British Science Blogging

What goes around comes around on the shameless blog-whoring front, I reckon. A positive spin-off from the Truth In Science debacle was the happy discovery of a number of excellent UK, or UK-based, science bloggers of whom I was previously unaware. I’m sure there is more excellent stuff out there, and I’d like to know where it is. So if you write about science and are from or are currently based on this side of the Pond (ex-pats also welcome), link to yourself in the comments and I’ll add you to the list below. Everyone else, tell me about the relevant people in your blog-roll.

The List

• Bad Science - Ben Goldacre keeps an eye on the relentless ignorance of the British media. Poor man.
  
• Bunsen Burner. Some excellent general science writing (it’s not been active for a couple of months though).
  
• Connaissances. A geologically-inclined poet currently living in France.
  
• Darren Naish: Tetrapod Zoology. A paleontologist who actually gets to study dinosaurs.
  
• Dr Petra Boynton - an evidence-based approach to sex and relationship issues.
  
• dotdotdot - contrary to the tagline, she apparently does now have a PhD.
  
• El Gentraso - Science writer focussing on evolution, ecology and conservation.
  
• Gooseania - surviving a Maths PhD in Manchester.
  
• homunculus - Philip Ball gets people to pay him to write about science. Bastard.
  
• inkyCircus - Still one third British, which is enough to qualify them for our football team (they'd probably be an improvement too).
  
• Leaves on the Line - Andrew Jaffe, an astrophysicist at Imperial College, London.
  
• The Neurophilosopher’s weblog - cognitive science and other things biological.
  
• Postblogger - biochemist/botanist riffing on the traumas of being a post-doc (except on Thursdays).
  
• Post Doc Ergo Propter Doc - chemistry postdoc, and not afraid to complain about it.
  
• Ramblings of a Scientist - of Dr. Jim, to be precise.
  
• Sane Scientist - not so sure of that myself...
  
• The Scientific Activist - an American biologist in Oxford.
  
• A Somewhat Old, But Capacious Handbag - Miss Prism opines on cakes and biology.
  
• Stoat - climate science commentary.
  
• Transient Reporter - survived British bording school, so academia holds no fears for him.
  
• The Unbearable Lightness of Being a Postdoc - Iknownotwhattodo, another biologist stuck in post-doc limbo.
  

Keep them coming - then who knows? We can coordinate on any more MP nagging, follow up on Postblogger’s suggestion for our very own carnival, and, more importantly, think about getting together in a pub somewhere…

Link to me or the puppy baby squid gets it

People are getting much more imaginative when coercing people to link to them. First we get Acephalous garnering plugs by the bucketloads in the name of science (I’m just hoping that he’s done a control experiment he hasn’t told anybody about), now Transient Reporter is not only begging for comments but getting other suckers to do it too.

Clearly, I need to up my game. I was going to get attention by threatening this sweet little fellow with an ugly demise:


But everyone knows that for the big boys, chordates are so last phylum. So I went down to the waterfront* this morning and took another hostage:


I’m not asking for much in return for letting the little guy to swim free, am I?

Mmmm… kraken crackling….

*look, I know the Solent is thoroughly scoured of all interesting animal life, but bear with me, hey?

Phases of belief

I’ve been puzzling over why what is a legitimate dispute between members of the pro-science camp, over emphasis and tone in the struggle against the forces of ignorance, always seems to break down into what could charitably be referred to as ‘arguing past each other’ (I’m not implying the coturnix is an offender here, by the way – he’s just got the best link summary).

A common framing of different theological positions is to represent the continuum from theism through agnosticism to atheism as a change in the relative importance of empiricism and faith in a particular person’s worldview. An atheist places a high value on tangible evidence; a theist is more concerned with the greater truths that they feel exist outside of the world we can subject to experimental verification.


I can see some fairly obvious flaws with this representation. Committed empiricists see all the theists, fundamentalist and moderate, lumped together at the far end of the spectrum, which can make them highly suspicious of someone like Ken Miller, who is clearly a man of deep religious conviction even though he just as clearly values science. Furthermore, as we’ve been so recently reminded, at that empirical end of the spectrum you find people who have little time for faith themselves but will tolerate it in others (provided that religious views are not being foisted too egreriously on the unwilling) jostling for space for people who argue that all faith is silly and even dangerous. The fact that a single axis does not usefully capture the range of viewpoints and how they relate to each other seems to make it all too easy to misunderstand other peoples’ positions.

Because of this, I think a third factor needs to be considered, which for want of a better word I’m referring to as ‘zeal’ (I also considered ‘passion’, which might be a less inflammatory choice). This is a measure of commitment to a particular worldview; how much do you care about it being true? Does it bother you that others don’t share it? Inspired by a recent treatise on ‘thermopienamics’, I’ve tried to map different theological outlooks onto a ternary diagram, with Empiricism, Faith and Zeal as the vertices. The advantage of this representation is that it (hopefully) emphasises that I’m not talking about absolute quantities here, but a relative measure of which attributes most control someone’s positioning in the theological menagerie: someone who plots near the faith vertex is not necessarily antiscientific per se, it is just that faith is far more important to them than empiricism.


In this representation, the Faith/Empiricism side of the triangle is dominated by agnosticism, because they generally don’t particularly care one way or the other about such matters (or at least aren’t too bothered by others disagreeing with them). The boundary between the theist and agnostic sectors reflects the fact that people who are more passionate about their religion can maintain their faith even when they have an appreciable regard for science and empirical reason, whereas less passionate theists are more likely to drift into agnosticism. Likewise, if you tend toward empiricism, the more you care about the existence or non-existence of God(s), the more likely you are to drift over into the realm of the actively disbelieving atheist. I’ve reserved the high end of the zeal realm for cranks and conspiracy theorists, whose passion is tempered by neither faith nor empiricism.

