Exciting news - Egypt's Great Pyramid is hiding secret rooms and passages. At least that's the latest claim put forward by the French architect and pyramid expert Jean-Pierre Houdin.

Houdin works with a 3D scientific software company called Dassault Systemes - using virtual reconstructions of the pyramids to put ideas about their construction to the test. In 2006, Houdin presented evidence for the theory (first proposed by his father) that building materials for the Great Pyramid were carried up an internal spiral ramp.

On Thursday he presented his latest results at a press conference in Paris - evidence for two hidden antechambers leading from the king's burial chamber.

The Great Pyramid was constructed by the 4th dynasty pharaoh Khufu, around 2560 BC. The only rooms known inside are the King's Chamber, Grand Gallery, Queen's Chamber, and an unfinished chamber cut into bedrock at the base of the pyramid (pictured right). Houdin thinks that the known corridors inside the pyramid were simply related to its construction and would have been impractical for the funeral procession to pass through. That would have required another - as yet undiscovered - passageway, as well as antechambers to store the furniture and objects related to the ceremony.

The pyramid of Khufu's father - the so-called Red Pyramid at Dahshur - has similar antechambers off the burial chamber, and Houdin points out that Khufu would have been likely to use the same architects for his own pyramid.

If these extra rooms do exist, Houdin says it would explain the strange positioning of the known passages - they had to avoid these antechambers. The theory would also explain how (as most experts believe) the only known door to the King's chamber was closed from the inside.

Houdin points to a stone block in the north wall of the burial chamber (pictured, the north wall is on the right) that does not bear any load from the course of stones above it. He thinks that this could be concealing the entrance to these secret rooms. Scientists who used ground-penetrating radar to scan the walls of the Queen's chamber saw what they thought could be a hidden corridor leading from the north wall. And this post on the Talking Pyramids blog points out that in later pyramids, the north wall was often decorated with the image of a false door.

One way to find out if Houdin is right would be to scan the walls around the King's burial chamber with non-invasive methods such as infrared imaging or radar. The Egyptian authorities have turned down Houdin's requests to do this.

However Xavier Maldague and his team from Laval University in Quebec City, Canada, have applied for permission to scan with infrared imaging - a technique that they could apparently carry out from a nearby hotel room. They are still waiting for approval but hope that they might be able to start making measurements in 2012.

I should say that it feels a little strange to be writing about ancient Egypt right now, with such dramatic scenes playing out in modern-day Cairo. I guess that archaeology is pretty low down on the list of the protester's concerns but it is still absolutely gutting to see the state of some of the Egyptian antiquities damaged by looters smashing their way through the National Museum in recent days. Among other things, a couple of stunning gilded statues of Tutankhamun, from his tomb, have been ripped from their bases (the bases are lying smashed on the floor, it's not clear from the photos I've seen where the statues themselves are). These precious objects survived more than 3,000 years in Tutankhamun's tomb before they were excavated, and we can't even keep them safe for a century.

I hope that Maldague gets permission to scan the pyramid. But if the researchers do find hidden rooms, perhaps there is an argument for leaving their contents undisturbed.

  *****

There's more on Houdin's theory at these blogs, all written by people who know far more about this than me:

Talking Pyramids

Pyramidales [in French]

Em Hotep

Few subjects in archaeology capture the imagination like Egyptian mummies do. These beautifully preserved bodies, particularly those of kings and queens, offer a tantalising window into the ancient past. And now, with state-of-the-art scientific techniques such as X-ray scanning and genetic analysis, we are finally getting definitive answers to questions relating to health, family relationships, and causes of death.

Or are we? Despite a string of triumphant headlines, the scientific analysis of Egyptian mummies remains incredibly difficult. The truth is that the latest studies are - so far - only making our understanding murkier. 

I've just written a feature for New Scientist (What killed Tutankhamun - sub required) about efforts to determine the cause of death of Tutankhamun, who died after a short reign in around 1333 BC. After decades of wild speculation about everything from birth defects to murder, 3D X-ray scans published in 2005 (see second pic, below) identified a broken leg (Annales du Service des Antiquités de L'Égypte, vol 81, p 159). Then a DNA analysis published in 2010 concluded that the pharaoh was an inbred genetic weakling, and infected with malaria (Journal of the American Medical Association, vol 303, p 638).

Both studies gained huge press coverage, including glitzy TV documentaries, and the findings have entered popular wisdom about Tutankhamun. But there is a large dollop of uncertainty associated with these results. For example, the broken leg could have been fractured after Tut's death, by the royal embalmers, or after the mummy was unwrapped in 1925. 

But it is the DNA findings that, behind the scenes, are causing the most debate, with some experts concerned that all the researchers have detected is modern contamination. I've written about this in a news story for New Scientist today (free to read) but as this is such a high-profile study I wanted to use this post to look at the arguments in a bit more depth, so you can make your own mind up!

This was a huge study of 11 royal mummies dating from around 1300 BC - the first DNA analysis of ancient Egyptian royalty - and it was carried out at great expense. The mummy samples aren't allowed to leave Egypt, so a state-of-the-art DNA lab was built at the Egyptian Museum in Cairo, funded by the Discovery Channel, which filmed the proceedings. The study was led by Zahi Hawass, the exuberant head of Egypt's Supreme Council of Antiquities, and carried out by an Egyptian team, with the help of two international consultants, Albert Zink of the EURAC Institute for Mummies and the Iceman in Bolzano, Italy, and Carsten Pusch of the University of Tübingen, Germany - both experienced mummy researchers. 

 The results were published with great fanfare in February 2010, alongside the Discovery documentary. The findings were suitably dramatic. As well as detecting DNA from the malaria parasite in four of the mummies, the researchers produced a family tree. Among other things, they identified Tut's father as the heretic pharaoh Akhenaten, concluded that Tut's parents were brother and sister, and found that two mummified foetuses found in Tut's tomb were probably his stillborn children.

 It was an unprecedented wealth of information about Tutankhamun and his family, and the authors described their work as heralding a new scientific discipline, of "molecular Egyptology".

