Thylacine mitochondrial genome

Just stumbled across this interesting paper in Genome Research, which documents the mitochondrial genome sequence of the extinct marsupial wolf/Tasmanian tiger/thylacine, but much else besides (human DNA contamination, nuclear genome from thylacine, an impressive microbial metagenome), all from some hairs from museum samples that have not been stored particularly well. 

All this is made possible by the use of so-called "next-generation" or high-throughput sequencing, which is exciting as we here at the University of Birmingham will be getting our HTS instrument soon (in fact, several instruments if the grant proposal I sweated blood to get in earlier this week is successful). 

It is a little frustrating that the authors don't provide chapter and verse on how many kits they used and how many sequencing runs they needed to do to get the ~1.1 million reads. But a quick back of envelope calculation suggests that one could replicate their study for around £20-30K today, which is astonishing. They point out in the paper that a full nuclear genome of the thylacine could be achieved for ~$1m, so I guess it is inevitable we will see one within a few more years. 

Sadly, it is very unlikely, despite a few die-hard believers and supposed sightings, that any of us will ever get to see a living thylacine. But if you want a good book to read on the subject, try the excellent Carnivorous Nights by Margaret Mittelbach and Michael Crewdson.

While we are on the subject of University Challenge...

This may be a little off-topic for this blog, but while the British media are in a feeding frenzy over Gail Trimble and her team on University Challenge, I thought I would share this with you. The quality is not perfect, but just about watchable. 

Imperial College in the University Challenge final 1995-6:

Watch out for the feature in today's Times 2 (you can access it via the free online trial or buy it in print).

Please help Darwin's medical students URGENTLY!

This week for the first time 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 seven 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:

• Erasmus Darwin: Physician or Poet or both?
  
• The Evolution of Lactose Tolerance
  
• Should being a creationist automatically disqualify applicants for admission to medical school?
  
• HeLa Cells: ethical nightmare, medical blessing, or evolution of a post-human species?
  
• What killed Annie Darwin?
  
• Why do humans reproduce sexually?
  
• Evolutionary trade-offs: sickle cell disease and malaria
  

The students have been given the option of delivering a conventional powerpoint presentation tomorrow morning or posting on a purpose-built blog, Darwin's Medical 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. At least three of them have taken up this option. 

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!

We will be meeting up to discuss what they have learnt this week tomorrow at 9.30pm, so please read and comment in the next 12 hours.

Guest Blog from Lauri Lebo: Darwin's Pilgrims 4

On our last full day in England (Friday 13th February), I visited Darwin's birthplace in Shrewsbury. It was the day after Darwin Day and the rest of this hodge-podge group of pilgrims had scattered by now for other sites and commitments. Only Alex Prodoehl, a 23-year-old hip-hop music agent, and I remained to the end.

Our larger group had toured the village of Shrewsbury earlier in the day. Our guide was Jon King, the director of the town's Darwin festival. He appeared to be a bit exhausted and perhaps hungover from the previous 24 hours of Darwin Day celebrations. Nonetheless, he was a terrific, gracious and exuberant storyteller.

I hate to say it, but Shrewsbury looks just like my mother-in-law's collectibles of Dickens' Houses. The buildings are 17th Century Tudor structures with steep-pitched gables and moss-lined roofs. Arched doorways lead to gardened courtyards and cobbled streets so narrow folks could lean out their windows and shake the hands of their neighbors.

King told us a story behind Darwin's acceptance of passage on the HMS Beagle to be a companion to the captain. After Captain Robert Fitzroy made his offer for the trip, which was due to embark in less than four weeks, Darwin's father first balked. Darwin was only 23 at the time (the same age as my youngest - a fact that never fails to give me pause) and had been an unambitious student, preferring riding, shooting and the gathering of beetles to the classroom. Robert Darwin considered the journey to be a waste of time.

Darwin wrote a letter of regret to Capt. Fitzroy. However, Josiah Wedgwood intervened on Charles' behalf and convinced his brother-in-law to let him go, arguing it would be good for the boy.

Here's where the story takes its dramatic turn: Darwin now had permission, but the letter of regret was already on its way to Fitzroy in London, 150 miles away. When he learned he could go, Darwin, as the story goes, immediately raced uphill from his home to The Lion, a pub that also chartered coaches. Breathlessly, he booked the next one leaving for London. As King said, the longest journey Darwin ever took wasn't on the Beagle, but was on that coach as he raced to beat that letter.

