Bio-friendly universe

12. February 2009 22:46

Comet Ikeya-Zhang, taken by Gerald Rhemann

I guess it gives a whole new spin to the phrase "Decoding the Heavens". I just went to a press conference here at the AAAS meeting at which Anthony Remijan of the National Radio Astronomy Observatory talked about using a radio telescope to sweep the sky for signs of complex organic molecules, to gain clues to how life first formed.

Scientists have spotted large molecules in space before, including sugars, alcohols and even antifreeze (ethylene glycol). But generally they had to decide what molecules they were looking for, then look for the particular radio signatures (called "spectral lines") emitted by those molecules. That works fine, but you can only find what you were already looking for. Remijan and his colleagues tried a new approach. They used the powerful Green Bank Telescope in West Virginia to scan a star-forming region near the centre of our galaxy across a wide range of radio frequencies. Remijan said they've found more than 720 spectral lines from a whole range of molecules, including 11 never seen in space before. Around 240 of the spectral lines come from molecules that still have to be identified.

The researchers have made the whole dataset available online, so anyone who's interested can start sifting through it for evidence of new chemistry. Molecules already identified by the survey include cyanoallene, methyltriacetylene, cyclopropenone and methylcyanodiacetylene - all quite complex carbon-based molecules, with lots of double and triple bonds.

What I find most interesting about all this is how it changes our perception of where the chemical precursors of life came from. Remijan mentioned the famous Miller-Urey experiment conducted back in 1952 here in Chicago. Stanley Miller and Harold Urey built apparatus that simulated the precise atmospheric and chemical conditions thought to be present on the early Earth. It produced several molecules thought to be precursors of life, including some amino acids. The assumption was that these precise conditions on Earth were necessary for these molecules to be formed, but scientists are increasingly discovering that there's all sorts of complex organic chemistry going on in outer space, including the formation of pre-biotic molecules. These molecules probably form on the surface of interstellar dust grains, then are carried onto planets by comets and meteorites.

A second talk in the same press conference also suggested that the universe is quite a bio-friendly place. David Wilner of the Harvard-Smithsonian Center for Astrophysics and his colleagues have been using the Submillimeter Array Telescope in Hawaii to look at dusty disks surrounding nine young stars in the constellation Ophiuchus. They wanted to know whether the material in these disks was distributed in the right way to form planetary systems like our own. They found that in all cases the disks were just right for making planets. What's more, two of the nine disks had a hole in the centre, suggesting that the dust had been cleared away by young planets already formed. So planetary systems forming around stars could be the norm, rather than the exception. And where there are planets, there's the possibility of life.


Neandertal genome announced

12. February 2009 17:14

Reconstruction of what a Neandertal child might have looked like, made by researchers at the University of Zurich, based on a specimen found in Gibraltar

It's the 200th anniversary of Charles Darwin's birth today, so a great day for a post about human evolution. I'm in Chicago this week attending the annual meeting of the American Association for the Advancement of Science. The conference has only just started but already some great results have been presented by ancient DNA expert Svante Paabo.

He and his colleages at the Max Planck Institute for Evolutionary Anthropology and the DNA sequencing company 454 Life Sciences told us (via satellite link from Leipzig, ahead of a talk that Paabo will be giving here in Chicago on Sunday) that they have completed a rough first draft of the Neandertal genome. The Neandertals were our closest relatives, so the genome promises to offer unprecedented insights into what makes humans different from any other species.

Paabo and his colleagues had already published the sequence of DNA found in Neandertal mitochondria (organelles inside cells involved in energy production, which have their own genes) but this is the first overview of the whole genome. Overall they have sequenced 3.7 billion base pairs of DNA from six individual Neandertals at four sites across Europe, and they have managed to cover 63% of the Neandertal genome at least once. The biggest challenge was getting enough DNA from the fossils to sequence, and separating it from contaminating DNA from bacteria and modern humans. At best only 4% of the DNA extracted from the fossils came from the specimen itself, compared to around 70% for mammoths frozen in permafrost.

From the sequence they have produced, the researchers confirmed that Neandertals were much more similar to humans than to other species of ape, and that Neandertals and humans diverged around 830,000 years ago. We already know about a lot of genetic changes that are unique to humans compared to other apes, so the researchers are now keen to check whether the Neandertals had the human or ape versions of these genes. That'll help them to home in on genes that make us uniquely human.

