Burying Carbon to Save the Planet

Recent research has highlighted the possibility of burying, or sequestering carbon dioxide in deep, disused coal mines. Not only might this allow us to reduce atmospheric carbon dioxide levels but the process would displace usable methane (natural gas) from the coal and extend the length of time we will have this resource available to us as a fuel and chemical feedstock.

However, I felt that the while the concept sounds viable initially, there are several loopholes in the whole carbon burial argument, especially when releasing methane is also brought into the equation. I asked team leader Thomas Brown of the US Department of Energy’s National Energy Technology Laboratory about my concerns.

First the whole process will require its own energy supply, which will in turn release CO2, as well as being expensive to undertake in practice. Moreover, most of the methane retrieved in this way will end up being burned as fossil fuel and adding still further to the global carbon footprint.

“You are correct,” Brown told me, “Cost projections for CO2 sequestration indicate it will be expensive and a great deal of research is currently underway to bring these costs down.” He points out the methane release process is quite encouraging because for every 2-4 units, or moles, of CO2 trapped, just one unit of methane is released.

“This suggests that [the process] has the potential to be more cost effective than the [alternative approach] of sequestration in deep saline aquifers,” Brown adds.

The coal bed methane will certainly be useful nevertheless and Brown points out that CO2 released by burning it will in turn have CO2 capture systems in place. “It is an additional energy source that can be utilized instead of venting it from coal seams to the atmosphere,” he says, “it also provides some offset for the cost of sequestering CO2 – methane is much more detrimental to the environment as a greenhouse gas than CO2.”

He adds that sequestration in coal seams my not be a viable option owing to low permeability values and swelling of the coal itself, which he discusses in his research paper. “More R&D is required,” he told me.

Bad Apples, Colds and Echinacea

Echinacea - Photo by Bruce MarlinRecent media reports seem to have strengthened the case for using echinacea to ward off or treat the common cold. But, are they based on valid new evidence?

The LATimes [item no longer available by link] for instance, says researchers carried out an “analysis of 1,600 patients pooled from 14 previously published studies found that echinacea reduced the chances of catching a cold by 58% and shaved 1.4 days off the duration of a cold.”

The researchers who carried out this analysis point out that none of the previous trials was large enough to be valid, but somehow they attempt to give them new credence by mixing together the data from lots more dubious studies. One bad apple can almost certainly spoil the barrel, but throw together a couple of dozen bad apples and that barrel is going to be humming before the day is out, surely?

Meta analyses of solid double-blind, placebo-controlled clinical trials certainly can shed new light on old findings, but what they do not do is create new data points, they are simply a re-analysis of old results pooled.

Craig Coleman of the University of Connecticut whose team carried out the meta analysis, point out that none of the trials analysed individually were big enough to reveal the benefits of Echinacea. Somehow his new analysis of old data demonstrates an almost two-thirds reduction in the risk of catching a cold compared to a person not using Echinacea. But, how could that be, if those earlier trials succumbed to serious wishful thinking and the placebo effect, then the whole argument is in doubt.

Wallace Sampson, an emeritus adjunct professor of medicine at Stanford University School of Medicine is quoted as saying that because the methodologies of some of the earlier studies are so suspect, this casts doubts on the pooled result. Exactly.

The team also reports that of 800 products containing Echinacea they investigated, there are large variations in the quality, which part of the plant was used – flower, stem or root – and how much so-called active ingredient is present. In addition, they suggest that more work is needed to check the safety of the countless formulations available. Their warning echoes other studies that have pointed to toxicity problems associated with long-term use of Echinacea products, although admittedly some of those studies might also be considered invalid because of poor methodology.

So, should we run to our local herbalist on the off-chance that we might catch a cold or if you’ve already caught one quickly down a dose of Echinacea to “shave off” 1.4 days or runny noses and sneezing? I don’t think so, not unless you don’t mind putting up with a whole lot of bad apples.

DNA Network

DNA Network logoSciencebase was recently invited to join the excellent DNA Network and as such our genetics news feed is now being pulled by the network’s feed system. If I had been a little slower off the mark, I could have been site number twenty in the list, but when I joined I think I jumped in at #18. There are, at the time of writing, nineteen members, no DNAying it.

