So what's next for high-energy physics? The LHC won’t be the end. Physicists will want to go to higher energies. The question is, how? The International Linear Collider -- a planned linac that will do for positrons and electrons what the LHC did for protons -- is what the community wants right now, but it won't go to any higher energies. It might be too expensive to build just to match the LHC's capabilities. Machines like the ILC struggle to achieve accelerating gradients of 30 MeV per metre, and the radio wave power delivered to the metallic cavities would melt them were they not supercooled and superconducting.
But all is not lost. SLAC's Mark Hogan gave a talk about all the novel accelerating technologies in the works. He presented the so-called Livingston chart, which at right shows the hard-won exponential increase in accelerator energies with time. Every few decades or so, an order of magnitude increase in energy is earned. But you can also see how each successive family of accelerator technologies – cyclotrons, synchrotrons, storage rings – leap to new heights, but taper off with time. Something has to be done. And Hogan thinks that wakefields will be the way to go -- using initial pulses to create a wave in a plasma, or a fiber, that in turn allow successive electron pulses to surf on the wake.
Of course, the technology is years away -- but it could offer gradients in the GeV per metre range. That would put desktop light sources within reach. Who knows -- maybe there could be desktop colliders, too. The future is wide open. But my future at Lepton Photon is quite limited. I am skipping out on Friday, the last day -- but have enjoyed my time in Hannover thoroughly. Thanks very much to the organizers.

Posted by Eric Hand on August 20, 2009
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So nearly all of the talks at this conference have been reviews -- not surprising, given the paucity of fresh data in the field. But there is one machine still chugging along -- the Tevatron -- and new results were presented by each of the main experiments, CDF and DZero. The new Higgs search results weren't all that surprising, just incremental advances on the last big rollout of results in the spring. But let's look at the latest results for CDF in the plot here. You can see that, even without combining their data together for a joint analysis, the individual teams are getting close to excluding certain ranges of Higgs masses. In particular, it is interesting how the plot shows observed values exceeding the expected values, especially in the low mass regime around 120 GeV -- precisely the region where many theorists expect to find the Higgs. Could this be the beginning of a signal? CDF spokesman Rob Roser says it's only a one-sigma difference from expectation -- barely a blip on the radar in the physics world. But nonetheless, he says it's a motivation to his team. This is precisely the part of the energy spectrum where the LHC is the worst at detecting the Higgs -- a place where the LHC will need a year or two of data to say anything. So it helps give Tevatron continued justification to run in 2011. And it means that, if the Higgs is in fact a low-mass particle, the race for priority is still on.

Posted by Eric Hand on August 20, 2009
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This year ACS hosted a two-day symposium on the National Ignition Facility and a couple of the other big nuclear fusion efforts. Given the audience, most of the talks focused on the role chemists could play in diagnostics, i.e. detecting whether fusion actually occurs, and on the different sorts of experiments chemists might be interested in, like nucleosynthesis and stellar burning processes.

NIF has had its share of delays, dilemmas and scandals, but finished construction in late March and looks to make its first attempts at ignition next year. At the conference, NIF science director Richard Boyd said they're currently running experimental implosions — up to two a day — to optimize all the parameters, and using “a bunch of tricks to make the process as efficient as possible”. For example, right now none of the experimental implosions are using deuterium-tritium targets, but Boyd notes that “with just a tiny bit of deuterium, we can actually go through most of the optimization procedures without producing neutrons, which are problematic because they activate things”.

Representatives from ITER and LMJ also spoke to give updates on their facilities. ITER, as Nature reported last month, will begin a “phased approach” in 2018 and not begin experiments with deuterium-tritium plasmas until 2025 or 2026, at least five years later than originally planned. Ned Sauthoff, director of the US ITER project office, said the next step is to get industrial input into the design of the facility, focusing on early-delivery and high-risk projects like the superconducting magnets and diagnostic instrumentation.

The Laser Mégajoule facility in France is much further along than ITER, and only slightly behind NIF. They've finished the buildings and have completed one out of four laser halls, and are hoping to have first light in 2014. Jean-Luc Bourgad of France's Atomic Energy Commission also noted that they're developing a numerical simulation facility in parallel, and are hoping to break a petaflop in 2010.

Image: LLNS/LLNL/US DEPT OF ENERGY

Posted by Lizzie Buchen on August 20, 2009
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While most of the talks here at Lepton Photon have focused on blowing up the Standard Model at high energies -- i.e., firing up the LHC -- Joerg Jaeckel of the University of Durham in the UK gave an interesting talk on how you can look for new physics at energies of just an electron-volt or so. The LHC might miss particles that only rarely interact with normal matter. And so Jaeckel extolled the virtues of exquisitely sensitive experiments that probe this alternative (and cheaper) 'low-energy' frontier.

One classic example is the GammeV experiment at Fermilab, which basically tries to shine a light through an opaque wall. On one side of the wall you can have a source that shoots 10^20 photons per second. On the other is a detector so sensitive that it could catch a single photon per second -- a full 20 orders of magnitude sensitivity. Now photons can't go through walls. But a weakly interacting particle could, something like an axion -- a hypothetical dark matter particle. And there are certain rare scenarios where photons could create axions. If that happened, the axion could pass through the wall and create a photon on the other side.

There are plenty of other low-energy experiments -- some have looked for slight differences in the way light is polarized in the vacuum, and some have looked for axions in the presence of a strong magnetic field. One has even found hints of an anomaly in the standard model by looking at that way the spin of a muon deviates in a magnetic field.

But these experiments in general get little attention. I suggested to Jaeckel that maybe it's because the LHC is guaranteed to discover new things, whereas these experiments could end up being as fruitless as the seemingly pointless effort of shining a light on a wall. Jaeckel had a nice analogy. "[The LHC] is digging a broad ditch. With a low-energy experiment, you're digging a hole. It's a very deep hole, but you may be drilling in the wrong spot."

Posted by Eric Hand on August 19, 2009
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It's the second to last day of the conference and the chemists are starting to head home. The hallways are quieter, the rooms less full, the Metro less forested by rolled up posters, the Power Bar options in the press room more limited. So I decided to give myself a little treat today: biological chemistry. As a life scientist by training, I've been rather out of my element the past week.

First Justin Gallivan from Emory in Georgia gave an entertaining talk about programming bacteria “to seek and destroy small molecules”. To control the cells, he's using riboswitches — fragments of RNA which, when bound to certain small molecules, will bind to DNA and control gene expression. He's now engineered riboswitches to respond to the molecules and regulate the genes of his choosing.

To do this, he scrambled portions of a well-studied riboswitch and screened for mutants that would 1) reliably bind DNA when not bound to the small molecule (real riboswitches are leaky), 2) recognize the herbicide atrazine but not its degradation product hydroxyatrazine, and 3) move toward atrazine.

The "movement" part was my favorite (and made for some cute videos of scurrying E. coli). E. coli naturally explore their environment via a "random walk", where they alternate between swimming in more or less a straight line and "tumbling" before changing directions, steering towards tasty chemicals when they sense them. But E. coli lacking the gene cheZ just tumble around the whole time. Gallivan engineered his riboswitch to bind to cheZ, blocking its transcription and leaving the poor little bacteria spinning around aimlessly. But when atrazine was around, it would bind the riboswitch, permit transcription of cheZ, and the bacteria would swim right for it. When engineered with an enzyme that breaks down atrazine, the bugs could both seek and destroy.

Dennis Dougherty then gave a great talk about nicotinic acetylcholine receptors to explain why smokers don't paralyze themselves everytime they take a drag. The receptors, which are activated by nicotine and acetylcholine, are located on our muscles and in our brains. This is fine — some would argue euphoric — in the brain, but if nicotine activated the receptors in muscles, one puff of a cigarette would cause every skeletal muscle to contract.

For better or worse, this doesn't happen, so Dougherty brought his chemistry into the mix to figure out why. He discovered that the nicotinic acetylcholine receptors in the brain and on the muscle are made of different types of subunits, which he published a few months ago in Nature. As a result of a subtle change in the binding site, the receptors in the brain make a tight bond, called a cation-π bond, with nicotine and acetylcholine, but those on the muscle only make this bond with acetylchonline.

Finally, Lilly Award winner Scott Silverman talked about making DNA catalysts, which don't occur in nature (the only naturally-occurring catalysts are protein enzymes and RNA enzymes (ribozymes)). Silverman's been taking a random pool of DNA sequences and selecting for catalytic activity. He's discovered deoxyribozymes that can ligate RNA — even forming "lariats" and "branched" RNA — and is now trying to find deoxyribozymes that will work with small molecules, proteins and sugars. It's all well and cool, but it's not clear to me what lariats and branched RNA are good for, or why DNA catalysts are superior in any way to ribozymes or protein enzymes. Maybe time will tell.

Image: NIH.gov

Posted by Lizzie Buchen on August 19, 2009
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Today I started with a talk by Jack Szostak from Massachusetts General Hospital and Harvard. I'd originally heard of Szostak because he co-discovered telomerase, but discovered he was no one-trick pony when he was name-dropped all over last week's NSF Minimal Life workshop for his work on artificial cells. He's trying to figure out the most basal brew of molecules capable of growing and dividing and even evolving.

He spent most of his time talking about a very pretty paper he published a year ago, where he created a super-stripped-down version of a cell that consisted of nothing but a self-assembling membrane and genetic material. His impressive protocells cells could grow and divide, and when he modified the nucleic acids he was able to get them to self-replicate within the membrane. Great stuff, but unfortunately he didn't present much of anything new.

In the afternoon I went to learn about a new type of nanostructured solar cells, presented by Yi Cui from Stanford University. Nanostructured solar cells — made from semiconductor nanoparticles — are very hot because they can be manufactured much more cheaply than semiconductor films, and offer finer control over their electrical properties, meaning they can potentially be much more efficient. Early this year Cui created an array of nanocones, which are dramatically black, compared with the flat films that look more like a mirror. Now he's made solar cells with the array, and they draw an impressive amount of current per unit area. Cui claimed it set a new record for current density — 17.5 mA/cm^2 — but turns out it merely ties the world record. Still, not too shabby.

These incremental increases (and ties) are certainly important, as people are still trying to work out the best way to make nanostructured solar cells — quantum dots, nanotubes, nanodomes, etc. Later, symposium organizer Stan Wong from SUNY Stonybrook told me that while he's "sure they will work in the future," nanostructured solar cells are "nowhere close to real commercialization or practicality".

Image: protocells, LANL.gov

Posted by Lizzie Buchen on August 19, 2009
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In the spirit of this year's theme at ACS, "Chemistry and Global Security", I decided to stop by the symposium "Sensing and Destroying Chemical Warfare Agents and Pesticides", where Kim Janda from Scripps was giving a talk about simple solutions to detecting weapons.

It's a pretty cool and important topic, and Janda's a big name, so I was pretty excited — but my excitement dropped when Janda began his talk with a disclaimer:

"The coolest stuff I've got I'm not allowed to talk about, and the really interesting stuff I'm doing with therapeutics doesn't fit with this symposium."

