Visit of Randal Keynes part two

Following on from the previous post, Randal has now sent me the speech he gave while receiving his honorary doctorate. Here it is:

Deputy Pro-Chancellor, Vice Chancellor, my fellow Graduates, Graduands and guests,

My thanks first to Professor Raine for his citation tracing all my relations and explaining my interests in conservation and science heritage.

Fellow Graduands, I’ve come here today to join you in this wonderful ceremony with a strong sense of the excitement of Birmingham Biosciences in 2012, your success in your courses, and what now lies ahead for you all in all the different fields in which you’ll be putting to use all the knowledge and understanding you’ve gained here through your studies.

For myself, thinking of links with the past as I do so often in my work on science heritage, the Lunar Society of Birmingham comes first to mind. Among its members were Joseph Priestley, Matthew Boulton, Josiah Wedgwood and Erasmus Darwin, scientists, doctors, manufacturers and inventors, each with different interests and skills, and all glad to talk freely together about their many interests. There must now be many echoings of those discussions in the collaborations that take place between the many teams in the School of Biosciences as they work today across its wide range of interests. I guess the School is working so well now just as the Lunar Society did before partly because these open exchanges are good ways to do innovative, productive science.

But why should young scientists like you today bother with science in history? Why do I and others go on about Darwin and the other historical figures?

I can suggest many answers. I’ll give you one of them quickly now because for me it’s one of the strongest, it starts here in Birmingham, and numbers of you may perhaps recognize the point one day in some scientific investigation you carry out or hear about.

So, there’s one meaning of science - its conclusions, the body of latest knowledge. There’s another meaning – the process, how the explanations are developed, tested and agreed.

On the process, Joseph Priestley was living here in the 1770s and in his experiments on electricity and gases he always used equipment that was cheap and easy to obtain, and described his experiments clearly and simply so that anyone could repeat them or vary them as they wanted. He was hoping to find clear and simple explanations that anyone else could test so that they could carry on from there. And he felt that the more experiments could be done by more people, the better the conclusions would be. Also, the best explanations would often be the simplest ones because with simplicity often came greater explanatory power. The value and power of his classic experiments on both electricity and gases were linked with these features of his method.

Now Charles Darwin, in his experimental work on plants and insects at his home in Kent some eighty years later, followed Priestley’s method exactly in all these respects, including simplicity for explanatory power.

When we look at the two men’s achievements together now, we can see a valuable approach that was used with great effect in two outstanding contributions to science. Yes of course, science has come a long way since then, but I’d suggest that key elements of that approach may still have great value in many areas of science today.

Deputy Pro-Chancellor, I’m deeply grateful for the honour you have conferred on me today, and for the special link it gives me now with Birmingham and its heritage of science.

Visit of Randal Keynes to University of Birmingham

On July 4th 2012, it was my pleasure to host a visit by honorary graduand Randal Keynes, with his wife Zelfa and mother Anne, to the University of Birmingham. Their day here included lunch with the Vice-Chancellor and others, a trip to the Special Colletions and Archives, along with Alice Roberts to see a first edition Origin of Species (thanks to Sue Worrall), and a visit to the Lapworth Museum of Geology (thanks to Ivan Sansom).

Randal received an honorary doctorate at the School of Biosciences graduation ceremony and the day concluded with a photo shoot of Darwin-descendent Randal alongside Huxley-descendent Adam Tickell, plus strawberries and champagne in the VC's office.

Here is a video record of selected snippets from the day:

 

Unfortunately I was not allowed to film the graduation ceremony, nor does the University seem to realise that "information wants to be free", so the only way to get footage of the ceremony is to fork out for a DVD!

At the graduation ceremony, Randal gave a speech in which he highlighted the links between the Lunar Society of Birmingham, his ancestors (Erasmus and Charles Darwin), Joseph Priestley and the birth of the scientific method. Randal was introduced with a speech from University orator Professor John Raine, which John wrote with help from Randal and myself. A hypertext-linked version of the speech follows.

Chancellor, Vice Chancellor, Graduates, Graduands and Guests, 

The concept of conservation is one that associates equally with the natural environment of plants and animals and with the human-created world of architecture and buildings. Most conservationists usually work in one arena or the other, but today before us stands an individual whose contribution spans both and who can therefore properly be described as a conservationist in the most comprehensive and generic of senses. 

Randal is from a renowned lineage of English families – notably the Keyneses, the Adrians, the Darwins and the Wedgwoods. Born on July 29th 1948, he is a great nephew of the eminent economist, John Maynard Keynes; and he is also the great-great-grandson of naturalist Charles Darwin. In 1839 Charles Darwin had married Emma Wedgwood, descendant of Josiah Wedgwood the 18th century founder of industrialised pottery manufacture, and who, along with his friend Erasmus Darwin and other prominent Midlands figures, were founding members of the Lunar Society of Birmingham which played such an important role in science for the Industrial Revolution. 

