My blog lives up to its name

Further update: Highly Allochthonous is now found at:

http://all-geo.org/highlyallochthonous.

I am beginning to theorise that this is a cast iron example of nominative determinism.

When I started blogging, I had no real idea where it would lead. I didn’t know whether I would, or could, produce regular content; or whether anyone else would read it if I did. After a sluggish start, I found that the answer to the first question was yes. As for the second, the number of visitors to this site has been slowly but surely increasing, especially over the last few months; I could hardly claim to be setting the blogosphere alight, but I was reasonably content with progress.

But then, in a rather bewildering fortnight at the end of January, not only do I get the Naturejobs gig, but an e-mail arrives out of the blue from Scienceblogs, inviting me to the top table. And, as such, Highly Allochthonous is on the move; please click through to its shiny new home at http://scienceblogs.com/highlyallochthonous/.

To be honest, I’m still not sure whether I’ll be able to hack it with the big boys (I certainly won’t be able to match the prodigious output that some of them achieve), but it’s an exciting opportunity to get a wider audience. Of course, I’m hoping everyone who has already discovered me will drop in every so often, if only to brag that you read me “in the glory days, man, before he decided to play it safe and post nothing but pretty pictures!”

The bureaucratic run-around

This morning, armed with my contract and my passport, I set out to register at my new academic home. I was told that I needed to go the International Office, which proved to be the starting point of a rather long and convoluted morning of being shunted around campus:

• The staff at the International Office tell me I need a student number from Biographics department.


• I head downstairs to the Biographics department, who tell me that before they can give me a student number I need to go to the Science Faculty Office to get the relevant form.


• Across campus at the Science Faculty Office, after some confusion I get given a form, which seems more like a student degree application form than anything else, and get told that at some point I will need to pay a fee to ‘unblock’ my registration.


• Back at the Geology department, after checking that I’m not literally on a wild goose-chase, I fill in the sections of the form which actually seem relevant.


• Back to Biographics, who tell me that the form needs to be stamped by the International Office.


• Upstairs at the International Office, they stamp my form, but tell me that my account must be unblocked my paying the fee at the Finance Office.


• I venture the other way across campus to the Finance Office, where I queue for 20 minutes or so to pay the fee.


• Back in once more to Biographics and finally get my student number.


• Return in triumph to the International Office – they give me yet another form to take back to Finance (I’m starting to think that my first visit – and payment – was unnecessary, but no-one seems sure).


• After shuttling between a couple of people in the Finance Office, they tell me I am now ok to register at the Science Faculty Office.


• I return to the Science Faculty Office, where they discover my account is still blocked. After 10 minutes of phoning around (what a novel concept!) I finally get registered.

I was an undergraduate at a University that has had eight centuries to perfect its administrative opacity, but I have to admit, I’m thoroughly impressed. At least I can say that I got some exercise this morning, and got a lot of practice in finding my way around the campus.

If at first you don't get published in Nature, cheat

Just a quick plug whilst I settle in down here in Jo'burg...

Actually, I've never even tried to get properly published in Nature - I've yet to stray into fields of study that are 'sexy' enough. Nonetheless, thanks to the mysteriously vanished Postblogger's heads-up, I'm getting the chance to sneak a few words of wisdom into print, as one of this years' four Postdoc Journal keepers. 200-250 words a month might not seem like very much wisdom, but I know some very long words...

My first entry was published the Thursday before last. Quite why I was deemed worthy is uncertain - I suspect that my exotic post-doc destination probably helped matters, but I suspect that all the writing practice I've had on these pages in recent months probably helped too.

In transit

The last week or so has been... intense. The speed at which moving to another country went from a theoretical possibility to imminent reality caught me completely unawares, and I suddenly had a million things to do and too little time to do them in. Somehow I got most things organised, I suspect more due to luck than judgement, and now - with a few hitches - I'm on my way.

What's weird is that not only do I not know what to expect when I arrive in Johannesburg, but I've been so focussed on the departure date that I haven't even thought about it until now. A 12-hour flight lies between me and finding out.

Valentine’s Day Massacre

Other people may have received cards telling them how wonderful they were yesterday – but not me. Instead, I got a nice long e-mail from JGR regarding two papers I submitted way back in June (which I have alluded to previously) which was about as far from ‘roses are red…’ territory as you could get.

I haven’t really talked about the research behind these papers on this blog (I guess I didn’t want to pre-empt publication, somewhat ironically), but they were basically presenting the major conclusions of my PhD project – a study of the tectonic evolution of New Zealand in the last 20 million years, using paleomagnetic measurements to look at crustal rotations. My first paper presented my dataset, which took a lot of work to amass, and the second was my attempt to construct a model of deformation to explain these data.

I’m still chewing over the reviews (they’ve hardly arrived at a convenient time!), but the basic gist seems to be that they don’t like my data - although they couldn’t really find much wrong with it – and they really don’t like my model. They were very keen to point out to me that accommodating the large and fast crustal rotations my data seem to indicate (much larger and faster than has previously been suggested) is not easy, and my suggestions for how it has happened are a little bit at odds with the well-established picture. Never… anyway, there’s a lot to filter and think about, which obviously I don’t have time to do at the moment, so for now I’m just going to have to go:

AAAAARRRRRRRRRRGGGGGGGGGGGHHHHHHHHHHHH!!!!!!

instead.

How to waste even more time with Google Earth

I dare you to visit this rather funky map quiz and not get addicted.

My only complaint is that the pictures containing nothing but ocean floor are a little bit too difficult...

(thanks to Ron).

Wasting your life, creationist style

I suppose as a geologist I should feel angry and aggrieved about this newly minted PhD student:

…Dr. Ross is hardly a conventional paleontologist. He is a “young earth creationist” — he believes that the Bible is a literally true account of the creation of the universe, and that the earth is at most 10,000 years old.

For him, Dr. Ross said, the methods and theories of paleontology are one “paradigm” for studying the past, and Scripture is another. In the paleontological paradigm, he said, the dates in his dissertation are entirely appropriate. The fact that as a young earth creationist he has a different view just means, he said, “that I am separating the different paradigms.”

Later in the article is becomes fairly clear that his motivation for getting his doctorate is to use “the fact that he has a Ph.D. from a legitimate science department as a springboard [for pushing a literalist viewpoint].”

