Thursday, July 31, 2008

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:

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:

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: 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):

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.

Wednesday, July 30, 2008

A new way of seeing The Origin and The Rough Guide to Evolution

I thank Carl Zimmer for pointing out the latest cool gadget on the net, Wordle, which lets you generate “word clouds” from text that you provide. The clouds give greater prominence to words that appear more frequently in the source text and, remarkably, you can feed it a whole book at a time!

Above is what you get from Darwin's Origin of Species (Click here to access the original word cloud from Wordle).

Darwin's main preoccupation with “species” is obvious! But many other important keywords crop up: varieties, forms, conditions, many, one, natural and selection...

And here is what I got from The Rough Guide to Evolution (original word cloud here).

Nice to see the key words I would expect to get. And “Natural” lining up parallel to “Selection” is cool too! Although (or should that be “however”) I am surprised how often I use "however" and "although"! 

Feel free to load all of Darwin’s other works into Wordle—you can access them all from Darwin online!

From so simple a beginning…

Why this blog? 

Well, the superficial answer is that I have just finished writing The Rough Guide to Evolution (well almost finished—a couple of chapters still left to edit, plus an introduction, glossary and index to put together) and now want to promote the book (due out late Dec or early Jan). But the deeper answer is that I want to share what I have learnt with a wider audience. 

In writing The Rough Guide to Evolution I have been exposed to the profound influence of evolutionary thinking on science and society as well as come face-to-face with Darwin’s life and works (which, despite Olivia Judson’s plea for us to stop talking about Darwinism, must surely be worth a mention in the run up to the Darwin 200 year!) 

In preparing the book, I have ended up visiting places other writers on evolution seldom go—looking at popular music inspired by Darwin and evolution, speculating what Darwin would have had on his iPod or preparing itineraries for the Darwinian tourist (do you know where to find Darwin memorialised in the local McDonalds?). I have been amazed by what I have learnt, but also puzzled at the survival of some common misconceptions as regards Darwin and evolution.

But writing The Rough Guide did not mark the start of my interest in Darwin and evolution—that began over twenty years ago, when I first read Stephen Jay Gould’s first collection of essays, Ever Since Darwin. I guess I have to admit my interest has over the years verged on the obsessional (I cited Darwin’s views on marriage in my wedding speech and my first two children are called Charles and Emma) and my own life has been intertwined with Darwin’s: I grew up in south London a few miles from Down House; my college in Cambridge occupies the house where Darwin’s wife lived after his death; my wife comes from Staffordshire, a short distance from the Wedgwood family home at Maer (where Darwin was married) and as I write this, I am sitting in Malvern, a few hundred yards from where Darwin stayed and less than a mile from where his daughter is buried.

In addition, both the book and this blog build on my experience during the last five years in organising our university’s Darwin Day event—an inter-disciplinary meeting aimed at celebrating Darwin’s life, work and influence on his birthday. In organising this meeting, I learnt of the wide influence of Darwin’s ideas and became acquainted with some of the UK’s foremost Darwin scholars. Our local Darwin Day events have covered a huge range of topics: the evolution of antibiotic resistance, of literary manuscripts (including The Origin of Species), of genomes and of the human face and gait. Plus we have had presentations on the Darwin Correspondence Project, evolutionary art, the end-Permian mass extinction, the hunt for the remains of HMS Beagle, the origin of Darwin's finches, the Wilberforce-Huxley debate. The three most memorable highlights of the meetings were:

  • Readings of anti-slavery prose and poetry from Erasmus and Charles Darwin by Rastafarian poet, Benjamin Zephaniah (who I had the pleasure of chaperoning for the day two weeks ago when he received an honorary degree from my university).
  • The creation of the Origin of Species in Dub with my Jamaican colleague, Dominic White.
  • A scintillating eye-witness account of the Dover trial from Nick Matzke, shortly after its conclusion.

As a professor of microbiology, I guess I possess the scientific credentials to write about bacterial and genomic evolution—in fact, I have written several research publications on the evolution of the bacterial flagellum (a favourite topic of the IDiot movement). But I also have a promiscuous curiosity, with an eye for the whimsical, which will guarantee that everyone, including even the most enthusiastic of Darwin fans will discover some new and unexpected in this blog. 

So, please sign up to the feed and join the ride and I’ll aim to deliver an average of one post a day!

PS: There are just 197 days to go until Charles Darwin's 200th birthday (12th February, 2009)!