In the next figure, I’ve tried to plot the positions of significant religious denominations and the major players in the recent spat (apologies to anyone who feels misrepresented).


Does this help us any? In my mind, it gives us a new perspective on some recurring problems. For example, the suspicion moderate agnostics seem to have of some of their atheist brethren can be understood to stem from their suspicion of too much zeal for any particular worldview; they feel it is divisive and polarizing. Both fundamentalist theists and the more vocal atheists lie in the same direction in this regard, even though the focus of their zeal is entirely different. This confusion between faith and passion may also be behind the theists’ “atheism is a religious belief too” argument.

Likewise, the snide remarks which sometimes get directed towards “timid” agnostics by atheists also reflects a misunderstanding – if you don’t personally find the existence (or not) of God particularly important, you are probably happy to stick to the more technically correct position with regard to non-corporeal entities that exist outside of space and time: “there almost certainly is no God, but we can never be 100% certain”, to adapt Dawkins slightly. The mainstream Anglican Church - which places great value on thoughtful, less boisterous faith, and is looked on with some contempt by the evangelical wing for just that reason - is more than happy to stick God into that gap, which science may make smaller but can never completely close (listen to the Archbishop of Canterbury talking to John Humphrys, for example). This is as close as you get to the ‘non-overlapping magisteria’ idea in the real world: there is still some overlap, but in practical terms it is very small, and allows people (if they wish) to reconcile their faith with the empirical world. This includes people like Ken Miller (who is, of course a Catholic, but the idea is the same). In contrast, for fundamentalists the magisteria overlap almost completely; because they regard revelation and scripture much more highly than science, in their minds science loses and is denied.

Another interesting feature of this representation is that it suggests that the more zealous theists, if something causes them to doubt their faith, may be more likely to move directly into the atheist camp without any intermediate stops in agnosticism. I think this is interesting in light of the widespread anger amongst the “deconverted” which surprised Dawkins so much on his recent US tour. Perhaps the more zealous Christians are more likely to feel betrayed or lied to if they lose their faith than the former Anglicans who Dawkins would more commonly encounter in the UK, which makes them a bit more passionate in their atheism. And, somewhat heretically, it might suggest that atheists can have a uniquely effective role in the conversation – in supporting and encouraging these refugees.

The other sector I’ve tentatively identified in the middle of the triangle is the realm of the ‘Einsteinian religion’ which Dawkins discusses in The God Delusion - where effectively, ‘God’ is the universe revealed by science, capable of inspiring wonder and awe but not so keen on the smiting or prying into peoples’ personal lives. I’m wondering if this is the true middle ground we should be aiming for – the triple point of the theological system. But for now, if you’re picking sides, by my reckoning I’m fairly sure that a lot of us can pick both (Update: i.e., this whole notion of "teams" is meaningless, there is just a slight difference in the theological outlooks that people are comfortable with - in this particular case I see Ed as uncomfortable with the overly zealous, and PZ as uncomfortable with the overly credulous):


All we need to do is get the moderates to see that a little bit of passion is not always a bad thing, and perhaps get the hardcore atheists to concede that people are always going to believe silly things, but some silly things are more harmful than others, and then we can all be one big happy creationist-bashing family again. Until Christmas, anyway.

Student incoherence

I’ve just finished marking some assessed practicals. Personally, I’ve yet to be convinced that formally assessing an exercise where they have three hours to wheedle the answers out of you has much educational value – I’d much rather use the class time to properly consolidate important concepts and then test it with an out-of-class exercise - but hey, I’m not in charge of teaching.

The good news for this year is that, on the whole, the marks were pretty good. Whether this is due to (a) smarter students, (b) A clearer idea of the set task (I’d rewritten the rather opaque set of instructions I inherited last year) or (c) I’d confused them less in lectures, is unclear, but hopefully I can justifiably take some of the credit.

However, a couple of things perplexed or annoyed me. Firstly, the Oceanography students (whose reasons for doing a tectonics course somewhat escape me) scored significantly higher than the Geology/Geophysics students. Perhaps my suspicion that the more sensible geology students prefer to go to proper geology departments has some merit. Secondly, the most annoying aspect of marking this year was the complete disorganisation of the submitted work. Almost universally, the relevant discussion and working for the individual questions were not collated in a sensible order, but scattered randomly throughout the submissions, making it very easy to miss things. It’s a good thing for the students that I was conscientious about checking through a second time when adding up the marks.

I didn’t actually penalise anyone for this, and I’m thinking that maybe I should have –being able to properly articulate your answers is almost as important as being able to produce them in the first place. My worry is that this work was produced under no time constraint, which doesn’t auger well for the exams after Christmas.

Return of the Megatsunami

Update: Further developments in this story can be found here.

It seems like megatsunamis are back in vogue, but this time a different culprit is in the frame. Around the turn of the millennium a lot of publicity was given to the suggestion that a 200 cubic kilometre-sized chunk of the western flank of Cumbre Vieja, an active volcano on La Palma in the Canary Islands, was poised to fall into the sea in a future eruption. Modelling suggested such a collapse would send a gigantic tsunami racing westward across the Atlantic, and the eastern seaboard of the US would be assaulted by 50 m high waves that would penetrate up to 20 km inland (for comparison, the Boxing Day 2004 tsunami produced waves 20-30 m high which penetrated 2-3 km inland on the Sumatran coast, a mere 160 km away from the epicentre).