So, here is a quick random selection of fellow network members. The links will take you to the individual RSS feed for each site whereby you can subscribe (for free) and get some great and timely information on DNA and the latest happenings and business news in genetics and DNA research.

VentureBeat Life Sciences

Discovering Biology in a Digital World

DNA Direct Talk

Epidemix

The Daily Transcript

henry: the human evolution news relay (genetics)

Mary Meets Dolly

Genetics News

Microarray and Bioinformatics

Gene Sherpas: Personalized Medicine and You

The Personal Genome

All excellent newsfeeds, all focused on one thing, DNA. You can find links to the others, including Eye on DNA, the owner of which led me to the DNA Network in the first place, via DNA Network. I’ll do another round-up of the remaining members later.

YASSE – Yet Another Science Search Engine

A new global science gateway – I’m sure they’d prefer me to display that phrase in blinking bright green text on a red background, but I won’t – has been launched by the US Department of Energy (DOE) and the British Library. The aim is in “accelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases.” Yeah, okay. But, isn’t this just yet another science search engine portal? Apparently, subsequent versions of WorldWideScience.org will offer access to additional sources as well as enhanced features.

That’s what they all say. I’m sure it’s a very worthy search tool and would like to hear from Chemspy visitors who have tried it out and found its results useful/useless (del. as applic.)

Incidentally, the webmaster risks a duplicate content penalty because the two canonical forms of the web address (WorldWideScience.org and www.WorldWideScience.org) both return “200 OK”. One of them should have a 301 redirect applied.

Ptaquiloside Redux

PtaquilosideAlmost ten years ago, I wrote a feature article on the cancer risk associated with the bracken toxins known as ptaquiloside for ChemWeb. The article was updated and mirrored on Paul May’s Molecule of the Month website at Bristol University, and quite bizarrely still draws a few readers to the Sciencebase site via my byline on the article. I suppose the reason it is still popular is that it makes it to page on in Google should you search for the word bracken.

Anyway, this article occasionally triggers some rather interesting correspondence with readers. Most recently, John Nayler emailed me to ask whether or not toxic chemicals from bracken might leach into groundwater beneath bracken-infested areas. I had to admit I did not know, but a paper published recently in the journal Chemosphere (2007, 67, 202-209) discusses the microbial degradation and impact of ptaquiloside on soil microbes themselves, which sheds some light on the potential impact of this carcinogenic toxin.

Another of Nayler’s concerns regards whether or not bracken is not simply an unpleasant weed with a cancer risk associated with eating the “fiddle heads” (a delicacy in Japan), but whether or not landowners, whose land is infested with bracken might be liable for public health lawsuits should those with a right to roam on their land be exposed to bracken spores. The risk may be small but that never stopped an ambulance-chasing lawyer in the past.

Cancer Research UK has a FAQ on the cancer potential of bracken. Despite isolated ptaquiloside coming up positive in carcinogenicity tests a decade ago, the latest research, according to Cancer UK is that there is no risk of cancer associated with eating bracken fiddlehead greens. So, what about those spores. Studies have shown bracken spores to cause cancer in mice, but those mice were given a lot of spores and to extrapolate to human cancer risk is (death)wishful thinking. A walk among the bracken is more likely to trigger a sneezing fit if the spores are high than anything else, and as CRUK points out, diet and smoking are far greater risk factors than bracken for cancer.

I Know What I Did Last Summer

This is what we were posting about a year ago this month, some of these are just plain silly, others are quite informative, but most just seem to lead to one thing on the mind:

Seat of Female Libido Revealed – Researchers found the organ in the brain responsible for female sexual response, I have to admit I hadn’t realized it had gone missing.

Keeping the lead in your pipesOrgans were being fiddled with in churches across Europe

Sperm and eggs – a sexy paradox…in fruit flies.

Erotic brain – Medical scientists discovered that women’s brains light up when they are exposed to erotic imagery, you don’t say?

Coca Cola Blonde – Yuck! (No Photoshop involved, by the way)

Beer vs wine – Beer is better, more B (vitamins)

I’m not sure if there is any kind of running theme here, (sex, booze…?), maybe it was just the time of year, the silly season was upon us, or you could probably even blame global warming.