Randal’s father was the eminent Cambridge physiologist Professor Richard Darwin Keynes and his father, Sir Geoffrey Langdon Keynes, was a distinguished surgeon and scholar whose work in developing blood transfusion saved thousands of lives in the First World War. On the other side of his family, Randal’s mother, Mrs Anne Pinsent Keynes, whom we are delighted to welcome here in the Great Hall with us today, is also of very distinguished lineage. Her mother, Hester, was Lady Adrian, a renowned penal reformer, and her father, Lord Adrian, was a Nobel Prize-winner in 1932 for his discoveries about the workings of the nerve cell. 

And Anne’s grandmother was Birmingham’s own Dame Ellen Pinsent – who is 1911 was the first woman to be elected to the City of Birmingham Council, and a pioneer in the education of children with special needs. She, for one, would have been delighted that last year Ofsted found the special school named after her in South Birmingham – The Dame Ellen Pinsent School – to be ‘outstanding’. Dame Ellen was awarded an honorary MA by this University in 1919, while her husband – Anne’s grandfather - Hume Chancellor Pinsent – a solicitor in this city, was Treasurer of this University until his retirement in 1913. 

It is also a great pleasure today to welcome Randal’s wife Zelfa Hourani. Unfortunately their two offspring – Soumaya and Skandar – are otherwise engaged today. Soumaya works as an economist and Skandar is at university (and is widely known, having played the character of Edmund Pevensie in the three Nania films – The Lion, the Witch and the Wardrobe, Prince Caspian; and Voyage of the Dawn Treader. 

But back to Randal. As a boy, he spent many of his summer holidays with his Darwin-side grandmother at her home in the Suffolk countryside, and it was there that he gained some of his earliest insights on his family ancestry as she talked of the holidays she had spent as a child with her grandmother at the Darwins’ home of Down House, just south of London. But it was some years later before Randal’s imagination was stirred to discover more about his Darwinian heritage. Indeed, for most of his adolescent years, Randal had found the pressures of his ancestry somewhat oppressive. When it came to university, for example, he broke away from the family tradition of reading science at Cambridge to study philology and anthropology at Oxford. 

On graduating he decided upon a DPhil, to explore the anthropological connections between some ideas in Anglo-Saxon and Ancient Icelandic writings. But when an attractive job came up in the Ministry of Defence he decided instead to join the civil service where he went on to pursue the significant part of his career. As well as working at the MoD in London, he had secondments to Northern Ireland during ‘The Troubles’ and so, last week he will no doubt have particularly appreciated the reconciliation of former foes epitomised in that historic handshake. 

He also served for a spell with the Parliamentary Ombudsman and in 1992 he was awarded an OBE for his work at the MoD during the Gulf War. It was while a civil servant that he began to devote more and more of his spare time to aspects of conservation. He became active in the Victorian Society, campaigning for the protection and restoration of our outstanding Victorian and Edwardian architectural heritage. And his campaigning took on a personal dimension in the 1980s, when the neighbourhood in which he lived, just east of Kings Cross station, became the subject of clearance proposals to make way for the new channel tunnel rail link into central London. Randal was at the forefront of a well-organised campaign – and which also involved debate in Parliament – that led to the line being re-routed into the adjacent St Pancras station, now the marvellous ‘St Pancras International’ with its fabulously restored Gilbert Scott-designed hotel on the front. Meanwhile, Randal’s previously condemned neighbourhood was sympathetically regenerated – and the full story of its rescue and conservation can be read in a soon-to-be-published book, King’s Cross: A Sense of Place, which includes a chapter by Randal. 

Since then, his attentions have turned to another piece of architectural heritage – again one in which Randal could claim a personal interest – Charles’ Darwin’s Down House in North Kent – where the great naturalist had spent the last forty years of his life, undertaken many of his studies of natural life and written his ‘Origin of Species’. Here, the conservation challenge has been to withstand the pressures for property development over the very landscape where Charles Darwin had conducted so many of his investigations of animals, insects and birds and where he had built his evidence base for his Theory of Evolution. To this end, Randal has provided the case which the Government has now put to UNESCO to make Down House and its surroundings a World Heritage Site for the history of science. More than this, Randal has played a leading role in gathering together and researching all the surviving material about Darwin’s life and work at Down House. 

