Nature Newsblog
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There was once little difference between equatorial and arctic climates.
A core of sediment pulled from the bottom of the Arctic Ocean has confirmed that, millions of years ago, the North Pole was as warm as a balmy summer day.
Read the story here.
Differences in sexual appetite might be partly determined by our genes.
Scientists in Israel have pinpointed a common genetic trait that could make some of us hungrier for sex than others.
Read the story here.
Tiny toolmaker or microcephalic? The 'hobbit' debate continues.
They may have been tiny, but the hobbits of the Indonesian island of Flores are still the focus of the biggest controversy in anthropology. The latest twist in the tale suggests that these one-metre-tall hominids, with a brain the size of a grapefruit, were the final members of a tool-making tradition stretching back more than 800,000 years. But amid fresh doubts over the species' evolutionary history, the idea that the curious creatures were deformed modern humans refuses to go away.
Read the story here, and have your say about the origins of these novel fossils.
The death of a French professor in a laboratory explosion in March was a shocking reminder that research can be a risky business. Mark Peplow and Emma Marris investigate whether chemistry deserves its reckless reputation.
Something that felt like an earthquake hit the French town of Mulhouse on 24 March. The explosion at the National Institution of Higher Learning in Chemistry (ENSCMu) killed Dominique Burget, a 41-year-old photochemist. It also sent ripples of concern around the world.
Read our story, plus horrifying stories of chemistry-lab accidents, here (you will need a subscription).
On 27 May an earthquake struck Java, Indonesia, about 25 kilometres south-southwest of the city of Yogyakarta, claiming more than 5,000 lives. News@nature.com takes a look at the situation.
Read the briefing here.
Watch this space for all the latest news from the human genome meeting in Helsinki. Claire Ainsworth will be posting diary reports here from 31 May - 3 June.
Mounting carbon dioxide could fuel more poisonous ivy.
Forests could become thick with more toxic forms of poisonous ivy and other noxious vines, thanks to rising levels of carbon dioxide.
Read the story here.
Easily pronounced stocks do better on the market.
For those of you struggling to pick a winner in the complex world of stocks and shares, help is at hand. A psychology study has found that, at least in the short-term, stocks with names that are easier to pronounce consistently outperform those with more confusing monikers.
Read the story here.
Nano paddle could, in principle, cool a pool of molecules.
Just the thing to keep your nano beers cold: an idea for the smallest refrigerator in the world.
Read the story here.
Web gurus and geeks descended on Edinburgh, UK, this week for www2006. Chairing the panel 'The Next Wave of the Web' was Nigel Shadbolt, an artificial intelligence researcher at the University of Southampton, UK, and deputy president of the British Computer Society. Declan Butler asks him about the Web's progress.
Read the interview here.
Mice with a hefty dose of a certain gut bacteria are fatter.
Scientists have identified a key microbe in our guts that helps us glean more calories from food. The discovery backs the idea that the type of microbes in our gut help to determine how much weight we gain, and that seeding the intestine with particular bugs could help fight obesity.
Read the story here.
Ban of veterinary drug should protect carion-eating birds.
India has announced it will ban diclofenac, a veterinary drug that has caused South Asian vulture numbers to crash by more than 95% over the past 15 years (see 'Switching vet drug could save vultures'). The birds are poisoned when they eat carcasses of treated cattle.
Read the story here.
Progress has been made but more is needed, report warns.
Almost all tropical forests are still in danger of degradation, according to the most comprehensive survey yet of how these resources are managed. Only 5% of tropical timber is managed sustainably, says the report.
Read the story here.
Two new recipes tell how to make objects vanish.
Two prescriptions for an invisibility cloak have been unveiled by physicists in the United Kingdom and the United States. The researchers say that in principle the technologies needed for building these devices already exist. "Invisibility is visibly close," says Ulf Leonhardt of the University of St Andrews in Scotland, one of the researchers behind the proposals.
Read the story here.
Discovery supports theory that human HIV pandemic came from African apes.
Scientists have spotted the signs of an HIV-like virus in chimpanzees in southern Cameroon, confirming the long-held suspicion that these animals are a natural reservoir for the virus in the wild.
Read the story here.
Supercritical hydrothermal vent found on Atlantic seabed.
Scientists working in the southern Atlantic Ocean have found a 407 °C hydrothermal vent, the hottest yet known on an ocean floor. Although only 5 °C hotter than the previous deep-sea high of 402 °C, recorded in the Pacific Ocean, the new hotspot bumps seawater into the strange state of being a supercritical fluid.
Read the story here.
Better hygiene could squelch transfer of disease to corals.
Scuba divers could inadvertently be carrying coral disease from one reef to another, say scientists, who have shown that bugs stick to wetsuits like glue. But a quick rinse in disinfectant can stop the spread.
Read the story here.
This week’s Nature Podcast looks at the outer shell of HIV, investigates scientific misconduct in China, asks why a little disorder might help the ITER fusion reactor, and has more on undersea volcanoes, a long-found Asian plesiosaur, non-mendelian inheritance, and lobsters with the lurgy. English language transcripts of each show are also now available.
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I think we humans should surrender: we are clearly surpassed by microbes.
Cold: ‘Snow mould’ thrive under packed snow in the Rockies.
High: In a Peruvian valley rimmed by 6000 metre peaks, bacteria bloom at the barren foot of a retreating glacier.
Ultrasmall: Many bugs pulled from an ice sample from a 120,000 year old Greenland glacier, 3000 meters down, were less than 0.2 of a micron (compared to a typical bacteria of some 1.5-6 microns). They are naturally tiny and don’t swell up, even when given the chance to gorge.
