Theories of evolution - 1000 years before Darwin

20. February 2009 12:45


Charles Darwin in 1854

We're all celebrating the 200th anniversary of Darwin's birth this month, but what isn't so well known is that centuries before he published his theory of evolution by natural selection, scientists in the Islamic world were discussing similar ideas. The earliest known example is from a science writer called al-Jahiz, who worked in Baghdad in the 9th century.

In The Book of Animals he wrote: "Animals engage in a struggle for existence [and] for resources, to avoid being eaten and to breed.... Environmental factors influence organisms to develop new characteristics to ensure survival, thus transforming into new species. Animals that survive to breed can pass on their successful characteristics to [their] offspring."

And in the 10th century, an Ismaili scholar called Muhammad al-Nakhshabi wrote: "While man has sprung from sentient creatures [animals], these have sprung from vegetal beings [plants] and these, in turn, from combined substance, these from elementary qualities, and these [in turn] from celestial bodies." 

Sounds familiar. Of course, coming up with the general idea of evolution is very different from the huge body of work that Darwin did to observe and test the mechanism of natural selection, but still, I think it's amazing just how long ago Islamic scholars were discussing such ideas. 

Science and Islam coverThe House of Wisdom

These quotes are given in Ehsan Masood's excellent book, Science and Islam, which I have reviewed for this week's New Scientist along with The House of Wisdom by Jonathan Lyons (you can read the review here). Both are well worth reading, and turn the all-too-common Western view that Islam is an "anti-science" religion on its head. A thousand years ago, it was Christianity that forbade its followers from enquiring into the natural world. For those in Europe, the idea that species could change and develop over time would have been unthinkable.


Searching for shadow life

16. February 2009 15:22

DNA double helix

It's the last day of the AAAS meeting today, and one of the most fascinating themes has been the sessions on various weird and wonderful types of life. All kinds of fundamental questions in biology -how likely is life to arise, does it have to be based on DNA, how you define life in the first place - are difficult to answer with a sample size of one, ie the life we know that has originated on Earth. So for biologists trying to answer these questions, the dream would be to have a second sample, an alternative kind of life to compare to the life we already know.

Many of them are working to make this a reality, by trying to synthesise different types of artificial life, and they're making good progress. For example, Tony Forster of Vanderbilt University and his colleagues started with a normal bacterial cell and worked out what would be the minimal components needed for it to survive. They reckon the least they can get away with is 151 genes, which is just one fifth the size of the smallest known natural genome (belonging to a bacterium called Mycoplasma). The plan now is to build all these components from scratch, and compile them into a working cell. That's a fair way off of course, but Foster is confident that it will be possible.

Meanwhile others are taking a more stripped down approach. Sheref Mansy of the University of Denver makes cell-like structures out of fatty acid molecules. Under the right conditions the fatty acids form a double membrane a bit like a cell membrane, and coalesce into spherical vesicles. The vesicles can grow in size, and Mansy has even managed to replicate short snatches of DNA inside them. Next he hopes to coax them to divide.

A key requirement in many definitions of life, however, is the ability to evolve by natural selection. And this is something that Steven Benner of the Foundation of Applied Molecular Evolution has been able to achieve. He and his colleagues synthesised RNA-like molecules using an alphabet of six different genetic letters (the four used by normal life, plus two artificial ones). They were able to get these molecules to replicate in a test tube. What's more, when errors arose in the replication, those errors were passed on to the next generation of molecules - just as occurs in Darwinian evolution.

Is this life? It meets nearly all of the requirements in NASA's formal definition of life: "A self-sustaining chemical system capable of Darwinian evolution." But it falls down on the "self-sustaining" part. Benner has to continually add a soup of raw materials and enzymes to keep the reaction going. Next he hopes to create a system in which the genetic template can catalyse its own replication. Then biologists could have an argument over whether the result should count as life. Even though it's not included in the NASA definition, many may feel that the system would also need to be enclosed inside cells, like Mansy's, before they hail it as living. I think this is a bar that will keep moving as the research advances.

But perhaps all we need to do to find new forms of life is to look around us. Physicist and astrobiologist Paul Davies pointed out that alternative creatures might exist on Earth already, right under our noses. If life originated on Earth once, he said, perhaps it originated several times, leading to two or more unrelated lineages. If so, this "other" life might have died out early on, or it might have integrated with the early organisms from which we are descended. But in his talk he focused on a third, more exciting possibility, that it might still be living alongside us today. He calls the idea a "shadow biosphere".

