pointing out a paradox (why do the ginger genes survive in the face of social stigma and an increased susceptibility to skin cancer) and sketching out three kinds of potential evolutionary explanation: sexual selection, genetic drift and natural selection. The film leaves out any detailed consideration of the other kind of answer to the “why ginger hair question?”, i.e. a mechanistic genetic explanation of the phenomenon—but one can only go so far in a six-minute film!

In fact, the explanation has been clear for over a decade. Ginger or red hair appears in people who have two copies of a recessive gene that encodes a mutant form of the melanocortin 1 receptor (MC1R) protein, a protein which regulates the production of various forms of the skin and hair pigment melanin. Over sixty different mutations that affect the function of MC1R can cause variously grades of red-ginger hair, usually accompanied by pale skin, freckles and a tendency for skin to burn rather than tan after exposure to sunlight—for an excellent introduction to the genetics of MC1R, see the relevant article from OMIM (Online Mendelian Inheritance in Man). Interestingly, a study published in May this year showed that red-headedness is what geneticists call the null phenotype in human, i.e. is what you get when you have no functioning MC1R at all.

The ginger complexion is very rare in humans, found in less than 1% of the world population. It is common in the North West of Europe, with the highest rates in Scotland and Ireland. As a result of Scots and Irish migration to the New World, the largest number of ginger-haired people occurs in North America; there are also many in Australia. A few years ago, during a trip to the Northern-Irish city of Derry/Londonderry, I visited a million-pound high-tech exhibition called “The Fifth Province” which is housed within the city’s Calgach centre. The exhibition focuses on the Irish Diaspora and features a series of Irish, North American and Australian ginger-haired freckled children as proof of a common Irish heritage. In fact, in Irish step dancing competitions, according to a friend from Northern Ireland, marks are awarded for how “Irish” girls look and the ginger complexion is considered so authentically Irish that girls often wear ginger-haired wigs.

Curiously, in Jamaica, native-born white people are usually termed “red men” by the rest of the population— a fact brought home to me earlier in year when Karen Nelson, a Jamaican-American expert on bacterial genomes, was introduced via e-mail and photo to my collaborator on the Origin of Species in Dub, Jamaican geneticist Dominic White (who has a Northern-Irish mother and Jamaican father). Her first comment was how “red” he looked!

But even more curiously, in Jamaica there are people from the self-identified black community, who have reddish hair, freckles, and a rusty complexion (they are sometimes called “red Ibos”). A study from the University of the West Indies has confirmed that this complexion is linked to mutations in MC1R.

Let’s now examine the claims in the film in more detail.

First of all, the idea that the genes for ginger hair and the ginger phenotype are destined to die out soon appears to be an urban myth/persistent meme that has little or no basis in reality. This topic has been explored repeatedly in the blogosphere:

• http://www.kqed.org/quest/blog/2008/03/31/redheads-are-here-to-stay/
  
• http://scienceblogs.com/gnxp/2007/08/red_hair_going_extinct.php
  
• http://scienceblogs.com/gnxp/2007/08/update_on_redhead_hoax.php
  

Working through the film’s explanations for ginger hair in reverse order…

What about the claim that ginger hair and pale skin provide a selective advantage by facilitating the synthesis of vitamin D in the skin? The idea that the pale skins seen in Europeans are the result of selection for increased vitamin D production (a process driven by UV radiation from the sun and masked by melanin) has been around for several decades, but is still the subject of some controversy. However, I can find no evidence in the scientific literature that specifically links increased vitamin D production to the ginger-haired phenotype rather than simply to European-style pale skin in general.

In addition, there is no evidence from molecular genetic studies to suggest that natural selection has been acting on the MC1R mutations associated with red-headedness. In fact, the opposite appears to be the case: in Africa at least natural selection seems to be acting to preserve the original dark-skinned dark-haired version of the gene. However, as an interesting aside, Darwin reported in The Descent of Man a claim that redheads were the best suited of all Europeans to working in an African environment!!

The second explanation discussed in the film, a relaxation in the selective pressure to maintain the original genotype in high latitudes, appears to be most likely according to genetic studies. In other words, what is not forbidden by natural selection is allowed.

