After referring to a paper in Agricultural and Forest Meteorology in the last post, I remembered something I read on Crooked Timber the other day. Many people have a pretty good idea of how toxic the world of academic publishing is — if you don’t, take a look at this recent Guardian piece by Mike Taylor, who lays out the issues pretty clearly.

But what can individual researchers do to fight the power and toxic influence of the big publishers? Personally, I only submit papers to journals with an open-access policy (the EGU journals like Biogeosciences are good here, especially with their “open peer review” process), and try to encourage co-authors to do the same. But I am among the tiniest of tiny fish in a very big pond, so what I do has an influence barely measurable in pico-Seldons¹. Now some of the big fish are taking an interest, and have started a movement! You should sign up if you’re involved in publishing scientific results and care at all about the free dissemination of knowledge.

One of the things I’m responsible for in my day job is a phenology webcam at our experimental site at Puéchabon. The idea of this is to observe colour changes in the canopy of the forest up there, with a view perhaps eventually to replacing manual phenological observations with information drawn from digital photos. In this sense, phenology means things like when flowers come out, when fruit forms, and so on. The Quercus ilex (holm oak) forest at Puéchabon is evergreen, so you don’t get the same spectacular seasonal changes in leaf colour that you see in deciduous forests, so we’re not sure whether this is going to work — the changes we’ll be looking at will be a bit more subtle.

We installed the webcam on the 20 metre tower at Puéchabon in July and have been collecting images every half hour since, apart from a few outages. The images aren’t all that exciting (below left), but it’s quite nice to watch the changing angle of the sun on the canopy throughout the day. Very preliminary data analysis indicates that we will at least be able to see something changing through the seasons, even if it’s not abundantly clear to the eye from the images. A recent paper by Sonnentag et al. (unfortunately behind the evil Elsevier paywall…) gives some ideas about how to analyse these images. In the plot below right is a time series of the mean chromatic green component of the part of the webcam field of view that covers the forest canopy. This is defined as $g_{cc}=G/(R+G+B)$, where $R$, $G$ and $B$ are the red, green and blue components of the digital image. There is definitely some seasonal variation, although with a lot of noise. I want a full year of data, so that we can see the new growth in the spring, before doing some more detailed analysis, since there are definitely still some scene illumination artefacts in what we’re seeing. It’s encouraging that we can at least see something though!

Webcam image

Chromatic green time series

The potential difficulties in data analysis aren’t helped much by the local criminal low-lives. We’ve had four major thefts at Puéchabon in the last six months, the latest of which involved break-ins at both of the sheds on site and theft of a load of gas analysis and data processing equipment (including the PC collecting the webcam images), as well as power conditioning equipment and batteries used with the generator we use to power the site. Until the third theft of the year, we did have a nice big set of photovoltaic panels for power, but some enterprising lads took a truck up there and carted them all away. Probably 20 square metres of panels, gone in one night. It’s pretty weird. Much of the stuff these idiots have taken is basically worthless to them. It’s hard to imagine them successfully fencing a gas analyser or a fluorometer at one of the local flea markets! They seem to be taking stuff just because it’s there and it’s shiny.

It’s not quite clear what’s going to happen at Puéchabon now going forwards: we can’t afford to have guards at the site 24 hours a day to protect stuff, and it’s getting kind of silly when Alain and Jean-Marc, the technicians who go up there weekly, come back more often than not with long faces and another tale of broken locks and missing stuff. The whole point of a site like this is to have continuous observations, and if those keep getting interrupted by equipment walking away, it reduces the value of the remaining data quite a lot. We’ll have to see what happens.

day-job

For a brief period some years ago, I worked for an engineering firm that did sonar work for the (UK) navy. Many of the people in the company were ex-submariners, who had served both on the Swiftsure/Trafalgar attack boats and on the Vanguard missile boats. These were all pretty solid people, and I remember one in particular who delighted in telling stories about his time working his way up from a “baby sailor” to naval attaché to the British embassy in Washington, D.C. His most amusing tales included a reenactment (with actions) of the joys of carrying soup tureens around crowded submarines, and the entertaining ability of US spy satellites to dip into the atmosphere to take a closer look at interesting sights, like Soviet mini-subs stuck on their motherships in their pens.