So it goes at big conferences. Janda ended up giving a review some of his work in this area, which was fine for me because I didn't know much about it.

Janda's developing antibodies to detect some of the nastier chemicals that could be turned into weapons: sarin, soman and vx. It turns out these all have the same "chemical signature", in that they all naturally degrade to methylphosphonic acid (MPA). The idea is this might translate into lab-based or even portable assays for detecting minuscule quantities of toxin.

Apparently MPA isn't the easiest target for antibody development, so Janda did some tweaking — modifying the protein to make it better at inducing an immune response, and eventually ditching the "classic" method of producing antibodies (using hybridoma cells) in favor of screening massive libraries in vitro. The library method uses viruses, which all display a different variant of antibody or other peptide on their surface.

Using this technique, Janda found antibodies not only to MPA, but also to anthrax, abrin and botulinum toxin. Using the MPA antibodies he could detect 1 pg/ml, while the "gold standard" (feeding it to a mouse and seeing how much time passes before it dies) can only detect if it's more than 10-20 ng/ml.

To screen for antibodies to botulinum toxin, he mentioned that he "used SPR [a type of biosensor] because a certain group that gives us money wants us to use it".

Posted by Lizzie Buchen on August 18, 2009
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Here are the several hundred physicists that made their way to Hamburg for the conference. It's a relatively small conference, and since there is only one plenary session at a time, with invite-only talks given, there is none of the helter-skelter feeling of something like an APS meeting. But several people complained to me that there are only about half as many people as usual -- and that that reflects the growing ennui, malaise even, of a community that hasn't pushed at the energy frontier in decades. You can see that more people made the trek out to Korea for the last Lepton Photon in 2007 in the group photo from that year.

High energy physics has been waiting for something like the LHC for 25 years, says Bob Cousins of UCLA, and a deputy spokesman on CMS. He remembers a DOE advisory committee in 1983 that outlined the need for a super-collider -- some machine that would reach beyond the TeV energy scales where the Standard Model breaks down. Sure, the Tevatron has done plenty of interesting things in the interim -- but there has been no upheaval to the overall picture. The community has watched as the Superconducting Super Collider got partway built and then was canceled. And it has waited patiently as the LHC worked its way slowly into existence. It really has taken a generation for the LHC, Cousins says. "The lost generation?" I asked. "Yeah, something like that -- my generation," he said. But if they can hold on a little longer, they could end up being the greatest generation.

Posted by Eric Hand on August 18, 2009
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So in all of the discussions of the status of the LHC, there has been little change to the new plan that emerged a few weeks ago: the machine will run at half-energy through most of 2010. The two general purpose experiments, Atlas and CMS, will just have to be patient. But at the end of an LHC status talk, the Atlas team's Mel Shochet, of the University of Chicago, had a question: how will the LHC fix the problem with the splices for good? Mel had heard a rumor that the LHC would be shut down for quite a while as the welded splices were replaced with clamps -- a simpler technology used effectively at Fermilab's Tevatron.

Would LHC engineers do the clamping over the course of several planned shutdowns each winter? If so, that could put the time when the LHC could operate at full 14 TeV energies way off in the future. On the other hand, shutting down to do all the clamping at once would mean that the LHC would have to be shut down for a long time -- maybe even a year -- which presents a problem of its own.

In the hallways, I found Rolf-Dieter Heuer, the Gandalf-like director general of CERN, and asked him for his sage thoughts. "Clamping hasn't been decided, but it very well could be an option," says Heuer, who is having a bit of a homecoming here -- he was the research director of DESY for many years. Heuer says the main thing is to get some data to the experiments and give engineers a feel for the machine. Deciding how to fix the bad splices will come later, he said.

Posted by Eric Hand on August 18, 2009
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This morning at the conference, Charles Arntzen from Arizona State University talked about transforming plants into little green vaccine-manufacturing machines using engineered viruses. He helped pioneer the technique a few years ago when he made a vaccine against plague, and now he's taken aim at norovirus, aka the “dreaded cruise ship virus”, which can hamstring people for a day or two with diarrhea and vomiting.

The disease may not seem like the worthiest target of vaccination efforts — especially compared with the last big vaccine produced by this technology, which targeted cancer. But in a way, that's the point. Pharmaceutical companies aren't going to waste their time with something that's elective and only lasts a couple days, and cruise-goers don't inspire much sympathy in disease-fighting philanthropists, so this technique provides a cheap and easy way to fill in the gap. And to be fair, “cruise ship virus” can also cause outbreaks in more heartrending locations, like hospitals, day care centers, homes for the elderly and, allegedly, football teams.

To get the tobacco plants to produce the vaccine, researchers insert genes coding for virus structural proteins into the tobacco mosaic virus, and infect plants with the engineered strain. The virus replicates and spreads through the plants, making the plant cells churn out the encoded particles, which can be used in vaccines.

The use of recombinant virus is an improvement over the more common method for producing plant vaccines, which uses transgenic plants and so is slower and generates a lower yield. (Arntzen has also been involved with that technology since its early days.)

More importantly, the recombinant virus approach has significant advantages over the traditional flu vaccine manufacturing technique, which uses chicken eggs and has been more or less unchanged for decades. Plant-generated vaccines don't involve any viral genetic material so they're noninfectious, can be scaled up easily and cheaply, and in some cases patients can vaccinate themselves simply by eating the plant.

Image: Flickr/richardmasoner

Posted by Lizzie Buchen on August 18, 2009
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ACS is spread out across hotels and centers over at least a nine block-by-nine block chunk of downtown DC. There are shuttles rolling around but they rarely beat walking, so when you venture to a new location it's best to be sure you want to stay for at least a few talks. I ended up grabbing lunch at one end of the stretch, so I thought I'd at least take a walk through the nearest ACS venue. Luckily I happened upon some fairly interesting talks about polymers — no huge breakthroughs, but certainly educational.

Richard Gross at the Polytechnic University at NYU presented some interesting work on sophorolipids — surfactants that are oozed out by yeast. Sophorolipids have been generating some interest with the increasingly eco-conscious pharmaceutical industry because they're biodegradable, naturally and renewably produced and non-toxic, or at least low-toxic.

Gross has been hooking these glycolipids into polymers for a few years now using ring-opening metathesis polymerization, and here he showed how versatile the process was, not just producing high molecular weight polymers but also giving him the power to vary the polymer's structure and "tune" its physical properties. He found that the polymers have similar physical properties to polylactic acid, an increasingly popular "green" plastic, but sphorolipids have unique potential because he can make them in funkier shapes.

I also checked out a talk about cavities with Joseph Antonucci from the National Institute of Standards and Technology, who's trying to develop antibacterial fillings. There's a recent trend to introduce antibacterial agents into fillings (and really, what industry isn't following this trend?), but there's a problem with leakage. A few years ago people started developing antibacterial materials that worked by contact with bacteria rather than releasing the agent, but these "biocidal" polymers were difficult to make.

Antonucci developed a new, one-step way to synthesize biocidal polymers — by adapting the "classic" Menschutkin reaction, which is apparently old hat for organic chemists. (Back in 1907 Nature ran an obit (pdf) on Prof Menshutkin if you're into that kind of thing.) One of the surprises for Antonucci was the antibacterial product ended up being a viscous liquid, making it all the more suitable for filling in your cavities.

Posted by Lizzie Buchen on August 17, 2009
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This cute little worm has constructed a tube around itself from beads of zirconium oxide. It's a pretty impressive feat by human engineering standards, as the animals have to stick together all the little bits (normally sand and pieces of seashell) while submerged in flowing water — not the best conditions for your average adhesive.

Russel Stewart at the University of Utah is looking to these innovative little carpenters for tips on synthesizing a glue with similar advantages. Gluing in wet conditions would be great for a number of reasons, especially for sticking together bloody human body parts like broken bones. Currently, Stewart says, there aren't any clinical adhesives for bone, only for superficial wounds.

When Stewart cloned the genes in the worm's protein-rich glue, he found that they all shared a key feature: they were very negative on one side and positive on the other. Instead of copying the exact genes, then, he'd just have to get the charges right.

After he made his synthetic protein goop, he tested it by sticking bones together underwater, and found that the glue bonded them together with a strength of 750 kilopascals — meaning a bond just over a square inch could hold a full keg of beer. While this isn't enough for a weight-bearing bone, it's probably adequate for reaffixing small fragments or bones in the face.

Posted by Lizzie Buchen on August 17, 2009
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Today DC is much more alive and crazy with chemists than yesterday, and the chaos was exacerbated by a mid-morning fire alarm that evacuated the convention center. Chemists (and journalists) spilled out onto the sidewalks and milled about aimlessly; some took it as a smoke break, a few awkwardly typed on the laptops that were teetering on their palms. Carmen Drahl at the C&EN blog captured the mayhem on video. Alas, it was a false alarm (apparently the second one of the conference — maybe some expo exhibits getting out of hand?) and five minutes later the chem fest continued.

I started the day learning about carbon dioxide reforming — converting CO2 and hydrocarbons into something useful, rather than stowing it away under the ground or ocean.

Chang-jun Liu from Tianjin University in China focused on CO2 reforming of methane, which produces synthesis gas or syngas, a mix of carbon monoxide and hydrogen. This can then be used like natural gas to power turbines, converted into liquid fuel or as a hydrogen source for fuel cells.

Liu's trying to make the process more efficient by improving upon nickel catalysts. These are cheaper than the more popular noble metal catalysts and are quite active, but the problem is they're easily deactivated by carbon deposits that choke up the reaction.

To make nickel less vulnerable to carbon deposits, Liu described a room temp plasma treatment that created super small particles — less than 10 nanometers. Due to their new size and structure, these catalysts resisted deposit formation and remained reactive, giving this cheaper alternative a possible future in CO2 reforming.

Posted by Lizzie Buchen on August 17, 2009
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Welcome to Lepton Photon 2009, the premier high-energy physics conference of the summer, this year taking place in Hamburg: Germany's second largest city and, with its system of rivers, dammed lakes and canals, the country's biggest port. It's also the place where the Beatles, back in the early 60s, cut their teeth, playing night after night in the city's famous red-light district.

Not sure where the title of the conference comes from, though I think it's pretty sweet. As one of my colleagues said, it could be a good name for a rock band. But at least here at the beginning of the conference, we're not going to be hearing about leptons or photons, but, rather, protons: updates on the status of the proton-smashing LHC, and its two main detector experiments, Atlas and CMS. As most know, the LHC fizzled out last year after a bad weld vaporized -- and so most of the people in the room have been closely following every detail of the machine's rehabilitation. Most of the plan is settled after a new energy schedule was set by LHC management on 6 August, so we're not expecting any new revelations, but let's wait and see.

Posted by Eric Hand on August 17, 2009
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This afternoon I went to the Presidential Plenary Symposium, hoping to get a nice overview of what chemistry really has to do with global security. The symposium was in a huge ballroom, which looked all the bigger because only about 5 percent of the seats were occupied.

