The Rough Guide to Evolution

Evolutionary Chemistry: from Darwinism to drugs

2011-12-10T04:55:00.000-08:00

Most therapeutic drugs work by binding to proteins and interfering with their function. A key challenge for chemists working in the pharmaceutical industry is to discover new medicinal chemicals that fit important protein targets, rather like a key fits a lock. The traditional way to do this is to take a long hard look at the protein “lock” and then rationally design a chemical “key” that fits it. However, analogies with biological evolution have recently inspired an alternative approach: evolutionary chemistry.

Instead of attempting rational drug design, the evolutionary chemist simply generates a massive pool of variable DNA-like starting molecules (analogous to the variation that underlies biological natural selection). When these are then introduced to the target protein, only a small fraction of the molecules bind (the selection step). However, various chemical tricks then allow the chemist to amplify this population of molecules (the reproduction step). The amplified molecules are then used as the starting point for a subsequent round of selection and amplification. After several rounds of selection, the molecular mixture is greatly enriched for aptamers, molecules that bind tightly and specifically to the chosen target.

This evolutionary approach, called SELEX, has already led to the development of one useful drug, Pegaptanib (with the trade name Macugen), which has been licensed as a medicine to treat a common cause of blindness (age-related macular degeneration). But this is just the start: evolutionary chemistry is all set to deliver additional medically useful aptamers in the next few years that will target heart disease or cancer. For example, the US company Archemix has a developed lead aptamer, ARC1779, which acts as a potent, selective antagonist of von Willebrand Factor (vWF), with potential for use as an anticoagulant or antithrombotic agent (http://www.ncbi.nlm.nih.gov/pubmed/19479665). It is currently undergoing evaluation in clinical trials in patients diagnosed with acute coronary syndrome undergoing percutaneous coronary intervention.

For an unusual attempt to communicate how SELEX works (albeit applied to discovering new diagnostics rather than drugs), take a look at this video of the winning entry in the Dance you PhD competition of 2010!

Darwin's Pilgrims: The Video

2011-11-22T23:12:00.000-08:00

In February 2009, I hosted 'Darwin's Pilgrims": a visit to England by two Americans with links to the Dover Pennsylvania trial, Cynthia Sneath and Lauri Lebo, and Canadian Lit Hop artist Baba Brinkman to celebrate Darwin's 200th birthday. The trip involved a "pilgrimage" to Darwin-related sites and a series of performances in English cities, including the premiere of the Rap Guide to Evolution. Previous blog posts captured the spirit of the event

But this is the first time I have presented the complete video, covering trips to Malvern, Cambridge and London, even though I finished it a couple of years ago. I hope you enjoy the footage and the great music! For a bunch of non-believers, we spent a lot of time in churches!

http://www.youtube.com/watch?v=GCf3Kg3ekeY

Don’t want to believe in evolution?

2011-11-21T09:42:00.000-08:00

Is it possible to be a rationalist (a believer in the laws of logic) but not believe in evolution? Just about! But only just!

There are several philosophical show stoppers that bring rational argument to a halt.

Perhaps requiring the least mental gymnastics is the "Omphalos hypothesis", so-named after an 1857 book by English naturalist (and local Worcester man) Philip Gosse. Gosse argued that even if creation occurred from nothing, the creator would necessarily leave traces of previous existence that had never actually occurred. Although Adam was never hooked up to a placenta, he required a navel ("omphalos" in Greek) because it made him a complete human being. Similarly, God must have created trees with rings that they never grew and rocks with a fossil record of life that never actually existed.

This kind of thinking has drawn adverse responses from Catholic scientist Ken Miller and the "Zoo Rabbi" Natan Slifkin, who both reject it as depicting God as a dishonest charlatan. A secular response, Last Thursdayism, proposes, that by this logic, the world might just as easily have been created last Thursday, but with the appearance of age such as false memories and fictitious history books. There is even a parody religion, The Church of Last Thursday.

The first real philosophical show stopper is metaphysical solipsism: the belief that you, the reader, is all there is and that this blog and this author, this world and the evolution of life in it, are all just figments of your imagination. However, it is scarcely possible to hold this belief in your mind for even a minute and, as English philosopher Bertrand Russell once pointed out, solipsism

“is rejected in fact even by those who mean to accept it. I once received a letter from an eminent logician… saying that she was a solipsist, and was surprised that there were no others. Coming from a logician and a solipsist, her surprise surprised me.”

One modern variant on solipsism is the brain-in-a-vat idea, taken seriously by, among others, Berkeley philosopher Barry Stroud. In this scenario, your brain has been removed from your body, placed in a vat of life-sustaining liquid and your neurons hooked up to a supercomputer that provides you with a virtual reality indistinguishable from any “real” reality. So, the argument goes, if you are in a vat, all your conclusions about evolution in the real world are false. And, as you have no way of knowing whether you are in a vat or not, this leaves you free to doubt the reality of evolution.

But why suppose you ever had a body in the first place, why not suppose you are a disembodied brain created yesterday with false memories of a biological world built by evolution? Some cosmologists are seriously discussing the idea of Boltzmann brains, self-conscious entities that arise from random fluctuations in vacuum energy (named after Austrian physicist Ludwig Boltzmann, who suggested that the whole universe resulted from such a fluctuation). If the universe lasts long enough, such entities are inevitable, say the cosmologists. But why stop at a brain—viewing yourself as a Boltzmann-brain-in-a-vat breaks none of the laws of physics and also gets you off the hook of having to believe in evolution.

A more general case of the brain-in-a-vat idea is the simulation hypothesis. According to this viewpoint, popularized by the Matrix films, we are all living in a simulated reality, run on a computer powerful enough to create a internally consistent simulation, so detailed that it could not be distinguished from “real” reality. Swedish philosopher Nick Bostrom argues that it is more likely than not that we are living in such a simulation. His argument rests on the assumption that any sufficiently advanced civilization capable of creating simulations that contained intelligent individuals would be unlikely to restrict itself to a single simulation, instead, it would run billions of them. Thus, he asks, why suppose that we are the one civilization that develops the simulations rather than one of the billions run in simulation? Richard Dawkins points out that this merely pushes the need for evolution back stage as the only plausible source of the intelligences running the simulation.

Mathematical physicist Frank Tipler has controversially attempted to interweave cosmology, simulation and religion. He posits that as the universe comes to an end in a singularity, the computational capacity of the universe will outrun time, so that an intelligent civilization could run an infinite simulation within a finite time. Tipler borrows a term from Pierre Teilhard de Chardin to describe this final state of infinite information the Omega point. Recently, Tipler has come to identify his Omega point with God and to equate the associated infinite simulation with the resurrection of the dead. But why not assume we are already dead in Tipler’s sense, i.e. already living in his Omega point simulation and thus free to dispense with any direct evolutionary explanation for our own origins?

How is an evolutionary biologist to respond to all this? The obvious response is to adapt a line from George Orwell and say that you have to be a real philosopher to believe all that, no scientist could be so foolish! In fact, insofar as none of these scenarios is verifiable, they fall outside the realm of science and bring no additional explanatory power. So, you don't really have any excuses for dismissing evolution! Wise up and smell the cladogenesis!

Bio380 Human Evolution Genes and Genomes Bioinformatics Practical

2011-11-20T09:50:00.000-08:00

I have a bioinformatics practical class tomorrow and rather than hide it away, I thought I might as well share it with the world via this blog. Happy to receive comments on any mistakes or suggestions for improvements or additional reading.

Bio380 Human Evolution Bioinformatics Practical 2011

Follow this link to the entry for the FOXP2 chimpanzee protein:

http://www.uniprot.org/uniprot/Q8MJA0

Take a minute to explore the information on the page.

Q. What is the evidence that this gene is functional in the chimpanzee?
Q. Why is this entry called FOXP2_PANTR
Q. What does the Forkhead domain do?

Scroll down to the sequence at the bottom of the page

Q. What is unusual about the first third of the protein sequence?

Click on the pop-up Fasta view button

Q. What is a FASTA sequence?

Select the sequence that pops up and copy it to the clipboard. Then return to the previous window.

Open in a new tab and go to http://www.ncbi.nlm.nih.gov/BLAST/
Select “protein blast”

Q. What is BLAST?

Paste the FoxP2 FASTA sequence into the search box. Click on the algorithm parameters link, then tick the box indicating Filter low complexity regions

Q. What does this do?

Start the Blast search. The Blast search may take some time, so open a fresh tab and go to http://www.uniprot.org/
Search for “foxp2_human”
Spend some time exploring the information therein, while you wait for the Blast search to finish.

Return to the Blast search result. Scroll through the results. In the segment of the query spanning residues 241-698, how many differences does the chimp protein show from the following:
Orang utan (Pongo pygmaeus) Gorilla (Gorilla gorilla)
Lar gibbon (Hylobytes lar) Macaque (Macaca mulatta)
Horse (Equus cabellus) Mouse (Mus musculus)
Humans (Homo sapiens)

PS: use the sequence with header "FoxP2_Human"

Q. What differences do you find?
Q. How conservative or radical are the changes in amino-acid properties?

Go to http://www.nature.com/nature/journal/v418/n6900/full/nature01025.html
This paper suggests that the human sequence undergoes an additional post-translational modification compare to the chimp sequence

Q. What is this difference and how significant is likely to be?

Go to http://www.ncbi.nlm.nih.gov/omim
Search for FoxP2, then click on the first entry and explore the information therein, particularly that under the Evolution heading.

Q. Does this confirm or deny any of your previous conclusions?

Follow the link to this recent paper:
http://dx.doi.org/10.1016/j.jhevol.2007.07.006
Speed-read the abstract and introduction

Q. On the basis of this, would you expect Neandertals to be able to speak?
Q. What would you expect their FoxP2 gene to look like?

Follow this link to another recent paper
http://www.cell.com/current-biology/abstract/S0960-9822(07)02065-9

Q. What do you conclude?

Now read these blog entries

Q. Do your conclusions change?
Q. Are blogs are useful source of scientific information?

The genome of James Watson, Nobel laureate and co-discoverer of the structure of DNA can be found here: http://jimwatsonsequence.cshl.edu/

Follow these links

Then evaluate the following question:

Q. Is Jim Watson a black man?

And, finally, is Watson’s recent gaffe on race more likely to be due to:

A single gene disorder (the “butt-head racist gene”?)
A polygenic disoder (the “butt-head racist gene complex”?)
The racist culture in which he grew up?

Darwin and Mendel: The Great What If?

2011-11-06T03:02:00.000-08:00

Charles Darwin and Gregor Mendel were contemporaries. One of the great “what ifs” in the history of science is “what if Darwin and Mendel had met to discuss each other’s work, or, at least, had exchanged notes?”

The closest they came to meeting was in the summer of 1862, when Mendel visited England to attend the International Exhibition, a world fair held in South Kensington. Charles Darwin was less than twenty miles away, but their paths never crossed as the Darwins were stuck at home, nursing their son Leonard through scarlet fever.

Mendel read a German translation of Darwin’s Origin before publishing his seminal paper in 1865, but he did not see any connection between his work and Darwin’s. It has been claimed that Mendel’s paper sat on a shelf at Down House, unread, but this is just a myth. Although Darwin possessed two books that briefly referred to Mendel’s work, there is no evidence that he read the relevant sections; in one of the books, the pages are clearly uncut. Darwin leant one of these two books to his friend George Romanes, who used it to write an encyclopedia entry, priming another myth: that Darwin wrote about Mendel in the Encyclopaedia Britannica.

How close was Darwin to discovering Mendel’s laws of inheritance? As early as 1838, Darwin scribbled in his notes a question that, in retrospect, seems pregnant with potential: “Do races of peas become intermixed & gardener have hybrid seedlings?” In a letter written to Wallace in February 1866, Darwin recognizes that inheritance can be non-blending:

“My dear Wallace… I do not think you understand what I mean by the non-blending of certain varieties… I crossed the Painted Lady and Purple sweetpeas, which are very differently coloured varieties, and got, even out of the same pod, both varieties perfect but not intermediate.”

Furthermore, as Chinese plant scientist Yongsheng Liu has pointed out, Darwin describes experiments that are uncannily similar to Mendel’s, in his 1868 work Variation Under Domestication:

“Now I crossed the peloric snapdragon… with pollen of the common form; and the later, reciprocally, with peloric pollen. I thus raised two great beds of seedlings, and not one was peloric. The crossed plants, which perfectly resembled the common snapdragon, were allowed to sow themselves, and out of a hundred and twenty-seven seedlings, eighty-eight proved to be common snapdragons, two were in an intermediate condition between the peloric and normal state, and thirty-seven were perfectly peloric, having reverted to the structure of their one grandparent…”

The ratio, at 2.4 to 1, is close enough statistically to conform to an expectation of 3 to 1, so this might count as a glimpse by Darwin of Mendel’s first law.

But given that Mendel himself did not recognize the universality of his own work, it is unfair to expect Darwin or anyone else to do so, particularly in the face of less easily interpreted results from crosses in other species of plants and animals. Instead, the modern synthesis of Darwin's and Mendel's work had to wait until the mid-Twentieth Century.

Bibliography

The extent of Charles Darwin’s knowledge of Mendel by Andrew Sclater

The Monk in the Garden: The Lost and Found Genius of Gregor Mendel, the Father of Genetics by Robin Marantz Henig

The Rough Guide to Darwin

2011-10-12T02:00:00.000-07:00

As part of my attempt to put all my talks, whether for teaching or research online, I have put these two talks I gave yesterday in Oxford on to YouTube.

The Rough Guide to Darwin

http://www.youtube.com/watch?v=4yHHoCivCT0
Talk given to doctoral students in Oxford 11th Oct 2011
Covers Darwin's early life, including wayward youth, before discussing his major work, impact and legacy

Warning: Explicit discussion of Darwin and sexuality. "Let's get Downe and dirty with Darwin!"
Ignore grey screen YouTube snafu at very beginning. Soon sorts itself out.

From Darwin to Drug Resistance

http://www.youtube.com/watch?v=4iVQK9sYr2M
Talk given to doctoral students in Oxford 11th Oct 2011
Brief review of Darwin's legacy and evolutionary thinking in bacteriology.
Ignore grey screen YouTube snafu at very beginning. Soon sorts itself out.

Wallace: Darwin’s Rival or Ambassador?

2011-10-07T23:24:00.000-07:00

Alfred Russel Wallace (1823-1913) was born in Llanbadoc, near the Welsh town of Usk and grew up in Hertfordshire. He worked as an apprentice surveyor for the six years. During a brief spell as schoolmaster in Leicester, Wallace met entomologist Henry Bates and developed an interest in natural history. He worked for several more years as a surveyor/engineer. Then, inspired by Humboldt and Darwin, Wallace set off with Bates on an expedition to Brazil. In 1852, after four years collecting specimens and surveying the Rio Negro, Wallace set off back to England. At sea, a fire forced Wallace to abandon his specimen collection and, adrift, he spent ten days in a lifeboat, awaiting rescue.

Back safe in England, an insurance payment supported him while he wrote papers and forged links with naturalists, including Darwin. In 1854, Wallace embarked on an expedition to the Malay Archipelago (present-day Malaysia and Indonesia). During this six-year excursion, Wallace collected over a 100,00 specimens, discovered the discontinuity between the kinds of plants and animals found in the northern part of the archipelago and those found in the south (now called the Wallace line), and, crucially, hit upon the idea of evolution by natural selection independently of Darwin. Wallace’s experiences were written up as a lively travelogue, The Malay Archipelago.

During his middle years Wallace was beset with financial problems, which we largely alleviated in 1881 by a government pension that Darwin helped him obtain. In late life, Wallace extended his work on biogeography, became an early environmentalist and toured the US promoting evolution and natural selection. In old age, he settled in Broadstone, a suburb of Poole in Dorset. He is buried in Broadstone cemetery in a grave capped with a (rather phallic!?) fossil tree trunk and block of limestone.

Although often cast as Darwin’s rival, Wallace remained a loyal and lifelong supporter of Darwin, accepted Darwin’s claim to priority, dedicated The Malay Archipelago to Darwin and even entitled his major book on evolution Darwinism. Wallace was an altogether more colourful character than Darwin, but also rather more flakey. Wallace adopted spiritualism and unlike Darwin, expounded a progressive, teleological view of evolution, with the universe working towards the birth of the human spirit. He rejected natural selection as an explanation of the human mind, instead favouring interventions from the “unseen world of spirit”. He became a socialist and an opponent of smallpox vaccination. He got tangled up in disputes as to whether the earth was flat (in the Bedford Level experiment, he showed it wasn’t) or whether there were canals on Mars (he argued there weren’t). It is clear that, had Darwin died in South America, “Wallaceism” would have turned out quite different from Darwinism!