I can’t bring myself to be angry about this, though (even though I can understand why others might). Instead, I find it sad; a waste of half a decade or more of someone’s life. Getting through a PhD is no picnic at the best of times; in my experience it’s only your fundamental enthusiasm and interest in your subject that gets you through. Forcing yourself through the whole traumatic process when you believe, deep down, that every word you write, every measurement you make, and every conclusion you draw is fundamentally mistaken – well, let’s just say that I can’t see it doing wonders for your mental well-being.

Over at PZ’s (where this story came to my attention - see also Chad's take), a large proportion of the comments are debating whether the University of Rhode Island would be justified in withdrawing his doctorate - or even, given that they knew about his young-earth beliefs before he applied, whether he should have been admitted to the PhD programme in the first place. I’d have to unequivocally answer no, and yes, respectively. In the context of a PhD you can only be judged on what you have submitted, and his supervisor tells us all we need to know:

His subject was the abundance and spread of mosasaurs, marine reptiles that, as he wrote, vanished at the end of the Cretaceous era about 65 million years ago. The work is “impeccable,” said David E. Fastovsky, a paleontologist and professor of geosciences at the university who was Dr. Ross’s dissertation adviser. “He was working within a strictly scientific framework, a conventional scientific framework.”
…
“We are not here to certify his religious beliefs,” he said. “All I can tell you is he came here and did science that was completely defensible.”

Presuming that this is an accurate representation of his dissertation, it’s a no-brainer: he came, he followed the rules, and he advanced his field: so he earned his doctorate, however galling it may be that he has proceeded to use his qualification in the manner that he has – to add a veneer of scientific authority to flawed creationist arguments.

Besides, there’s something else interesting about this story: the fact that when push came to shove, to get his qualification he had to follow the ground rules of science. And when he did that, what happened to all those big, obvious, gaping holes in the scientific picture of an old earth and common descent that we hear so much about? Did he try, even slightly, to cast some light on those holes with his research? It doesn’t look like it to me. Rather than a bold assault on the evil Darwinian empire, we get some meandering about “working within a particular paradigm of earth history”. Likewise, despite his self-declared mission to destroy Darwinism, it seems that Johnathan Wells kept his powder dry during his time at Berkeley. In both cases, the choice to use the PhD qualification as a rhetorical weapon, rather than the PhD research, pretty much tells you all you need to know.

Contestants, raise your hammers...

From the Berkeley Geological Association blog (with some snipping):

Geolympics is the ultimate in field geologist competition. This yearly event should put to the test all the field practices geologist's are trained to perform with accuracy and time contraints as parameters of success.

1) The Brunton: Imagine 5 or so rocks with varying strikes, dips, slickenlines, etc. that need measuring whilst being timed.

2) Rock Demolition: Imagine a line of geologists armed with a basketball size chunk of granite and their favorite rock hammer. They are timed to see who can smash their rocks into chunks no bigger than a baseball.

3) Twisted Map Folding: Imagine a new crisp map completly unfolded and a geologist blind folded who must then, by feel alone, fold the map into its original orientation while being timed.

4) Gear Up Gear Down: Imagine a geologist pulling up his/her truck when the clock starts and they must exit the vehicle and gear up with boots, hand lens, brunton, hammer with loop, acid bottle, map, rain gear, the works then when complete screaming ROCK IT! and then undressing again into street clothes, packing away the gear and firing up the truck again.

A few more potential events occur to me:

• Contact free running: A test of mapping skill and athleticism. Contestants have to precisely follow a contact between two formations, across hill, dale, ravine, cliff face, river, bracken, and bog. Points for speed, accuracy and style.
  
• Drilling time trial: One for the paleomagicians amongst us. Contestants are given an hour to drill, orient and extract as many core samples as they can. Scoring is based on the length of the cores as well as the number (i.e. an 8cm core which yields 3 standard paleomagnetic samples scores the same as three cores which yield only one each). Solo and pair events.
  
• Geo-orienteering: Like orienteering, except you have a geological map and specified rock samples must be gathered from each control point.
  

I'm sure you guys can come up with some more events...

Reality intrudes on blogging

You might have noticed that things fell silent here only two days into my promised seven-day epic. As it has turned out, the reasons I prevaricated about signing up to the Just Science challenge in the first place have defeated me: exam marking to get through, a couple of presentations to give, and, due to the fact that next week is my last week here in Southampton, lots of departmental loose ends to tie up. As if that weren’t enough, just when I’d figured that the South African Consulate were going to tell me to get lost, on Wednesday my passport came back with a nice visa stuck in it. It’s really happening – in two weeks, I shall be arriving in South Africa to start my new job. Which means that I have quite a lot to get done between now and then...

Anyway, although I had a number of half-completed posts lying around, and I believed that I would have enough time to polish and post one up every day, I have ended up being too busy, or too tired, to really give them they attention they deserve. And, if I’m honest, my motivation was also sapped by the realisation that for some reason, my posts were appearing in the Just Science aggregator dated as 1969 or something, and were not appearing in the RSS feed either.

However, whilst I have failed miserably, at least one geoblogger is making a good fist of it: Brian is going from strength to strength with a great series of posts on sedimentary geology. I particularly liked Wednesday’s post about the modelling of depositional systems in big tanks.

Stalagmite records individual storms and intensities

In last months’ post about climate records from stalagmites and other speleothems, I concentrated on their potential for giving us detailed regional climate information over long time periods: 10s, and even 100s, of thousands of years. However, this article at Mongabay.com highlights some research concerned with records preserving climatic variations over much shorter timescales, and one of the more contentious issues in modern climate research: how the frequency and intensity of hurricanes is affected by our warming climate.

It seems that the towering storm clouds and humid atmosphere associated with hurricanes and other tropical cyclones produce rainwater which is extremely light isotopically (it has &delta¹⁸O 6 per mil more negative than normal precipitation), and a lot of it falls in a short time when a storm hits land. Amy Frappier and her colleagues decided to test if this pulse of storm water could affect the &delta¹⁸O of the groundwater enough to leave a signal in speleothems growing in underlying caves.

We used a computer-controlled dental drill to carefully mill off layers of powder from a fast-growing stalagmite [from Actun Tunichil Muknal caves, Belize], where each sample reflects cave drip water over periods of a week to a month. Analyzing these rock powders using standard techniques, we were able to detect brief spikes from recent hurricanes and tropical storms that produced rain over the cave - even when those storms struck only weeks apart!"

