Metagenomics on YouTube
September 25, 2007, 7:46 am
Filed under: Uncategorized

It always feels a bit tedious to point out that science can be fun but it’s worth repeating when doing so is quite fun itself. Here (via Jon Eisen) are some people having fun telling the world about their science. I’m quite charmed that this seemed like a good way to spend an Oregon afternoon, and the questions and concepts make me think I’ll keep an eye on the lab. You might think a few powerpoint slides could have done the trick, and you may be right. But I bet the vibe in the lab was better the day after they did this than it would have been if they’d just done that…

If you want some of the hard stuff to go with this, here’s a review from Nature Reviews Microbiology by lab chief Jessica Green and others on the need for theory if one is to understand microbiological biodiversity, a goal that matters for studies of soil, of ocean phytoplankton, and of much else. (abstract | PDF)

Incidentally, David O’Connell and his colleagues at Nature Reviews Microbiology have just brought out a terrific special issue on marine microbiology (thanks to the support of the Gordon and Betty Moore Foundation and the Agouron Institute, it’s free, I believe). I have been intending to blog about it for a bit and still hope to get round to, but go and have a look anyway if that’s your sort of thing.

Update: here’s some backstory on the video


Ken Macleod’s “Learning the World”
September 24, 2007, 7:58 am
Filed under: Books

When I said a little while back that I would be posting occasionally on related books I meant that quite broadly — so broadly, indeed, that quite a lot of science fiction that makes no reference to photosynthesis at all might fall into the category. I quite often think of what I do as a writer as “non-fiction SF”, and I feel myself to be more explicitly in conversation with the genre than most popular science is. As it happens, though, a central image of Ken Macleod’s most-recent-but-one book, “Learning the World” (Amazon UK|US) is photosynthetic: a pair of batlike alien astronomers wondering why the starts in one particular direction in their sky are turning green. The implicit answer is that vast post-human colonization efforts are turning whole planetary systems into habitats, and if not creating Dyson spheres then at least putting enough of the starlight to photosynthetic use to shift the colour balance of the remainder. The action in the novel centres on a starship/spore from these green stars coming to the system of the alien space bats (and what a fine phrase that is); as the UK subtitle says, it is “a novel of first contact”, though it is also, rather cunningly, a novel of second contact. (In the US it’s subtitled “a scientific romance” instead).

I don’t think it’s Ken’s best book, but there’s a lot to like about it and some things to love. There’s a mixture of homage and critique towards Heinlein (and earlier Heinlein influenced work, such as Panshin’s “Rite of Passage“, I think, and maybe even Mike Ford’s “Growing Up Weightless“, but I’m out on a limb there, because I’ve never read the Ford, though typing this reminds me that I should); Constantine the Oldest Man has clear links to Heinlein’s Lazarus Long, though he is a lot less gabby, while Atomic Discourse Gale (a lot of the characters have names like that) reads like a protagonist from a Heinlein juvenile. At the same time the idea of human exceptionalism is interestingly subverted with the help of some ideas revealed right at the end that feel like a hybrid of Lee Smolin and David Brin (which I agree sounds scary). And its allied concept of manifest destiny is given very short shrift. There’s a nice feeling in the background about the simultaneous inevitability and costliness of progress, which I understand to be a theme of Winwood Reade’s “The Martyrdom of Man“, which provides both the epigraph and, movingly, tailpiece to the novel, and which I shall now endeavour to learn a little more about.

And there’s the fact that the vast spaceship is called “But The Sky, My Lady! The Sky!” For me, that’s terrific (not just in a gimmick way, but as an artfully delivered further reflection on progress). Your mileage may differ.

The book’s biggest problem, perhaps, is that it is just too close in set-up to Vernor Vinge’s “A Deepness in the Sky“, which seems to me to have set the bar for such entertainments high enough that to fail to clear it is no evidence of slacking. If you have read neither and imagine yourself likely to read only one, my strong advice would be to read the Vinge. If you have read neither but like first contact novels enough to feel sure you will read both then it might be best to read Learning the World first. (If there’s anyone who meets this description and follows my advice, which I’ll admit sounds unlikely, do let me know how that works out for you.)