Infinite: There are probably more bacteria in our gut then there are cells in our bodies.
Bacteria are so yesterday. Today I’m all over fungi. I just spent two hours taking a crash course in a room full of fungus-lovers.
I would guess that most people’s interactions with skin fungi are limited to a bout of athlete’s foot. Be grateful. After a slide show of the gruesome, scaling, pustulating, havoc that pathogenic fungi can wreak in the dead cells that crown our skin, I will never complain about itchy toes again.
Actually, Trichophyton rubrum, the worldwide agent of athlete’s foot (in countries that favour sweaty shoes and socks) tops the list of skin-loving pathogenic fungi. Tricophyton tonsurans (ringworm of the scalp) comes in at number two.
But in the last decade or so the number of really invasive, dangerous infections from fungi is rising, mainly because of the growing number of patients whose fungi-fighting immune systems are dampened down by drugs in order to accept an organ or tissue transplant.
Michael Rinaldi, of the University of Texas Medical Center, showed one case in which a kidney transplant patient turned up with glaring red patches all over his body. It turned out that Trichophyton rubrum – the athlete’s foot fungus – had eaten its way into his skin and internal organs. “They do whatever the hell they want in immunocompromised people,” Rinaldi said. “It’s the way it’s gonna be – we’re creating living Petri dishes.”
I came away with mild nausea but also the feeling that fungi research is a bit of a backwater. These people figure out which fungi is which by growing a mouldy culture and examining what shape it is under the microscope. They debate whether to use genetic sequencing – imagine! – to better identify their fungi.
In the other room, people are talking about sequencing genes of hundreds or thousands of bacteria at a time. Maybe this thinking hasn’t fully invaded the fungi world yet.
Creatures steer clear of their infected friends.
Caribbean spiny lobsters have a cunning way to avoid catching disease: they seem to be able to sniff out the scent of illness in their peers before infected neighbours show any symptoms.
DNA's cousin, RNA, may also pass information down the generations.
In a discovery that rips up the rulebook of genetics, researchers in France have shown that RNA, rather than its more famous cousin DNA, might be able to ferry information from one generation of mice to the next.
Read the story here.
Using RNA interference to shut down harmful genes can have fatal flaw.
New studies on the safety of a gene-silencing mechanism highlight the need for caution before clinical trials, scientists say.
Read the story here.
DNA's cousin, RNA, may also pass information down the generations.
In a discovery that rips up the rulebook of genetics, researchers in France have shown that RNA, rather than its more famous cousin DNA, might be able to ferry information from one generation of mice to the next.
Read the story here.
Conference discusses voluntary code of conduct.
Researchers in the field of synthetic biology are to issue a declaration of intent about professional behaviour and organization in order to ensure good practice and to address a range of concerns about their research. The scientists hope to ensure that controversy doesn't choke the field just as it begins to make progress. But critics are likely to be unimpressed — a coalition of organizations concerned about the technology released an open letter ahead of the meeting calling for the field to be externally regulated.
Read the story here.
Find blog entries from the synthetic biology conference here.
Planetary scientists debate where to land next.
More than 125 planetary scientists will gather in Pasadena, California, next week to begin planning NASA's next steps on Mars — or rather, where that step should fall. The workshop will rank more than 40 candidate landing sites for the Mars Science Laboratory (MSL), a rover slated to depart for the planet in September 2009. There will be no hasty decisions: NASA plans three more workshops after this one, and will choose the final site a month before launch.
Read the story here.
The last weird bacterial factoids for today. David Relman of Stanford University has examined the bacteria lurking in twelve different spots of the same person’s mouth and used genetics to identify the types of bacteria living there.
Relman found that each spot in the mouth – and even four spots on the same tooth – host hundreds of bacterial species and a completely different collection of them. Our mouths, it seems, are not just one sea of saliva washing a few bacteria back and forth. It is more of a collection of rock-pools, each holding a different collection of bugs.
It’s pretty mind-boggling to think that different spots of the human body, only millimeters apart, attract these diverse groups of bacteria. Now I’m imagining a whole bacterial country mapped out on the body with cities home to different species.
So far, Relman has little idea why the mouth is so patchy. Is it something strange about enamel? Could the different inhabitants explain why gum disease crops up in certain places?
He is now exploring how these populations are established from the start, by studying the same spots in a sparkling clean mouth (after most of the bacteria were scraped with a dental cleaning) and then later as the bacteria build up.
Walk around for too long at this meeting and suddenly everything seems to be swarming with potentially evil bacteria. But orange juice? Could they deprive me of that?
Oh yes. Once, food poisoning was the realm of chicken and eggs and greasy joints with roach-ridden kitchens. Not any more.
Food microbiologist Larry Beuchat of the University of Georgia tells me that there have been several outbreaks of Salmonella from orange juice (like the freshly squeezed kind). The bugs were picked up, who knows where, during harvesting or handling. Orange juice was once considered safe because it is so acidic, but in fact the hardy Salmonella can survive in there. You’re OK with pasteurised stuff though.
Other foods to cross off the shopping list (if you are the worrying kind): chocolate, peanut butter, cake mix. All have been linked to food poisoning. Even dried infant formula. And tomatoes are definitely on the borderline.
Come on, I say, do you drink unpasteurised orange juice? No, Beuchat says, nor apple juice or oysters.
But hell, I’m feeling reckless. I might just order up a PB&J and a glass of OJ anyway.
MRSA (Methicillin resistant Staphylococcus aureus, to use its full name) is rife in hospitals, prisons and pretty much everywhere else.