A slightly less amusing story revolved around the hubris of submarine commanders. He sent some of us a photograph showing £20 million of towed sonar array snarled up around a mooring buoy, all because the sub commander couldn’t be bothered to wait for the divers to help reeling the thing in. A sad navy man with a big beard stood gazing at the pile of expensive spaghetti, looking like he might burst into tears at any moment. Not the navy’s finest moment.

One of my main jobs was to work on sonar system performance measures, which were used by the Ministry of Defence to try to ensure that they weren’t being diddled by the main contractor for the sonar system in question. Terrifyingly large amounts of money were involved, and some terrifyingly bad engineering decisions. The contractor decided to “buy British” for microprocessors for the beamforming hardware and designed a system using the Inmos Transputer. Oops. Inmos were assimilated into SGS Thomson, the Transputer shortly thereafter became extinct, and a sharp about-turn was needed to redesign the whole processing chain to use off-the-shelf PC components instead of the custom hardware that they had planned for.

It was an interesting little period for me, though I hadn’t wanted to work on the naval side of things. The company also did a lot of aerospace work, and I had nominally been hired to work on that. The structure of the company meant that I got poached for sonar stuff, got grumpy and left.

This company did have one extremely good thing they did though, one that I’ve not yet seen anywhere else (although it may be a standard approach in some kinds of engineering companies). All of the details of all non-classified projects that the company had going, in all of the fields where it worked, were available for perusal via the company’s accounting and time tracking software. Each engineering employee kept track of the time they spent on whatever projects they were assigned to (no surprises so far), but it was also possible to look through any other projects, see what work remained to be done, to see who was assigned to do the work, to see any open slots where people with particular skills were needed, and if you had spare time, to put yourself down to do that work. It was a very efficient system, and it actively encouraged people to talk and cooperate across project boundaries within the company. I think that was probably one of the biggest lessons I took from my time there. That, and, if you have 1500 m of towed array to reel in, wait for the divers…

Some interesting things that passed through my RSS reader recently:

Food pairing and flavour networks
This is kind of interesting. Why do cheese and bacon (if you eat that kind of thing) go together so well? Or asparagus and butter? Or caviar and chocolate? (Apparently. If you’re Heston Blumenthal.) The hypothesis was that these “paired” foods had many flavour compounds in common. The data presented in this preprint seems to confirm that idea for Western cookery, but contradict it for Asian cuisine. There’s a lot more in there about the evolution of recipes, clusters of ingredients, and other network analysis goodness.

Economists doing something right?
The people at Crooked Timber always have a lot of interesting things to say. This is a summary and some discussion of a meeting at the New Economics Foundation talking about the need to cut consumption and spread wealth around by redistributing working hours. From a personal point of view, the idea of earning a reasonable salary from a 21-hour working week and having time to work on personal projects, do some volunteering, spend time with Rita and Winnie, all sounds great. From a social point of view, a gradual redistribution of working hours to reduce unemployment and spread income around more fairly also sounds fine. It seems unlikely to happen, if only because NEF seems to be the only group of economists who can bear to think about the end of economic growth and a transition to a steady-state economy. When I listen to mainstream economists speak, I have this image in my mind of a train racing along a bridge which is being frantically cobbled together bit by bit as the train approaches. Sometimes the train gets closer to the edge, sometimes it backs off a little way. But in the long run, the bridge builders can’t win. They’re just going to run out of stuff to build more bridge.

Some good news
To leaven the economics misery, this is really good. Polio is on the way out in India: not one new case in the last year!

Carnedd Llywelyn, North Wales. January 2006.

Along with a lot of other people, I’m a big fan of cephalopods. I’ve dived with squid and cuttlefish and have watched octopus while snorkelling. I particularly remember following one cuttlefish across a reef in the Philippines, watching its mesmerising pattern display, until it got bored of the clumsy and noisy thing with too few appendages plodding along behind it and made off for deeper water.