The effect is clearly illustrated by this figure from a paper Frappier et al. have just published in Geology [1]. Tropical cyclones which have hit Belize in the last 30 years (A) correlate well with short negative excursions in &delta¹⁸O (B). These excursions are superimposed on a longer-term pattern related to the El Nino Southern Oscillation (the 15 month offset with the El Nino record in C represents the time it takes rainwater to percolate from the surface to the cave). The accompanying carbon isotope record also shows the El Nino variation, probably due to changes in soil respiration rates, but not the storm events, showing that they are due to a separate forcing (heavy storm precipation).


The final subfigure D is interesting, as it indicates that stronger storms (plotted in A) seem to produce larger excursions. Going back to the Mongabay piece:

"We also found that the relative size of spikes that we measured was related to the intensity of the storm, which is encouraging for the prospect of reconstructing the intensities of pre-historic landfalling storms.."

There’s currently a lot of debate over possible changes in storm numbers and/or intensity as a result of anthropogenic climate change (RealClimate has a good summary of the science) – some people claim there is already a clear signal, but others say that the historical data just isn’t good enough. Speleothem records can’t help resolve one of the major issues, the detection of non-landfalling storms, but it seems that they can potentially give us a much longer term record of trends in tropical cyclone intensity than is currently available; and a better idea of how much natural variability there was in the past can only help.

[1] Geology 35, p111-114 (doi).

This post was published on Day 2 of the Just Science challenge – a full week of science and only science. You can subscribe to the RSS feed at http://www.justscience.net/?feed=rss2.
All my posts for this week

Spot the planetary difference

There are many differences between Titan’s atmosphere and Earth’s, in terms of temperature (a couple of hundred degrees lower) and composition (no oxygen, more methane), but the cloud formation recently snapped above Titan’s north pole by Cassini, shown in the top image above, doesn’t look too dissimilar from storms snapped from our own planet’s orbit, as the lower image (source) illustrates. At 2400 km in diameter, it is quite a whopper - it would fill most of the North Atlantic.

It’s not that clouds haven’t been imaged on Titan before; we managed that even before Cassini arrived in Saturnian orbit, and Cassini itself has imaged some before now as well. But those previously observed cloud systems were mainly located around the south pole of Titan; what’s interesting about this one is that it is in the opposite hemisphere, directly above the lakes which have caused so much excitement. This makes it extremely tempting to link the two phenomena. The northern hemisphere of Titan is now entering its spring after a seven-year winter, so evaporation from these lakes in the rising temperatures could easily have contributed to the formation of clouds.

The key question, though, is what happens then: do significant amounts of hydrocarbons rain back out of the atmosphere to complete the “methanological cycle”? Is this precipitation intense enough be actively eroding out the landscapes imaged by the Huygens lander on its descent, and produce standing bodies of hydrocarbons in depressed topography? Or, rather than being refilled from above, are lakes on the surface more to do with hydrocarbon release from either subsurface “methanifers”, or cryovolcanic venting?

Some of these questions are still open. During Huygen’s descent, it measured variations in atmospheric methane concentration and temperature which, when examined in detail, indicated the presence of thin methane clouds capable of generating a persistent light drizzle [1]. Such weather makes the surface of Titan the natural location for any British extraterrestrial colony, but it is not really energetic enough to carve new drainage channels or any other new topography. And although attempts to model Titan’s atmosphere do suggest that strong storms can occur [2], how common or important they are in reality is unclear. Effectively, what we need is more observation time. Just like continuous observations of Mars over several years have revealed changing features which might indicate actively flowing water, if Cassini is able to observe Titan for long enough, we might not only see a few storms but also be able to assess their effect on the landscape.

[1] Tokano et al., 2006. Nature, 442, 432-435, [doi].

[2] Hueso and Sánchez-Lavega, 2006. Nature, 442, 428-431, [doi].

This post was published on Day 1 of the Just Science challenge – a full week of science and only science. You can subscribe to the RSS feed at http://www.justscience.net/?feed=rss2.
All my posts for this week

Prepare for 7 days of pure science

After a lot of dithering, I've signed myself up for the Just Science Challenge:

we would like to propose a Week of Science, to begin on Monday, February 5, and end on Sunday, February 11. During that time each blogger should post about science only, with at least one post per day. Furthermore, issues which are favored by anti-scientific groups (creationism, global warming, etc.) should be either avoided, or discussed without reference to anti-scientific positions.

I like to think I am fairly science-focused anyway, or at least that my digressions into other realms do not overwhelm the geology. But I like the idea of having a week where we don't let creationists, denialists and the other forces of antiscience dictate any of our output. Besides, it's always nice to stretch myself, and a post a day is enough of an increase in my average output to be a nice challenge, even if I've cheated a little by putting in a fair amount of preliminary groundwork.

A day in the life

Lab Lemming wants to know what I do in a typical day. I’m not sure I have a “typical day”, but today is as good as any other I suppose.

Job title: Paleomagnetism technician (bear this in mind for what follows)
Insitution: School of Ocean and Earth Sciences, National Oceanography Centre, Southampton.
Date: Friday 2nd February, 2007

Prevailing conditions:

• The deadline for handing in the third year mapping projects is Monday
  
• Semester 1 exams have just finished
  
• Our cryogenic magnetometer is not being used this week because we need a helium refill (which was going to be done this morning but has been put back to Monday).