His own family home had itself been something of a treasure-house of Darwinian material and, in his adult years, he took on the task of sifting systematically through his father’s inherited pieces. In doing so, in a chest of drawers, he happened upon a writing case that had belonged to Charles Darwin’s daughter, Annie, containing her pale yellow ribbon stitched with small glass beads, her goose-feather quills with which she wrote, her sealing wax, a thick lock of her fine brown hair, a fold of paper on which was written ‘April 23rd 1851’ - the date of Annie’s death at the age of just ten - and a leaf from a pocket book with a map of the churchyard in Malvern where she is buried. The story of that personal tragedy and the experience that influenced Darwin’s revolutionary understanding of humankind’s place in nature, has been painstakingly researched by Randal and crafted into his biography ‘Annie’s Box’, first published in 2001, and described by one literary critic as ‘ the best non-fiction book I have read all year’. 

And of course Randal’s research on Darwin and his commitment to conservation has had to encompass the Galapagos Islands – which unlike Down House, already enjoys the status of being a World Heritage Site. Even so, the archipelago is still facing extreme dangers as a result of rapid growth in eco-tourism and immigration from the Ecuadorean mainland. Randal is a member of the Board of Directors of The Charles Darwin Foundation for the Galapagos Islands – an international scientific organization that leads the science for the conservation of their uniquely valuable wildlife. He travels there frequently and is focusing particularly on communicating the Island’s story and its inestimable importance to the world. 

He is also a Board member of the Charles Darwin Trust which promotes the use of Darwin’s inspiration in science education. He works hard helping young people around the world to grasp the legacy of Darwin through his life in science and, in the Darwin bicentenary year, he took part in the national Evolving Words initiative, which here in Birmingham culminated in poetry recitals by children from inner city neighbourhoods. He has also provided invaluable support to the Rap Guide to Evolution, a Wellcome Trust-sponsored celebration of Darwin’s life and legacy through the unlikely medium of Hip Hop! 

Chancellor, there are, as indicated, significant connections between Randal’s family and this great University and City of Birmingham. Indeed, his ancestors in the Lunar Society were part of a select group of individuals that could perhaps be said to have provided the genesis for the modern world here in the heart of England. Charles Darwin’s statue is, of course, to be found in the line of distinguished individuals that form the frieze over the entrance to this Aston Webb building, and our special archive collections here include a first-edition copy of his ‘Origin of Species’. But irrespective of such historical connections, the contribution of Randal Keynes to conservation, to education and to outreach, locally, nationally and internationally, itself deserves to be recognized and marked by this University – an institution that shares with him a commitment to diligent research and to respecting, protecting and making best use of important heritage. 

So to you, and to the University, I present Randal Hume Keynes, deemed worthy to be awarded the degree of Doctor of the University, Honoris Causa.

Interesting video and paper from Nature

From the Nature video feed:

A few million years ago, our ancestors stopped climbing trees and started walking upright, on two feet. To work out how and when this happened, researchers look for fossils -- and recently they found a surprising set of foot bones in Ethiopia. The foot is about 3.4 million years old, making it roughly the same age as 'Lucy' and her species, Australopithecus afarensis. But while Lucy's species had feet much like modern humans, the new foot has an opposable big toe, like a chimp. So do the foot bones represent a new species of hominin? Watch the video and decide.

Read the original research paper: www.nature.com/nature/journal/v483/n7391/full/nature10922.html

The ‘Annie Hypothesis’: Did the Death of His Daughter Cause Darwin to ‘Give up Christianity’?

The paper that I wrote with John van Wyhe on what we call "the Annie Hypothesis" is now out here:

http://doi.wiley.com/10.1111/j.1600-0498.2012.00256.x

Here is the abstract:

This article examines one of the most widely believed episodes in the life of Charles Darwin, that the death of his daughter Annie in 1851 caused the end of Darwin's belief in Christianity, and according to some versions, ended his attendance of church on Sundays. This hypothesis, it is argued, is commonly treated as a straightforward true account of Darwin's life, yet there is little or no supporting evidence. Furthermore, we argue, there is sufficient evidence that Darwin's loss of faith occurred before Annie's death.

During peer review, the paper was criticised for mixing history with historiography and for being overly positivist, but what can you expect of a scientist! We are all positivists!

Sadly, the paper is not open access: if anyone wants a copy but cannot access it, please email me (m.pallen@bham.ac.uk).

Allow me to thank John van Wyhe for beating the paper into shape and nursing it through to publication!

Other previous posts on this topic:

• http://roughguidetoevolution.blogspot.co.uk/2008/12/annie-darwin-and-darwins-loss-of-faith.html
• http://roughguidetoevolution.blogspot.co.uk/2009/07/spread-of-annie-myth-its-worse-than-i.html
• http://roughguidetoevolution.blogspot.co.uk/2009/06/emma-darwins-poignant-diary-entry.html

Rap Guide to Evolution: new "I'm a African" video

Back in the run-up to the Darwin bicentenary year, I persuaded Canadian Lit-Hop artist Baba Brinkman (creator of the Rap Canterbury Tales) to "do for for Darwin what he had done for Chaucer". He rose to the challenge majestically to create the Rap Guide to Evolution and I was thrilled to experience his premier performances at small poetry workshop in Hinxton near Cambridge in early 2009. The video below provides a glimpse of this earliest version of the show. In the week that followed I arranged for Baba to tour England, with shows in Cambridge, London, Birmingham and Shrewsbury.