But after a crash course in Staphylococcus aureus, it seems that the picture is far more complicated (when is it not?). Not all S. aureus are created equal, as Vance Fowler, of Duke University, told me.
There are actually all kinds of different strains of S. aureus spreading around the world – and some are far more fearsome than others. A harmless type of S. aureus is hitchhiking around in the noses of one third of us, with no ill effects. Other strains can kill – and scientists want to know what distinguishes the nasal companion from the killer.
To this end, Fowler has been collecting samples of S. aureus from patients since 1994, along with a DNA sample and a 17-page medical history. He now has a bank of around 2000 bacterial strains, one of the most extensive collections of this bacterium in the world.
He and his colleagues are homing in on the genetic differences between these strains. They first divided up a bunch of patients into three groups according to the severity of their symptoms. Some were perfectly healthy (these samples. Fowler told me, were partly collected from undergraduate students willing to have their noses scraped while they lined up to watch a basketball game). A second group had mild symptoms; a third had the most dreaded of symptoms such as bone or joint infections.
Fowler’s team next analysed seven genes in each patient’s S. aureus, and placed them into groups according to how similar they are. They found that all the strains fall into eight different families – and that two of these groups appear to be linked to more dangerous infections. One called CC5, for example, caused severe infections 60% of the time, compared with some 15% in another group.
Fowler is working with collaborators to find the exact genetic alterations that make these strains nastier in the human body. They examined 419 genes in more detail and homed in on four regions which seem to be more common in the nastier strains. These regions – which are known to jump from one bacteria to another – contain several genes, such as ones that make immune-provoking molecules.
The idea now is pinpoint more precisely which changes in these genes might transform an innocuous strain of S. aureus into a destructive one.
Armed with such information, doctors might be better equipped to battle infections: perhaps by testing someone’s strain in hospital and decide whether to treat early and hard. Another hope is to identify people who are most susceptible to infection – and perhaps offer them a vaccine, should one ever be made.
Bug-eating bugs destroy life-threatening biofilms.
Little-known predatory bacteria can suck out the innards of bugs that cause lethal lung infections, microbiologists have shown, raising the hope that they might one day provide an alternative to conventional antibiotics.
Read the story here.
Alex Mallet, from Drew Endy's lab, gives his take on the whole meeting here. And a student at Davidson college has lots of entries summarising specific talks on cis-action. In the long run, I expect the easiest way to browse them will be on the May archive.
Four active bloggers at a small biology meeting: the shape of things to come? or an outlier produced by an over-representation of geekiness in this very specific field?
Posted on behalf of Oliver Morton
2006 predicted to have more storms than usual, but less than 2005.
The United States and Mexico should brace themselves for another set of powerful hurricanes this year, forecasters have warned.
Read the story here.
Drug could overcome brain shutdown caused by trauma.
Clinical researchers have discovered that they can rouse semi-comatose patients by giving them, bizarrely, a common sleeping drug. If more wide-ranging tests are successful, the drug could become the first effective treatment for ‘persistent vegetative state’, the condition at the centre of the US legal battle over sufferer Terri Schiavo last year.
Raed more here
An Inconvenient Truth showcases science of climate change.
An Inconvenient Truth, a feature film starring former vice-president Al Gore as Al Gore giving his PowerPoint presentation on climate change, opens in New York and Los Angeles on 24 May and elsewhere throughout the summer. News@nature.com tackles the big questions surrounding this much talked-about film.
Read our review here.
Amidst all this dispassionate science, there’s nothing like a personal story to raise a round of applause.
Microbiologist Joan Bennett worked in New Orleans before Hurricane Katrina slammed into the city last summer -- so she had a particular interest in the mould that invaded her home after the floodwaters subsided.
Her pictures were pretty graphic. Imagine the type of fungal growth experiment you find at the bottom of a severely neglected coffee cup or fruit bowl – and amplify that to the size of a living room.
Mould coated the ceiling. It extended its furry tentacles up the walls. A thick, lush variety upholstered the sofa. The carpet was a thriving Petri dish.
Bennett grew some of the moulds on a real Petri dish and found at least 20 different types. She says she is searching for a brand new one: “it would make me very happy if I could find Aspergillus Katrinansis,” she said.
Ruined furniture aside, some people think that these moulds are taking a toll on people’s health: moulds have been linked to allergies and sometimes worse.
Lots of rumours circulated about the bacteria and viruses that might run wild in the aftermath of Katrina, from cholera to hepatitis. But in the event, mould probably won.
Joint-crippling disease threatens to spread across the globe.
Scientists have found clues as to why a little-known virus is disabling hundreds of thousands of Indian Ocean island dwellers, in an outbreak that threatens to spread further around the world. It seems the virus has adopted a genetic change that may make it more efficient at invading the mosquitoes that carry it from person to person.
Read the story here.
Here’s a cautionary tale for microbiologists everywhere. The bacteria you put to bed at night may not be the same as the ones that you awake in the morning.
This is news to me. I thought an E. coli was an E. coli, whichever way you cut it. Beloved, trusty, experimental ally of molecular biologists. Only get really interesting when they acquire the suffix 0157 and swarm over contaminated meat.
Steven Finkel of the University of Southern California presented a whole host of evidence showing that E. coli are far more fickle than we thought. In one experiment, he started out with 50 identical cultures of the bugs, left them to grow for ten days and then examined the sequence of one gene in each. Three-quarters of them picked up mutations in that gene, and these mutations were of 180 different types.
When he left the bacteria for several months, many of them had chopped out large chunks of their entire genome, discarding 50 or 60 genes like they were unnecessary baggage. Finkel says that the bugs even smell different after ten days, and turn different shades of yellow.