 What hasn't made the news until now is that for many in the ancient DNA community, this study has triggered not excitement but scepticism and frustration.

To start with, some researchers are convinced that it is theoretically impossible for DNA to survive so long in such a hot environment. The warmer the conditions, the faster DNA degrades. So although DNA has been recovered from frozen mammoth or Neanderthal remains that are tens of thousands of years old, it is not expected to last as long in a hot tomb (probably around 30 ˚C). Ian Barnes, a molecular palaeobiologist at Royal Holloway, University of London, and his colleagues have calculated that in such conditions it would only last a few centuries at most, and certainly not for 3,000 years (American Journal of Physical Anthropology vol 128, p 110).

Because of this, Barnes and others say that they would expect the resulting paper to provide extensive information about the methods used, and the efforts taken to rule out modern contamination. They would also like to see the raw data, to judge the validity of the results for themselves.

Unfortunately, perhaps because the paper was published in a medical journal rather than one that specialises in ancient DNA, such information was not included. "There's a lack of detail which I find quite puzzling," says Eline Lorenzen of the Centre for GeoGenetics at the Natural History Museum in Copenhagen, Denmark, who wrote to JAMA in June, expressing caution over the results (vol 303, p 2471). "I would be surprised if any of the paper's reviewers were within the field of ancient DNA," she says. "Many of us in the DNA community are really surprised that this has been published."

Critics are especially concerned by the method that Hawass's team used to analyse the mummy DNA. The DNA in ancient samples is generally degraded, present in very small amounts, and contaminated with modern DNA. This is a particular problem for human samples, where you have to work out whether the DNA you have belongs to the original individual or to other people who have come into contact with the body in modern times.

Ancient DNA researchers usually start by trying to amplify and sequence mitochondrial DNA (mtDNA). There are thousands of copies of this in every cell, so it is much easier to work with than genomic DNA, of which there are only two copies in every cell.

Mitochondria are passed down the maternal line, so they provide information about family relationships. And sequencing the DNA gives a sense of the quality of the sample - for example it will be obvious whether you have just one sequence, or a mix of contaminating DNA from different individuals.

But the JAMA paper doesn't mention mtDNA. Instead, the researchers used genetic fingerprinting to construct their family tree. You might think that genetic fingerprinting, famous for its use in criminal investigations, should give black-and-white results. But it can actually be very subjective, particularly for poor quality samples (for example see Linda Geddes' excellent investigation).

 Genetic fingerprinting involves testing variable regions of the genome called microsatellites. These are made up of short sequence repeats, the exact number of which differs between individuals and is inherited from parent to child. Each microsatellite region is amplified using a technique called polymerase chain reaction (PCR), then researchers estimate from the size of the product how many repeats it must contain. By comparing individuals over a number of such regions, it's possible to work out whether or not they are related. 

The problem is that PCR amplifies modern contamination as well as ancient DNA, and simply checking the size of the products offers no way to distinguish between the two. "With microsatellites, it is very hard to establish if there is contamination," says Barnes. "They don't give you the sequence, it is just a coloured band on a computer screen."

To make matters worse, the PCR can slip on the sequence repeats, producing "stutter bands" of different sizes. For modern, good-quality samples, researchers can usually work out which are the stutter bands and which are the real ones. But for poor quality samples, especially when mixed with contamination, where there may or may not even be any original DNA present, teasing out which bands are real and which aren't is fraught with difficulty. "Very few ancient DNA studies have used microsatellites because they are so prone to genotyping errors," says Lorenzen.

She and Barnes are both keen to see the raw data so they can judge its quality for themselves. But the JAMA paper simply gives the genotypes that were eventually derived for each mummy.  

As well as the raw data, Lorenzen wants more information about the precautions taken to guard against contamination in the first place: "How were the DNA samples taken? What measures were taken to ensure no contamination from the individuals doing the sampling? In modern-day Egypt, what are the frequencies of these alleles? If anything else was found in the graves, have they genotyped that? As far as I can tell they did not carry out any pre-treatment precautions. There is a complete lack of information about how this was done. It rings alarm bells." 

Barnes agrees. "We know that the material has been handled in the past by quite a lot of people, and we know that DNA preservation is theoretically poor in this material. You have to assume that the material is already contaminated and then explain why the results tell you that you haven't got contamination."

So what do the researchers have to say about all this? Hawass (pictured left, with Tut's mummy) sees no cause for concern. He told me that he is confident in the conclusions reached, and describes the recent studies as "the final word" on Tutankhamun. "We announced everything that we discovered only after the findings had been reviewed by scholars connected with respected scientific journals."

For a more in-depth response to the criticisms, I went to Pusch and Zink, who designed and oversaw the JAMA study. On how the DNA could have survived, both agree that DNA from a body simply buried in the sand would probably not survive from ancient Egyptian times. But they argue that in the royal mummies, the embalming process used by the Egyptians must have acted to preserve the DNA. This included drying out the body with a naturally-occurring mixture of salts called natron.

"The Egyptians really knew how to preserve a body," says Zink. "The worst thing for DNA is humidity. They got rid of the humidity very fast, and then protected the body from the re-entry of humidity, by covering it with oil, wax and bandages." 

Pusch also believes that the embalming materials may themselves be acting to protect the DNA. "Nobody has thought about the components of the resin," he says. He says he is currently working with chemists at the University of Tübingen to investigate what different substances are present, and hopes to publish on this in mid-2011.

Regarding contamination, Pusch says that the team took their samples from deep inside the mummies' bones, where modern contamination could not have reached. (It's hard to see how this would have worked on the thin, fragile skeleton of Tutankhamun though, not to mention the tiny bones of the mummified foetuses.) They also genotyped the eight lab staff who carried out the genetic analysis to make sure that their DNA wasn't being picked up, and they checked every result in two independent labs. But as for Lorenzen's idea of using non-human remains as a negative control, "that would be a little bit stupid", Pusch says.