One objection to this neutralist explanation is that the ginger phenotype is associated with an increased risk of skin cancer, so one would expect it to be selected against. A counter-argument here is that such cancers typically occur after reproductive age and so will not affect reproductive fitness. However, when discussing similar arguments on pale skin more generally, Jared Diamond has pointed out a counter-counter-argument—that in human societies individuals might still contribute to the fitness of genes in their descendants long after birth of their children (the what-use-is-a-grandmother argument)

What of the first explanation: sexual selection? As pointed out in the film, this was the explanation favoured by Darwin in the Descent of Man for differences in human skin colour and in this context has recently been re-visited in a review article by Aoki (which I have not been able to obtain: can anyone e-mail me a PDF?). The folk wisdom is that redheadedness is attractive in a woman, but unattractive in a man. But I can find no papers that attempt to document or quantify the attractiveness of ginger hair colour or that describe any mathematical model that would explain current gene frequencies through an interplay between the negative effects of natural selection and female-specific positive effects of sexual selection Perhaps, someone out there can start a collaboration between psychologists, geneticists and mathematical modellers that would deliver the ultimate truth on this tricky question!

And before closing, let me throw in two final pertinent points.

Firstly, ancient DNA studies on Neanderthals have shown that provided evidence that at least some Neanderthals had MC1R mutations that although not seen in modern humans, probably resulted in red hair.

Secondly, our close relatives the orangutans have ginger-red hair, provoking the two “why” questions:

• Why in genetic terms? These apes have been shown to have a functional MC1R, suggesting that the mechanism of red hair generation in orangs is different from the prevalent mechanism in European human populations. One hopes that the orang genome sequence will soon deliver the answer.
  
• Why in evolutionary terms? Sexual selection again? Or genetic drift? But as they live in the Tropics, one might argue that the selection would favour a darker complexion?
  

Clearly, the evolution and genetics of red hair will keep scientists busy for a few more years yet!

---

Further Reading

The wikipedia article on red hair is surprisingly informative. Also there is a recent book on this subject (although I have not read it).

Exciting stuff from the BBC for the Darwin bicentenary

Andrew Marr, the British political journalist who championed Darwin in the Greatest Britons series...

Here is a snippet from the programme:

...is returning to the life and works of the great man of evolution for a joint Open University/BBC production, tentatively entitled On Darwin's Legacy, which will appear in the bicentenary year.

More details here...

Religious polymorphism: blame it on the parastites?

In the book, I blame parasites for pornography, in that we wouldn't need sex if parasites were not driving genetic diversity. But for an interesting twist on this issue, check out this post from the Economist:

Praying for Health: Religious diversity may be caused by disease

And if you are after the paper, it is available here

Assortative sociality, limited dispersal, infectious disease and the genesis of the global pattern of religion diversity

.

Could life play fairy chess?

[This is a snippet from the cutting room floor of the Rough Guide to Evolution, rejected by the editors for being too long and too technical for the educated layperson. I like to think that most blog readers are a cut above the average, so I posting it here]

Thomas Huxley once likened the world to a chessboard, in which the pieces were the phenomena of the universe and the rules the laws of Nature. Shortly after teaching my children the rules of chess, I let slip that there was a variant of chess, named fairy chess, in which one was allowed to vary the rules just slightly. Soon afterwards, whenever my son was stuck in an awkward chess position, he would make an illegal move to get out of trouble and then confidently declare that he was playing fairy chess! 

Fairy chess is almost identical to conventional chess, except that one feature of the standard game is changed, for example, by altering the layout of the board (making it a cylinder or torus), by introducing non-standard pieces, such as the grasshopper (a kind of hobbled queen that can moves along ranks, files, and diagonals but only if it can hop over another piece to reach its destination), or the nightrider (a kind of super-knight that can make an unlimited number of knight moves in any direction) or by modifying the rules (e.g. in Andernach chess, a piece changes colour after capturing another piece, while in Einstein chess, a piece is demoted with every move unless it captures another piece, in which case it is promoted).

