Hurray, ancient DNA is back in the headlines. When the genome sequence of the mammoth was announced in November, I talked a bit about the possibility of using cloning to resurrect extinct creatures from their DNA, and suggested that the next genomes to be published in this area maybe those of the Neanderthal and the cave bear. Clearly inspired by the same thought, New Scientist has a light-hearted feature this week listing its top ten candidates, apart from the mammoth, for species to be brought back to life.

The main issue is preservation of the DNA. This means dinosaurs are out, because they are too old - no genetic information is likely to survive for more than a million years. So ideal candidates would have lived less than 100,000 years ago, and there will be specimens preserved in permafrost. It's also helpful to have a closely-related species alive today, that can provide eggs for the cloning process, and serve as a surrogate mother. Finally, New Scientist based its selection on a made-up measure called "megafaunal charisma" (how exciting the prospect of resurrecting these animals is) which basically means it chose the candidates it thought would be most interesting to write about.

Here is the top 10, in no particular order:

Sabre-toothed tiger

Neanderthal

Short-faced bear

Tasmanian tiger

Glyptodon (a giant armadillo the size of a Volkswagen Beetle)

Dodo

Woolly rhinoceros

Giant ground sloth

Moa

Irish elk

Gorilla (not extinct yet but could be soon)

Out of those, my favourite has got to be the Glyptodon (pictured), although the lack of a suitable living surrogate (today's armadillos aren't going to be able to carry one of those to term) would be a huge challenge. In fact the hurdles for resurrecting any of these species are still enormous, but then the science is progressing dizzyingly fast. Just 55 years ago when the structure of DNA was discovered, the idea of sequencing an entire genome in just a few months, for example, or of cloning a new individual from an adult cell, would have seemed impossible. So who knows what will be doable in the next 50 years.

Of course the ethical issues surrounding bringing back any of these species, especially the Neanderthal,  are much harder to dismiss. If they wouldn't have anywhere to live - the reason many of these animals went extinct in the first place - what's the point? But then as New Scientist says, "let's not spoil the fun". Car-sized armadillos would certainly give a trip to the New Forest a whole new edge.

So what would you bring back, and why? 

How much are researchers' interpretations of tantalising ancient remains affected by their own prejudices? It has certainly been a significant factor in studies of the Antikythera mechanism. Several scholars from naval backgrounds, who studied the fragments soon after they were retrieved from a shipwreck in 1901, were convinced it must have been a navigational instrument. Later, Erich von Daniken, the Swiss author who thinks ancient civilisations got much of their technology from visiting extraterrestrials, concluded that the clockwork machine was used in alien spaceships. Even today, experts disagree over whether the device was primarily a planetarium or an eclipse predictor, depending partly on which part of the mechanism they discovered.

A story reported in the Guardian today suggests that archaeologists working on sites across ancient Greece may be suffering from a similar problem. They often find the remains of homes that contain hundreds of drinking cups, and it is generally assumed that these must have belonged to wealthy families who threw lavish parties. But Clare Kelly Blazeby of Leeds University, who is due to speak at the Archaeological Institute of America meeting in Philadelphia on Saturday, reckons a more plausible explanation is that the buildings were owned by working class residents, who earned extra money by turning their houses into drinking dens. This would also solve the mystery of why so little physical evidence has been found of Greek tavernas, even though they are so often mentioned in classical literature. Kelly Blazeby thinks that archaeologists may not have recognised the bars when they found them because the sites didn't fit with their ideas of how domestic houses should be used. "It's amazing how entrenched people in the field are," she told the Guardian. "We are trying to change archaeologists' minds by pointing out that houses could be used economically as well as being residences."

Kelly Blazeby probably has a good point. But then her specialist field is the anthropology of working class drinking, so just maybe she too is finding what she's looking for. 

[Picture credit: Gorivero] 

Sorry for the long wait between posts, I took a break over Christmas and New Year. Thought I'd catch up with a great story about Stonehenge from while I've been away - the finding by Rupert Till, an expert in acoustics and music technology at Huddersfield University, that the ancient stone monument is perfectly designed to amplify certain sounds, even producing a "repetitive trance rhythm" in some circumstances. Till thinks that the builders of Stonehenge purposely shaped and positioned the stones for the best possible acoustics. The story was covered first in the Yorkshire Post on 2 January, then made international news over the past few days, somehow morphing into the idea that Stonehenge was a "concert venue" or (according to MSNBC) a "totally awesome rave location".