I was a little disappointed in these talks, in part because they didn't have much chemistry in them. But there was certainly an interesting cast of speakers with impressive resumes. The talks started with Vahid Majidi, who's the assistant director of the Weapons of Mass Destruction Directorate at the FBI. He's also been chief scientific officer of the Department of Justice and the leader of the chemistry division at Los Alamos.

Majidi started out trying to relate global security to chemistry: while chemists work with moles per liter, he works with humans per area of land; chemists think about the nature of the analyte, he thinks about intent. “We both suffer from heterogeneous analyte distribution,” he says, along with “interfering species”— good people who look like bad people. I appreciated the attempted empathy but was still waiting for the connection to actual chemistry.

To that end, he went no farther than showing a few slides of case studies in which the FBI caught people with chemical WMDs — pufferfish toxin, ricin, uranium, chlorine. Pretty interesting cases, but after the overviews he focused on the FBI's general strategy of stopping WMDs (various steps of intervention). There must be loads of fascinating research going into new ways of detecting and destroying chemical and biological WMD's but it looks like I'll have to seek out a different session for the real stuff. (Luckily, the schedule's full of such goodies.)

After Majidi came Mark Wrighton, who was delivering the academic perspective on chemistry and global security. He's chancellor of Washington University in St Louis, Missouri, and as advertised had a different view of global security than Majidi. To him, the greatest threats to global security are energy and the environment, problems which “will be with us for the remainder of the century,” he says. “Chemists will play a vital role," he added.

This year he vice-chaired a National Research Council committee on America's energy future, and spent much of his time at the symposium going over the committee's analysis. He started out setting the rather grim stage of our current energy situation — our overreliance on fossil fuels (85 percent of our energy needs), scary population growth stats for India and China, mounting volatility in fossil fuel market prices, and of course climate change, which Wrighton calls the most compelling argument.

He listed the ways chemists could help with the CO2 problem — geological storage, photobiological reduciton of CO2 to fuels (i.e., biofuels), electrochemical reduction of CO2 to something more useful. All very interesting stuff, but he too left out all the juicy bits. I would have really liked to see Stephanie Burns give the business perspective, as she's president, chairman and CEO of Dow Corning, but she wasn't able to make it.

Overall, both talks were nice and easy. Though pretty shallow on the details, they gave some non-chemistry context that suggests potential global applications. I've got the next four days here to get all the details.

Image: ACS President Thomas Lane. ACS.org

Posted by Lizzie Buchen on August 16, 2009
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I thought I'd ease my way into the conference in as macabre a way as possible — with the smell of decaying flesh.

Grad student Sarah Jones and her advisor Dan Sykes at Pennsylvania State University presented their work on the volatile chemicals that waft from dead pigs' bodies during the earliest stages of decay. The idea is to determine the chemical profiles of a body's aroma at different time points after death, which might help crime scene investigator-types accurately determine the time of death.

Jones kicked off the show with some gnarly descriptions of the various stages of decomposition, starting with “fresh” and ending with “dry decay”, during with the bones finally turn to dust, as it were. My personal favorite was called the “black putrefaction” stage, at which point the body cavity — bloated from the gases and fluids produced by invading bacteria — ruptures, transforming the carcass into a wide open rotting flesh-fest for hungry insects and microbial scavengers. I should note that during Jones's descriptions, a smiling Sykes held up large color images of decaying pigs in each respective stage.

These different stages of decay are very well studied — people even know which insects invade which orifices at which timepoints. Decaying flesh is the focus of America's fascinating “body farms”, where universities in Tennessee, Texas and North Carolina recognize the scientific merits of having dead human bodies rotting away on their campuses.

But although people know all the gory visual details of decomposition, they're less certain about the smell. This would be helpful, says Jones, for developing a portable electronic device that could determine time of death on-site and in a quick and accurate way.

The researchers set up freshly-dead pigs in special smell-catching death chambers. They used pigs because they're about the same size as humans, rot in a similar fashion and can be studied immediately after death — no need to politely pause for mourning family members.

The chambers are outfitted with solid phase microextraction (SPME) fibers, which catch the volatile organic compounds. Jones and Sykes say the use of these fibers is the biggest advancement of their work, as previous studies of death smells used sorbent tubes, which are bulky and inconvenient, meaning they can't be used "in the field".

Jones didn't really go into the details of the chemical profile, though it included names like "putrescine" and "cadaverine" and the more subtle "indole precursors". So far, the research hasn't turned up any big surprises, but the SPME fibers will let them go out into the field to check volatiles in different environmental conditions, which may turn up some new scents. Jones also repeatedly insisted that the work is in its "very very early stages".

Image: FBI.gov

Posted by Lizzie Buchen on August 16, 2009
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Aloha, chemistry! This weekend, more than 10,000 chemistry-philes descended upon the nation's capital for the American Chemical Society's 238th semi-annual meeting. The location is perfect because a) this year's theme links chemistry to global security, a subject near and dear to Washington's heart, and b) it's about half a mile from Nature's DC office.

Presentations have been going since 8 this morning, but at early afternoon the conference center's still at a pretty low buzz. I expect it to pick up over the course of the day or by tomorrow.

I'll try to blog the goods as best I can, but also check out The Sceptical Chymist, Chemical and Engineering News and #ACS_DC on Twitter for more ACS news.

Image: DOE.in.gov

Posted by Lizzie Buchen on August 16, 2009
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US President Richard Nixon threw a 1440-guest dinner in honor of the Apollo 11 crew in Los Angeles on 13 August 1969, a day which saw the astronauts hop between New York, Chicago and Los Angeles. Nixon himself oversaw details including a newly commissioned song by the Marine Drum and Bugle Corps and table decor, according to Time Magazine.

The guests included government officials, astronauts, entertainment figures and other celebrities, but notably lacked Jacquelyn Onassis, former President John F. Kennedy's First Lady, who declined Nixon's invitation. The mood, while celebratory, was also valedictory, according to space journalist Andrew Chaikin. The astronauts were well aware that Nixon was no fan of the manned space program, which he saw as a legacy of his predecessors Kennedy and Johnson. Chaikin wrote in A Man on the Moon that one cynical astronaut at the dinner raised a pre-emptive memorial toast to the moon landings: "Here's to the Apollo program. It's all over."

This is the final blog post of the @ApolloPlus40 series, which accompanied the ApolloPlus40 Twitter project by Nature News, a re-telling of the Apollo 11 lunar landing, 40 years later.

Thanks for following!

Posted by Lucas Laursen on August 14, 2009
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On the afternoon of the second day of NSF’s Minimal Life workshop, Eric Smith of the Santa Fe Institute in New Mexico provided a much-needed synthesis.

He examined the trade-offs of having a super-pared-down genome and the need to leech off of the environment — parasites, for example, can only survive with bare-bones genomes because they farm out most of their metabolic needs to their hosts. He presented his not surprising, but necessary, quantitative data showing that the more dependent an organism is on its environment, the less metabolically complete its own genome is.

Smith discussed the metabolic and biosynthetic pathways that seem to be universally needed for life, which all involve the same five precursors (the famous CHNOPS from high school chemistry), the same cofactors, and produce pretty much the same amino acid nucleotides. But while it’s hard to find the complete networks for all these necessary bits and pieces at the level of an individual species, they are indeed wrapped into a nice little package at the level of the ecosystem. The boundary between organism and ecosystem, then, is more fluid and less important than most people assume.

“What species lineages are doing is breaking up the universal metabolic costs, and creating behavioral links that allow species to get what they don’t make within an ecosystem,” he said. Even the cell theory of life, Smith says, is “not as fundamental as we take it to be”.

Andy Ellington from University of Texas in Austin was next, and, following his discussion yesterday, opened with a diatribe against the concept of life. As “the only person in the room from the deep south…where people think differently”, he said he understood the consequences of the word’s sentimentality, which was due in part to the difficulty of defining it.

“For me, life is like pornography,” he said. “We know it when we see it, but we can’t actually define it with any precision.”

But that didn’t stop him from commenting on “the magic of life”: that complex function arises from the interaction of simple components. To understand the black box in between, he’s trying to create the minimal artificial system capable of evolving, a process which even viruses are capable of.

“I’m a genomic emperialist,” he said. “If T4 [virus] DNA gets in [a host cell], makes more T4 DNA, and gets out, it’s doing its job. It replicates. Whether I call carbon and nitrogen and some water my home or a big bag of nucleotides and enzymes and other fun things my home, it doesn’t matter to me. My DNA replicates.”

Thus he removes a pesky hurdle that holds back many bottom-up, engineering approaches to biology: the cell. “I don’t like the cell,” he said, “and I don’t think it makes any difference whether you have a cell or not to think about these things.”

Instead, he’s trying to engineer his evolvers in in vitro replicating systems — droplets of watery solution bobbing in a sea of mineral oil. Each droplet has the basics for DNA transcription and translation, and gets an evolutionary nudge from a self-splicing intron that jumps around the genome disrupting code, and can even do so in a targeted fashion.

To test the ability of his ascetic droplet worlds to support protein evolution, he provided genes for streptavidin and biotin, which normally bind very tightly. He scrambled the biotin binding site of streptavidin and distributed different mutants among some 10^12 little droplets. The system “responded like a champ,” he said, evolving novel interactions between the proteins.

Moreover, these novel proteins, which had “never seen the inside of a cell, just the black oily night, for their entire evolutionary lives”, were more soluble than wild-type proteins in the in vitro system. The protein had learned to fold better in its oily environment than in a cell.

One novel binding site is all well and good, but Ellington wants to “take my pathetic little one-feedback loop and extend it out” by evolving an operon or even an enzyme that amplifies its own gene.

“The goal is to make increasingly complex replicators that have nothing to do with cells, but have replicating functionality," he said. "It’s a subsystem of a cell but it evolves.”

Ellington concluded that these replicators that undergo evolution “challenge the intuition that cells are important for life”. He also pointed out to Smith that, contrary to his discussion, “there’s no ecosystem here. It’s its own selfish self, trying to make more of its own selfish self. It is what it is.”

Posted by Lizzie Buchen on August 11, 2009
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On the first day's afternoon at the NSF workshop on "minimal life", discussants took an engineering approach to understanding the simplest forms of life. Here, engineers are sort of the “cheaters” of the group — unlike the other scientists, they get to understand the minimum required for life by looking at things that are simpler than what naturally occur in nature.

Clyde Hutchison of the J Craig Venter Institute said the ultimate goal of his work was “a complete description of biological systems in terms of the laws of chemistry and physics.” While physicists have the hydrogen atom as their simple model organism, biologists must use minimal cells. He's not talking about chunky, complicated yeast — his cell of choice is Mycoplasma genitalium, the smallest cell that can be grown independently in the labroatory, and its 580 kb genome, the smallest known genome of any bacterium capable of independent life, he says. And even that's not little enough for his fancy: he wants to see how much of it he can trim away and still have the tiny thing function.

“Are there cells that can live in the lab that are significantly simpler than cells that exist in nature?” he asks.