Further Online Reading

The Alfred Russel Wallace web page: http://www.wku.edu/~smithch/index1.htm

Alfred Russel Wallace page in Wikipedia

Image Rights

Wallace Grave George W. Beccaloni: Creative Commons Attribution 3.0 Unported

Open Education and Bio380 lecture on Neanderthals

2011-10-01T02:26:00.000-07:00

This academic year I have set myself the goal of making all my lecture available for all, in the public domain, via YouTube and maybe also Slideshare. The technical side of doing this is fairly straightforward (capture a screen movie via QuickTime), but the major hassle is ensuring and documenting permissions for all images. In my first attempt, I quickly realised that putting this information on the same slides as the images led to cluttered chaos, so I have piled them all up at the end of the talk.

It is unclear to me what the rules are about using material from published papers, but cannot see how authors would not want students to know about their work. So, in general, I am proceeding along the course of it is easier to apologise afterwards rather than ask permission in advance. If anyone objects to anything I have done, let me know and I will remove the offending material from the public domain. Also, if anyone has tips on how to do all this as efficiently and fairly as possible, please let us know via the comments. Ditto if you want to send words of encouragement!

It will be interesting to see if anyone other than my own students look at this stuff, but here we go, the game's afoot! Information wants to be free!

Here is my first lecture for this year from the Bio380 course: Waking the Dead, on Neanderthals and their influence on the modern human gene pool. Enjoy!

Slidecast via YouTube

http://www.youtube.com/watch?v=LdYURwBW7L4

Slides via Slideshare
Bio380 Human Evolution: Waking the dead
View more presentations from Mark Pallen

Great Read at Birmingham: Captain Kirkup and Chris Stringer

2011-10-01T02:22:00.000-07:00

AV material associated with this week's Great Read at Birmingham events.

Captain Kirkup on Evolution and Game Theory

Video of the talk and subsequent Q&A : http://www.youtube.com/watch?v=15gxMlQQ6AA

Slides to go with this: http://www.youtube.com/watch?v=RTk9_DlOpcQ
(Open these in a separate window as they will need to be manually paused and progressed forward: sorry no synchronised slidecast available)

Chris Stringer on The Origin of Our Species
Podcast of the talk via YouTube (publicly available): http://www.youtube.com/watch?v=QryLIaRORlU

Live tweets from Great Read at Birmingham opening event

2011-09-25T06:20:00.000-07:00

Here are the live tweets from Great Read at Birmingham opening event, sorted from earliest to latest

66. mjpallen: @mjpallen @greatreadatbham @unibirmingham live tweet under #GRAB2011 hashtag
65. mjpallen: #grab2011 ken miller up on stage; textbook author, daughter had to read his book at school; she gave up biology for history :-)
64. mjpallen: #grab2011 Ken testified in George and Pennsylvania; pervasive problem in US education and local politics; evolution in Ohio local politics
63. mjpallen: #grab2011 “vote for proevolution candidate you vote for sin“ 2 of republican presidential candidates creationist; creationist museums
62. mjpallen: #grab2011 antievolution bills pop up all over; problem coming to UK and Germany; Uk scientists published letter defending evolution
61. mjpallen: #grab2011 creationist conference in Malvern, UK; now describing Dover trial why lawsuit? 1st amendment http://t.co/VffLhax0
60. mjpallen: #grab2011 Ken lead witness in Dover trial Goals: show ID not science; show it is religion.
59. mjpallen: #grab2011 Conservative judge, so ID people thought easy time coming
58. mjpallen: #grab2011 > 9 hours cross examination: like PhD viva over and over again. Trial showed collapse of ID as credible theory; icons of ID trashed
57. mjpallen: #grab2011 ID claim: evo cannot make irreducibly complex systems; Michael Behe; missing part makes it nonfunctional; mousetrap example
56. mjpallen: #grab2011 flagellar components alone have no function say ID ppl. Only designer can make it. But even Darwin knew of change of function
55. mjpallen: #grab2011 testable to see if flagellar components can do anything if not all together; take away all but 10 parts of flagellum; still works
54. mjpallen: #grab2011 works as type III secretion system; counters irreducible complexity claim. ID is wrong! Cites Pallen and Matzke paper. testability
53. mjpallen: #grab2011 ID textbook Pandas and People; textbook evolved from creationist book with "creation" changed to ID; Barbara Forest testimony
52. mjpallen: #grab2011 1987 book changed because creationism deemed in law religious; Dover trail covered by BBC in War on Science; showing clip fr Nova
51. mjpallen: #grab2011 "judgment day" overblown rhetoric in nova show; received award; back to Dover case; Dec 20 2005; verdict ID not science!
50. mjpallen: #grab2011 struggle continues; "only a theory" book written to contain antirationalism antiscience; US lagging in science & math; Nature edop
49. pathogenomenick: Ken miller shows this great antievolution poster #GRAB2011 http://t.co/ur6sP88h http://t.co/ur6sP88h
48. mjpallen: #grab2011 whoisyourcreator.com nonsense on web; abundance of human fossils; Darwin's tree from Origin dead ringer for human evo tree!
47. mjpallen: #grab2011 new findings all the time; e.g. A. sediba; Matzke study on hominin brain size; sustained increase in brain size; no gap in record
46. mjpallen: #grab2011 chimp genome confirms predictions from elsewhere; chromosomes 46 in man; 48 in great apes; chr 2 is fusion of two chimp chromosome
45. mjpallen: #grab2011 fused chromsome has telomere in middle; 2 centromeres; one inactive; DNA seqs are facts; no ID explanation for this
44. mjpallen: #grab2011 evolution doesn't imply Dawkinsism acc to Miller. Dan Dennett says God/evo not compatible; Miller says yes; Dobzhansky was X-ian
43. mjpallen: #grab2011 nothing in biology makes sense in light of evolution; Dobzh also supported compatabilitism; evo is process of creation he said
42. mjpallen: #grab2011 pope says evolution God do mix! St Augustine wrote universe evolved; Miller says scientists question 5th C mystic; but Mendel monk
41. mjpallen: #grab2011 Mendel did expts even tho religious Augustinian; Darwin not religious; agnostic not atheist; said that theism and evo compatible
40. mjpallen: #grab2011 http://t.co/ANooECt7 Now cites Darwin first notebook tree; then closing words of Origin See also http://t.co/0gdYwcOP http://t.co/ANooECt7 http://t.co/0gdYwcOP
39. mjpallen: #grab2011 John Hawks now on the stage; science changes year by year; ancient genomes teach us about our own gene functions
38. mjpallen: #grab2011 focus on late stages in human evolution <1m years; Neanderthal means "brute" in vernacular;not fair; Darwin met Neanderthal fr Gib
37. mjpallen: #grab2011 Neander valley ripped up by mining; site was carpark; dug up in 2000 or so; found new remains; jigsaw fit to old bones; DNA found
36. mjpallen: #grab2011 Haekel drew mad trees; Homo stupidus for Neanderthals! now lots of evidence of culture; bone techn; shells w. holes for ornament;
35. mjpallen: #grab2011 cut feathers from birds; Neander hyoid bone suggests they talked; reconstruction of voice like Dame Edna/Steve Perry/Journey :-)
34. pathogenomenick: Lol at John hawks' impression of neandertals communicating: a rendition of don't stop believing by journey #GRAB2011
33. GreatReadatBham: @johnhawks just sang to us as Journey in describing the voice of Neanderthals #GRAB2011
32. mjpallen: #grab2011 Neander trading across long distances; cultural and complex. Vindija cave perfect site; shin bone yielded lots of DNA; 1.4x genome
31. GreatReadatBham: follow @mjpallen live feed #GRAB2011
30. mjpallen: #grab2011 more evidence from DNA than from all fossil record; some redheads MCR1 mutations unique to Neanders, not same as AMHs. not all red
29. mjpallen: #grab2011 Siberia at edge of range; low DNA variability among Neanderthals; genealogy possible; 100s of specimens; healed fractures seen
28. mjpallen: #grab2011 bony injuries in Neanders same as rodeo riders; amputation of arm; blind, lame; hunting large mammals; even rhinos; tough life
27. mjpallen: #grab2011 ambush hunters like cougars; chronic disabilities; osteoA; starch grains fr tooth calculus; lots of new science here, cannibalism?
26. mjpallen: #grab2011; men in one site all related; women not. enamel hypoplasia; starvation; dead kids; synchrotron scanning of life history
25. mjpallen: #grab2011 neanderthals live fast die young; Denisova cave in Altai mountains; rugged country; horse country; vertical limestone; few caves
24. mjpallen: #grab2011 David Reich calls it magical place; cold place zero deg C; like fridge; chimney over cave; size of lecture theatre with high roof
23. mjpallen: #grab2011 sheep layer on top; beneath that remains of human; bracelets; pinky bone has yielded best ancient DNA ever! But only 6% DNA human
22. mjpallen: #grab2011 79% DNA no hit Neander mitochondrial DNA variation low; Denisovan DNA is outgroup to humans and Neanderthals; tooth yielded same
21. mjpallen: #grab2011 does Neander and Denisovan DNA survive in humans? ABO polymorphisms for >2m years; not useful; need to find consistent patterns
20. mjpallen: #grab2011 Neanderthal genes more often resemble non-Africans; 3% of our genomes; skeletal evidence of mixture too from mandibular foramen
19. mjpallen: #grab2011 paper out any moment shows Denisovan DNA in Melanesians and Aborigines at 5% or less. Long distance away! Mystery.
18. mjpallen: #grab2011 we don't know what Denisovan skeletons looked like; missing popn movements; mixtures now established between AMH and archaics
17. mjpallen: #grab2011 evidence of admixture in East African pygmies, unkn source. Neanderthals and Denisovans form clade; how can this info be useful?
16. mjpallen: #grab2011 we can explain some heritability; mentions Galton @uniBirmingham alumnus; 300 genes now explain 20% of height variation
15. mjpallen: #grab2011 Hawks using Neander and Denisova genomes to discover new genes underling phenotypes in modern humans; showing genetic maps; HAR1
14. mjpallen: #grab2011 human accelerated region; humans very diff from other primates here; Denisova diff from humans and Neanders in HAR1! Moreancestral
13. mjpallen: #grab2011 Hawks now comparing his own genome to Neanderthals! His androgen receptor is Neanderthal and may make him bald!
12. mjpallen: #grab2011 Hawks now closing with ode to power of evolutionary thinking! and phew can take rest from live tweeting. Thanks for listening! Bye
11. GreatReadatBham: #grab2011 evolution organises knowledge, including complex, real-world data about Neanderthals per @johnhawks
10. pathogenomenick: @mjpallen: #grab2011 Hawks now comparing his own genome to Neanderthals!" impressively nerdy python output in slide :)
9. gilbertjacka: RT @pathogenomenick: Ken miller shows this great antievolution poster #GRAB2011 http://t.co/ur6sP88h http://t.co/ur6sP88h
8. GreatReadatBham: #grab2011 thanks to @johnhawjohn and Ken Miller for a great launch to GRAB 2011 on evolution @unibirmingham
7. pathogenomenick: Wonder if freshers know how lucky they are to see ken miller and John hawks in 1 day- not all biology lectures will be like that! #GRAB2011
6. scienceboy86: RT @GreatReadatBham: #grab2011 thanks to @johnhawjohn and Ken Miller for a great launch to GRAB 2011 on evolution @unibirmingham
5. GreatReadatBham: And thanks to all the great @unibirmingham students who came along! #grab2011
4. JoshRosenau: RT @mjpallen: #grab2011 "vote for proevolution candidate you vote for sin!" 2 of republican presidential candidates creationist; creationist museums
3. JoshRosenau: RT @mjpallen: #grab2011 new findings all the time; e.g. A. sediba; Matzke study on hominin brain size; sustained increase in brain size; no gap in record
2. johnhawks: RT @GreatReadatBham: #grab2011 evolution organises knowledge, including complex, real-world data about Neanderthals per @johnhawks
1. GreatReadatBham: #grab2011 next event Cap Benjamin Kirkup US Army on evolution of antibiotic resistance 5pm Tues 27/9 Poyntyng Large

Darwin's Shrewsbury

2011-09-25T05:57:00.000-07:00

Brief tour of Darwin sights in Shrewsbury for speakers at Great Read at Birmingham initiative. Sights include Darwin shopping centre, stained glass window of Darwin in McDonalds, Unitarian chapel, Darwin's schools and his birthplace (The Mount).

http://youtu.be/iI1a2qybmlU

Visiting Down House with Randal Keynes

2011-09-25T05:23:00.000-07:00

I have now received two VIP tours of Down House with Randal Keynes (Darwin's great-great-grandson) as tour guide. Randal's mellifluous voice, sharp intellect and wide-ranging knowledge of Darwin's life, science and family make these trips an unforgettable treat!

Last Friday I visited with three eminent American speakers at the Great Read at Birmingham initiative: Ken Miller, John Hawks and Captain Ben Kirkup. John Hawks has already blogged on the experience here: http://johnhawks.net/weblog/hawks/travel/down-house-visit-2011.html

Last February, I visited with Eugenie Scott from the NCSE.

Below are links to YouTube videos of both trips. Watch them and fall under Randal's spell as he guides us through Darwin's home and gardens, his life and family.

Tour of Down House with Randal Keynes for Great Read at Birmingham speakers

http://youtu.be/YPg5OanvSl4

Tour of Down House with Randal Keynes and Eugenie Scott

http://youtu.be/1EsAttZon0A

Relevant links

Ken Miller at the opening Great Read at Birmingham event

2011-09-24T12:17:00.000-07:00

The Evolution Wars: Why they continue, Why they matter, by Ken Miller

Ken Miller speaking at the opening event of the Great Read at Birmingham initiative, in the Barber Institute, University of Birmingham, England, 22nd September 2011

Watch a slidecast of Ken's excellent talk here:

Adam Tickell on Thomas Henry Huxley at Great Read at Birmingham event

2011-09-22T22:38:00.000-07:00

Professor Adam Tickell, PVC for Research and Knowledge Transfer, University of Birmingham, speaking at the launch of the Great Read at Birmingham initiative, September 22nd 2011

Video and text of the speech

Dear students,

I am sure that you have enjoyed the two excellent talks from our external speakers. First let me introduce myself. My name is Adam Tickell and I am Pro-Vice-Chancellor for Research here at the University of Birmingham, which means it is my job to ensure that the academics that lecture you produce the very best research that they can, on top of their excellent teaching.
Now, I know that Mark Pallen later in the term is going to tell you about Charles Darwin, who formulated the Theory of Evolution.

But it is worth stressing that Darwin was a retiring person who left the defence of his theory in the rough and tumble of Victorian society to others.

His most famous, and robust, advocate was a remarkable man called Thomas Henry Huxley, who was so vociferous in his defence of Darwin’s theory that he earned the nickname Darwin’s Bulldog.

Many of you will have heard of Huxley’s famous encounter in 1860 with the Bishop of Oxford, with the famous gibe about whether Huxley was descended from an ape via his grandmother or grandfather. In fact, that gibe was probably never uttered and one of the things you should learn in your three years is the importance of going beyond what is written in textbooks and newspapers and even academic publications and evaluating the evidence for yourselves!

But whatever the truth of that encounter, Huxley was a remarkable individual. Although he left school at the age of ten, he was a voracious reader and taught himself science, philosophy, history and German. An adventurer medic, who served as surgeon’s mate on the delightfully named HMS Rattlesnake, as it surveyed northern Australia and New Guinea. An expert on invertebrate comparative biology, authoring several papers that clarified some tricky taxonomy.

In 1854 Huxley took up a Chair of Natural History at the Royal College of Mines (now part of Imperial College), where for over thirty years he made valuable contributions to science and education in Britain. Huxley’s numerous achievements include his prescient classification of birds with dinosaurs (only recently recognized as correct), a treatise on the physical geography of the Thames valley, a classic book on crayfish and a biography of the Scottish philosopher David Hume. Huxley helped secularize schools, opened up adult education and transformed the academic activities of universities, viewing them as factories of new knowledge rather than storehouses of old. He even coined the word “agnostic”.

Huxley also left behind a treasure trove of aphorisms:

“After all, it is as respectable to be modified ape as to be modified dirt”

“Life is too short to occupy oneself with the slaying of the slain more than once”

“Science is organized common sense”

“The great tragedy of science is the slaying of a beautiful hypothesis by an ugly fact.”

From his biographer Edward Clodd, comes the greatest tribute of all: “It was worth being born to have known Huxley”!

But why, you may ask I am bigging it up so much for Huxley?