Pusch and Zink admit that their data, as to be expected for such difficult samples, was not always 100% clear. So they tested every microsatellite several times in samples from different locations on each mummy, and used a "majority rule" to decide on the result. "If we do the experiment 30 times on one mummy, we might get 18 the same," says Pusch. Then they used a computer programme to work out the most probable family tree for the resulting genotypes.

Zink says that he would be happy to discuss the results with other researchers but that he would be reluctant to share raw data, because the need to use the majority rule means "there could be a lot of arguing".

What about mtDNA? In fact, the researchers say that they have isolated mtDNA, but chose not to include it in the JAMA paper as they are still working on it. "We face problems getting clear results," says Zink. MtDNA sequences would give researchers their first insight into the genetic origins of the pharaohs - a potentially explosive issue - so "we want to be 100% sure", says Zink. He and Pusch are planning a paper on this, along with an analysis of the male mummies' Y chromosomes - later this year. The JAMA paper was "just the opening ceremony", says Pusch.

Overall, Pusch says he is disappointed by the criticism that the paper has received. "I don't understand people's harshness," he says. "These people have never worked on royal mummies. Give us a little bit more time, to show people that more is to come." 

But Lorenzen is not swayed. "There has been so much coverage of this, but no mention of the criticisms," she says. "It is very frustrating."

So, is this one of the most exciting developments in Egyptology, and will 2011 bring our first insight into the genetic origins of the pharaohs? Or is this a case of researchers under huge pressure for results seeing what they want to see? Pusch and Zink seem to me to be talented and tenacious researchers working in very difficult circumstances. But they need to provide the methodological details and raw data that will convince other experts of the validity of their work. When publishing such important results you cannot expect to be given the benefit of the doubt.

Here's a mystery regarding the Antikythera mechanism. If you've seen photos of the largest surviving piece of this ancient calculator (such as the one on the left), you'll be familiar with its largest gearwheel. It's clearly recognisable because it has four pieces cut out of it, giving it wide spokes in the shape of a cross. Antikythera scholars call this wheel b1.

The four spokes on b1 have some small holes in them, suggesting that some other structure was once attached to - and therefore carried around on - this wheel. But what? And for that matter, why does this wheel even have spokes? All of the other surviving gearwheels in the mechanism are solid discs.

Back in the 1990s, the mechanic and curator Michael Wright came up with the idea that b1 carried other gearwheels - a type of gearing known as epicyclic - and that this was used to model the motions of the planets. The Greeks thought that each planet moved in little circles, called epicycles, as it traced a larger orbit around the Earth. Wright built a model to show how these gears would have worked (see video).

As for the spokes, Wright reckons that the maker of the device cut out the spaces in this large wheel simply to save on valuable bronze.

Although no trace of Wright's epicyclic gearwheels survives, it's a brilliant and plausible suggestion - the inscriptions on the mechanism suggest that it did model the planets somehow - and other Antikythera experts have assumed that he was probably correct.

But now there's a rival theory. I wrote last week about a study suggesting that the Antikythera mechanism didn't model the epicycles of the planets after all - that it was actually modelling earlier astronomical theories.

 So if this cross-shaped gearwheel wasn't carrying around epicyclic gearwheels, what was it carrying?

Jim Evans, an expert in the history of astronomy at the University of Puget Sound in Tacoma, Washington, and the lead author of the latest study, suggests that four little statues or figurines could have been mounted on the spokes of b1, perhaps representing the four seasons, or winds associated with those seasons.

As b1 turned in the course of a year, one after the other of these figures would have appeared in a small window on the front face of the device. For example, the Greeks associated Boreas, god of the north wind, with winter; Zephyros, god of the west wind, with spring; and the Etesian winds with later in the summer.

As well as explaining what b1 was carrying, Evans says this theory also explains why it had spokes.

"The figurines would have ridden around on b1, and would usually have been flat against the wheel," he told me. "When one of them reached the window, a mechanism attached to the plate below b1 would have pushed an arm up through one of those large gaps in b1, to cause the figure to come forward and appear out of the window." He adds that he and his colleagues have been working on some mechanical designs for exactly how this might have worked.

I love the idea of little deities popping up through a window in the front of the Antikythera mechanism, like the world's first cuckoo clock! But how likely is this?

When I asked Alexander Jones, a historian of astronomy at the Institute for the Study of the Ancient World who has studied the Antikythera mechanism, he described the idea as "a little bit desperate". And Evans himself admits that the whole thing is "highly conjectural".

That said, Evans points out that displays involving moving figures were very popular in Medieval astronomical clocks (for example see detail from the Prague astronomical clock, above), which may be directly descended from devices like the Antikythera mechanism. And we know that the ancient Greeks did use automated figures too. For example, Hero of Alexandria, working in the first century AD, was famous for his steam-powered devices, that among other things drove miniature people, animals and birds.

The idea also reminds me of the Tower of the Winds (which I've blogged about before). It's an octagonal tower in the ancient Greek marketplace in Athens and it dates from the first or second century BC - just the same time as the Antikythera mechanism. It originally had a weather vane on top, and you can still see carvings of the gods associated with the eight winds at the top of its outer walls (see pic, left). Inside was an impressive water clock.

No physical trace of this clock remains save for the holes in the floor where it once stood, but Derek Price - a historian of science who also spent decades working on the Antikythera mechanism - reconstructed its workings in the 1960s. From the positions of the floor markings he concluded that this water clock was of a known type that included a revolving astronomical display, and he suggested that it probably had moving figures that struck the hours.

So although there is no direct evidence for the existence of pop-up figures in the Antikythera mechanism, the idea is at least possible, consistent with the surviving remains of the device, and in the spirit of the type of thing that Greeks were doing at the time. Evans also says he hopes that his suggestion will serve as a reminder to keep an open mind about the mechanism's features: "An ancient mechanic may have seen more possible uses for those holes on the spokes of b1, as well as the spaces between the spokes, than we might."

The Antikythera mechanism is by far the most sophisticated piece of technology that survives from the ancient world. This corroded mass of battered bronze gearwheels languished at the bottom of the sea for more than 2000 years, before being salvaged by sponge divers in 1901.

