Heliophage


Frankenbug
May 23, 2010, 11:22 am
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"I tell you, it's just the beginning"

So Venter’s artifical bacterium is finally upon us (Science paper). Economist article (not by my hand) here:

Like Shelley’s protagonist, Dr Venter and Dr Smith needed some spare parts from dead bodies to make their creature work. Unlike Victor Frankenstein, though, they needed no extra spark of Promethean lightning to give the creature its living essence. Instead they made that essence, a piece of DNA that carries about 1,000 genes, from off-the-shelf laboratory chemicals. The result is the first creature since the beginning of creatures that has no ancestor. What it is, and how it lives, depends entirely on a design put together by scientists of the J. Craig Venter Institute and held on the institute’s computers in Rockville, Maryland, and San Diego, California. When the first of these artificial creatures showed that it could reproduce on its own, the age of artificial life began.

The announcement is momentous. It is not unexpected. Dr Venter’s ambition to create a living organism from close to scratch began 15 years ago, and it has been public knowledge for a decade. After so much time, there is a temptation for those in the field to say “show us something we didn’t know.” Synthetic DNA is, after all, routinely incorporated into living things by academics, by biotech companies, even by schoolchildren. Dr Venter—a consummate showman—and the self-effacing Dr Smith (uncharacteristically in the foreground in the picture of the two above) have merely done it on a grand scale.

But if it is a stunt, it is a well conceived one. It demonstrates more forcefully than anything else to date that life’s essence is information. Heretofore that information has been passed from one living thing to another. Now it does not have to be. Non-living matter can be brought to life with no need for lightning, a vital essence or a god. And this new power will allow the large-scale manipulation of living organisms. Hitherto, genetic modification has been the work of apprentices and journeymen. This new step is, in the true and original sense of the word, a masterpiece. It is the demonstration that the practitioner has mastered his art.

Fine take from Ken Macleod (@amendlock)  in the Guardian:

Vitalism isn’t a doctrine of any major faith, besides new age theosophies and other forms of muddled thought. In my teens I caught the virus of vitalism from reading Arthur Koestler’s The Ghost in the Machine – and was cured of it, ironically enough, by a creationist tract that extolled the wondrous complexity of cellular machinery: complex and wondrous enough, I realised, for life to need no other explanation. That tiny machine didn’t need even the tiniest ghost.

Synthetic life, then, creates no problems even for creationists (after all, it’s intelligently designed!) let alone more sophisticated theists. This won’t, of course, spare us the usual TV studio parade of clergy (why them?) asked to comment – though they may find it easier than usual to give answers less stupid than the questions.

More significant than the clerics are their secular successors, the ethicists – paid to worry so we don’t have to. They’re already on the case.

Jamais Cascio (@cascio) makes some useful distinctions. More responses, many with insight, curated at Practical Ethics (@ethicsinthenews) and a set of very worthwhile opinions at Nature (free pdf) in which Steen Rasmussen makes a useful distinction:

The radical ‘top-down’ genetic engineering that Venter’s team has done does not quite constitute a “synthetic cell” by my
definitio…

The top-down community seeks to rewrite the genetics program running on the ‘hardware’ of the modern cell, as Venter and his colleagues have done. Bottom-up researchers, such as myself, aim to assemble life —  including the hardware and the program — as simply as possible, even if the result is different from what we think of as life.

There is so far nothing up at Rob Carlson’s Synthesis, but it will be worth checking when there is

(UPDATE: Here it is, and it was. This bit particularly pointed:

I doubt very much that the JCVI team, or the team at Synthetic Genomics, will be using this or any other genome in any economically interesting bug any time soon.  As I note in Chapter 8 of Biology is Technology, Jay Keasling’s lab and the folks at Amyris are playing with only about 15 genes.  And getting the isoprenoid pathway working (small by the Gibson et al standard but big by the everyone-else standard) took tens of person years and about as much investment (roughly ~$50 million in total by the Gates Foundation and investors) as Venter spent on synthetic DNA alone.  And then is Synthetic Genomics going to start doing metabolic engineering in a microbe that they only just sequenced and about which relatively little is known (at least compared with E. coli, yeast, and other favorite lab animals)?  Or they are going to redo this same genome synthesis project in a bug that is better understood and will serve as a platform or chassis?  Either way, really?  The company has hundreds of millions of dollars in the bank to spend on this sort of thing, but I simply don’t understand what the present publication has to do with making any money.

End update.)

I spent a fair chunk of the past week with Rob’s book Biology is Technology (Amazon US|UK, sample here) and if you want to grok this development  in its fullness you would do well to do the same. For a different take with a lot to offer, check out Denise Caruso’s Intervention, too (Amazon US|UK).

