Wednesday, 21 December 2011

Charles Darwin's Gap Year(s)

A few months back I finally got hold of a copy of On the Origin of Species.  I had become a bit embarrassed by the fact that after four years of centering my studies on the ideas of Darwin, I still hadn't read the work.  When my mum picked a copy up at a charity shop and gave it to me, I immediately dived in.   Though enjoyable to finally read Darwin’s great theory in his own words, the best part was the sister book preceding it.


This is The Voyage of the Beagle, a diary describing Darwin’s journey around the world aboard the HMS Beagle as Ship’s Naturalist, straight out of university.  This was the 1830s and it is amusing to see the early nineteenth century gap year (or five) tour of the world.  The twenty-two year old Darwin’s description is vivid, enthralling and makes for a fascinating read.  You begin to admire his pluck and spirit of adventure (and admire his persistence in carrying on through many bouts of seasickness).  You also see his fascination with everything that surrounds him – both animals and people.  He writes in an honest voice, full of wonder and quite often, fun.   His prose is very accessible as well which surprised me - scientists are not often the best adventure writers!

He empathises with every living thing around him no matter how small and (in my opinion) frankly boring a species it may be.   His passion takes him on three month detours through the wilderness to collect samples, leads him to meet the military leader of a revolution in Patagonia and to live through an earthquake in Chile.  Though there are moments that grate with modern sensibilities (such as the derogatory description of indigenous South Americans he encounters), it is hard to fault him when those were the commonly held views in British society at the time.  He does redeem himself in several places further on by expressing his shock at the treatment of native slaves and a wish for equality among men (man being the operative gender).

To finish  - some of my favourite anecdotes:
  •  Fox Murder on San Pedro Island, off the coast of Chile: In which our hero notices a curious fox watching the men of the Beagle surveying the coast.  Whilst it is distracted Darwin creeps up on the animal and knocks it over the head with his geological hammer.  As Darwin puts it: “more curious or more scientific, but less wise, than the generality of his brethren”.  He later donated the specimen to the Zoological Society in London.  The fox is today known as Lycalopex fulvipesor or Darwin’s Fox. Sadly, it is critically endangered.
  • Giant Tortoise Surfing in the Galapagos:  Yes, Darwin was about twenty six by the time he reached the famous Galapagos Islands off the coast of Ecuador.  This does not stop him behaving like a student and riding a Giant Tortoise, albeit rather unsuccessfully.  A vital part of the research process I’m sure.
  •  Hanging with the Gauchos of Patagonia – In Argentina, Darwin makes friends with Gauchos (cowboys) who ride with him when he is collecting specimens.  They show him how to hunt with the traditional bolas, a type of lasso with ball weights attached to entangle the legs of the prey.  Darwin has a little accident with playing with one of these and manages to catch his own horse with him still on it, which amuses his companions greatly.  Another interesting anecdote is the locals distrust of his habit of daily face washing.  Not the done thing in nineteenth century Argentina apparently!


I would urge anyone who has an interest in evolution, Darwin or simply a good story to give The Voyage of the Beagle a go.  It is a fascinating read!

Tuesday, 18 October 2011

Denisovans and Depilation: New Thoughts On Modern Human Migration

Over the past few weeks a bewildering number of papers on human genetics has been released.  I have endeavoured to keep up with the almost weekly revelations that occurred in September and early October, but will no doubt have missed some vital points along the way.   To summarize briefly; a newly recognized human species discovered in early 2010 has a genome that overturns one of the most widely accepted models for Homo sapiens provenance and migration. Add some additional genetic studies and a lock of 88-year-old human hair from Western Australia and the palaeoanthropological world turns upside down.  To explain further I have to go back to the beginning and describe the two polarized models for modern human evolution that previously held sway.


'Out of Africa' v. The Multiregional Hypothesis
Since the 1980s there have been two main models of human migration, which I will over simplify here.  The first 'Multiregional Hypothesis' states that Homo erectus evolved in Africa and moved into Eurasia about one million years ago.  It then explains that Homo sapiens independently evolved from these H. erectus populations spread out across the globe.  The idea of ‘gene flow’ or migration is proposed to explain how complete speciation didn’t take place in each region and that homogeneity was maintained.


Out of Africa also describes an initial waved of migration by Homo erectus, but suggests that about 100,000 years ago modern humans originating from Africa then spread out across the globe and replaced all other hominin species that had come before it. I would say that the majority of academics in recent times agree with the 'Out of Africa' model (or some variant of it), especially after a paper was published that seemed to prove a single origin for modern humans in a shared common female ancestor who lived in Africa about 200,000 years ago (Cann, Stoneking and Wilson 1987). 