The device was originally a mechanical computer (some people prefer to say calculator), which used Greek astronomers' state-of-the-art theories to model the movements of the Sun, Moon and planets in the sky.

Well that's what scholars thought, anyway. But a new paper on the mechanism, published earlier this year in the Journal of the History of Astronomy, suggests that they might have got things back to front. Jim Evans, an expert in the history of astronomy based at the University of Puget Sound in Tacoma, Washington, and his colleagues Alan Thorndike and Christian Carman have made the most accurate measurements yet of the Antikythera mechanism's zodiac dial, used to display the positions of celestial bodies in the sky.

Evans described his work at an event held in March at the Getty Villa in Los Angeles, at which he and I discussed the Antikythera mechanism (see video). His analysis has various technical implications for the way that the device displayed information - to be honest when I first heard him speak I thought it was the kind of thing that only true Antikythera geeks would get excited by. But when I went through the paper in more detail I saw this knock-out sentence, right at the end:

"Finally, if the maker of the Antikythera mechanism used gears to model Babylonian astronomical cycles, and if, as is likely, the mechanism reflects a craft tradition going back to the time of Archimedes, this raises the fascinating, but unprovable, possibility that epicycles and deferents entered Greek astronomy, not because of natural philosophical considerations, but because some geometer applied a geometrical image of gearing to a cosmic problem."

The theory of epicycles - the idea that celestial bodies moved in small circles as they traced larger orbits around the Earth - is arguably the most famous aspect of Greek astronomy. Although often scoffed at, it was actually very good at explaining the apparent movements of the Sun, Moon and planets through the sky, and it pretty much defined our view of the cosmos (see top three pics for various examples) until Kepler came up with the idea of elliptical orbits in the early 17th century AD.

What Evans and his colleagues are suggesting is that geared devices like the Antikythera mechanism didn't model this theory after all. They inspired it.

That's huge. It would give mechanical models a starring role in the history of astronomy, in other words in the way that we have come to understand the universe around us. If Evans is right then without models like the Antikythera mechanism, there would have been no epicycles, and for 2000 years we would not have seen the cosmos in the way that we did. Our modern understanding of how the solar system works would presumably still be the same, but the history of how we reached this point would be dramatically different.

I've written a feature about this latest work in this week's edition of Nature. But here's a summary of what led Evans and his colleagues to suggest this idea.

First, a bit of background about epicycles. The Greeks generally thought that the celestial bodies in the solar system - the Sun, Moon and five known planets - were orbiting Earth. They saw these celestial bodies as divine, and believed that their orbits must therefore consist of perfect circles.

But this isn't what you see when you look at the sky. The Sun and Moon (because the orbits of the Earth and Moon are actually ellipses, not circles) appear to speed up and slow down. And the planets (because they're orbiting the Sun, not the Earth) have a rather inconvenient habit of changing direction.

To explain this, the Greeks came up with the idea that celestial orbits were made up of different circles superimposed on one another. For example they reckoned that each planet traced a small circle - an epicycle - at the same time as moving around its larger orbit - the deferent. Similar theories of the Sun and Moon's motion involved superimposing one circle onto another with a slightly different centre.

When researchers who had X-rayed the surviving pieces of the Antikythera device published a reconstruction of its workings in 2006, they noted a crucial piece of gearing that was used to drive the Moon pointer. A "pin-and-slot" mechanism allowed one gearwheel to drive another around a slightly different centre, giving an undulating variation in speed. This pin-and-slot mechanism was itself mounted on a bigger 9-year turntable, effectively modelling how the orientation of the Moon's ellipse rotates around Earth.

This seemed to be a lovely demonstration of an epicyclic lunar theory used by the Greeks, translated into wheels of bronze. This type of gearing, in which gear wheels ride round on other wheels, is still described as epicyclic.

Although the relevant gearing for the Sun and planets does not survive, researchers assumed that if the mechanism was using epicyclic gearing to model the motion of the Moon, it was probably doing the same thing for these other bodies too. The photo on the left shows the epicyclic gearing that models the motions of the planets in a reconstruction made by Michael Wright (see how it works in this video).

So here's the new bit. Evans has now shown that the Antikythera mechanism may not have worked this way after all. He used X-ray images to accurately measure the divisions on the device's main dial. This dial has two concentric scales, one showing the 360 degrees of the zodiac, and one showing the 365 days of the year, so that pointers moving around it can show both the date, and the position of celestial bodies in the sky.

Just less than a quarter of this dial survives. The 360 zodiac divisions should of course be very slightly wider than the 365 day divisions. But Evans found that although evenly spaced, the zodiac divisions in this surviving portion are actually closer together. To make a full circle, other parts of the zodiac scale must compensate by being extra widely spaced.

This was done on purpose, Evans believes, to model the uneven progress of the Sun through the sky. Instead of the Sun pointer moving at varying speed around an equally divided dial, it moved at constant rate around an unequally divided dial.

Evans' analysis suggests that half of the zodiac dial had extra-narrow divisions - a "fast zone" - and half had extra-wide divisions - a "slow zone". This scheme would have modelled the Sun's motion reasonably accurately and is identical to an arithmetic theory that Babylonian astronomers used for the Sun, known as System A. The Greeks borrowed other Babylonian astronomical theories, so it's not a huge stretch to think that they used this one too.

If Evans is right (and others in the field are taking his suggestion seriously) then the Antikythera mechanism did not use epicyclic gearing to model the movement of the Sun after all. It used conventional geartrains to model much older astronomical theories.

This may therefore be the case for the planets too. Evans thinks that they were shown on five individual dials, perhaps showing the timings of events in their cycles rather than their position in the sky - again, no epicycles required.

As discussed above, the Antikythera mechanism did use epicyclic gearing to model the varying motion of the Moon. But Evans points out that the amplitude of variation encoded in the pin-and-slot mechanism is closer to that used in older arithmetic theories than in the epicyclic theory used by the Greeks.

He believes that rather than modelling epicycles directly, a mechanic looking for a way to represent an older, arithmetic theory of the Moon's motion may have hit upon the idea of using gearwheels mounted on other wheels to produce the cyclic variation that he was after. In other words the inventor of epicycles was not an astronomer, but a mechanic.