Sick of nature
September 21, 2007, 7:25 am
Filed under: Nature writing

WaldenIn a flattering post that takes up the ideas I went into here, Back40 draws our attention to Sick of nature, an essay on nature writing and its problems by the author David Gessner (his website) in which he lets off considerable, amusing and thought provoking steam about his craft/calling/curse/whatever

I AM SICK of nature. Sick of trees, sick of birds, sick of the ocean. It’s been almost four years now, four years of sitting quietly in my study and sipping tea and contemplating the migratory patterns of the semipalmated plover. Four years of writing essays praised as “quiet” by quiet magazines. Four years of having neighborhood children ask their fathers why the man down the street comes to the post office dressed in his pajamas (“Doesn’t he work, Daddy?”) or having those same fathers wonder why, when the man actually does dress, he dons the eccentric costume of an English bird watcher, David Gessnercomplete with binoculars. And finally, four years of being constrained by the gentle straightjacket of the nature-writing genre; that is, four years of writing about the world without being able to use the earthier names for excrement (while talking a lot of scat).

Worse still, it’s been four years of living within a literary form that, for all its wonder and beauty, can be a little like going to Sunday School. A strange Sunday School where I alternate between sitting in the pews (reading nature) and standing at the pulpit (writing nature). And not only do I preach from my pulpit, I preach to the converted. After all, who reads nature books?

Gessner goes on to discuss Thoreau‘s Walden and Abbey‘s Desert Solitaire (which should have been a bigger influence on Mapping Mars than it was) with an insightful eye and a great turn of phrase, before concluding thus:

The best writing in this genre is not really “nature writing” anyway but human writing that just happens to take place in nature. And the reason we are still talking about “Walden” 150 years later is as much for the personal story as the pastoral one: a single human being, wrestling mightily with himself, trying to figure out how best to live during his brief time on earth, and, not least of all, a human being who has the nerve, talent, and raw ambition to put that wrestling match on display on the printed page. The human spilling over into the wild, the wild informing the human; the two always intermingling. There’s something to celebrate.

Meanwhile at Back40 our host, who works the land for a living, talks about the local and global.

Though I am in fact rooted in particular land, fully engaged in a specific place, it is global in Oliver’s sense. I have long seen it this way too. It isn’t only the carbon but also the nitrates, synthesized in electrical storms and that falls in rain, and other minerals that fall from the dusty skies, carried across the Pacific from China on high altitude wind currents, as well as the things I put on that land – everything from Dutch grass seeds to British cattle genes via New Zealand. Even the weeds are immigrants from every continent – as am I.

I prize a vision of natural systems that explicitly acknowledges all of this in dynamic relationship. To truly see it you need to somehow split your focus to include the micro and macro, the very far and the very near, the past, present and future, all at once. It’s hard to do, but worth the effort I think.

That last bit is my point exactly.

Picture of Walden Pond plaque from Mary Ellen Goodwin, picture of David Gessner from his site, all rights presumably reserved.

Review: Richard Fortey in Nature
September 19, 2007, 8:51 pm
Filed under: Reviews received

A kind review (subscription required) by Richard Fortey in Nature (I had nothing to do with it). Here’s the top and bottom and a potted precis of the bits in between:

All the greatest monsters are green. The Incredible Hulk had to turn green before going on the the mekonrampage and the Eagle comic featured a supremely evil green being called the Mekon, who was opposed in almost every issue by the chisel-jawed space hero, Dan Dare. One explanation for this odd association of colour with character is that green belongs to the vegetable kingdom. Humanoids have no right to have chloroplasts in their tissues — and if they do have them, well, they are probably not quite right. In the plant world, green is a heroic tint. It’s a measure of the presence of chlorophyll and a sign that an organism captures energy from the Sun to convert it into organic matter. This is the basis of almost all life on the planet, and is arguably the single most important biochemical pathway there is.