Paabo didn't want to talk too much about specifics ahead of publising a formal paper, but he did confirm that Neandertals did not have the lactase gene that many humans have, meaning that they would not have been able to digest milk once they were weaned. But when it comes to the FOXP2 gene, known to be involved in speech and language, Neandertals had the same version as humans, which no other apes have. This doesn't prove that Neandertals could talk, as several other factors would have been required as well, but Paabo said there's no reason to assume they couldn't.

In general, the Neandertal genome is extremely similar to the human genome, so in most regions, it falls within the normal variation that you see in humans (this confirms evidence from other fields, such as the pictured reconstruction, created by researchers from the University of Zurich who used computur modelling techniques to add flesh to the bones of a specimen found in Gibraltar). But the researchers are now looking for particular areas where the Neanderthals are completely chimp-like. Such regions must have evolved in human ancestors after they split from Neandertals, and could contain genes that make our species unique. They've already found one such region on chromosome 7, so will be looking more closely at the individual genes there. Overall, it sounds as though there's going to be a flood of interesting data coming out of this project over the next few months.

Most of the reporters at the press conference wanted to know about the evidence for inbreeding between humans and Neandertals. We already knew from mitochondrial DNA that Neandertals made very little or no contribution to the modern human gene pool. Now the researchers can check whether any genes from our own ancestors infiltrated the Neandertal genome. The results aren't in yet, and Paabo says this is an "open question".

Other questions involved whether we can now clone a Neandertal (no, but we could put individual Neandertal genes into other species to see what physiological effect they have) and what this tells us about Neandertal behaviour (not much - and for the time being at least, archaeological evidence is likely to tell us more about this than genes will). Negative news too about the prospects for analysing the DNA of Homo floresiensis, the little "hobbit" people who lived as recently as 13,000 years ago in Indonesia. Paabo's team visited the site where their remains were found, but have been unable to extract any DNA at all from the fossils. Excavations are ongoing there so there's still a possibility of getting some DNA, but Paabo says he fears that the site is just too hot and too humid for the DNA to have survived intact.

By the way - I haven't forgotten about last week's Whipple conference on the Antikythera mechanism - it was a fascinating day, and I'll post on it shortly.


Alien hands

4. February 2009 11:06


Children holding hands, taken by Elizabeth Ann Collette

Yesterday I was in a taxi on the way to a BBC studio to chat about Decoding the Heavens on the BBC Radio Scotland show Radio Cafe (you can hear it here until next Monday) when I had an intriguing conversation with the driver. We started off wondering why a lot of people seem so desperate to attribute any ancient achievements they don't understand to aliens. The Antikythera mechanism has suffered from this a lot, starting with the Swiss author Erich von Daniken, who wrote about it in his books Chariots of the Gods and Odyssey of the Gods. In his view, the device was clearly a navigational instrument used in alien spaceships, which "tells us how little we know about the wisdom which the gods whispered into the ears of their darlings". Funnily enough, von Daniken didn't offer a single piece of evidence for his amazing claim that the device was made or influenced by aliens, or for why the aliens would have inscribed it in perfect Greek! The closest I can find is his argument that because the mechanism was made to be a portable size, "it could easily have been transported from one 'god's' palace to another". Ancient history is amazing enough, I really don't understand how someone could have so little faith in human ingenuity that they feel the need to invoke such a crazy theory. Still, von Daniken has sold millions of books, and his championing of the Antikythera mechanism may be one reason why it was ignored by mainstream historians for so long.

That's not to say intelligent alien life couldn't be out there somewhere, of course (there just isn't any evidence that such beings have visited Earth). So the taxi driver and I got on to what intelligent extra-terrestrials might look like. I reckoned that we can't just assume we would even recognise them as life-forms - exotic types of aliens that have been proposed include everything from gaseous clouds communicating via radio waves to beings based on spin configurations in a sea of liquid hydrogen. My driver was much more pragmatic, though. He argued that if there's one thing intelligent life forms would have that's similar to us, it would be their hands. To build a civilisation you need technology, he said, and for that you need to be able to manipulate the environment around you. That's something no other life form on Earth can do anywhere near as well as people. You're not going to build computer chips with fins or tentacles or giant insect feet. It's an interesting point. Even among robots and other technology, is there any design that can manipulate objects with as much dexterity and versatility as the human hand? 


Is the Pantheon a gigantic sundial?