Some of the more extreme headlines are rather ridiculous - archaeologists don't think that the primary purpose of Stonehenge was music. But the events going on there would certainly have involved sound, and the idea that neolithic Britons finetuned the acoustics of their monuments isn't surprising, according to Dave Batchelor, who is an archaeologist working at the Stonehenge site. He told 24 Hour Museum: "The use of music, drums and those types of instruments is well-known from archaeological records going back tens of thousands of years to Paleolithic cave art. People were making simple flutes and rums out of animal and bird longbones and things like that."

There are also lots of other examples of ancient monuments that incorporated sound. Rock art expert Steven Waller has taken sound recordings of echoes at more than 300 archaeological sites in France, Australia and the US. At many of them, including Horseshoe Canyon in Utah and Hieroglyphic Canyon in Arizona, he has found that rock paintings tend to be located where the echoes are most intense. He thinks that the artists interpreted the eerie natural sound effects as the spirits speaking to them, and that this motivated them to create the paintings.

Thomas Ault of Indiana University, Pennsylvania, thinks that an elaborate two-storey structure in Orissa, India, that dates from the third century BC (previously interpreted as a place for meditation) is actually a theatre, after measuring its acoustics and finding that a person speaking anywhere on the "stage" area (but nowhere else) can be heard clearly throughout the site. 

And then there's my favourite - acoustic expert David Lubman has studied the Mayan site at Chichen Itza in Mexico, and believes that the Mayans designed the staircase of the main pyramid (pictured) so that its echo sounded like the chirp of their sacred bird, the quetzal. Click here to listen to two quetzal chirps, followed by the echoes of two handclaps at the pyramid.

The sad news is that at many sites, these ancient sound effects aren't recognised, let alone protected, so they are being lost through erosion, vandalism, noise pollution and alterations. The amplification that Till discovered no longer works at Stonehenge, for example. He only discovered it after visiting a full-size concrete replica of the monument in Maryhill, Washington.

Everyone's talking about two tombs just discovered in Saqqara, which is just south of Cairo in Egypt. The tombs are about 4300 years old, and date from the time of Unas, who was the last king of the 5th Dynasty. The contents of the tombs have long since been stolen but hieroglyphics at the entrances show that they belonged to two high officials - a woman who was in charge of music and entertainment for the pharaohs, and a man responsible for the quarries that supplied the stone for nearby pyramids.

The BBC has a nice video showing the tombs, with commentary from Zahi Hawass, head of Egypt's antiquities authority. The tombs themselves aren't particularly stunning but archaeologists are excited because they were found in a little-explored area of Saqqara, and their presence suggests that the necropolis there could be much larger than thought.

Meanwhile a fascinating paper to be published in next month's issue of Tunnelling and Underground Space Technology suggests that the ancient Egyptian tomb diggers must have had a sophisticated understanding of natural ventilation techniques. It's by Don Gribble, a student at Carleton University in Ontario, Canada, and he focuses on tombs dug during the New Kingdom (1570-1070 BC) in the Valley of the Kings, which is hidden in the mountains on the west bank of the Nile, 900 km south of Cairo.

Many of these tombs were dug as corridors into the mountain, with only one opening that served as both entrance and exit. The most impressive tomb found so far, called KV5, was built for the sons of Ramses II. It houses up to 150 underground chambers, and stretches more than 200 metres into the mountain. Archaeologist Kent Weeks surveyed it in 2006 as part of the Theban Mapping Project and found something puzzling: part of the floor of the central chamber had been lowered during the tomb's construction, and later raised again to the original level. Why?

Gribble thinks he has the answer. He points out that because the tombs had only one opening, ventilation would have been a huge problem for the tomb builders. He estimates that a medium size tomb of 500 cubic metres would contain enough air to support 35 workers for just eight hours. Unless the air could be refreshed, they would be forced to stop digging... or die of suffocation.

Luckily the conditions in this part of Egypt are just right for natural ventilation. The air temperature drops dramatically at night, causing a draught of cool air to flow into a tomb, flushing out stale air and dust and replacing it with fresh air. Gribble thinks the alterations to the floor of KV5 show that the Egyptians understood this and used it to their advantage.

KV5 is unique because it has two corridors that point backwards under the entrance, as well as areas that progress forwards into the mountain (you can see plans of the tomb plus a video here). With the chamber floor at its original level, cool air would have flowed forward into the tomb each night, but not into the backwards-pointing corridors. By lowering part of the floor, the workers created a wall that would have acted as a barrier and deflected the cool air into this lower part of the tomb. Once they were done with these corridors, they replaced the floor.