Search on Steroids

Researchers at Xerox Corporation have developed new text mining software that goes beyond conventional keyword search, enabling it, in effect, to hone in on the one or two golden nuggets among the trash in the garbage pit. I asked the developers how applicable the system might be to science searching as it is originally aimed at administrative, legal and business type environments. Apparently, the FactSpotter software will be just as well matched to searching out elements of risk in scientific documents, for instance.

Is the Web Awake?

The web's awakeA vast underground network exists in the American North West. The network is composed of the usual hubs of major activity with numerous interconnections, a complex packet-based communication system, and peer-to-peer sharing. But, this is not the familiar kind of network of BitTorrents, search engines, and wikis. This is a living organism, perhaps the biggest living organism. A fungus known as Armillaria ostoyae. we know almost instinctively that A. ostoyae is alive. It is an ordered entity, it assimilates nutrients and excretes waste products, it grows, it reproduces. Its metabolic pathways carry packets of chemical information along its network of tendrils. It exists beneath a 9 square kilometre area east of Prairie City in a remote corner of Oregon’s Blue Mountains at about 2000 metres.

So, asks Philip Tetlow in his latest book The Web’s Awake, can we similarly define the World Wide Web as being somehow alive, and more philosophically, aware?

Seemingly not. Tetlow draws together a network of evidence but comes to no more solid a conclusion than we cannot yet know whether or not the Web is awake, aware, or simply awash with random clusters of information and interlinks. His title would imply that he had evolved an answer to one of computing’s quintessential questions, can a true Turing machine exist? If the Web were awake, then it would be as parasitic as any fungal sprawl. But, it not only feeds on us, it offers us a symbiotic relationship in which we feed on its digital gifts.

The Armillaria ostoyae network would not exist if it were not for the roots of its forest host, but we still feel it to be alive. In the same way, the Web would not exist without the information and power we feed it. Nevertheless, we do not feel that the Web is alive. Of course, we do not yet know what future structure and organisation may emerge within the Web, maybe its offspring will be autonomous, a parasite or symbiote, maybe it will feed on us just as A. ostoyae feeds on the forest above and will ultimately destroy it.

There are no straight answers to Tetlow’s questions. Maybe we should JFGI. Just Flipping Google It!

Down, down, deeper and down

TL:DR – Deep-sea explorer Alvin is finally being laid to rest, so David Bradley salvages a few thoughts on deep-sea exploration from scientists who don’t seem to mind the pressure.


Alvin - Image from NOAAHow do scientists cope under pressure? In the depths of the ocean? In a place where the only natural light is the product of bioluminescence, where high-pressure sales has an altogether different meaning?

Plumbing the ocean depths began in earnest in the 1930s with the invention of the bathysphere. Built by New York explorers William Beebe and Otis Barton it was little more than a 2-tonne steel ball dangling from cables attached to a ship. Beebe and Barton dived to almost a kilometre below the surface off the coast of Bermuda in 1934 and piped details of their findings through a telephone to the crew up top. They reported sightings of fish and invertebrates the likes of which science had never seen before and have inspired a generation of scientists to explore deeper.

Paul Tyler of Southampton University’s Oceanography Centre is a marine biologist who regularly dives and has tried out all the deep-sea submersibles except the Japanese Shinkai craft. ‘It’s like sitting in a refrigerated VW Beetle without the seats,’ he told us, ‘there are normally three of you in a 2 metre sphere with three portals to look out of, as you get deeper you put more and more clothes on, but it’s fantastic, priceless’. But, a 4000m dive can take three hours to reach the seabed, ‘so you sleep, read, or chat, but once you reach the bottom, time flies past because you don’t want to waste a second, you’re so busy, you’re either collecting, photographing or setting up experiments,’ Tyler adds.

Even graduate students can go deep. Coral biologist Scott France of the College of Charleston made an early start in diving, ‘My PhD studies included research on dispersal of crustaceans between hydrothermal vents,’ he explains, ‘Within eight months of arriving at the Scripps Institution of Oceanography, I made a dive in Alvin to 3800 meters.’ Alvin is a submersible operating out of Woods Hole Oceanographic Institution. France realised that no amount of reading would have prepared him for the experience, ‘I was ecstatic,’ he exclaims, ‘I was an explorer venturing to a place on Earth that virtually no other human had seen before, witness to an environment completely alien to most people.’