This apocalyptic scenario was put forward by Bill McGuire and his colleagues at the Benfield Hazard Research Centre. McGuire has become the go-to guy when you want a geological scare-quote for your breathless documentary about how we’re all doomed, whether by megatsunami, supervolcano, or some other hyperbolically titled geological phenomenon. Here in Southampton, some people who have studied past collapse events in the Canaries think that the risk is being a tad…overhyped (see also here for the Benfield team’s counterargument, because you seem to get a series of much smaller landslides rather than one big one which will wipe out the whole of Western Civilisation.

Now Phil calls our attention to an article in the New York Times (free registration required) which highlights another potential source for really big waves - oceanic asteroid impacts, which a group of scientists led by Dallas Abbott have proposed as the source of some interesting wedge-shaped deposits, referred to as ‘chevrons’, you find on some shorelines, particularly around the Indian Ocean. Firing up Google Earth, we can find them on the West Australian coast (the line on this and the following images is 5 km long:


and here are the stars of the NY Times article, in Fenabosy bay, Madagascar:


and some similar structures I’ve spotted on the east coast of South Africa:


From a distance the chevrons resemble large dunes, but when you look closer things don’t fit. Studies of the Australian chevrons (see here and here) reveal that although they’re largely made up of sand, they also contain shell debris and cobbles (clasts of rock about 10-20cm in diameter), and sometimes are associated with much larger boulders, which appear to have been transported a considerable distance.


These observations are consistent with the chevrons being formed by a violent surge of water – a storm surge or a tsunami – sweeping the shells and other marine material inland. The strength of current required to transport the large boulders, and the distances inland (several km) and height above present sea level (10s of m) this material now crops out, have led some people to favour a tsunami origin.

So where do the asteroids come in? Look at this animation of the propagation of the Boxing Day 2004 tsunami (for those with lots of bandwidth, go here for the high resolution Quicktime version), and compare the wave directions radiating away from the Sunda Trench with the orientation of the chevrons found around the Indian Ocean. It’s clear that the former cannot cause the latter, so the chevron-causing tsunamis were not generated by subduction zone earthquakes (all of the other plate boundaries in the Indian Ocean are spreading ridges). Even if the orientation wasn’t wrong, the size of wave required to form structures on the scale of the chevrons dwarfs even the tsunami generated by the magnitude 9.2 earthquake two years ago.

Hence we need another source, and Abbott and the other members of the ‘Holocene Impact Working Group’ reckon that source is an asteroid impact, specifically the one which formed the 18-mile wide Burckle Crater, located in the centre of the Indian Ocean (31°S, 61°E). To support this hypothesis, they cite analysis of some of the marine fossils found in the Madagascar chevrons, which are fused with metallic flecks enriched with elements common in chondritic asteroids but rare in the Earth’s crust (as Lab Lemming explains rather better than the NY Times article).

This is not the only recent large impact Abbott and her colleagues have proposed – you can find chevrons on the eastern coast of Australia and southern New Zealand which they’ve linked to a crater on the New Zealand continental shelf. That’s at least two major impacts in the last 10,000 years, which is a bit at odds with the current estimated frequency calculated from astronomical surveys of near-earth asteroids.

In the midst of this contradiction, then, it is worth noting that the evidence is still slightly ambiguous. From the information I can find online there is reasonable evidence that at least some of the chevrons are caused by tsunamis, but the orientation of many of the Australian chevrons seems a little too north-south to be obviously traced back to Burckle Crater, which is almost directly to the east; and in the second of the two papers I linked to above, carbon dating of coral and shell debris in the chevrons suggests that together they record at least three events, roughly 700, 2000 and 6000 years ago - Burckle Crater is thought to be about 5000 years old - rather than one big event, although this may be complicated by reworking of older debris. Perhaps, then, we are looking at evidence for a number of smaller impacts, perhaps mixed in with submarine landslides, rather than a single big one forming all the chevrons. Such an interpretation would probably be more consistent with the astronomical data – there’s probably more uncertainty in impact rates of smaller asteroids, as they’re harder to spot (while we’re on that subject, it seems that estimates of the size of tsunami generated by an impact of a given size vary widely, which introduces additional uncertainties) . However, only time, and some careful dating work, will tell.

Scientific writing for beginners

A letter at the core of a recent bruhaha at MIT, where a prospective hire was caught in the cross-fire of egos higher up the academic food chain (see Adventures and Ethics in science for analysis and links to more), has been brilliantly dissected by wildtype over at Transient Reporter. It's all good, but this bit is a particular favorite with me:

I am most happy to support you if you and I are going to work with some distance between us.
Stay where you are and I won’t cut your grant proposals down during study sessions, or hold up your manuscripts.

because it is a prefect illustration of scientific writing, where withering intellectual assaults (as well as speculative handwaving) are deeply buried beneath a veneer of understatement and superficial politeness. As a semi-homage, I thought I'd reproduce a handy translation guide for certain key phrases in scientific papers, which I originally put up on my now defunct pre-blog website. It dates from those heady undergraduate days when I read many more papers than I have time to now.

A novice or outsider might expect the average scientific paper to be a clear and coherent document. Far from it. Little research produces clear-cut or easily understandable results (it would be quite dull if it did), but a combination of ego and desire for further funding means that few scientists will readily admit this. Fortunately for them, the somewhat formal prose traditionally used in a publication provides many opportunities for deliberate obfuscation (as well as the lobbing of a few choice insults at people who happen to disagree with you).

The list below exposes and translates some of the more common phrases you're likely to find.