29. January 2009 17:27


The Pantheon in Rome

The Pantheon in Rome is one of the most stunning and well-preserved buildings that survives from antiquity. But could it have been more than just a temple? In today's issue of New Scientist I've written a news story about the idea that this domed building was actually a colossal sundial. An opening in the roof of the dome lets through a dramatic shaft of sunlight. During the six months of summer the noon sun falls on the walls and floor of the temple, and in winter (when the sun is lower in the sky) it falls onto the inside of the roof itself. But at the exact moment of the two equinoxes, in March and September, the sun falls at the junction between the roof and the walls, directly above the northern doorway, and shines through a grill there onto the porch floor beyond. The idea that the building was purposely designed to mark the equinoxes was suggested in the 1970s, but no one really picked up on it. Now an expert in timekeeping called Robert Hannah, who's based at the University of Otago in New Zealand, has discussed the idea in detail in his latest book, Time in Antiquity. Equinoxes occur when the Sun is on the celestial equator, and Hannah reckons that the Romans may have seen the equinox as a sacred time, when the Emperor could be raised up to dwell there with the gods.

Hannah now plans to look for other buildings and landscapes from the ancient Greek and Roman worlds that could have similar celestial significance. For example, he points out that if you stand at the Pnyx, which was the ancient political assembly area of Athens, to the west of the Acropolis, the midsummer sunrise appears directly behind the peak of Mount Lykabettos, a prominent hill to the northeast. The summer solstice was the point in time from which the Athenians measured the start of their calendar year. Hannah argues that ancient civilisations were much more aware then we are of how natural events signalled the passing of time, and he thinks they could well have used the sunrise behind Mount Lykabettos to mark the arrival of the new year.

I've written a short review of Time in Antiquity in the same issue of New Scientist. It's a lovely book about how the ancient Greeks and Romans marked the passing of the seasons and told the time. Among other things, Hannah gives a detailed analysis of the various calendars used on the Antikythera mechanism. But what makes it for me are the anecdotes from plays and poems, which give you a vivid taste of daily life in these societies. One play has a character who is a prostitute, nicknamed Clepsydra, which was the name for a type of water clock, because she used one to time her sessions with clients. Another features a guest invited to dinner when his shadow measures twenty feet long, but he's so eager for food that he measures it at dawn instead of dusk, and arrives hours early. But my favourite is probably a poem written by a Roman disgruntled that he can no longer eat when he wants because meal times are being set by new-fangled sundials. I used it in Decoding the Heavens too, here's that version:

The gods confound the man who first found out

How to distinguish hours! Confound them too,

Who in this place set up a sundial,

To cut and hack my days so wretchedly

Into small portions! 


New model of the Antikythera mechanism

28. January 2009 14:17


Close up of front dial

After letting you know about the upcoming conference featuring members of the Antikythera Mechanism Research Project, today I can update you about Michael Wright, who has been working on the Antikythera mechanism since the early 1980s. He made the first working model of the mechanism (I've previously posted a video of it on youtube). Now he's working on a second model.

The first version was made out of packing crate wood and recycled brass plates from a pub door. Michael built it bit by bit, reworking and replacing different sections over the years as he studied his X-rays of the original Antikythera fragments, and worked out how the machine was put together.

Model of Antikythera mechanism, front view

Now that the structure of the mechanism is generally agreed upon (the surviving parts at least), Michael is making a smarter display version, and he has kindly sent me some photos of it. The case is made of maple, with wood panels above and below the front dial instead of the old brass strips. The dials are pretty similar to the older model, but the new ones are neater, and Michael says he has worked out how the calendar ring was held into the front dial, which he wasn't sure about before.

The top two photos show the mechanism from the front - the pointers show the Sun, Moon and the five planets that the Greeks knew about, as they circle through the sky. The inner dial is a zodiac scale, while the outer dial shows the days of the year. In the close up you can see the engravings better - look for the Sun pointer (second from left, labelled "Helios"). On the zodiac scale you should also be able to recognise Parthenon on the left (the Greek name for the sign Virgo) and Chelai on the right (meaning "claws", this is what the Greeks called the sign of Libra).

Close up of upper back dial, showing inner Olympiad dialThe third picture is a close up of part of the upper back dial - it was a spiral calendar inscribed with local month names, with a tiny 4-year dial inside it showing the timing of the Panhellenic Games, including the Olympic Games. Below this is a second spiral (not shown) which displayed the details of upcoming lunar and solar eclipses.