For some the experience can be quite out of this world. ‘It takes a few hours to descend to the bottom and is very eerie,’ says Emma Jones a fish behaviourist at the FRS Marine Laboratory in Aberdeen, Scotland, ‘the sub tends to creak as it sinks which can be a bit disconcerting!’ She revisited a dead whale that had been ‘planted’ on the sea floor 18 months previously. ‘The skeleton was a very spooky sight,’ she says, ‘we were collecting bone samples to see what had colonized them, sediment samples, sucking up amphipods and filming.’
Submersibles are certainly not the most luxurious way to travel, says geologist Paul Aharon of The University of Alabama, Tuscaloosa who has just returned from the Atlantic diving in Alvin. ‘It is an uncomfortable ride inside the submersible with three people crammed in among the oxygen tanks, carbon dioxide scrubbers and electronic consoles,’ he explains. ‘Last dive I almost got hypothermia because I forgot to take long pants with me,’ he revealed to us, ‘I worked at 3 Celsius with no possibility of moving my legs for over 8 hours!’

He and Tyler also point out that there are some rather personal problems that face anyone on a submersible. ‘There is always the question of vital body functions such as urinating…’ Aharon muses, ‘In addition, the air we breathe has less oxygen and more CO2 than the atmosphere to prevent sudden ignitions. The results are headaches, memory lapses and slowdowns in brain functions.’

Alvin is a titanium-hulled submersible and can remain submerged for 10 hours under normal conditions, although its life support system will allow the sub and its occupants to remain underwater for 72 hours. It makes about 150 dives every year. There are several other equally adept submersibles including – Clelia and the Johnson Sea-Links I and II, which are run by Harbor Branch Oceanographic Institution. And, the Japanese craft Shinkai 6500, which weighs almost 26 tonnes and goes down, obviously, to a depth of 6500m. Shinkai, like the others, carries the requisite TV cameras, temperature and depth sensors, stills cameras and various navigational devices. But, riding Shinkai can be a lonely life since there is room for just one diver.

Discomfort aside, it is the wonder that keeps the scientists going back for more. ‘You don’t realise what a unique experience entering ‘inner space’ is,’ explains Tyler. ‘I went to Axial Seamount on the Juan de Fuca Ridge, which is actually the shallowest of my study sites, at about 1550 m,’ says Maia Tsurumi who works with Verena Tunnicliffe on hot vent ecology at the University of Victoria, ‘Getting to go down to the bottom in a sub was amazing – definitely one of the highlights of my grad career.’ The sites can be almost beyond belief, it seems, ‘The most fantastic biological site I have seen in my life is a tubeworm pillar,’ adds Tyler, ‘it is just unbelievable, 14 high and five meters in diameter, it’s just enormous covered in these tubeworms.’

In October, visual ecologist Tamara Frank of HBOI was about to set sail, when October’s Hurricane Iris and Tropical Storm Jerry scuppered her plans. She made her first dive in 1992, and is now studying the effects of light on the daytime depth distributions of organisms with colleague Edie Widder. Their dives need go no deeper than 1000m at the moment, but she is hoping to collect benthic animals too, which would mean much deeper dives. ‘Most dives in the submersible are fascinating, seeing these spectacular organisms in their natural habitat is just the most amazing experience in the world.’ she told us, ‘Once you pass through the air-water interface, you’re surrounded by seawater, and don’t even realize that you’re looking through a Plexiglas sphere because the refractive index of Plexiglas is the same as that of seawater…there’s none of this “looking out of little tiny portals” if you’re lucky enough to be in the front of the JSL; and the seats are very comfortable!’

‘There are too many rewards to count,’ Aharon also enthuses. ‘First, we descend for hours without lights to conserve electricity and you’ll see all kinds of eerie bioluminescence with psychedelic colours. It is a wonderful experience!’ he exclaims. ‘I wish I had more time to just sit and observe,’ laments Frank, ‘but on most of our dives in the Gulf of Maine, we immediately have to start transects, which are exhausting, because you’re straining to identify organisms that pass through the transect area as the sub goes through the water.’ She confesses that science sometimes obstructs the view! ‘Both Edie and I have seen beautiful gelatinous organisms during these transects, but couldn’t stop and film or observe them because data collection always has priority, and that’s sometimes frustrating.’ Takeshi Matsumoto of the Japan Marine Science and Technology Center (JAMSTEC) which operates the Shinkai submersible agrees that it is a busy game, ‘The most serious problem during a dive is the restriction of diving survey time,’ he explains, ‘observers have to accomplish everything within a few hours during the dive. Planning and preparation are essential.’ Jones agrees, ‘Because research vessels cost so much to run, and weather can change so quickly, you do feel you have to make use of every minute available to do your science.’

