Heliophage


Review: Jim Endersby in the Sunday Telegraph
October 16, 2007, 11:12 am
Filed under: Reviews received

A thoughtful (and wonderfully positive) review which, like The Economist’s, goes long on the entropy angle. Surprisingly for the Telegraph, which is meant to be all media to all people these days, it is not on line, at least not yet. (In print, though, it has a very striking sunflower picture, so I’ve prettied up this entry with something similar). Update 18/x/07: the whole review is now online (though without sunflower). Here’s how it begins:

Perhaps the greatest achievement of Victorian physics was the formulation of the laws of thermodynamics and in particular the first law, which states that energy is conserved; it can neither be created nor destroyed, only converted from one form (such as the chemical energy locked up in coal) into another (the heat that powers steam engines). The ‘dark side’ of thermodynamics, as Oliver Morton puts it in his highly original study of photosynthesis, is entropy. The conversion is never completely efficient: whenever energy is converted from one form to another, some of it decays from an organised form (in which it can do work) to a disorganised one (in which it cannot).

Here’s his conclusion:

sunflower by joolz perryPhotosynthesis is, as Morton eloquently describes it, ‘an everyday miracle, needing nothing but sunlight, air and leaves — and eyes taught to make sense of them’. This book will, quite literally, change the way you see the world as it teaches you to understand the importance of that everyday miracle that we all depend on.

In among the kind words leading to this, Endersby also expresses some doubts about the workings of the book’s first part.

Morton has opted to break the photosynthetic process down into its various components and explain how each of them was discovered, which results in a series of chapters in which the reader is constantly brough up to date with one part of the story and then sent back to an earlier period to follow the parallel but distinct story of another part of the sun-eater’s intricate machinery. Despite Morton’s immense expertise and exemplary clarity, the story is occasionally a confusing one.

However, once the history and basic principles of photosynthesis are out of the way, Eating the Sun really takes off, ranging from the search for life on other planets to the Gaia hypothesis and the historic role of plants in making this planet habitable. Morton is as compelling and eloquent in describing the evolution of landscape as he is at describing the evolution of life itself.

The idea that the book lifts off late is one that I have come across elsewhere (Andrew Brown makes it too, in the most generous way possible) and I can see the sense of the critique. I’ll have to think more about whether I could have managed the narrative more elegantly, and whether my feeling that the first part of the book needs to be as it is in order for the last part to work is really justified.

I don’t know Jim Endersby, but we turn out to have a lot in common, including the HPSLewes arms department at Cambridge (his connection more eminent than my undergraduate sojourn) and living by the South Downs (he’s a lecturer at the University of Sussex). Like Mapping Mars, his first book has been long listed for the Guardian First Book Award (A Guinea Pig’s History of Biology, Amazon.co.uk | Amazon.com) and received a recent review by Georgina Ferry. I think I should probably buy him a pint of Harveys.

Image from Joolz Perry under a creative commons licence with thanks

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My brother won the Nobel prize
October 13, 2007, 12:27 pm
Filed under: Global change

…along with a few thousand other people, and some movie guy. Although I am not uncritical of the IPCC process, I do think it is a grand and important project, and I’m proud of him and the role he played in it as an author on Chapter 5 of Working Group II in the fourth assessment report.

John in the field



Jatropha and biofuels beyond corn
October 13, 2007, 12:12 pm
Filed under: Farming, Interventions in the carbon/climate crisis

JatrophaSome things we have in Nature this week prompt me to a catch-up post on biofuels.

If you’re talking about photosynthesis as an energy source, then you’re talking about biofuels, and you have to respect both their promise and their pitfalls. They cannot be a wholesale replacement for fossil fuels. But they are already a large part of the energy economy in many poor countries, where the rural population relies on gathered firewood. Enhancing the efficiency of this biomass use (and replacing it with other renewable sources where possible) would be a worthwhile development goal simply in terms of reducing indoor air pollution. Beyond that, solid and liquid biofuels may have potential in various situations and niches. And by enriching soils, growing biofuels may also draw down some carbon from the atmosphere and tuck it away.

To make this work, though, we need to do two things. One is to find out how best to grow and use the most promising biofuel crops. Another is to stop wasting time and money and goodwill on corn-based ethanol and various low efficiency temeperate-climate-based biodiesel schemes.

We addressed both of these issues in Nature this week. My colleague Daemon Fairless reports from India on jatropha, a much touted oil crop.

Although there is reason to be enthusiastic about jatropha’s potential as a biodiesel feedstock in India and beyond, there is one rather sobering concern: despite the fact that jatropha grows abundantly in the wild, it has never really been domesticated. Its yield is not predictable; the conditions that best suit its growth are not well defined and the potential environmental impacts of large-scale cultivation are not understood at all.jatropha plantation “Without understanding the basic agronomics, a premature push to cultivate jatropha could lead to very unproductive agriculture,” says Pushpito Ghosh, who has been working on the plant for the best part of a decade, and who is now director of the Central Salt and Marine Chemicals Research Institute (CSMCRI) in Bhavnagar.

