Monday, 30 June 2008

AMEMR photos

A couple of group shots from our Plymouth Extravaganza ...

Moi, Mark Baird and Steve Emsley. The Cambridge '96 Planktonic Drinking Club (well, 3/4 of it) re-united.

Chris Wood (NOCS), David Keller (US), Alex Forryan (NOCS), Charles Stock (US), Bablu Sinha (NOCS), Ben Ward (NOCS), Katya Popova (NOCS), Karen Wild-Allen (AU), Mark Baird (AU).

Duck update

While away at AMEMR, both duck families survived and prospered, with no losses over the whole week. However, arriving at work today, it appears that two of the new chicks have perished, and that we're back to two mothers with three chicks between them. On the up-side, the two surviving chicks from the original brood are coming along in leaps and bounds. Both are now quite large and have begun developing their flight feathers. No sign of them taking to the air just yet, but it can't be too long now.

In other news, some of the nesting seagulls have finally produced some chicks. On the roof opposite we appear to have three actually quite large chicks. They're not as appealing as the duck chicks are/were, but they still have some charm. Photos to follow.


Another AMEMR conference ticked off (23rd to 26th June). As conferences go, I've never really been to anything quite as singularly focused on modelling as the AMEMR series. Most other conferences slip modelling in alongside more observational work, or at most have a specifically modelling session, but AMEMR is wall-to-wall modelling. Admittedly with only a single session (~18 talks per day for 4 days).

So it should be something like modeller's heaven, right? Well, at best a mixed bag. The first AMEMR conference in 2005 has left little impression on me beyond a loathing for super-narrow regional modelling (e.g. a dreary discussion of a bog-standard model in a boring provincial region). If a theme arose out of it, then it was a questioning of the justifiability of the complex end of marine ecosystem models. Up until that point, the continual increase of model complexity was seen as natural and right, with nary a second thought given to whether the resulting models could be robustly validated. Furthermore, when it came to validation, simply showing a side-by-side comparison between a highly-abstracted observational field and a carefully (= dubiously) colour-intervalled model field was a fairly acceptable strategy. Some speakers didn't even do that, and were content to simply show model output as if it were gospel truth.

While AMEMR 2008 also suffered somewhat from regional talks, and from some weak model-data comparison (of which, my poster was something of an example!), things were generally better. There were echoes of the last meeting's anti-complex model sentiments, but the absence from the conference of one of the major offenders on this count kept this particular "discussion" more low-key. An interesting development this time was the inclusion of more higher trophic level modelling. In aquatic circles, this specifically means fish models. Which, given the socio-economic importance of fisheries made for more anthropocentric sessions towards the end of the conference.

Although only a few fisheries modellers made an appearance at AMEMR, they had a couple of good talks and two excellent keynote speakers. The best research speaker summarised what must have been a massive piece of work with an emsemble size of thousands of individual simulations (for reference, Sarah Gaichas). Applying a generic fisheries model of the North Pacific to three specific locations, she was able to show the consequences of perturbations of different fish species on the whole food web, and to demonstrate that the three locations behaved differently to management despite the imposition of the same strategy everywhere. A real tour-de-force. The two keynote speakers both brought home the necessity of modellers to take in the bigger picture, and not to lose themselves in the detail. While they recognised the importance of advances in model realism, the socio-economic problems that they find themselves dealing with simply cannot wait until all of the modelling details can be resolved. They advised that modellers need to bear the wider context in mind, and to explore model behaviour (or "have fun", as one of the speakers put it; Beth Fulton) while recognising the limits of their models. Stirring stuff.

In summary, and to paraphrase terribly, there were a couple of take-home messages from this year's AMEMR:
  • From the biogeochemical modelling end: Be aware of model limitations and perverse/pathological details
  • From the fisheries modelling end: Be aware that the world cannot wait for perfection, and that second best models may have to suffice

On a more social note, I was able to catch up with both MEB and SME on several evenings. Mark, as ever, was doing sterling work with his size-based model. Meanwhile, Steve retains his animosity to models because of their inadequacy as a means of representing reality. We had some philosophical fun thrashing that one about.