What a wonderful piece of machinery. I've had quite a few emails from people asking where they can buy an Antikythera mechanism for themselves, but as far as I know there are no plans to make them commercially.


Upcoming conference on the Antikythera mechanism

24. January 2009 09:24

Main fragment of the Antikythera mechanismJust a quick note today to let you know about a conference that's coming up on the Antikythera mechanism. It's open to the public and it's being held in Cambridge on 6 February (more details here). The speakers include Mike Edmunds and Tony Freeth, who headed the latest team to image the fragments of the Antikythera mechanism, as well as Yanis Bitsakis and Alexander Jones, who both helped to read the inscriptions that were revealed. Because it's a public meeting I don't know if they'll be giving away any as-yet unpublished secrets, but it should be a wonderful opportunity to hear about the latest work on this fascinating device, from the researchers who carried it out. I'll certainly be there, so I'll post about it afterwards, but I imagine they'll be focusing on their most recent paper, published in Nature last July. In it they reported that the mechanism had a 4-year dial on it that showed the timing of the Panhellenic Games, including the Olympic Games, as well as a local calendar which hinted that the mechanism might have come from Syracuse, on the island of Sicily in the western Mediterranean. This was a huge surprise because all the indications from the shipwreck on which the mechanism was found suggested that it came from somewhere much further east, perhaps Rhodes. (See this news story I wrote about it at the time for New Scientist, or my more recent feature.)

If you can't make it on the day, there's also an associated exhibition dedicated to the Antikythera mechanism, at Cambridge's Whipple Museum of the History of Science until spring 2009. The mechanism itself is on display in the National Archaeological Museum in Athens, but the exhibition has information about the latest research by Tony Freeth's team, as well as this beautifully-made video.


Galileo next for DNA treatment

23. January 2009 11:41

Portrait of Galileo Galilei by Justus Sustermans painted in 1636There's a story doing the rounds at the moment that Italian scientists are seeking permission to exhume Galileo's body to see if they can extract DNA from it. Galileo was known to have suffered from a degenerative eye disease that left him blind before he died, so they want to look for evidence in his DNA of what the disease was, and exactly how it might have affected what he saw through his telescope. Paolo Galluzzi, director of the Institute and Museum of the History of Science in Florence, says this might help to explain certain mistakes Galileo made, such as why he described Saturn as having "lateral ears" rather than rings. But really, this project has to be an incredible longshot, even if the researchers do get permission to open Galileo's grave. As one expert in ancient DNA comments in ABC's version of the story: "If you put a human corpse in a coffin and seal it inside a slab of granite, which appears what happened to Galileo's body, there is going to be a huge amount of purification [I assume this is meant to say putrefaction] and decomposition," he says. DNA was recently used to identify 16th-century human remains buried in Poland as belonging to the astronomer Copernicus, but simply checking for a match between two sequences isn't as challenging as trying to identify specific mutations within the genes associated with blindness. Still, it's all great publicity for International Year of Astronomy, organised this year by the International Astronomical Union and UNESCO to celebrate the 400th anniversary of Galileo's first use of an astronomical telescope.


Eyes to the stars

22. January 2009 16:38

Star cluster NGC 290, taken by Hubble Space TelescopeBack in November, I posted about an initiative to allow astronomy sites to be recognised on the World Heritage List. I think this is a long overdue project (and part of a broader need to recognise scientific heritage more generally) so I invited Clive Ruggles, an archaeoastronomer and chair of the working group that will decide how these astronomy sites should be chosen, to write a comment piece for New Scientist about why he thinks ancient astronomy is so important for our cultural heritage. You can now read the result here, as well as view a photo gallery showing some of the world's most striking astronomical sites, as chosen by leading archaeoastronomy experts. Old favourites such as Stonehenge in the UK and Chichen Itza in Mexico are covered, but also lesser known sites like the Big Horn Medicine Wheel in Wyoming (an oval arrangement of stones aligned to the summer solstice) and a 7th-century observing tower in Cheomseongdae, South Korea. 