So, what is the motivation for cramming oneself into a tiny capsule and diving to the bottom of the sea? ‘I was always fascinated by the abyss and grabbed the opportunity when it came my way,’ Aharon told us, ‘I guess my initial attraction started in childhood when I read about Captain Nemo.’ Tsurumi agrees that the deep can affect you profoundly, ‘There is nothing so romantic and exciting as going somewhere seemingly totally inaccessible,’ she says. Aharon is totally hooked, ‘It’s an addiction, once you start going down (and hopefully, coming up again),’ he says.

It is not always so dreamy though. One of the more frustrating aspects of deep-sea science is not diving as Southampton University oceanographer Mark Varney explains, ‘I went on an expedition to the central Indian Ocean in June, and found the entire trip something of an ordeal. The weather was bad for most of the period, and the science wasn’t terribly successful.’

Indeed, extremely rough conditions are perhaps the worst aspect of doing research at sea. ‘On our Indian Ocean trip we were blown out on two occasions (to Indonesia and then towards Australia – both took several days to get back on to station,’ adds Varney. Tyler points out that, ‘Bad weather and very occasionally malfunctions are the only things that stop us diving.’ But, Frank notes, the hazards of diving are overrated, ‘I find it much more terrifying driving in Boston than diving in a submersible,’ she asserts, ‘At least in a submersible, you’re being ‘driven’ by a professional, there’s no ‘traffic’ to worry about, and you know the vehicle has been through an enormous number of safety checks.’

France too is not perturbed by the potential dangers, ‘My desire to see the deep sea and its organisms first hand represses rational consideration of the dangers involved,’ he says, ‘Of course there are dangers involved in travelling to such great depths. One can’t simply call for a tow-truck if the sub is stuck.’

‘The longest cruise I have been on was slightly over five weeks,’ says France, ‘and this was as a graduate student. At that time everything was an adventure and so the time passed quickly. Now that I am married, being away for that length of time would be an emotional hardship.’ However, at the end of a trip, the coming home can be a problem for some, ‘I often get “post cruise blues” after a cruise,’ admits Frank, ‘as do many of my colleagues, because you go from this exciting, noisy, “happening” environment, where there’s always someone to talk to, to a very quiet home.’

But, one question remains…how do they cope with those ‘personal’ problems during a dive? Jones had her own method, ‘I found out I was diving in Alvin at 4pm the day before so I deliberately stopped drinking any fluids from then on as I didn’t want to be squirming and crossing my legs for 10 hours,’ she says. Aharon, however, explains the standard approach, ‘We take capped bottles fitted specially for men and women. Not a pretty site, but we are all human.’

This article originally appeared in HMSBeagle, which has since sunk without trace…ironically enough, although it was fun while it was still afloat and is sadly missed by its trusty crew of writers and even those who had to swab the decks.

Also in Issue 75
The growing problem of biopiracy
Research assistants under contractual obligation

Previously, in Elemental Discoveries:
Accidents will happen
Predicting climate change
Green silicon production
P2P for scientists
Women in science
Academic poaching of researchers
Permanent implantable contact lenses
Profile of ETH Zurich
Paradoxical ozone

White Biotech

Is it just me or is the title of the latest paper published on Chemistry Central rather unfortunately politically incorrect when taken out of context? I suspect it is just me, as Google throws up almost half a million entries for “white biotechnology” and the phrase itself was apparently coined in 2003 or thereabouts.

Anyway, the paper’s full title is “Relevance of Chemistry to White Biotechnology” and it is authored by Munishwar Gupta and Smita Raghava of the Indian Institute of Technology in Delhi. They discuss the emergence of novel biotechnological approaches to the bulk production of fine chemicals, biofuels, and agricultural products. It is, as the authors say, “a truly multidisciplinary area” with “further progress depending critically on the role of chemists.” The authors outline the state of the art and in so doing hope to encourages chemists to take up some of the challenges thrown up by this area of chemical science.

You can read the pre-press version of the paper here (as a pdf).