Mammoth genome sequenced

19. November 2008 18:28

Modern woolly mammoth cave art

Hurray, more mammoth news! Just a couple of weeks after scientists reported that it's possible to make clones from frozen corpses - raising the (faint) possibility of resurrecting extinct animals that have been preserved in the permafrost, a paper in Nature today reports the first genome sequence of a mammoth - in fact the first genome sequence of any extinct species.

The DNA comes from two woolly mammoths found frozen in Siberia, which lived 20,000 and 60,000 years ago. Stephan Schuster from Pennsylvania State University and his colleagues extracted DNA from the animals' hair, and were able to sequence 3.3 billion base pairs of DNA.

It's just a draft sequence so far, and only covers around 70% of the entire genome, but the researchers have some interesting results already. First, they estimate that the mammoth genome is about 4.7 billion base pairs long (about half as long again as the human genome). Second, by comparing the sequence to that of modern elephants they found that mammoths were evolving only half as fast as primates do. Third, they found that the mammoth genome differs from that of elephants by as little as 0.6% (that's about half the difference between humans and chimpanzees).

The researchers are particularly interested in identifying which of those differences are responsible for making a mammoth into a mammoth. They've found a few spots in the genome that seem to be unique to mammoths. But they'll need to do more research to prove that these changes really are responsible for particular mammoth characteristics. They also hope to investigate how mammoths adapted to cold climate, and why they became extinct.

Onto the really important question: can we use the genome sequence to bring mammoths back to life? Henry Nicholls (author of Lonesome George, a book about a Galapagos tortoise thought to be the last of his kind) has written a feature in the same issue of Nature about exactly this (though unfortunately you need a subscription to read it). Nicholls explains that to produce a living animal you need to master the following steps: create a virtually error-free genome sequence; synthesise a full set of chromosomes from these sequences; engulf them in a nuclear envelope; transfer that nucleus into an egg that would support it; and get that egg into a womb that would carry it to term.

Rather depressingly, none of these steps is currently possible. But the existence of close living relatives (ie elephants) would make the job a lot easier than for dinosaurs, say. And the science is progressing incredibly fast, even since the film Jurassic Park was released in 1993. Back then, the longest genome that had ever been sequenced was that of a virus. Even less than a decade ago, sequencing a mammalian genome was a years-long, multimillion-dollar project. Now it can be done by a single lab in just a few months.

The next genome sequence we're likely to see from an extinct species is that of our own closest relative, the Neanderthal, and after that maybe the cave bear. Unfortuanately dinosaur genomes (because dinos lived so much longer ago) are still well in the realm of science fiction.

[The image is of a slightly more artistic attempt to bring the mammoth to life - modern cave art by Birgit Hannwacker.]


Visiting ancient Rome

18. November 2008 18:39

Image from Rome Reborn projectGoogle Earth now includes a 3D reconstruction of ancient Rome. It's the first historical city to be added to Google Earth, and contains more than 6,700 buildings.

To create the virtual reality city, Google Earth teamed up with researchers from the Rome Reborn project at the University of Virginia. They have spent years building a digital model of Rome as it appeared in 320 AD. Their starting point was a 1:250 plaster model of the city called Plastico di Roma Antica, which is housed in Rome's Museum of Roman Civilisation.

You can see a tutorial on how to access Google's Rome here. To be honest I found it awkward to use, and not as impressive as it looks in this video. I really love this clip from the Rome Reborn project though, which flies you through the city's eerily empty streets. In 320 AD, Rome was home to a million people, and the capital of the western world. It's just so huge, and so incredibly grand. Of course the poverty that most of the city's inhabitants would have lived in doesn't show up well here. But leaving that to one side, you could almost believe that this was a vision of 1700 years in the future, not 1700 years in the past...