8:30-8:45: Walk into work
8:50: Switch on my computer and open exam paper to mark.
8:55: Computer beeps – student has e-mailed wanting me to check their map before they print it
8:55-9:15: In computer room consulting with stressed and sleep-deprived student.
9:20: Get back to my office to find another pile of exam scripts on my chair. This lot really liked my question, it seems.
9:20-10:00: Marking
10:00-10:15: Another student wanting help with his cross-sections
10:30-10:45: Yet another student; this one wants his report abstract checked, and reassurance regarding the word limit.
11:00-11:20: In lab to show a fourth year undergraduate how to do susceptibility measurements (for their dissertation project).
11:30-11:45: Get fed up with constant interruptions and go and have coffee.
11:50-12:00: Dragged back to the lab by panicky student who thinks she’s broken the computer. She hasn’t, it’s just so old (DOS, no less) that she doesn’t really get how it works.
12:00-12:45: Marking.
(12:25: Course co-ordinator pops in to check that I have got the latest batch of exam scripts. He’d like them back early next week (!) )
12:45-12:50: Some more students, this time people doing 4th year dissertation who want to book some lab time.
12:50-1:30 pm: Lunch.
1:30-2:45: Finally get a moment of quiet to get through some marking. Promisingly, most appear to be written in a language resembling English.
2:45-3:00: Start sending out e-mails about laboratory schedule for the coming weeks (given that it’s going to be chaos when I leave, I want to make sure everyone has some machine time).
3:00-3:30: Reinvaded by stressed students.
3:30-3:45: A bit more marking.
3:45-4:30: More mapping consulation down in the computer room with even more stressed and sleep-deprived students.
4:30-4:45: Need caffeine.
4:45-5:00: Work on lab schedule for those who have bothered to respond to my e-mails.
5:00-5:30: Finalise marks on first exam question. Two more to go!
5:30-5:45: Tidy stuff up before heading to the pub for a well-earned pint or three.

It’s not like this every day – Thursday was spent mainly trying to sort out someone’s misorientated sample data, Monday will mainly be spent sorting out the helium refill. The common theme, perhaps, is that of me doing a lot running about on other peoples’ behalf.

I’m passing this on to Transient Reporter (assuming that he’s not snowed under changing nappies, I don’t really want to hear about that) and Thermochronic, but everyone should pile in. Now, where's that pint...

Linking up

Philosophia Naturalis #6 is up at Science and Reason. Lots of physical science goodness, but scandalously no geology - which is at least partly my fault for not getting around to submitting any suggestions. Perhaps our growing band of geobloggers should fortify ourselves with gin and tonic and gatecrash next months edition at Geek Counterpoint.

On that subject, you may or may not have noticed the new occupant of my sidebar - an amalgamated feed of recent posts from all the geobloggers I'm aware of, created using Google Reader's nifty 'share' function. I thought it was a convenient way of making all (any) of my readers aware of what everyone else in the geoblogosphere is up to. At the rate it's been ticking over in the last week, quite a lot.

Anyone is welcome to hijack the feed (if you can't find the relevant script in my source page, let me know and I'll send it to you) - the more cross-linking the better for all of us, I reckon. And if you write (or know of) a geoblog I've yet to include, drop me an e-mail.

Lusi – the man-made mud volcano

The latest from Lusi

In May 2006, an exploratory gas well being drilled in eastern Java hit a limestone aquifer. Because the lower part of the well had not yet been ‘cased’ - sealed off from the surrounding rock - a surge of overpressured water was released into the mudstones higher in the borehole, fracturing them and mixing them into a hot mud which eventually made its way to the surface near the drilling rig.

Since then, since then, 7,000-150,000 cubic metres of mud* a day has been disgorged from a vent dubbed ‘Lusi’, burying surrounding villages. I found this video on You Tube showing the encroachment of the mud – a rising tide which shows no sign of stopping.

From a more elevated perspective, here’s a satellite image. I think those huts on the bottom left of the second panel are the ones you see at the end of the video


This is from a recent GSA Today paper by Davies et al.[doi], which confirmed that the drilling into the aquifer was probably responsible for the eruption; the company operating the well (understandably) tried to implicate an earthquake which occurred two days beforehand, but any seismogenic effects should have been immediate (and detectable as a pressure change in the borehole), and ‘liquefaction’ tends to affect less cohesive sands more than mud.

You can read more on this at PhysOrg. Then read how they’re planning to put a stop to it:

Indonesian geophysicists hope to stem the flow of a destructive mud volcano on East Java by dropping chains of concrete balls into its mouth…

… Last week, the government team tackling the disaster approved a plan that will use 1,000 steel chains to try to slow the flow of mud. Each chain is 1.5 metres long and links together four concrete balls — two that are 40 centimetres across and two that are 20 centimetres across. Each ball and chain set will weigh about 300 kilograms. The balls themselves will be modified to maximize their friction with the mud.

Apparently, they think this will restrict the flow without just causing it to divert somewhere else. I suppose it depends on how fractured the rock is, but I’d say it’s a long shot at best.

Update:And, a month later, this rather bizarre plan swings into action. On Saturday, they only managed to drop one chain because a steel cable on the hoisting mechanism broke. They managed sixteen more on Monday, but then they hit another potential snag when they looked at the telemetry from sensors attached to the chains, as another site has reported under the arresting title ‘Volcano consumes concrete balls’:

The balls slid one kilometre into the crater, roughly twice the depth anticipated, so many more than planned may be required to staunch the mudflow, said the operation's spokesperson Rudi Novrianto.

"Based on our monitoring of Monday's operations, we may later decide to add to the number of ball chains, but the decision will only be made once the initial target of 374 chains have been dropped into the mud hole," he said…

…Basuki Hadimuljono, the head of the team trying to plug the steaming crater, was quoted by the Koran Tempo newspaper as saying that the number of chains required may rise to 1 000 from the initial estimate of 374.

I remain unconvinced that this is going to work, but you can’t fault their perseverance.

(Thanks to Geology News for the heads-up which led to the update).

*In media units, that’s up to 40 olympic swimming pools.

Fiddling while my blog burns

I've been putting off the switch to the new blogger template system because, like Propter Doc, I've been having trouble getting the expandable post summaries to work properly. Rewriting the javascript which did the trick on my old template to use the new metadata labels, and get past a seemingly much fussier XML parser, proved to be a long exercise in fiddling, but I've finally managed it. For those who are interested, this is the code I used. You have to be in the HTML view with the widgets expanded to insert it:

<script type='text/javascript'>
var memory = 0;
var number = 0;
</script>

Then scroll way down the page until you find the div for the post-body and insert the stuff in bold:

<div class='post-body'>
<b:if cond='data:blog.pageType == "item"'>
<style>span.fullpost{display:inline;}</style>
<p><data:post.body/></p>
<b:else/>
<style>span.fullpost{display:none;}</style>
<p><data:post.body/></p>
<script type='text/javascript'>
var permlink='<data:post.url/>';
var title='<data:post.title/>';

var spans = document.getElementsByTagName('span');
var number = 0;
for(i=0; i <spans.length; i++){
var c = " " + spans[i].className + " ";
if (c.indexOf("fullpost") != -1) {
number++;
}
}

if(number != memory){document.write('<p><a href=' + permlink + '>"'+ title + '" continues...</a></p>') }
memory = number;
</script>

</b:if>

<div style='clear: both;'/> <!-- clear for photos floats -->

The bit in brackets in the document.write statement can be changed if you want it to say something different. Now, when you're writing a post, you just stick the bit you don't want to appear on your front page between <span class="fullpost"> and </span>, and off you go!