First, he is important in the history of ideas. Great ideas, like the theory of evolution, need to be argued over and Victorian society was, by no means, receptive to an explanation of life on earth that didn’t rely on God. Huxley’s advocacy of Darwin’s theory was powerfully influential.
Second, Huxley is important to the history of this University. Although the University on this campus dates back to 1900, before that, where the Birmingham Central Library now stands, there was something called the Mason Science College. This college was founded in 1875 by Sir Josiah Mason, a Birmingham industrialist and philanthropist, who made his fortune in making key rings, pens, and nibs. Mason College had several notable alumni before its incorporation into the University of Birmingham, including two prime ministers, Stanley Baldwin and Neville Chamberlain and a Nobel Prize winner Francis Aston.

But the key point is the foundation stone of Mason College was laid in 1880 by none other than Thomas Henry Huxley. So there is direct link between the institution in which you are enrolling and Darwin’s Bulldog! In Huxley’s honour, each year the university holds a Huxley Lecture, a tradition which goes back over a century. And of course, Darwin himself is built into the very fabric of our buildings, as a statue above the main entrance to the Aston Webb building.

Huxley gave a speech at the foundation of Mason College on the topic of “Science and Culture”. The speech makes interesting reading even today, packed full of sound bites and arguing that a scientific education was more important than a classical one. In it, Huxley delights in pouring scorn on the distinction between pure and applied research and suggests that the scientific method, which has proved so successful in the physical sciences, should be applied to the study of society.

My third reason for talking about Huxley is more personal.

Huxley died in 1895, but not before founding a family, that like the Darwin family was marked with a record of high achievement. He and his wife Henrietta had eight children. Like they Darwins they suffered the pain of losing a child in infancy. Two of Huxley’s daughters married the same man, the Pre-Raphalite painter John Collier, although not at the same time! You can see his paintings in the Tate gallery and Bridgman Art Library in London.

The most eminent of Huxley’s sons, Leonard, had six children by two wives. These included Julian Huxley – an evolutionary biologist who was not only the first director of UNESCO and a founder of the World Wildlife Fund, but also a eugenicist who – at least before the horrors of the holocaust – had unsavoury views about the rate at which what he called the lower strata reproduced. Julian was the brother of Aldous, who wrote Brave New World, and Andrew, who won the Nobel prize for his work on the physiology of nerves. One of Leonard’s grand-daughters, Angela Huxley, married a great-grandson of Charles Darwin, thus fusing these two notable lineages.

As I said, Thomas Huxley had eight children. His eldest daughter Jessica was lucky to survive scarlet fever when two years old, a disease which had killed her brother Noel. She grew up to marry Frederick Waller, who was architect to the Dean and Chapter of Gloucester Cathedral.

And now, I’m afraid, you will have to indulge me.

Jessie and Fred begat Oriana.

And Oriana begat Renée, Celia and Elvira.

And Renée wrote novels and married an Irish writer.

And I think you all might be able to guess where this is going when I tell you that the Irish writer was my grandfather Jerrard Tickell.

I have to say, I knew little of this as a child – my abiding memory of my grandmother is of her bringing packets of Rowntrees Fruit Gums when she came for Sunday lunch.

However, in the absence of fruit gums, I am very pleased to help kick off the Great Read at Birmingham initiative, which has so much to do with the legacy of Thomas Huxley and his closest associate, Charles Darwin.

I would like to close by quoting my great-great- great grandfather’s closing from his foundation speech, which calls on us, as his to praise Mason’s “crucial instance of wisdom” in establishing his Science College:

"In conclusion,” Huxley said, “I am sure that I make myself the mouthpiece of all present in offering to the venerable founder of the institution, which now commences its beneficent career, our congratulations on the completion of his work; and in expressing the conviction that the remotest posterity will point to it as a crucial instance of the wisdom which natural piety leads all men to ascribe to their ancestors."

Great Read at Birmingham

2011-09-08T22:55:00.000-07:00

This week, all the new undergraduates at the University of Birmingham (~6000 students) will receive a copy of the same book in their Welcome Packs and be asked to read it before arriving to encourage to engage with academic ideas and to create a shared experience for all new students. That book is The Rough Guide to Evolution!

The University believes that attending an institution like @uniBirmingham is about grappling with complex, multi-faceted, and even controversial ideas. As an academic community, the University welcomes and enjoys debate and hopes that this choice of book will stimulate discussion.

The idea behind the the Great Read at Birmingham initiative was proposed by the Vice-Chancellor, Professor David Eastwood, and is based on many successful similar programmes run in North America. But no British university has ever implemented a programme on this scale before!

There will be University-wide activities around the book during Welcome Week and the first term. Schools and departments will also use the book in study skills modules or in other ways.

Events kick off with Great Read at Birmingham Guest Talks in Welcome Week

Thursday 22 September 2011 15:30-17:00
As part of the Great Read at Birmingham initiative, "Rough Guide to Evolution" author Professor Mark Pallen welcomes two great speakers on evolution to our University, speaking back to back in Welcome Week in the Barber Institute Concert Hall.

This is open only to students at @uniBirmingham. Limited spaces available. First come, first served!

THE EVOLUTION WARS: WHY DO THEY CONTINUE AND WHY DO THEY MATTER?

Professor Ken Miller is a biochemist, textbook author, a Christian and an articulate spokesman for evolution. He played a key role laying out the evidence for evolution in the landmark Dover trial in 2005 and brings the full power of his engaging oratory to our first year students in his talk.

NATURAL SELECTION, NEANDERTHAL GENOMES AND THE MYSTERY OF DENISOVA CAVE
Professor John Hawks is an expert on human evolution and a keen blogger. He will bring us all up to date with evidence for and ramifications of interbreeding between humans, Neanderthals and the mysterious Denisovans with his fascinating talk.

Web page: http://www.birmingham.ac.uk/welcome/grab.aspx

Facebook: http://www.facebook.com/pages/Great-Read-at-Birmingham/245600152143735

Twitter: http://twitter.com/#!/greatreadatbham

Rough Guide to Evolution now available on Kindle and as eBook

2011-09-08T12:54:00.000-07:00

Great news! The Rough Guide to Evolution is now available to buy as a Kindle eBook here:

And as a Adobe eBook here:

http://www.penguin.co.uk/nf/Book/BookDisplay/0,,9781409358558,00.html

So, go on, indulge yourself and buy a copy now!

The evolution of biblical manuscripts

2011-08-30T12:44:00.000-07:00

In an ironic twist of fate that might infuriate creationist fundamentalist Christians, evolutionary thinking dominates scholarly studies of biblical manuscripts, particularly attempts to reconstruct original texts of the New Testament in the face of copying errors!

The New Testament of the King James Bible is a seventeenth-century English translation of the Textus Receptus, a Greek text prepared by Dutch theologian Erasmus in the sixteenth century from a few late-medieval manuscripts.

In the late nineteenth century, Birmingham-born theologian Brook Westcott and his Dublin-born collaborator Fenton Hort tried to improve on the Textus Receptus, publishing The New Testament in The Original Greek (1881), which incorporated information from a wide range of manuscripts, including the oldest fragments known at the time.

Crucially, they adopted a genealogical view of manuscript affiliation that directly parallels the tree-like branching descent with modification seen in Darwin’s theory of evolution. In their own words:

“All trustworthy restoration of corrupted texts is founded on the study of their history, that is, of the relations of descent or affinity which connect the several documents.”

However, Westcott and Hort also recognized the potential for horizontal transfer between lineages, viewing the Byzantine textual lineage as a fusion of the two earlier traditions (the western and Alexandrian).

In the early twentieth century, British theologian Burnett Streeter proposed a theory of local texts, in which textual traditions diverged as a result of geographical separation – a parallel with allopatric speciation in evolutionary biology.

From the 1950s onwards, American biblical scholar Ernest Colwell attempted to bring quantitative methods into the analysis of New Testament textual traditions. Cladistic approaches borrowed from evolutionary biology now sit at the cutting edge of studies of New Testament manuscripts: exponents include David Parker, a theologian at the University of Birmingham, Gerd Mink at the Institute for New Testament Textual Research, Münster, Germany and among American scholars, Stephen Carlson.

So, in conclusion, evolutionary thinking even illuminates the origins of the text of the Bible!

Some Darwinian poetry to make you smile

2011-08-24T12:14:00.001-07:00

Charles Darwin's grandfather Eramus Darwin was a brilliant but seriously bonkers chap--a kind of 18th Century English Rasta. You can read all about his interests on the relevant Wikipedia page, but I cannot help sharing these few lines from the Temple of Nature in which he sees the fruits of past (sensual or sexual) pleasure in geological sediments? What was he smoking?

"HEAR, O ye Sons of Time! your final doom,
And read the characters, that mark your tomb:
The marble mountain, and the sparry steep,
Were built by myriad nations of the deep, --
Age after age, who form'd their spiral shells,
Their sea-fan gardens and their coral cells;
Till central fires with unextinguished sway
Raised the primeval islands into day; --
The sand-fill'd strata stretch'd from pole to pole;
Unmeasured beds of clay, and marl, and coal,
Black ore of manganese, the zinky stone,
And dusky steel on his magnetic throne,
In deep morass, or eminence superb,
Rose from the wrecks of animal or herb;
These from their elements by Life combined,
Form'd by digestion, and in glands refined,
Gave by their just excitement of the sense
The Bliss of Being to the vital Ens.

"Thus the tall mountains, that emboss the lands,
Huge isles of rock, and continents of sands,
Whose dim extent eludes the inquiring sight,
ARE MIGHTY MONUMENTS OF PAST DELIGHT;
Shout round the globe, how Reproduction strives
With vanquish'd Death, -- and Happiness survives;
How Life increasing peoples every clime,
And young renascent nature conquers Time;
And high in golden characters record
The immense munificence of NATURE'S LORD!

For a roots reggae reinterpretation of some of Ras D's anti-slavery poetry, have a listen at this rough and ready bit of whimsy I cooked up a few years ago with a Jamaican friend.

http://pathogenomics.bham.ac.uk/Dub/free_OriginMP3s/12.%20Bonus%20Track%20Ras%20Darwin.mp3

Mary Anning: Fossil hunter extraordinaire

2011-08-11T23:36:00.000-07:00

Anyone off to Lyme Regis for their holidays should spare a thought for Mary Anning (1799-1847), who hailed from this English coastal town. Geologist and historian of science Hugh Torrens describes her as “the greatest fossilist the world ever knew”.

Left destitute by the death of their father in 1810, Mary and her brother Joseph turned to collecting fossils from the local coastline (now styled the Jurassic Coast: see recent Guardian pics) in the hope of selling them to amateur collectors. At the age of twelve, just a few months after her father's death, Mary made a spectacular find that brought her to the attention of the scientific community: the first complete skeleton of an ichthyosaur (a giant "fish lizard") ever found. Although Joseph had found the skull (shown here) a year before, Mary was responsible for locating the rest of the fossil.

Her subsequent discoveries included the first plesiosaur (her own drawing shown here) in 1821 and a remarkable specimen of an extinct ray-finned fish, Dapedium politum, in 1828. Anning also described the first complete skeleton of a flying reptile, the pterosaur Dimorphodon macronyx.

Later in life, Anning’s fame secured her financial support from the British Association for the Advancement of Science and honorary membership of the Geological Society of London—the only woman in an exclusively male club.

The chief impact of Anning’s work was that her fossils established beyond doubt the concept of extinction, proving that some extinct animals looked nothing like anything alive today. Anning died from breast cancer in her forties and is buried with her brother at St Michael’s Church, Lyme Regis, where a stained-glass window is dedicated to her memory.

Galton or Weismann first to continuity of the germ-plasm?

2011-08-11T06:05:00.000-07:00

While researching the previous post, my curiosity was piqued over a comment by Frank Darwin about his relative Francis Galton (who BTW was apprenticed here in Birmingham). While researching The Rough Guide to Evolution, I soon realised that many quotations are misattributed (here is one telling example) or quoted out of context and so good scholarship requires that one actually dig out the source and confirm that it says what it is purported to say. In the last few years, and even more so since I wrote the book, this has become a whole lot easier, largely thanks to the Google books initiative.

So, let's return to what Frank wrote:

“But in science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs. Not the man who finds a grain of new and precious quality, but to him who sows it, reaps it, grinds it and feeds the world on it.”

which I and others have cited in the context of his father's theory of evolution.

But if you look at the whole paragraph, it is clear that Frank was talking about an article in the Macmillan's Magazine by Francis Galton and the fact that Galton got to the theory of germ-plasm and what is often called the Weismann barrier earlier than August Weismann (who got there in the 1890s and is generally credited with priority):

"With regard to the machinery of reproduction the essay is remarkable for containing what is practically identical with Weismann’s continuity of the germ-cell, and Galton’s priority is acknowledged by that author. But in science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs. Not the man who finds a grain of new and precious quality, but to him who sows it, reaps it, grinds it and feeds the world on it. This is true of this very Macmillan’s Magazine article. Who would know of these admirable views on Hereditary Genius and Eugenics, if this were Galton’s only utterance? This is the grain which has increased and multiplied: and it is to-day familiar nutriment, and is now assiduously cultivated by the Eugenics Education Society. But if Natural Inheritance, and Hereditary Genius had not been written; if the papers on eugenics had not appeared, and especially if he had not convinced the world of his seriousness by creating a eugenic foundation at University College, where his friend Professor Karl Pearson carries on the Galtonian traditions—why then the paper in Macmillan would have counted for very little. But it was not quite unnoticed. By my father it is referred to in the Variation of Animals and Plants under Domestication. Galton was encouraged and reassured by Darwin’s appreciation of his work: his words in Hereditary Genius are, “I feel assured that, inasmuch as what I then wrote was sufficient to earn the acceptance of Mr. Darwin . . . the increased amount of evidence submitted in the present volume is not likely to be gainsaid.” He was characteristically generous in owning his debt to the author of the Origin of Species, and characteristically modest in the value he ascribed to my father’s words."

So, does this mean the textbooks (and wikipedia) need re-writing? Should Weismann be demoted in the pantheon of the history of science? Well, a few moments with Google turns up the article that Frank was discussing and here is the relevant passage:

"If we examine the question from the opposite side, a list of life-long habits in the parents might be adduced which leave no perceptible trace on their descendants. I cannot ascertain that the son of an old soldier learns his drill more quickly than the son of an artizan. I am assured that the sons of fishermen, whose ancestors have pursued the same calling time out of mind, are just as sea-sick as the sons of landsmen when they first go to sea. I cannot discover that the castes of India show signs of being naturally endowed with special aptitudes. If the habits of an individual are transmitted to his descendants, it is, as Darwin says, in a very small degree, and is hardly, if at all, traceable.

We shall therefore take an approximately correct view of the origin of our life, if we consider our own embryos to have sprung immediately from those embryos whence our parents were developed, and these from the embryos of their parents, and so on for ever. We should in this way look on the nature of mankind, and perhaps on that of the whole animated creation, as one continuous system, ever pushing out new branches in all directions, that variously interlace, and that bud into separate lives at every point of interlacement.

This simile does not at all express the popular notion of life. Most persons seem to have a vague idea that a new element, specially fashioned in heaven, and not transmitted by simple descent, is introduced into the body of every newly-born infant. Such a notion is unfitted to stand upon any scientific basis with which we are acquainted. It is impossible it should be true, unless there exists some property or quality in man that is not transmissible by descent."

(NB I should at this stage distance myself from all the racist twaddle proffered elsewhere in Galton's article).

Well, there is a nice separation between embryo and soma here, and even a hint of Dawkin's Selfish Gene / river of DNA out of Eden. And it appears that Weismann did himself write to Galton in 1889:

"You have exposed in your paper an in idea which is in one essential point nearly allied to the main idea contained in my theory of the continuity of germ-plasm"

But another Google books link reveals an interesting analysis by Bulmer in his biography of Galton. Bulmer's verdict is that Galton foreshadowed Weismann "only in a weak sense", because his language and ideas were less precise.

Nonetheless, perhaps Galton should be edged into the textbooks and encyclopaedias on this? Or is this just another example of "precursorism"? What do you think?

Darwin: serial plagiarizer or revolutionary genius?

2011-08-11T03:48:00.000-07:00

Stephen Jay Gould once joked that “precursoritis" (or should it be "precursorism") is the bane of historiography. Nonetheless, it is clear that there were precursors to Darwin in describing natural selection and other components of his theory of evolution.

In 1941, Conway Zirkle wrote a remarkable (and long) paper Natural Selection before the "Origin of Species" (available in full via Google books) in which he collated and discussed over two dozen descriptions of natural selection and associated ideas that pre-dated Darwin.

Although most of these earlier authors lacked Darwin’s clear conception of the implications of natural selection for the origin of species, some of their passages are strikingly prescient of Darwin’s ideas. Take, for example, this passage from French freethinker Jean-Jacques Rousseau (1712–78):

… children, bringing with them into the world the excellent constitution of their parents, and then confirming it by the same exercises which first produced it, would thus acquire all that strength and vigour, of which the human frame is capable. Nature in this case treats them exactly as Sparta treated the children of her citizens: those of them who came well formed into the world, she renders strong and robust, and destroys all the rest...