Once astronomers realised that epicyclic gearing could closely model what was going on in the sky, they could have borrowed the idea of superimposed circles, and incorporated it into their own theories of how the cosmos was actually arranged. The clockwork universe was born.

Not much is known about when and how the idea of epicycles first arose, but the credit is traditionally given to an astronomer called Apollonius of Perga who lived in the third century BC. Geared astronomical devices seem to have arisen at around the same time - although the Antikythera mechanism itself dates from the second or first century BC, the Roman author Cicero wrote that Archimedes made one in the third century BC. So the timing is about right for such machines to have inspired the idea of epicycles.

Over the following centuries, there could have been an ongoing interaction between mechanics and astronomers as the theory was developed and refined. "Maybe we need to rethink the connection between mechanics and astronomy," says Evans. "People think of it as purely one way, but maybe there was more of an interplay."  

If this had happened, wouldn't somebody have written about it somewhere? Not necessarily, says Evans. He points out that the history of astronomy has generally been written by philosophers, who would have downplayed the role of mechanics.

Greek astronomy, he says, combined "a low road of nitty gritty arithmetical calculations", with "a philosophically-oriented high road" that was based on aesthetically pleasing geometric theories. "The people who wrote the history were philosophers of the high road. If there were the influence of something mechanical, it's not surprising that it wouldn't be there in the history. The historians emphasised the clean, the pure, the philosophical."

As Evans admits, it is impossible to prove where the idea of epicycles came from. But his analysis is fascinating food for thought. And a reminder, if we needed one, not to take anything about the Antikythera mechanism for granted.

"Usually in archaeology there's an elite focus on the majestic cities that we can wonder at. But the burning question is aways how did they feed these populations."

That's Stephen Houston, an expert on Maya civilization at Brown Unviersity in Providence, Rhode Island. He's commenting on a story on Nature's website today about how the ancient Maya used an elaborate system of canals to reclaim vast swamps and turn them into farms.

The Maya lived in the Yucatan Peninsula in central America, from before 1000 BC, with the civilisation reaching its height from about 400 BC to 900 AD. They're famous for their impressive stone pyramids, such as at Chichen Itza in Mexico, or Tikal in Guatemala, and for their achievements in maths and astronomy. But they lived on rough, rocky terrain, mixed with huge areas of wetland (see satellite photo) created by rising sea levels. So, as Houston says, how did they manage to grow enough food for their huge populations?

Timothy Beach and his wife Sheryl Luzzadder-Beach, both physical geographers, have been studying the remains of irrigation canals in northern Belize for the past twenty years, and reported on some of their latest work at the Geological Society of America meeting in Denver, Colorado, this week. The canals have been studied before, but the pair are using tools such as satellite imaging and isotope analysis combined with more than 60 excavations to try to work out how widespread the canals were, and exactly how they were employed.

The researchers reckon that this canal system in Belize covered an area 100 kilometres across, and was used to divert water and create new farmland. The water table in this area varied throughout the year - sometimes it was two metres below the surface, sometimes the land was completely flooded. The Maya responded by digging canals and throwing the soil onto adjacent land, creating raised fields on which they grew crops such as avocado, grass and maize.

Some of the efforts seemed piecemeal, but Beach says that others were "preplanned, large-scale efforts" involving ditches up to 900 metres long. And if the Maya were doing this in northern Belize, it seems likely that they were using the same methods elsewhere too - today around 40% of the Yucatan peninsula is swamp.

Ingenious. But sadly there was a downside - one of the theories for what caused the downfall of the Maya civilisation is that by converting the wetlands to avoid floods, they induced a catastrophic drought.

Every so often an idea comes along that is so mind-blowing it transforms your perception of reality. Yet, once you've been exposed to this new worldview, it becomes hard to see how things could be otherwise.

Here's one of them.

Most people who follow the progress of physics have heard of "dark matter". It is made up of particles that we can't see or feel. Cosmologists only know it is there because they can detect the gravitational pull it exerts on distant galaxies, but they reckon it makes up around a quarter of the mass of the universe.

But what if there are other types of matter that don't interact with any of the particles and forces that we know, not even gravity? What if these particles interact with their own forces, and form more than a few featureless clumps? What if there is a whole "dark universe" with stars and planets and even life forms, that we are oblivious to?

The idea is discussed in a book called Massive: The missing particle that sparked the greatest hunt in science, by journalist Ian Sample. It's out in the US today (and was published in the UK in June).

The book is about the hunt for the Higgs boson - a particle whose existence was first suggested in the 1960s to explain why fundamental particles have mass. Massive tells the story of this elusive entity from the first scribbles in the notebook of a young father called Peter Higgs, to the multi-billion-dollar atom smashers (most recently the Large Hadron Collider at CERN, near Geneva) built in the hope of creating it.

I really enjoyed Massive because it weaves the physics into a compelling human story; it's a science book that reads like a novel*. But for anyone who has been wondering why scientists care so much about the Higgs, the final chapter is also the best discussion I've read of what it will mean if they do finally manage to make the Higgs boson, and what finding it might tell us about the nature of the universe.

For me the most fascinating possibility Sample describes is that the Higgs could reveal the existence of dark, hidden worlds. He points out that until now, particle physics has been completely anthropocentric, focusing on the particles that make up our bodies, or that we can detect.

But, he says, some physicists are starting to question whether this is all there is: "Why should the particles of matter we have found and the four forces of nature we are aware of be the only ones there are? There is no reason why the human body should be equipped to sense everything in the universe, and the existence of dark matter proves it is not. The extraordinary possibility is that there could be a host of particles and forces that are going about their business in a world that is entirely beyond our perception." 

If so, there's no reason to think that this hidden world should be any less complex than the one we know, or even that it, too, shouldn't harbour life. If the physicists are right, "what we call reality - that is, everything we know - is part of a much greater and more complex reality that we are completely oblivious to."