It's a lovely theory. At the moment there's no direct evidence for it, but Gribble suggests that archaeologists could analyse other tombs in the valley with this approach in mind. He also wonders whether any words exist in the ancient Egyptian language to describe this nightly airflow - something like "tomb breath", "living (breathing) rock" or "breath of the tomb Gods". Does anyone know?

If you've ever been to Athens, you're probably familiar with the Tower of the Winds, an octagonal marble tower in the Roman marketplace at the foot of the Acropolis. What's less well-known is that it held one of the largest and most elaborate water clocks of Greek and Roman civilisation.

The tower is one of the only buildings from ancient Greece or Rome that has never been buried or demolished, or even lost its roof. It was built at the beginning of the first century BC by a Macedonian astronomer called Andronicus of Cyrrhus. Carved on its faces are eight winged demigods, representing each of the eight winds, with a sundial beneath each one.

The inside, by contrast, has been completely gutted and the only sign of its original function is a mysterious pattern of holes and grooves carved into the floor and walls. In Roman texts, the tower was referred to as an horologium, which means "hour indicator". And the ancient name of the spring that runs above the tower in the hill of the Acropolis is Clepsydra, which means "water thief" and was a name often used for water clocks.

This much is fairly easy to find out. But what did this water clock look like? For nearly a century after the tower was first described by archaeologists in 1870 scholars didn't even attempt to answer this question because its mechanism had completely disappeared. Even today, descriptions of the tower tend to give only the shadiest of details about the clock itself. While I was researching Decoding the Heavens, however, I managed to unearth a couple of papers from the 1960s, in which a British science historian called Derek de Solla Price - better known for his work on the Antikythera mechanism - reconstructed it. The papers were published in the American Journal of Archaeology in 1966, and in the April 1967 issue of National Geographic (neither are online I'm afraid).

Price reckoned that deciphering what the floor markings once supported was like "recreating the workings of a suburban kitchen in an empty room, using the relative positions of the sockets, pipe holes and rectangular floor stains as evidence". So he drew a plan of the holes and grooves in the tower, then compared them to the water clock designs described in ancient texts. He found a match.

Water from a nearby stream poured into container that was engineered to keep a constant water level - either by overflow pipe near the top or a ballfloat that blocked the inflow pipe when the tank was full. Water then dripped from hole in the bottom of this container at a constant rate into a cylindrical vessel beneath. The rise in this water level over the day was used to measure the passing hours, and it was emptied and started again with each new dawn.

This type of clock was designed by the Greek engineer Ctesibius in the third century BC, and used throughout the Greek and Roman worlds. But the scale of the Tower of the Winds suggests that this one was huge.

A float in the measuring tank would have turned an axle as it rose, and this in turn was connected to a large bronze disc, marked with the constellations in the sky, which rotated behind a set of curved wires that represented the position of the horizon and the hours of the day - it might have looked a little like the Prague astronomical clock (pictured), although driven by water and not clockwork. From the front, an observer would see the Sun and stars riding clockwise through the sky as time passed, mirroring the movements of the heavens. Price also found channels in the floor where the overflow from the water tank fed three fountains, and grooves that held marble railings to keep spectators away from the clock's machinery. Knowing the Romans, the clock was probably also surrounded by elegant statues.

The gleaming bronze star disc turning inexorably and mysteriously in line with the sky must have been the main attraction of the bustling Athens marketplace. This was much more than just a timepiece. It was a spectacular celebration of the beauty of the heavens, and of man's understanding of it.

Time for another shipwreck story - scientists think they have solved the mystery of why the Mary Rose sank.

The Mary Rose was Henry VIII's finest warship, but she sank on 19 July 1545 while engaged in battle with the French Fleet, just off the southern coast of England. She took 415 men to their deaths, and Henry himself watched her disappear beneath the waves. But why did such a well-respected vessel sink so suddenly? The French navy claimed they had holed her, while the English said she tipped over while making a sharp turn, causing water to pour in through her open gun ports. Other theories have included everything from an unruly crew to an outbreak of dysentery.