Mitochondrial DNA, which is passed only down the female line, was examined in 147 individuals from five major ethnic groups across the globe.  Two major conclusions were reached from the investigation.  The first was that there was the existence of two major groups  - one with very similar mtDNA of African origin; the other contained the four non – African groups.  The second conclusion was that the African group had a far greater level of variation than the other four, indicating it was the oldest DNA as it had had the most time to accumulate mutations (ibid).   This led to the ultimate conclusion that there was one original ancestor of modern humans alive about 200,000 years ago, supporting the out of Africa hypothesis.  She is referred to as Mitochondrial Eve.
On the right is the Out of Africa model showing replacement of earlier popualtions. On the left is Multiregional Theory showing gene admixture (Source: Scientific American) 
Out of Africa is not completely inflexible.  It's supporters allowed that some degree of interbreeding might have taken place between modern humans and other similar species they encountered on the way, such as Neanderthals, but that such encounters had left no lasting genetic legacy in the world population today.  I even went as far as writing an undergraduate dissertation on the reasons that two such similar species wouldn't have mixed, suggesting a biological phenomenon known as Behavioural Character Displacement.


How wrong I was.

A possible encounter in Late Pleistocene Europe? (plawiuk.blogspot.com/2006_10_29_archive.htm)
The first alarm bells began to ring when Green et al (2010) published a paper showing that up to 4% of the human genome of modern non-Africans contained Neanderthal DNA.  In genetic terms this is a massive amount and was pretty conclusive evidence that Neanderthals had not only bred with us - they are us.  With the addition of the 'X-woman' find, 2010 heralded a whole new worldview in Palaeoanthropology...and a whole new species - the Denisovans.


Who are the Denisovans?!
A human population identified from a single bone in the finger belonging to individual nicknamed 'X-woman'.  


This bone was found in a cave in Denisova, Siberia and was dated to between 50,000 and 30,000 years ago, making it contemporaneous with modern humans and Neanderthals, previously thought to be the only two hominin species left on earth by this date.  The DNA sequenced from this finger suggests that it was significantly different from both Neanderthal and modern human DNA and should therefore belong to a group of its own, which palaeoanthropologists refer to as the Denisovans.  They would have shared a common ancestor with modern humans and Neanderthals between 750,000 and 1.3 million years ago (Krause et al 2010).


Since this first study was released subsequent genetic investigations have shown that the Denisovans contributed 5-6% of the DNA in the genome of present-day Melanesians (Reich et al 2010).  A further study published this year (Reich et al 2011) shows that many South East Asian populations contain Densiovan DNA. It suggests that with a range stretching from the far North of the globe to South East Asia, the Denisovans were as flexible to changes in environment as modern human populations famously are.  


Finally, Hammer et al (2011) have shown that even in present-day African populations, such as the San, genetic material from an unknown archaic hominin makes up 1-2% of the genome, further implying we are genetic mix of different species.  


It seems likely that this fraternization between species actually benefited Homo sapiens in the long run.  An investigation of Human Leukocyte Antigens (HLAs), proteins coded for by genes essential for a healthy immune system, shows that many were 'picked up' by non-Africans from Denisovans and Neanderthals they interbred with as they moved across the globe.  Migrating Homo sapiens would have not survived the new diseases they were exposed to without these vital genes.


A Lock of Hair and the Earliest Modern Human Migration
In 1923 an Australian Aboriginal man gave a lock of his hair to an anthropologist.   This year DNA was collected from a strand of the hair and the entire genome of the man analysed.  Rasmussen et al (2011) concluded that this individual's ancestors had separated from the ancestors of all other human populations between 64 and 75 thousand years ago.  Thus Aboriginal Australians were the first modern humans to leave Africa and migrate across the globe into Asia and then Australia.  This is great news for the indigenous populations of Australia, who can now prove that they have the longest association with their land, or indeed any human population has had with any area of land.  The diagram below shows how the earliest migrations might have been timed and which groups moved where.


Early spread of modern humans outside of Africa (Science/AAAS)
To Conclude...Rather than one sweeping migration of modern humans leaving Africa 100,000 years ago that trampled on all other hominins in their way, migration seems to have occurred in numerous fits and spurts with the existing populations interbreeding with new arrivals.  Each area of the globe has a unique genetics admixture, to the benefit of all - a veritable 'melting pot' of species.


A Little Disclaimer...I must stress that genetics studies are not always to be trusted.  Mistakes have been made in the past when sampling living human populations and when dealing with contamination of fossil material. However such work can certainly contribute a great deal to Palaeoanthropology if treated with caution.