His basic strategy is to first synthesize and assemble the entire chromosome, then start hacking away and sticking the trimmed down versions in Mycoplasma cytoplasms to see if they still grow. So far he's working on getting the recipient cells to accept the synthetic genome — a tricky feat because the genome is synthesized in yeast, and it's difficult to get it out intact. But he's been able to get the system to work using naked whole genomic DNA as the donor and another bacterial cell as the recipient, "putting us well along the way of making a synthetic cell".

Tom Knight of MIT, a leader in synthetic biology, was up next, and talked about engineering organisms from the smallest number of simple parts. He spoke of the necessity of standardized parts for engineering, and specifically of the Biobricks project that he helped found.

His strategy seems similar to Hutchison's — start with a simple organism and systematically take stuff out until it breaks. He chose “an organism which absolutely no one cares about”, he said — Mesoplasma florum, commonly found in insect guts. The bacterium has a genome less than 800 kb long and an impressive lack of functionality: It can't make any of its own amino acids or cofactors, or carry out the citric acid cycle. Basically all it does it make and break down proteins. So far he's sequenced the genome and is currently developing “genome engineering tools” like custom transposons.

Next came Sheref Mansy of the University of Trento, in Italy, with perhaps the most minimalistic, bottom-up approach. If you want to create the simplest replicating cells, forget proteins and phospholipids (the primary components of our cell membranes). Last year, he was able to create a protocell that replicated its DNA using only four components: fatty acids to make the membrane, and DNA template, primer and activated nucleotides. There are many limitations to his protocell, such as the inability to use support the function of proteins, but it seems pretty exciting to get even these properties from such a barren bag of chemicals.

Posted by Lizzie Buchen on August 11, 2009
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This week at the National Science Foundation headquarters in Arlingon, Virginia, a small group of researchers got together for a workshop about “minimality” in biology. Participants considered the teeniest living cells, the shortest genomes, the simplest engineered systems — basically asking, how low can you go and still have “life”?

The morning sessions on 10 August focused on “unusual life”. Stephen Giovannoni of Oregon State University in Corvallis talked about SAR11, a clade of tiny planktonic bacteria that happen to be the most numerous microorganism in the ocean's uppermost waters. Evolution has done an impressive job trimming the fat from SAR11's genomes — the genome of one member, Pelagibacter ubique, has no introns, extrachromosomal elements, transposons or non-coding genes, and has the shortest between-gene “spacers” known. With only 1.3 million base pairs, its genome is the smallest of any free-living microorganism — although a similar claim was made by almost all the speakers today about their organisms — and makes up 30% of their teeny cell bodies.

Such a barren genetic code means SAR11 is pretty dependent on its environment. It may not be a traditional parasite, in that it isn't constantly sucking the life force of another organism, but it does make you wonder where to draw the line between an organism and its environment. SAR11 depends on seawater for five essential cofactors, as well as for the amino acids glycine and serine. And as reported last year in Nature, it must get reduced sulfur compounds that are made by other plankton.

Howard Ochman of the University of Arizona talked about the evolutionary processes that might lead to small cells and genomes. He postulated that bacteria have a “pervasive mutational bias toward deletion”. In contrast, when a mutation deactivates a gene in eukaryotes, the “pseudogene” remains, accumulating and filling the genome with noncoding DNA.The bacteria's progression toward a compact genome doesn't appear to have a purpose. “It doesn't matter how many genes there are to the overall replication rate,” he says.

Many think about evolution as leading from simple organisms to complex, but bacteria don't seem to have taken this path. When ancestral, free-living bacteria with chunky genomes moved into nutrient-rich hosts (like humans), many of the bacteria's genes became superfluous and become inactivated. Through an unknown mechanism, according to Ochman, the bacterial bias for deletion removes these “dead genes”. Such bacteria, with tightly-packed coding regions, can have genomes nine times smaller than Giovannoni's Pelagibacter. It brings up an interesting difference between bacteria and eukaryotes: In bacteria, genome size is tightly linked to gene number, but while mice and humans have about the same number of genes, the mouse genome is about 15 percent smaller than ours.

The audience (which, by the way, was composed entirely of men, except for the meeting coordinator, an NSF representative, and your Nature reporter) got excited when Krastan Blagoev, the NSF program coordinator, suggested talking about the ethics of “engineering life”, which was the subject of the afternoon sessions. Tom Knight led the discussion, and wanted to talk about how to present the work to the public. “For a lot of people,” he said, “it sounds like we're taking over the reins of creation. We can talk all we want about how safe it is, what we plan to do it, how to assure that the things we do are constructive and not destructive, but there will still be a hwole set of people out there who will look at it from the perspective of, are we playing God?”

To which Andy Ellington of University of Texas in Austin replied: “Why don't we just ignore it?”

“We have to be honest with what we're doing, and speak as scientists,” Ellington said. “NSF is walking into a minefield by talking about minimal life. By stating that we're creating, defining, minimizing life, we're by necessity saying that we know what life is, and immediately taking on the religious connotation of life. It's a hugely loaded term, and brings up Frankenstinian stuff about mucking with life.”

“I'd prefer the term be eliminated from biology books,” he said, favoring a more specific term.

Eric Smith of the Santa Fe Institute in New Mexico argued that “we shorten the discussion of things we don't understand by substituting inadequate smaller ideas” — such as minimal 'cells', as the cell theory of life isn't always adequate.

“I'd hate to lose the term life when we don't know what it means,” Smith said.

Clyde Hutchison of the J Craig Venter Institute in San Diego, California, said that they are, in fact, interested in the question of what 'life' is. “So are religions. Different approaches lead to different conflicts. Religions wouldn't like the idea of no difference between life and not life.”

Ellington responded, “by saying we're both interested in learning about life, we're saying that there's something special about life. That's a profound limitation. This is like the virus/non-virus debate that was ultimately useless.”

Harold Morowitz of George Mason University, the lead organizer of the event and a venerable big gun in the field of minimal life, quieted things down when he said “there was nothing implied” in using the l-word in the title of the workshop. “It's a way of asking questions about biotic systems, organisms and ecosystems, and how they function. That gives us plenty to talk about.” With which he dismissed the group to lunch.

Posted by Lizzie Buchen on August 11, 2009
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So I hiked up to the famous quarry itself on Saturday, on a day with remarkably clear blue skies and cool mountain air. It's relatively strenuous - about 3 or 4 hours uphill, with a few steep sections, and then an unremitting 3 hours of knee-pounding downhill switchbacks. If you fancy seeing the quarry for yourself, you'll need to sign up for a guided tour. The quarry is a national herritage site, so you can't wander in there alone, nor can you take any fossils away with you. This was, of course, a source of great despair to the paleontologists on our hike, who found fossils (some relatively rare) and were forced to simply put them back on the ground and walk away. (If truly interesting pieces are found, they are put in a locked cupboard in the quarry for study and/or to show tourists like us some good specimens from the site.) There aren't exactly fossils on every bit of loose shale, but there are a reasonable few scattered around. Enough that, for example, I ate my lunch whilst sitting on a trilobite. We spent our time in the quarry marvelling at the view (we didn't know which way to look - out towards Emerald lake and Walcott peak, or in towards the quarry), taking commemorative pictures with Derek Briggs (who famously helped to recognise the strange character of many Burgess shale fossils) and with a toy model of opabinia, which one of the researchers had brought up with him specifically for the photo-op. Marianne Collins was also on our tour -- the artist who drew many of the recreations of these creatures, including the five-eyed, long-snouted opabinia. A glorious end to a fantastic meeting.

Image: Your intrepid blogger with Derek Briggs

Posted on behalf of Nicola Jones

Posted by Ananyo Bhattacharya on August 11, 2009
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One presentation that stirred things up a bit suggested that Anomalocaris wasn't the fierce predator it is usually portrayed as (see my news story here). This animal is almost always shown munching on a hard-shelled trilobite, but it seems that maybe it was incapable of such attacks. Opinion is still divided, but even Simon Conway Morris threw up a picture of a classic reproduction of Cambrian life during his talk, featuring an Anomalocaris gripping onto a trilobite, and quipped "so here we see an Anomalocaris putting a trilobite gently to bed...". This was met with many chuckles - not, I think, because the idea of a gentler Anomalocaris is laughable, but simply because people don't know quite how to respond to classic ideas about Cambrian life being overturned. If the 'gentler' image holds up, they'll have to redraw all the Cambrian life pictures.

Posted on behalf of Nicola Jones

Posted by Ananyo Bhattacharya on August 11, 2009
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The Apollo 11 crew, along with 20 other NASA personnel quarantined with them at the Lunar Receiving Laboratory in Houston, completed their health quarantine on 10 August 1969. They emerged to cheers from 300 NASA employees and the embraces of their families, who they had seen and spoken to through windows for the duration of the quarantine.

The Apollo 11 crew's last day at home was 7 July 1969, in the run-up to the launch, and they would only enjoy a few hours back home before embarking on an international public relations tour to celebrate their mission's success.

Video: http://bit.ly/2pH6m

Photo: NASA

This blog post is part of the @ApolloPlus40 series, which accompanies the ApolloPlus40 Twitter project by Nature News, a re-telling of the Apollo 11 lunar landing, 40 years later.

Posted by Lucas Laursen on August 10, 2009
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Geoengineering — the deliberate manipulation of climate to counteract global warming — might not be taking off just yet, but the push to fund more research into it is increasing. Read the full story here on Nature News. And that wraps up our coverage of the 2009 Ecological Society of America meeting.

Posted by Alex Witze on August 08, 2009
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I'm writing this after a few drinks (which, as you'll soon see, is perfectly appropriate) and after being inspired by Simon Conway Morris's talk on the origin of body plans. I wish I could do Conway Morris's talk justice in this blog – he is an eloquent, and funny, speaker. Suffice it to say that he recounted some of his arguments against Gould (read about that here); fought back, good-naturedly, at several other speakers at this conference who have called him wrong about some particular matters of creature identification; threatened to drink a bottle of commemorative 'Shale Ale' whilst at the podium in spite of Canada's draconian laws against drinking in public; and responded to one confession of love. Of course, he also addressed some serious points of biology, concluding that perhaps, “at long last, biology is going to become predictable”. There's one prediction I would bet money against.

If there's one thing I have learned at this conference, it's that Cambrian animals are unpredictably, wonderfully silly. Quite a lot of them have ridiculous spiky bits, funny amounts of fur and legs and antennae. My personal favourite thus far is Canadia, if only for the name (yes, I am Canadian), which Martin Brasier has called a “worm in drag” thanks to its feathery cloak. But it's a close call. Halluciginia, with spiky bits both as feet and back spines, owes its name to the fact that it seems as if its creator was on acid. Opabina has five eyes, and a long nose with a claw on the end. That's just odd.

The people who draw scenes of these creatures seem to really embrace their oddity, by painting them up in cartoon colours – primary yellows and blues, with bright orange and purple and everything in between. Many of the reconstructions bring childrens' bath toys to mind (You can actually buy toy versions, suitable for ages 5 and up).