As it turned out, Fitzroy had received the letter, and had offered the position to another person, who had declined. Darwin was given another chance.

While others, including Cyndi, took in a bit of shopping, Alex and I walked to the edge of town to The Mount, where Darwin was born. Today, the expansive brick building is home to a government accountant agency, but one of the employees, Lorraine, was only too happy to invite us in to see the room where Susannah is believed to have given birth to Charles.

A steep hill from the house leads down to the slow-moving Severn River. Alex and I hiked down the hill and walked along the muddy banks. This used to be a garden when Darwin's family owned the land. Today, it is overgrown with brambles. As a young boy, Darwin collected bugs and other critters down here. This is where he was born a naturalist - as they say in Shrewsbury.

As Alex and I walked back to the hotel, we stopped in a shop selling bottles of Darwin's Origins, a rich brown ale brewed for the bicentenary. We asked the salesman if he might open the bottles for us. Outside, Alex raised his bottle and offered a toast, "To Darwin and his magical idea."

Home now. Took hike today with husband and flopped down on the ground in the sunshine in an open field at the top of a hill. Five turkey vultures started circling over us, spying possibility in our prone bodies. Apparently, my feigned death throes weren't convincing enough to hold their attention - Jeff noted that carrion doesn't typically giggle.

The turkey vultures glided off.

Baba Brinkman on Radio Shropshire talking about the Rap Guide to Evolution

http://www.youtube.com/watch?v=tGc1GNxGqg4

Obama name-drops Darwin

OK, he is mainly celebrating the Lincoln bicentennial, but listen out for Darwin and support for science at around 6 minutes 20 seconds.

Visit msnbc.com for Breaking News, World News, and News about the Economy

H/t Greg Laden and the Beagle Project.

Guest Blog from Lauri Lebo: Darwin's Pilgrims 3

February 12th 2009
Happy Darwin Day!

Disclaimer: I've been drinking red wine to Darwin's amazing contribution to science tonight. Forgive me if more than a bit of sloppiness creeps into this note. Much fun in Birmingham. However, didn't start out that way. Spent much of afternoon in a science conference at University of Birmingham listening to, among other things, a professor discuss, I think, the snot-like secretions of hagfish and the cell-structures of conodonta as part of the evolutionary history of vertebrates. These events always serve as a great reminder for those times I start to think I have any idea of what's going on.

Cyndi and I visited Westminster Abbey in London yesterday. We paid our respects. Cyndi lit a candle.

We had to wind our way through the maze of the cathedral, the site of which has been a place of worship by Benedictine monks since the 10th Century. We just don't have the long-view concept of history in America. Britain's greatest historical figures - Chaucer, Charles Dickins, Winston Churchill and 17 kings and queens - are all buried here.

Finally, we found it, a gray slab of granite near the exit in what is called the Nave. In simple script, it says only: Charles Robert Darwin. Born 12 February 1809. Died 19 April 1882.

I enjoy this passage from the Abbey's web site:

The Dean of Westminster, George Granville Bradley, was away in France when he received a telegram forwarded from the President of the Royal Society in London saying "…it would be acceptable to a very large number of our fellow-countrymen of all classes and opinions that our illustrious countryman, Mr Darwin, should be buried in Westminster Abbey". The Dean recalled " I did not hesitate as to my answer and telegraphed direct…that my assent would be cheerfully given".

It was a Christian funeral service. Alfred Russel Wallace, who came up with his own theory of natural selection before the publication of On the Origins of Species, was one of the pallbearers (as was the American ambassador to the UK, James Russell Lowell). I'm struck by the naturalist's graciousness. Despite the fact that Darwin's theory of natural selection might easily been Wallace's, he never exhibited any petty jealousy and remained, to the end, one of Darwin's greatest supporters.

Tomorrow: On to Shrewsbury and Darwin's birthplace...

Guest Blog from Lauri Lebo: Darwin's Pilgrims 2

Tuesday 10th February, 2009
Visited King's College Chapel in Cambridge yesterday. Henry VI was only 19 when he laid the first stone of the foundation on Passion Sunday, 1441. Built for a few dozen students attending the newly formed college, it is a place of overwhelming opulence - filled with stained glass and gold statues.

William Wordsworth wrote of the Chapel,

'...where music dwells
Lingering – and wandering on as loth to die;
Like thoughts whose very sweetness yieldeth proof
That they were born for immortality.'

