Saturday, 31 October 2009


Now this is pretty cool ...

It's a kind-of cloud generated from the content of Strange News using an online Java package called Wordle. I particularly like that it displays "Arse" prominently - didn't notice that I'd used it that much. Although I've fed it this blog, it can be fed any large block of text. Here's what happens when you give it the entire text of Moby-Dick (for APM, of course) ...

Marvellous. Given that it identifies major themes in the text it's fed (cf. "Whale" above), perhaps it's a quick way to generate a short-hand summary of a technical paper or long newspaper article? :-)

Return of the Wanderer

For someone as poorly observant as me, it's difficult to know for sure, but I'm pretty sure that this year's successful seagull (last blogged here and photographed here) is currently hopping around its birthplace on the roof opposite (I'm in work wrapping up a review for the NSF). The gull, which still has juvenile plumage, arrived with an adult, possibly its parent. I don't know how gull families work, but they're a veritable model of the nuclear family compared to the dysfunctional ducks. Anyway, wearing my anthropomorphic hat, I suspect that animals as big and seemingly clever as gulls are probably smart enough and interested enough to recognise and return to places that once were important to them. So, who knows? It could be them.

Monday, 19 October 2009

The naturalness of age

We caught an excellent exhibition at the Civic Centre yesterday. The BP Portrait Award 2009 is on tour, and is spending a month and a half in Southampton.

While the subjects range widely, taking in everyone from children to heavily tattooed Portsmouth supporters, painting the elderly was quite a popular choice. Some of the pictures were really striking, and the material accompanying such painting usually made vague references to the naturalness of the ageing process or the cycle of life or some such.

Seeing such commentary repeatedly made me reflect on, not so much how natural ageing is, but how natural our acceptance of it is. In part, this sometimes strikes me as being a reflexive dismissal of efforts to ward off ageing and a dislike of the denial of age by those of a more materialist (in the social sense) disposition. All well and good, but as a biologist I can't help but think that ageing, far from being something that we should relax into, is something that we really should resist.

Rather than seeing it as a necessary part of life, senescence should instead be seen for what it is: a predictable outcome for the throwaway machines that are built to service the unconscious and uncaring needs of immortal strands of digital information. If we value ourselves, that is our minds, above the ceaselessly shuffled genes that built the machines that we both are and occupy, then we should take a far less sanguine view of our fate.

In a way, ageing truly exposes our serf-like existence as mere temporary vessels for more permanent passengers. Once they have disembarked, off to newer, cleaner vessels for the next leg to eternity, the fate of the decaying hulks left behind is irrelevant, and the concomitant blindness of natural selection is to be expected. In this view, we should be more than a little annoyed by senescence, and a whole lot more questioning of the common wisdom that, just because something is natural, it should be uncritically accepted.

The shallow pursuit of youth should be viewed suspiciously, but it is wrong to view ageing as some benign part of some abstract "cycle of life". What ageing is really telling us, if we're prepared to listen, is "you're fired".

Sunday, 18 October 2009

More drinking in Eastleigh

Further to last month's evening in Eastleigh, last night saw another, albeit more refined, quaffing-session in the town. This time it was a wine-tasting evening - at least that's the formal excuse. Last time's winner, Dan, was both defending the Golden Arse and co-hosting the evening with Rachel. Unfortunately, as has occurred time and time again, he was unable to retain the Arse, which went to repeat-winner June ...


While June won with an impressive score of 15/18, I trickled in way down the table with a paltry 7/18 points. And, even then, some of those I only got because I played the numbers game and guessed the same wine multiple times. Though I have won the Arse in the distant past (and on my first tasting evening to boot!), my performance in the last few evenings has left a lot to be desired. I think I'll be taking tips from June next time though (and/or copying off of her sheet).

Wednesday, 14 October 2009

Carbon cooperation

Another very interesting seminar today. This one, by David Beerling from Sheffield, dealt with the geological cycle of carbon (weathering; CaCO3 burial; vulcanism) and the role that terrestrial vegetation plays on top of it.

Essentially, for a couple of decades it's been known that there's a neat feedback loop between CO2 and climate, which is mediated through rock weathering on land. Vegetation on land is known to be associated with enhanced weathering, and the evolution of land plants (first in getting onto the land; later the advent of the angiosperms) is believed to be responsible for two significant decreases in atmospheric CO2 in the Phanerozoic.

This was the background to the talk, but it went off in quite a different direction. Beerling then introduced the arbuscular mycorrhiza (AM) and the ectomycorrhiza (EM), two groups of fungi with strong mutual symbioses with land plants. While I knew that these played an important role in nutrient acquisition for some plants, I'd no idea quite how big a role this was. Apparently around 12% of photosynthate produced by a plant can be channelled to its symbiont.