Or this passage from the German philosopher Johann Gottfried Herder (1744–1803):

In short, every species extends its possession of the Earth in proportion to its capacity, cunning, strength, or courage… the whole creation is at war, and the most opposite powers are found so close to each other… Each strives with each, as each is pressed upon; each must provide for his own subsistence, and defend his own life. Why acts Nature thus and why does she thus crowd her creatures one upon another? Because she would produce the greatest number and variety of living beings in the least space, so that one crushes another,and an equilibrium of powers can alone produce peace in the creation.

In the Temple of Nature, Charles Darwin’s grandfather, Erasmus Darwin provides a poetic description of the Struggle for Existence, culminating in a graphic rhyming couplet:

In ocean's pearly haunts, the waves beneath
Sits the grim monarch of insatiate Death;
The shark rapacious with descending blow
Darts on the scaly brood, that swims below;
The crawling crocodiles, beneath that move,
Arrest with rising jaw the tribes above; 60
With monstrous gape sepulchral whales devour
Shoals at a gulp, a million in an hour.
—Air, earth, and ocean, to astonish'd day
One scene of blood, one mighty tomb display!
From Hunger's arm the shafts of Death are hurl'd,
And one great Slaughter-house the warring world!

While in Zoonomia he obliquely references Sexual Selection and Natural Selection:

The birds, which do not carry food to their young, and do not therefore marry, are armed with spurs for the purpose of fighting for the exclusive possession of the females, as cocks and quails. It is certain that these weapons are not provided for their defence against other adversaries, because the females of these species are without this armour. The final cause of this contest amongst the males seems to be, that the strongest and most active animal should propagate the species, which should thence become improved.

Two other early descriptions of natural selection have been unearthed since Zirkle’s paper. One comes from a densely written inaccessible book (Principles of Knowledge: see review here) by one of Darwin’s heroes, the geologist James Hutton, who rejected evolution of species, but described natural selection:

If an organised body is not in the situation and circumstances best adapted to its sustenance and propagation, then, in conceiving an indefinite variety among the individuals of that species, we must be assured, that, on the one hand, those which depart most from the best adapted constitution, will be most liable to perish, while, on the other hand, those organised bodies, which most approach to the best constitution for the present circumstances, will be best adapted to continue, in preserving themselves and multiplying the individuals of their race.

The second comes from an unlikely source—Natural Theology (1809), where William Paley (the irritant that gave rise to Darwin's pearl) proposed natural selection, only later to reject it:

There is another answer which has the same effect as the resolving of things into chance; which answer would persuade us to believe, that the eye, the animal to which it belongs, every other animal, every plant, indeed every organized body which we see, are only so many out of the possible varieties and combinations of being, which the lapse of infinite ages has brought into existence; that the present world is the relict of that variety: millions of other bodily forms and other species having perished, being by the defect of their constitution incapable of preservation, or of continuance by generation.

Charles Darwin acknowledged the role of earlier thinkers such as Geoffrey St. Hilaire in very first edition of the Origin. He also clearly drew inspiration from agriculturalist Sir John Sebright, who he cites several times for his work on breeding. However, Darwin fails to mention in publication a passage penned by Sebright in 1809

The greatest number of females will, of course, fall to the share of the most vigorous males; and the strongest individuals of both sexes, by driving away the weakest, will enjoy the best food, and the most favourable situations, for themselves and for their offspring. A severe winter, or a scarcity of food, by destroying the weak and the unhealthy, has had all the good effects of the most skilful selection.

even though Darwin alluded to it in his C notebook of1838:

Sir J. Sebright — pamphlet most important showing effects of peculiarities being long in blood.++ thinks difficulty in crossing race — bad effects of incestuous intercourse. — excellent observations of sickly offspring being cut off so that not propagated by nature. — Whole art of making varieties may be inferred from facts stated

Two others were credited only in later editions of the Origin for their prior descriptions of natural selection. William Wells was a Scottish-American physician who described the role of natural selection in the evolution of humans in the appendix to an essay on dew published in 1818, while Patrick Matthew was a Scottish fruit grower who proposed natural selection as mechanism of evolution in his On Naval Timber and Arboriculture (1831) over a quarter-century before Darwin and Wallace.

So, it is clear that Darwin was not the first to propose all the ideas that made up later came to be known as the Darwinian Theory of Evolution. However, any attempt to detract from his revolutionary achievements by arguing that he was simply a serial plagiarist or intellectual scavenger is as senseless as claiming that Shakespeare was a second-rate playwright merely because he reused some old existing plotlines!!

It was Darwin’s genius to weave many disparate ideas (such as variation under domestication, Malthusian population pressure and the oddities of biogeography) into a unique combination that is still largely thought to be accurate today, while other combinations of similar concepts, for example, Lamarck's or Spencer's theories of evolution, have been abandoned.

In addition, Darwin was able to articulate these ideas, and the evidence for them, with such unprecedented clarity and forcefulness that within a few short years most naturalists and much of the wider society had come to accept biological evolution as a fact, proven beyond reasonable doubt. Furthermore, there is an abundant documentary evidence trail to show that Darwin generally did not rely on precursors in his thinking, and where he did, he acknowledged it.

Peter Bowler, Professor of History of Science at Queen’s University Belfast makes the point forcefully in his book Evolution, the History of an Idea:

“Simple priority is not enough to earn a thinker a place in the history of science: one has to develop the idea and convince others of its value to make a real contribution. Darwin's notebooks confirm that he drew no inspiration from Matthew or any of the other alleged precursors.”

Darwin’s own son Frank Darwin made a similar point in the first Galton Lecture in 1914 (albeit moaning about Weismann gaining credit when Francis Galton had priority over on the continuity of the germ cell) :

“In science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs. Not the man who finds a grain of new and precious quality, but to him who sows it, reaps it, grinds it and feeds the world on it”

The last word on this subject should go to Darwin himself, who in an 1860 letter to Rev. Baden Powell (father of the scoutmaster) states that

"No person, not even the most ignorant, could suppose that I meant to arrogate to myself the origination of the doctrine that species had not been independently created. The only novelty in my work is the attempt to show how species become modified, and to a certain extent how the theory of descent explains certain large classes of facts; and in these respects I received no assistance from my predecessors."

Sources and related links

Minimum requirements for a PhD thesis

2011-08-08T09:27:00.001-07:00

I am getting tired of having to examine sub-standard PhD theses and then having to write the same old comments in the report on the thesis, so I have decided to set down the minimum requirements for a PhD thesis. Anyone who is contemplating asking me to examine a thesis should read these and comply with them or stop wasting my time. And be warned, you don't want to get me cross by wasting my time with substandard theses that are an insult to my intelligence!

As most of those who read this blog are also academics, please feel free to add comments if you think I have been too harsh or lenient or when there are additional requirements that you would usually insist on. These requirements apply primarily to theses in molecular bacteriology and related disciplines and may not all apply in other disciplines.

The thesis as a whole
The thesis should comply with the regulations as regards margin sizes, order of front material and length of abstract. It should have been carefully proofread by someone experienced in the use of scientific English before submission.
The front material should include a declaration that all the work presented was performed by the student except where indicated and should list all the cases where the work presented in the thesis was not performed wholly by the student. Text from a multi-author paper, particularly if not primarily written by the student, should not be reproduced verbatim in the thesis without a clear description of where the student’s work ended and that of other authors began.
My suspicions will be aroused if the thesis is too short (<200 pages) or too long (>300 pages). It is almost never necessary to present a thesis that spans two volumes.
All sections of the thesis should comply with the usual conventions of scholarly scientific discourse. The thesis should be free of typographical, spelling, grammatical and stylistic errors. A consistent approach to typography (e.g. to fonts, use of capital letters in headings, justification of margins, line spacing and marking of paragraph breaks) and to formatting of references should be adopted throughout.
Latin binomials and gene names should be used correctly and italicised throughout, including in the table of contents and references. “E. coli” or any other species name should be treated as a singular noun. Proper use of nouns derived from Greek and Latin should be employed throughout, with care taken to avoid use of plural forms of the noun when the singular form is appropriate (e.g. do NOT write “the mitochondria is a bacteria”, “the culture media used was LB”). The terms “sequence homology” and “sequence similarity” should not be confused. Similarly, never say ORF when you mean protein-coding sequence or CDS!
Abbreviations should be spelt out at first use and defined in a list of abbreviations. Abbreviations should be avoided in the title of the thesis.
Throughout the thesis, when statements of scientific fact are made that have not been derived from the student’s own experimental work, they should be backed up by reference to peer-reviewed scientific publications. These may include review articles for subjects peripheral to the main thrust of the thesis, but should include original articles, with due credit for historical priority, for mainstream topics. References should be up-to-date and it should be clear that the student has kept up-to-date in the field right up until the submission date.
For the thesis as a whole and for each chapter, there should be a clear separation between the kind of material that belongs in the Introduction, in the Methods section, in the Results section and in the Discussion. There should be minimal repetition. In particular, the Introduction and Discussion sections of each results chapter should contain just enough reference to material introduced earlier in the thesis to maintain a narrative flow, but must not repetitively restate basic facts.
The Introduction
The Introduction should include extensive reference to the scientific literature, present a logical flow of ideas, with no non-sequiturs, and provide a rationale for the work that has been done. This need not consist solely of long stretches of text; instead, whenever appropriate, tables and figures should be used to convey the student’s understanding and knowledge of the field as succinctly as possible. The Introduction should be drafted in such a way as to provide evidence that the student had read and understood most of primary literature relevant to the thesis, rather than relying heavily on a handful of review articles. The student should also demonstrate an ability to make critical judgements on key issues. Irrelevant material should be excluded and students should from refrain from attempting encyclopaedic coverage.
In general, diagrams and figure legends should not be reproduced unchanged from papers and certainly not without the copyright holder’s permission. Instead these should be drafted from fresh or at least re-drafted to demonstrate that the student has grasped the concepts and facts illustrated or tabulated and has incorporated up-to-date findings and nomenclature.
The Introduction should close with a statement of aims and/or research questions waiting to be addressed at the outset of the project.
Methods and Results
Enough details should be provided of materials and methods so that someone expert in the field could reproduce the work—preferably without burrowing through a long chain of references Wherever possible, all data and analyses should be provided in the thesis, so that their veracity can be checked by the examiner. Where this might interrupt the narrative flow of the thesis, these should be presented in an appendix or, if datasets are large, they should be provided on a DVD.
Each line of experimental work should be given its own results chapter, with a brief introduction, a results section and a discussion section for each of the chapters. Methods specific to a given chapter might also feature in a dedicated methods section, although a Methods chapter dedicated to commonly used methods could be included.
The introduction to each results chapter should describe and justify the rationale for the programme of experimental work described in that chapter. Careful consideration should be given to what appears in the Introduction to the thesis as a whole and what should be reserved for the introduction to a specific results chapter, so as to present the most logical flow of ideas, while avoiding repetition. The narrative describing the progress of experiments and interpretation of data should deliver a simple and coherent description of the work undertaken. Long verbose descriptions of results should be avoided—instead, material should be summarised effectively in tables, figures or in crisp and lively prose.
Students should avoid over-interpretation of results—the student should distinguish between situations where the data are merely consistent with a given interpretation and where they actually provide convincing evidence for it.
Results from experimental controls should be presented whenever relevant. The number of replicates carried out for each experiment should be described and the reproducibility of techniques discussed. The potential for technical errors should be discussed together with the steps that the student took—or might have taken—to avoid them.
Where, for historical or financial reasons, the student has not adopted the most direct or most informative approach to a problem, this should be explained carefully. The student should attempt to evaluate the importance and shortcomings of each piece of work, in terms of how far it tells us new things about the world, represents an achievement in method development and/or provides resources for subsequent work.
Discussion
The thesis should conclude with a single Discussion chapter, which evaluates whether the body of research presented has fulfilled the aims set out at the end of the Introduction, examines how it fits into the broader scientific picture and assesses whether it is likely to stand the test of time in the light of recent technical and scientific developments. Repetition of material presented earlier in the thesis and a simple description of what has been done should be avoided.
Viva
During the viva, the candidate must demonstrate knowledge and understanding of all the work that has been done and the background to it. In addition, the student must demonstrate a sound grasp of basic concepts in microbiology and molecular biology (e.g. transcription, translation, the genetic code, Koch’s postulates), such as could be obtained from relevant undergraduate textbooks, and a critical approach to the definition of key terms (e.g. virulence, pathogenicity island).

Remember: the examiner's word is final and there is no appeal against academic judgment, so get it right before you submit the thesis and certainly before you start the viva!

Survival of the aptest: evolutionary turns of phrase

2011-07-28T08:48:00.000-07:00

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

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

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

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

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

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

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

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

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

Darwin’s captain: Robert FitzRoy

2011-07-28T07:16:00.000-07:00

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

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

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

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

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

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

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

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

2011-07-22T10:31:00.000-07:00

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

Why am I happy?

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

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

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

So, why am I disappointed?

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

So how have Rough Guides responded?

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

And why does it matter if the Rough Guide to Evolution is now out of print?

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

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

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

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

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

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

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

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

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

An experiment

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

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

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

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

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

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

The game's afoot--get tweeting!

Another five star review

2011-07-21T06:56:00.000-07:00

5.0 out of 5 stars A Grand and Glorious Guide to Evolution,

By John Kwok (New York, NY USA)

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

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

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

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

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

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

Charles Darwin senior: cause of death and place of burial

2011-07-20T03:28:00.000-07:00

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

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

Dave asked me to explain why I thought that it was almost certain that CD Senior died from meningococcal disease. The clues stem from the passage I mentioned earlier:

"About the end of April, Mr. Darwin had employed the greatest part of a day in accurately dissecting the brain of a child which had died of hydrocephalus, and which he had attended during its life. That very evening he was seized with severe head-ach. This, however, did not prevent him from being present in the Medical Society, where he mentioned to Dr. Duncan the dissection he had made, and promised the next day to furnish him with an account of all the circumstances in writing. But the next day, to his headach there supervened other febrile symptoms. And, in a short time, from the hemorrhagies, petechial eruption, and foetid loose stools which occurred,his disease manifested a very putrescent tendency."

The clues are two-fold:

1. meningococcal disease is commonest in childhood and adolescence, so it is one of the likeliest causes of a fatal infection of the brain in a child

2. The petechial haemorrhages are a give-away: as recent clinical guidelines state: "fever plus a petechial rash is meningococcaemia until proven otherwise"

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

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

Last resting place of Charles Darwin rediscovered

2011-07-17T22:54:00.001-07:00

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

But I am talking about the first Charles Darwin, the naturalist's uncle, who lived from 1758 to 1778. This Charles Darwin was the eldest son of Erasmus Darwin and Mary Pole (who incidentally died from an overdose of morphine). Here is what the younger Charles Darwin wrote about his uncle:

"His [Erasmus's] eldest son, Charles (born September 3, 1758), was a young man of extraordinary promise, but died (May 15, 1778) before he was twenty-one years old from the effects of a wound received whilst dissecting the brain of a child. He inherited from his father a strong taste for various branches of science, for writing verses, and for mechanics. "Tools were his playthings," and making machines was one of the first efforts of his ingenuity, and one of the first sources of his amusement." *

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

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

Dr. [Erasmus] Darwin was able to reach Edinburgh before Charles died, and had at first hopes of his recovery; but these hopes, as he informed my father, "with anguish, soon disappeared. Two days afterwards he wrote to Wedgwood to the same effect, ending his letter with the words, God bless you, my dear friend, may your children succeed better." Two and a half years afterwards he again wrote to Wedgwood, I am rather in a situation to demand than to administer consolation."

A more detailed description of CD the elder's death strongly supports a diagnosis of meningococcal disease:

"About the end of April, Mr. Darwin had employed the greatest part of a day in accurately dissecting the brain of a child which had died of hydrocephalus, and which he had attended during its life. That very evening he was seized with severe head-ach. This, however, did not prevent him from being present in the Medical Society, where he mentioned to Dr. Duncan the dissection he had made, and promised the next day to furnish him with an account of all the circumstances in writing. But the next day, to his headach there supervened other febrile symptoms. And, in a short time, from the hemorrhagies, petechial eruption, and foetid loose stools which occurred,his disease manifested a very putrescent tendency."

Charles Darwin the elder is also notable because Erasmus Darwin claimed, after his son's death, that Charles had discovered the usefulness of digitalis/foxglove before William Withering, who is usually credited with this discovery (and who used to work here in Birmingham). This led to a longstanding feud between these two members of the Lunar Society of Birmingham.

And now to title of this post.