I'd never really thought about this before, but now that Sample has made the point, it makes sense. It even starts to seem pretty unlikely that the stuff that we happen to be able to detect and measure should be everything there is, or even a significant fraction of everything there is. I guess it's just one more logical step in realising that we're not the centre of the universe after all.

Where does the Higgs come in? According to Sample, physicists think that the Higgs boson, and the field with which it is associated, will be tenuously linked to other Higgs fields that give mass to particles in the hidden world, forming a "bridge that provides a way to peer into the hidden world and look at the kinds of particles from which it is made".

If hidden worlds exist, then any Higgs boson made in the LHC could decay into invisible hidden-world particles, which might then break down into "real" particles that we can see. To the LHC's detectors, this would look like a sudden burst of particle tracks coming from nowhere. Scientists could then work backward to build up an idea of the kinds of hidden-world particles the Higgs boson must have decayed into.

Until then we'll just have to imagine what ghostly goings on could be passing through our bodies right now...

* As I know the author rather well I am probably biased in favour of this book. But I honestly think I would have loved it anyway.

Circular tattoos on the neck of a Peruvian mummy suggest that a medical treatment similar to traditional Chinese acupuncture was being used in south America in ancient times.

I covered the research for New Scientist recently, but I really don't think the story works without pictures of the tattoos so here they are, along with a bit more information about ancient tattoos...

The 1000-year-old mummy was found unwrapped in the sand of the desert at Chiribaya Alta in Southern Peru, in around 1990. She has decorative tattoos representing birds, apes, reptiles and symbols on her hands, arms and lower left leg.

Decorative tattoos are fairly common in human mummies. The oldest known tattoo dates from 6000 BC from the south American Chinchorros culture, and shows a thin pencil moustache tattooed onto the upper lip of a male adult.

But this mummy also has some tattoos that don't appear to be decorative - circles of different sizes placed at irregular positions on her neck. They aren't particularly pretty, and would have been hidden by her hair.

Konrad Spindler, an archaeologist best known for his excavations of Otzi the Iceman, wondered if they might have been part of a medical or therapeutic ritual, perhaps to ease neck pain. He made drawings of the tattoos (see top pic) and brought them back to Europe, along with samples of skin punched from the tattoos.

Maria Anna Pabst from the University of Graz, Austria, and her colleagues used various microscopy techniques to investigate what the tattoos were made of. The decorative markings were made of soot, which is quite common for ancient tattoos. But the dye in the neck circles consisted of partially burned plant material. It's the first time that two different kinds of tattooing materials have been found in the same mummy (Journal of Archaeological Science vol 37 p 3256).

Pabst told me that this is strong evidence the neck circles were meant for a separate purpose from the decorative tattoos. "If you use different materials, they have different functions," she says.

The idea that tattoos could have a medical purpose has been suggested before. For example, Otzi himself has the oldest tattoos ever found on a European mummy - some 15 groups of lines and shapes on his back and legs.

Spindler and his colleagues pointed out in the Lancet in 1999 (vol 354 p 1023) that Otzi's tattooed lines are located very close to classical acupuncture points, and suggested that there might have been a medical system similar to acupuncture practised in Central Europe 5200 years ago.

X-ray scans have shown that Otzi had chronic wear in his hip, knee and ankle joints and his lower spine, and the team concluded that his tattoos matched the acupuncture points that would be used to treat these ailments. They could have been part of the treatment itself, or used as a guide to self-treatment, showing Otzi where to stick the needles when he was in pain.

Of course this evidence is circumstantial, and it's extremely difficult to know what was really intended. But Pabst's comparison of two types of tattoo in the Peruvian mummy adds another useful line of evidence. It is one of only two mummies known with both decorative and what appear to be medicinal tattoos. (The other is a Scythian nomad prince from the Altai mountains, dating from around 500 BC, who has pictures of mythical creatures tattooed on his arms, shoulders, chest, back and right leg, as well as a series of dots down his spine and on his ankle - see pic, left.)

Pabst points out that in her mummy too, the circles match very well with traditional Chinese acupuncture points (see second pic, above), which is a surprise because China and south America are on different land masses. The knowledge must either have been carried far north via the Bering Strait, or developed independently.

The neck therapy would have used needles in the same way as acupuncture, Pabst reckons, but burning medicinal plants into the skin at key sites was perhaps thought to confer extra benefits. For further clues Pabst even showed Spindler's drawing of the tattoo circles to a modern-day shamanic healer in Peru - he said that the designs suggested to him a strengthening ritual, that would have been carried out on an upper class subject.

In case you're wondering, Otzi's tattoos were made of soot - Pabst carried out microscopic analysis of them in 2009 (Journal of Archaeological Science, vol 36, p 2335). But it seems unlikely that much more information will come to light on this topic. Spindler died in 2005, and Pabst has now retired, so the project has sadly come to an end.

What's like rockclimbing, and listening to an allegro molto? Being a bee, according to behaviour researcher Rodrigo De Marco. I've just written a short news story for New Scientist about a study in which De Marco and colleagues used high-speed video inside a hive to glean information about the honeybee's waggle dance. When I interviewed De Marco about his research he had some lovely insights into the mind of a bee, as well as the challenges of decoding its famous dance. His comments didn't fit into the story so I thought I'd post them here as a q&a.

First some background - that honeybees use an ingenious dance to communicate the location of nearby food sources was discovered in 1946 by Karl von Frisch. Each dance consists of a series of "waggle phases" during which the bee shakes its body from side to side (see video). Von Frisch subsequently worked out that the dancer's orientation relative to gravity during each waggle phase gives the direction to the food relative to the sun's position, while the number of side-to-side movements the dancer makes gives the distance.

But in the decades since von Frisch's work, researchers have made little progress in working out other bees decode the information in the dance. Studies have shown that followers can sense vibrations and flows in the air around the dancing bee, however they also touch the dancer directly. De Marco's work, published in Animal Behaviour, is an attempt to solve that mystery...