Abi-Rached et al (2011): 10.1126/science.1209202

Cann, Stoneking and Wilson (1987): 10.1038/325031a0

Green et al (2010): 10.1126/science.1188021

Hammer et al (2011): 10.1073/pnas.1109300108

Krause et al (2010): 10.1038/nature08976

Rasmussen et al (2011):10.1126/science.1211177

Reich et al (2010): 10.1038/nature09710

Reich et al (2011): 10.1016/j.ajhg.2011.09.005

Sunday, 2 October 2011

Darwinism in the Sheffield Jungle

A few months ago I wrote an article for the Sheffield Jungle, a research project run by the National Fairground Archive at the University of Sheffield. The Jungle was a travelling menagerie run by a showman called Frank Bostock that stayed in Sheffield from 1910-1911 and returned in later years. The project gives an interdisciplinary look at the menagerie and its cultural and physical legacies.  It's worth taking a gander at the website, which holds a variety of tales (including a wealthy manufacturer taking home a lion cub to his family of five young children!). The project will run until 2013 and involves weekly updates from local newspaper articles of the time.


My own contribution discusses Bostock's use of Darwinism in the showground and the grim truth behind animal exhibits.

Tuesday, 20 September 2011

A New Ancestor?

In the past few weeks there has been a great amount of publicity about a new discovery from caves in Malapa, South Africa - a hominin named Australapithecus sediba represented by two fossils excitingly named MH1 and MH2.  In fact its been so well publicized that a fair amount of work colleagues have mentioned it to me, knowing my area of interest.   My automatic reaction has been to bristle and growl a bit, especially when the phrase 'missing link' is bandied about in the press so much.  The fossil description was first published back in April 2010 when I was doing my Masters.  We discussed it at some length at uni and finally dismissed it as a variant of A. africanus, rather than as a new species ancestral to Homo.  Now, after seeing the more detailed papers, I'm not so sure...
Artist's impression of Australopithecus sediba (source: Science)
Dating
One of the original reasons for rejecting the Australopithecine fossils as a Homo ancestor was an age considerably younger than the oldest known Homo fossils.The two fossils discovered were originally dated to between 1.78 and 1.95 million years ago, based on fauna present and uranium and geomagnetic dating of the strata (Dirks et al 2010).  QED, they could not be ancestral to a genus that was older than them.  However the more recent paper gives a case for a much tighter date of 1.977 +/- 0.002 million years ago.  As the authors point out, this new dating conveniently places A. sediba much earlier than the earliest uncontested evidence of Homo in Africa (Pickering et al 2011).  I know nothing about the finer points of dating, so I can't offer much comment on the reliability of the methods used.  However this is a very, very opportune turn of events for those arguing for A. sediba to be recognized as a transitional species between Australopithecus and Homo.


Anatomy
There are several papers, each focusing on a specific area of A. sediba's anatomy including the hand, foot, pelvis and cranium.  I'm going to start with the foot, because I like feet.


The Foot and Ankle
Well preserved foot and ankle bones are fairly rare in the hominin record so the remains associated with A. sediba are very exciting.  The question palaeoanthropologists want to answer are: what form of bipedalism did A. sediba possess and how does the structure of the foot compare to Homo and other Australopithecine species?  Calcaneus, talus and tibia were all preserved in association with the adult fossil MH2 (Zipfel et al 2011).  A right talus and calcaneus show an interesting mix of mosaic features, including a cuboid facet angled like that of a modern human foot and suggesting an arched foot (apes have flat feet).    Yet, the calcaneus itself is very ape-like as are the thickened malleoli on both tibia, suggesting some form of arboreal locomotion was still important.


Remains of the foot and ankle. A=tibia,talus and calcaneus cemented together, B=distal tibia, C= fourth metatarsal (right), D=fifth metatarsal (right) (source: Science)
Overall the mosaic foot and ankle morphology suggests a bipedal gait unique to the species.


Pelvis
The pelvis is wider than that that of other Australopiths and similar to the shape of Homo erectus (Kibii et al 2011). However, A. sediba only has a cranial capacity of 420cc - that's over a hundred cubic centimeters smaller than the smallest cranial capacities measured in Homo habilis.  Until now it has always been assumed that widening pelvises were related to an increase in brain size.  In A. sediba this is obviously not the case and raises questions about how important the relationship between brain size and pelvis shape actually is.


Hand


A. sediba hand - very human-like (source: Science)


The diagram above gives an excellent idea of the features of the hand. As well as being amazingly complete for a fossil 2 million years old it also shows some clear human-like features such as shorter fingers and a longer thumb than apes, allowing for greater manipulation of objects and perhaps tool-making (Kivell et al 2011). A. sediba may not have been spending as much time in the trees as its other Australopith relatives.