Oliver Morton has written a biography of this organic greenery. He takes us on a grand tour from molecules to biosphere, and a very impressive journey it is. He tackles the difficulties of explaining how photosynthesis works … goes on to outline the 3.5-billion-year-plus history of photosynthesis on Earth … no escaping a kind of modified Gaia outlook here: life, nutrient cycles and rock weathering are all locked together in one inescapable dance … very good on what is needed to turn an alga into a land plant, and then to prop up that plant so that it can bathe in air and light to make a tree. The greening of the ancient continents was the final triumph of the chloroplast … proceeds smoothly to an account of climate history … describes with admirable dispassion the different hypotheses detailing how the biological and human world might cope with this challenge … of several recent accounts of what might happen to climate in the next decades, Morton’s is among the most balanced, but I am still left crossing my fingers and recycling a few plastic bags …

Morton’s account of the ubiquitous importance of photosynthesis is an original viewpoint for looking at the world. It is written with verve and an eye for detail. His breadth of scholarship could leave other science writers green — with envy.

I should mention that he also notes he would have liked more diagrams. I should probably also mention that, as it happens, I reviewed one of Richard’s books many moons ago.

Picture (which is of the Mekon, not Richard) added a day late and taken from DanDare.org, where there is also a fine Mekon poster. Copyright not inquired into…

The road to Barton
September 18, 2007, 5:37 pm
Filed under: By, with or from EtS

The road to BartonChris Surridge knows a lot about plants and has been kind enough to instruct me now and then. He used to work at Nature (before I moved here) and now works for PLoS ONE up in Cambridge. He recently put these pictures up on Facebook and I thought I’d link to them because they recapitulate in part a little detail in Eating the Sun — the ride from the city centre to the village of Barton. This is the ride that Robin Hill used to take every day going home from the biochemistry department, though he would not have gone along Kings Parade, and I Robin Hillwould imagine probably not down Newnham Avenue, either. Hill made a number of fundamental contributions to the science of photosynthesis, most notably the “Hill reaction” (which rather becomingly he did not refer to as such himself) in which isolated chloroplasts are induced to release oxygen and the Z-scheme, which explains how the two photosystems work together. Maybe some of the inspiration for one or other came from the cycle ride (which took him past the house of his friend and mentor David Keilin). Even if it didn’t, it’s a very nice ride to take on a dry afternoon at this time of year, and Hill’s destination, Vatches Farm, would be a lovely place to come home to:

Hill had admired, perhaps loved, Vatches for some time. As an undergraduate he had more than once cycled out to Barton to sketch it. Following in his bike-tracks on one of those perfect afternoons with which Cambridge so often and somewhat misleadingly sees in the new academic year, it was easy to understand the attraction. The main building is a long whitewashed farm-house just across the road from the duck pond on the village green. The south-facing garden—now divided between a few different properties, as the farm was broken up after Robin and Priscilla died in the early 1990s—is a lovely mixture of lawns, flowers and orchards, lit by warm, low sun. Under the old fruit trees he used to tend to the fallen apples perfume the air. Between two small lawns in the eastern part of the garden (for which its new owners have justly won awards) stands a striking, proud beech tree that Hill must have planted not that long after he and Priscilla bought the place. Nearby is what seems to be a relic from the trip to Singapore: an amelanchier of some sort, the current owner tells me, which in the spring fills the air with a scent of almonds and coconut. At the end of the main lawn a farm gate set in a line of trees opens on to farmland. A grassy track leads through a field already ploughed for winter wheat; a mile or so away, the dish of the university’s radio telescope at Lord’s Bridge Road slowly sweeps the skies.

I quite like commuting in over the Thames and past St Pauls, but those pictures do make me envy Chris a little.