Octopus, in particular, are smart little critters. One of the saddest things I’ve ever read was a section of a book about octopus physiology¹ that talked about the effect of certain nervous system lesions on the behaviour of octopus — these were lesions induced by human experimenters, of course. The writer talked about how the cephalopod victims cowered at the back of their tanks and clearly were less than keen on being used as experimental subjects. It stuck in my mind as the only place in the book (otherwise a good and thorough treatment of octopus physiology) where the author seemed tempted in any way to anthopomorphise or to ascribe emotions or feelings to the octopus. That’s why Octopus vulgaris is the only invertebrate protected under the UK’s animal experimentation laws…

Anyway, octopus are very cool and a fascinating model for non-human (and non-vertebrate!) intelligence. A recent article in Orion magazine does a great job of getting across just how amazing these creatures are. Go and read it. If they lived a bit longer and could be trusted not to molest the dog, I would love to have an octopus to live with us. Alas, I don’t like to imagine what would be the result of Winnie versus a Pacific giant octopus. Messy, for sure.

I’ve been thinking for a long time, mostly privately in my idle moments, about the sort of house I’d one day like to build for myself. I have some ideas that I think are pretty cool: multiple small wooden buildings, connected by walkways, with the main building on a slope with a stepped living area; a separate Japanese-style bathhouse; an octagonal library/study with windows all around; a cellar dug into the side of the hill.

Of course, all of this is nothing more than idle daydreaming. Recently though, Rita sent me a link to some pictures of cabins (sheds, huts, that sort of thing) that capture a lot of the spirit of what I’ve been thinking of. You can see them here (yes, the link is safe!). Some of these places look heavenly.

Uh-oh. Getting a bit behind on this 30-day challenge. Time for some shorties…

Not really a “past life” as such, but something interesting I did a while ago that was brought back to mind by the Costa Concordia cock-up. I’ve not spent a lot of time on big ships, indeed until 2007, I think the only larger vessels I’d been on were ferries, cross-Channel or around the Greek islands.

In April 2007 though, I went to Canada for a big trip, mostly to visit some potential future places to live and work and to attend a workshop at the Banff International Research Station. I flew out to Vancouver, took a ferry to Vancouver Island where I visited UVic (ended up working there for a couple of years afterwards), then travelled east by train. I made it as far east as Halifax, Nova Scotia, all by train. That was a pretty cool experience in itself, but I’d had a wacky idea for how to get home from Canada to the UK. It’s possible to book passage on container ships under some circumstances, which I decided to do. It’s a tricky process, not super cheap, and the logistics of making the rendezvous with the ship turned out to be a bit more “interesting” than I expected.

At this time, the M/V Flottbek was sailing a triangular route between Montreal, Liverpool and Antwerp, so my plan was to meet the ship in Montreal and spend a week travelling to Liverpool. Four days before the ship was supposed to sail, I called the port agent from Halifax, letting him know who I was, that I was sailing with the Flottbek in a few days and asking what to do about getting to the ship. “Eh, if you’re sailing on the Flottbek, you won’t be sailing in a few days! You’ll be sailing tomorrow. She’s loading in Montreal right now!” Oh dear. Massive panic. Ran to a travel agent, luckily got a ticket for a flight back to Montreal that evening, taxi to airport, flew back to Montreal, six hours sleep then presented myself at the gates of the container dock in the morning (after a complicated explanation in French to a Québecois taxi driver that yes, I really did want to go to the container port).

I spent seven days on the Flottbek, under the capable care of the German master and chief engineer and they Philippino crew. It was a very interesting experience, though the life of a crewman on a container ship isn’t one that I would want to share any time soon: 9 months on, 3 months off for the men, or a generous 3 months on, 3 months off for the senior officers. Being away from home for that length of time, all the time, sounds more like something out of a Patrick O’Brien novel than real life. Still, for seven days, in spring, with calm seas and beautiful sunsets, it’s something I’d recommend to anyone who has the time.

Everyone on the Flottbek seemed extremely competent and the captain was a serious serious man who’d been a seafarer all his life, having grown up on Heligoland and having a little boat of his own as a boy. I can’t, not in a thousand years, imagine him or any of his crew doing what the master of this Italian cruise ship did. The Flottbek had run aground once, on a shoal in the St. Lawrence River, on the way from Montreal to the open sea, but that was the fault of the Lawrence River pilot (thankless job: shifting shoals and big ships don’t make for a stress-free life).

I’m a sucker for nature photos. One of our annual outings when we lived in Bristol was to the Nature Photographer Of The Year exhibition at the city museum. Going by the crowds there, we aren’t the only ones who like this stuff.

So, here’s some eye candy.

Mt. Cain, Vancouver Island. New Years, 2010/2011.