So, one is encouraged to think: 'Boy things were weird in the Cambrian'. But, to be fair, perhaps we should trawl the bottom of today's oceans and the far corners of the continents, do up some primary-coloured cartoons of the weirdest things we find, and put them in a lineup against the Cambrian beasts. My bet is that most people wouldn't be able to ID the Cambrian culprits. I mean check out the star-nose mole (which has also inspired a toy). I can't vouch for the reality of everything on www.oddanimals.com, but isn't it interesting that it's hard to tell real weird animals from fake ones?

I'm not trying to downplay the Cambrian – it's a fascinating time. But with this next drink I'll just say cheers to all of modern life's oddities (humans, perhaps, being the strangest).

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 07, 2009
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Martin Brasier of Oxford University jokingly referred to the 'MOFAOTYOF Principle' in his talk – the 'My Oldest Fossils Are Older Than Your Oldest Fossils' phenomenon. He makes fun of it (such competitions can perhaps get a bit silly), but it is the business that Brasier and his team are in – hunting down those oldest fossils of the old.

Certainly you can't get older than the Ediacaran when it comes to animal fossils, and this was the subject of Brasier's talk – the strange squished creatures preserved in the rocks of Mistaken Point, Newfoundland. At the end of his talk, Brasier threw up a slide showing some 'trace fossils' – the fossilized tracks that some worm-like or snail-like creature left behind. Such tracks are more common in younger fossil beds, when animals were more likely to be mobile (the most commonly talked about Ediacaran beast looks like a feather stuck in the seabed, and certainly didn't get around too much). And they're more common in shallow waters. If such tracks are from the Ediacaran deep waters, as implied, then that would be quite exciting to those in the field. It could even push back the date of complex mobile creatures – things that move intentionally in a single direction, perhaps in search of food, with a sensory system and complex muscles – by tens of millions of years. Maybe. “A lot of people have looked at a lot of rock very hard and not seen anything like this,” I overheard Guy Norbonne, an Ediacarian expert, say over coffee. “I understand it's under review. Let's see the paper, and see how it stands up.”

Brasier sees a bit of a shift in how people are looking at the Ediacaran. At first there was an awed acceptance that all these squishy creatures must have been the ancestors of modern animals (so there would be a soft coral, and a squidgy early worm, etc). Then the Ediacaran creatures were seen as a 'failed experiment', most of which went extinct. Now there is a more sober period of working out what they all were, and which ones died out and which lived on, Brasier says. This shift is one of the reasons he wrote his recent book Darwin's Lost World, about the Ediacaran fossils (Darwin lamented that pre-Cambrian fossils had never been found; but they have been found since, and so are not a 'lost world' to us).

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 07, 2009
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I was slightly shocked to see a slide of 'fossilized brains' from the Cambrian thrown up on a slide. Brains? From the Cambrian? Turns out I was right to be shocked. “People find it hard to swallow” says Nicholas Strausfield, a neuroanatomist from the University of Arizona. He was trawling through Burgess Shale fossils of Waptia – a small shrimp-like creature from the Cambrian – looking for hints of the evolutionary relationship between insects and crustaceans, when he found 3 samples that seemed to have brain-shapes in them. “I have flattened a lobster brain, and it looks like that,” he says. You can't tell too much from these fossils, except that the brain was apparently big enough to handle some complex sensory information from the antenae and simple eyes. Still, it's fascinating. Strausfield (who, as the recipient of a McArthur grant, unofficially counts as a 'genius') switched from looking at insects to crustaceans on the principle that you ought to be able to eat what you study. Sadly, he notes, Waptia is so small it wouldn't even make a good soup.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 07, 2009
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The annoying thing about fossils is trying to work out what the heck the creature looked like before it was trapped in a mudslide, lost some limbs, got squashed flat, and was chemically altered by millennia of burial. This is not easy. And as Robert Sansom of the University of Leicester points out, it's made extra difficult by the fact that some discriminating features used to identify these creatures decay faster than others. That introduces a bias in how organisms are classified, he warns. His group is doing lab tests of decay rates of different bits and pieces of animals to sort these biases out.

The lucky thing is that Burgess Shale fossils and others from the same time period around the world are strangely well-preserved. I had assumed that this was just a lucky accident of some Cambrian beasts being swallowed by a mudslide, and Walcott finding the result. But it seems to be more complicated than that. The preservation of organic carbon from these beasties is a highly unusual phenomenon, and is very rare (possibly absent?) in the fossil record for animals of younger eras. Why is this? No one knows for sure. But it might have been a combination of those animals being swamped with fine-grained clay that kept the oxygen out, and the oceans being low in sulphate, which stopped other bacteria from eating up the remains. An intriguing thought, with evidence to support it from Emma Hammarlund of the University of Southern Denmark.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 07, 2009
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Roughly 100 billion cubic meters of groundwater is overexploited around Beijing. Nine years ago, that figure was 8 billion cubic meters.

Such were the dire numbers coming out of a presentation today by Ge Sun, a hydrologist at the US Department of Agriculture in Raleigh, North Carolina, on the state of China's water crisis. In the Daxing district of Beijing along, the water table has dropped 1.3 meters per year between 2001 and 2007. (I checked my notes three times to make sure that 'meters' is correct there, hard as it seems to believe.) More than 1,000 natural lakes have vanished. Forty percent of the country's rivers have become ephemeral. The rivers that manage to hang on are, more than half of them, polluted.

The factors are many: among them are population growth, mismanagement of land, increasing urbanization and low efficiency of using water, Sun said. And it was hard to miss the sense of urgency in his voice. Water resource issues and environmental disasters have become so rote in China over the past decades that it can be difficult -- at least for me, a jaded journalist -- to comprehend them getting any worse. But the economic boom in China is a whole new matter. Look at that number again of overexploited water in Beijing: 8 billion cubic meters in 2000, 100 billion cubic meters today. Where will we be in 2020?

Image: The 2,000-year-old Dujiangyan irrigation system in Sichuan province

Posted by Alex Witze on August 06, 2009
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Day and night are not equal when it comes to warming, Shiqiang Wan of the Chinese Academy of Sciences' Institute of Botany reminded the audience today.

Since 2005 Wan has been part of a team looking at how ecosystems change in Inner Mongolia, along the gradient that runs from meadow to typical (grassy) to desert steppe. They've set up big experimental plots (right) that alter precipitation, temperature, and other inputs, then see what happens. The idea is to simulate how climatic change might affect various ecosystem responses.

Among many questions they tackled a fairly thorny one: what difference it makes whether warming occurs during the night or during the day. Many computer models, Wan told the meeting, rely on a 24-hour average to sum up the expected effects of warming. His team, however, split out these factors, warming some of their plots during the day only, some during the night only, and some during a 24-hour cycle.

The differences were fairly dramatic, his team reports in a paper in press in Biogeosciences. Plots warmed only during the night turned from being a net carbon source to a net carbon sink; the extra warming at night stimulated leaf respiration rates, which meant they sucked down more carbon than before.

The take-home message? It might sound familiar: climate change could affect the world's ecosystems in unpredictable and currently little-understood ways.

Image: Research Group of Global Change Ecology

Posted by Alex Witze on August 06, 2009
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Remember the latest addition to the periodic table, copernicium, element 112? Well the fall out from the name choice has begun.

The abbreviated symbol that discoverer Sigurd Hofmann chose was Cp. This hasn't been confirmed by IUPAC yet, and this is the body that has the say in the end, but it seems appropriate that here at the IUPAC congress that the discussion over this shortened symbol should be aired.

The problem is that for many synthetic chemists Cp already means something - it is used as a shorthand form for the cyclopentadienyl ring, a 5 carbon and 5 hydrogen ring that is aromatic like benzene and often used as a ligand.

So some chemists are inevitably unhappy about the use of Cp for another purpose. One of these is Paul Chirik from Cornell University who in his talk about main group chemistry apparently said he wanted to start a campaign to have the abbreviation Kp, not Cp used for element 112. This, apparently is etymologically correct, because Copernicus was actually Polish and his name was spelled Mikolaj Koppernigk.

Chirik assures me he said this in jest and is by no means an expert in this area. But I wholeheartedly encourage this kind of campaign! Come on chemists, stand up for the rights of cyclopentadienyl ligands! Kp vs Cp - what do you think?

Posted by Katharine Sanderson on August 06, 2009
Categories: International Union of Pure and Applied Chemistry 2009 | Permalink | Comments (0) | TrackBacks (0)

The plenary lecture this morning was by Peter Bruce, from the University of St Andrews, over on the east coast of Scotland. His message was an appeal to chemists to open their minds in order to save the world from climate change. Free yourselves from thinking of the immediate applications, he said, and this challenge can be faced. "The chemistry to tackle this is still going to be fundamental chemistry," he says. Chemists should forget the immediate technical challenges.

Stirring stuff. And he had some very good reasons for saying this. Bruce has spent many years looking at ion transport in polymer electrolytes, and along the way has invented a better way to probe the structure of these large crystalline polymers that are otherwise too large to get x-ray crystal structures of.

How can this help climate change? Well these fundamental chemistry advances have found their way into lithium batteries - the things that charge our laptops, mobile phones, as well as powering tiny implantable medical devices of the future.

Bruce is now looking at ways that might - eventually - make the charging and recharging process of batteries much much faster. This process involves lithium ions moving from one material to another. They travel one way when the battery is being used, and when it's plugged in again to recharge, they hop back over from whence they came. As many of you will know, this can take hours.

Bruce's work on solid crystalline polymer electrolytes could help. But to understand how these materials work their molecular-scale structure needs to be understood. The problem has been getting single crystals to do crystallography on. So Bruce developed a powder diffraction technique that worked a treat.

He's also spent a lot of time investigating why and how these crystalline polymers can conduct. The reason is that ions in crystalline polymers hop, which is very different to the way floppy non-crystalline systems work, he says. The conductivities they show are way too low for industry, he says, but doesn't much care. "Scientifically it opens up new avenues," he said. And curiosity has led his group to investigate other metals in the same group of the periodic table as lithium.

Next is the challenge of making the energy density of the materials better. To try and get a ten-fold improvement in energy, Bruce has developed a lithium-air battery, where oxygen from air reacts to start the ion motion. It's a neat idea, and you never know, it could work.

Posted by Katharine Sanderson on August 06, 2009
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Some of the weirder Ediacaran species might not be species after all, Alexander Liu of Oxford University has told the conference. There's a brand of squidgy Ediacaran fossils known collectively as 'pizza discs'. They are all round, and have bumpy bits – of up to 1-cm height in the fossil record – randomly scattered in the middle. These bumps are not consistent from one pizza disc to the next – each disc is individual. This makes it hard to identify the characteristics that define the creature that left the fossil print. So hard, in fact, that Liu wonders if it's not a specific creature after all. Some tell-tale hints in some pizza discs hint that maybe they are the slightly-decayed remnants of other, already-known species, he told the conference. Liu, who works in Martin Brasier's group, has even rotted some modern jellyfish and seaweed bits in the lab and made modern fossils of them, to confirm that this does indeed create irregular, lumpy shapes (no huge surprise there). His conclusion – that blobby bits that don't look like much might, in fact, be blobby bits that aren't anything much special – is so intuitively obvious that I can't help but think he's right. Depending on who you talk to, though, downgrading the Pizza disc from a creature to a bit of garbage might be slightly controversial.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 06, 2009
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Yet more history from Desmond Collins, who talked today about the work that has gone on in the Burgess Shale since the 1970s or so. Collins himself was in charge of many further explorations of the shale, and even has a quarry named after him (as does the original discoverer Charles Doolittle Walcott, and a handful of others, but only a handful). Collins is clearly on a first name basis with both all the people who have explored the shale, and also all the creatures who have turned up in the rocks. He showed a fabulous slideshow of weird and wonderful creatures preserved in the shale, most of which you can see in the Royal Ontario Museum's online photo collection. Surprisingly (to me), many of the creatures revealed have still not been properly described – including the one called the 'Collins monster'.