To find this weird life, he suggested looking in environments where normal life can't survive, such as extremes of temperature, salt, or radiation. Or you could run an experiment with conditions that would kill off normal organisms, for example by disrupting the normal genetic code, and see if anything grows.

Davies thinks these shadows would have to be microbes, or we'd have noticed them already. He points out that only a fraction of microbial species have ever been cultured in the lab, in fact many of them seem impossible to grow, no matter what conditions researchers try - so maybe some of them are living by different rules. I used to be a microbiologist, and I'd get very frustrated when my cultures didn't grow. It never occurred to me that I might be dealing with aliens.


One Earth among billions

14. February 2009 18:11

The blue marble

The ancient Greeks had some pretty sophisticated astronomy, but as far as I know they never speculated about the possibility of life on other planets (apart from the general idea that the cosmos as a whole could be seen as a divine, living organism).

Now astronomers are going to the other extreme, and seeing the potential for life literally everywhere. I just went to a press conference at the AAAS meeting here in Chicago where planet expert Alan Boss gave his latest views on how many habitable planets may be out there (that means rocky planets roughly the size of Earth, orbiting at the right distance from their star to have liquid water). The numbers were quite astounding - he reckons there could be one habitable Earth for every Sun-like star in the universe, an incredible 100 thousand billion billion of them, and 100 billion in our galaxy alone. Boss also thinks there's a high chance of life evolving on such planets. "Life is so tenacious and hard to stop," he told the press conference. He reiterated the point Anthony Remijan made here yesterday, that comets continually carry rich mixtures of prebiotic organic molecules onto the surface of planets. "If a habitable planet is sitting around a star for billions of years - something is going to come up."

Of course, many astronomers aren't nearly as optimistic about the chances for life elsewhere. So far it's hard to settle the argument as it hasn't been possible to detect directly any Earth-sized planets orbiting other stars, but Boss is basing his estimate on the 300 or so larger planets that have been detected, as well as computer simulations of how planets form. We know that bigger hotter "super-Earths" seem to form around a third of stars like our Sun, and Boss reckons that normal-size Earths should form much more easily. There are some kinds of solar system in which it would be very difficult to image a habitable Earth-like planet forming - for example when there is a huge gas giant, like Jupiter, orbiting close to the star. But so far this type of system has only been seen in around 15 per cent of solar systems, leaving 85 per cent in which an Earth (or several) could form.

He was speaking just 3 weeks in advance of the launch of NASA's Kepler mission, which aims to detect Earth-like planets for the first time. Three or four years from now, we should have enough results to give us a much more solid estimate of the number out there. Boss said he'll be "absolutely astounded" if the mission doesn't find any.

Once we find some planets that look habitable, the next step will be to build better telescopes so that rather than simply detecting their presence, astronomers can get more detailed images. Even a picture just ten pixels across would enable us to look for the presence of oceans and continents. And directly detecting light from these systems should tell us something about the different chemicals in the planets' atmospheres - the presence of oxygen, for example, would be good evidence that life has already evolved.

If we do see signs of life, Boss thinks we should send a small (unmanned) spacecraft to check it out. Even if the planet was relatively close, say 30 light years away, it would take a couple of thousand years for the spacecraft to arrive. But once it was there it could beam back detailed images - if there's anyone still here to receive them.

Boss has just written a book all about the search for habitable planets, called The Crowded Universe.


Antikythera mechanism may be even older than thought

13. February 2009 22:36


Main surviving fragment of the Antikythera mechanismLast Friday I caught the train to snowy Cambridge for a half-day conference on the Antikythera mechanism, organised by the Whipple Museum of the History of Science. Several of the researchers from the Antikythera Mechanism Research Project spoke about their work on the device, so it was a good opportunity to catch up with them and find out where things have got to.

First, Mike Edmunds of Cardiff University and his London-based colleague Tony Freeth summarised the project so far. They didn't add much to what has been said before, however, and it was Alexander Jones, over from the Institute for the Study of the Ancient World in New York, who gave the most interesting talk of the day. He has been collaborating with Tony Freeth and others to decipher the inscriptions on the mechanism, particularly those letters hidden beneath the surface of the surviving fragments and revealed only recently by 3D X-ray imaging.