If we adapt Huxley’s metaphor to molecular biology, life can be seen as a biochemical game of chess, in which the behaviour of the molecular pieces is seemingly governed by universal rules. In the DNA of all living organisms, the same deoxyribose-phosphate backbone is always used, with the same four “standard” bases. And the deoxyribose is consistently in the right-handed D-sugar form, never in the mirror image L-DNA form. The same genetic code is used everywhere (aside from occasional minor changes in organelles, and rare changes elsewhere), and always according to the same principle: three-base codons read consecutively into amino-acids by the tRNA-ribosome combination. The same twenty “standard” amino acids are added to proteins by the ribosome in all organisms (with just three additional spare amino acids used only in some organisms: N-formylmethionine, selenocysteine and pyrrolysine). And the amino acids handled by the ribosome are always in the left-handed form, never the mirror image D-amino acids. 

The evolutionary explanation for the universality of life’s pieces and rules is universal descent from a common ancestor. But the forcefulness of this argument depends on whether the pieces and rules could have been different. Could life play fairy chess? Evidence from the natural world and from the laboratory suggests the answer is yes!

Even in natural organisms many alternatives to the standard building blocks exist. The ribosome uses less than two dozen “standard” amino acids to build proteins, but several hundred “nonstandard” amino acids are used by living organisms in other settings (for example, the amino acid gamma-aminobutyric acid is used as a neurotransmitter); many find their way into proteins by modifications to standard amino acids after the ribosome has finished its work (the amino acid citrulline is created from arginine in this way). Similarly, although in nature DNA is always made by a polymerase from the same four standard bases (adenine, guanine, thymine and cytosine), over a hundred non-standard bases are used in tRNA molecules, with many non-canonical base pairings.

However, it is from the laboratory that the most compelling evidence for the “life didn’t have to be this way” argument comes. For a start, scientists have created many alternatives to the standard DNA backbone. Peter Nielsen from the University of Copenhagen has created peptide nucleic acids, in which the four standard bases are used in canonical base pairings, but the backbone is created from amino acids. Swiss biochemist Albert Eschenmoser and others have created nucleic acid backbones using alternatives to deoxyribose—examples include homo-DNA (which contains a six-carbon sugar, instead of the conventional five-carbon sugar), pyranosyl-RNA (pRNA), threose nucleic acid (TNA), and, simplest of all, glycerol nucleic acid (GNA). In each case, conventional pair bonding of bases remains possible (although structural studies have shown why conventional DNA may be preferable to homo-DNA).

Several groups have shown that it is possible to expand the alphabet of bases used in standard nucleic acids—Japanese biochemist Ichiro Hirao has even created unnatural base-pairs (y-s instead of A-T or G-C) that can be transcribed by RNA polymerases in a template-dependent fashion and then translated using artificial tRNAs to add a non-standard amino acid (chlorotyrosine) to the resulting protein. Floyd Romesberg at the Scripps Research Institute has created artificial base pairs do not rely on hydrogen bonding. Peter Schultz, also at the Scripps Research Institute, has created several “fairy chess biochemistries” which include oddities such as quadruplet codons. He has made yeast and bacteria that incorporate non-standard amino-acids into their proteins, and has even evolved several novel tRNA synthetases that couple non-standard amino acids to tRNAs.

Thus, there is strong evidence that the biochemical building blocks of life, and the rules used to assemble them, could have been different: life could have played any one of a myriad varieties of fairy chess. Given that any hypothetical intelligent designer would have had such a rich palette to draw upon, the very paucity of variation at the molecular level provides compelling evidence that instead of each being independently designed, all living organisms have evolved from a common ancestor. 

But, to return to the topic of a previous post,  the ultimate proof will come when we discover or create the biological equivalent of the Klingon: an organism devoid of any historical link with natural terrestrial life. This might seem a long shot, but I would bet on this becoming a reality in my lifetime.