Cranium

As mentioned before, the cranial capacity (420cc) is typical of an Australopithicine. However, Carlson et al (2011) produced a virtual endocast for the MH1 skull and observed some very interesting features of the hominin's brain. This includes a more human-like frontal lobe, intermediate between A. africanus and early Homo. The authors suggest that this is brain reorganization that occurred just before brain size expanded. The video below, featuring a very excited Lee Berger, shows how the skull was scanned to create this view.



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I am certainly prepared to accept A. sediba as a species in its own right after reviewing this excellent and comprehensive selection of papers. There are some clear unique traits, such as the very modern shape of the talus and the overall structure of the hand, that do not fit into the range of A. africanus. Yet, I still withhold my judgement on its status as an ancestor to species such as Homo erectus. More fossils are needed and more comparative studies should be carried out before such conclusions are made. Nevertheless, there is no doubt that these are extremely important specimens dated to just before the emergence of Homo.

To Close...
A final fascinating titbit is that there may be soft tissue preservation from Malapa! Astonishing and brilliant. A whole project has been devised to investigate this - the site is here, if you wish to take a look. It certainly looks like an exciting time for Palaeoanthropology. I only hope that I can get PhD funding for next year and get back in the game!

Carlson K, Stout C, Jashashvili T, de Ruiter DJ, Tafforeau P, Carlson K and Berger LR (2011) 'The Endocast of MH1, Australopithecus sediba' Science 333: 1402-1407.

Dirks PHGM, Kibii JM, Kuhn BF, Steininger C, Churchill SE, Kramers JD, Pickering R, Farber DL, Mériaux A-S, Herries AIR, King GCP and Berger LR (2010) 'Geological Setting and Age of Australopithecus sediba from Southern Africa', Science 328:205.

Kibii J, Churchill SE, Schmid P, Carlson KJ, Reed ND, de Ruiter DJ, and Berger LR (2011), 'A Partial Pelvis of Australopithecus sediba' Science 333: 1407-1411.

Kivell TL, Kibii J, Churchill SE, Schmid P, and Berger LR (2011) 'Australopithecus sediba Hand Demonstrates Mosaic Evolution of Locomotor and Manipulative Abilities' Science 333: 1411-1417.

Pickering R, Dirks PHGM, Jinnah Z, de Ruiter DJ, Churchill SE,Herries AIR, Woodhead JD, Hellstrom JC, and Berger LR (2011), 'Australopithecus sediba at 1.977 Ma and Implications for the Origins of the Genus Homo', Science 333: 1421-23.

Zipfel B, DeSilva JM, Kidd RS, Carlson KJ, Churchill SE, and Berger LR (2011) 'The Foot and Ankle of Australopithecus sediba', Science 333: 1417-1420.

Saturday, 10 September 2011

A Medieval Pleasance

Towers at Tregruk
Whilst doing the housework, I decided to also get  my Saturday morning fix of Time Team repeats.  I am not always impressed by their programs, but I had a surprise.   The episode focused on a little known castle in South Wales called Tregruk or Llangybi, which belonged to the rich and powerful de Clares.  The pictures below give an idea of how wild and overgrown the site is! It reminds me of Sleeping Beauty's castle.


Tregruk - very large curtain wall

Doorway at Tregruk
Mysteriously, for a site the size of Windsor Castle, there is very little evidence of buildings or activities inside the massive bailey.  After three days of puzzlement the team concluded that rather than being an important military site, it was probably in fact a 'pleasance' - a romantic medieval retreat.  The empty space may well have been full of gardens and fountains for the amusement of the rich owners.  Not an image usually associated with medieval fortifications!  It is certainly a place I'll put on my list of things to visit.
Photos are taken from: http://www.flickr.com/photos/ben_salter/sets/72157622527948039/with/4040172480/

Friday, 9 September 2011

Become A Nun

It's twelve months since I finished university and I'm living at home on minimum wage.  I have today lost my final chance of funding to do a PhD.  In addition the application for the dream job I've wanted since I was five has just been rejected. To be frank - the future looks bleak.  

At times like this, I always think, what would happen if I lived in a book?

This would be the turning point in which our heroine either applies successfully to become a governess in a remote location, consoled by the grandeur of the landscape and convenient attractiveness of her rich and enigmatic employer. Or....through a uncanny turn of fate, involving an incident with a runaway pram, earns the undying gratitude of a woman who happens to have a vacancy in her small-yet-up-and-coming-business-complete-with-group-of-eccentric-but-ever-so-loveable-employees.  

On the other hand, if you're me, you do a Guardian job search and get the result 'Become A Nun'.  I knew my Masters was useful for something.