Since then the various songs have undergone "descent with modification", with two versions of the album now out there (original and revised) and a sell-out live show which ran off Broadway for many months. Also, thanks to an encounter during the very first performance, Baba won financial support from the Wellcome Trust (and did a bit of his own crowd-funding) to create educational and entertaining videos to accompany each track. This has been a slow process, as he has to wait for the animators and actors to find time in their busy schedules to contribute, but the videos have been steadily appearing on YouTube and a dedicated website.

When I first suggested that Baba create the Rap Guide to Evolution, I asked if he could do something to communicate and even celebrate the Out-of-Africa theory, i.e. the idea first proposed by Chris Stringer and others that all modern non-African humans are descended from a small band of humans who left Africa 60-70 thousand years ago (pace John Hawks and Svante Paabo who now emphasise that a few percent of the non-African human genomes originated from archaic hominins from outside Africa). To me this theory gelled nicely with the pan-Africanism that permeates both reggae (check out this Black Uhuru track) and some rap music. Baba did a great job on this, with his track "I'm a African".

A few months back Baba visited Birmingham to perform the Rap Guide to Evolution for our students. During his visit he solicited my help in finding a multi-racial cast of volunteers to appear in the video for "I'm a African". From amongst students and colleagues, we managed to find two Indians, two Greeks, an Afghan, a Chinese, a number of Europeans (including me!), plus some people with African ancestry more recent than 70Kya, all willing to lip-sync along to the track against a green background, hastily assembled Blue-Peter-fashion from some card and sticky tape. Filming all this within our Centre for Systems Biology was a truly surreal experience!

Well, yesterday, just as Nick Loman was stoking our other blog up to blistering heat with the news of Oxford Nanopore, I received a note from Baba saying that the video for "I'm a African" was now finished and available online. So, here it is! Enjoy! Mine is the ugly mug a few seconds in!

A few notes on the video:

1. It's "I'm a African" rather than "I'm an African" for good reason, as Baba explains here.

2. The track is modelled on a track from Pan-Africanist Hip-Hop group Dead Prez. Listen to that track here if you want to compare and contrast.

3. Be sure to wait right until the end of Baba's video to see the architect of the out-of-Africa theory, Chris Stringer, make a cameo appearance, thanks to some footage I captured when he visited the University of Birmingham!

4. I suspect that the Dead Prez track was influenced by a speech "I'm an African" by Thabo Mbeki. Although later deeply flawed as a president, in 1996 Mbeki gives a great speech.

5. A few years back, in similar vein, with a Jamaican colleague, I created "Light be Thrown", a celebration in reggae format of our recent African origins and Darwin's predictions about how light will be thrown on human origins.

Evolutionary Chemistry: from Darwinism to drugs

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

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

• http://roughguidetoevolution.blogspot.com/2009/02/guest-blog-from-lauri-lebo-darwins.html
• http://roughguidetoevolution.blogspot.com/2009/02/guest-blog-from-lauri-lebo-darwins_13.html
• http://roughguidetoevolution.blogspot.com/2009/02/guest-blog-from-lauri-lebo-darwins_842.html
• http://roughguidetoevolution.blogspot.com/2009/02/guest-blog-from-lauri-lebo-darwins_16.html

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?

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

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.

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Bio380 Human Evolution Bioinformatics Practical 2011

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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

• http://itre.cis.upenn.edu/~myl/languagelog/archives/005038.html
• http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/foxp2_krause_el_sidron_2007.html
• http://johnhawks.net/weblog/reviews/genetics/brain/foxp2-bushman-variant-2010.html
• http://johnhawks.net/weblog/reviews/denisova/foxp2-denisova-humanlike-2011.html
• http://blogs.discovermagazine.com/loom/2011/11/14/neanderthal-neuroscience/
• http://discovermagazine.com/2011/oct/08-the-brain-language-fossils-buried-in-your-cells/article_print

• 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

• http://www.independent.co.uk/news/science/fury-at-dna-pioneers-theory-africans-are-less-intelligent-than-westerners-394898.html
• http://www.nytimes.com/2007/12/12/science/12watson.html?_r=1
• http://isteve.blogspot.com/2007/12/james-watson-and-passing.html
• http://johnhawks.net/weblog/topics/biotech/testing/watson_african_dna_2007.html

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:

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

Darwin and Mendel: The Great What If?

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

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?

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

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

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

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/ANooECt7http://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