Note that I didn't write the original code - I've just (I think) bodged it to work in the new system. Here's another way to do it, from someone who looks like he might know what he's talking about, although for some reason I couldn't get that to work either.

I'll be fiddling with other bits of the template in the next few days, so apologies in advance for when I break the HTML (Update: which I see is already the case for IE users. Bloody Microsoft! OK, have fixed it (sort of) although all the posts vanish to the bottom of the page if you shrink the window too much. Seriously, people, get a better browser.

New data on the revision habits of the modern student

In one of the courses I taught last semester, the exam has asked pretty much the same questions every year for the last five years. This doesn’t exactly reflect well upon those doing the teaching, and this year (my second of covering these lectures) I made a deliberate decision to do something a bit different with the questions from my part of the course. The exam is divided into two sections: a ‘numerical’ part focussed on data manipulation and calculating things, and an ‘essay’ part. For the former, instead of asking the usual question about triple junction stability and migration, I gave them a question where they had to assess the quality of some paleomagnetic data and use them to calculate when a terrane (a highly allochthonous one, no less) collided with a larger continent.

I realised at the time that this alteration could potentially act as a useful survey of the study practices of our undergraduates. The question I set was actually pretty easy – if you’d bothered to revise the part of the course about paleomagnetic field tests and calculation of paleolatitudes (I’d even, after some debate, given them the relevant equation, and therefore wondered if it wasn’t a little too easy). However, students in thrall to the art of ‘question spotting’, who only revised the small bit of the course about triple junctions, might be in a little bit of trouble.

Today I received the scripts from the exam; no-one had answered my numerical question. Not one student.

Although that means I have less marking to do, part of me can’t help but find that a little bit depressing. The weird thing is, plenty of people answered one or both of the essay questions I set – both of which asked about parts of the course which previous years' questions hadn't, and at least one of which requires some knowledge of paleomagnetic techniques to answer properly. Maybe then, this just indicates a degree of mental inflexibility (‘It’s not a triple junction question! Panic!’) rather than damagingly limited revision practices. I suppose I’ll find out when I read the essays…

Update: OK, after a bit of investigation, it seems there are a number of factors at play here:

• Of the other two questions in the relevant section, one, on seismic moment and earthquake hazards, has been mixing and matching the same three subsections for at least the last four or five years; the other, on elastic bending of a plate in response to seamount loading, must have been seriously highlighted by the lecturer because I was asked to help with exactly the same question a week before the exams.
  
• I have some testimony to the effect that the students pretty much assumed that ‘my’ question would be of the same type as it had been in previous years (despite the fact that someone else had taught the course for most of those years), and revised (rather selectively) with that assumption in mind.
  
• If I’m scrupulously honest with myself, the way the question was worded might have made it seem that it was a lot more work than it actually was: not every step was explicitly spelt out, and the style (“This is the scenario. This is your data. Calculate stuff” style, rather than “Calculate x. Calculate y. Calcuate z.”) was perhaps a little intimidating. I’m open to the possibility I was also asking to much for a 45 minute question, but sadly I have no data to test that.
  

So, faced with two other questions they had prepared for, and one which they hadn’t and might have looked like a lot of work, the students opted to shun me. I’m not sure anyone comes out of this particularly well, to be honest. In my own defence, I have a fair number of essay questions to mark, so obviously I wasn’t being a fully bastard examiner from hell.

Milankovitch goes solar?

From New Scientist:

Robert Ehrlich of George Mason University in Fairfax, Virginia, modelled the effect of temperature fluctuations in the sun's interior. According to the standard view, the temperature of the sun's core is held constant by the opposing pressures of gravity and nuclear fusion. However, Ehrlich believed that slight variations should be possible [due to instabilities caused by interactions with the Sun’s magnetic field]…

…Ehrlich's model shows that whilst most of these oscillations cancel each other out, some reinforce one another and become long-lived temperature variations. The favoured frequencies allow the sun's core temperature to oscillate around its average temperature of 13.6 million kelvin in cycles lasting either 100,000 or 41,000 years. Ehrlich says that random interactions within the sun's magnetic field could flip the fluctuations from one cycle length to the other.

These two timescales are instantly recognisable to anyone familiar with Earth's ice ages: for the past million years, ice ages have occurred roughly every 100,000 years. Before that, they occurred roughly every 41,000 years.

The paper is up on arXiv, and his model also has an oscillation in the 22,000 year range as well. This strikes me as a mighty big coincidence; it’s not like we’ve pulled the frequencies of variations in the Earth’s orbit - the Milankovitch cycles generally held to control long-term climate fluctuations - out of thin air. One thing I’d really like to know how sensitive the periods of these solar oscillations, if they exist, are to changes in the temperature structure of the sun, which I suspect we haven’t constrained with absolute precision. That said, a solar oscillation in the 100,000 year range might solve the problem of why it’s such a dominant signal in the climate record.

Anyone care to guess how long it will take for someone to claim this somehow has a bearing on the reality of anthropogenic climate change?

Update: Those of you who don't see the disconnect should head over to Open Mind for a clear explanation of why we think that the current short-term warning we're all worried about cannot be attributed to solar variability)

The writing in the cave walls

There’s a really nice post up on RealClimate about extracting climate records from stalagmites. Stalagmites and other speleothems form when water, percolating down from the surface and picking up dissolved carbon dioxide and other minerals on the way, penetrates into a cave system. When it reaches the cool, dry air of a cave, the carbon dioxide can escape from solution and carbonate minerals precipitate out. Take a steady drip of water, leave for a few thousand years, and voila:


The exciting part comes when we look at a cross-section through a stalagmite: just like tree rings, chemical changes in the different carbonate layers - particularly changes in the oxygen isotope values – reflect changes in the water falling on the land above the caves when that layer was deposited, and hence potentially give us high-resolution information about climatic variations over tens of thousands of years. Even better, you can determine the age of deposition using uranium-thorium dating; so what we potentially have is a source of climate records comparable to those we can get from ice cores (allowing us to independently check their chronologies), but globally distributed; you get caves on every continent, not just Antarctica and Greenland.