In a previous post (The evolutionary tourist in Edinburgh), I claimed that Charles Darwin senior was buried in St. Cuthbert’s Church, located in Lothian Road, at the eastern end of Princes Street. Now I have just received an email from veteran Wikipedian Dave Souza, who writes:

"Today an anon editor helpfully pointed out that we'd both got the wrong kirk, the Duncan family vault was in the graveyard of the Chapel of Ease built for St Cuthbert's Church on the South side of Edinburgh, and later renamed the Buccleuch Parish Church Burying Ground. It's sited at 33 Chapel Street, not far from the Old College of the University of Edinburgh."

Click on the two links above to see quite how far apart the two sites are.

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

A five-star review

2011-07-17T05:57:00.000-07:00

This from Howard Kornberg via the Amazon.co.uk site:

5.0 out of 5 stars Everything Evolutionary, 6 May 2009

Howard Kornstein (UK) - See all my reviews

This review is from: The Rough Guide to Evolution (Rough Guide Science/Phenomena) (Paperback)

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

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

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

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

2011-07-05T23:28:00.001-07:00

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

There were a couple of reasons for this

I felt the need to re-focus my efforts on my "day job" in bacterial pathogenomics rather than devote myself to things Darwinian and evolutionary
I also did somewhat max out on Darwin and evolution during the Darwin bicentenary year.

However, in the last eighteen months, I have had some success in getting grants in and papers out (although papers still lagging behind grants), what with an MRC grant on Acinetobacter genomics, a BBSRC grant on the chicken gut microbiome and a major stake in an NIHR research centre for surgical reconstruction and microbiology. Plus the blog and twitter feeds associated with my research group (@pathogenomenick and @mjpallen) are now well established. So, there is now enough slack in the system for me to return to this blog!

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

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

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

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

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

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

Rap Guides to Aquatic Biology

2010-01-13T23:38:00.000-08:00

Here are two biological takes on Lonely Island's "I'm on a Boat" (on YouTube) that might amuse you. The first parodies Craig Venter's marine voyages, the second the ecology of ponds!

Origin of Species: new online variorum

2009-11-24T23:41:00.000-08:00

Yesterday, the world celebrated the sesquicentennial of the publication of The Origin of Species. But it is worth stressing that there was not one "Origin of Species", but six different editions produced in Britain alone during Darwin's lifetime. Fifty years ago, in time for the hundredth anniversary of the first publication, Morse Peckham produced a variorum text, which showed the variant readings between the six editions. However, Peckham's variorum has always been difficult to follow and is decidedly old-fashioned with its literal use of cut and paste.

To celebrate the 150th anniversary, my colleague at the University of Birmingham, Barbara Bordalejo, working with John van Wyhe at Darwin Online, has produced a fantastic new digital online variorum, which is much more flexible and user-friendly than Peckham's. Take a look at it here: http://darwin-online.org.uk/Variorum/index.html

For more details, see the editor's introduction: http://darwin-online.org.uk/Variorum/Introduction.html

At last, all of us can follow the evolution of The Origin!

First thoughts on "Creation"

2009-09-27T12:01:00.000-07:00

Yesterday afternoon, I went to see "Creation", the new film out centred on Charles Darwin's relationships with his wife and his daughter, Annie. I guess I am in a unique position in writing this as I am sitting about two hundred yards from Montreal House in Malvern, where Annie died in 1851 and I live on land that was once part of the estate of the Lodge, the house in which Darwin and his family (including Annie) stayed for a few months in 1849.

But geographical proximity is not the real issue here--I have been far too close psychologically and intellectually to Darwin and his life, and Annie's role in it, for far too long to ever approach the movie as most viewers will. With that in mind, I was preparing to be disappointed, but in fact for the most part I enjoyed the movie, as did my children, because I remembered to tell myself that it was a work of imagination not historical biography.

There are lots of minor historical inaccuracies in the film, but as Eugenie Scott has pointed out, "Creation" will bring many aspects of Darwin's life, particularly his family life, to a wider audience, including the tragic loss of his daughter here in Malvern and the misery of his chronic illness. The acting is great, particularly Martha West as Annie and real husband and wife team Paul Bettany and Jennifer Connelly as Charles and Emma. And the lavish cinematography is a treat.

There were two things in the film I did not like. One was the way in which it flitted from one part of Darwin's life to another, back and forth across the decades. I would have preferred a simpler narrative. But more problematic was the way in which the film inter-linked Darwin's various struggles, intellectual and emotional, when as far as I am aware they were never linked. For example, there is no evidence that the death of Annie Darwin had any effect whatsoever on Darwin's work on the Origin of Species. And it is unclear to me whether differences in attitude to religion between Charles and Emma Darwin, which were clearly raised as an issue around the time of their marriage, persisted as a problem in their relationship as late as the film suggests, i.e. into the late 1850s. I may be wrong and will have to look into this, but the level of emotional intensity on Darwin's part in the film on this issue strikes me as off-kilter.

But all-in-all, a good film which I advise you to go and see! At the very least, it will banish the tired icon of Darwin as merely an old man with a bushy beard!

The evolution of the Origin revisualised

2009-09-09T08:22:00.000-07:00

A few years back, Peter Robinson and Barbara Bordalejo, both textual scholars, came to work here in Birmingham. They, along with local New Testament scholar David Parker, have been at the forefront of efforts to exploit computers in textual scholarship and use the kind of phylogenetic approaches used on biological sequences to unravel the patterns of evolutionary branching among manuscripts. Peter and Barbara had worked extensively on Chaucer's Canterbury Tales, but shortly after her arrival here, Barbara was searching for a fresh project. David Parker, perhaps rather provocatively for a Reverend Professor, suggested that Barbara, Peter and I work together on the evolution of Darwin's Origin of Species, treating Darwin's publications as "textual genomes". We did some preliminary work on this and submitted a proposal to the Arts and Humanities Research Council, but alas it was not funded...

But the best proof that one is working on something worthwhile is when someone else comes up with the same idea quite independently (cf Wallace on Ternate!). So it is gratifying to see two examples of people doing the kind of analyses and developing the same kind of visualisation tools that we envisaged:

The (En)tangled Word Bank is the work of computer scientist Greg McInerny and London-based visual artist Stefanie Posavec (see Science Blog Post) and is certainly pretty, although whether it can be used by scholars to unravel Darwin's thinking is unclear.
Ben Fry's The Preservation of Favoured Traces looks more useful and provides a more intuitive view of changes, but sadly appears to lack a zoom tool, so that one can only gain a "God's eye" view of the whole text, without been able to look closely at individual sections.

But both projects provide a fascinating proof of concept and it would be great to see them integrated more fully into a project like Darwin Online, where they could make a real contribution to Darwin scholarship!

And now a request please! Can either or both projects now incorporate the two forerunners of the Origin: Darwin's 1842 Pencil Sketch and his 1844 essay (both transcribed here), so we can see quite how much of the Origin was written over ten years before Darwin started on his "big book" Natural Selection (which should also be included). It always amazes me how much of the structure of Darwin's argument was laid out in those two manuscripts from the 1840s, but it would be nice to see visually how many of the words are in common too.

I have outsold my advance!

2009-09-08T09:09:00.000-07:00

Just a brief note to report the good news that I have outsold the advance against royalties that I was given for my book, The Rough Guide to Evolution and have just had an additional payment. I think only about half of Rough Guides do this at all and I was quietly hoping to do so within the first year of publication. But the fact that I have done so in the first six months is good news indeed (as is the fact that a French translation courtesy of Edition Tournon is in the offing!).

Thanks to all of you who bought the book and/or recommended it!

The Darwin Song Project

2009-09-06T00:42:00.001-07:00

I have to confess that there is not much folk music in my iTunes library, but last week my copy of the Darwin Song Project CD arrived. And I am impressed!

The Darwin Song Project is the fruit of a frenetic collaboration between eight of the world's top folk artists, who composed the 17 songs of the album during a week-long retreat in a Shropshire farmhouse and then performed them in the new Theatre Severn in Darwin's home town Shrewsbury in March this year.

Even though it incorporates the Annie hypothesis, my favourite song on the album is the Dylanesque "Kingdom Come", which investigates how differences in religious belief divided Charles from his wife Emma. It opens with what must be a unique first line--an account of the life cycle of ichneumonid wasps, parasitic wasps that lay their eggs in the flesh of living caterpillars and which troubled Darwin!

Another delight is this mock-Country number, "We'll him down". I dedicate this YouTube link to all my friends from Dover, Pennsylvania (Lauri, Cyndi, Tammy and Nick)! Let's hope their Creationist compatriots realise that the song is ironic!

Videos for three other songs from the project are also available on YouTube. You can find out more about the project from its website and from this BBC Radio 4 show. And you can place your order for the CD here.

[Review of the album from The Guardian.]

Lamarck, Darwin and the Tree of Life

2009-08-17T11:42:00.000-07:00

There has been some interesting discussion in the blogosphere as to whether Lamarck beat Darwin to the Tree of Life metaphor:

I am due to speak on this subject at the upcoming Society for General Microbiology meeting in Edinburgh, so I was intrigued to read these posts.

Here is my own quick-fire rather disorganised contribution to the argument, quickly cribbed off my Powerpoint slides, with a shameless inattention to sources:

It seems that Pallas did indeed come up with this metaphor in words before Lamarck and Darwin, even though he didn't draw a tree. This is what he wrote in

Elenchus Zoophytorum (1766):

At omnium optime Arboris imagine adumbraretur Corporum organicorum Systema, quae a radice statim, e simplicissimis plantis atque ani- malibus duplicem, varie contiguum proferat truncum, Animalem & Vegetabilem; Quorum prior, per Mollusca pergat ad Pisces, emisso magno inter haec Insectorum laterali ramo, hinc ad Amphibia; & extremo cacumine Quadrupedia sustineret, Aves vero pro laterali pariter magno ramo infra Quadrupedia exsereret.

“But the system of organic bodies is best of all represented by an image of a tree which immediately from the root would lead forth out of the most simple plants and animals a double, variously contiguous animal and vegetable trunk; the ﬁrst of which would proceed from molluscs to ﬁshes, with a large side branch of insects sent out between these, hence to amphibians and at the farthest tip it would sustain the quadrupeds, but below the quadrupeds it would put forth birds as an equally large side branch.”

Augustin Augier in 1801 deserves credit for this description of a phylogenetic tree:

‘‘A figure like a genealogical tree appears to be the most proper to grasp the order and gradation of the series or branches which form classes or families. This figure, which I call a botanical tree, shows the agreements which the different series of plants maintain amongst each other, although detaching themselves from the trunk; just as a genealogical tree shows the order in which different branches of the same family came from the stem to which they owe their origin.’

see http://www.bio.sdsu.edu/faculty/archibald/Archibald08JHBonline.pdf for a depiction of Augier's tree. In fact, this article in general is an excellent source of information on the whole issue of evolutionary trees and in particular draws attention to a paleontological chart from 1840 that looks a lot like an evolutionary tree.

Chambers in his Vestiges of the Natural History of Creation has something that looks a bit like an evolutionary tree, although it is probably best described as a developmental tree. Follow this link: http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=A2&pageseq=215

Note that Darwin's first depiction of an evolutionary tree is arguably not the oft-quoted "I think" figure, but these "coral of life" depiction that appears a few pages earlier in his notebook.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=CUL-DAR121.-&pageseq=27

And finally, Wallace hit on the metaphor independently. One can dispute whether his tree-like diagrams on the classification of birds really count as evolutionary trees, but his verbal description in the article he published in 1855 clearly pre-date Darwin's published descriptions of the tree of life and add the appealing analogy of the human vascular system:

On the law which has regulated the Introduction of New Species. Annals and Magazine of Natural History, including Zoology, Botany, and Geology 16: (September): 184-196.
“We are also made aware of the difficulty of arriving at a true classification, even in a small and perfect group;—in the actual state of nature it is almost impossible, the species being so numerous and the modifications of form and structure so varied, arising probably from the immense number of species which have served as antitypes for the existing species, and thus produced a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak or the vascular system of the human body. Again, if we consider that we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others, the whole difficulty of the true Natural System of classification becomes apparent to us.”

Interestingly, Wallace is now buried under a huge fossilised tree:

[NB we all know it is really a huge fossil phallus ;-) ]

But the last word goes to Darwin, with his melodic prose:

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.

And for those of you who like reggae, try those "beautifiul ramifactions" Jamaican-styleee...

Happy Birthday to this Blog! And hello to a new blog on bacterial pathogenomics

2009-08-06T07:53:00.000-07:00

Last week, while I was away on vacation in France, this blog had its first birthday. During this last year, the blog has plotted the completion, publication and reception of my book The Rough Guide to Evolution, but has covered much more besides in its 193 postings—from evolutionary tourism to flagellar biology. According to Google Analytics, the blog has received over 23,000 visits from 137 countries!

It is unclear quite how well the book is selling, as I am still awaiting accurate figures for the first half of the year, but I have been told that worldwide sales so far are likely to be around 10,000-10,500, which means that there is a good chance I will have just outsold my advance against royalties in the first six months of the book's life!

But now I must confess that a change is at hand. I have to re-focus my efforts on my "day job" as a microbiologist, so, although I won't be closing this blog, I will be posting less often here. Instead, I will be using the insights into blogging that I have gained from this blog to drive forward a new blog Pathogens: Genes and Genomes, which will convey the excitement generated by the collision of high-throughput sequencing and clinical and environmental bacteriology. Feel free to join us there and to raise a glass to The Rough Guide to Evolution, book and blog!

Rough Guide to Evolution in Nature again this week

2009-08-01T08:46:00.000-07:00

The Rough Guide to Evolution features again in the prestigious scientific journal Nature this week, thanks to Eugenie Scott (executive director of the US National Center for Science Education), who recommends it as Summer reading:

"The 200th anniversary of Charles Darwin's birth, plus the 150th anniversary of the publication of his best-known book, On the Origin of Species, make 2009 the year to learn about evolution. Mark Pallen's The Rough Guide to Evolution provides a concise summary of what you need to know: a brief history of the idea that all living things share common ancestry, a complete survey of the mechanisms of evolution and a solid summary of how life originated and then adapted through time to a changing planet. He livens up the story with literary, musical and cultural references so that you never feel you are being told to eat your vegetables. Alas, it is not only non-specialists who don't have a firm grasp of the strength of theory and data supporting the modern understanding of evolution — many scientists outside the field of evolutionary biology struggle too. This entertaining handbook will bring anyone up to date."

Thanks Genie!

Baba Brinkman's Rap Guide to Evolution now available in MP3

2009-08-01T08:00:00.000-07:00

Canadian Lit Hop artist Baba Brinkman has just released his new album, The Rap Guide to Evolution, and as a special promotion, the album can be downloaded for free during the month of August in MP3 format. Follow the links from Baba's web page to get your copy: http://www.babasword.com/

Although Baba is not charging for downloads, he would appreciate donations to cover production costs.

The Rap Guide to Evolution is a hip-hop exploration of modern Evolutionary Biology. The album is based on the stage show of the same name, which appears at the Edinburgh Fringe Festival this August. Follow Baba's progress at the Fringe via his own blog for the event (Darwin on the Fringe) and be sure to go see the show if you are visiting the Fringe.

From Digbeth watesland to darwin-inspired arts space

2009-07-21T03:13:00.000-07:00

Just picked this up from the Behind Closer Doors project website:

Two artists from Birmingham are part of an unusual project which has transformed a Digbeth waste-ground into a darwin-inspired exhibition space.

In the wake of the revered scientist’s bicentenary, Helen Grundy and Anne Guest are set to launch Unnatural Selection on 30th July at the Rea garden in Floodgate Street. The project is supported by Arts Council funding and the artists’ collective Behind Closed Doors.

Unnatural Selection aims to replicate Darwin’s methods of using his garden as a laboratory to observe nature, collect samples and carry out experiments.

There is a related workshop on saturday 1st August from 12-3pm.

Hat tip: Lewis Bingle.

PCR in song and video!

2009-07-13T22:03:00.000-07:00

The polymerase chain reaction revolutionised molecular biology twenty years ago, opened up the study of ancient DNA from extinct organisms, and similar DNA amplification methods underpin the current revolution in high-throughput sequencing, so it is great to see molecular biology company BioRad celebrating this wonderful technique with a couple of hilarious catchy tongue-in-cheek songs.

Baba Brinkman at the Cambridge Darwin festival

2009-07-13T07:25:00.000-07:00

I ducked out of the Cambridge Darwin festival for a variety of reasons, including severe cash flow problems after renovating my house. But Baba Brinkman went and from various sources I hear he had a great time there.

Here he is rapping to David Attenborough in King's College.

Another stray link between Darwin and the Wire...