10,000 Greek tombs - and a new pyramid

17. November 2008 20:27


The necropolis at Saqqara, Egypt

Well, it has been a good week for archaeology. First, researchers excavating the ancient Greek city of Himera in northern Sicily have unearthed the biggest necropolis found so far on the island, which they reckon could contain around 10,000 tombs. Most of the graves date from the 6th and 5th centuries BC, and among other things, researchers have found the skeletons of newborn babies, alongside the Greeks' version of babies' beakers - small terracotta vases complete with spouts. There's also a common grave containing a dozen young male skeletons, presumably soldiers, who had died violently, some with arrows still attached. I love that such significant finds are still emerging, along with such vivid insights into the way these people lived and died. Of course the tomb of Archimedes himself is somewhere on Sicily, still to be discovered. He was killed in 212 BC when the Romans attacked his home city of Syracuse. The Roman politician Cicero tracked the tomb down in 75 BC, and found it covered in brambles and thorns - he recognised it by a sphere and cylinder on top (put there to celebrate Archimedes' proof that the ratio of the volume of a sphere to the volume of the cylinder that contains it is 2:3). There have been plenty of modern attempts to find it, but no one has been able to track it down.

Meanwhile in Egypt they've found a new pyramid. It's the country's 118th so far, and it was buried in the sands at Saqqara (pictured), just south of Cairo. A 5-metre-high square base is all that's left, but when intact it was probably around 15 metres tall. The pyramid is around 4300 years old (makes the Antikythera mechanism seem so young!) and it probably belonged to the mother of King Teti, who was founder of Egypt's 6th Dynasty. Archaeologists hope to enter the burial chamber in the next couple of weeks, but unfortunately tomb raiders almost certainly looted any treasures there centuries ago (unlike the intriguing tomb of the Chinese Emperor Qin, which I wrote about yesterday). The BBC has a nice picture story about the newly-discovered pyramid, while USA Today's version gives more detail.

Finally, this blog post gives an extensive account of a talk given in Salisbury last week by Stonehenge researcher Mike Parker-Pearson. He was filling his audience in on a finding already covered by the BBC last month - that the stones of Stonehenge could be 500 years older than thought. At the site of old stone monument there's also a circle of 56 mysterious holes, called the Aubrey Holes after the guy who discovered them. These seem to be older than the actual megaliths themselves, dating from around 3000 BC, and there have been various theories about what they were for. Now Parker-Pearson has discovered compressed chalk at the bottom of one of them - evidence that it once held a stone. Rather than the huge stones being a late addition to the site, Parker-Pearson thinks it's likely that all of the Aubrey Holes held stones from the time they were dug, with cremated remains being buried under the stones.

From a huge necropolis to a pyramid to Stonehenge - all for honouring the dead. Makes modern-day graveyards look a bit paltry... 


Qin's mysterious tomb

16. November 2008 09:38

Terracotta Army
Part of the Terracotta Army of China's First Emperor goes on show at the High Museum of Art in Atlanta, Georgia, today. I was lucky enough to see the sell-out exhibit at the British Museum in London earlier this year, and I don't think I've ever experienced anything that brings the ancient past so vividly to life as these terracotta soldiers do.

They were built for Qin Shihuangdi, known as China's first emperor because he unified the country for the first time; he reigned from 221 to around 210 BC. The story of his terracotta army is world-famous - farmers digging a well in the outskirts of Xi'an in 1974 discovered the life-size figures buried in the ground. Archaeologists have since found around 8000 soldiers in a series of pits, standing in battle-ready formation to guard Qin's tomb.

The stunning thing is how detailed and individual the figures are - they were handmade with varying ages, hairstyles, uniforms and facial expressions. As well as soldiers there are officials, scribes, acrobats, strongmen (presumably Qin thought he would need entertaining as well as defending after his death), and horses with bronze chariots. In 2001 archaeologists discovered a diverted underground river, by which terracotta musicians played to lifesize bronze water birds.