Friday, 20 June 2008

When there were three ...

After a die-back from 18 chicks to just 2, things have taken a turn for the better and 3 new chicks have appeared ...

Swimming in their water dish.

Sunning themselves.

Following their mother to the pond.

Meanwhile, the two surviving chicks from the first brood are getting big.

Thursday, 19 June 2008

Career bunk

I was contacted today by our PR person about a potential interview with some new magazine, The Sea. Although, this is unlikely to come off, I duly responded. I might as well record my science-lite responses to the interview questions here ...

Why did you decide to become an oceanographer?

I actually came into oceanography by accident. Although my main interest has always been with biology, I've also always enjoyed mathematics. So I when I heard of theoretical ecology at high school, I thought "that's where I want to be" and aimed myself that way. After completing my first degree in conventional biology, I selected a doctorate in ecosystem modelling that would let me continue with biology, but would allow me to explore mathematics more. As it happened, the ecosystems I wound up modelling were those of the open ocean, so I came to learn about (and love!) plankton. Although I'd not considered oceanography until my doctorate, I've not looked back since. My parents find this "return to the sea" funny, since my dad was a marine engineer and spent much of his working life on the ocean.

How did you prepare or train for it?

I grew up in Scotland, so at high school, alongside maths and english, I was able to take all of the sciences (biology, chemistry and physics) when I did my Highers (similar to A-Levels). I did have a favourite science subject, biology, and this is what guided my choice when I went to do my honours degree at university. While there, I did a fairly conventional mixture of botany and zoology, but as I'd always liked maths at school, I also took a few maths courses and applied these to my biology studies. As it happens, this came in handy afterwards when I decided to continue my studies with a doctoral degree in ecological modelling. This brought together both my biology training and my interest in mathematics. It also introduced me to oceanography, a subject I've stayed with ever since. After completing my doctorate, I've been involved in a number of projects covering a diverse range of interesting topics, from the ecology of important plankton groups, to the intricacies of the ocean's carbon cycle, and to the wider earth system, past, present and future. These latter experiences have been both rewarding, and have underscored that science really is a career of life-long learning.

What does you current job involve?

At the moment I'm involved in a project to work out how much anthropogenic carbon dioxide – that’s carbon dioxide created by human activity – is being absorbed by the ocean. Every year the amount of CO2 in the atmosphere rises but by less than it should do, and one of the reasons is that some of it is being dissolved and going into the ocean. We want to know how much because that will help us to predict what will happen in the future.

You can’t tell the difference chemically between anthropogenic and other CO2, you can just tell that there is CO2 there, but some people have worked out little tricks to tell where it is. For example they use information from CFCs, which also go into the ocean and also have a recent history but don’t occur naturally. They see where in the ocean they are distributed and use that to guess where we might also have anthropogenic CO2.

What I am doing is testing their theories using my model. I’ve simulated the last 200 years, which is about how long we’ve been using fossil fuel, and anthropogenic CO2 has gone into my model ocean. I know where it is, because I can separate it out using an accounting trick, but I pretend that I don’t know. Then I use the methods that they use in the real world to see if they can find the CO2 in my model. This tests whether the assumptions they are making in the real world are accurate.

How much do you earn?

Approximately £30,000, although there's a graded pay scale, so I've earned less in the past and will (hopefully!) earn more in the future.

What's the best part of your job?

The best part is the variety in the work. While I've stayed an ecosystem modeller since my doctorate days, each project has brought new challenges both in terms of learning about new things, and in gaining experience of new ways to tackle and solve problems. Furthermore, although I'm mostly focussed on one or two projects at a time, there's a lot of scope and freedom for developing my own work or for collaborating with other scientists.

And the worst?