Darwin, as a young seminary student at nearby Christ's College, didn't attend the services, but he used to slip in here in the evenings to listen to the choir hymns. He was not exactly a devout student. Our host Mark Pallen described a story of Darwin staying up late drinking with a friend until the two young students fell asleep in their easy chairs.

I imagine him sitting quietly in one of the back pews, drawing inspiration, not from the sermons, but from the music. I find these glimpses into his contradictory nature make me feel connected to him in some way.

Later, Heidi Bernhard-Bubb came out to our talk that was held tonight. For those who might not remember her, she was the York Dispatch reporter slandered by Dover's school board members, who was compelled to testify to the accuracy of her articles. She moved to England about a year after the trial and had a third baby. She looks terrific and stays home raising her babies, while her husband runs a school for autistic children.

Also, the first performance of Rap Guide to Evolution was performed tonight by Baba Brinkman - a Vancouver rapper touring with Cyndi and me.

Amazing summation of Darwin's theories, natural selection, sexual selection...Cyndi and I are blown away - the guy raps the phrase Australopithecus afarensis!

Sample rhyme:

No I wasn't born in Ghana but Africa is my mama
'Cause that's where my mama got her mitochondria
You can try to fight if you wanna, but it's not gonna change me
'Cause it's plain to see, Africans are my people
And if it's not plain to see then your eyes deceive you
I'm talkin' primeval; the DNA in my veins
Tells a story that reasonable people find believable
But it might blow your transistors; Africa
Is the home of our most recent common ancestors
Which means human beings are all brothers and sisters

Tomorrow, on to Westminster Abbey and Darwin's grave.

Guest Blog from Lauri Lebo: Darwin's Pilgrims 1

Sunday 8th February, 2009

Visited the grave this afternoon of Charles Darwin's daughter Annie, who died of an infection here when she was 10. Her simple gravestone says, "A dear and a good child." A small rosebush has been planted at the foot of the stone and a single pink rose blooms. Her father had brought her here in 1851 to a house perched on the Malvern Hills overlooking the expansive Severn River Valley, which is covered in fog today, to try to save her. The family had spent a summer in Great Malvern, a Victorian-era spa in western England, two years earlier. Darwin, who suffered from chronic stomach ailments, had found the water restorative. Emma, pregnant, had remained behind in London. And Annie died without her mother. Darwin did not wait for the funeral - instead, he let the servants bury Annie - and rushed back to London to be at his wife's side.

Our host, Mark Pallen, a Birmingham University microbiologist, has taken us to the graveyard, which stands under towering ancient Norfolk pines brought here by the church. Now sitting in hotel lobby waiting for dinner at the local pub, drinking coffee and watching it snow over the Malvern Priory (a Middle Age church cut from blocks cut of red and tan sandstone.) The snowflake clusters are so big, one would cover the palm of your hand.

It's cozy and sleep beckons seductively, but Cyndi Sneath and I gamely fight off its advances. (But unable, apparently, in my jet-lagged state to resist heavy-handed metaphors.)

Tomorrow, we head for Cambridge.

Wow, we made it into a Science magazine blog!

Now that things are quietening down on the Darwin bicentennial front, I was intending to write a bit more about our Devil in Dover/Rap Guide to Evolution show (on for the last time tonight in Shrewsbury). 

But I don't need to, because the whole show has been given a perfect review over on the Origins blog on the Science Magazine web site. Check it out here:

http://blogs.sciencemag.org/origins/2009/02/rapping-with-darwin-and-dawkin.html

Happy 200th Birthday Charlie!

So the long-awaited bicentenary is here! Happy Birthday Charlie. I have a busy day ahead, so will stick to reminding readers that it is also Abraham Lincoln's 200th birthday and ask you to re-read this earlier posting. 

Plus let's listen to Suzi Quatro one more time:

Happy Darwin Day!

Fluffed lines and the wandering A: from Neil Armstrong to Randal Keynes

Still very busy do the Darwin's Pilgrims tour, so little time to blog. Have now done shows and visits in Cambridge and London. Tomorrow Birmingham and Friday Shrewsbury. Will supply a fuller account when it is all over. 

But this morning we visited the Darwin's Big Idea exhibition at the Natural History Museum, which was fantastic (as was the behind the scenes tour of Darwin's fishes from Karen James: thanks!). And to see with one's own eyes the "I think" image from Darwin's notebook was amazing.