So what? Well, if you’re a microbiologist – analyzing a particular gene in your bacteria, say – this might matter. Many people throw their cultures in the fridge overnight, and come back to analyse them in the morning, or next week, or next month…
Finkel’s results suggest that such a neglected culture might have changed, so that it now contains numerous different bacteria with different genetic make-ups; ten identical cultures could have become ten different ones, although most people don’t know it. He says that microbiologists get nervous when they hear his talk.
There are certainly a lot of perspiring scientists around. But I think that’s more to do with this being sticky Orlando in summer.
US committee recommends that FDA approve the jab for girls.
A vaccine against cervical cancer has made it one step closer to the doctor's office. On 18 May, an external advisory committee recommended to the US Food and Drug Administration (FDA) that they allow one such vaccine, called Gardasil, to be licensed for use in girls from the age of nine.
Read the story here.
Slow-release treatment could mop up carcinogens in the mouth.
It freshens breath, protects teeth and even, if you believe the commercials, makes you immensely popular. But Finnish researchers are hoping that chewing gum could soon pull off an even more ambitious trick: helping to stave off cancer.
Read more here
Study shows that proposed carbon nanotube cables won't hold up.
Is it possible to make a cable for a space elevator out of carbon nanotubes? Not anytime soon, if ever, says Nicola Pugno of the Polytechnic of Turin, Italy. Pugno's calculations show that inevitable defects in the nanotubes mean that such a cable simply wouldn't be strong enough.
Read the story here.
A big difference between this meeting and the one two years ago is the stress on medicine, which has been taking up quite a lot of Sunday. Wendell Lim, of UCSF, chairing the session, started it off with a serious, provocative vision. The medical implications of synthetic chemistry have been in making small molecule therapies; the medical implications of synthetic biology will lie in making "living therapies". Living therapies are creatures designed, with the help of synthetic genomes or parts of genomes, to do medicinal stuff. Examples from today: therapeutic bacteria that target tumours (bacteria seem attracted to tumours, which I didn't know before, and I'd be interested in finding out if anyone knows why), viruses for delivering genes, engineered immune system cells.
The immune cells came from David Baltimore's talko on Sunday afternoon which dealt with various aspects of his project to "engineer immunity". The logic here is that it is difficult to develop vaccines against diseases such as AIDS and malaria because the immune system just isn't very good at dealing with them; if it were, the diseases wouldn't be such a problem. The fact that the natural immune response is so poor makes it hard to provoke a good response using vaccines. Wouldn't it be nice, goes Baltimore's argument, if we could get round this by going in and telling the immune system exactly what it should be doing, rather than just giving it a sketch of the problem -- that is, a vaccine -- and leaving it to its own insufficient devices. So, for example, give it blueprints of specific antibodies that are known to have a neutralising effect on HIV, rather than make do with the less impressive specimens it comes up with on its own. Or give it some stem cells that will make T-cells that we know will deal with a specific tumour.
Baltimore admits that this is ambitious stuff; it effectively combines immunotherapy, stem cell therapy and gene therapy, none of which, to put it kindly, are exactly established successes. But there are some encouraging results, and the potential pay offs are obviously vast.
Two thoughts here: one is that Baltimore's project, which has attracted the attention of the Bill and Melinda Gates Foundation, might be seen to some extent as old wine in new bottles -- ideas that have been around for a while and perhaps lsot some lustre rebadged in shiny up-to-date livery. Gene therapy has, after all, been in trials since 1990. In fact, though, I think re-examining the idea as synthetic biology makes sense. Synthetic biology is largely about reprogramming biological systems, and that's what gene therapy tries to do. If including gene therapy makes you reexamine what you think synthetic biology is, then maybe it should -- maybe synthetic biology is a bigger, broader thing than people are mostly taking it for.
Second thought: as these technologies get nearer to medicine, they also get scarier. Making viruses less likely to be recognised by a pre-existing immune response is a good idea for gene therapy, but it obviously has other potential implications. Likewise getting bacteria to last longer in the bloodstream and to express new proteins, such as invasin, that get them into cells, as described in one of the talks, is something that might be quite unpleasant in the wrong hands. So might associated systems that trigger pathogenic behaviour with an external cue. Imagine a harmless bacteria that could be spread through a population unobserved and then be triggered to turn nasty by a gas -- a gas that was not in itself a weapon, and so not recognised as such. That would be seriously nasty stuff.
The people doing this work are devoted to trying to do good. But systems for getting "living therapies" into the body to do good are obviously going to have overlaps with techniques for getting living weapons in to do harm. As I argued last year, biology has a dark side. This is not a reason for not doing such research -- but it is a reason for staying careful and thoughtful while doing so. This is something that the meeting will be returning to tomorrow.
(There are other worries, too. As Baltimore pointed out when he was talking about his expectation that lentiviruses would not have the leukaemia-causing problem that has dogged some gene therapy, it seems possible that the gene which was used in those trials was itself an oncogene. As Baltimore said, this was unfortunate. Also a little sobering.)
Posted on behalf of Oliver Morton
Eating dairy seems to up the chance of having multiple births.
Eating milk and other dairy products could increase a woman's chance of having twins, a US doctor is proposing, based on a study of vegan women.
Read the story here.
...is Rob Carlson, a friend who I met at the first of these meetings. Rob, like Drew Endy, used to work at Roger Brent's Molecular Sciences Institute, just down the road from here, and he's now at the University of Washington. He may well be the only person in this pretty eclectic audience whose interests roam from detecting single proteins in cells to building space elevators. More on Rob here.