Collins' stories are full of freak snow storms during trips up to the shale, accidental finds of great fossils, and lovely little details that make the stories come alive: from the rat (which he also knows the name of... Robert I think it was) who licked their dishes clean for them when they were short on water, to the goats who licked the salt left on the rocks by the camp's mandated bathroom site (the goats would unfortunately kick bits of shale onto the camp in the process, until the researchers got permission from the park authorities to move the camp and pee wherever they liked). In 1995, while shoveling out vast amounts of fallen shale from the original quarry site, they found a block of ice encasing newspapers left behind on Walcott's expeditions.

Photos show how the Burgess Shale sites have changed and expanded over time – the original Walcott quarry is now some 3 times bigger than it originally was, thanks to researchers attacking the rocks with crow-bars, jack hammers and circular saws (they weren't allowed to use dynamite, as Walcott did, much to Collins' dismay). About half of Walcott's original quarry ledge has been preserved for historical reasons. The rest has been hacked away to reveal yet more finds. Looking at the panoramic shots of the mountains, one can't help but think there must be many, many more possible quarry sites – it's fantastic to imagine what weird wonders remain to be found.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 06, 2009
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Quote of the day goes to Kevin Peterson of Dartmouth College, who began his talk with a dedication to Wonderful Life, the book that popularized Cambrian creatures. “If it weren't for Wonderful Life we all wouldn't be here. Or at least I wouldn't be,” he said. “I brought this book to a bar in Montanna and read it in one sitting, over 12 beers. I developed my first man crush – I was in love with Simon Conway Morris.” (He means this as a joke, of course... no actual romance here). Conway Morris was one of the researchers who reinterpreted the Burgess Shale fossils in the 1960s, unveiling their truly bizarre characteristics, and is giving a talk here tomorrow... perhaps someone should warn him of Peterson's unrequited feelings.

Meanwhile Peterson has gone on to work on annelids – which he confesses are really just 'boring segmented worms'. There has been a problem in the worm world that genetic evidence gave a different sort of family tree than did morphology... in fact genetics seemed to put molluscs and other distinctly non-wormy creatures nested in within marine worms, which was surely not right. Indeed it would have meant there were a bunch of worms missing from the Cambrian fossil record. Peterson's group has been using micro-RNA evidence to sort it out, showing that the earlier genetic evidence was simply wrong in this part of the family tree (though he still doesn't know why). Worm dilemma sorted. Micro-RNA analysis, it seems, has a great potential for sorting out such family tree mysteries, though of course you need modern, living species to analyze – it doesn't exactly help to identify Ediacarian creatures.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 06, 2009
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A session this morning took on one intimate intersection between ecology and medicine. As Brendan Bohannan put it, “Some of the most exciting and interesting communities to study have been right under our noses all this time. In fact, they have been in our noses, and our guts, and the rest of our bodies.”

The microbes of the human biology form diverse communities, and each is a miniature ecosystem, presumably following all the same basic rules as the large ecosystems outside our windows. These communities do much more than merely hitch a ride. They help train human immune systems, help suck nutrients out of food, and so on.

For example, babies usually get their first gut microbes from the vaginal canal, as they are born. Babies born via Cesarean section bypass the canal, and tend to have predictably different communities of gut microbes until they are seven years old. According to Deborah Wohl, there is some research to suggest that Cesarean babies as a consequence have slightly higher rates of immune-related conditions such as asthma, eczema and allergies.

One fascinating talk was about catheter infections, which are apparently very common in hospitals. The general idea about them is that the urethra is more or less sterile, so the infection must proceed when microbes climb up the inside of the catheter tube and reach the bladder, where they then cause harm. But in a small pilot study, Betsy Foxman and her colleagues found evidence to suggest that microbial communities on the inside of catheter were stable over time, whereas communities on the outside of the tube—the surface touching the urethra tissue—shifted from day to day. She suggests that infection may result from disturbances in the regular microbial community inside the urethra.

And other conditions, including inflammatory colitis, periodontal disease, and bacterial vaginosis may not be the result of one bad pathogen coming from the outside, but disturbances in the normal microbial communities of the colon, mouth and vagina. Future treatment may look more like ecological restoration than the blunt instrument of antibiotics.

So is the medical establishment ready for ecological medicine? The panel was hopeful. Patrick Seed, an infectious disease specialist, said “One might argue that really the future is going to be restoring ecology with things like anti-virulence drugs. But even with that precise knife, if you take out a member of the community, my guess it that you will affect the community very broadly. We need to feed the good bacteria—keystone or cornerstone organisms that bring about a healthy ecology.”

See also: Why your teeth are like tropical islands.

Posted by Emma Marris on August 06, 2009
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How many bee species do you think live in New York City? Would you believe 227? You would if you heard Kevin Matteson of Fordham University give his talk on urban pollination in the Big Apple.

Most of those bees, he admits, are rare, or live in parks. But a surprisingly tough cohort of bees, wasps and flies do make their living buzzing around the flowers planted in postage-stamp gardens in Brooklyn or window boxes on cafes in Manhattan.

Matteson found, though, that 40% of the flowers they are visiting are the kind you buy at a big hardware store like Home Depot. They are showy, pest-resistant, and often sterile. That means that while the urban pollinators are there, ready to spread the floral love around the five boroughs, there are no plants taking them up on the offer.

He also mentioned that many of the cities rarest insects live in the often scrubby and exotic “meadows” that dot the city—some of which may be targeted for removal under the city’s highly praised Million Trees campaign.

This bee isn’t from NYC but from Missouri. If any wild bee fans want to tell me what kind of bee it is, I'd be thrilled to know.

Posted by Emma Marris on August 06, 2009
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Disaster struck at the poster session tonight. I thought that the session organisers had decided to extend the reach of refreshments provided to include rose wine (a summer drink) and I gladly took a glass full of the pink stuff. To my horror I discovered it was cranberry juice. Tsk.

Luckily, to calm my nerves I had the pleasure of talking to Charlotte Mallet a PhD student from the University of Angers, France. She explained to me that she was trying to take biomass - cellulosic waste from agricultural processes - and make electronic devices.

So far she has managed to make oligomers based on furans, derived from the fructose molecules she gets from the biomass. From this she can make an organic plastic and from that a transistor. The properties of this device aren't quite good enough for industry, Mallet says, because they have low mobility, which means they can't carry electrons very well. But she is working hard to improve this and hopes to have a news device by September.

I'm not sure how seriously this proposition will be taken in attempts to save the world from burning fossil fuels, but perhaps every little helps.

Posted by Katharine Sanderson on August 05, 2009
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On Friday, before the meeting properly started, I went along on a field trip to Los Alamos, New Mexico. If the name rings a bell, it is probably because the town was once a secret government enclave, r&d hub of the Manhattan project, and so the intellectual home of the atomic bomb.
There is still an active government lab there today, home of, among other things, this week’s world’s fastest computer.

But Los Alamos is also famous in New Mexico for being partially destroyed by the 2000 Cerro Grande fire. The blaze was massive--190 km²--and it torched 400 houses and bits of the lab. It was also started on purpose, as a “controlled burn”.

Before 1880, the arid forests of New Mexico burnt regularly, in fires started by lightning and local peoples. These were thought to be mostly low-intensity fires which stayed on the ground, burning out smaller plants but leaving trees unscathed (see image of such a low-intensity fire).

The controlled burn was part of an effort to mimic this regime, but a history of fire suppression left many areas thick with potential fuel, and a severe drought left that fuel as dry as bone. So a fire started to clear out low fuel and help reduce the threat of big fires turned out to start a big fire itself.

As we drove through the area that burnt nine years ago, we saw many dead ponderosa pines, black and white, covering the hillsides in the Jemez mountains. Underneath grew grasses that had been seeded via small planes to help fight erosion. The fire sterilized a good thick layer of soil, which then promptly washed downhill in the next big rain, choking water drainages. Our tour guide, Randy Balice, Fire Hazard Assessment Specialist for Los Alamos looked over the scene gloomily.

But Belice had good news to share as well. This year, a lightning-started fire “burnt just like fires should burn, if you like those pre-1880 type fires.” While parks department and other officials kept a careful eye on it, it rippled through the undergrowth, clearing out dry fuel, and then got rained out.

“That fire was a renewal,” said Belice.

Posted by Emma Marris on August 05, 2009
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Looking about me with ecologist’s eyes, I begin to see the convention center and the surrounding infrastructure as a thriving ecosystem. In the morning, ecologists disperse to the convention center site in pulses via shuttle busses and more gradually by walking. This movement could be viewed as diurnal migration, a common feature of many animals.

Although one could follow a food chain in the traditional sense, it would be fairly dull. In essence, the Starbucks at the Hyatt concentrates various energy-rich products of photosynthesis, and the ecologists graze thereupon, until there are no more strawberry-banana smoothies available.

Perhaps more interesting is following the path of information. As the first presentation of the day unfolds, information flows from one ecologist to many. This information, if deemed interesting, is further spread throughout the day from audience members to their friends and colleagues, with a peak of information transmission occurring after 5 PM at local bars. Simultaneously, posters sessions transmit information over an hour or two via one-to-one interactions.

This information flow reverses the familiar “pyramid of numbers” in which one top predator—an orca whale, say—eats several smaller animals, who in turn eat many more even smaller organisms, until one works down to something tiny, photosynthetic and numerous like plankton. Here, the producers of information—the plankton—are presenters, and the many more numerous receivers of the information are the attendees who fly away from Albuquerque stuffed with new ecological knowledge.

And I suppose that is the fundamental difference between food energy and information. Food energy is finite, and in fact never makes it from prey to predator without lots of it being lost. Information can be reproduced endlessly.

It would be very interesting to me if it were somehow possible to track which research leaves the conference in the largest number of brains. Would sessions with largest audience always win out? Or would there be sleeper research, communicated to a paltry crowd but then enthusiastically retold by that audience to friends over dinner and strangers on the shuttle bus? And which brain would leave with the largest amount of new research lodged therein? Would it be a devoted session attendee, who sits in dim ballrooms from 8 AM to 10 PM every day? Or would it be the popular and chatty friend of many, who haunts the halls and beer halls, having conversations with other attendees all day? Who is the ESA orca whale?