"It has long been known"	I didn't look up the original reference.
"A definite trend is evident"	These data are practically meaningless, even when you squint.
"Whilst it has not been possible to provide definite answers"	An unsuccessful experiment, but I still hope to get it published.
"Three of the samples were chosen for detailed study"	The other results didn't make any sense.
"Typical results are shown"	These are the only results which prove my theory.
"These results will be in a subsequent report"	I might get around to this sometime, if pushed/funded.
"In my experience"	Once.
"In case after case"	Twice.
"In a series of cases"	Thrice.
"It is believed that"	I think.
"It is generally believed that"	A couple of others think so, too.
"Correct within an order of magnitude"	Wrong, but I'm not going to admit it.
"According to statistical analysis"	Rumor has it.
"A statistically-oriented projection of these findings"	A wild guess.
"A careful analysis of obtainable data"	Three pages of notes were obliterated when I knocked over a glass of beer.
"It is clear that much additional work will be required before there is a complete understanding of this phenomenon"	I don't understand it. AND/OR Give me more money.
"After additional study by my colleagues"	They don't understand it either.
"Thanks to Joe Bloggs for assistance with the experiment and to Cindy Adams for valuable discussions"	Mr. Bloggs did all the work, and Ms. Adams explained to me what it meant.
"Contrary to the interpretation of Jones (1997)"	Jones is an ignorant fool.
"A highly significant area for exploratory study"	A totally useless topic selected by my committee.
"It is hoped that this study will stimulate further investigation in this field"	I quit.

Of course, these rules sometimes break down - in print, most often in the 'Comment and Reply' section. This is one of the more formal ways that peer review continues long after publication - people who disagree with you, or want to engage in a bit more cite-napping (I do like that term), can submit a short rebuttal to the publishing journal, which is published together with any response (re-rebuttal?) you might have. Outbreaks of 'contrary to the interpretation of' are common, but I am especially reminded of a particular response, which pretty much dropped all pretense at politeness:

Westaway [2004] adds details on the deformation rates in the eastern Mediterranean that do not affect the results of our paper, and need no further comment. He is wrong in saying we suggest no surface uplift of the Turkish-Iranian plateau or Greater Caucasus since 12 Ma, and we refer readers to sections 4 and 11 of our paper for the details [Allen et al., 2004]. We do not cite Westaway's papers on lower crustal flow because we do not believe them and see no need to refer to them: He suggests crustal flow from areas of thin crust to thick crust, against the gravitational buoyancy forces. Our reply is brief because we do not think this was a constructive comment on our paper, and not worth a response on the same scale.

Ouch.

My democratic experiment concludes

...and, I have to say, the result is surprisingly positive. As promised in his last response, I received a follow-up letter from my MP John Denham, which I reproduce below. Bolded words were underlined in pen in the original.

Thank you for contacting me regarding the "Truth In Science" resource packs.

Neither the Department for Skills and Education nor the Qualifications and Curriculum Authority (QCA) have been involved in the development or distribution of the "Truth In Science" resource packs to schools.

It is up to schools to decide what teaching resources they need to help them deliver the national curriculum. However the Minister agrees with you that the "Truth In Science" information is not a suitable resource for the science curriculum.

The programme of study sets out the legal requirements of the national curriculum. There are two programmes currently operating in key stage 4 sciences:

• Pupils in year 11 are following the 2000 programme of study
  
• Pupils in year 10 are following the 2006 programme of study
  

Both programmes include a focus on the nature of science as a subject discipline including what constitutes scientific evidence and how this is established by experimentation. Pupils also learn about scientific theories with extensive supporting evidence from established bodies of scientific knowledge.

The Minister would like to assure you that he is working with the QCA to find a suitable way of communicating to schools that the "Truth In Science" is not part of the science national curriculum.

Yours sincerely,

For non-Brits, Year 11 are 15/16 year-olds (the last year of compulsory education, at the end of which the students sit GCSE exams), Year 10 are 14/15 year-olds. Follow the links to compare the relevent parts of the 2000 programme of study, and the 2006 version. The troubling section 1 b) is being changed significantly in the newer standards, which is in itself somewhat reassuring.

When I started this little experiment I was not exactly optimistic about a positive outcome - but I have been very pleasantly surprised. Not only did my MP acknowledge my communications, but he actually took action based on my concerns. Even better, it seems that those in a position to actually do something are aware of and concerned about the actions of Truth In Science (lets just hope that they don't have to run it past the PM first). This is more due to the efforts of others, I suspect, but every little helps, and this whole episode demonstrates that, through tools like writetothem, it isn't hard to supply that little.

Although the experiences of others show that I may be quite lucky to have a conscientious and savvy MP (he's even started a blog specifically to get feedback from his constituents), I find myself in the happy position of having had a cynical prediction - about politics, no less - proved wrong. In my next post: gravity defying pigs.

Update: Unbearable Lightness has also got a positive response; postblogger is still drumming his fingers, and has finally named and shamed his rather up-of-himself MP.

Ego boost

A recurring referral in my sitemeter log indicates that I've been nominated for an award. I'm flattered to find myself in some pretty distinguished company, which means that I've not a hope in hell of winning even if the nomination goes forward - unless PZ and Phil really go at it in a tentacles vs telescopes deathmatch...

Real peer review

Peer review is the sacred core of the self-correcting machinery of science. Before it can be published, a new paper must pass muster with qualified experts in the field it covers, ensuring that dodgy results and poorly supported conclusions do not make it out into the literature to impede the grand progress of the scientific enterprise.

Well, that’s the theory – but what’s it like in practice?

