A crappy thing about Nature (the journal, not the concept)
August 15, 2012, 5:55 pm
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I’m very happy to have worked for Nature. I’m proud of some of the stuff I did in my time as Chief News and Features Editor there and — even more so — of the stuff I helped my excellent colleagues there to do. I have huge affection for many of the people who work there, and I think it is a great magazine and journal. I think that by and large it navigates the difficult territory that comes from being a profit-making organisation providing a public good and a cultural necessity reasonably well. I think it has served science faithfully for 143 years, and that the world would be a much worse place without it it.

However the fact that a personal subscription to Nature does not allow you access to its archive is simply crappy.

Yes, you get access to articles back to 1997, which is better than nothing. But science didn’t start in 1997. Nature didn’t start in 1997. Ideas that are important today are not all rooted in the very shallow post-1997 horizon of intellectual history. The random selection of articles I just looked at  in a recent issue all had references to pre-1997 work, some of it published in Nature.

Sometimes pre-1997 observations are as current as they come. Today I was looking into various aspects of the Pinatubo eruption of 1991. Around the world scientists looked into the eruption and sent their observations and ideas to Nature. The best of them got published. Have there been any better observations since? No – there haven’t been any comparable eruptions to observe since. So I can’t read the most recent relevant observations on a topic of current interest  in a journal to which I have paid to subscribe.

Not an isolated instance. A friend recently asked me about the origin of a fundamental concept in molecular biology. With a little work, I tracked it down to a Nature paper from the 1960s. That was helpful to him — but I couldn’t get the full context because I couldn’t get the bloody paper. (The friend could – irony of ironies, he works for Nature.)

I admit that I’m probably unusual in the amount of pre-1997 stuff that I want to read.  I have a greater interest in the roots of scientific discussions than most. I am interested in the continuities and lack of same between science now and science in its past. I like the day before yesterday.

But a) I think, all other things being equal, it would be better if more people moved a little way towards my approach to these things. Too many people read only the most recent publications in their field, and lack a long perspective.

And b) I BOUGHT A SUBSCRIPTION. I should be able to read the archive.

Now, I should note that this policy, while stupid, is not sneaky. The subscription page makes it clear that you don’t get the archive. And I should also note that the subscription is worth it anyway for a beautifully produced magazine that never fails to inform and fascinate.

But it is still a bad policy. And not just because it inconveniences me and leaves me feeling ripped off by an institution I esteem so highly. Because Nature should be about all of Nature. It should be about making you a part of the process of which it is, and has been, a great exemplar. And it shouldn’t salami slice that process in search of a quick buck.

I remember speaking with quite fierce pride at my leaving party about the experience of being at the head of a spear  with a haft centuries long behind it. But if you want to appreciate the haft, it will cost you £22 quid a glimpse, even if you’re a paid up member of the spearhead. That’s wrong. If you’re part of Nature‘s wonderful ongoing conversation you should be part of all of Nature‘s wonderful ongoing conversation.


Some Mars stuff
August 4, 2012, 9:01 am
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In honour of MSL/Curiosity, which descends towards the surface of Mars at breakneck speed tomorrow morning with about a five in seven chance of ending up in one functional piece, I’ve put a couple of relevant pieces up at the mostly defunct MainlyMartian. If you want to try and hold your breath through the “seven minutes of terror” they start at 05.31 UT Sunday Monday morning.

A question about the history of ecology
July 13, 2012, 7:01 pm
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I’ve been reading a bit of ecological history for a column, and I was struck by some dichotomies. Here’s Ron Doel, in 2003

By the 1960s, two distinct ‘environmental sciences’ had emerged: one biology-centered, focused on the problems in ecology and population studies, and funded in part on the problems in ecology and population studies, and funded in part by agencies and managers concerned about human threats to the environment; the other geophysics-centered, focused on the physical environment, and responsive to the operational needs of the military services that support it.

I can see that, and I can see how it would map in part on to a distinction between critical and industrialised science of the sort that Ravetz discusses.

But here’s a different dichotomy, in a different context, as ascribed to G. Evelyn Hutchinson by Joel Hagen in “An Entangled Bank”

Population biologists tended to take a merological perspective, focusing upon independent individuals and assuming that population phenomena determined higher level community properties. In contrast to this bottom up approach, other ecologists, particularly those who later studied ecosystems, took a holological approach by studying the flow of materials and energy through food webs without considering the individuals that made up the web. Hutchinson, an eclectic biologist, seemed capable of making the transition from one perspective to the other effortlessly. Most other ecologists have not been so adept.