Now researchers analysing the remains of some of the crew have come up with another idea - she sank because many of her crew were foreign, so language difficulties meant they were unable to understand orders in the heat of battle. Lynne Bell from the School of Criminology in Simon Fraser University in Burnaby, Canada, and her colleagues analysed oxygen isotope ratios in the bones and tooth enamel in 18 of the sunken sailors, and what they found was completely unexpected. Most naturally occurring oxygen exists as 16O, ie with 8 protons and 8 neutrons in the nucleus of each atom. But there are also tiny amounts of 18O, which has two extra neutrons. Water molecules containing 18O are heavier than normal, and condense more easily. So as moist air masses are carried away from the equator by prevailing winds, the heavier molecules are lost more easily as rain. The closer you get to the poles, the less 18O there is in the water. This ratio is carried over into the plants that grow in a region, and anything that eats those plants, so by looking at the ratio of 18O in someone's skeleton, you can tell where they spent most of their life.

Bell and her colleagues found that 30-60% of the sailors on the Mary Rose had 18O ratios too high for them to have been from England. They came from much further south, somewhere like Mediterranean Europe. In that case, their English probably wasn't great. As the Mary Rose turned, perhaps they weren't able to understand the order to close the gun ports in time to save her from sinking.

Those of you alert to archaeology news may have heard this before - a Channel 5 documentary mentioned it in the summer. But Bell's study is now being published, in next month's issue of Journal of Archaeological Science, so I thought it was worth mentioning again. Historians have uncovered documents refer to 600 Spanish mariners who had been stranded penniless at Falmouth 4 months earlier, and taken into the service of the King. Perhaps Henry, struggling to create Britain's first real navy in response to the French threat of invasion, was forced to use foreign crew on his prized warship - with tragic consequences.

Bell's detective work is about to hit the headlines again, by the way. She has also been studying the remains of a killer called the Mad Trapper who was caught and shot by the Mounties after a dramatic manhunt across the Canadian Arctic in 1932. This is where the expression "The Mounties always get their man" comes from. But who was he? Bell has carried out similar isotope tests on his exhumed body, to check his geographic origin and diet in the hope of establishing his true identity. The results are to be revealed in another documentary, apparently due to be shown on the Discovery Channel this month.

I was on Radio 3's Night Waves programme on Monday to chat with Jim al-Khalili about his new TV series Science and Islam (you can hear it here for the next few days). Jim is a physicist at the University of Surrey, trained in the western scientific tradition, but he was born in Baghdad. In the series, he explores the contribution of the Islamic world to the history of science. Are there Medieval Muslim scientists who should be spoken about in the same breath as Galileo, Newton or Einstein, he asks.

I've written here before about the influence of Islamic science and technology, and Jim is absolutely right that the achievements of these scholars are under-recognised today, in their home countries as well as the West. We're taught that once the ancient Greek and Roman civilisations fell, not much of importance happened in science until 1543, when Copernicus suggested that Earth orbits the Sun, and the anatomist Vesalius corrected longstanding misconceptions about the human body.

But during this time the Islamic world covered a vast kingdom that at its height stretched from Spain to northern India. Within this region, Muslims, Christians, pagans and Jews all worked together in the common language of Arabic. They had access to past knowledge from Greek, Egyptian, Persian, Indian and Chinese scholars, and starting in the eight century the Muslim rulers began a huge effort to translate, synthesise and disseminate this knowledge. It was a wonderful flowering of civilisation, openness and learning.

Much of the ancient knowledge that inspired European scientists in the 16th century reached them via Arabic translations, and for this alone western science owes a huge debt to its Islamic counterpart. And in many areas scientists working in the Islamic world improved significantly on the learning they inherited. Take the 13th-century astronomers of the Maragha school who developed mathematical techniques to describe the motions of the planets that were later used by Copernicus. Or the 9th-century Baghdad scholar al-Khwarizmi, who invented algebra (the picture shows a page from his book on the subject). In fact, pretty much any scientific word starting with "al" - such as alcohol, alkali, algorithm - probably comes from Arabic. 

Jim's series is showing on BBC4, starting on 5 January. It's a joy to watch - beautifully shot and full of fascinating ideas, stories, people and places. I'm so pleased that he's drawing attention to this crucial chapter in the history of science. But while Jim emphasises the unprecedented feats of Islamic science, I would argue that the big achievement of this period was synthesis, not revolution.

The Maragha astronomers developed the maths to improve Ptolemy's models of planetary motion, for example, motivated by the idea that celestial orbits were divine and should involve only perfect circles. But for the most part they didn't attempt to make accurate astronomical observations and then explain what they saw. Chinese astronomers wrote detailed descriptions of the Crab Nebula, dramatically formed by a supernova in 1054. But scientists in the Islamic world barely mentioned it. And they never questioned the idea that the Earth was at the centre of the universe.