While I work in a building full of other oceanographers, oceanography is a big field, and we're often working on quite individual and isolated projects. So while it may appear like we're always working closely together, occasionally you're the closest to an expert in the building on a particular topic, and so have to dig yourself out of holes when they come up. But even then, it's often very satisfying to rely on yourself this way.

Monday, 16 June 2008

Unusually positive

Some unusually positive news from the quad today. Firstly, both of the remaining chicks are still with us, and are still getting bigger. That means a period of more than a week when there have been no further chick fatalities. Secondly, and more impressively, we additionally have a newly-hatched brood of 3 chicks. We've been expecting this for a couple of weeks, but nothing has happened until now. Seeing newly-hatched chicks again, it's clear how much the survivors from the original batch have grown. They positively tower over the new arrivals. We're now just hoping that competition for resources doesn't make the new batch appear too much like disposable rivals to the original batch.

Sunday, 15 June 2008

Digging hills

Neal Asher seems to be cranking books out at quite a rate, so I'm no longer sure which is his latest. Hilldiggers has to be up there though.

Hilldiggers again takes the reader to Asher's Polity universe. However, similar to the books in his Spatterjay series, Hilldiggers is not part of the main series of Polity novels that feature the agent Ian Cormac. Instead it takes place in a solar system outside the "Line of Polity" (the Polity's border), originally populated by humans at a time before the formation of the Polity. However, the Polity is now bordering on the system, and has sent ambassadors, overtly and covertly, to contact the civilisation there.

But things are complicated in this system. Two Earth-like worlds exist, and while colonised together, their early history was marred by distrust and clouded in mystery. This distrust grew until both planets engaged in a seemingly endless war that occurred sporadically when the two planets were in orbital alignment with one another. The war only ended when an alien entity, the Worm, was captured by one side, the Sudorians, and its technology exploited to give that side a decisive edge over their rivals, the Brumellians. Though the war ended, it did so brutally, with the Sudorian military exacting a near-genocidal final blow. The novel picks up twenty years after the end of the war, with peace apparently firmly established.

The main narrative strand follows one of the Polity's ambassadors, David McCrooger (another Scottish-sounding protagonist), on a direct mission to establish relations with the victorious Sudorians. Distrusted by the Sudorian military, who fear a Polity take-over, McCrooger is caught in an assassination attempt that strands him on Brumal. Captured by the Brumellians, he begins to learn an alternative version of their history and that of the war.

The novel has a number of other narrative strands, including four quads (two sisters and two brothers) whose origins are related to the Worm, and have all risen far in Sudorian society. McCrooger's path intersects with each, and it becomes clear that something is driving each to their position, while also trying to effect changes in that society. The chapter frontpieces in the novel take the form of short excerpts from a revisionist history of the Sudorian-Brumellian system written by one of the quads.

Finally, the novel includes a Polity AI narrator, Tigger, who covertly watches over the solar system, and who takes an interest in one of the quads. While officially on a Polity mission, Tigger (who, unsurprisingly given the name, takes a copyright-violating form) is not averse to following his own conscience, and begins his own investigations into the Sudorian-Brumellian war, an investigation that unearths some truths that the Sudorian military want to keep buried.

As normal for an Asher novel, these strands start out fairly separate, but gradually wind together as connections form or are revealed. Also as usual for Asher, the novel is something of a page-turner, as one is quickly drawn into the world he creates. However, while the novel in part tackles a "big theme" (genocide), as is also normal for Asher, it gets bogged down in a rather long-winded yet carefully-described series of violent events. This culminates and an over-long space battle involving the Hilldiggers of the novel's title. Editing this section down could have vastly improved it, but I suspect that Asher likes describing such events. That's something of a shame, since in other respects the novel is more successful than his other books. Particularly the gradual revelation of the history of the settling of the system and its century-long war.