One thing I found particularly interesting about Ruggle's article was the idea that rather than simply preserving ancient sites in isolation, we should try to look after the environments in which they were placed. For astronomical sites that of course includes the sky - an ancient observatory can't be truly appreciated without the starry sky to go with it, yet today an undimmed view of the stars is distressingly rare. The last time I saw a properly dark sky was several years ago, sitting on the beach of a tiny island in Fiji, far from any artificial lights. It was one of the most beautiful things I've ever experienced; far from being dark the sky seemed alive and pulsating, an awesome (and colourful!) display of shimmering, bursting light - it's easy to see why ancient people thought they saw gods up there. "To those of us in the modern, lit-up world, the first time that we see a truly dark night sky can be breathtaking," says Ruggles. "But until relatively recently, most people experienced this spectacle every clear night, wherever they lived. If we want to appreciate the beliefs and practices reflected in the architecture of ancient temples and tombs, we cannot ignore their relationship to the sky."

This obsession with the sky was also what drove the development of much ancient technology including the first scientific instruments, from sundials to astrolabes, and of course the Antikythera mechanism.


Ancient parchment gives up its secrets

20. January 2009 17:29


First page of the Rijmkroniek by Melis Stoke (Manuscript A, 14th century) Parchment, 90 pages

A few sources over the past week have picked up a story about DNA being extracted from very old parchment. Made from dried animal skin, parchment was a popular writing material in the ancient world and through Medieval times. The story reported last week was that researchers from North Carolina State University in Raleigh tested five pages from a 15th-century French manuscript and found genetic material from two closely related calves. Tim Stinson will be presenting the results of the research at the annual meeting of the Bibliographic Society of America on Friday. The hope is that identifying DNA from manuscripts of known origin could shed light on ancient trade routes or herding practices. Alternatively, comparing the DNA of manuscripts for which the date or source isn't known with others for which it is, might help provide clues as to their origin.

DNA has been extracted from old parchment before. One of the key studies was published in 2007 by Greek researchers including Yanis Bitsakis and Agamemnon Tselikas at the Centre for History and Palaeography in Athens. Bitsakis and Tselikas are experts in deciphering ancient lettering - they were both involved in reading the inscriptions revealed when the mysterious Antikythera mechanism was X-rayed in 2005. I visited them at the centre when researching Decoding the Heavens, and it's a lovely place, hidden in an Athens back street and filled with piles and piles of beautiful old books and manuscripts. While I was there they told me how they had teamed up with ancient DNA expert Nikos Poulakakis from the University of Crete to extract DNA from some of the collection. They were able to identify DNA from three Greek manuscripts dating from the 13th and 16th centuries AD, which turned out to come from three different goats.

The US and Greek researchers are now in contact. Bitsakis tells me they hope to build a database of DNA sequences from manuscripts, using Tselikas's collection as a starting point.


Uncrackable codes

19. January 2009 15:27

Close up of Phaistos Disc (picture credit: asb)

Another top ten today - there's a fun blog post over on Beauty of Earth, with a list of the ten most famous uncracked codes. They range from Kryptos, a 1990 sculpture installed in the grounds of the CIA in Langley, Virginia, to Linear A, one of two linear scripts used in ancient Crete. (The other script, Linear B, was deciphered in 1952 by a British architect called Michael Ventris, when he showed that it was used to write Greek. Reading about Ventris's work was what inspired a young London schoolboy called Michael Wright to find a mystery of his own to solve. Decades later, he went on to decode the Antikythera mechanism.)

It's an intriguing list, although the reason that some of the codes have never been cracked may well be because they are meaningless hoaxes. Unfortunately it's impossible to know which! One entry that has been called into question recently is the Phaistos Disc. This flat disc of fired clay is stamped on both sides with an uneven spiral pattern of mysterious pictographic symbols. It was found in 1908 in the Minoan palace of Phaistos in Crete, alongside remains dating from around 1700 BC. Because of the way the symbols were stamped into the clay, it has been described as the earliest ever example of movable type.

But no one has ever been able to decipher the symbols. And last summer, Jerome Eisenberg, a specialist in faked ancient art, published an article in the magazine Minerva arguing that the disc was fired too perfectly to be authentic. He reckons that the Italian archaeologist who supposedly found it, Luigi Pernier, may have faked the disc because he was desperate to unearth something at Phaistos that would outdo the fabulous artefacts that his rival, Sir Arthur Evans, was discovering at the nearby site of Knossos.

Plenty of enthusiasts are still convinced that the disc is real, though, and I for one really hope that it is. The mystery could be solved by a technique called thermoluminescence dating, which would give a rough date for when the object was last fired. Unfortunately the authorities at the Heraklion Museum, where the disc is held, have apparently refused permission for this to be done. The test involves heating a sample of the object, so they may be concerned about damaging such a precious artefact. Or perhaps they know something we don't.