A source of constant amusement (and some trepidation) to me is the way that some of the most vital jobs in your academic career seem to be just dropped into your lap: you are asked, told, expected to do them and do them well, but no-one thinks to provide much in the way of guidance, or even check that you’re vaguely competent, before gladly dumping the workload in your lap*. That’s certainly been the case for lecturing (for instance, no-one on the teaching staff has ever bothered to sit in on one of my lectures to see if they are actually coherent), and my introduction to the ‘review’ bit of the peer review process has been suspiciously similar. My two helpings of review fodder to date, the second of which I polished off yesterday, have both come to me in the same way - the editors sent a paper to my supervisor/boss and he fobbed them off in my direction (so that’s exactly like the teaching then...). Whether their eagerness to do so was confidence in his opinion (scary) or desperation (scarier) is hard to tell.

That’s the first dose of reality – willingness to review other papers is a grudging quid pro pro for other people reviewing yours, and the abstract realisation that we have to do it to make the system work isn’t much of an incentive when you have other, more concrete, demands on your time. This is especially true for the people most frequently solicited for reviews - prominent scientists at the forefront of their field, who want to spend their time staying at the forefront rather than carefully checking the work of current or potential competitors. Hence, with one important exception, one of three things will happen:

1. They review it by skimming the paper and banging off a few line which quote your abstract back at you, and say its all fine. A nice ego boost, but hardly constructive.
   
2. They stick it in their in-tray and leave it there for 5 months**.
   
3. They offload the task onto a lesser minion (sometimes promptly, sometimes only after nagging by the journal editor, if they are still too busy to bang out the cheap and cheerful review described in (1)).
   

The second dose of reality comes when considering the exception, which is when the submitted paper treads on the toes of one of the reviewer’s pet theories, or (worse) pre-empts something that he is working on himself. Whilst such situations can motivate a prompt review, they can also lead to the concept of objective assessment getting a little…strained, meaning that such a review is going to have a strong focus on the negatives. Common examples: a minor problem is talked up as a fundamental flaw, or an unrealistic amount of extra analysis is demanded (a hostile reviewer for one of my papers suggested that to properly establish one of my ‘assumptions’ – in reality the major conclusion to the paper - I would need to undertake elemental analysis of every Miocene outcrop in New Zealand). And as Lab Lemming astutely reminds us in the comments, even where your reviewer is managing to quell the urge to trash your work, you're still liable to an unhealthy dose of cite-napping: it seems that somehow you've missed the key contribution of every paper they've written since 1977, and it's their duty to point this out to you.

In the former case this can be annoying, but is to a certain extent healthy – who better to test your ideas to destruction than someone not inclined to believe them? The problem is that papers within a given subfield tend to always get sent to the same people, meaning that if they are hostile to certain ideas or interpretations, it can be very difficult to get them published in a top journal. However, even if publication is slowed by such antics, good science will generally out in the end. The latter case is more difficult, because it is not altogether unheard of for someone to hold up someone’s paper while manoeuvring to scoop it, especially in competitive fields like paleoclimatology***. And then, basically, you’re shafted.

All things considered then, since anyone more than a year into their PhD should have had a healthy amount of practice at critically assessing the scientific merit of a paper (I’ve been scribbling sarcastic comments in the margins since my undergrad days), delegation is perhaps the best outcome; indeed, for lesser lights such as myself the novelty value of actually being asked for my opinion probably motivates us to be more conscientious, compensating for our relative lack of experience (I may generalise too much here, given that my pedantic nature forces me in that direction anyway). Now, however, the problem is reversed, because the reviewer finds himself in the position of passing judgement on the work of people who are far more important than he is. A glorious victory for egalitarianism, to be sure, but should you identify any serious flaws you have to bear in mind that in the small world of academia, just because the review process is supposedly anonymous doesn’t mean they won’t find out it was you who trashed their precious paper. You have to choose your words carefully, and even then some people may not be too happy with you, should they find out who you are.

Hopefully, it won’t come as too much of a surprise that scientists are human beings, and thus the peer review process is witness to as much sloth, incompetence and back-stabbing as any other human activity. The question is, how much does it matter? The trumping issue aside, not as much as some people think. The ‘official’ peer review process is really just a preliminary; the real peer review occurs after publication, when everyone gets to see your opus, read it, write sarcastic comments in the margin, and (if it’s any good) use and cite it in their own work. This is something that ID ‘theorists’ and other pseudoscientists constantly misunderstand: somehow getting a paper ‘peer reviewed’ and published does not automatically convert bad science to good. It might make scientists pay some attention to your ideas, but it doesn’t require them to agree that they are valid; and if they don’t think they are, they will say so. Good ideas are good ideas and bad ideas are bad ideas, whether they’re ‘peer reviewed’ or not, and will gain traction – or not - accordingly. However scientific publishing adapts to the internet age, whether with “open reviews” or some other system, that will always remain the real test

*This is my experience, anyway – I’d be interested to whether this is actually fairly common, or my department’s unique approach to training is shining through.
** Yes, I’m talking to you, the JGR reviewers who have been sitting on a couple of my papers since June…
*** Which might explain why so many of the paleoclimatologists I’ve met are constantly in a bad mood.

Where have all my pictures gone?

I've just realised that one of the webhosts I use to host some of the images used on this blog (I don't host them on Blogger much because (a) you can't list them and (b) it converts everything to crappy jpegs) has seen fit to erase everything from my account space. Without warning. I don't know how long its been since this happened, so apologies to anyone who's been image-less (although it's partly your fault for not telling me).

I've restored all of the broken images I've found bar one (the Java strain partitioning figure, which I'm going to have to redraw). Let me know if you find any more. I'm off to find an e-mail address which I can impotently express my displeasure at.