Image from Tricia Helfer’s blog, used with thanks but no permission



Carbon-negative volcanism
April 18, 2010, 8:57 pm
Filed under: Uncategorized

The excellent Michael Tobis points to this infographic from Information is Beautiful which compares the CO2 emitted by Eyjafjallajokull to the amount of carbon not being emitted by the planes now grounded in Europe, and asks if this is the first carbon-negative eruption.

The answer is surely no: other volcanoes have done much more on the carbon front. There’s a fairly clear flattening in the Keeling Curve in the early 1990s which is equivalent to about 2 gigatonnes of carbon missing. It’s associated with Pinatubo temporally, and there are two separate global mechanisms with which to explain it. The first is that it because Pinatubo reduced the temperature it reduced soil respiration, a major source of CO2. The second is that plants like diffuse light, and the stratospheric sulphate veil produced by Pinatubo provided it. As a result the plants sucked down more CO2 while the bugs beneath them were  producing less.

The importance of the two different effects is debated. The diffuse light effect is now widely accepted as real, but how much of the Pinatubo effect it accounts for is not fully agreed. It’s also a little hard to get rid of the effects of the El Nino happening at the same time (there are a lot of climate scientists who would really like a Pinatubo without an El Nino in order to isolate the influence of the volcano). Here’s a very good post by Tamino that lays the arguments out.

Either way, Pinatubo is a big time carbon-negative winner.



Five weeks in a (heath)row
April 18, 2010, 8:55 pm
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Rather oddly, I’ve been at or very close to Heathrow for the past five Saturdays in a row — going to Asilomar, coming back from Asilomar, attending Eastercon for the George Hay lecture, and doing a couple of legs of the London Loop. Last week, on Hounslow Heath, an A380 flew right over my head. It was a great deal quieter this week. And, as the Loop often is, rather pretty.

Cranford church, among the trees and under an empty sky



Sheila Schaffer, 1927-2009
January 17, 2010, 10:04 am
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With many other people, we gathered in the Meeting House at the University of Sussex yesterday to mourn the loss and celebrate the life of Sheila Schaffer, mayor, activist, mother, grandmother, mother in law, socialist, friend, cricket enthusiast, environmentalist, walker, art lover, cyclist, sometime potter and inspiration.

Update: Obituary in the Guardian (which is the proximate source of the picture)



Green view
January 13, 2010, 10:14 pm
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The Economist has a weekly online environment column called Green.view. Here’s a taster of what’s been up there in the past month.

This week, there’s a piece about the current cold weather, what it means, and what it doesn’t mean

One possible implication is a change in the prospects of the current poster child for climate change—Arctic sea ice. The extent of summer ice in the Arctic Ocean has been decreasing at a rate of about 8% per decade. In 2007, as the result of prior losses, peculiar sunniness in some areas and a particular disposition of winds, the ice levels fell spectacularly. That particular alignment of circumstances did not hold sway over the following years, which accordingly saw the ice bounce back somewhat. The current cold in mid latitudes might, counterintuitively, reverse that trend and reduce the ice cover further.

The atmosphere cannot make heat, or even hold that much of it. There is more heat stored in the top four metres of the oceans than in all the Earth’s atmosphere. So when the atmosphere cools down one part of the globe, it is a good rule of thumb that it is warming some other part. In the case of the current mid-latitude chill, it is the high latitudes that are seeing the warming. In Greenland and the Arctic Ocean, December was comparatively balmy. The air above Baffin Bay and the Davis Strait was 7ºC warmer than usual (though that still left it pretty cold).

Last week, we saw in the new year (and sort-of-decade) with a piece about a proposal to add some more time to the beginning of earth history

Rocks from 3.8 billion years ago to 2.5 billion years ago are assigned to the Earth’s earliest geological eon, the Archaean. Anything earlier—a few lumps of Greenland and Canada, and rock-residues preserved now only as inclusions in larger, later, rocks—are referred to as belonging to the Hadean, an informal and ill-defined but useful and evocative term.

The new proposal suggests not just that the Hadean should be formalised, but also that a new aeon, the Chaotian, should be recognised as extending extend further back in time than the Earth itself. The Chaotian would begin with the beginning of the cloud’s collapse, be punctuated in the middle with the ignition of the sun and come to an end with the collision that created the Earth-moon doublet in its sort of modern form. In a fit of further distinctions, the authors—Colin Goldblatt, a young researcher at NASA’s Ames Research Centre, and three older colleagues with considerable previous form in the framing of provocative hypotheses—suggest the Nephelean and Erebrean for the periods before the sun’s ignition, the Hyperitian and Titanomachean for those after.