Possibly just by a quirk in my reading order, the novel seems to share a theme with Alastair Reynolds' Chasm City, with their common backgrounds of the settlement of a solar system and the resulting bloody war. Unfortunately for Asher, this shows clearly the gap between the two novelists. Reynolds handles the revelations more carefully and with much more panache in his writing. While it's still enjoyable, Asher seems satisfied with just revealing material artlessly to the reader. Reynolds also (generally, but not always) avoids the pitfall of describing action in great detail and at great length. On this count, Asher seems to be falling into a classic trap that affects series novelists: the exponential growth in size of later novels.

Anyway, notwithstanding the above, Hilldiggers is still an enjoyable page-turner. And while flawed, hopefully its better aspects reflect a growth in Asher's writing. Since he's now cranking novels out at full speed, this should be a testable hypothesis in fairly short order!

Friday, 13 June 2008

Friday photos


Quad patrol.

Identical twins?

Thursday, 12 June 2008

Holding steady

Though last week saw the continuing decline of the chicks in the quad, this week has seen no further losses. Since last Friday we've stabilised at 2 chicks belonging to a single mother. As it happens, the chicks have started to get quite large now. However, there's been no sign of any other mothers in the quad this week. And not a hint of further broods of chicks. The quad's output may be restricted to two this year.

Monday, 9 June 2008

Mike Fasham

We got some sad news at work today concerning Mike Fasham, the great god of plankton modelling. After a prolonged period in hospital the past month, Mike died on Saturday the 7th June.

I add that rather light-hearted appellation above because that's how I first knew of Mike, and because I think he would have been amused by the over-egged awe that my fellow plankton modelling students held him in. Working in Warwick and in Leeds, we knew only of Mike from his work in far-off Southampton. Many such distant greats of science that one comes to know through their published work turn out to be dull as dishwater or mean-spirited workaholics when finally encountered in the flesh. Not so Mike.

While I got to know him somewhat during an extended workshop in Cambridge in the summer of 1996, it wasn't really until I left Warwick and moved to Southampton that I got to know him well. In fact, since my PhD. was founded on a model that he published in 1993 (a descendant of his most famous model, FDM90), I chose to move to Southampton specifically to work with him. As it turned out, we didn't work directly together at first, but we were still able to collaborate on a paper together (albeit on the rather arcane topic of off-shelf carbon transports).

However, despite only limited work contact, Mike and I would still chat together at length, particularly on his frequent visits to NOCS after his retirement. While oceanography would be an occasional topic for discussion, it was usually a minor one. Mike saved his ideas for those who could best work with them; rarely me. Instead, we'd usually trawl over politics, often drifting onto films, books or more general science topics. A recurrent, comic topic was that of my PhD. supervisor, who Mike had come to know while organising that 1996 conference. Between us, we had plenty of stories to trade there.

Although Mike had cancer for almost all of the time that I knew him, he never gave in to it, and would occasionally arrive at NOCS with novel haircuts "inspired" by his bouts of chemotherapy. While the last year saw Mike confined to home, we were still able to visit him on-and-off, and he was always in good spirits whenever we saw him. As ever, these visits were not frequent enough, but they were always highly enjoyable occasions for us and, I hope, Mike.

I'll miss him without a doubt.

Friday, 6 June 2008

Graphing the horror of the wild

As intimated earlier ...

The plot uses data culled from the blog here.

One week later

Chick numbers this week are still asymptoting towards zero. We began the week, we believe, with 4; this then dropped to 3 by Wednesday; and today, Friday, we appear to have only 2 chicks remaining. Ironically, one of the photographs I took several weeks ago appeared in NOCS News this week with a cheerful note about NOCS being the host to two duck families and 18 chicks (which there were when the photograph was taken and passed to our PR department). I must remember to plot this attrition rate up as a graph. Whichever way you cut it, it's not good.

Sunday, 1 June 2008

Dr. Morris

We had a very welcome visit from Dr. Morris. The weather was quite good on Saturday, so we took a trip to Portsmouth and its Spinnaker Tower.

From a distance ...

A giddy upward shot ...

Comedy use of a (defused) torpedo ...