But remember my alter ego, grumpy old Victor Meldrew. Well, I got nearly to the end of the exhibition, before I experienced the "I don't believe it" moment! 

Randal Keynes misquotes his own great-great-grandfather!!! Instead of "There is grandeur in this view of life..." he says "There is a grandeur..."!

How can this be? 

Well, I have a slightly silly explanation. Remember how Neil Armstrong fluffed his lines when stepping on to the moon: "one small step for man, one giant leap for mankind" instead of what he meant to say "one small step for a man". Well the missing "a" must have been cycling on in hyperspace for thirty or more years, before suddenly landing in Randal's mouth. How else could such an eloquent man make such a mistake.

Or alternatively, we could invoke a catch phrase of English comedian Al Murray, and playfully shout "shame on you Randal!"

I don't believe it!!

English Comedian Harry Hill on Attenborough and Darwin's Finches

I am not usually a fan of Harry Hill, but this is worth watching

Hat-tip: Nick Loman

Evolving Words, Randal Keynes and The Rap Guide to Evolution

Life is rather too frenetic to blog much lately. Have just returned from a science/poetry workshop at the Hinxton Hall conference centre organised by Elizabeth Lynch as part of a Wellome Trust-sponsored project called Evolving Words. The aim of the project is to get poets and scientists working together to get young people from five UK cities to create poetry celebrating Darwin and evolution. The project will play out over most of 2009, culminating in performances in London in November. The aim of the workshop was to kick the whole project off and get everyone inspired, which it did perfectly!

In attendance on the first day was Randal Keynes, Charles Darwin's great-great-grandson and a keen devotee of the great man. I had never met Randal before, but was familiar with his work and shared several mutual acquaintances. But he embarrassed me (but in a nice way) when, during a Café Scientifique, he suddenly starting telling everyone how good my book was:

Later in the bar Randal and I had some interesting discussions of the (lack of) influence of Annie Darwin's death on Darwin's work and of the "Darwin's delay" myth. 

In the evening, there was a wonderful poetry session led by Michael Horovitz. Michael was great, but the highlight for me was Baba Brinkman performing three tracks from The Rap Guide to Evolution, the culmination of my attempts to persuade Baba to move from Chaucer to Darwin. 

Baba did a splendid job, as you can see and hear for yourself with the following three YouTube movies.

These were great! But it is going to be even better with a musical sound track and a larger stage, which is what we will have when we take Baba's show and a talk entitled The Devil in Dover (from Lauri Lebo) on tour to four UK venues (Cambridge, London, Birmingham and Shrewsbury). In the first three venues we are using university premises, so it is not clear to me whether I can open the shows up to the general public, but if you want to attend, e-mail me on m.pallen@bham.ac.uk and I will see what I can do. The gig in Shrewsbury is open to the public: get your tickets from The Hive.

I will try and post updates of our tour, which will include plenty of Darwinian tourism, but cannot promise to do so every day. I am looking forward to Lauri Lebo and Cyndi Sneath (one of the plaintiffs in the Dover trial) arriving in Malvern tomorrow. Cyndi has never left the USA before, so I will roll out the merry olde England tourism by putting her up in a grand hotel right next to the Priory Church yard where Annie Darwin is buried. 

And in case you were wondering about Greydon Square, it turns out sadly he is not coming. But I am confident that Baba will single-handedly deliver a great Rap tribute to Charles Darwin!

Darwin's struggle: It's OK, but still makes me grumpy!

I have just watched the BBC 4 programme "Darwin's Struggle: the Evolution of the Origin of Species". In general it is nicely put together and doesn't get wholly embroiled in the "Darwin's delay through fears of impact on religion" myth, giving airtime to various other threads in the story (e.g. Darwin's experimental and breeding work; his principle of divergence). But it still makes me grumpy!

Firstly, why is it that a professional film-maker and a professional actor cannot quote Darwin accurately! In the closing words of the Origin of Species, he does not write "whilst this planet has been cycling along"! He writes "whilst this planet has been cycling on"! OK, I quibble, but if they cannot even get that right, it undermines one's faith in their ability to get the less obvious stuff right!