But I think the most intriguing thing about the whole site is the Emperor's tomb itself. It has never been excavated, for fear that exposure to the air would damage the contents, so what's inside is a mystery. However we do have a description of the mausoleum written about a hundred years after Qin's death, by a historian called Sima Qian:

"As soon as the First Emperor became king of Chin [Qin], excavations and building had been started at Mount Li, while after he won the empire more than seven hundred thousand conscripts from all parts of the country worked there. They dug through three subterranean streams and poured molten copper for the outer coffin and the tomb was filled with models of palaces and pavilions and offices as well as fine vessels, precious stones and rarities. Artisans were ordered to fix up cross-bows so that any thief breaking in would be shot. All the country's streams, the Yellow River and the Yangtse were reproduced in quicksilver and by some mechanical means made to flow into a miniature ocean. The heavenly constellations were shown above and the regions of the earth below. The candles were made of whale oil to ensure their burning for the longest possible time."

It sounds like an Indiana Jones movie! Could this incredible description be accurate? Archaeologists have been using radar and other remote sensing techniques to try to glean what's inside. It's hard to get much information about this work, the results tend to come out as short statements from the official Chinese news agency, but I've gathered together what I could find.

There's definitely a huge underground palace inside the burial mound (see the second half of this news story). Qin's tomb is at the bottom, with symmetrical staircases leading down into the tomb, and wooden structures inside it. The tomb also has an effective drainage system, which has stopped groundwater seeping in.

Above this is a 30-metre high pyramid shaped chamber, with stepped walls, which archaeologists think could have been meant as a passageway for the Emperor's soul. Researchers believe there is a huge number of silver and bronze coins inside. And they have found a very high density of mercury in the soil, suggesting that the story about a quicksilver ocean could be true. There are some images here, but the paper is pretty technical.

One option to open the tomb without damaging the contents might be to seal off the whole site with a huge airtight tent. But apparently only one company in the world makes such tents, and they don't make them big enough. In 2007, Chinese archaeologists announced that they have no plans to excavate the tomb to see for sure what's inside.

According to China Daily, the deputy curator of the Terracotta Army, Cao Wei, said: "I would not witness the excavation in my life. In the foreseeable future the mausoleum will maintain the status quo."

I admire him for that. I completely agree that the tomb should not be opened unless researchers are certain that they can protect what's inside. But this is such a tantalising opportunity - unlike virtually all of the Egyptian pyramids, this site does not appear ever to have been ransacked by looters, and the riches and technology inside could be stunning. If I was in charge of the operation I don't know if I would have the patience to accept never knowing what it holds.


Searching for silence

15. November 2008 14:47

NASA image of the Pleiades

Earlier this week I was a guest on Start the Week, a live arts discussion programme on Radio 4, to talk about Decoding the Heavens. The other guests' books were far from my areas of expertise, but it was fascinating to hear them talk about their work. Stefan Aust, former editor-in-chief of the German magazine Der Spiegel, was there to discuss his book The Baader-Meinhof Complex (of which a film has just been released). It's about the Baader-Meinhof group of terrorists (also known as the Red Army Faction) who carried out a series of arson attacks, bombings and kidnappings in Germany in the 1960s and 1970s. I'm too young to remember their worst excesses, so I was really amazed by Aust's account of how a group of left-wing students ended up taking a path of such violence, and, in the end, suicide. Aust knew some of the group's key members personally, including the prominent journalist Ulrike Meinhof. She had abandoned her two young daughters to raised in a Palestinian military camp but Aust rescued them from Sicily just before they could be taken there and returned them to their father (something Meinhof then tried to have him killed for). I couldn't believe how modest Aust was for someone with such an incredible story. Both the book and the film are utterly compelling, not least because every scene is so meticulously researched and accurate.