I think it’s a fine and thought provoking read (and benefits from the fact that our recent redesign has encouraged sometimes robust discussion in the new comments threads).

We also have a leader on biofuels more generally, posted here in its entirety

Kill king corn

Biofuels need new technology, new agronomy and new politics if they are not to do more harm than good.

Zea mays has become the very emblem of plenty, with rich golden cobs of corn (maize) overspilling from some of the most effectively farmed arable lands on the planet. Jatropha curcas, on the other hand, is an unprepossessing and indeed toxic plant, better suited to scrubland and hedges. Yet in the world of biofuels, ugly-duckling jatropha has the potential to be, if not a hero, then at least one of the good guys, and a harbinger of better things to come. The golden-headed siren corn, on the other hand, is inspiring a wrong-headed gold-rush — to a dead-end of development that is polluting the modest aspirations the world might have for biofuels in general.

The common complaints about biofuels — and they seem to become more common by the day — are that they are expensive and ineffective at reducing fossil-fuel consumption, that they intensify farming needlessly, that they dress up discredited farm subsidies in new green clothes, and that they push up the price of food. All these things are true to some extent of corn-based ethanol, America’s biofuel of choice, and many are also true of Europe’s favoured biodiesel plans.

As far as the greenhouse goes, figures from the International Institute for Sustainable Development’s Global Subsidies Initiative put the cost of averting carbon dioxide emissions by using corn-based ethanol at more than $500 a tonne of carbon dioxide. What’s more, the heavy use of nitrogen fertilizer in growing corn leads to significant emissions of nitrous oxide, an even more potent greenhouse gas.

Despite this, the generous tax allowance of 51 cents a gallon given to ethanol blenders in the United States has made corn peculiarly profitable (provided that tariffs continue to keep out far more efficiently produced ethanol from the sugar plantations of Brazil). In a recent article in Foreign Affairs, C. Ford Runge and Benjamin Senauer of the University of Minnesota in Minneapolis point to estimates that this artificial price-hike will drive world corn prices up by 20% by 2010. This has a knock-on effect on other staple crops — more land for corn means less for wheat, for example. Higher prices are good news for farmers, including some of those in developed countries. But they can be bad news for the very poor, who spend a disproportionate amount of their income on food. According to World Bank studies, for the poorest people in the world a 1% increase in the price of staple food leads to a 0.5% drop in caloric consumption.

This sorry state of affairs has the small benefit of providing a stark, contrasting background against which to sketch out what a successful and sustainable biofuels industry might look like. It will be based not on digestible starch from staple crops such as corn or cassava, but for the most part on indigestible cellulose, with some room for biodiesels that, because they grow on marginal land, do not compete with food production. In the medium to long term, it will not seek to produce ethanol — a poor fuel — but a range of more complex fuels delivered by carefully designed microbes.

A rosy biofuels future will enjoy the benefits of free trade, allowing the countries and peoples of the tropics to ship some of their abundant sunlight north in the form of fuel. It will also require serious amounts of agronomic research — as we report on page 652, one of the most significant problems with jatropha is that, as yet, remarkably little is known about how best to grow and improve it. One focus of such research must be in the development of plants, such as jatropha, that make do on little water, and those that require low inputs of nitrogen. This is inherently more feasible in the case of fuels, where all that needs to be taken out of the system are carbon and hydrogen, than in the case of food, where there is a need to export nitrogen in the form of protein as well. Another focus will be on systems that actively store carbon in the soil, improving it for future agricultural use and at the same time doing a little bit more to take the edge off the carbon/climate crisis.

Biofuels are unlikely ever to be more than bit-players in the great task of weaning civilization from Earth’s coal-mine and oil-well teats. But they may yet have valuable niches — including some that allow them to serve some of the world’s poor, both as fuels for their own use and as exports. Provided, that is, that someone kills king corn.

A few links for those wanting more: Biofuels : Is the cure worse than the disease? (pdf), is a much talked about recent document from the OECD, and the ins and outs of its reception are discussed on the FT’s website. The point about greenhouse emissions from heavily fertilised biofuel crops was made recently by Paul Crutzen and others in this paper (pdf) discussed by Chemistry World and Futurepundit; the conversely optimistic point about biofuel plantations not needing to export nitrogen and thus opening up low intensity options has recently been raised by Robert Anex of Iowa State in work discussed here on the Biopact site. Biomass polycultures leading to increased soil carbon is the subject of a much discussed paper by David Tilman and colleagues in Science last year. This summer the FT ran an op-ed by Jacques Diouf of the UN Food and Agriculture Organisation on trade and development issues around biofuels. And then there’s John Mathews’ thought provoking Energy Policy article Biofuels: What a Biopact between North and South could achieve (subscription required), which is I think the first place I’ve seen the term “ergoculture” contrasted with agriculture.