Secondly, we have the usual old nonsense from Jim Moore about Annie Darwin's death and its influence on Darwin's religious belief and what he wrote in the Origin. Not a jot of direct documentary evidence for any of it. I will attempt a detailed dissection of these claims later in the month, but for now, let's just examine the two passages from the Origin which Moore thinks were influenced by Annie's death:

Passage 1

The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F373&pageseq=82

Well, Darwin came up with the first version of this years before Annie was even born! Here is what he wrote in his Notebook in 1838:

One may say there is a force like a hundred thousand wedges trying [to] force every kind of adapted structure into the gaps in the oeconomy of nature. or rather forming gaps by thrusting out weaker ones.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F1574f&pageseq=36

He didn't need the death of Annie to come up with that violent image!

Passage 2:

We will now discuss in a little more detail the struggle for existence. In my future work this subject shall be treated, as it well deserves, at much greater length. The elder De Candolle and Lyell have largely and philosophically shown that all organic beings are exposed to severe competition... We behold the face of nature bright with gladness, we often see superabundance of food; we do not see, or we forget, that the birds which are idly singing round us mostly live on insects or seeds, and are thus constantly destroying life; or we forget how largely these songsters, or their eggs, or their nestlings, are destroyed by birds and beasts of prey; we do not always bear in mind, that though food may be now superabundant, it is not so at all seasons of each recurring year.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F373&pageseq=77

But the progenitor of this passage in the 1844 essay carries the same misleading-glad-face-of-nature theme:

De Candolle, in an eloquent passage, has declared that all nature is at war, one organism with another, or with external nature. Seeing the contented face of nature, this may at first be well doubted; but reflection will inevitably prove it is too true. The war, however, is not constant, but only recurrent in a slight degree at short periods and more severely at occasional more distant periods; and hence its effects are easily overlooked. It is the doctrine of Malthus applied in most cases with ten-fold force.

http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=F1574f&pageseq=36

OK, there is a little more detail in the Origin, but in some ways the earlier talk of war and ten-fold force is more violent. I cannot see any effect of Annie's death here! Can you?

Case NOT PROVEN!

Cambridge: Darwin's rooms and the Rap Guide to Evolution

What was that we were saying about forgetting about Darwin? What nonsense! In fact, readers might be interested to know that Darwin's rooms in Cambridge are being nicely restored for the bicentenary. Read John van Wyhe's ongoing accounts of the process here:

http://www.christs.cam.ac.uk/alumni/distinguished-alumni/charles_darwin/darwin_room/

With luck, I might get to see the rooms when I visit Cambridge a week today, leading a "Darwin's roadshow" party of visitors, which will include two hip-hop artists, Baba Brinkman and Greydon Square and two people involved with the Dover trial, Lauri Lebo and Cyndi Sneath (one of the plaintiffs). 

We will be doing a bit of Darwinian tourism before the show in the evening. The show will include one hour on "The Devil in Dover" from Lauri and Cyndi and then will conclude with the world premier of "The Rap Guide to Evolution". 

I have seen some of the early drafts of the material from Baba and it looks very exciting, particularly as Baba has grafted some of the evolution material on to existing hip hop tracks. For example, here is a snippet of the lyrics from Baba's I'm a African (which draws on a Rap song of the same name by Dead Prez--if you follow the link, watch out for explicit lyrics).

I’m a African, I’m a African
And I know what’s happenin’
I’m a African, I’m a African
And I know what’s happenin’

1 No I wasn’t born in Ghana but Africa is my mama
2 ‘Cause that’s where my mama got her mitochondria
3 You can try to fight if you wanna, but it’s not gonna change me
4 ‘Cause it’s plain to see, Africans are my people
5 And if it’s not plain to see then your eyes deceive you
6 I’m talkin’ primeval; the DNA in my veins
7 Tells a story that reasonable people find believable
8 But it might blow your transistors; Africa
9 Is the home of our most recent common ancestors
10 Which means human beings are all brothers and sisters

You can pick up a sample of Baba's music here: a track called Natural Selection here (complete with samples of Dawkins as Darwin!).

After Cambridge, we take the show (and our Darwinian tourism) to London (Tues 10th), Birmingham (Darwin Day itself) and Shrewsbury (Fri 13th). The shows are aimed mainly at schoolkids and students, but if anyone lives near these venues and wants to come along, let me know. It is going to be an awesome bicentenary celebration!

Oh and I must remember to thank the British Council for making this all possible!

Steve Jones on forgetting about Darwin

Steve Jones, like me, is in rant mode, but he goes one step further in today's Telegraph and says let's just forget about Darwin entirely: Can we please forget about Charles Darwin?

I can see where he is coming from, but I will wait two more weeks before I join him in this position, after our Darwin roadshow and Darwin Day is over (of which more exciting details later)!