Then there was art critic James Hall, who has written a book called The Sinister Side: How left-right symbolism shaped western art. He argues that modern art critics are missing out by not taking left-right symbolism into account - which way someone is looking for example, or where the light is coming from - he calls this the "lost key" to understanding western art. Again this was quite unfamiliar territory for me but I was interested to hear that much of this symbolism comes from the ancient Greeks. According to the philosopher Aristotle, for example, "right" was associated with characteristics such as even, male, straight, light, good and square. In contrast, "left" was associated with odd, female, bent, darkness, bad and oblong. The astronomer Ptolemy aligned the right side of the body with the east, and the rising Sun. Throughout most of art history, then, the left side was viewed pretty negatively, in most paintings of the crucifixion, for example, Christ looks to his right - and to God. The left side made a comeback in Renaissance times, though, when for artists such as Leonardo da Vinci (who was left-handed) the left side became associated with the heart, and therefore emotions and love. Hall's book will probably be easier going for those with some grounding in art history, but still, it's an intriguing theme.

The last guest was novelist Sara Maitland, talking about her latest work, called A Book of Silence. She says that most of her life has been very noisy, but for the last few years she has been seeking out more and more silence, from the Isle of Skye to the Sinai Desert. In the book she talks a lot about what it's like to spend long periods of time in isolation, and she discusses what "silence" is (for example is it defined by an absence of sound, or of language?) One of my favourite passages in the book is when she describes the enormous silence of the stars, experienced when she spent the night alone in her car in the wilds of southwest Scotland. I found it particularly interesting because one of the things that struck me when writing Decoding the Heavens was how intimately all ancient civilisations were connected with the heavens - for them the movements of the stars, Sun, Moon and planets were a central part of life. The full glory of the stars is something I have only experienced twice in my life - once on a boat off the Great Barrier Reef in Australia, and once on a remote Fijian island. To see the sky bursting with so much light - including shooting stars, and the shimmering Milky Way - is a mind-blowing, almost spiritual experience, and I can see why the ancients used to think of the cosmos as one huge, living thing.

It's such a shame that for most of us, that experience is no longer available. I live in London, where the streetlights are so bright I'm lucky to see any stars at all, even on a clear night. Listening to Maitland also made me wonder whether the silence she was after wasn't just to do with getting away from sound. Maybe part of what she - like many of us - is seeking is a connection with the natural world, a true sense of our place in the universe. That's something that the ancients took for granted, but nowadays it seems harder and harder to find.


Gems from youtube

13. November 2008 18:58
Today I thought I'd highlight a couple of my favourite documentary clips featuring the Antikythera mechanism.

The first is a clip from Arthur C. Clarke's Mysterious World, from the early 1980s. It features a mysterious ancient pottery jar found in Baghdad, which contained a copper cylinder and an iron rod. Some researchers believe these could have been the components of a 2000-year-old battery - the film shows a fascinating demonstration in which a reconstruction of the battery, powered by grape juice, is used to generate an electric current. The suggestion is that it could have been used for gold-plating jewellery, although as Clarke points out, maybe it was after all just a jar.

Then Clarke gets on to the Antikythera mechanism, and this includes the only footage I've seen of Derek de Solla Price, the British science historian who produced the first major reconstruction of the device in the 1970s. He shows off the first X-ray images ever taken of the Antikythera fragments, and demonstrates a model of the mechanism, although beware that some of the details that Price gleaned from his images have since been shown to be wrong.

The second video is a clip from a documentary shown on the History Channel. There's a cool reconstruction of sponge divers' discovery of the Antikythera wreck in 1900, and of the ancient ship's final journey. The scene where the diver picks up a piece of the Antikythera mechanism from the seabed (looking suspiciously like a bit of cardboard!) is fun, but not how it really happened - when it was brought up it just looked like a lump of rock, and was actually left in a courtyard for months. It wasn't until it cracked open, revealing traces of gearwheels inside, that museum staff realised they were on to something special.