Images from Valerio Pillar, www.jatropha.org and ~dabbler~, formerly jowo under creative commons license with thanks



Review: The Economist
October 13, 2007, 9:56 am
Filed under: Reviews received

This one delves a little further into the ideas:

PHOTOSYNTHESIS is the basis of life on Earth. Thermodynamics is the order and disorder in the universe. Put them together and you have the makings of a book that may re-order the way you think about the world. And that is what Oliver Morton, news editor at Nature (and who once worked for this paper), has done.

Mr Morton’s thesis is that modern biology has become so focused on the movement of information, in the form of genes, that it has neglected the processes needed to move that information around: in essence, thermodynamics. People talk glibly of “using up” energy when in fact they are doing no such thing. What is actually used up is order. An energy flow drives the process, but it is disorder (or “entropy”, to use the jargon) that changes, by increasing.

A highly ordered system such as a living thing thus needs an abundant supply of negative entropy (or unentropy, or call it what you will) to maintain its internal order. That negative entropy comes from the sun and is captured by photosynthesis, which uses light to split water molecules and combines the resulting hydrogen with carbon dioxide to form sugars. The sugars are a store of negative entropy that can be used elsewhere. The waste product, conveniently for the animals of Earth, is oxygen.

The book, then, is in part a refrain in praise of photosynthesis, the Earth’s energy and order currency-exchange market. It is also an entertaining history of how the subject arrived where it is today—and an illuminating insight for the non-scientist into how the magisterial pronouncements of science are every bit as much the result of sausage-making as Bismarck’s description of the process of legislation.

Here’s the review in full

Update: No, I don’t know what the words “currency exchange market” are doing in that paragraph either. 



Review: Georgina Ferry in the Guardian
October 2, 2007, 5:01 am
Filed under: Reviews received

A full review, nicely titled “Living colour”, that sets out a lot of what’s in the book. Excerpts:

[For Oliver Morton] the joy of looking at a tree or a landscape comes from knowing, from the level of individual molecules to the level of planetary evolution, how it came to be the way it is … You might think you know all about photosynthesis from secondary school biology lessons. You know that carbon dioxide plus water plus energy from the sun equals glucose plus oxygen. But from the earliest years of the 20th century, scientists were not satisfied with this cookery-book approach, and neither is Morton. The first section of his book introduces the key figures whose experiments arrived at today’s consensus about how photosynthesis really works … Morton enlivens what can at times be a hard read by vividly describing the passions and rivalries that drove the scientists who tracked these elusive games of pass the parcel…

Astrobiologists tend to agree that whatever forms [complex] life might take, on Earth or elsewhere, it will always need oxygen. The trick, then, is to develop telescopes that can detect oxygen in the atmospheres of planets orbiting other stars. How many of these there might be, in Morton’s view, is “the biggest question that we currently have it in our hands to answer”…

In his final section Morton looks at the planet since the industrial revolution – the lifetime, perhaps, of an average tree. We cannot understand what impact our activity will have on the climate unless we take into account how plants will react to – and possibly exacerbate – alterations in the carbon, nitrogen and water cycles.

Hard-nosed science writer though he is, Morton does not shrink from the word “crisis” to describe what is going on in our atmosphere. Unlike many in the green movement, he is willing to put his faith in technology to solve the problem, but only given a massive investment of resources and political commitment. If just some of the energy that scientists have devoted to understanding photosynthesis goes into low-carbon technologies, we might just be able to do it. If we fail, it won’t be their fault.



Yet more excited geology
September 28, 2007, 6:39 am
Filed under: Warning: contains molecules

About a day after I posted on excited geology my esteemed colleague Phil Ball pointed out this paper in GRL to me about the possibility that soil bacteria share electrons with each other through networks of nanowires — an idea that would always seem extremely cool and in the circumstances seemed steeped in syncronicity too. Phil looked into the work and wrote us a fine news story for this week’s Nature. Excerpt:

Last year, Gorby and his colleagues discovered that Shewanella oneidensis bacteria can grow long filaments, just 100 nanometres (a hundred millionths of a millimetre) thick, which conduct electricity (Y. A. Gorby et al. Proc. Natl Acad. Sci. USA 103, 11358–11363; 2006). The researchers presented evidence that the microbes use these ‘nanowires’ to shunt electrons produced during metabolic reactions onto the surface of mineral grains in the soil, to be taken up by metal ions. Without an electron acceptor, the bacteria cannot function properly and die. The researchers found that several other bacterial species also produce such nanowires.