Posted by Emma Marris on August 05, 2009
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When will society let go of a land that's lost? Not until long after it should, as I was reminded by a talk by Robert Twilley of Louisiana State University.

Twilley is an expert on the vast delta of the Mississippi River that feeds Louisiana coastal wetlands with both freshwater and rich sediment. Or rather, it used to -- until decades of water diversions choked off much of the water supply. Hurricanes such as Katrina and Rita in 2005 have also wiped out hundreds of square kilometres of land. Sea level rise, and land subsidence, conspire further to threaten to drown much of the coast.

A Nature Geoscience paper published in June argues that relative sea level rise will wipe out 10,000 to 13,500 square kilometres of coastal land by the year 2100 -- and there's apparently nothing we can do about it. The Mississippi River has simply been too dammed up and altered for it to ever provide enough sediment back to the delta to rebuild coast or even counter much of the decline. In other words, Twilley told the ESA meeting, we're past the point of no return. "We've decreased the capacity to adapt," he said. "We are now outside of the adaptation envelope because of the way we've mismanaged the river."

What's left to do? One idea is to look at how much coast could be restored if we tried as hard as we could. The Wax Lake Delta (pictured) started forming from sediments around about 1973, as a result of water diversions along Louisiana's Atchafalaya River. Studying how it builds up over time provides one test system to understand the land-building capacity of the coast, Twilley says. Moving a model of how Wax Lake is built to the Mississippi, he says, suggests that 1,000 square kilometres of wetlands could be created in the next century if sea level rise and land subsidence together amount to 7 millimeters per year -- a sort of middle-of-the-road estimate.

Society has put its mind to greater tasks, Twilley argues. Whether battling a vanishing coastline is worth it is a difficult question, however. Restoring Louisiana could be a great environmental triumph -- or a great societal folly. What do you think?

Image: National Center for Earth-surface Dynamics

Posted by Alex Witze on August 05, 2009
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The exhibit hall here at the ecological meeting seems oddly empty -- or maybe that's just because I hit it at a down time when free beer wasn't being offered. I did spend some time flipping through the fancy new materials at the unstaffed booth of the Encyclopedia of Life (EOL), the ambitious effort to catalogue the planet's species onto a one-page-per-species website.

The site is still in its early days -- a little browsing uncovers skimpy entries for many species, but such is the nature ofa work in progress. But I was intrigued by one new social-networking push to get more content. If you've got a Flickr account, you can add your pictures of various animals and plants to the EOL. Just join the EOL group, upload your pix, and change the license. You then tag the photo with the common and/or genus and species name of the organism in the picture. Et voila!

One thing not clear to me: what happens if you misidentify your critter?

Image: Canis lupus familiaris, common name Angie

Posted by Alex Witze on August 05, 2009
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In the largest experiment of its kind to date, ecologists have found that the wetter the Arctic tundra becomes, the more carbon dioxide it gives off. See the full story on Nature News here.

Posted by Alex Witze on August 05, 2009
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If you can't tell the difference between an embryo and a giant bacterium, then things have got to be pretty bad. But Frank Corsetti of the University of Southern California, Los Angeles, gave the audience a persuasive argument today that at least some spherical bodies found in the fossil record, thought to be eggs or embryos, are indeed probably giant sulphur bacteria instead. Certainly I can't tell the difference from the pictures, and nor, apparently, can the experts.

These particular fossils are not from the Burgess Shale, nor even from the Cambrian, but from the Neoproterozoic Doushantuo Formation in China, which holds fossils from some 600 million years ago. Not only do some spherical blobs in this record look a lot like a modern sulphur bacterium called Thiomargarita, but this little bug is also known to spit out phosphate, which is required for the particular kind of fossilization found in this formation. Coincidence? Corsetti thinks not.

This kind of confusion about what the heck a fossil represents – plant or animal, whole animal or part of one, egg or bacterium – is rampant throughout paleontology. Peoples' notions of what they expect to find can deeply influence their description of morphology and identification of fossils, notes famous Yale paleontologist Derek Briggs over lunch. I comment that what you need is a kind of blind experiment, whereby naïve graduate students who know nothing about the subject are asked to describe the morphology of some new fossil. “That is, actually, what happens,” is the witty rejoinder (not, it has to be said, with noble intentions, but by happy accident as a result of students not doing their homework). Seriously, Briggs notes, it would be interesting to see what would happen if scientists could approach fossils without any baggage. That's a difficult experiment to conduct. Instead of facing such challenges, we go for dessert.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 05, 2009
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Back in my youth, when deciding what subjects to study at school and university I wanted to make sure that I would come out versed in something that would be of use to the wider world, perhaps even do some good. I chose chemistry. It's clear from conferences like this that many chemists are interested in the subject for similar reasons.

Climate change is a big topic that chemists are tackling. This morning's session on carbon capture and storage being a good example.

This is a technology intended to clean up coal-powered power stations by scrubbing out carbon dioxide from flue gas, and compressing it to be stored elsewhere - anywhere but into the atmosphere.

There are a number of problems that chemists are looking at. Today kicked off with a talk by Gary Rochelle from the University of Texas at Austin. He took us through the major considerations that are needed for the solvent that is used to collect the carbon dioxide from the gas. The standard at the moment is something called MEA, monoethanolamine. Rochelle's fundamental physical chemistry calculations on this and other candidate solvents showed that there isn't a simple one-size-fits-all solvent. The considerations are: capacity of the solvent to hold carbon dioxide; how much the solvent degrades when heated; how fast the reaction is; how much heat it requires.

Some of these properties are better in different solvent, he says, which are again different in different plants. Another good candidate solvent looks to be piperazine.

Then we heard from Trevor Drage from Nottingham University, UK, about using solids not liquid solvents to strip out the carbon dioxide. His systems are a long way from being scaleable but show promise. On paper, he said, solid sorbets could reduce energy loading in the systems by 30 - 50%. These systems are amine polymers loaded onto porous silica-based materials, or basic nitrogen in an activated carbon matrix.

One area that is often overlooked, says Drage is the regeneration of these sorbents and how the carbon dioxide is removed so they can be reused.

Matthew Hunt is from Doosan Babcock, a Scottish-based company
spending a lot of effort in scaling up CCS technology, with demonstration plants in Canada. This is just a 4 tonne plant so far, which is no real use for a power plant which will need to porcess 850 tonnes of carbon dioxide a day, he said. But according to Hunt, the company is on track to full-scale post-combustion carbon dioxide removal by 2014.

Of course, the impetus for these small demonstration scale plants needs to come from government, and the feeling in certain quarters of this meeting at least, was that not enough push, and not enough decisiveness is being shown to make the technology viable.

My hope is that in 2014 we are not still at the stage where academics working in small groups are showing results of small scale CCS projects and saying that scale up is needed urgently.

Image: representation of MEA

Posted by Katharine Sanderson on August 05, 2009
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If you happen to swing by the Nature stand at the IUPAC congress exhibition, you'll have a rare treat. In the booth opposite is the stand for the next IUPAC congress, which will be in Puerto Rico in two year's time. 2011 is also going to be the International Year of Chemistry.

The stand there has on a loop a video of Puerto Rico's most famous (?) export Ricky Martin, as well as Marc Anthony (J. Lo's husband). This really is a rare treat in a chemistry conference, let me tell you.

Another treat is bumping into the congress chairman over a glass of wine at the poster session. Paul O'Brien from Manchester University seemed to be feeling the pressure of constant dinner engagements over the week. He said the whole experience made him nervous. From where I was standing listening to the gentle murmur of happy chemists I would say that any nerves were unfounded.

Posted by Katharine Sanderson on August 04, 2009
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While most of the conference's 150 participants are paleontologists, geologists or biologists, a handful are interested hobbyists, at least one of whom has an entire basement museum of fossils he has collected over the years. Keynyn Brysse's talk was fantastic for the more general audience - including myself.

Brysse is not a paleontologist, but a historian of science (she did her BSc in paleontology, and was headed in that direction, but found she couldn't abide the field work thanks to extreme and persistent sun stroke). She spelled out clearly the different ways in which scientists have been inclined to label the Burgess Shale creatures over the years. From about 1890 to the 1960s is what could be called 'Phase I', or, as Stephen J. Gould termed it in his seminal book Wonderful Life, the 'Shoehorn Phase'. During this time, the creatures seen in the shale were lumped into whatever phylum they were most similar to. Though that may sound sensible, it put many creatures into categories where they clearly did not perfectly fit. In 'Phase II', from about 1970 to 1985, such oddball creatures were instead granted their entirely own phyla. Gould called this the 'Weird Wonders' phase, and it resulted in a proliferation of more than 20 new categories of life – something, perhaps, of an over-enthusiastic response. Today, Brysse points out, we are in Phase III, or what Gould disparagingly called the 'Straightening Rod' phase (as it doesn't fit with his ideas). In this period, life forms do not necessarily have to fit neatly within a given phylum – they can instead be a 'stem' group, branching off from some more familiar 'crown' group. This falls into the now-popular form of biological classification called cladistics.

While that may all sound like semantics, Brysse argues that it has a fundamental impact on how scientists think. “The way you classify Burgess Shale animals determines your view of evolution,” she says. An explosion of new phyla, and later a mass extinction of phyla, sounds like a much more major event than an explosion of new species and the dying off of some of those species. They may describe the same events – the same beasts may be born, live and die. But one sounds more extreme than the other, and has implications for whether we think of evolution as a slow or dramatic phenomenon, gradual or step-wise. “Gould has no evidence of a mass extinction; it's just required by his theory,” she points out. Brysse has just completed her PhD on this topic with the University of Toronto (she jokes that Derek Briggs, one of the critical players in phase III and also at this conference, would often call her the girl who was doing her PhD on his PhD), and intends to turn it into a book. “It would be about what happened after Wonderful Life”, she says. What will it be called? “I don't know. It's a shame 'Wonderful Strife' has already been taken,” she laments.

Aside from the book, there aren't many fossils in Brysse's future – for her post-doc at Princeton, she's currently studying the history of scientific understanding of the ozone layer.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 04, 2009
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Yesterday it was 30 degrees and sunny, leading to violent thunder storms, torrential rain, and today's wet drizzle. This demonstration of the changeable weather in Canada's Rockies gives me a new appreciation for the early explorers of these mountains. In some ways they had it easier than today's field geologists and paleontologists, in that they had pack horses to carry their gear (several participants at today's conference have lamented not having their own pack horses). But clearly it was not easy, negotiating up scree slopes of shale, through dense forest, in at times horrendous conditions.

When Charles Doolittle Walcott arrived on the scene in 1909 (the event which this conference is commemorating) he had his family with him – including his wife, in full skirt, and some of his children. How they managed I'll never know.

Desmond Collins opened today's talks with an historical account of Walcott's adventures – a version of which will appear, with further details and a more modern take on the shale's significance – in an essay in the 20 August edition of Nature (closer to the actual date of Walcott's discovery of Burgess Shale fossils, which was 31 August 1909).