Rob's latest post from the meeting points out its commercial vibe. I must say that I wish I'd noticed Craig Venter and Vinod Khosla talking over lunch -- or indeed heard what they were saying... Rob also catches up with a couple of this morning's chemistry talks, so for the time being at least I won't.
Posting on Rob reminds of something I wrote about the biosecurity implications of synthetic biology in the New York Times last year. It seems particularly apposite right now, because the past two talks have been about designing bacteria and viruses for therapeutic purposes, part of which might involve making them less susceptible to the immune system. Subscribers can find it here, and everyone else can apparently find it for free here, but I should point out that the free version contains an error that crept into my copy through miscommunication with the Times, and which the Times itself has corrected: though Rob was a key player in the conception of very sensitive detection molecules called "tadpoles", there are a bunch of other people who should share credit, most specifically Ian Burbulis. The relevant paper is Burbulis, I.E., Yamaguchi, K., Carlson, R., and Brent, R. "Using protein-DNA chimera to count small numbers of molecules". Nature Methods Vol. 2, 31-37, 2005
Posted on behalf of Oliver Morton
Tim Gardner, of Boston University, gave an interesting talk on Saturday morning on the "network biology" approaches he's using in his lab. Interesting in two distinct ways.
One: interesting in itself. Looking for networks by comparing the RNA expression of cells in different conditions and looking for correlations (or, more precisely, according to Gardner, "mutual information") between the expression of regulatory sequences and genes is a neat way of learning more about how cells actually work, a subject on which we are often remarkably ignorant. Key factoid (if I understood it correctly): in E. coli, the best studied bacterium, researchers currently don't have any idea of how three quarters of the genes are regulated. And that shouldn't be taken as meaning that we understand fully how the other quarter is regulated -- just that in those cases we have some leads on the subject (and, to be fair, in some of those cases much more than that).
Second interesting thing: Gardner's take-home message is the exact opposite of the view taken by Drew Endy and his colleagues. Gardner argues that because we have very few well characterised "components" with which to build entirely novel mechanisms and don't really understand how to do so we should concentrate on learning how natural cells work through building network models and get our miracles by tweaking these natural systems. Endy's position is that working out how natural systems actually work is extraordinarily hard (remember that ignorance over three quarters of E. coli) and that we should instead try and build simple things which we do understand. In this respect synthetic biology exists as a counterpoint, or alternative, to systems biology, network biology and other attempts to uncover the ways life actually works.
In part, this is the division between science and engineering. Endy and many of his colleagues at MIT are engineers, and they think in terms of designing well characterised systems, not of understanding very poorly characterised systems such as those that four billion years of evolution have left littering the face of the earth. As Endy puts it, if you were faced with a very complex, very buggy, awesomely antique software system which had been re-worked billions of times, with no notes at all to reveal what all that rewriting was meant to accomplish, or any really well understood sense of what its operating principles were, wouldn't you rather design something new from scratch?
The idea that synthetic biology offers that ability to do wholly new things is often seen as underwriting its practical or commercial possibilities. But it is also, at a more fundamental level, an epistemological distinction that sets this new discipline apart from its predecessors, offering real intellectual novelty. If, that is, Endy and his engineering colleagues can really deliver. Otherwise, it's biology as usual -- even if that biology is, as Gardner's talk was, very interesting in its own right.
I'll try and get a sense of which side of this debate the people attending the conference can be found on; if I turn up anything, I'll report back.
Update: I originally characterised the "mutual information" approach as a way of looking at things "more loosely but more productively", but Rob Carlson put me right.
Posted on behalf of Oliver Morton
An interesting addition to the various agendas surrounding this conference is an open letter from a variety of NGOs concerned about the implications of the technology and the limitations of scientific self governance, which can be read here. I hope some of those involved will be able to present their position in person during the debates on these issues that will take place on the third day of the conference -- I understand there are currently some invitations in the ether.
As I mentioned in a previous post, I'm chairing a session on that third day, which puts me in a position which might be seen as leading to a conflict of interest. For what it's worth, I do think there are issues with journalists reporting on conferences at which they are also participating, but I don't think those issues mean that such reporting is always a no-no, provided that the appropriate disclaimers are in place. But it does mean that I don't think I'm going to express my opinions on these particular issues right now.
Posted on behalf of Oliver Morton
A fascinating first presentation from Steve Chu, who runs Lawrence Berkeley Lab, one of the sponsors of this event, on the challenge of finding technologies for clean energy production and the possibilities that various synthetic-biology technologies offer for meeting that challenge. There was lots of talk of artificial photosynthesis, and some wonderfully far out ideas, such as redesigning plants so that their carbon-dioxide intakes and water outputs are separated, rather than being combined in the magnificently subtle mechanisms of the stomata.
I suspect that this is not in fact practical or desirable, but maybe I've been hanging out too long with the plant scientists who Chu has found critical of this idea. Chu, in response, says the plant people might benefit from learning to think like physicists or science fiction authors, and I'm not one to play down the possibilities of learning from SF. What's more, the fact that the set of "things which are subtler than physicists think" is pretty much equal to the observable universe doesn't mean that physicists don't have wonderful insights to offer to everyone else, even if the tone in which those insights are offered can, occasionally, be a little hard to take. Anyway, even if the disambiguated stomata never come to pass, or don't deliver advantages, they still represent an idea about photosynthesis that I, as someone with a book on the subject inching towards publication, have never come across before, so lots of extra credit for freshness.