Q: How does a honeybee move during its waggle-phase?
A: Imagine yourself rock climbing, with your hand and feet held, and moving your backpack from side to side in a controlled manner. Like that! We also know that the dancer does not keep all its feet still while wagging its body from side to side; it moves them in a systematic fashion, pretty much as you would need to move your hands and feet in order to climb up. A single waggle-phase can last from a fraction of a second to several tens of seconds, whereas an entire dance can involve from a single to hundreds of waggle-phases.

Q: You describe the question of how information from the dance is transferred to followers as a "major gap" in understanding. Why has it been so difficult to work this out?
A: To start with, there is a grave lack of understanding of the sensory horizon of honeybees. What is meaningful input for a honeybee? How are different meaningful inputs combined? Answering this question also involves solving several separate puzzles. For example, what is the nature of the uncertainty that the dancers' audience experiences prior to and during dance following? What are the relevant cues and signals associated with the dance? How are such cues and signals being integrated from the sender's and the receiver's side of the communication process? To make matters worse, it is difficult to observe the behaviour of both dancers and followers simultaneously, and even more difficult to observe them both inside and outside the hive. So it is very hard to track the ultimate effect that the dance has on the behaviour of the individual followers.

Q: You used high-speed video to record more than 40 dances, with nearly 400 followers. What did you find?
A: We found that the higher the number of the dancer's wagging movements, the higher the number of the followers' antennal deflections.

Q: So in a sense the followers use their antennae to "count" the number of wagging movements?
A: Using the word counting would imply that followers can compute deflections of a certain size as discrete events, but we do not know whether this is how the deflections are processed by the brain. I think that instead the bees may be sensing the length of time over which the stimulation occurs, as a person might estimate the duration of a piece of music. Imagine the difference between listening to either a short or a long allegro molto.

Q: How do the followers estimate the orientation of the dancer with respect to gravity?
A: We found that the type of stimulation the followers receive depends on their position relative to the dancer. For followers who face the dancer from the side, contacts are more obvious and regular, and involve both antennae, whereas from behind they are more subtle, a bit less regular, and involve one antenna at a time. The followers might be able to use this information, combined with knowledge of their own position, to figure out the dancer's orientation. Imagine a situation in which you can easily orient your body either vertically or horizontally, and that when you find the right orientation, this is signalled to you by the occurrence of music, or a certain kind of motion. You would only need to figure out what the orientation of your body is when the music (or motion) occurs to find out what the relevant orientation is.

Q: Are the antennal deflections sufficient to transmit all the information that the followers need, or are they using other information sources too?
A: It would be unwise to imagine that honeybees rely on a single pathway. I think that we would learn a great deal by looking at how honeybees interact with each outside the hive. Can they follow each other? If yes, to what extent? The dance may be great advertisement, but it might well be that more is needed to bring the audience to the actual target.

Q: Why do you find these dances so fascinating?
A: Because their occurrence and shape can be predicted by a human observer. Hence, they are useful to gather insights about how information flows in nature. There are other communication systems in nature that humans can interpret, but in most cases the function they serve isn't so obvious. With the dance, the ultimate goal is simply to recruit comrades. Bees also have quite a restricted repertoire of behaviours. So we can observe the behaviour of dancers and followers and make very clear predictions about what we expect to see. That gives us a good chance of finding ‘meaningful' correlations. A panacea for ethologists! However, there is a danger here too: the study of the honeybee dance has frequently led to oversimplified interpretations about communication and behaviour. It seems that, sooner or later, students of the honeybee dance tend to find themselves embracing their own hypotheses a bit too kindly, instead of fighting them properly. I still fail to understand why - could it be that the idea that honeybees ‘read' the dance as we do becomes at some point irresistible?

PS De Marco carried out this research at the Freie Universität Berlin, however he is now at Max Planck Institute for Medical Research in Heidelberg, studying behaviour development and the development of neuronal circuits underlying the so-called stress response.

PPS OK so this doesn't have anything to do with the Antikythera mechanism. But De Marco's paper does have "decoding" in the title :-)

OK, now I'm obsessed with Paleodictyon. I mentioned this mysterious hexagonal entity briefly in my last post as an example of a trace fossil drawn by Leonardo da Vinci (see his sketch, left). But what is it - undersea mushroom garden, or the world's weirdest sponge?

Paleodictyon is a fossil found in sedimentary rocks that once formed the deep seabed. It consists of a network of tunnels or tubes that would have sat a few millimetres underground, with vertical shafts leading up to surface. Palaeontologists traditionally interpret it as a burrow system, dug by an unknown maker. But Paleodictyon forms a perfectly regular hexagonal pattern, like a honeycomb (see fossil cast made by Yale palaeontologist Adolf Seilacher, left). What kind of animal could have dug such geometrically perfect tunnels?

Now it turns out that this hexagonal structure may not be a burrow system after all, but the remains of a bizarre creature.

The story starts in 1976, when marine geologist Peter Rona of Rutgers University was using a giant sled carrying cameras and echo sounders to map the seabed of the Mid-Atlantic Ridge, around 3.5 kilometres down. In an area populated by black smoker hydrothermal vents, he found some strange patches of dots. The dots were holes, arranged in a "strikingly symmetric" hexagonal pattern. The patches were quite small, around 5 centimetres across, but there were thousands of them (see one of Rona's photos, below).

The patterns were so regular, and so odd, that Rona apparently even wondered for a moment whether he had stumbled across the footprints of aliens from outer space. Then Seilacher got in touch and pointed out the similarity to Paleodictyon. Seilacher and other palaeontologists had assumed that whatever made Paleodictyon, it went extinct 50 million years ago. But Rona had found the modern-day equivalent.

Between 1990 and 2003, Rona made several trips down into the abyss, in the tiny manned sub Alvin, to scoop up cores of mud that contained the mysterious hexagonal structure. The project was featured in IMAX film, Volcanoes of the Deep Sea, in 2003, and Rona finally published his results in September 2009.

Rona's work was covered in this New York Times article, but I found it frustratingly light on detail regarding Paleodictyon itself so I thought I'd summarise the main findings here.