Pictures courtesy of Chis Surridge and the Howe lab, University of Cambridge, rights reserved

Excited geology
September 17, 2007, 9:33 pm
Filed under: Uncategorized

In a post on soil chemistry over at Transect Points, (via Gary) Philip Small delves into the mysteries of pH and pE, buffering and poise. It’s interesting stuff which I point you to in part because how microbes do their stuff is something it’s important to understand, in part because this sort of thinking has relevance to the Terra Preta stuff I was extolling a while back, and in part because of a fear that some readers of Eating the Sun will feel that I downplay the importance of soil, and I’d like to show I appreciate it. On top of all that, though, it’s because I just liked reading him pivot fact into image as elegantly as this:

To many of us, what makes soil different than geologic material is that it is in an excited state, excited mostly by solar energy as facilitated by living processes.

Power-station-fed algae
September 16, 2007, 2:29 pm
Filed under: Interventions in the carbon/climate crisis

They sound, I’ll admit, a little less appetising than corn-fed chicken. But they might be a source of fuel for some, and there was a short article about them in The Economist‘s Tech Quarterly last week. The idea is to take effluent CO2 from power stations and bubble it through some sort of bioreactor in which there are photosynthetic algae. CO2 enrichment makes the algae grow faster. You then harvest the algae and turn them into something useful — such as biodiesel (the oil yield can be up to 30% for some algae). The Economist story highlights two companies working on this, GS Cleantech and GreenFuel Technologies. There’s more on algal biofuel in general in a recent Popular Science article.

I remember getting into a discussion about this on Synthesis, Rob Carlson’s blog a little while back. (As the biological technology archive on Synthesis shows, Rob knows a lot about this sort of stuff and keeps insightfully abreast of new developments, which is probably why he is quoted in the Economist piece). Looking back on it, I now think the discussion was somewhat at cross purposes. I was trying to think of the algae in terms of carbon capture and storage — as a way of cleaning the power station’s waste stream. Others were seeing it as a way of making biofuels better. Algal bioreactor in closeupFossil-carbon based biofuels might be cheaper to produce than whole-plant biofuels, and as such could form part of the solution for some problems, such as energy security. They would also help a little with global warming, by displacing the use of fossil fuel oils.

But I don’t think The Economist is quite right in saying that “Using photosynthesis to capture exhaust gases from power plants could reduce the emissions produced by coal-fired stations.” The emissions stay the same — it’s just that an extra loop is put into the process, potentially making things more profitable. The original electricity generator takes out of the dug-up coal the energy that plants put into it in the past, oxidising the coal into carbon dioxide in the process. Then the algae reduce that CO2 to fuel by putting put some fresh sunlight back in. Then internal combustion engines in diesel vehicles reoxidise it. If the use of this biodiesel displaces the use of fossil diesel, there’s a net effect on global warming. But all of the carbon dioxide from the original electricity generator still gets into the atmosphere eventually. The advantages from the system are the same as those for any other biofuel — there’s no real decrease in the electricity associated emissions.

There might be a way of doing something similar, though, in a genuinely carbon neutral way. If the electricity generation is done with a small CHP plant fired by using biomass — say eucalyptus — it could simultaneously generate electricity, heat for domestic or industrial use and diesel for motor vehicles. The generating plant + algal bioreactors system becomes a way of making diesel out of a biomass that is efficiently grown but not good as a liquid fuel, while at the same time producing electricity. That might me quite a nice low/medium tech locally supported generation and transportation solution, if anyone wants such a thing. Of course you’d have to show that the diesel produced was more than enough to power the trucks bringing the wood to the generating plant to start making much of an impression, and there are other ways of turning wood into vehicle fuels, through pyrolysis and the like. But in a place with enough sunlight to grow serious amounts woody biomass and drive efficient algal growth in photobioreactors such a system might be in with a chance.

Image of algae in a photobioreactor by Dan Bihn, who probably reserves all rights