The seminar then delved into some experimental work in which the strength of this relationship was examined (largely through 14C-labelling of plant photosynthate). This was augmented by some very elegant and clever growth experiments in which the potting medium was differentially composed of soils of different mineral value. These trials showed not only the strong link between the two species, but also how tenacious fungi are at locating and "mining" minerals for their plant partners. Some of the photographs showing the fungal growth were really impressive on this point.

Finally, the talk returned to the geological cycle of carbon, and armed with this new quantitative knowledge about the plant-fungus relationship, suggested instead that the underlying factor in the downward "jumps" in past atmospheric CO2 was the evolution of the two groups of fungi. Fossil evidence points (as much as it can given large uncertainties) to the appearance of each group around the time that CO2 drops.

Anyway, it was all quite a nice challenge to the "interesting-but-not-significant" view I'd formed of AM and EM during my biology degree. And intriguing to see cooperation, which I also typically view as "interesting-but-not-significant", put pole position in such key biogeochemical processes.

Sunday, 11 October 2009

Evil corporates

Judging from this weekend's films, anti-corporatism is still in vogue, and still makes for enjoyable cinema (which may say more about me than Hollywood).

First up was State of Play, a remake of an excellent TV series we saw a couple of years ago. Somewhat surprisingly, the film largely mirrors the original, albeit with a few nips and tucks. The core story is retained, though some of the plotting is rather fast, and we don't get to know some of the characters quite so well. This does tend to move things along a little too quickly for the viewer to try to guess ahead, surely one of the pleasures of the genre, but it was still an enjoyable film. The story's central messages about the corrupting influence of the bottom line and the creeping corporatisation of military services are retained, and still timely, although as with the TV series, get overshadowed as the narrative twists its way to the finish line.

Much more interesting, and viscerally enjoyable, was District 9, an ostensibly science fiction film about alien visitors to Earth who have overstayed their welcome. Told as a mixture of conventional cinematic narrative and through interspersed documentary footage and interviews, the film follows Wikus, an administrator tasked by Multinational United (MNU) to evict the aliens from their Johannesburg (and eponymous) slum. However, while serving eviction notices to the brutalised aliens, Wikus is accidentally exposed to an alien technology and begins to undergo a genetic transformation that gradually turns him into an alien. This transformation is of great interest to MNU, who have long been searching for a means to successfully operate alien weaponry, and Wikus quickly becomes an expendable resource for the corporation's biotechnology department. Escaping from MNU, Wikus becomes a hunted fugative, and while desperate to return to normal life and his loving wife, he gradually becomes aware of the true plight of the aliens. Ultimately, he selflessly helps one alien and his son to escape to, and activate, the mothership that has hovered unresponsively over the city for 20 years.

While the film is solidly enjoyable as a science fiction romp, particularly when Wikus begins to use alien technology to fight back against MNU, its real themes run very close to the surface. In this respect, setting the film in post-Apartheid South Africa is something of a master-stroke, one that harmonises perfectly with the anti-racist subtext (practically the sur-text). The film did strike me as channelling the spirits of Robocop and Alien Nation, but by marrying the best themes from both (together with the rather enjoyable violence of the former) more than stands on its own two feet. And, as ever, it's hard not to like a film which ends hopefully.

Saturday, 10 October 2009

Not so autotrophic now

We had an interesting inaugural seminar in yesterday's Friday Seminar Series. MVZ was in the barrel, as was I, since I was on introducing duty through my new membership of the Series' organising committee. He gave a quite revelatory (and impressively brief) overview of some work he's done on less-than-autotrophic behaviour of phytoplankton. After starting with an introduction that took in the evolutionary history of prokaryotes and the endosymbiosis that led them to eukaryotes, we jumped to a conundrum in the nutrient and carbon budgets in the modern North Atlantic. Basically, eukaryotic algae are doing a fair fraction of the carbon fixation, but are only responsible for a small fraction of phosphate uptake. Given that there should be parity between these, something is up. Bactivory, apparently, is what that "something" turns out to be. By carefully labelling prokaryotic cells by providing them with an isotope-labelled amino acid, MVZ was able to show that, within hours, this label wound up in some interesting places. Even card-carrying autotrophs like the coccolithophorids have a sideline in getting phosphate in a less-than-first-principles manner. The idea is that, in highly nutrient stressed environments like the oligotrophic gyres, bacteria provide an excellent source of phosphate, and other useful molecules to boot. That said, my favourite phytoplankton, the diatoms, are still hardcore-autotrophs, with no whiff of bactivory on their part (at least in the open ocean), but this probably stems from their adaptation to high nutrient environments (plus their frustules would probably impede dining). In the environments that MVZ studied, it turns out that eukaryotic phytoplankton are as important at grazing bacteria as bona fide protistan microzooplankton. Quite a turn up for the books [*], although pleasing to see that, despite billions of years of autotrophic life, the eukaryotes are hanging on to their phagotrophic machinery ... just in case.