Earth – dwarf planet

I’m somewhat chagrined than I didn’t pick up on this myself, but I’m amazed that no-one else did: in all the furore over whether Pluto was a planet or merely a borrowed geological term, no-one stopped to think of the nominative consequences for our own fair sphere. Anjana Ahuja reports in The Times on the views of the editor of Sky and Telescope magazine, Richard Fienberg:

According to the IAU’s General Assembly, which met in Prague this year, a celestial body can be called a planet only if a) it is in orbit around the Sun; b) it is round (in other words, is massive enough to be shaped into a ball by its own gravity); and c) it has cleared the neighbourhood around its own orbit.

It is c) that has proved awkward. The IAU meant that planets should orbit the Sun in isolation, rather than whizzing around with other bodies, such as asteroids. This clause did for Pluto, because it resides in the Kuiper Belt, a girdle of icy bodies that lies beyond Neptune.

But, Fienberg points out: “Our own world is threatened by . . . a host of other near-Earth asteroids whose paths around the Sun intersect ours. By strict application of the IAU’s new rules, this means Earth is no longer a planet either. Ditto for Mars, Jupiter and Neptune, all of which are accompanied in orbit by little asteroids. Ridiculous!”

Special plead your way out of that one, IAU. I confidently predict the appearance of a modified sub-clause which defines 'cleared' as 'not having any other bodies above a certain percentage of the size of the candidate planet' – if there isn’t one already. It’s not so much I’m convinced by this argument, but it just shows how easy it is to tie yourself in knots when you start preferring semantics to science. And this closing line is priceless:

Fienberg has come up with a fresh mnemonic, forged in pure bitterness, to describe the new Pluto-less planetary octet: Many Very Egotistical Malcontents Just Screwed Up Nomenclature.

Carnival(s)!

• Edition #3 of the physical sciences carnival Philosophia Naturalis is up at Geek Counterpoint. Lots of interesting stuff there - and I'm not just saying that because my Hawaii earthquake post is included.
  
  
• The new installment of the more venerable Tangled Bank is also up over at Easternblot.
  
  
• And it seems there's enough cool anthropology stuff out there in the blogosphere to merit a dedicated carnival - The Four Stone Hearth - three stones of which are currently piled up at Afarenis.
  

Nuclear seismology

A barely remembered anecdote, the recent talk of detecting nuclear explosions, and a Web of Knowledge search combined to bring this paper up on my screen:

Seismic tomographic inversion of Russian PNE data along profile Kraton [1]

The acronym ‘PNE’ is made more explicit in the next result:

Origin of upper-mantle seismic scattering – evidence from Russian peaceful nuclear explosion data [2]

That’s right – PNE stands for ‘peaceful nuclear explosion’, a phrase from a simpler time when people seriously advocated using nuclear explosives to dam rivers, create new anchorages, and release gas from underground reservoirs (which, shockingly, turned out to be radioactive). Both the USA and USSR engaged in this interesting pastime, but the Soviets detonated 239 PNEs against the Americans’ 28, a disparity that is probably due more to the relative power of each country’s citizenry (I suspect even in those days. if given the choice very few people would fancy a close-up view of mushroom clouds) than a difference in official enthusiasm.

Anyway, it seems some Russian geologists had the bright idea of using PNEs to undertake controlled source, wide-angle seismology on a scale not achieved before or since. They arranged to have a series of nuclear explosions set off along a number of lines (with names like 'Quartz' and 'Kraton') stretching several thousand kilometres across the USSR, along which they also deployed seismometers. Unlike reflection seismology, where only the reflected seismic energy coming directly upwards from buried discontinuities such as boundaries and faults is collected, wide-angle seismology deploys seismometers a long way from the source in order to pick up refracted seismic energy; because the speed of sound generally increases with greater depth (and pressure) in the Earth, due to Snell’s Law of Refraction downward-travelling waves eventually curve back upwards towards the surface. If you get far enough from the source, not only will a seismometer pick up these deep-diving waves when they reach the surface, but because of their higher average speed these waves will actually reach that seismometer before ones that have travelled at shallower depths. The distance from the source at which the ‘first arrivals’ from different depths first appear provides a great deal of information about the velocity structure, and hence the physical structure, of the subsurface rocks along the survey line (simply put, earlier appearance of deep waves=faster velocities – although obviously it’s a bit more complicated than that, especially when you factor in the presences of sharp discontinuities in wave-speed across lithological boundaries).

Methodology wise, there is quite a large overlap between these wide-angle techniques and earthquake seismology. However, because the source in this case is man-made, you minimize some of the major uncertainties which limit resolution when your source is a natural earthquake: the exact time and location that the source wave was generated, and the nature of the original signal (as I’ve discussed in the context of the North Korean test, man-made seismic signals are generally much shorter and simpler than an earthquake signal). The frequency of the signal is generally higher, too, which also improves resolution. There is however, one major drawback: the airguns (or less commonly nowadays, conventional explosives) used in seismic experiments produce orders of magnitude less energy than an earthquake does, meaning that pretty much all of the waves penetrating below the crust-mantle boundary (Moho) –about 35-40 km below the surface in normal continental crust - dissipate before they can get back up to the surface. The figure below shows the inferred paths of seismic waves picked up along a wide-angle survey line in the Aleutian Islands (the source is located in the centre, the scales are in km) [3].