 

Watch out for Dawkins on Darwin on Channel 4 on Monday

The Genius Of Charles Darwin

Monday 04 August 

8:00pm - 9:00pm 
Channel 4

Richard Dawkins presents a guide to Charles Darwin and his revolutionary theory of natural selection, which Dawkins considers the most important idea ever to occur to a human mind. On the 150th anniversary of the theory's publication, Dawkins explains who Darwin was, how the theory was developed, what it is and why it matters. He also explains how the theory changed the way in which humans see themselves, and the reasons why he believes Darwin's theory is fact.

VIDEO Plus+: 7159

I would hope US viewers might be able to pick it up from:
http://www.channel4.com/watch_online/

Cumulative cultural evolution in the laboratory: An experimental approach to the origins of structure in human language

Just as I finished the last post a link to this remarkable paper arrived in my inbox:

Cumulative cultural evolution in the laboratory: An experimental approach to the origins of structure in human language
Simon Kirby, Hannah Cornish and Kenny Smith

We introduce an experimental paradigm for studying the cumulative cultural evolution of language. In doing so we provide the first experimental validation for the idea that cultural transmission can lead to the appearance of design without a designer. Our experiments involve the iterated learning of artificial languages by human participants. We show that languages transmitted culturally evolve in such a way as to maximize their own transmissibility: over time, the languages in our experiments become easier to learn and increasingly structured. Furthermore, this structure emerges purely as a consequence of the transmission of language over generations, without any intentional design on the part of individual language learners. Previous computational and mathematical models suggest that iterated learning provides an explanation for the structure of human language and link particular aspects of linguistic structure with particular constraints acting on language during its transmission. The experimental work presented here shows that the predictions of these models, and models of cultural evolution more generally, can be tested in the laboratory.

I note that Ed Yong over at Not Exactly Rocket Science has already written a long post on it, so I won't write an elaborate post of my own (and Jonah Lehrer covers it too) But neither bloggers nor authors note the historical roots of the idea that languages might be subject to natural selection (the authors look-back horizon seems to be limited to John Maynard-Smith!)

Here is what Darwin wrote in the Descent of Man:

..as there is a limit to the powers of the memory, single words, like whole languages, gradually become extinct. As Max Müller has well remarked:—"A struggle for life is constantly going on amongst the words and grammatical forms in each language. The better, the shorter, the easier forms are constantly gaining the upper hand, and they owe their success to their own inherent virtue." To these more important causes of the survival of certain words, mere novelty and fashion may be added; for there is in the mind of man a strong love for slight changes in all things. The survival or preservation of certain favoured words in the struggle for existence is natural selection.

(emphasis added by me)

What was it Marcus Garvey said (albeit in a different context): "A people without knowledge of their past history is like a tree without roots"! But all said and done, Darwin would have loved the paper!

In a similar vein see: 

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history

And if you want a neat modern tree of Indo-European langauges, see the tree in this paper: 

Language-tree divergence times support the Anatolian theory of Indo-European origin

And as a takeaway project for readers, how many mistakes can you spot in this tree (published in Nature):
http://www.nature.com/nature/journal/v449/n7163/fig_tab/449665a_F1.html

Language and life: from evolution to Esperanto

Yesterday my wife was searching for sites that mention Darwin, Esperanto and Klingon and sent me some links she found: she does that kind of thing, claiming that it is a tongue-in-cheek effort to outdo me in obscure obsessions (but while she was obsessing, I was engaged in the ordinary family activity of watching the Poseidon Adventure with the children!).

One of the links was to a discussion on the EvC (Evolution versus Creationism) forum on the parallels between the evolution of languages and biological evolution. I was all fired up to make that the basis of a blog post, until I realised that the discussion was three years old. But now I have started, I might as well get on with it.

The link between evolution, Esperanto (which I speak) and Klingon (which I don’t) comes from a paragraph at the end of one of the posts:

Right, I'm just rambling now, but just this last point: its quite fun. It just occured to me that linguists have already made Chimeras! Klingon and Esperanto are good examples. Ah! And Klingon in fact gives us a really interesting example of a language where a cultural force (Trekkiness) makes a language that was deliberately made difficult to learn, very popular.

This draws out some interesting analogies, but I think, to some degree, misses the mark. Natural chimaeras do exist in biology, particularly in microbiology. Karen Nelson and her colleagues surprised the world back in 1999 with their description of the genome of Thermotoga maritinum, a bacterium, but with a quarter of its genes most closely related to equivalents in archaea (the third major branch of life alongside eukaryotes and bacteria).