Much more practical is the two-pronged strategy Chu outlined for improving biomass systems: re-engineer the plants to be more easily converted into fuel (eg less lignin), and re-engineer various microbes to be better at carrying out that conversion directly. It makes a lot of sense, though there are some fairly subtle questions of sustainability that need to be addressed, at least as far as I'm concerned, before we can safely assume that large-scale agricultural systems will provide a significant fraction of our future fuel needs.
What didn't make a lot of sense, to European ears, was the way in which some of this was expressed. "Gallons per acre"? Please! They'll be talking about BTUs per bushel next. 21st century science and technology really shouldn't be expressed in sixteenth century units.
Posted on behalf of Oliver Morton
It's always fun to come to a conference where something is afoot -- where there's not just a bunch of presentations, but a genuine agenda. The first synthetic biology conference, at MIT two years ago, was such a conference -- an attempt to bring together a whole bunch of people working on a diverse bunch of technologies and scientific approaches that are made possible by cheap DNA synthesis, and to some extent to establish the pre-eminence among those approaches of the vision of synthetic biology then being championed at MIT. That vision is of a world where biological circuits can be designed from scratch, using
"biobricks", in an analgous way to electronic circuits, but with standardised sequences of DNA and the proteins they describe taking the place of resistors, transistors, diodes and the like. The conference was the basis of a feature I wrote on synthetic biology for Wired in my previous existence.
Two years on, here we all are at Synthetic Biology 2.0, the followup conference, at UC Berkley. And again its a conference with an agenda. Or, more properly, many agendas. The main one, I think, is to reassert the message of Synthetic Biology 1.0 -- that lots of different things people are doing with different biological systems can be treated as a coherent emerging discipline. But there are also a bunch of other things going on, among them: an attempt to show that this sort of stuff has real world applications, especially in the energy arena; a showcase for the fact that this technology has commercial possibilities (various companies have sprung up in the field in the past two years, including Craig Venter's Synthetic Genomics and Codon Devices, which boasts on its board Drew Endy, the most eloquent of the proponents of the "MIT vision" described above; an attempt to get the nasc ent community to agree how to regulate itself and to avoid this technology being used for naughty purposes; a window to show the world that this technology, well regulated, can be a force for good.
Not all these agendas are necessarily aligned. For example, without being unduly cynical, there could be commercial applications, at least in the short term, even if there aren't dramatic real world applications. And self regulation could easily co-exist with, or indeed reinforce, public worries. And not everyone here will sign up to all or indeed any of them. So it will be interesting to see how it all unfolds, especially on the third day, where the science and society implications are going to be discussed. (Disclaimer: I will be moderating one of the sessions on that day.)
Posted on behalf of Oliver Morton
Oliver Morton reports back from the Second International Conference on Synthetic Biology (SB2.0) at the University of California, Berkeley, from 20-22 May.
Due to a technical glitch, some of these comments will be posted by Nicola Jones back in London, though they are being written by Oliver at the conference.
To post a comment about any of these posts, simply click on the headline.
Recipe for making symmetrical holes in water is easy.
Bizarre geometric shapes that appear at the centre of swirling vortices in planetary atmospheres might be explained by a simple experiment with a bucket of water.
Read more here
Now that China's massive dam has been built, what will it mean for the environment?
The last load of concrete is due to be poured at China's Three Gorges project on 20 May, completing the main wall of the world's biggest dam. Although the huge structure promises to control flooding on the Yangtze River and provide copious hydroelectric power, many fear that it could also have damaging social and environmental repercussions.
Read the briefing here.
Everyone who’s anyone in the study of bacteria, fungi and viruses will be at the American Society for Microbiology meeting in Orlando, 21 -25 May. Helen Pearson will be learning what's new in germs, and recording her thoughts here.
(To add a comment to any of these posts, simply click on the headline)
Coincidence, or the fault of cell-phone masts?
A Melbourne university has emptied the top floors of one of its buildings after a spate of brain-tumour cases were reported during the past month. Most affected staff worked on the top floor, raising fears that cell-phone masts on top of the building are responsible. But experts say it is far more likely to be an unfortunate coincidence.
Read the story here.
A mock tsunami this week let Pacific countries put their emergency warning systems to the test. Emma Marris talks to Brian Yanagi, who helped to develop and monitor the test, to find out how it went.
Read the interview here.
Early stages of testing should be made public, say public-health experts.
The World Health Organization (WHO) has rebuffed requests from the pharmaceutical industry to tone down its plans for openness in drug testing.
Read the story here.
This week’s bumper Nature Podcast features the discovery of a new antibiotic, the first nuclear Neanderthal DNA, and a trio of Neptune-sized exoplanets, finds that human ancestors and chimps may have been closer than we thought, cashes in on climate change models, and loses out to cheating bacteria.
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Scientists today publish the sequence of chromosome 1: the largest and last of the human chromosomes to be done and dusted. News@nature finds out what this latest milestone means.
Read more here.
Novel citation index highlights hot topics.
Are you working on the hottest topic in your field? Many scientists may think so, but it has been a tough assertion to prove — until now, that is. A German physicist has devised a way of answering the 'Hot or not?' question for his discipline. If it stands up to scrutiny, it could be used to rate topics across the sciences. In physics, the results show that hotness — measured by a parameter known as m — correlates well with the promise of future wealth... and that promise is greatest in nanotechnology.
Find the physics top five here. (You'll need a password)
Disagree with the results? Tell us why.
Lava dome could crack any day, but many locals refuse to flee.
Indonesia's Mount Merapi, which has been belching lava since 4 May, sprang back to life today after a few days of relative calm. Scientists are warning that it is imperative to evacuate many thousands of people who remain in the area.
Read more here.