Whatever your feelings about the rationality of using nuclear bombs in this way, you can’t deny that they’re going to generate a hell of a lot more energy, allowing signals from deep in the mantle to be received back at the surface. Here’s a similar figure for the ‘Kraton’ PNE seismic line (from [1]. Note the change in horizontal as well as vertical scale: whereas seismometers 2500 km away from the source are fairly pointless for normal wide-angle surveys, for a PNE shot this is about the point that first arrivals from the 660 km discontinuity start arriving. Which I can’t help being a little bit impressed by.


The second of the two papers I’ve cited concentrates on the uppermost mantle, 100-200 km beneath the Earth’s surface. The waves travelling through this region appear to be travelling slower than in the overlying rock, and are also being scattered a lot, resulting in noisy first-arrivals data (the relationship between the arrival time and the distance from the explosion is not linear). The authors propose that this is because the mantle at this depth is partially molten. It seems that the unique data generated by these 30-40 year-old experiments is still reaping dividends, now that scientists worldwide can access them and apply the latest processing tricks.

References
[1] L Neilson et al., Geophysical Research Letters 26(22), p 3413-16, 1999.
[2] L. Neilson et al., Geophysical Journal International154, p 196-204, 2003.
[3] D Shillington et al., Geochemistry Geophysics Geosystems 5, Q10006, 2004 [doi]

Lego weapons redux

This must be a real pain to reload...

My democratic experiment continues

In slightly more encouraging news, I received a response to my e-mail to John Denham about the activities of Truth In Science. I reproduce it below:

Thank you for your email asking me to sign EDM 2708.

Although Early Day Motions can be a helpful expression of back bench parliamentary opinion, I feel that they are somewhat over used and their impact somewhat diluted. For this reason I only very occasionally add my name to EDM's.

Nonetheless your letter has prompted me to consider the issues you have raised carefully and I have therefore written to the relevent ministers on your behalf.

I will contact you as soon as I receive a detailed reply,

Yours sincerely

JOHN DENHAM MP
SOUTHAMPTON ITCHEN

Well, it's slightly up on 'John thanks you for your interest and will take the matter under consideration', but it still has a slight form letter quality to it, doesn't it? It's a little disappointing that he won't sign the EDM, but the fact that he has forwarded my concerns up the chain of command means that my letter pretty much had the desired effect. Besides, I can see his point - EDM 2708 has collected 39 signatures so far, which isn't nearly enough to make it stand out from the crowd, and his spell as a government minister (before resigning over the Iraq War) has possibly given him some insight into how muchlittle EDMs actually register at the highest levels of government.

So, a cautious thumbs up to my local MP; it will be interesting to see what, if any, response will be forthcoming from 'the relevent ministers'.

Update: I’m not the only one who’s been writing to their MPs about this, and via Pharyngula, I see that Postblogger is currently leading the ‘most unhelpful response’ category: his un-named (Tory?) MP responded with

I would be very happy to act on this matter as soon as you can prove beyond all reasonable doubt that Creationism is not true, and I look forward to hearing from you as soon as possible.

Two apparent successes though: Mark Frank’s MP Sandra Gidley, a Liberal Democrat, told him she was signing up (although she’s yet to appear on the on-line list of signatories), and outeast seems have had a hand in getting Liam Fox to sign (as he’s the Shadow Defence Secretary, we can safely say that not all Tories are with the forces of ignorance on this one). I’d be interested to hear of any other successes or failures, which I'll add below

• Sharon Hodgson (Labour) at prompting of Jim Windram.
  

Tony Blair likes science, but he doesn’t understand it

Not, at least, if this interview with New Scientist is anything to go by (there’s even a podcast if you want to hear everything, and discussion continues at the New Scientist newsblog). The interview starts with Mr Blair telling us that he was ‘very poor at science at school’, and has only really started to appreciate its importance after he became leader of the Labour Party and PM. Sadly, it quickly becomes apparent that this appreciation is limited to the economic benefits. In a series of questions, the interviewer, New Scientist Editor Jeremy Webb, gives Blair numerous opportunities to exhibit some understanding of science as a process of discovery, but he doesn’t get very far. Here’s the best we get:

How do you bridge the gap between science as an academic interest-discovering more about the universe-and science as an commercial enterprise?

You need a certain amount of pure research, and the excitement and creativity of scientific discovery. But if you also have universities and research centres sufficiently in tune to what is going on in the private sector, then hopefully discoveries will be made that have a real utility.

I actually have few problems with a political leader wanting to maximise the practical and economic benefits of cutting-edge research; what does concern me about this exchange is the Prime Minister’s apparent conception of ‘pure research’ as a nice add-on to the scientific enterprise, rather than its foundation; the most novel, and therefore valuable, innovations are generally unexpected spin-offs from untargeted research into general problems. As an example, who would have thought that studying bacteria which live in hot springs would eventually lead to PCR?

Far more disturbing, however, are the later parts of the interview, which show that this misunderstanding is merely an expression of a much deeper malaise: Blair doesn’t get science as a way of thinking. Take this suggestion that scientists should pick and choose their interventions:

My advice for the scientific community would be, fight the battles you need to fight. I wouldn’t bother fighting a great battle over, say, homeopathy. It’s not going to determine the future of the world.

That’s right: we should just ignore the fact that homeopathy is rubbish. We should stay quiet while practitioners both cynical and deluded convince people to accept comforting myths (you don’t need nasty drugs to get better, just specially treated water!) in preference to reality, promote anecdotal and testimonial evidence over properly controlled experiments, and assert unopposed that the products of modern science are ‘unnatural’, and that its practitioners are either blinkered or corrupt. And then we should wonder why they don’t accept our arguments that the MMR vaccine doesn’t cause autism, that GM food is safe to eat, and that we are going to have to seriously change our lifestyles to prevent catastrophic climate change.