But though history looms large at this conference, which is held close to Walcott's Burgess Shale discovery, the science being presented here is on a broader topic: the Cambrian explosion – the eruption of a vast number of new forms of life, including most animal groups alive today, starting some 530 million years ago.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 04, 2009
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100 years ago this month, the fantastically-named geologist Charles Doolittle Walcott wandered up into the Canadian Rockies and stumbled on one of the world's most amazing fossil beds - the Burgess Shale. In those rocks, Walcott and those following him found a stunning collection of preserved soft-bodied animals from 505 million years ago, from worms to jellyfish to things unknown on modern Earth. For decades, it stood as essentially the only showcase of animals from the Cambrian - a time when life exploded into many different (and often odd) lifeforms.

I'm in Banff, Canada, this week for the commemorative conference of this event (from 4-7 August), blogging talks on everything from water column-chemistry to modern fossil finds. Simon Conway Morris will be there, as well as other big names in this field. I'm keen to see what they have to say. And, to top it all off, I'll be heading out on a hike to the Burgess Shale itself (weather permitting), so will hopefully have some photos for you of that. If I'm lucky I'll stumble on something even stranger than what Walcott found... but no hammers are allowed, and I won't be bringing any fossils home with me.

Posted on behalf of Nicola Jones

Posted by Mark Peplow on August 04, 2009
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Chemists love to talk about the details of a synthetic reaction: swapping this carbon atom for that one, changing the angle between sulfur atoms by 2 degrees and so on. So during this morning's talk by Daniel Rabinovich from the University of North Carolina at Chapel Hill, I was happy to listen to him talking about tinkering with ligands to try and recreate the chemical environment that a copper atom finds itself in the small protein methanobactin thinking no more of it other than "chemists like to try and do this kind of thing".

Methanobactins are a small part of the large bacteria called methanotrophic bacteria that use methane to make their own carbon and energy. At their heart is a copper binding compound, which has fairly unusual chemical groups called thiones around it. As far as I could tell, the interest was in the synthetic challenge in recreating these unusual chemical group around the copper atom.

I mean, if chemists want to try and mimic nature's functions they tend to go after big things, like photosystem II, or a huge protein structure.

But I was wrong. It turns out that a patent was granted (to other scientists unrelated to this work) on the small copper-based protein methanobactin because it is a potent antibacterial agent against S. aureus, although this is a delicate protein that will be hard to recreate in its natural form.

Whilst trying to recreate the chemical geometry of the copper atom in this small delicate protein, Rabinovich actually found a way to make a synthetic version of an antibacterial, and that is what he's working on now.

Rabinovich has a better chance of making large amounts of the stuff. His work was all based on known procedures - albeit some obscure ones.

Posted by Katharine Sanderson on August 04, 2009
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Powerpoint presentations at ecology conferences are usually dominated by pretty landscapes: flowering plants, cute little pikas, soaring mountain vistas. So it was a bit of a shock today to sit through pictures of corpses at the Civil War battle of Gettysburg, American warplanes spraying deadly Agent Orange on Vietnam, and refugees lining up at camps in Darfur.

The cheerful topic of the morning: warfare ecology, a newly-dubbed sub-field of ecology. Gary Machlis, an ecologist at the University of Idaho, gave an impassioned lecture about why all scientists should care about warfare and why ecologists should help figure out how to restore devastated landscapes.

The litany of environmental disasters was depressing: General Patton scarring the delicate landscape of California's Mojave desert with thousands of tanks. Bombings of chemical plants in Serbia that sent pollutants coursing downstream into non-combatant nations. Saddam Hussein draining the marshlands of Iraq to destroy the livelihoods of the Marsh Arabs there. Elephants that stampeded over the border from Uganda into the Congo, then back, as war raged back and forth.

But in his oddly infectious, impassioned-professor sort of way, Machlis seemed to get the audience - primarily younger researchers, with a smattering of military types - inspired. "Like conservation biology in the 1970s, or restoration in the ecology in the 1980s, warfare ecology reflects an interdisciplinary approach to a global challenge," he said, pacing back and forth. "The scientific community must continually evaluate its ethical responsibility toward warfare."

Ecologists might engage, he said, by figuring out how to build a refugee camp with the right resources to save lives. Or supporting swords-to-ploughshares restoration efforts like restoring the Korean demilitarized zone. Or working with remote sensing to better monitor war's impacts on civilian populations. Only then, Machlis argued, can scientists truly be responsible.

What do you think? What responsibility do scientists have to salve society's ills? And how best might they go about it?

Image: Car bomb in Iraq, DoD

Posted by Alex Witze on August 04, 2009
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The always-controversial notion that a comet or asteroid slammed into North America some 13,000 years ago got a severe tongue-lashing today from a Wisconsin researcher.

The idea, put forth two years ago, suggests that an extraterrestrial impact somewhere over the Laurentide ice sheet abruptly terminated the last ice age and lead to the extinction of the continent's great mammals, like mammoths (right), and some early peoples. A recent paper in Science proposes that physical evidence of the impact has been found in the form of nanodiamonds scattered across the continent. But both impact experts and paleoecologists have been reluctant to accept the idea.

Jacquelyn Gill, a graduate student at the University of Wisconsin in Madison, laid into what she called the "impact" (with quote marks heavy in her voice) today. Sediment cores at two locations in Indiana, and one in Ohio, are ideally located to preserve evidence of the environmental chaos such an impact would have caused. But no such traces are present, she reported at the meeting. In fact, declines in the abundance of a particular spore marker appears to take place more than 1,500 years before the purported impact would have happened, she says.

"We don't see a real trend here that would suggest a physical impact," she said.

Supporters of the impact idea have argued that no physical evidence of the impact itself -- eg a crater -- might be expected to remain. But evidence of massive environmental disturbance seems also remarkably slim, at least to researchers like Gill.

Image: Royal BC Museum, Victoria, Canada (where you can listen to a mammoth!)

Posted by Alex Witze on August 04, 2009
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While the idea of green roofs sounds lovely and eco-friendly, keeping those plants alive on your rooftop is easier said than done. That's the message given the ecology meeting today by Colleen Butler, who's been growing experimental green-roof plots at Tufts University in Boston for the past few years.

Atop the campus library she's been planting various species to see which ones do best. "People assume that if it grows in your garden, it'll grow on your roof," she says. But the high temperatures and variable rainfall can often do in even the best-meant plants. One that seems to do well is the Sedum species of low-growing flowering plants. In fact, Sedum might even be bullying out its neighbors in certain circumstances.

Butler's test plots suggest that when drought comes, Sedum might help its neighbouring plants survive. But in normal rainfall years, it seems to out-compete its neighbours and hog the green roof all to itself. The lesson, she says? Be sure you know what you're planting up there.

Image: The California Academy of Sciences' green roof, in San Francisco

Posted by Alex Witze on August 04, 2009
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On my way up to Glasgow from London I did a spot of sailing. On the trip from Fleetwood, Lancashire, to Whitehaven, Cumbria, for a long time we could see the nuclear fuel plant Sellafield. It spans a vast area of the Cumbrian coast line.

So it was with interest that I spotted a poster by PhD student Sarah Wallace from Leeds University in the UK.

She has been looking at how strontium, a waste product from Sellafield, will move in the sediment near the plant, and if it might make it into the groundwater.

The contaminant plumes from the plant tend to have a high pH, and what Wallace had found so far is that in these conditions strontium-90 likes to stick to sediment. This could actually be good news for Sellafield because the half life of strontium-90 is such that as long as it sticks to the ground it will have decayed within 300 years or so.

Strontium is potentially nasty because it's in the same chemical group as calcium, a major bone component. So if strontium gets into the water and into the body, it can compete with calcium in the bones and cause diseases such as leukemia.

Wallace's work involved a fake contaminated bit of land - taking normal soil and untouched groundwater from the area and spiking it. In future she hopes to see what the longer term effects of strontium-90 are.

Posted by Katharine Sanderson on August 03, 2009
Categories: International Union of Pure and Applied Chemistry 2009 | Permalink | Comments (0) | TrackBacks (0)

Who'd have thunk it - a chemistry conference full of space news. It's not that weird really, when you consider that the search for life = search for molecules.

Lars Kristensen from Leiden University in the Netherlands today showed us his maps of methanol in space. He is making these maps so he can see how methanol is distributed in the material that young stars are made from. Methanol is used as a tracer for early star formation and forms on the surface of interstellar ice-covered dust grains. He'll also soon be able to compare his methanol maps with results of water abundance from Herschel, which set off recently to check out the most distant objects in the universe.

Methanol forms as ice on dust grains. According to Kristensen, the major way that the methanol escapes from the surface of these grains is not by heating thermally, but by a non-thermal mechanism, be that activation by UV light, or other methods.

The abundance of methanol in the areas that Kristensen looked at, using the Harp B instrument on the James Clerk Maxwell Telescope in Hawaii, was constant throughout those areas, he says.

Check below the fold for one of his maps.

Posted by Katharine Sanderson on August 03, 2009
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Hello from Glasgow, Scotland. Home to the deep fried mars bar, Charles Rennie Mackintosh, Gordon Brown MP, and now for one week only the IUPAC congress.

I'm here to delve into the finer points of chemistry and to see what is getting chemists salivating this year.

The first session I went to was about artificial photosynthesis. The process that plants carry out with ease - turning sunlight into stored energy - is causing a major headache for scientists trying to mimic the process.

Rather than try to rebuild the molecules used by nature for photosynthesis, chemists are looking at systems that they can build and understand better, and use them to do the same jobs that plants do with their complex molecular machinery.

In these systems, sunlight is used to power the separation of charge - from a neutral molecule to one with a positive and negative component. But the big problem is keeping those charged states apart from one another for any length of time. If they recombine, the charge separation, which could lead to electric current, is lost.

Today I got to see how making the molecules really long with the charged ends separate from each other in space can help. Ken Ghiggino from the University of Melbourne, Australia, uses a set of four porphyrins, which are big ring-shaped molecules. One end has a zinc atom sitting inside the ring and the other a gold atom. These two metals can shunt a charge from one end to the other. The trouble is that this kind of system is far too complicated to ever be manufactured on a large scale.

Another suggestion is simple dyad systems with one charge donating and one charge accepting part. But as Andy Benniston from Newcastle University showed us, to separate the charge with these systems is also not as easy as hoped. He suggested that when previous chemists have claimed to have a long lived charge separated state what they had actually done was form a different quantum state called a triplet state. This is something else entirely.

All this is yet more evidence that nature is unfathomably clever in its use of molecular processes to gain energy, and that humans are way behind in our understanding. But thanks to chemists who refuse to get depressed by this notion, one day we may just be able to take sunlight and produce energy that we can store and use at will, without destroying our world.

Posted by Katharine Sanderson on August 03, 2009
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Nature reporters Alexandra Witze and Emma Marris will be in Albuquerque, New Mexico, from Aug. 3-7, 2009, to cover the annual meeting of the Ecological Society of America. They'll be posting updates here on In the Field, Nature's news team blog from conferences and events.

Posted by Alex Witze on August 03, 2009
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