One thing this lets us look at is the variations in the strength of the monsoon through the last few glacial cycles. In the northern hemisphere summer, air rising above the warming land draws in moist air from the oceans to the south. The resulting rain is isotopically light (it has a negative &delta¹⁸O) because it has become fractionated by more evaporation and transport. A longer, wetter, stronger summer monsoon should therefore lead to lighter groundwater &delta¹⁸O than a shorter, drier, weaker, one; and that is exactly what we see in stalactites in the relevant regions. Here’s a record for most of the Holocene from Oman [1], showing both long term (over thousands of years) and short-term (over decadal and centennial timescales) variations in monsoon strength:


And here’s a longer term record, going back through a number of 21,000 year precessionary cycles, compiled from three overlapping stalagmite records from the Hulu Caves in China [2]. This second figure also plots the average summer insolation (black curve), and the Greenland ice core &delta¹⁸O (which tracks temperature – blue curve). The correlation is very good (especially if you look at a better version of the figure) – suggesting that the monsoon is stronger when it is warmer in Greenland. Centennial scale variations in Greenland have been linked to changes in the themohaline circulation, so these data give us some indication of the global effects such changes can have.


The variations in the monsoon being studied in these papers is a very strong climate signal, but as measurement and analytical methods get more sensitive and sophisticated (for example, the Hulu record has recently been extended back to 180,000 years ago [3]), tracking smaller regional variations in climate will become much easier. These results clearly show how, as this recent Science editorial [4] argues, “the age of the speleothem” could be upon us.

[1] Fleitmann et al., Science 300, 1737-1739 (2003)
[2] Wang et al/, Science 294, 2345-2348
[3] Hai Cheng et al., Geology 34, 217–220, 2006
[4] Henderson, Science 313, 620-622, 2006

The vacuous quantify the nebulous (again)

The news on the radio this morning informed me that today is apparently most depressing day of the year.

Being contrary, I was actually feeling pretty good today. A proper weekend off, visiting some friends in Salisbury and visiting the Avebury stone circle, meant I actually had a fairly productive Monday. So, other than the continuing lack of news on the South African visitor permit front, the only depressing thing about today was the media's insistence on not only running with a supremely silly 'yes kids, in science there really is an equation for everything' story, but also recycling it from previous years.

If taking a few values we can quantify (debt and income levels, time elapsed since Christmas), at least as many which you most certainly can't ('general motivational levels'? 'the need to take action'? Please.) and randomly planting them in a forest of brackets wasn't vacuous enough, both the culprit (a serial offender it seems) and the media seem to have missed the fact that this magic formula was quite comprehensively falsified last year...

Did you know your irony meter could go 'whee'?

It seems that the MP-nagging activities of your friendly neighbourhood science bloggers has caught the attention of Truth In Science, although I was a little puzzled that they directed their readers to this post rather than the one with the letter from my MP. The one that quite clearly states that the Truth In Science packs are “not a suitable resource for the science curriculum”.

Ah. That’s because they’re trying to spin the Department of Education’s response. A pinch of selective quoting (‘not an appropriate resource to support the science curriculum.’ becomes ‘not “appropriate…to support the science curriculum.”’), and off we go!

The national curriculum is a minimum standard. It exists to guarantee that every young person receives a basic education. Teachers are free to go teach more than the minimum requirements of the national curriculum. Even if intelligent design is “not included in the science curriculum,” this simply means that it is not compulsory in all schools. It does not constitute a ban.

So a statement that a certain teaching pack can’t be used as part of the science curriculum really means that it’s ok to use it - you just don’t have to. How kind.

But, thanks to this sterling bit of reasoning, today I learnt that my irony meter can go ‘whee’. It’s a whole new setting that I wasn’t even aware of.

Updating the geoblogosphere

Those coping with the sad loss of Down to Earth, rejoice - a couple of other new(ish) earth science oriented blogs have been brought to my attention:

• Apparent Dip (thanks to Lab Lemming).
  
• ...Or Something, which is especially notable for several cool geological photos.
  
• Olelog. Lots of general geological goodness.
  

Meanwhile, Kevin Vranes is jumping the Scienceblog ship, but thankfully he'll still be treating us to his climate change/policy musings at Prometheus, and going all wildernessy on us at NoSeNada.org.

Finally, if RealClimate doesn't slake your climate blogging thirst, try Open Mind (via Tim Lambert) or Head In a Cloud.

Precambrian black smokers

These are pretty cool – some excellently preserved black smoker chimneys from a 1.43 billion year-old massive sulphide body in northern China:


Hydrothermal vents occur at mid-ocean ridges or volcanic hotspots: seawater, permeating down through cracks in the crust, comes into contact with hot rocks above the magma chamber, and reacts with them as they are heated to a couple of hundred degrees C - leaching out metals such as lead, copper, zinc and iron. These hot, buoyant fluids then return to the surface at vent sites, mix with sulphate-rich seawater and rapidly cool, leading to the precipitation of iron sulphides in chimney-like structures. Here’s a more typical view:


Individual vents are generally short-lived, and when the upwelling hot fluids inevitably migrate somewhere else, the fragile spires tend to collapse under their own weight. Massive sulphide bodies – valuable sources of metal ore - are built from the debris of many generations of collapsed smokers in a long-lived vent field. So it’s quite rare to see such well-preserved fragments. I just wish the authors had included some pictures of the things in situ.

Under the microscope, you can even see evidence of fossilised microbes: on the outside of the chimneys are stromatolite-like ‘microbialites’ – layered deposits of sulphides and organic carbon, sometimes containing mineralised filaments similar in morphology to bacteria found in and around modern vents.


Hydrothermal systems - where interesting chemistry is driven by geothermal energy – is considered to be one place on the early Earth where life could have perhaps arisen; those favouring such a scenario (which includes those hoping for extraterrestrial life in places like Europa) will be happy to see evidence of a flourishing ecology in such environments so long ago.

Source: Li and Kusky (2007), Gondwana Research, in press [doi]

Too windy for wind turbines?