However, the correct linguistic analogy here is not with an artificial language like Esperanto, but with English (a Germanic language), a natural language, which has borrowed a huge vocabulary from French (a Romance language) or perhaps with Yiddish, a Germanic language which has borrowed extensively from Hebrew and Slavic languages (an alternative heretical view from Paul Wexler is that Yiddish is a “re-lexified” Slavic language).

Esperanto, although offered considered artificial, is in fact based on European languages (a mashup of Romance, Germanic and Slavic), both in terms of vocabulary and syntax. The biological equivalent of Esperanto would be an genetically engineered organism that draws its gene set and regulatory networks from a range of existing organisms. As far as I can see nothing quite like that exists, although it soon will if the proponents of synthetic biology have their way.

The Klingon language (tlhIngan Hol in Klingon) is another kettle of fish—a made-up language deliberately created by linguist Marc Okrand to be as different as possible from existing languages in many important ways. Creation of the biological equivalent of Klingon, say with DNA and RNA polymerases nothing like anything seen in biology, would be a remarkable achievement, scarcely on the horizon, even for synthetic biologists.

Curiously, the discussion on EvC neglects the existing and historical literature on biological/linguistic evolution. The idea goes back to the mid-nineteenth century, when German language expert August Schleicher saw languages as organisms and started to borrow ideas from Linnean taxonomy in his linguistic classifications. Schleicher embarked on a genealogical classification of languages that incorporated a branching-tree model, uncannily similar to Darwin’s and Wallace’s later view of biological evolution.



In fact, even Darwin noticed the analogies. 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…

And then Schleicher read The Origin and immediately saw its relevance to his own work on languages. In 1863, he published a paper, Darwinism and the Science of Language, in which he draws a tree of indo-European languages and comments on Darwin’s work:

First, as regards Darwin’s assertion that species change in course of time, a process repeated time and again which results in one form arising from another, this same process has long been generally assumed for linguistic organisms… We set up family trees of languages known to us in precisely the same way as Darwin has attempted to do for plant and animal species.

In return, Darwin elaborated at length on the parallel between languages and species in The Descent of Man:

We find in distinct languages striking homologies due to community of descent, and analogies due to a similar process of formation. The manner in which certain letters or sounds change when others change is very like correlated growth. We have in both cases the reduplication of parts, the effects of long-continued use, and so forth. The frequent presence of rudiments, both in languages and in species, is still more remarkable.

Bizarrely, Darwin’s intellectual opponent, Swiss-born Harvard geologist Louis Agassiz accepted the analogy between biological and linguistic evolution, but was then driven to deny that Latin, Greek and Sanskrit shared a common ancestor, because he refused to accept biological evolution!

Anyhow, to return to Esperanto. Despite rumours of its demise, the language is still going strong and hit the news headlines recently after its alleged use in a Littlewoods advert.




In fact, whatever language that is, it ain’t Esperanto!

Information about Darwin and evolution can be found in Esperanto on the Vikipedio. And Klivo Lendon has translated the whole of the Origin of Species into Esperanto: la Origino de Specioj. In the Origin of Species in Dub, we used a slightly modified version of his translation of the concluding words of the Origin to close one of the tracks:

Estas grandiozeco en ĉi tiu perspektivo de la vivo, kun ĝiaj pluraj povoj, kiu originale enspiriĝis en kelkajn formojn aŭ unu; kaj en tio, ke dum ĉi tiu planedo orbitadis laŭ la fiksa leĝo de gravito, de tre simpla komenco, senfinaj formoj, plej belaj kaj plej mirigaj, evoluis, kaj evoluadas.

[and following on from previous post here is a Wordle view of the Origin in Esperanto]

I did, at one stage, manage to get someone to start translating the passage into Klingon, but the job was never finish and it would be hard to find anyone who could read it out! Any takers?

PS. John van Wyhe, of Darwin Online fame, has written a nice piece on The Descent of Words, which covers some of the above topics.