When Rona studied Paleodictyon in the lab, he confirmed that the holes he had seen on the seabed are indeed the openings of vertical shafts, which lead to a honeycomb pattern of horizontal tunnels beneath the surface, just as seen in the fossil version (see model made by Hans Luginsland, left). The surface of the structure forms a raised shield-shaped dome in the seabed.

Disappointingly Rona found no trace of any organism associated with the tunnel structure - no body parts, biological material, or DNA. Little sediment lands on this part of the seabed, so it may be that fresh-looking holes can persist on the seafloor for hundreds of years, even after the owner/inhabitant is long dead. But intriguingly, when Rona tested a model of the structure in a flume tanks, he found that the shield-shaped profile makes it self-ventilating - in other words, water currents are deflected through the structure in a way that keeps all of the tunnels aerated and supplied with organic particles.

The study has left Rona and Seilacher with completely different views on how the structures are formed. Seilacher sees Paleodictyon is an especially complex member of a group of fossils called graphoglyptids, which palaeontologists believe are all burrows. They come in a dizzying array of shapes and patterns, including hexagons, spirals and tree-like structures (there's a nice paper showing the range of graphoglyptids here). But they all divide a given surface into equal subunits, just as human-made drainage systems do.

Seilacher reckons that graphoglyptids are basically subsurface mushroom gardens, in which foods (bacteria or fungi) are cultivated by unknown animals, probably some kind of worm. So in theory it might be possible to send a robotic sub to sit for hours next to a fresh burrow and wait for the unknown tracemaker to visit its farm.

Rona, on the other hand, thinks the hexagonal pattern of tubes represents the remains of the organism itself. His tests found that levels of bacteria are no higher inside the tunnels than outside - evidence against the farming theory.

It is also hard to imagine how any creature could have dug such a regular pattern. You can get hexagonal patterns in nature from closely packing regular subunits, such as soap bubbles, eggs, corals or honeycomb cells. To weave or burrow them is much harder, yet defects such as elongated sides or missed vertices are very rare. A computer simulation carried out in 1993 showed that the burrower would need "outstanding navigational skills" including the ability to execute 60-degree turns with an accuracy of 2 degrees, and to measure the length of the hexagon sides with an accuracy of less than 1% (Journal of Geological Education 41, 159-163; 1993).

More recently, another study applied graph theory to the tunnel network. The researchers calculated the total tunnel length for networks of varying sizes, and used a theory originally developed by the mathematician Euler to work out the shortest path an animal would need to take to visit all the parts of its burrow. One fossilised example of Paleodictyon is a metre across. Its hexagons have a side-length of just 5 millimetres, with a tube diameter of less than 1 millimetre, so the animal that dug this burrow could not have been more than 5 mm long, or more than 1 mm across. The researchers calculate that the total tunnel length in this fossil is around 230 metres, and that the burrower would need to revisit previous parts of the path at least one third of the time. To maintain its burrow system, the organism would need to move an improbably long distance relative to its own size, perhaps 46,000 times its own length and 250,000 times its width.

Instead, Rona thinks that the hexagonal tube system is all that remains of a strangely adapted form of sponge. Once the animal dies, its body parts get eaten away, leaving just the imprint of its body shape.

Rona suggests the most likely candidate is a hexactinellid sponge. These are also known as glass sponges, and have an internal skeleton made up of a four- or six-pointed silica lattice (see dried skeleton of the deep sea glass sponge Euplectella, above left). Perhaps one of these sponges, flattened into a horizontal layer, might form a hexagonal network of tubes like Paleodictyon. The vertical shafts would then allow aerated water and food particles to circulate through the animal's body.

Both ideas seem quite mind-boggling but I reckon Rona's explanation is the most convincing. But if Paleodictyon is a sponge, not a burrow, what does this mean for other graphoglyptid "burrows"? Are they actually creatures too?

After those lovely X-ray images of the shipwrecked watch in my last post, here are some more pictures. I recently wrote a feature article for New Scientist about how Leonardo da Vinci was deciphering trace fossils hundreds of years before mainstream palaeontologists caught up with him. The feature is here... the images that go with it are missing from the online version though, so I thought I'd post them here instead.

It's fairly well-known that da Vinci worked on body fossils (the direct remains of prehistoric organisms) but trace fossils - the tracks and trails these creatures leave behind - are much trickier to interpret. In da Vinci's time, scholars were arguing over why stone seashells were being found in the rocks on top of mountains. Trace fossils formed a key part of his arguments against the two prevailing theories - that the lofty seashells were the remains of sea creatures deposited during the Biblical flood, or that they had spontaneously grown inside the rock (yes really!)

Palaeontologist Andrea Baucon picked all this out of Da Vinci's cryptic notebooks, in particular the Codex Leicester. The top pic shows an extract - the highlighted text translates as: "Between one layer [of the rock] and the other there remain traces of the worms that crept between them when they had not yet dried. All the sea mud still contains shells, and the shells are petrified together with the mud." Baucon's analysis is published in Palaios (vol 25, p 361).

Baucon believes that da Vinci may also have included some trace fossils in his art. He has identified two possible candidates - slithery-looking tracks in "Madonna of the Yarnwinder" (second pic, just at the bottom of the stick) and "Virgin of the Rocks" (third pic, marked by arrow). When I asked Martin Kemp, an expert in da Vinci's art based at the University of Oxford, he reckoned that the marks in the Madonna are actually threads of yarn, but couldn't rule out that those in the Virgin were meant to represent trace fossils (although he was pretty sceptical).

 

There is one other example though that does seem quite convincing - a scrawled hexagonal pattern (last pic; left) which appears alongside some sketches of body fossils in another of da Vinci's notebooks, Codex I. Baucon points out that it looks just like Paleodictyon, one of the most common and characteristic trace fossils of the area of Italy where da Vinci was working (last pic; right). It is a network of burrows, originally dug into the sand of the seabed, made up of vertical, hexagonal shafts. The organism responsible is still a mystery. Scientists recently sent the submersible Alvin looking for it at 3500-metre-deep underwater vents. They found modern-day versions of the burrows, but no creatures were inside.

Thanks to Andrea Baucon for sending over the images.