And back in 2009, a look at the gap between the emissions that are reported and the levels of greenhouse gas that are measured.

ONE of the many sets of initials being bandied about at the climate conference in Copenhagen is MRV—monitoring, reporting and verification. In theory, it seems fairly straightforward: if countries commit themselves to limiting the production of particular greenhouse gases, they need to be able to keep track of what they are doing and to tell the rest of the world, which must in turn be able to verify the claims. In practice, there are any number of problems, one of which is that when you start to look at what is actually happening in the atmosphere, it does not necessarily resemble anything that is being reported. Countries therefore commit themselves to actions without any real idea of the current state of play. As Ray Weiss of the Scripps Institute of Oceanography put it at one of the many side events surrounding the negotiations on the Kyoto protocol and its eventual successor, it is like going on a diet without weighing yourself.



The great things had been there all the time…
January 1, 2010, 9:18 pm
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In a Polish field

There’s something peculiarly wonderful about reading and enjoying a book that you would never have found for yourself. My friend John gave me Robert Kee’s A Crowd is Not Company (Amazon UK|US) for Christmas, a memoir of time spent as a POW in the Second World War. It’s a moving and fascinating read, and in its insights into how the world looks when you are separated from it it contains a passage which would have made a wonderful epigraph for Eating the Sun

Suddenly I awoke to the fact that I was staring at a tree on the other side of the road and that this tree was green and delicate. For a few moments I was intensely conscious of the tree and saw nothing else. Then I thought of all the trees I had taken for granted in the past — beside the Cherwell at Oxford or on the pavements of a Surrey suburb. Always I had regarded them as only incidental to the main theme, the real great things that were to happen to me. At the time I had wondered why this main theme somehow always eluded me, why the great events never materializes. Now as I looked at the tree I saw that the great things had been there all the time but I had mistaken them for the background.

A happy new year to you all

Images from Flickr user Hampshiregirl, used under a creative commons licence



The Copenhagen Accord
December 23, 2009, 4:41 pm
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Catch-up blogging, part 2: Copenhagen, or Cop15, if you prefer, was a wild introduction to the diplomatic (I use the term loosely) side of climate politics. Here’s a brief note on the outcome from The Economist, which also ran a correspondent’s diary. What it all means is still sinking in, but I think the most helpful two pieces for a real understanding to date are Mark Lynas’s behind-the-scenes blame China piece in The Guardian and Sam Hummel’s 5 common misconceptions piece in Grist.

Update: Here’s a longer, fuller take from The Economist, and also a leader



Change of address
December 23, 2009, 4:33 pm
Filed under: Uncategorized

Catch-up blogging, part 1: As of a few weeks ago, I have become Energy and Environment Editor at The Economist. This means I have a new email address — first and last name, unpunctuated, at economist.com — which everyone is free to use for business relevant communications. What it means for my blogging here it is too early to say.



Efficiency is not enough
November 3, 2009, 3:23 pm
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The FT is doing a lot of climate stuff at the moment, not all of which I have caught up with, and much of which I am sure is excellent, but this para in yesterday’s broadly fine leader on following the science is flat wrong:

Fortunately the science becomes much clearer when we move from predicting the climate itself to assessing how best to reduce carbon dioxide in the atmosphere. Forget about esoteric “geo-engineering” proposals to cool the earth. Technology that already exists (or is in development) can do the job perfectly well by increasing the efficiency with which we use carbon-based energy.

The point here is not that I disagree with the notion of ignoring geoengineering — reasonable people can and do differ on that, as noted last week. But the idea that the earth can be cooled by using carbon-based energy more efficiently is just not true. Efficiency can slow the rate of warming — but any meaningful cooling will need  zero-emissions energy and probably a fair bit of direct air carbon capture too.

Unsuprisingly, the letters in today’s issue do not point out this error, because they are from people objecting instead to following the scientific consensus — including one from a chap who claims that there was once a scientific consensus that the world was flat. Can we get a better class of sceptic please?



Bruno Latour, the other world, and this world otherwise
October 28, 2009, 8:36 am
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Not by me, not my leg...

This thought from Bruno Latour seems spectacularly apposite to my work:

 

The dream of going to another world is just that: a dream, and probably also a deep sin.

But to seize, or seize again, this world, this same, one-and-only world — to grasp it otherwise: that’s not a dream, that’s a necessity.

 

 

Image from flickr user Enro, used under a creative commons licence




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