[*] Actually, as MVZ pointed out, people have known for a long time (probably for almost as long as they've known about microplankton) that eukaryotic phytoplankton engage in grazing activity. What's new here is that the scale of this has been established. I certainly wouldn't have expected algae to be such enthusiastic players in the grazing business. It's definitely something for future generations of ecosystem models ...

Friday, 2 October 2009

Day 6, drivearound

Rather than exhaust ourselves on another walk on our last day on holiday, we decided to go on a drive around several places that we had on our list but which we never got around to visiting. Any future trip out this way, not unlikely given how successful this trip has been, might take some of these in more closely.

Day 6, drive around

Our first stop was Goudhurst, a village on top of a little hill. Definitely something of a nice stop for a hike, but a little empty for us in culture-vulture mode. As with many of the East Sussex / Kent villages, it has a great church bang in the centre of town. Although this, and the town in general, was under siege from Jehovah's Witnesses while we were visiting, we had a good look around and in it ...


Next up was Lamberhurst, actually immediately to the north of Bewl Water. We didn't stop in the village itself, but instead dropped by its church ...


After an abortive trip to Scotney Castle, a nearby, but dull-looking National Trust site, we then headed back east to Cranbrook, a much larger village that afforded lunch and another church visit. This time the church was all decked out in its harvest festival finest, as can be seen in the scattering of apples and adornments to the baptismal font here ...


Cranbrook also sports a great windmill near its centre. It's essentially a museum these days (one that was shut when we visited), but I believe that it's still functional when it wants to be ...


Our final stop for the day was at a nearby vineyard. We had a quick look around the vines (which were being picked while we were there), before exploiting its shop as a source of birthday / holiday presents. Rather nicely, we also got to sample a few whites, a red and a rose that they produce. The whites were very nice, but the red wasn't as full-bodied as we're used to - possibly on account of more limited growing conditions for red grapes.

Full set of drivearound photographs available here.

On returning to Burwash, we chilled out to make the most of another beautiful sunny day, before getting ourselves ready for the trip back to Southampton. Burwash has been a great holiday venue, particularly because of the barn itself. Needless to say, a round of holiday home snaps resulted.

Full set of barn photographs available here.

Thursday, 1 October 2009

Day 5, Bewl Water

Looking around for a walk to do, we spotted nearby Bewl Water. It's another reservoir, much like Darwell Reservoir on our Brightling walk, but has an activity centre and a full round-lake path.

After ruling out cycling around the path on grounds of prohibitive cost (you'd think such an operation might drop its prices off-season), we decided to just walk out one edge of the lake then back, and then to try our luck elsewhere. But easy walking, nice views of oast houses over water and an impressive (early) average walking speed (3.5 mph), persuaded us to do all 20 km (12.4 mi) ...

Day 5 Bewl Water hike

As mentioned above, one of the attractions for us, and one of the reasons that it mutated from a 3-mile round trip into the full 12 miles, was because it had no shortage of attractive views of the aforementioned oast houses. And because, as the track picture above shows, the path wriggled its way around the lake, we often got multiple views of these. This one we saw from far and near ...


Actually, there isn't a huge amount more to say about the walk. The path was, with a few roadwork-related hiccups, extremely easy to follow. And the weather was, again, excellent. So it was a enjoyable and straightforward walk around a rather inlet-heavy, but pretty, lake ...


... At least for the first 10 km! The second 10 km, while still very easy walking, gradually became more of a chore. But the walk did give us something of a sense of achievement since it's the longest one-day walk we've done for quite a while. Some days we've come quite close in length when summed up over the full day, but this is the longest formal route we've walked in years (and it isn't even all that long!).

Anyway, it was very pleasant to return to the activity centre and claim our coffees. It was also surprising to find that, including a lunch stop, we'd managed to maintain an impressive (for us) average speed of 3.1 mph. Admittedly, the path, being around a lake, was largely flat walking, but this is still a good speed for our walks (our moving average even stuck at 3.5 mph).

The evening's entertainment this time was the glossy, nonsense techno-thriller Swordfish, another hauled from the barn's large DVD library. Unlike Mystery Alaska, which somewhat surprised us as a minor success, this time we got more-or-less what we expected. Its saving grace was that its running time was sub-100 minutes, so it only just outstayed its welcome.

Full set of photographs available here.