It was the Europeans, for whatever reason, who broke free of their dependence on ancient texts and finally made the leap to seeing knowledge as something to be gained by observing and experimenting on the natural world. Now science, not God, was the fundamental source of knowledge. That really was a revolution.

I posted the other day about a feature I've written for this week's issue of New Scientist, about Archimedes' links to the Antikythera mechanism. The device embodied the ancient Greeks' latest knowledge about the nature of the cosmos, so I was happy to see another feature in the same issue that discusses state-of-the-art thinking from today's cosmologists. It's the idea that our universe did not begin with the Big Bang. Instead, it bounced into existence when a previous universe collapsed in on itself. Rather than collapsing to nothing, this previous universe shrank to a fiery state of almost unimaginable density and temperature (equivalent to squeezing a trillion Suns into the space normally occupied by a proton), then rebounded and started expanding again. Physicists think this could be part of an eternal series of expansions and contractions, with no beginning and no end.

There's as yet no experimental evidence for this idea but the model is gaining increasing support - alternative theories simply break down when they get too close to the moment of the universe's creation.

The Greeks may not have been surprised by the Big Bounce. One of their main schools of philosophy, Stoicism, held that the history of the universe was an endless series of cycles, in which the entire cosmos was periodically destroyed in a huge fire, or "conflagration", before being created anew.

An extremely rare astrolabe quadrant has been rescued - for the second time. Back in 2007, I wrote a news story for Nature about this intriguing device after it was plucked from a junk pile during building works in the historic British city of Canterbury. Foundations were being dug for an extension to a restaurant that was housed in a period property, and Andrew Linklater of the Canterbury Archaeological Trust, who was assigned to watch over the works, found the dirty brass plate nestled among shards of pottery in a 14th-century rubbish pit.

Linklater couldn't identify the plate, so he took it to the British Museum. The experts there "held their hands up and went wow", he told me. It turned out to be only the eighth astrolabe quadrant ever discovered. The way it had been found was even more unusual - the device would have been the height of technology at the time, and such instruments are usually handed down through collections, not found discarded in archaeological sites.

Astrolabes were used for making astronomical observations and allow their owner to tell the time and calculate latitude. They are normally circular, but the rarer quadrants were "pocket" versions - more complicated to use but easier to carry around. Back in the 14th century, the street where the quadrant was found was lined with inns for pilgrims coming to Canterbury, so perhaps it belonged to one of these travellers.

I'm writing about it again now because the UK Reviewing Committee on the Export of Works of Art and Objects of Cultural Interest has just released its annual report. This committee defers export licences on precious artistic and cultural artefacts in danger of being sold abroad, so that they remain in the country until money can be raised by a British buyer (I bet the Greek government wishes it had had such powers back when the Elgin marbles were being shipped to the UK). Eight items were saved last year, and the Canterbury quadrant was one of them. When I wrote my news story, the quadrant was about to be sold by London auctioneers Bonhams, and it was expected to net the restaurant owners between £60,000 and £100,000. The British Museum wanted to buy it but was outbid by an anonymous telephone bidder, so the government acted. In the end, thanks to the temporary ban on export (and some generous grants) the British Museum was able to buy the quadrant at a second auction in July 2008 - for £350,000!

The extension to the restaurant is now complete by the way, and the owners have apparently named it the Quadrant Bar. 

This week's issue of New Scientist includes a feature I've written about the Antikythera mechanism, you can read it for free here. I wrote a long article about this 2000-year-old device for Nature a couple of years ago, which described researchers' efforts to decode it. I wanted to do something different this time so I focused on the possibility that Archimedes could have been the original inventor of this technology (as suggested by new readings of the inscriptions published this summer) and on how astronomical models like the Antikythera mechanism existed alongside a parallel tradition of modelling living creatures such as people, animals and birds. These models affirmed the ancient Greeks' idea of a divine order, as well as being used to demonstrate basic physical laws in pneumatics and hydraulics. The Greeks have often been derided as wasting their technical ingenuity on mere toys, but as I say in the feature, these models weren't toys, they were a route to understanding and demonstrating the nature of the universe - they represented a way to get closer to the true meaning of things. To what better use could technology be put?

New Scientist also has a souped-up version (see above) of the video I posted a couple of weeks ago showing the first complete reconstruction of the Antikythera mechanism, plus some new images and graphics. The Guardian has picked up on the video today as well, with this blog post. "I defy you not to be amazed," says Guardian science correspondent James Randerson.