Despite his assertion to the contrary, I think Tony Blair still sees science as ‘something that the “boffins” do’. It’s not. In the modern world everyone needs the informed scepticism of scientific thinking in their mental toolkit. People need to be encouraged to rigorously test their opinions against the ultimate arbiter, reality, and be open to refining them when the facts require it; to not take assertions at face value, no matter how charismatic or authoritative the proponent; and to be aware of the biases and prejudices which can cloud their perceptions. Believing that homeopathy is a valid ‘alternative’ to modern medicine is anathema to this kind of thinking, an indicator that people have, at best, a poor grasp of science, and are therefore unlikely to come to informed and rational opinions on other scientific issues; at worst, they are suspicious of and even openly hostile to phrases like ‘scientific consensus’. How can we not fight to correct that?

Blair expresses a similar attitude with regards to the teaching of creationism, it’s not a problem really, not a battle we need to fight:

This can be hugely exaggerated. I’ve visited one of the schools in question and as far as I’m aware they are teaching the curriculum in a normal way. If I notice creationism become the mainstream of the education system in this country then that’s the time to start worrying.

Sorry, but this is weasel. I don’t care if they’re being subtle about it, I don’t care if it’s just a few faith schools or academies: anywhere where creationism is taught in science class, you mangle whatever meagre understanding of science, and scientific thinking, that person might have got out of our education system. The present situation is worrying; when it becomes mainstream, that’s when you emigrate, because (as others have rightly opined) it’s too late.

I’m sure it’s completely coincidental that these comments come in the face of heavy criticism of the government’s recently implemented policy of labelling homeopathic treatments as if they’re real medicines (which is rather handily smacked down by Sarah over at Bunsen Burner), and their current evangelism for faith schools and letting suspected creationists fund new academies. And that Blair’s suggestions of important issues where he thinks scientists should engage the public – climate change and genetics – are the ones where scientific opinion tends to chime with government policy. The Prime Mininster is betraying his legal background: contrary to his enthusiastic noises, he does not seem to want a electorate that is truly scientifically literate, but one that will accept scientific authorities as expert witnesses in support of government policy.

Sadly, he doesn’t seem to realise the inherent danger in the idea that you can selectively use science to support the ideas that you agree with, and ignore it when it conflicts with them; if you pick and choose, what’s to stop other people doing the same – and choosing differently? That, Prime Minister, is the essence of antiscience.

THC not as weak as we thought (most of the time)

Following up from last month, the first results from the real-time monitoring of the thermohaline circulation were presented by Harry Bryden at the RAPID conference in Birmingham last week. I wasn’t there, so you should go to RealClimate and read Gavin’s analysis, as he was. This quote sums up the major news:

There were two key observations: first, that the approximations that had been used in the Bryden et al study were actually valid, and secondly, that the variations day by day varied by around 5 Sv (1 Sv is about 10 times the flow of the Amazon). The mean over the year for the MOC was 18 Sv.

It seems that over timescales of a few days there are fairly sizeable shifts in the amount of North Atlantic Deep Water (NADW) crossing the 25^oN transect. These results pretty much destroy any hope of extracting any meaningful long-term trend from the existing data set of decadally spaced, one-time snapshots of the circulation; the ‘weakening’ from 23 to 15 Sv since 1957 proposed in Bryden et al.’s Nature paper last year is very close in magnitude to the observed natural variability (and their 2004 hydrographic section underestimated the average strength of the present circulation by 2 Sv). In an interview with the BBC, Bryden still seems fairly convinced there is some weakening of the circulation (by 10% in the last 25 years rather than 30%), but I think the jury’s out on even that at this stage.

I’m wondering whether Nature is going to follow up on the fact that one of their headline papers was a little premature (no luck so far...), but as Gavin points out, the media seem to have missed the down-sized estimate in their excitement over the curious 10 day period in November 2004 when the southwards flow of NADW was weak to non-existent (see here, for example). According to someone else I know who attended the talk, Harry Bryden ‘just dropped this in’, and it’s certainly not in his abstract. Why? Because at the moment no-one really has any idea how this could happen. To understand the confusion we need to look a little further north. NADW is principally formed by cold saline water sinking in the Norwegian Sea, but as the figures below shows, the route south is not simple, because it’s path is along the seabed is blocked by the Greenland-Scotland Ridge (GSR), part of the volcanic edifice which Iceland sits atop of. The top figure[1] shows how the GSR acts as a sort of dam, with three or four ‘sills’ at bathymetric lows acting as spillways which spilt the NADW into different currents. The bottom figure [2] shows how these currents all join back together at the southern end of Greenland and head south as one big water mass.

Why is this important? It means that the apparent shut down of the THC is not because there was a temporary hiatus in NADW production (due to, say, freshening of the surface waters due to particularly strong seasonal melting in the Artic). The different routes taken by the NADW over the GSR all take different times, so any cessation in downwelling would not simultaneously cut off all the currents coalescing south of Greenland. There will always be some water. So, if this is a real signal, the whole water mass seems to have somehow been held up in the northern Atlantic somewhere, which seems a little weird. We scientists like weird, or course, but at this stage we need more data: how often do these ‘mini-shutdowns’ happen? Are they seasonal/cyclical or random? I think much more interesting stuff is going to come out of this array over the next few years – not least a robust estimate of the longer term trends in the circulation.

Newer developments:
The Case of the THC "Shutdown"


[1] From Wright & Miller (1995), Paleoceanography 11(2), p157-170.
[2] From Dickson & Brown (1994), JGR 99(C6), p12319-41.