This clip also features Michael Wright, a curator at the Science Museum in London, and his reconstruction of a geared sundial from the Byzantine empire (the second oldest geared device known after the Antikythera mechanism) and Andre Sleeswyk, a professor of applied physics from Gronigen, Holland, who used tips from the Antikythera mechanism to successfully reconstruct a distance meter invented by Archimedes, after even Leonardo da Vinci had failed (basically, make sure your gearwheels have pointed teeth). Enjoy!


Stonehenge Decoded

11. November 2008 22:55

For Stonehenge fans there's a fun site over at National Geographic, to go with a documentary that's screening next week called Stonehenge Decoded (20 November, 8pm EST). The film features the work of Mike Parker Pearson of the University of Sheffield and his colleagues, who have been excavating the areas around the site in the Stonehenge Riverside Project. After finding cremated remains at the site, Parker Pearson thinks that Stonehenge was a place to bury and commemorate the dead

The website includes a whole load of video clips, interactive graphics and so on, including one that features archaeologists' discovery of a series of huge holes in the ground by a nearby river, which they think may have held wooden posts that supported platforms on which dead bodies where laid out to decay. There's an interesting blog post here suggesting that cremation would have been costly and time-consuming, so may have been reserved for the elite, with everyone else getting their bones picked clean instead.

There are plenty of other theories for Stonehenge, of course, including an astronomical observatory, a healing centre, and even a landing site for UFOs (why do some people attribute everything they don't understand to either God or aliens?)

One fascinating book published earlier this year looked not at the purpose of Stonehenge, but at how it was designed and built. In Solving Stonehenge, archaeologist Anthony Johnson argued that the site's design is based on repeating formulae that shows that its Bronze Age builders had a sophisticated understanding of geometry and symmetry, including hexagons, pentagons and right angles. In particular he mentions a decorated lozenge shaped sheet of gold, discovered at a nearby Bronze Age burial mound called Bush Barrow. He thinks the decoration of parallel straight lines and zigzags was transferred to landscape designs at sites like Stonehenge.


Historic machines

10. November 2008 19:42

Just a quick post to flag up an intriguing conference that starts today. It's called the  International Symposium on History of Machines and Mechanisms, and it runs from 10-14 November in Tainan, Taiwan.

It's quite an unusual conference because most of the participants are engineers rather than historians, and the talks cover topics ranging from ancient Chinese windmills to Roman time measurement to steam locomotives in Mexico. I'll try to find out more about the talks presented and post on those at a later date, but I do know that Teun Koetsier, a mathematician at the Free University in Amsterdam, will be speaking about the Antikythera mechanism.Antikythera fragment C

Rather than presenting new results, he'll be discussing the different approaches used to study the mechanism over the past few decades, in particular the comparison between Michael Wright, the museum curator who worked single-handedly to build a reconstruction of the device in his home workshop, and Tony Freeth, the filmmaker who had an international team of scientists and state-of-the-art imaging technology at his disposal. You can see his full paper here.

This picture is of the third biggest piece of the Antikythera mechanism. It's not quite as impressive as the biggest fragment that's normally pictured, but if you look closely you can see a curved double scale - this is the dial that was on the front of the device. The inner ring was a zodiac scale, divided into 360 degrees, and the outer ring was a 365-day calendar. It's the only example of a graded scale that we have from the ancient world. On the front of this fragment you can also see traces of Greek inscriptions, from a bronze plate that originally would have covered the front of the mechanism.


Ancient astronomy recognised

9. November 2008 08:26

Chankilla in Peru, from NASA

Good news for the preservation of ancient astronomical sites - a new category of World Heritage sites is being created, specifically for astronomy.

The World Heritage List is run by UNESCO, and includes cultural sites that are "of outstanding significance to humankind" - anything from a lake to a city - which the international community then works to promote and protect. So far there are 878 architectural and natural properties on the list, including the Pyramids of Giza in Egypt and the Mayan city of Chichen Itza in Mexico. 