Oxygen molecules act as convenient electron dumps for bacteria that lie near the soil surface. But little air penetrates to some environments, such as deep lake sediments or waterlogged soils. Now, Gorby and his team think they have found evidence that the bacterial nanowires can link up into a network, conducting electrons to the aerated surface. The researchers filled plastic columns with wet sand infiltrated with a nutrient compound (lactate), and allowed S. oneidensis to grow in this ‘fake soil’. Only the top of the column was in contact with air.

Electrodes inserted at various heights up the columns revealed that, after about ten days, electrical charge was coursing up the column. Gorby’s team examined the sand under a microscope and found that it was threaded by a web of filaments between the bacterial cells. These are wires that provide the pathways for electron transport up to the surface, they suggest.

In contrast, when the team grew a colony of mutant cells that could spawn only very thin, frail and non-conducting filaments, the electrodes in the column remained uncharged.

Phil goes on to note some caveats about the work, notably from Derek Lovley at University of Massachusetts, Amherst, and it does seem quite possible that this sort of wiring is not a major feature of the real world. Redox shuttles in biofilms may be a much more central phenomenon. But it’s definitely thought provoking. For some context to that thought, try “Microbial ecology meets electrochemistry: electricity-driven and driving communities“, a recent review in the ISME journal by many hands, including that of Ken Nealson, quoted in Phil’s piece. And if this wired-up stuff is for real, what are the implications, not just for natural phenomena, but for technologies like the microbial fuel cells (subscription) my colleague Charlotte Schubert wrote about last year? (This blog is not devoted to bigging up Nature; but we do do a pretty good job.)



Lovelock, Rapley and big ocean pumps
September 27, 2007, 12:59 pm
Filed under: Geoengineering, Interventions in the carbon/climate crisis

There’s a letter to the editor in this week’s Nature from Jim Lovelock and Chris Rapley (late of the BAS, now at the Natural History Museum) suggesting that pumping up nutrient rich water from below the mixed surface surface layer of the oceans would increase the rate of photosynthesis in the seas above and thus pull down carbon from the atmosphere. Key para:

The oceans, which cover more than 70% of the Earth’s surface, are a promising place to seek a regulating influence. One approach would be to use free-floating or tethered vertical pipes to increase the mixing of nutrient-rich waters below the thermocline with the relatively barren waters at the ocean surface. (We acknowledge advice from Armand Neukermans on engineering aspects of the pipes.) Water pumped up pipes — say, 100 to 200 metres long, 10 metres in diameter and with a one-way flap valve at the lower end for pumping by wave movement — would fertilize algae in the surface waters and encourage them to bloom. This would pump down carbon dioxide and produce dimethyl sulphide, the precursor of nuclei that form sunlight-reflecting clouds.

There will be a lot of people who don’t like this suggestion for a lot of reasons (I wrote about some of the generalised disapproval of “geoengineering” in a Nature feature a few months back, and see also these blog posts (first | second) over at Climate Feedback). As well as the generalised mistrust of engineering interventions, though, I suspect that there will be some pretty specific criticisms, as my colleague Quirin Schiermeier notes in a news@nature article on the subject. Here’s his take on the downside:

“The concept is flawed,” says Scott Doney, a marine chemist at WHOI. He says it neglects the fact that deeper waters with high nutrients also generally contain a lot of dissolved inorganic carbon, including dissolved CO2. Bringing these waters to the lower pressures of the surface would result in the CO2 bubbling out into the air. So contrary to the desired effect, the scheme could result in a net ‘outgassing’ of CO2, he warns. “There is no technological fix for this problem,” he says.

Others say such a project would have no net effect on CO2 in the atmosphere. “At every meeting I’ve been to, when they have talked about this idea for surface ocean CO2 removal, the point has been made that you would bring up nutrients and inorganic carbon in the same ratio as you remove as biomass,” says Ken Buesseler, a marine chemist at WHOI. And there are potentially many harmful impacts on sea life, he says.

I haven’t taken on board the wider press coverage, but I hear that various oceanographers — including some who are not ideologically averse to a touch of geoengineering — share these or similar doubts. One encouraging thing is to learn from Quirin that David Karl (author of a fine review that touches on some of the science behind all this in the Nature Reviews Microbiology oceans special I was enthusing about earlier) will soon be trying out a pump along these lines made by Atmocean and seeing what effects it has. That experiment will surely teach us something, just as the iron fertilization experiments being discussed at Woods Hole this week have. And just as in the iron case, there should be exciting science on how the oceans work here even if there’s no world-saving breakthrough.

Update: There’s a fairly full and convincing account of the issues in a comment made by Peter Williams of Bangor over at Climate Feedback