Seals in San Diego

I've just read on BBC news the distressing news that the authorities are going to try and clear the Seals from La Jolla beach. I've been there twice now, once last year on holiday and once about 5 years ago while working. I only went the second time because I wanted to see the seals again. The reason seems, frankly, daft. The pool was gifted to the city if it became a "public area". But, apparently, it isn't public if kids shouldn't swim in it because the seals don't clean up after themselves. Well, yes, okay, this is true. But just become some philanthropist in the 1930s made a statement doesn't mean that we should live be this now; new knowledge has arisen. While a seal reserve might not be the original intent use, it's still allows the obvious public use of watching the seals.…

Thoughts on a Holiday

I'd never been to either Romania or Turkey before my holiday. A new country is always a new experience. In this case, the east Europe is much closer than many places I've been to, but I was still very unsure what to expect. Both countries were wonderful, confusing and full of contradictions. Romania is a beautiful and bountiful country. On the way to the delta, there were miles and miles of fertile ground, a breadbasket of corn and sunflower. Passing through the villages where we crossed the Danube for the first time, men on the road sides made a strange sign, moving their hands apart like an prayer in reverse; actually, they were miming the fish they have caught and were selling. Despite the natural wealth, the poverty in Romania is obvious; horse-drawn carriages are common. Some of the t…

Buyukada

The hassles and bustles of Istanbul came to their completion with a scrum for the one of the regular ferries to the Islands. It turned out to be unnecessary, though because it wasn't that full and there were plenty of seats. The journey was calm and pleasant except for the occasional waft of diesel fumes and a fractious child behind me. First impressions of Buyukada were not great; but this just turned out to be the feeding frenzy of merchants surrounding the arriving boat. The island itself is small, calm and relatively peaceful. They have no cars except for essential services; this means lots of bikes and the ever present smell of horse dung which, thankfully, I have become used to now. The place is lovely (with a few cheesy bits --- the noises upstairs sound distinctly like people danci…

Crisan

Am in Crisan, a small village on the delta of the Danube in Romania. It's a strange village because it is two dimensional; spread out across up and down the shore of a narrow spit of land, trapped betweeen one of the two main branches of the Danube in front and a reed bed behind. All around the river branches and reforms. It's just a short boat ride till you are on a stream with banks lined with reeds, travelling through large ponds choked with water ferns and lily pads. As the boat travels through, frogs leap for safety, out of the path. And there are birds everywhere; I'm not one of lifes twitchers, but here you can see the motivation. Pelicans, herons and ibis are common. Occasionally in the distance, a flash of blue is the most you are likely to see of the kingfisher, elusive, but at l…

Delta Nature Resort

Now in the grandly titled Delta Nature Resort which is about 20km upstream of Tulcea. We were bought here by a bloke called Vlad; fortunately, he had none of the xenophobic nature of his namesake; rather, he was a jovial, engaging man with a slightly old car. He drove us here carefully, except for a perilous moment when he tried for the dubious extra security of his seat belt while travelling at 50kph. The Nature resort. Well, it's a big wetland lake like so many of the others that we have seen over the last few days, reed beds, hanging trees and, of course, birds. The resort has been embedded on the side of the hill, not really adding to the place, but not detracting too much from it either. It's has pretentions to being five star; we were given a fruity cocktail when we walked through th…

Istanbul

Have been in Istanbul now for several days. Been down the Bosphoros, up a castle and in a mosque. It's an impressive place. The central tourist trap, Sultanahmet, is also overloaded with places to go and see, from many different ages. From an Egyptian needle (1500BC according to the guidebook, 400BC according to the plaque), through to the Byzantine hippodrome which used to house a huge swimming pool where they raced the beasts after which it was named, to the Palace which housed the Ottomans, through to the Blue and Aya Sofia Mosques. This city, perched across the straits, gateway to two continents has been the centre of several huge empires for many centuries, robbed only of it's crown when Ataturk decided that Ankara was the place for his capital, on the basis that finding somewhere to …

Blogpost Fiddling

I think I now have my blogging environment as I want it. I've been using blogpost.py to do my posting. I couldn't let go of my text only environment. I don't care if it's old fashioned, but I like the separation of editing and viewing. In this case, I've even had to learn asciidoc, but it was worth the effort. Today, I think I have fiddled with blogpost.py for the last time. I can now set both categories and status (published or unpublished) from within the blogfile. I'd added a post command previously; originally, blogpost used to have a create and update command. The big advantage with this is that all the information about the blog is apparent from the file; this means I can use a single make file to compile the lot. Any changes that I make while on the road will automatically publish t…

Talk Finished

Thankful, the talk is over. It went okay, didn't stumble too much and most importantly, got a few laughs. The main questions where about the things that I thought they would be. First, was the question about the apparent circularity of the definition; I thought to take this out, because I knew it might cause trouble, but it produces a much more unwieldy definition. A second, was the question about orphan functions --- genes with new functions or functions of duck-billed platypus. My answer is that all things have homologues even if they don't exist any more. Not sure people were entirely convinced; if you look at the axiomatisation, then my feeling is that it doesn't make much difference anyway. You build your process hierarachy; functions and roles then just drop out because they are defi…

Publication by Blog

Blogs are generally seen as a slightly dubious part of the scientific publishing landscape. This is not, of course, unreasonable. I put stuff up here, for example, such as my idea for IDs that I've thought about for a few days, but that I am unlikely to follow any further, or stuff opinion pieces on bees about which I have as little expertise as the average journalist. Fundamentally, though, despite it's current use, a blog is just a media channel; you can use them to transfer anything you like. A scientific paper, for instance. This might be useful. While, for instance, I love open access publication, it's quite expensive particularly as the cash tends to come out of my own budget, at least until I can get the library to pay. So, I've been thinking about a cheap and cheerful blog-based sy…

To Bio-Ontologies 2009

So, this year of Bio-Ontologies is upon me; I'm sitting in the airport waiting to fly in the wrong direction; although I've noticed that the airport signs no longer call this "waiting time" but "shopping time". It's 12 years on now; I can't remember whether this makes it the oldest SIG at ISMB, but it must be close. Perhaps it is surprising that a small meeting like this has lasted so long, but during it's time the use of ontologies within biology has blossomed; to some extent, this is true of the outside world also. This year has carried on with the trend. Gone are the days that we used to get enough papers to fill the day, but no more; we've stretched the day out, we've added a poster session but still we get more. The number of attendees has gone up somewhat also. It…