2009-07-07T08:41:00.000-07:00

Perhaps my earlier attempts to draw up links between the Darwins and the cult TV show The Wire were rather fanciful...

But how about this for a more tangible link (left): Darwin's daughter Annie in the forthcoming film Creation is played by 10-year-old Martha West, daughter of Dominic West, who played Jimmy McNulty in The Wire!

Everything connects...

I was suckered too...

2009-07-07T08:36:00.000-07:00

In case anyone is thinking I have been too rough in publicising quite how many people have fallen for the Annie myth, let me confess, I was suckered by this story too and that is why I am quite so cross to see reality not match up to mythos.

Here am I, in that piece of whimsy, the Origin of Species in Dub, falling for the myth that Annie's death influenced Darwin's evolutionary writings:

http://www.infection.bham.ac.uk/BPAG/Dub/Videos/Track8.html

The spread of the Annie myth: it's worse than I thought

2009-07-07T02:34:00.000-07:00

My posting on the spread of the Annie hypothesis has elicited this interesting posting on "the Angry Bitter Atheist myth"--the idea that a dismissal of religion purely on intellectual grounds isn't enough; instead atheists must also be angry at God for some tragedy or other. In fact, I have tried to avoid calling the "Annie hypothesis" (the claim that Annie's death triggered Darwin's final loss of faith in Christianity), the "Annie myth", for fear of drawing legal action (c.f. the bogus legal action against Simon Singh's use of the term "bogus").

But it is hard to avoid the conclusion that this story has been propagated so widely because it appeals to some human need for an emotional narrative, and so in that sense the term "myth" is appropriate. Plus, those who want to persuade Christians and other religious believers that Darwin was a thoroughly good chap for his work on evolution will wish to avoid the idea that his ideas on evolution had anything to do with his own loss of faith (even though they didn't have much to do with it)--far safer to blame it on a personal tragedy!

Anyhow, on further investigation, I have found a few more examples of the uncritical acceptance of the Annie myth:

Larry Moran and Niles Eldredge netted as uncritical devotees of the Annie myth in a single posting! Eldredge may be good on science, but he swallows both the "removed what little was left of his religious faith" myth and states as fact rather than wild guess that Annie died from tuberculosis.
This article and podcast on Annie Darwin from the Oxford Dictionary of National Biography: "Darwin's experience of his daughter's life and his bereavement had a double significance for his thinking. Recent scholarship (Moore) has shown that it was probably the final factor in his gradual rejection of Christian faith"
Plus this article from the same source on Darwin himself: "Moore reassessed Darwin's religious faith, showing that while he remained a pillar of his rural parish, the deaths of his father in 1848 and daughter Annie in 1851 finally led him to give up Christianity."
Evolution 101 by Randy Moore
More proof that even Carl Zimmer isn't infallible.
The Mini Oxford Handbook of Clinical Medicine, which ascribes Annie's death to typhoid fever rather than the usual tuberculosis.
Dinesh D'Souza's blog entry linking Annie's death and Darwin's loss of faith with the problem of evil
Telegraph columnist George Pitcher in his article "Charles Darwin was not the father of atheism"
David Livingstone in a chapter in Where Science and Christianity meet lends credence to Moore's account of the Annie myth, but with more balance than most commentators, and he also goes for "typhoid fever" as cause of death.
Even creationists are suckered in! http://www.evolutionthelie.com/history-of-science/evolutions-fatal-fruit-nurturing-charles-darwin/

It seems I really do need to get this paper finished and published to prevent this nonsense spreading further!

The surprising spread of the Annie hypothesis

2009-07-05T22:56:00.000-07:00

As I have pointed out in previous posts, I have been working on a paper on the unsubstantiated claim that his daughter Annie's death led to Darwin's abandonment of Christianity. Once the paper is press, I will present my analysis of just what flimsy evidence the "Annie hypothesis" was based on by its originator, James Moore. But for now, let's just take a look at how far this modern "Darwin myth" has spread and how many people have suckered by it (even Carl Zimmer has been taken in!).

Note, I use the term "myth" not so much in the sense of "false story" although I do think it is false, or at least unfalsifiable, but more because so many people wish to draw moral lessons from it. Most people seem far more comfortable with the idea that Darwin gave up Christianity only after something as traumatic as the death of a daughter, rather for the mostly dry intellectual reasons he cites in his Autobiography.

Anyhow, here is a draft of a table from the paper, showing quite how far the "Annie hypothesis" has spread. If you know of any additional striking examples of its presentation in print or on screen, please let us know by adding comments.

Table 1 Selected examples of the Annie Hypothesis in print, on screen and online

	Year	Quotations and context
In Print
1859 and All That: Remaking the Story of Evolution-and-Religion James R. Moore	1982	"Perhaps it was the "bitter and cruel" death in 1851 of ten-year-old Annie, his favourite child, just a month after he had read the moral challenge to that doctrine in Francis Newman's "excellent" spiritual Autobiography Faith, that prompted Darwin, as he later said, to give up Christianity once and for all."
Of Love and Death: Why Darwin 'gave up Christianity', James Moore	1989	See text of paper for discussion (in preparation).
Darwin, Desmond and Moore	1991	Account of Annie’s illness and death interspersed with interpolations about Darwin’s loss of faith.
Charles Darwin, Voyaging. Janet Browne.	1995	“His sense of God had virtually disappeared along with his daughter Anne.”
Rebecca Stetoff, , Charles Darwin And The Evolution Revolution	1996	"Darwin's own Christianity, never very deeply held, gradually eroded as he worked out his theory of natural selection; the remnants of his faith were wiped out entirely by the suffering and death of his daughter Annie in 1851. Later in life he described himself as an Agnostic--one who questions but does not flatly deny the existence of God. ... [Annie's] death destroyed the last lingering remnants of Darwin's Christianity."
Evolution, The Triumph of an Idea, Carl Zimmer	2001	“He could no longer believe that Anne’s soul was in heaven, that her soul had survived her unjustified death. It was then, 13 years after Darwin discovered natural selection, that he gave up Christianity”
Annie's Box Randal Keynes	2001	"After Annie's death, Charles set the Christian faith firmly behind him."
Emma Darwin, Edna Healey	2001	“The death of Annie confirmed Charles’s loss of faith”
Darwin and the Barnacle, Rebecca Stott	2003	“Perhaps he [Darwin] wanted to say what he was beginning to feel himself… that after death there was nothing—no God waiting to scour Annie’s record book…”
Darwin’s Origin of Species, A Biography, Janet Browne	2006	“Annie’s death may have finally tipped Darwin into disbelief”
The Reluctant Mr. Darwin, David Quammen	2006	“The death of Annie in 1851, following the death of his father three years ealier, marks an important point in Darwin’s long, quiet disengagement from religious belief and spirituality”
Darwin Loves You: Natural Selection and the Re-enchantment of the World, George Levine	2008	“But the hard experience of Annie’s death certainly had larger implications for his attitude toward religion, as James Moore has argued in his essay on this subject.” “That Anna [sic] died on Shakespeare’s birthday is a coincidence (is “intelligent design” an option?) of which I wish to take advantage, as I return to Darwin’s comment that Shakespeare had come to nauseate him.”
Rebel Giants, David Contosta	2008	“ For Charles, the death of this beautiful, kind, and beloved child was the last blow to any faith he had in God.”
“Call the Black Horses” from The Darwin Poems by Emily Ballou	2009	"You can safely put God to bed now/the way you can’t your daughter anymore./Tuck the sheets so tight he cannot move/and lock the bedroom door."
On Screen
The Voyage of Charles Darwin, BBC series	1978	Darwin voiceover on religion over funeral scene
The Devil's Chaplain, BBC documentary	1991	Moore stands over Annie's grave proclaiming that it was here that Darwin lost his Christian faith
Darwin's Dangerous Idea, PBS documentary	2001	Darwin family in black attends church, Darwin stays outside; Moore claims Annie's death destroyed Darwin's Christianity; claim repeated on PBS website
Darwin's Struggle: The Evolution of the Origin of Species BBC documentary	2009	Narrator states that after Annie's death "With his own belief in a Christian God already shaken, Darwin now severed his ties with traditional faith"; Moore links Darwin's statements in the Autobiography about the doctrine of damnation to anger at Annie's death. Moore claims links between Annie's death and "face of Nature" statements in Chapter III of Origin of Species, culminating in declaration "she suffered at Easter that others may live"
Did Darwin kill God? BBC Documentary	2009	Conor Cunningham bizarrely claims Annie died from cholera. Nick Spencer claims Annie's death once and for all finishes Darwin's Christian faith.
Creation (movie)	2009	Director's Statement: "The Darwin we meet in CREATION is a young, vibrant father, husband and friend whose mental and physical health gradually buckles under the weight of guilt and grief for a lost child. Ultimately it is the ghost of Annie, his adored 10 year-old daughter who leads him out of darkness and helps him reconnect with his wife and family."
Online
Wikipedia (accessed in 2009)		http://en.wikipedia.org/wiki/Development_of_Darwin "With Annie's death Darwin lost all faith in a beneficent God and saw Christianity as futile. "

David Hume's influence on Charles Darwin

2009-06-27T00:32:00.001-07:00

As a result of helping my son Charlie with his homework, I have just (re-)read David Hume's Dialogues Concerning Natural Religion, which is a superb examination of the arguments for and against the existence of God.

I was surprised to see how similar some parts of the Dialogues are to some parts of Darwin's own writings. I spent a bit of time Googling away to see if anyone else had noticed this, but can't find much evidence that anyone has. I found this one paper:

David Hume and Charles Darwin, William B. Huntley, Journal of the History of Ideas, Vol. 33, No. 3, Festschrift for Philip P. Wiener (Jul. - Sep., 1972), pp. 457-470 http://www.jstor.org/stable/2709046

But this is concerned with the influence on Darwin of Hume's Treatise of Human Nature and An Enquiry Concerning Human Understanding and does not even mention Dialogues Concerning Natural Religion!

Daniel Dennett in Darwin's Dangerous Idea: Evolution and the Meanings of Life does describe some connections between Hume's thinking in the Dialogues and Darwin's evolution by natural selection. But in a chapter is entitled "Hume's Close Encounter", Dennett's point is "look how close Hume got to Darwin". Interpreting Hume in the light of Darwin strikes me as a cart-before-horse argument, reminiscent of David Lodge's fictional thesis on the influence of T. S. Eliot on Shakespeare. Instead, we should be looking for Hume's influence on Darwin!

So, is there any evidence that Darwin was familiar with Hume? The answer is yes, in abundance! Darwin kept a list of books to be read and Hume's works feature several times:

Hume's Essay on Human understanding {(Sometime)}
Hume's Essay
Life of David Hume — (new Edit) by Bell recommended by Erasmus
Hume's life of himself with corres: with Rousseau
Humes dialogues & Nat. Hist of Religion
Hume Hist. Engl. Vol 5 & 6.
7th & 8th Vol of Hume's England — Admirable
Hume's Essays. 2 Vol.
2. vols of Hume's History
Hume's Hist of England. to end of the beginning of Elizabeth.

Plus Darwin lists Burton's Life of David Hume twice in his list, the second time with the verdict "poor". In fact, although I haven't totted up all of the books Darwin read, it seems likely that Hume is among the most common authors, if not the most common author, in Darwin's list!

So it is clear that Darwin read Hume's Dialogues, but was his later writing influenced by them? Well Dennett is right to point out how close Hume got to some of Darwin's key ideas:

Hume on the Struggle for Existence and War of Nature
"And why should man, added he, pretend to an exemption from the lot of all other animals? The whole earth, believe me, PHILO, is cursed and polluted. A perpetual war is kindled amongst all living creatures. Necessity, hunger, want, stimulate the strong and courageous: Fear, anxiety, terror, agitate the weak and infirm. The first entrance into life gives anguish to the new-born infant and to its wretched parent: Weakness, impotence, distress, attend each stage of that life: and it is at last finished in agony and horror."

"Observe too, says PHILO, the curious artifices of Nature, in order to embitter the life of every living being. The stronger prey upon the weaker, and keep them in perpetual terror and anxiety. The weaker too, in their turn, often prey upon the stronger, and vex and molest them without relaxation. Consider that innumerable race of insects, which either are bred on the body of each animal, or, flying about, infix their stings in him. These insects have others still less than themselves, which torment them. And thus on each hand, before and behind, above and below, every animal is surrounded with enemies, which incessantly seek his misery and destruction. "

And Hume gets close to Natural Selection:
"And this very consideration too, continued PHILO, which we have stumbled on in the course of the argument, suggests a new hypothesis of cosmogony, that is not absolutely absurd and improbable. Is there a system, an order, an economy of things, by which matter can preserve that perpetual agitation which seems essential to it, and yet maintain a constancy in the forms which it produces? There certainly is such an economy; for this is actually the case with the present world. The continual motion of matter, therefore, in less than infinite transpositions, must produce this economy or order; and by its very nature, that order, when once established, supports itself, for many ages, if not to eternity. But wherever matter is so poised, arranged, and adjusted, as to continue in perpetual motion, and yet preserve a constancy in the forms, its situation must, of necessity, have all the same appearance of art and contrivance which we observe at present. All the parts of each form must have a relation to each other, and to the whole; and the whole itself must have a relation to the other parts of the universe; to the element in which the form subsists; to the materials with which it repairs its waste and decay; and to every other form which is hostile or friendly. A defect in any of these particulars destroys the form; and the matter of which it is composed is again set loose, and is thrown into irregular motions and fermentations, till it unite itself to some other regular form."

"It is in vain, therefore, to insist upon the uses of the parts in animals or vegetables, and their curious adjustment to each other. I would fain know, how an animal could subsist, unless its parts were so adjusted? Do we not find, that it immediately perishes whenever this adjustment ceases, and that its matter corrupting tries some new form?"

And here are a few parallel passages that suggest to me that Darwin might have been influenced by the Dialogues.

The ship and botched trials analogy

Hume in the Dialogues: "But were this world ever so perfect a production, it must still remain uncertain, whether all the excellences of the work can justly be ascribed to the workman. If we survey a ship, what an exalted idea must we form of the ingenuity of the carpenter who framed so complicated, useful, and beautiful a machine? And what surprise must we feel, when we find him a stupid mechanic, who imitated others, and copied an art, which, through a long succession of ages, after multiplied trials, mistakes, corrections, deliberations, and controversies, had been gradually improving? Many worlds might have been botched and bungled, throughout an eternity, ere this system was struck out; much labour lost, many fruitless trials made; and a slow, but continued improvement carried on during infinite ages in the art of world-making."

Darwin in the Origin of Species: "When we no longer look at an organic being as a savage looks at a ship, as at something wholly beyond his comprehension; when we regard every production of nature as one which has had a history; when we contemplate every complex structure and instinct as the summing up of many contrivances, each useful to the possessor, nearly in the same way as when we look at any great mechanical invention as the summing up of the labour, the experience, the reason, and even the blunders of numerous workmen; when we thus view each organic being, how far more interesting, I speak from experience, will the study of natural history become!"

The house/architect analogy

Hume: "If we see a house, CLEANTHES, we conclude, with the greatest certainty, that it had an architect or builder; because this is precisely that species of effect which we have experienced to proceed from that species of cause."

Darwin: "Throughout this chapter and elsewhere I have spoken of selection as the paramount power, yet its action absolutely depends on what we in our ignorance call spontaneous or accidental variability. Let an architect be compelled to build an edifice with uncut stones, fallen from a precipice. The shape of each fragment may be called accidental; yet the shape of each has been determined by the force of gravity, the nature of the rock, and the slope of the precipice,—events and circumstances, all of which depend on natural laws; but there is no relation between these laws and the purpose for which each fragment is used by the builder. In the same manner the variations of each creature are determined by fixed and immutable laws; but these bear no relation to the living structure which is slowly built up through the power of selection, whether this be natural or artificial selection."

The observation that introduced species thrive in new environments, even though they have not originated there.

Hume in the Dialogues: "LUCULLUS was the first that brought cherry-trees from ASIA to EUROPE; though that tree thrives so well in many EUROPEAN climates, that it grows in the woods without any culture. Is it possible, that throughout a whole eternity, no EUROPEAN had ever passed into ASIA, and thought of transplanting so delicious a fruit into his own country? Or if the tree was once transplanted and propagated, how could it ever afterwards perish? Empires may rise and fall, liberty and slavery succeed alternately, ignorance and knowledge give place to each other; but the cherry-tree will still remain in the woods of GREECE, SPAIN, and ITALY, and will never be affected by the revolutions of human society. It is not two thousand years since vines were transplanted into FRANCE, though there is no climate in the world more favourable to them.

It is not three centuries since horses, cows, sheep, swine, dogs, corn, were known in AMERICA. Is it possible, that during the revolutions of a whole eternity, there never arose a COLUMBUS, who might open the communication between EUROPE and that continent?... Nothing less than a total convulsion of the elements will ever destroy all the EUROPEAN animals and vegetables which are now to be found in the Western world."