Most recently the research group has been studying the text on the front of the mechanism, and they have a paper planned on this very soon. Unfortunately Jones didn't pass on any juicy advance details and instead focused on the back of the mechanism, which was the subject of a Nature paper published in July last year.

In that paper, the team reported that the month names used on a 19-year calendar on the back of the mechanism came from a civil calendar, not an astronomical one as assumed, and that a smaller dial didn't show a 76-year calendar as previously thought, but a 4-year cycle marking the timing of the Olympic and other Greek games.

In his talk, Jones told us how surprised he had been to learn that this civil calendar was tightly regulated to lunar and solar cycles. Previously it had been thought that only astronomers used such sophisticated calendars, whereas the calendars used by ordinary people were much more ad hoc. But that clearly wasn't the case. Among other things, the mechanism's dial explained which months should have 29 days and which should have 30 days, and exactly which days to skip.

Jones also talked about the month names used on the calendar, including Phoinikaios, Kraneios, Lanotropios and Machaneus. Different month names were used in different regions of Greece, so in theory these should help pin down where the mechanism was made. Unfortunately knowledge of exactly what months were used where is very patchy, but the closest matches to the ones on the Antikythera mechanism are with regions colonised from the city of Corinth - candidates include Corfu, Illyria and Epirus in northwest Greece, and Syracuse in Sicily. Syracuse is a particularly exciting prospect because this is where Archimedes lived - and ancient writings suggest he once made a device similar to the Antikythera mechanism. But Jones revealed a hint that may implicate northwest Greece instead.

It's on the 4-year Olympiad dial. The different games listed on the dial are Isthmia, Olympia, Nemea, Pythia and Naa (plus one other that hasn't been deciphered). Isthmia, Olympia, Nemea and Pythia were all major games, of importance across the Greek world. But the Naa games, held in Dodona, were a much smaller affair, of only local interest. So Jones speculates that the dial might have been designed for someone who lived nearby. Dodona was in Epirus, one of the regions also implicated by the month names on the calendar, so perhaps the device was made in Epirus. Deciphering the final name on the list might help to confirm or rule out this theory.

Jones said he thinks the Antikythera mechanism wasn't so much a computer, designed for making specific calculations, as a simulator, intended to demonstrate the workings of the universe to a broad intellectual audience. He also revealed that it may be even older than thought, perhaps from the early second century BC. The inscriptions have been dated to around 100 BC. But because we don't know where the device is from, that's only a very rough estimate. Jones pointed out that many of the Corinthian colonies were devastated or taken over by the Romans well before 100 BC: Syracuse in 212 BC, Epirus in 167 BC, Corinth in 146 BC. After Roman conquest the inhabitants would presumably have stopped using their Greek calendar, suggesting that the Antikythera mechanism was built earlier than this. I think he's right when it comes to northwest Greece, but Syracuse was still Greek-speaking and relatively prosperous into the first century BC so its inhabitants could have carried on using this calendar for quite a while.

Also still unanswered is the question of how the mechanism ended up on the ship on which it was found.This was a Roman ship sailing from Asia minor in the eastern Mediterranean, carrying valuable goods (probably war booty) back to Rome. Yet the Corinthian colonies were all in the western Mediterranean. This caused a bit of discussion after the talks between Jones and Edmunds, who believes that devices like this, if not the Antikythera mechanism itself, were being made at the time in Rhodes in the east. I think he's probably right, and that the tradition of these devices spread across the Greek world.

Paul Cartledge, professor of Greek classics at the University of Cambridge, wrapped up proceedings with some entertaining comments about the wider significance of the Antikythera mechanism. In particular, he's interested in what the device tells us about the culture and mindset of the ancient Greeks. His main point was that although historians have often viewed the Greeks as not very technologically minded, the Antikythera mechanism shows that science and technology were central to their world. What's more, it suggests they were moving away from belief in superstition and omens towards a much more modern mindset in which the universe is explainable, and operates according to predictable rules.

I still find that astounding. More than two thousand years ago, you could say that the Greeks were having their own Scientific Revolution.


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?