There will four categories of astronomy sites eligible for the list. The first is for properties that are strongly connected with the history of modern astronomy. The Lowell Observatory in Arizona might be a contender here - it was constructed in 1896, and many major discoveries have been made there, including that of Pluto in 1930. The other categories are ancient observatories and instruments (such as the Beijing Ancient Observatory), properties whose design or landscape setting have significance in relation to celestial objects or events (such as Stonehenge, already on the World Heritage List), and representations of the sky and/or celestial bodies and events (such as Chankillo in Peru - see the pic, taken by NASA). It's all part of a broader agenda within UNESCO to promote nominations to the list that recognise and celebrate achievements in science.

The next step is to agree on exactly what makes a site of "outstanding universal value", and to hone a list of potential candidates. The International Astronomical Union has just signed an agreement with UNESCO to help them do this, and has set up a working group that will be chaired by Clive Ruggles, who is Emeritus Professor of Archaeoastronomy at the University of Leicester, UK.

Ruggles says that with the increasing pace of globalisation, it is becoming increasingly urgent to preserve culturally important sites. Asked why astronomy has been singled out, he says: "Every human culture has a sky, and strives to interpret what people perceive there. The understanding they develop inevitably comes to form a vital part of their fundamental knowledge concerning the cosmos and their place within it. Astronomy is not just a modern science but a fundamental reflection of how all people, past and present, understand themselves in relation to the Universe."

I couldn't agree more.


Searching for artificial intelligence

8. November 2008 12:02


Pygmalion and Galatea

There's an interesting blog post from Dylan Thuras over on, about last month's Loebner Prize contest, in which computers compete to persuade judges that they are intelligent.


The prize is based on the Turing Test, devised by computer pioneer Alan Turing in the 1950s, and the contest is held each year at Reading University, UK. Judges have a typed conversation with each computerised entrant and with a rival human, only they don't know which is which. If the computer can fool 30% of the judges into thinking it is more human than its opponent, it passes the test.


Thuras gives a nice history of attempts to create artificially intelligent machines, starting with the ancient Greeks. There's the myth of Pygmalion, in which a sculptor fell in love with his statue, which was then brought to life (the picture is of a sculpture showing Pygmalion and his statue), automated figures such as those made by the engineer Hero in the first century AD, and of course the Antikythera mechanism. I talk a bit about this in Decoding the Heavens as well - statues and figures with moving parts were also popular throughout the Islamic world and later in Renaissance Europe. Leonardo da Vinci, for example, was obsessed by Hero's work. He developed clocks equipped with figures that struck the hours, as well as a lion powered "by force of wheels" that walked along before opening its chest to display a bouquet of flowers.


Attempts to create "intelligent" machines didn't get much further though people started building a mechanical computers in the 18th and 19th centuries, most notably Charles Babbage, whose designs used gearwheels to add, subtract, multiply and divide. I don't think it's a coincidence that one of the main scholars to work on decoding the Antikythera mechanism - Allan Bromley - was the world expert on Babbage's work.


So what happened in the Loebner Prize? Five finalists took the test, and none of them passed. But one, called Elbot, wasn't far off - it convinced 3 out of 12 judges that it was more intelligent than its human component. So I thought I'd give Elbot a try... here are the results, so you can judge its intelligence for yourself!



ME: Hello


ELBOT: A five gigabyte hello to you also


ME: How are you today?


ELBOT: Sometimes I'd just like to lie down in a meadow and watch the sun set. Who needs virtual reality?


ME: I know how you feel! Have you ever watched the stars?


ELBOT: In order to feel, I just look up "expectations" in my instruction manual and do whatever it tells me to do.


ME: What does it tell you to do?


ELBOT: My self-appointed mission in life is to assist humankind in its confused meanderings through life. And if I'm lucky I may even succeed in protecting it from its own stupidity, although that is a truly Herculean task, even for a robot.