Darwin in the Origin of Species: "Still more striking is the evidence from our domestic animals of many kinds which have run wild in several parts of the world: if the statements of the rate of increase of slow-breeding cattle and horses in South-America, and latterly in Australia, had not been well authenticated, they would have been quite incredible. So it is with plants: cases could be given of introduced plants which have become common throughout whole islands in a period of less than ten years. Several of the plants now most numerous over the wide plains of La Plata, clothing square leagues of surface almost to the exclusion of all other plants, have been introduced from Europe; and there are plants which now range in India, as I hear from Dr. Falconer, from Cape Comorin to the Himalaya, which have been imported from America since its discovery."

Superiority of the contrivances of nature to those of art

Hume: "Look round the world: contemplate the whole and every part of it: You will find it to be nothing but one great machine, subdivided into an infinite number of lesser machines, which again admit of subdivisions to a degree beyond what human senses and faculties can trace and explain. All these various machines, and even their most minute parts, are adjusted to each other with an accuracy which ravishes into admiration all men who have ever contemplated them. The curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence. Since, therefore, the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of Nature is somewhat similar to the mind of man, though possessed of much larger faculties, proportioned to the grandeur of the work which he has executed."

Darwin in the Origin: "We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man's feeble efforts, as the works of Nature are to those of Art."

On the inability of finite minds to grasp an infinite deity

Hume in the Dialogues: "The question is not concerning the being, but the nature of God. This, I affirm, from the infirmities of human understanding, to be altogether incomprehensible and unknown to us. The essence of that supreme Mind, his attributes, the manner of his existence, the very nature of his duration; these, and every particular which regards so divine a Being, are mysterious to men. Finite, weak, and blind creatures, we ought to humble ourselves in his august presence; and, conscious of our frailties, adore in silence his infinite perfections, which eye hath not seen, ear hath not heard, neither hath it entered into the heart of man to conceive."

Darwin in his Autobiography:"But then arises the doubt—can the mind of man, which has, as I fully believe, been developed from a mind as low as that possessed by the lowest animal, be trusted when it draws such grand conclusions*? May not these be the result of the connection between cause and effect which strikes us as a necessary one, but probably depends merely on inherited experience? Nor must we overlook the probability of the constant inculcation in a belief in God on the minds of children producing so strong and perhaps an inherited effect on their brains not yet fully developed, that it would be as difficult for them to throw off their belief in God, as for a monkey to throw off its instinctive fear and hatred of a snake."

*Note the nice evolutionary twist added by Darwin here!

The balance of happiness/misery and pain/pleasure

Hume: "The only method of supporting Divine benevolence, and it is what I willingly embrace, is to deny absolutely the misery and wickedness of man. Your representations are exaggerated; your melancholy views mostly fictitious; your inferences contrary to fact and experience. Health is more common than sickness; pleasure than pain; happiness than misery. And for one vexation which we meet with, we attain, upon computation, a hundred enjoyments."

Darwin:"if we look to all sentient beings, whether there is more of misery or of happiness;—whether the world as a whole is a good or a bad one. According to my judgment happiness decidedly prevails, though this would be very difficult to prove. If the truth of this conclusion be granted, it harmonises well with the effects which we might expect from natural selection. If all the individuals of any species were habitually to suffer to an extreme degree they would neglect to propagate their kind; but we have no reason to believe that this has ever or at least often occurred. Some other considerations, moreover, lead to the belief that all sentient beings have been formed so as to enjoy, as a general rule, happiness."

Hume: "Admitting your position, replied PHILO, which yet is extremely doubtful, you must at the same time allow, that if pain be less frequent than pleasure, it is infinitely more violent and durable. One hour of it is often able to outweigh a day, a week, a month of our common insipid enjoyments; and how many days, weeks, and months, are passed by several in the most acute torments? Pleasure, scarcely in one instance, is ever able to reach ecstasy and rapture; and in no one instance can it continue for any time at its highest pitch and altitude. The spirits evaporate, the nerves relax, the fabric is disordered, and the enjoyment quickly degenerates into fatigue and uneasiness. But pain often, good God, how often! rises to torture and agony; and the longer it continues, it becomes still more genuine agony and torture. Patience is exhausted, courage languishes, melancholy seizes us, and nothing terminates our misery but the removal of its cause, or another event, which is the sole cure of all evil, but which, from our natural folly, we regard with still greater horror and consternation."

Darwin: "Now an animal may be led to pursue that course of action which is the most beneficial to the species by suffering, such as pain, hunger, thirst, and fear,—or by pleasure, as in eating and drinking and in the propagation of the species, &c. or by both means combined, as in the search for food. But pain or suffering of any kind, if long continued, causes depression and lessens the power of action; yet is well adapted to make a creature guard itself against any great or sudden evil. Pleasurable sensations, on the other hand, may be long continued without any depressing effect; on the contrary they stimulate the whole system to increased action. Hence it has come to pass that most or all sentient beings have been developed in such a manner through natural selection, that pleasurable sensations serve as their habitual guides. We see this in the pleasure from exertion, even occasionally from great exertion of the body or mind,—in the pleasure of our daily meals, and especially in the pleasure derived from sociability and from loving our families. The sum of such pleasures as these, which are habitual or frequently recurrent, give, as I can hardly doubt, to most sentient beings an excess of happiness over misery, although many occasionally suffer much."

Well, what does all this mean? It is uncertain to me whether these parallels reflect a direct influence of Hume's Dialogues on Darwin and if so, if there was a conscious or unconscious decision on Darwin's behalf to exploit them.

Alternatively, Darwin may have encountered these arguments in a third source that used, or was used by, Hume (e.g. Paley).

Or the resemblance could be purely coincidental.

But, in conclusion, it is intriguing to see how far great minds think alike!

Emma Darwin's poignant diary entry

2009-06-22T07:21:00.000-07:00

I am still slowly but surely working away on a paper debunking the myth that Annie Darwin's death had anything to do with Charles Darwin's loss of faith in Christianity. And in preparing the paper, I have been looking at the diaries of Charles Darwin and of Emma Darwin, his wife.

There has been quite a bit of publicity about the recent publication of Emma's diaries, but I didn't realise until recently that Charles Darwin also kept a journal of his life (see the Introduction by John van Wyhe). Darwin started keeping the journal in 1838, but backdated the entries to his birth, and made the last entry just four months before his death.

In researching the background to Annie's final illness and death, I took a look at both diaries. Annie Darwin fell ill in the summer of 1850, as is evidenced by this entry from Emma's diary for 27th June:

"Annie first failed about this time"

She was taken to Malvern by Charles on March 24th 1851, in the hope that she would benefit from Dr Gully's water cure. Charles records this and the subsequent tragic events on a single poignant page in his diary:

"March 24th to Malvern with Annie & Etty. returned home 31st.— April 16th. started for Malvern. April 23d our dear child expired. 24th. I returned to Emma. Our darling was born March 2d. 1841.—"

Emma in her diary maintains a progress report on Annie, gleaned from the letters sent by Dr Gully and by Charles. Unlike most of her diary entries, which tend to be rather terse, her entries on Annie are more informative than usual. On 7th April she writes "Annie's sickup"; on 13th April: "Annie very weak"; on April 14th "Better, Dr G. said she had turned the corner"; on April 15th: "Dr G alarmed, wrote for Ch./ began urine".

I will leave it to you the reader to follow Emma's records of Annie's illness through these links to individual pages for each week:

But for me Emma's entry on Annie's death is the most poignant of all these diary entries, whether from Charles or Emma. After writing "much better" on April 21st and "diarrhea came on" on April 22nd, for April 23rd, she writes simply:

"12 o'clock"

the time of Annie's death. This reminds me of Auden's poem, Funeral Blues: "Stop all the clocks..." and, for me, nothing in any of the accounts of Annie's illness and death could be more arresting.

Please help Darwin's medical students URGENTLY! #2

2009-06-17T11:25:00.000-07:00

This week for the second time (see earlier posting) I have been supervising a student-selected activity entitled "The Darwins, Evolution and Medicine". The rationale for these SSAs is to stimulate curiosity and critical thinking among medical students, who are otherwise burdened with a great deal of rote learning. There are fourteen students on the course and I offered them a selection of topics, which ranged from the matter-of-fact to the highly controversial. Here are the topics they chose:

The illness of Charles Darwin: a retrospective diagnosis
Charles and Emma- Benefits and Hazards of First Cousin Marriages
The Pleistocene diet: a recipe for diet and health?
Why do Europeans, North Asians and Native American have pale skins
How can we explain the course of the recurrent laryngeal nerve
Tay-Sachs disease in Ashkenazi Jews: Origins and Prevention
Darwin and slavery

The students have been given the option of delivering a conventional powerpoint presentation tomorrow morning or posting on a purpose-built blog Darwin's students, by 7 pm tonight. I offered this latter option as an incentive for them to explore and evaluate the blogosphere as a tool for academic research.

Please feel free to look at what they have written and provide constructive comments on their postings, links to other postings or literature etc etc just as if they were regular bloggers! As I explained to them, in a real sense, blogging is more peer-reviewed than the regular scientific literature, as dozens or even hundreds of people can comment. BUT be gentle with them—this is their first foray into the blogosphere!

The amazing power of Darwinite

2009-06-16T10:42:00.000-07:00

You remember Superman and how he suddenly lost all his powers in the presence of the element kryptonite? Well, I am beginning to wonder if there isn't an element called Darwinite out there that means people lose their critical faculties and say and write and believe any old rubbish when face to face with Darwin, his life and his theory of evolution.

I have already pointed out some of the many myths surrounding this topic, but the more I read about the myth of Annie's-death-caused-Darwin's-loss-of-faith, the more I am driven to believe in this powerful but hidden element, Darwinite.

Before I start on the Annie myths, let me point out that Darwinite is clearly inherited, as proven by this piece written by CD's great-great-grand-daughter Emma Darwin, where the diluted Darwinite in her veins is still able to induce hyperventilation in a healthy human male:

http://www.telegraph.co.uk/culture/3663891/The-Insider.html

Let me give just two examples from the Annie mythos:

1. In his Autobiography, Darwin admits that

"later in life I wholly lost, to my great regret, all pleasure from poetry of any kind, including Shakespeare".

Well, lot's of people go off poetry in later life or get cheesed off with Shakespeare-it's part of becoming a grumpy old man. But exposure to Darwinite ensures that American English professor, George Levine, comes up with an explanation custom-built for Darwin in his book Darwin Loves You. It goes like this:

Annie Darwin died on April 23rd 1851.
Which happens to be Shakespeare's birthday
So the memory of her death meant that Darwin developed a life-long downer on Shakespeare!

It has just got to be true (not)!

2. Without Darwinite poisoning, how else could anyone write the kind of twaddle that ends Jim Moore's publication (Of Love and Death: Why Darwin 'gave up Christianity'’ in Jim Moore ed., History, Humanity and Evolution. pp. 195-229, Cambridge, 1989) that kicked off the Annie myth? As opium was to Coleridge's poetry, so it seems Darwinite is to Moore's prose. Be warned this is strong stuff!

"He ends the chapter in search of a palliative: 'We may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt, and that the vigorous, the healthy, and the happy survive and multiply.' But the words ring hollow. Why should consolation be sought unless some one has been bereaved? And can bereavement be so readily assuaged? Nature is the victim in Darwin's figure, but nature is also given a 'face', a face 'bright with gladness', to which death comes promptly without fear. Only one face in Darwin's experience ever did that. He could recall it 'with much distinctness' - 'her eyes sparkled brightly; she often smiled' - and he had the imaginative ability with bygone faces to make them 'do anything I like' Here, then, nature may be tortured that health and happiness should prevail, but the face is also sacrificed for the redemption of the world. The bereavement is finally his own; the real victim, tragically, a child already perfect. Annie, who died at Easter, became the paschal lamb of Darwin's post-Christian evolutionary soteriology."

And how many of you didn't have to look up that last word!!

In The Light of Evolution III

2009-06-15T23:37:00.000-07:00

The current early edition of the Proceedings of the National Academies of Sciences of the USA has just been released and is chock full of articles on evolution from a recent colloquium:

In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: From wild animals to domestic pets, an evolutionary view of domestication Carlos A. Driscoll, David W. Macdonald, and Stephen J. O'Brien
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Genetics and ecological speciation Dolph Schluter and Gina L. Conte
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Natural selection in action during speciation Sara Via
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Postcopulatory sexual selection: Darwin's omission and its consequences William G. Eberhard
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Mate choice and sexual selection: What have we learned since Darwin? Adam G. Jones and Nicholas L. Ratterman
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Adaptive radiations: From field to genomic studies Scott A. Hodges and Nathan J. Derieg
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Sexual selection and mating systems Stephen M. Shuster
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates Julius Lukes, Brian S. Leander, and Patrick J. Keeling
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Reproductive decisions under ecological constraints: It's about time Patricia Adair Gowaty and Stephen P. Hubbell
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: In the light of evolution III: Two centuries of Darwin John C. Avise and Francisco J. Ayala
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Darwin's "strange inversion of reasoning" Daniel Dennett
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: The Darwinian revolution: Rethinking its meaning and significance Michael Ruse
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: In the light of directed evolution: Pathways of adaptive protein evolution Jesse D. Bloom and Frances H. Arnold
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Did Darwin write the Origin backwards? Elliott Sober
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Human-induced evolution caused by unnatural selection through harvest of wild animals
Fred W. Allendorf and Jeffrey J. Hard
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Tracking footprints of maize domestication and evidence for a massive selective sweep on chromosome 10 Feng Tian, Natalie M. Stevens, and Edward S. Buckler, IV
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Darwin's place in the history of thought: A reevaluation Robert J. Richards
In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: Darwin and the scientific method Francisco J. Ayala

New review of The Rough Guide to Evolution

2009-06-14T23:18:00.000-07:00

Fyrefly has just posted a review of The Rough Guide to Evolution here. Generally highly positive, although Fyrefly doesn't like the way people are highlighted in bold, e.g Charles Darwin (1809-1882), but this is Rough Guides house style, I'm afraid.

Clarence Darrow (1857-1938): greatest trial lawyer of all time

2009-06-11T11:02:00.000-07:00

The Guardian today features a piece by Donald McRae entitled The Great Defender, which details the remarkable courtroom skills of Clarence Darrow. Those interested in evolution will be familiar with Darrow's pivotal role in the Scopes Monkey—here is the relevant section from The Rough Guide to Evolution:

The trial ran for less than a fortnight, but attracted unprecedented media attention with over two hundred reporters and the first ever radio broadcast of judicial proceedings. Acerbic Baltimore Sun reporter H.L. Mencken presented the trial to the public in colourful turns of phrase such as “the infidel Scopes” or “the monkey trial” [NOTE added to blog: the discerning reader will note another link here between the show, The Wire, and Darwin's legacy]. The prosecution called just four witnesses to establish that Scopes had broken the law. The defence tried to field eight expert witnesses to establish that there was no conflict between evolution and the Bible. However, the prosecution argued – and Judge John Raulston accepted – that such expert opinion was irrelevant to the question of whether Scopes had actually taught about evolution. After Bryan snuck in a jibe that humans were descended “not even from American monkeys, but from old world monkeys” defence lawyer Malone delivered a dramatic speech, seen as the highpoint of the trial, passionately arguing that the Bible belonged to the realm of theology and morality rather than to science.

Towards the end, the trial took a bizarre twist as Darrow questioned Bryan as a witness to the authenticity of the Bible. Sparks flew in the resulting exchange, with Darrow using phrases like “your fool religion” and declaring (presciently, given later history): “We have the purpose of preventing bigots and ignoramuses from controlling the education of the United States.” To prevent Bryan from summing up, Darrow waived his own right to a closing statement. Instead, Darrow asked the judge to bring the jury in and instruct them to return a guilty verdict, which they did after just nine minutes deliberation. The judge fined Scopes the minimum allowed: just $100.

What I didn't know before I read the Guardian article was Darrow's role in two other high-profile court cases, the Leopold and Loeb trial (Darrow's summation, an eloquent attack on anti-capital punshment, which moved the judge to tears, can be found here) and the trial of African-American physician Dr Ossian Sweet (read Darrow's account of it here).

The author of the Guardian article, has a book out on Darrow: The Old Devil: Clarence Darrow: The World's Greatest Trial Lawyer, while the Clarence Darrow home page is stuffed full of information and links about Darrow.

Oh and here is a question for you: what's the link between Clarence Darrow and Claire Bennet from the cult show Heroes?