Genetic analysis suggests a messy split between the two lineages.
The evolutionary split between humans and our nearest evolutionary cousins, chimpanzees, may have occurred more recently than we thought, according to a new comparison of the respective genetic sequences. What's more, it might have been a messy divorce rather than a clean break — leading to the controversial theory that our two sets of ancestors may have interbred many thousands of years after first parting company.
Read more here
Monkeys string sounds together to create meaning.
It may not be exactly poetry, but a species of monkey has demonstrated an unsuspected level of articulacy. Researchers working in Nigeria have found that putty-nosed monkeys can use their two warning calls as 'building blocks' to create a third call with a different meaning. It’s the first example of this outside humans, say the researchers.
Read more here
Scientists debate role of air pressure in deep vein thrombosis.
A study of the effects of low oxygen levels on 'economy class syndrome' has re-opened the debate over how long-haul flights increase passengers' risks of deep vein thrombosis (DVT), the formation of potentially fatal blood clots.
Read the story here.
WHO's fight against resistance to artemisinin faces uphill struggle.
Five months ago the World Health Organization (WHO) called for a voluntary ban on the distribution of the antimalarial drug artemisinin on its own as opposed to in a combination treatment. But only one-third of the 40 targeted pharmaceutical companies have agreed to comply, with others remaining silent on the issue.
Read the story here.
Geologists blame climate change for disappearing equatorial glaciers.
The picture on the right shows the Elena glacier in East Africa’s Rwenzori Mountains. It is part of one of the world’s handful of equatorial ice fields — ice that geologists think has been been a permanent fixture here for 300,000 years. But in two decades, they say, it will be gone.
Read more here
Online review process aims to clear patent backlog.
The scientific community depends on peer review to make sure that papers are tip-top; could it work for inventions too? That's the question being pondered by the US Patent and Trademark Office, as it mulls over a peer-review programme for patent applications.
Read the story here.
Bonn meeting tackles emissions limits and the push for technology.
Delegates from 189 countries have descended on Bonn, Germany, for two weeks of talks aimed at spurring on the United Nations-led effort to fight climate change. The lynchpin of these efforts remains the Kyoto protocol. But some feel that the totemic agreement is in danger of being marginalized by nations with different agendas, not least Canada, whose environment minister is chairing the talks.
Read the news@nature.com briefing here.
Industry emitted less than allowed in 2005; but that isn't good news.
The first year of the European Union's emissions trading system, a scheme by which industries can buy and sell 'carbon credits' to stay under their yearly quota of greenhouse gas emissions, has yielded a surprise. On 15 May, the European commission released data showing that Europe's major industries actually emitted 44 million tonnes less CO2 in 2005 than they were allowed.
Read the story here.
Bonn meeting tackles emissions limits and the push for technology.
Delegates from 189 countries have descended on Bonn, Germany, for two weeks of talks aimed at spurring on the United Nations-led effort to fight climate change. The lynchpin of these efforts remains the Kyoto protocol. But some feel that the totemic agreement is in danger of being marginalized by nations with different agendas, not least Canada, whose environment minister is chairing the talks.
Read more here
The record for the fastest rise in temperature has just been topped.
With the heat of a burning sun, a laser pulse has ripped through pure sapphire, heating it faster than any explosion ever recorded.
Read the story here.
Health-conscious coffee drinkers offered reassuring test.
Nervous consumers who are addicted to the taste of coffee but desperate to cut down on their caffeine will welcome the development on offer from a team of US chemists: a molecule, extracted from llamas, that can easily detect caffeine in a hot or cold drink.
Read more here
Ship logs and pottery show how the geomagnetic field has changed.
While sailors plied the Seven Seas in the seventeenth and eighteenth centuries, little did they know that their ships' logs would one day help scientists to reconstruct the history of the Earth's magnetic field.
Read the story here.
Movie about a future pandemic in the United States has ruffled some feathers.
REVIEWED:
Fatal Contact: Bird Flu in America
Written by Ron McGee and directed by Richard Pearce
ABC Worldwide release on May 9, 2006
Bird flu has yet to hit the United States, but TV producers, with their minds on ratings, are already speculating about what would happen should the avian influenza virus mutate to a form that can be passed from human to human.
Read the review here.
Scientists haul up a hefty chunk of ancient asteroid.
A soccer-ball-sized chunk of a several-kilometre-wide asteroid has been found deep inside an ancient crater in South Africa. Finding such a large piece of a huge impactor is extremely rare, since these speeding giants are usually almost completely destroyed when they crash into the Earth.
Read the story here.
This week’s Nature Podcast features eusocial slackers, a seawater secret, the RNA pseudoknot, and a tale of meteoric survival, discusses Arctic data loss, Qatari science, asks how prepared the US is for bird flu, and gets in a spin about Saturn. You can listen to the show from here or subscribe with our RSS feed. Either way, it’s free.
To subscribe for FREE, type this URL into iTunes or your preferred RSS reader: www.nature.com/nature/podcast/rss/nature.xml
Wells flooded with salt and pollution, survey finds.
The devastating tsunami of 26 December 2004 is still making itself felt in Sri Lanka; though more than 16 months have passed, the well water in many coastal areas of that country is still undrinkable, a study has found.
Read the story here.
Looking for the point of seemingly pointless research.
Did you see these headlines this week? "Secret report says UFOs DO exist", screamed one. "UFOs don't exist, says MoD", said another. Confused, intrigued and potentially a little disappointed, I tried to find out what was behind the flurry of flying-saucer excitement.
Read the column here.
Space challenges aim to entice young women into science.