And this, it seems to me, also bears on the Clements/Tansley dispute, as to whether there was a sort of teleological holism in ecology (the notion of the climax ecosystem), or simply sets of relations between populations and their physical environments which could be studied rather as those in physics could be.

Now it’s pretty clear to me that these aren’t all the same cut and dried dichotomy. You can be a military-linked energy-flow kind of guy and believe in climax systems (I think the Odums did this). But elements of it do seem to be consistent. I wonder if anyone can guide me to deeper thought on this?

Promises promises
January 3, 2012, 9:51 pm
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It’s not saying much to say that there might be more blogging here this year than there was last year. It may also have more film stuff than was its original intention, though I might get some planetary anthropoceney geoengineeringish photosynthetic stuff up too. Let’s just see how it goes, shall we?

Not in my Oxbridge name…
May 30, 2010, 6:13 pm
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Reading Sarfraz Mansoor’s review of Gary Younge’s “Who are we” over coffee this morning I was struck (and who wouldn’t be) by the sentence

Of the 23 members of the new cabinet, 22 are white, 18 are millionaires, 15 are Oxbridge graduates and 13 went to private schools.

Which really is pretty disheartening. But it also piqued my slight irritation, because I tend to bridle somewhat at “Oxbridge” as a category (non UK readers: Oxbridge is a portmanteau word denoting the universities of Oxford and Cambridge). There are obviously great structural similarities between Oxford and Cambridge, as well as architectural ones and social ones. I remember that the first time I ever visited Oxford, having spent three years as a student at Cambridge, I had the odd feeling that someone had taken a townscape I was at home in, shuffled it, and redealt it  in an odd new pattern. But there are also distinctions, and though I’ll admit that the narcissism of small difference (my absolutely favourite Freudian concept, and one of the great undervalued explicators of life) magnifies them, they may matter. While the variation within both universities is far greater than the difference between their means, from my utterly subjective view point Oxford tends more towards the worldly, the glib, the rosy, the rhetorical, Cambridge to the provincial, the constrained, the cold, the logical.

Linked in my mind to these prejudiced distinctions is the notion that, as well as being more conservative than Cambridge, Oxford is also more central to the political establishment. Evidence: all the UK’s university-educated post-1945 prime ministers had degrees from Oxford (a second degree in the case of Gordon Brown), none had degrees from Cambridge. (Less impressive evidence: I remember a nice joke in Yes Minister about the Oxford preponderance explaining its transport links, though on checking I find that’s actually rather more a joke about civil servants).

So, cappuccino finished, I decided to test out my hunch that the cabinet was in fact dominated not by Oxbridge, but by Oxford. Unfortunately, not so much. Of the 65% of the cabinet that went to Oxbridge 6 are from Cambridge, 9 from Oxford, a 40:60 split. A preponderance, yes, but not a significant one (one-tail p-value 0.30). Expand the universe to include the six people who, while not cabinet ministers, attend, or may attend, cabinet and you find that of 29 people 20 (69%) went to Oxbridge, 8 to Cambridge, 12 to Oxford — 40:60 again, p-value now down to 0.25.

Then it struck me that the problem might be that the Lib Dems in the cabinet were masking a true Tory Oxfordness. Superficially plausible, in that of the 5 Lib Dems in cabinet proper, all of whom went to Oxbridge (and all but one of whom were privately educated), the ratio is reversed, 60:40 in Cambridge’s favour. If a fully Tory cabinet replaced them with 5 Oxford graduates, the p-value would fall to 0.06. Alas, assuming they would be replaced only from Oxford stretches plausibility. In fact if you assume, following James Forsyth on the Spectator’s blog, that the Tories who were denied true cabinet seats by the advent of the Lib Dems are David Willets, Chris Grayling, Theresa Villiers, Greg Clark and Nick Herbert, you find that that quintet is also, as it happens, 60:40 Cantab.

Since I started writing this, the resignation of David Laws has slightly pushed things further against Cambridge. The Oxbridge subset of the cabinet is now 36:64 Oxford, p value 0.21. (The Scottish Lib Dems, from among whose ranks the new Scottish seccretary had to be chosen, are a decidedly un-Oxbridge lot.) Of the 7 people attending cabinet from Cambridge, two of them, Francis Maude and Owen Patterson, went to my college, Corpus Christi. Corpus is one of the smallest of the 20 odd colleges, so that is a truly striking result.

No one in the cabinet, alas, went to Hull. (Though one is, to my previously ill educated surprise, a former member of the NUM.)

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

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
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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.


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