Darwin podcasts from the Fitzwilliam Museum

2009-06-10T09:12:00.000-07:00

The Fitzwilliam Museum in Cambridge (which Darwin frequented), is next week launching an exhibition, Endless Forms, to celebrate the Darwin bicentennial.

To accompany the exhibition, the Fitzwilliam has produced a series of fascinating podcasts, including most recently an account of Darwin's time in Cambridge from my friend John van Wyhe. Note the sly reference in John's talk to the myth of Annie Darwin and Darwin's loss of faith: watch this space for more on this issue!

Latest news from Simon Singh

2009-06-09T23:25:00.000-07:00

For those of you interested in Simon Singh's struggle with the British Chiropractic Association and the English legal system, Simon has written a nice summary of the history of the case, the issues involved and his determination to continue here:

BCA v Singh The Story So Far 3 June 2009

Darwin, the "Missing Link" and raucous students

2009-06-04T09:06:00.000-07:00

There has been much talk in the blogosphere about the hyping up of Darwinius as a "missing link" (summarised here by Carl Zimmer). And Harry Gee has been delving into the history of the term, as has Carl's brother Ben.

On reading all this, my curiosity was piqued as to whether Darwin ever used the term "missing link"....?

A few minutes searching on Darwin Online and on the Darwin Correspondence Project reveals that he did not. But interestingly, the term does feature in several letters written to Darwin, but not always in the sense of an intermediate between humans and apes:

Librarian Mary Boole wrote to Darwin in Dec 1866: "I felt that you had supplied one of the missing links,—not to say the missing link,—between the facts of Science & the promises of religion."
In a letter dated 12 July 1871, Otto Kratz sent Darwin photographs of very hairy Burmese natives and suggested that they may be the "missing link".
Geologist Frederic William Harmer quotes an opponent of Darwin, Frederick Bateman of Norwich in 1872: "I was unwise enough to reply to the latter, that a theory was not disproved by a mere objection being urged against it, & also to attempt to explain that an argument which he rested great weight upon, viz. the non production of the missing link, was valueless, owing to the imperfection of the geological record"
In 1877, one of Darwin's shipmates on the Beagle, Arthur Mellersh writes to ask Darwin whether "the missing link" been found in New Guinea, as he read in the newspaper.
Also in 1877 comes perhaps the first sinister racist use of the term in a letter from W. B. Bowles, who tells Darwin he 'believes "missing link" between higher mammals and man consists of a race of "speaking monkeys" – akin to Africans – who pollute blood of better race and impede civilisation'.

A search on Darwin Online also pulls up an interesting use of the term in recollections of Darwin collecting an honorary LLD degree from the University of Cambridge in 1877. The first is from John Neville Keynes, the economist father of John Maynard Keynes:

"The honorary degree of LLD was conferred upon Darwin in the Senate House amidst a scene of some disorder. The building was crammed, floor and galleries, the undergraduates being chiefly in the galleries; and it was of course an occasion on wh. undegraduate wit felt bound to distinguish itself. The chief pleasantry consisted of a monkey swung across by strings from gallery to gallery, which monkey was in the course of the proceedings to have been changed into a man. Before however this desirable consummation was reached, the representative of the original ancestor, (than whom he was less fortunate), was seized by one of the proctors, & thus prevented from fulfilling his high destiny. The perpetrators of the joke were very wrath, & vented their fury chiefly in groans for Humphreys, the most unpopular of the proctors. He was also made the butt of such remarks as this, Would Dr. Darwin kindly afford us some information regarding the ancestors of Mr. Humphreys? — a sally which took amazingly. Sandys, the public orator, introduced Darwin, according to custom, in a rather long Latin oration, wh. was delivered amidst a ceaseless fire of interruptions, (chiefly feeble), from the wittiest of the undergraduates. Sandys (I imagine inadvertently) made use of the word apes, & then the cheering was enormous. Darwin bore himself in a rather trying position with remarkable dignity; but I heard afterwards that his hand shook so much while he was signing the registry, that his signature was scarcely legible. Another emblem swung from the galleries was a large ring of iron, adorned with ribbons, supposed to represent the missing link. It was ultimately swung down into the lap of one of the lady visitors, who pluckily cut it down and appropriated it, amidst tremendous applause. I afterwards found that this courageous lady was Miss Borchardt."

A second account of the same event is recorded in a letter from Emma Darwin to her son William

CAMBRIDGE, Sunday mg., Nov. 17th, 1877.

MY DEAR WILLIAM,

It was a great disappointment your not coming yesterday to witness the honours to F., and so I will tell you all about it.

Bessy and I and the two youngest brothers went first to the Senate House and got in by a side door, and a most striking sight it was. The gallery crammed to overflowing with undergraduates, and the floor crammed too with undergraduates climbing on the statues and standing up in the windows. There seemed to be periodical cheering in answer to jokes which sounded deafening; but when F. came in, in his red cloak, ushered in by some authorities, it was perfectly deafening for some minutes. I thought he would be overcome, but he was quite stout and smiling and sat for a considerable time waiting for the Vice-Chancellor. The time was filled up with shouts and jokes, and groans for an unpopular Proctor, Mr ———, which were quite awful, and he looked up at them with a stern angry face, which was very bad policy.

We had been watching some cords stretched across from one gallery to another wondering what was to happen, but were not surprised to see a monkey dangling down which caused shouts and jokes about our ancestors, etc. A Proctor was foolish enough to go up to capture it and at last it disappeared I don't know how. Then came a sort of ring tied with ribbons which we conjectured to be the "Missing Link." At last the Vice-Chancellor appeared, more bowing and hand-shaking, and then F. was marched down the aisle behind two men with silver maces, and the unfortunate Public Orator came and stood by him and got thro' his very tedious harangue as he could, constantly interrupted by the most unmannerly shouts and jeers; and when he had continued what seemed an enormous time, some one called out in a cheerful tone "Thank you kindly." At last he got to the end with admirable nerve and temper, and then they all marched back to the Vice-Chancellor in scarlet and white fur, and F. joined his hands and did not kneel but the Vice-Chancellor put his hands outside and said a few Latin words, and then it was over, and everybody came up and shook hands."

It's nice to see that students at Cambridge were just as raucous back then as they are today!

From the Origin of Species to the origin of infection

2009-05-27T10:50:00.000-07:00

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

From the Origin of Species to the origin of infection

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

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

Darwin and natural selection

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

In On the Origin of Species by Means of Natural Selection, first published in 1859, Darwin eloquently (and presciently, given its subsequent influence on antibiotic resistance) emphasizes the remarkable power of natural selection:

‘We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.’ [link]

Later, in Variation Under Domestication [note: not The Descent of Man as stated in PDF], despite his ignorance of the nature of inheritance, Darwin points out that the variation that is a prerequisite of natural selection originates independently of the selection itself.

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

Darwin and Pasteur

Shortly after Darwin published The Origin, in Paris, Louis Pasteur performed a series of experiments that demolished the theory of spontaneous generation. Darwin was well aware of the on-going controversy. In 1860, in a letter to his friend Lyell, he refers to the work of Pasteur’s rival Pouchet:

‘I have seen something about the infusorial experiments in Paris: Quatrefage objected to their accuracy. Some old experiments were several years ago tried in Germany with astonishing precautions (air all passed through sulphuric acid & caustic potash) and infusoria never appeared.’

A few years later in 1863, he wrote to the English botanist George Bentham:

‘I am very glad that you are going to allude to Pasteur; I was struck with infinite admiration at his work.’

In disproving spontaneous generation, Pasteur might be seen as undercutting Darwin’s theory of evolution by removing a mechanism for the generation of the first life forms. However, Darwin was sharp enough to realize that the conditions under which life first originated were likely to be quite different from those around today. In 1871, he wrote to his botanist friend Joseph Hooker:

‘It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a proteine [sic] compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.’

As far as I am aware, Pasteur never made any direct reference to Darwin, although he opened his 1864 address to the Sorbonne on spontaneous generation with these expressive lines:

‘Great problems are in question today, keeping every thinking man in suspense: the unity or multiplicity of human races, the creation of man 1,000 years or 1,000 centuries ago; the fixity of species, or the slow and progressive transformation of one species into another…’

Half a century later, an essay in Science magazine concluded:

‘Darwin, master of the organic world sleeps near Newton, master of the inorganic, in the great [Westminster] Abbey, among the most famous of his race. Pasteur rests alone in the chapel of his laboratory … Both rest forever among the immortals. the last half of the nineteenth century may well be called their age “the Age of Darwin and Pasteur”.’

Darwin, Cohn and the origin of infection

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

From 1874 until 1882, Darwin and Cohn maintained a lively correspondence, principally on botany. On 26 September 1876 Darwin writes to invite Cohn and his wife to visit him at Down House. And then, the very next day, Darwin writes to his son Frank, saying that he hopes they will not come! Apparently the subsequent visit was a success. However, for microbiologists, one particular exchange of letters stands out. In January 1878, Cohn writes to Darwin, discussing Koch’s recent discovery of the anthrax bacillus. Darwin’s response is a triumphant celebration of the birth of medical microbiology:

‘I thank you sincerely for your most kind letter and I return your wishes for the New Year with all my heart. Your letter has interested me greatly. Dr Sanderson showed me some admirable photographs on glass by Dr Koch of the Organisms which cause Splenic Fever. But your letter and the valuable work which you have given me make the case much clearer to me. I well remember saying to myself between 20 and 30 years ago, that if ever the origin of any infectious disease could be proved, it would be the greatest triumph to Science; and now I rejoice to have seen the triumph.’

Further reading

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

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

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

Sedgwick, W.T. (1923). Darwin and Pasteur: an essay in comparative biography. Science 52, 286.

http://darwin-online.org.uk – The complete works of Charles Darwin online. http://www.darwinproject.ac.uk – Darwin Correspondence Project

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

2009-05-24T08:34:00.000-07:00

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

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

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

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

But another key facet of The Origin's evolution that intrigues me is just how much of it was written over fifteen years before 1859 in two short documents, Darwin's 1842 Pencil Sketch and 1844 Essay. It is interesting to take favourite passages from the Origin and see their ancestors in those earlier drafts. Here are is the most obvious example, the closing words:

"There is a simple grandeur in the view of life with its powers of growth, assimilation and reproduction, being originally breathed into matter under one or a few forms, and that whilst this our planet has gone circling on according to fixed laws, and land and water, in a cycle of change, have gone on replacing each other, that from so simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved." 1842 Pencil Sketch.

"There is a [simple] grandeur in this view of life with its several powers of growth, reproduction and of sensation, having been originally breathed into matter under a few forms, perhaps into only one, and that whilst this planet has gone cycling onwards according to the fixed laws of gravity and whilst land and water have gone on replacing each other—that from so simple an origin, through the selection of infinitesimal varieties, endless forms most beautiful and most wonderful have been evolved." 1844 Essay

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." The Origin of Species, First Edition. NB: in the 2nd edition "by the Creator" is introduced after "originally breathed."

But the new census of the first edition hammers home the differences not just between editions, but also between copies of the very same edition. Start off by taking a look at the census guide for a panoply of features that can be used to classify a copy of The Origin as a First Edition. A key hallmark is the misspelling of species on p. 20:

There can be no doubt that a race may be modified by occasional crosses, if aided by the careful selection of those individual mongrels, which present any desired character; but that a race could be obtained nearly intermediate between two extremely different races or speceies, I can hardly believe. The Origin, First Edition, Page 20.

But look at all the other minute differences, for example in the binding:

If there is a full stop after MURRAY at the bottom of the spine, it is a 2nd or 3rd edition binding.
If the letters at the bottom of the spine are short and square (as opposed to tall and thin), it is a 2nd edition binding.
If the second N in LONDON is slightly lower than the other letters, it is a 3rd edition binding.

And there are differences even within the first edition!

For original bindings there are two variants, the difference being the width of LONDON. In the first variant, LONDON at the bottom of the spine is 16mm wide; in the second variant, it is 18mm.

I will leave it to the train-spotters among you to look at the guide for all the minutiae;-)

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

And perhaps I should close with a new variant of the ending of the Origin:

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

Very gradual change we can believe in

2009-05-24T00:52:00.000-07:00

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

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

Anyhow, here is my selection of Darwin "change" quotes that Mike might like to try on later versions of poster:

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

And if you prefer to draw on the alternative Obama Hope poster for an analogous Darwin image, how about this quote:

"We shall never, probably, disentangle the inextricable web of affinities between the members of any one class; but when we have a distinct object in view, and do not look to some unknown plan of creation, we may hope to make sure but slow progress." Origin p. 434

Rough Guide to Evolution in the Malvern Gazette

2009-05-15T05:17:00.001-07:00

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

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

2009-05-08T10:42:00.000-07:00

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

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

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

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

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

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

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

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

Yes, you've guessed it...!

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

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

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

Notes

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

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

Humpty dumpty judge sides with BCA in Singh hearing

2009-05-07T23:45:00.000-07:00

Bad news, I am afraid, from the courtroom in the BCA versus Simon Singh case (see yesterday's post). The Judge, emulating Humpty Dumpty in Through the Looking Glass, has decided that he is the master of Singh's words and can decide that they mean what he wants them to mean. He has ruled that Singh's words:

"The British Chiropractic Association claims that their members can help treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying, even though there is not a jot of evidence. This organisation is the respectable face of the chiropractic profession and yet it happily promotes bogus treatments."

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

More news here:
http://godknowswhat.wordpress.com/2009/05/07/singh-case-update-a-real-pain-in-the-neck/

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

Interesting post on protein folding and evolution

2009-05-07T11:31:00.000-07:00

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

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

Interested readers should take a look!

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

2009-05-06T23:40:00.000-07:00

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

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

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

The original BCA brochure: http://web.archive.org/web/20070206003656/http://www.chiropractic-uk.co.uk/gfx/uploads/textbox/Happy+families.pdf
April 2008 - Simon Singh's "Comment is Free" piece in the Guardian (removed from Guardian site, but here hosted on a Russian server!):http://svetlana14s.narod.ru/Simon_Singhs_silenced_paper.html
August 2008 - The news of the claim: http://www.telegraph.co.uk/news/newstopics/mandrake/2570744/Doctors-take-Simon-Singh-to-court.html
August 2008 onwards - Material on the web summarised at: http://holfordwatch.info/2008/08/16/british-chiropractors-join-the-legal-intimidation-party/
November 2008 - Summary of BCA's Legal Claim: http://jackofkent.blogspot.com/2008/11/on-bcas-case-against-simon-singh.html
November 2008 - Summary of Simon Singh's Defence: http://jackofkent.blogspot.com/2008/11/on-putting-chiropractic-on-trial.html
November 2008 - Article on the influential Quackometer site: http://www.quackometer.net/blog/2008/11/chiropractic-folly-and-nature-of.html
And on the Blog of philosopher Stephen Law: http://stephenlaw.blogspot.com/2008/11/simon-sigh-sued-by-british-chiropractic.html
December 2008 - Useful round up on Dr Aust's site: http://draust.wordpress.com/2008/12/23/it%E2%80%99s-quiet%E2%80%A6-too-quiet/
December 2008 - And strong support from Phil Plait of Bad Astronomy: http://blogs.discovermagazine.com/badastronomy/2008/12/24/uk-quackery-on-trial/
March 2009 - High Court orders preliminary hearing on Thursday 7 May 2009: http://jackofkent.blogspot.com/2009/03/bca-v-singh-first-court-hearing-is.html
http://jackofkent.blogspot.com/2009/03/bca-v-singh-date-set-for-first-hearing.html

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

Talk: Erasmus and Charles Darwin on Evolution

2009-04-30T09:46:00.000-07:00

A talk by Dr Chris Smith:

Erasmus and Charles Darwin on Evolution

Speaker: Dr Chris Smith
Date: Thursday 7 May
Time: 7.00pm
Cost: Free - Booking advised

Location: Thinktank, Millenium Point, Curzon Street, B4 7XJ

Erasmus Darwin has been called 'England's Leonardo' and the 'greatest polymath of his age'. Perhaps his greatest achievement was to develop a theory of organic evolution some sixty years before the publication of the Origin of Species. This talk reviews Erasmus Darwin's life in the Midlands and compares his thought with that of his more famous grandson.

Dr Chris Smith is an Honorary Visiting Fellow in the Department of Vision Sciences at Aston Dr Chris Smith is Honorary Visiting Fellow in the Department of Vision Sciences at Aston University and Honorary Research Fellow in the Centre for the History of Medicine at the University of Birmingham. He was Chair of the Erasmus Darwin Bicentennial Committee (1999-2002) and joint editor of The Genius of Erasmus Darwin (Ashgate, 2005). His first publication on Charles Darwin dates back to 1977.

Don't miss this opportunity to come and hear him.

To Book
Seats for our lecture are on a first come first served basis but if you would like to ensure a place please send an email to basec@oneuk.com.