An unmanned rocket built by a 13-year-old UK girl guide successfully took off on 6 May at the National Space Centre in Leicester. The craft, made from paper and sticky tape, and powered by pressurized carbon dioxide from an indigestion tablet packed inside an empty film cartridge, reached a height of several metres before it fell back to Earth.
Read the story here.
Neural networks used to self-reflect are dulled in autistics.
Autistic patients may lack the ability to daydream normally, say researchers who have found that these people's brains act differently when they are taking a break.
Read more here.
Underwater whistles give bottlenoses their own moniker.
We are not the only animals to give ourselves names, says research on bottlenose dolphins. The dolphins' distinctive whistles may function as individual calling cards, allowing them to recognize each other and even refer to others by name.
Read more here
Protein from genetic mutation helps wounds to heal.
Researchers have concluded that a gene responsible for most cases of hereditary deafness may have an unexpected benefit: it may protect you from infection.
Stella Man, a member of David Kelsell's team at Queen Mary, University of London, spoke at the European Society of Human Genetics meeting in Amsterdam today, 8 May. She announced that the Cx26 protein encoded by a deafness gene might help wounds to heal.
Read the story here.
European workers strike against system to boost efficiency.
Patent examiners don't exactly have a reputation for staging angry protests. But on Tuesday 9 May they plan to hold a half-day strike at the European Patent Office (EPO) in Munich, Germany, to defend their right to work to a high quality.
Read more here
Survey reveals diversity of marine creatures.
Small can be beautiful, as these pictures of tiny marine animals testify. Marine biologists took the stunning snaps on a research cruise to survey the small creatures of the deep that support the ocean's food chains.
Read more here
Wobbles in transmissions help to create weather data.
They have prompted protests at school gates, led to calls for planning procedures to be overhauled and have even been disguised as trees in the hope that people don't notice them. But now it seems that mobile-phone masts might inadvertently help to improve the accuracy of weather forecasts.
Read the story here.
Big bounces may make the Universe able to support stars and life.
A bouncing universe that expands and then shrinks every trillion years or so could explain one of the most puzzling problems in cosmology: how we can exist at all.
Read the full story here.
Imaging shows that anticipation can be as horrible as the event itself.
The paralysing dread one feels before an injection or tooth extraction fires up some of the same brain regions involved in feeling pain itself, say researchers who subjected plucky volunteers to electric shocks. Their discovery supports the idea that distraction could ease a nasty wait.
Read the full story here.
Does the ghostly Casimir effect really cause ships to attract each other?
Some stories are just too good to be true. And according to physicist Fabrizio Pinto, that's exactly the case for an analogy routinely used by physicists to illustrate the mysterious Casimir effect.
Read the story here.
No wave - but also no warning - in Tonga.
A precautionary tsunami warning was issued on 3 May (GMT) for Tonga and the nearby South Pacific, after a 7.8 earthquake struck off the coast of that island. Thankfully the quake didn't trigger a large wave, and both Tonga and the surrounding coasts were spared devastating damage. But the event tested the newly revamped Pacific tsunami warning system, which did fairly well to disseminate the information — with a few glitches.
Read the story here.
Dwindling circulation could worsen El Niño effect.
Climate change is weakening a vast system of circulating winds that traverses the Pacific Ocean from coast to coast, say climate experts. Global warming has caused the system, which is crucial for monsoon rains in Southeast Asia and fisheries in South America, to decline since the advent of industrial times.
Read more here
Scientists concerned by online publication of IPCC draft.
Climate experts have expressed surprise and concern about a US government decision to release a politically sensitive report when it is still in draft form.
Read the story here (you will need a subscription).
US judges are starting to acknowledge that lethal injection could be an excruciating way to die. Emma Marris investigates whether the medical community's refusal to assist could help end the practice.
Do no harm. Nearly all US MDs and PhDs recite this three-word oath instinctively when asked why they object to helping with executions. "It violates our ethical oath and erodes public trust," says Priscilla Ray, head of ethics at the American Medical Association (AMA), which prohibits members from participating in executions. Even helping to design a more humane protocol would disregard the AMA code, Ray says. "Formulating a way to kill somebody would violate the spirit of the policy."
Read the story here.
Faked data, fudged numbers, filched ideas. We take a look at what prompts those ethical missteps in science, and what can be done about it.
Note: You'll need a password to access many of these stories.
Your cheatin' heart: what makes a scientist deceive?
Where are they now? The stuff of folklore.
What is misconduct?
Catching the crooks
Fraud follows the funds
Plagiarize or perish?
So you suspect someone of fraud. What now?
Misconduct Mahem
FAQ: Can you tell when someone is hiding the truth?
FAQ: How to make your own desktop crime lab
Canadian study shows early onset of painkiller's side-effects.
The controversial painkiller Vioxx (rofecoxib) may cause heart attacks within just two weeks of starting the drug treatment, a study of Canadian patients claims.
Read the story here.
Global menace of climate change and pollution add to local hunting concerns.
They are one of the emblems of international conservation, but polar bears are on thin ice. The 2006 edition of the global guidebook for species in danger, the IUCN Red List, published today, has officially upgraded the bears’ status from ‘conservation-dependent’ to ‘vulnerable’.
Read more here
Fish starved of air more likely to turn into boys.
Aquatic 'dead zones', oxygen-depleted areas throughout the world's waterways, are not only suffocating marine life but may also be transforming female fish into males.
Read the story here.
Researchers struggle to explain trans-Atlantic divide in health.
Middle-aged Americans are in much worse health than their English counterparts, suggests a trans-Atlantic comparison, and scientists are at a loss to explain why.
Read the story here.