Certain witty and erudite public figures here in the UK have an annoying habit of making somewhat ignorant pronouncements on anthropogenic climate change, preferring to deny that it's happening at all rather than talk about the more complicated (and valid) issues of how badly it might affect us (or not), or what mixture of adaptation and mitigation would best serve us. Jeremy Clarkson is one such person. The Radio 2 DJ Terry Wogan is another. Despite his form, I was intrigued by one item of discussion (or, more accurately, lengthy mockery) on his breakfast show this morning, namely that in the stormy weather that we're currently enjoying, 'it's too windy for the wind turbines!' Ha ha ha.

It turns out that wind turbines are shut down at wind speeds above about 65 mph, because the faster rotation of the blades at high wind speeds can either overheat the generator, or cause 'overspeed' problems whereby the blade rotation becomes impossible to control or stop (see p20 of this pdf). This is a simple consequence of optimising the turbines to the usual (slower) wind conditions, but it does raise an important issue. Other forms of renewable energy such as wave and solar are also compromised by stormy weather, meaning that during a serious storm, even without damage to the distribution system a renewables-heavy generation mix could well leave a lot of us without power.

To avoid such problems, you either need enough non-renewable (nuclear, gas, coal) capacity to act as a backup, which places fundamental (low) limits on renewable generation, or you need to somehow store the energy produced by the renewables in better weather. The latter is currently impractical at a large scale, which is one argument in favour of distributed generation (where batteries and heat sinks can be used). However, it seems that people are experimenting with using wind generators to produce hydrogen fuel. Using renewable power to produce energy-rich chemicals would be an interesting way of getting round the problem; in pure speculation mode, I wonder if you could use wind turbines to turn atmospheric CO2 back into hydrocarbons?

Feel free to say hola

Higher powers inform me that this week has been declared as Delurking Week. An invitation to any normally mute, semi-regular browsers to say hello, say them; a cunning use of emotional blackmail to garner praise and validation, say I.

Still, self-assessment is a difficult thing, so in addition to random hellos, I would be interested to hear any comments, impressions, or suggestions on possible topics you might have.

Westminster: bastion of scientific illiteracy

Miss Prism’s MP favours ”a balanced approach to the various theories of origin." in secondary school science classes. Odd, I thought we were talking about evolution, not the origin of life.

So far, 2 out of the 7 MPs that are known to have been contacted about the Truth in Science packs appear to be comfortable with mixing up empirical science and religious faith. This is admittedly a small sample size, but taken with the fact that more MPs felt moved last November to rejoice about 100 years of Rugby League than register their support for the Early Day Motion about Truth In Science, it doesn’t exactly instil great confidence in our elected representatives. At least the Department of Education were prompted to action, making a strong statement which my MP gave me a preview of (update: and people coming here via the Truth In Science should definitely read). And heartening scepticism of the commentators on this short article by Truth In Science member Richard Buggs is a nice contrast to the norm, too.

Best endorsement ever?

Apparently Highly Allochthonous is 'harder to pronounce than "Pharyngula" '. It's almost tempting to change my tagline...

Titanian shores

Details of the proposed polar lakes on Titan first announced in July, have been published in Nature by Stofan et al. (see also the accompanying News and Views article). The “lakes” are found in topographic depressions, and are thought to be filled with liquid based on their very low radar backscatter, which means whatever is in them is very smooth and reflective. This might seem counter-intuitive until you realise the radar beam is being sent towards to surface at an angle, rather than just straight down. A smooth surface therefore acts as a tilted mirror, reflecting energy away at the incident angle rather than back towards Cassini; a rough surface will contain parts with the correct orientation to return radar energy.

These features are by far the smoothest and most reflective found on Titan, and the contrast with the surrounding regions is quite sharp, as the figure below shows: the top row are false colour radar data with and without noise correction, and the bottom row are horizontal and vertical profiles of the normalised radar cross section (NCRS – a measure of the returned radar energy) along the white lines shown in b. -25 dB is about the level of instrument noise.


What’s also clear in the radar images is a very lake-like morphology, with irregular edges and what look like channels draining into the main body. The similarity is really brought home by this lovely image from the JPL press release:


It’s important to note that radar can’t tell us for sure that what we are seeing here are liquid hydrocarbons, although it does indicate a material with a low dielectric constant (i.e. it’s not a polar liquid, like water), as you’d expect. The authors also note:

Our inference that the northern-hemisphere lakes discovered by Cassini radar are at least partly liquid methane is consistent with various other considerations. If such lakes cover at least 0.2–4% of Titan's surface … they will buffer the atmospheric methane's relative humidity at its observed value, removing the requirement for a putative steady drizzle at the equator. If the abundance of lakes seen in [these] data are typical of their coverage poleward of about 70° in both hemispheres, then the fraction of Titan's surface covered by lakes is within this range. More recent polar radar data from Cassini support this assertion.

It is also unclear how these lakes are filled: is it by methane rain, or do the depressions cut into a subsurface methane aquifer? If the former, you would expect seasonal variations in how large and full the lakes are. Hopefully Cassini will keep collecting data long enough for us to observe, or rule out, such variations.

Philosophia Naturalis #5: Some sciblogging New Year’s Resolutions

The New Year may merely represent an arbitrary point in the Earth’s orbit with no intrinsic significance, but the flipping over of the digits on the calendar seems to have a real psychological effect, compelling us to dream up grandiose promises to improve ourselves and our lives. Of course, we then spectacularly fail to keep most of them, but this month’s edition of Philosophia Naturalis attempts to mirror this spirit of self-improvement by asking: what makes science blogging good science blogging? A trawl through the past month’s activity in the science and technology blogosphere suggests that, at their best, scibloggers perform a number of vital functions, which we can all try to emulate:

To augment the media coverage of science

It’s an unfortunate fact that you don’t have to know anything about science to be a science correspondent for a major newspaper or news channel – if anything, having a science degree probably counts against you. The very best people overcome this, of course, but a lot of mainstream science reporting seems to consist of slightly rewritten departmental press releases (which may also have been ‘rewritten for clarity’ by non-scientists). If you want nuance and context, science bloggers are on hand to pick up those vaguely explained findings in the mainstream media – be it reports of running water on Mars, the latest results from the Stardust probe, the origin of weird gamma ray bursts, the topology of the Universe, or the year’s top 5 nanotechnology breakthroughs - and run with them.

To talk about the ‘unsexy’ science the media does not reach

Reports of cutting-edge breakthroughs are all very well, but to really understand what those breakthroughs mean you need to know the basic science as well. Blogging gives us scientists the opportunity to talk about the nuts and bolts of their disciplines, such as how particles detectors work (in the run up to the LHC being switched on next year), or how stars manufacture the elements that form us all. We can also rectify the puzzling lack of media interest in our particular (and, obviously, intensely interesting) subfield by waffling to our heart’s content about strange correlations between the structure of the Cosmic Microwave Background and the orientation of our solar system, or the ‘interpretation question’ in quantum mechanics.

We can also compensate for the media’s notoriously short attention span; the results being breathlessly publicised are only a snapshot of research programmes which can play out over decades, as various hypotheses are proposed, tested, then discarded or modified. For example, there was a lot of excitement a few months back about possible liquid water on Enceladus, but it is interested bloggers who now tell us that this is not the only possible explanation for those geyser-like plumes.

To show that scientists are people too

It’s a sad fact that the common caricatures of scientists – as soulless reductionists with no empathy, social skills, or ethical qualms (with a nice sideline in big frickin’ lasers and maniacal laughter) are not often recognised as exaggerations. Blogging gives scientists a chance to express their real voices and personalities, and show that our lives are in fact, fairly normal: OK, we may talk about methods of solving Rubik’s cubes as well as soap operas, and we may have appalling taste in T-shirts, but our jobs have both good days and bad days. And worse days. And days when our experiments produce stupid results. We make mistakes. And, of course, we have arguments. Big arguments. Over things like whether string theory is the best thing since sliced bread or a half baked blind alley, or whether the entire universe can usefully be described as a computer, or if worries that climate change science is being stretched too far to gain political traction are justified. We find the idea that we're all engaged in a battle to suppress The Truth about global warming, or evolution, or the age of the Earth, rather hilarious - any 'orthodox conspiracy' of more than two scientists would undergo a schism faster than you could say, 'splitters!'

To fight the forces of ignorance and antiscience

There is a lot of silly science out there. The media sometimes shoots itself in the foot by giving silly answers to nonsensical questions, or giving free publicity to pointless mathematical concepts (though we can also be slightly more generous).

But darker forces, which don’t just mindlessly mangle science but actively slander it, are also at work. Defending against these attacks might be like playing whack-a-mole, but it must be done: and it’s nice to see that even if the US National Park Service’s are somewhat coy over the age and geological history of the Grand Canyon, there are science bloggers willing to step into the breach.

To provide the wow factor

Who better than scientists to inspire people with their tales of just how cool the Universe is? Not enough of us take the time, which is why we still miss Carl Sagan ten years after his passing. However, if a picture speaks a thousand words, then Phil has amassed ten thousand spectacular words over at Bad Astronomy (plus a few more of his own), and the HiRise team also do their bit with more stunning images from the Mars Reconnaissance Orbiter. Us geologists produce some very cool pictures too, so maybe I should take this one particularly to heart in the coming year.

Thus concludes this month’s edition of Philosphia Naturalis - may science blogging continue to flourish in 2007. Thanks to you all for reading, and to the contributers (willing and unwilling) for writing. PN #6 will be hosted by Charles Daney at Science and Reason on Thursday, February 1. Send your nominations and suggestions to carnival@scienceandreason.net, as explained here. We’re also looking for bloggers with a physical sciences/technology focus for hosting future editions; more information, and links to past editions, can be found at the Philosophia Naturalis site.

A geo-historical revolution

I’m actually in work today, despite the building being Officially Closed: you can still come in, but there’s no heating or canteen staff to provide coffee. However, an opportunity to engage in some warming ROFL’ing is provided by Adamant (via Pharyngula): a merging of the sequence of events in the geological record, scaled according to the biblically-based timescale of Archbishop Ussher, and human history. Here are some highlights which appeal to the paleogeographic nerd in me:

• 1384 B.C.: Shang Empire scraps compass research when China drifts over south magnetic pole.
  
• 1314 B.C.: On his way home from Troy ,Odysseus makes wrong turn into Tethys Ocean ;Homer writes it up.
  
• A.D. 1492: Panama's rise from sea thwarts Columbus's discovery of Japan.
  
• A.D. 1522: Sneak asteroid attack by Hernan Cortez smashes Aztec Empire
  
• A.D. 1588: Spanish Armada frustrated by continuing absence of English Channel.

Of course, the Young Earth Creationists think that most geology was confined to the year of Noah’s Flood, so this parody suffers from being rather less ridiculous than the ideas it is parodying.

Why 2007 might be better than 2006

If I was asked to sum up my life last year, the phrase ‘treading water’ would seem appropriate. Although I passed my PhD and had two papers published at the beginning of the year, the work that went into them was mostly done in 2005. Since then, my research output has stalled a little, other than a couple of co-author credits. This hasn’t been helped by two first-authored papers submitted in June being consigned to review purgatory, but the depressing reality was that my position was not designed to help me build my own scientific career, rather to support others’ (my boss, other members of the group). This was far more depressing, and irksome, than the strange disconnect between my position (and salary) and my teaching responsibilities. Worse, my attempts to find a new job (both academic and non) had all fallen flat, so much so that offers from someone I know in the exploration industry to join the Dark Side were starting to seem tempting – a sure sign of dissatisfaction. Some have it much worse than me, of course, but I was starting to feel trapped and seriously demotivated.

Suddenly, though, a change is in the air, with an almost-to-good-to-be-true job offer from a research group in South Africa. They need a postdoctoral paleomagician to work on some really old cratonic sequences, and come February, work permit permitting (I seriously hope I’m not jinxing this by mentioning it), I’m it. Exotic fieldwork? Check. Potentially interesting reseach? You got it. A chance to escape my current not-so-inspiring job? Woohoo!

This move is not without risks, of course. I’ve gone from a permanent, if degrading, job to a fixed term (one or two years, depending on circumstances and progress) postdoc. Although the guys I’ll be working with seem to have a decent output, South Africa is not exactly the centre of the academic universe. And I’ll be living in Johannesburg, which hasn’t exactly acquired a reputation for cosiness in the past few years. However, I feel that if I turned down this opportunity just because I found the idea a bit intimidating, I’d likely spend the next few years, maybe decades, regretting it. Whatever happens, at least for now I have something to look forward to in 2007.