Sunday, February 27, 2011

An Ethical Foreign Policy

Saddam Hussein helped me to understand the role of the UN and the nation state when he gassed the inhabitants of the Iraqi town of Helabja in 1988. I was 18, and it was the first time I ever saw a dead body on TV. The attack killed something like 5,000 people and injured many more. The reaction of my own country, the UK, it’s allies and the UN was muted and in some quarters seemed to involve trying to blame the Iranians, with whom Iraq was at war.

Then the realisation struck: the UN pretty much leaves you to your own devices within your own borders because to do otherwise would seriously worry its member states. Fancy mandating the interference of a league of nations into your country’s affairs? Because once the principle is established then quite a large fraction of the members of the UN could find calls for interference within their borders. And if you think that sort of response is just for nasty countries like Russia and China, then observe the British response to European Court of Human Rights judgements against it.

Another formative event for me was the end of the first Gulf War: after Iraqi forces had been ejected from the recently invaded Kuwait. The Allied forces were heading towards Baghdad, the Iraqi people were rising up against their leader. And then we stopped and I remember John Major giving a press conference saying, when asked about supporting the Iraqis against their leader, “I don’t remember asking them to revolt” or words to that effect. Surely this, more than any other, was a time to act ethically, to depose the tyrant rather than pop him back in his box with the people of Iraq, a bulwark against our greater Satan: Iran. Invade another country: very bad, but do what you want inside your own borders.

A motivating factor for this post is the wave of revolutions across North Africa and the Middle East in Tunisia, Algeria, Egypt, Yemen, Bahrain, and Libya triggered, it seems by poor economic circumstances, and perhaps the success of other democratic revolutions. Largely these are countries with whom we’ve been happy to do business, Tunisia and Egypt are even popular tourist destinations.

Libya has been ruled by Gaddafi for the last 42 years, he has always seemed to be genuinely quite bonkers and was a great enemy of the UK for a number of years (supporting the IRA, and responsible for the shooting of Yvonne Fletcher outside the Libyan embassy). More recently he has been back in favour but now he’s back out of favour again. Who can keep up with all these changes? His return to favour in 2004 was stimulated by his renunciation of “weapons of mass destruction” and support for the “War on Terror”. It’s interesting that in his recent speech he tried to hit that button again to regain support from his old allies in the West.

Egypt has long been a friend of the West, largely because it has taken the lead amongst Arab nations in maintaining diplomatic relationship with Israel. For this we conveniently ignore its not particularly good democratic and human rights record. Now the people have managed to oust Hosni Mubarak it turns out that as a nation we weren’t all that keen – who knew? It must be more than a little galling to the opposition in Egypt that we’re willing to show how much we support them just when that support is no longer needed.

Mixed in with all this is David Cameron is off to the Middle East for an arms fair; we’re often told that the weapons, tear gas, rubber bullets that we sell to nations will definitely not be used to suppress their own populations. Quite why we should think this is even remotely plausible I don’t understand. Did the nice dictator promise not to use them against his own population? What else is he going to do with them?

It would be nice to think we could run a foreign policy whereby we didn’t support people who weren’t very nice and in fact actively sought their removal from office perhaps by more widespread use of travel restrictions and financial embargoes on the leadership, as we seem to be heading with Libya now.

Working out which countries are nice and which are nasty shouldn’t be too hard: we could use the Democracy Index, perhaps the Press Freedom Index, or even the use of the death penalty as a proxy. Indices such as this are always going to be a bit subjective but the same cast appear at the bottom again and again.

I can’t help thinking that across the world people of many nations remember; they remember who we supported and who we didn’t. We in Britain remember, just look at our media regarding Germany, and that was over 60 years ago. Just think what the people of other countries will remember in the years to come.

Saturday, February 19, 2011

Photographs, videos and GPS

02 February WestendorfThis post is in part a memory aid but it may be interesting to other amateur photographers, and organisational obsessives.

My scheme for holidays and walks out is to take cameras (Canon 400D, Casio Exilim EX-S10), sometimes a video camera (Canon Legaria FS200) and a Garmin GPS 60 which I use to provide information for geotagging photos rather than navigation, although I once used it as an altimeter to find the top of a cloud covered Lake District mountain. Geotagging is the process of labelling a camera image with the location at which it was taken.

I save images as JPEG, I should probably use RAW format on the SLR but the workflow is more complicated and I rarely do anything particularly advanced with images after I’ve taken them other than cropping, straightening and a little fiddling with contrast. Once home I save all the images from a trip to a directory whose name is as follows:

Z:\My Pictures\[year]\[sequence number] – [description] – [date]

So for my recent skiing trip:

Z:\My Pictures\2011\003 - Hinterglemm – 29jan11

I leave the image file names unaltered. Padding the sequence number with zeroes helps with sorting. The idea of this is that I can easily find photos of a particular trip just using the “natural” ordering of the file system, I don’t rely on 3rd party software and I’m fairly safe from the file system playing sneaky tricks with creation dates. The Z: drive on my system is network attached storage, so it can be accessed from both my desktop and laptop computers. I back this up to the D: drive on my desktop PC using Syncback and I also copy it periodically to a portable drive which I keep at work. Syncback synchronises the files in two directories, I use this in preference to “proper” backup because it doesn’t leave my files in a big blob of an opaque backup format (I got burnt by this when using NTbackup in the past). The drawback is that I can’t go back to a snapshot in time but I’ve never felt the need to do this.

In addition to the images, I also save the GPS file in GPX format to the directory, this is downloaded and converted using Mapsource which is Garmin’s interfacing software. GPX is a format based on XML so is easy to read programmatically and even by humans. I do little inside Mapsource other than converting, and for a multi-session trip, stitching all the tracks together into a single file. Another handy tool in this area is GPSBabel which converts GPS data between a multitude of formats.

I use Picasa for photo viewing and labelling: it’s free, it has basic editing functions, it allows labelling and geotagging of photos in a fairly open manner and it does interesting stuff like face recognition too. As well as all this it links to Google’s web albums, so I can share photos, and it talks nicely to Google Earth.

Both geotagging and labelling images use EXIF (Exchangeable image file format) this is a way of adding metadata to images; nice because it’s a standard and the data goes in the image file so can’t get lost. EXIFtool is a very useful command-line tool for reading and writing EXIF data, and it can be integrated into your own programs. Software like Picasa, and websites such as Flickr are EXIF aware so data saved in this format can be visible in a range of applications. 

It is possible to geotag photos manually with Picasa via Google Earth but I’ve collected a GPS track so this is not necessary. There are free software packages to do this but I’ve written my own for fun. The process is fairly simple: the GPS track has a timestamp associated with each location point and the photos from the camera each have a timestamp. All the geotagging software has to do is find the GPS point with the timestamp closest to that of the photo and write that location data to the image file in the appropriate EXIF fashion. The only real difficulty is matching up the offset between image time and GPS time - for this I take a picture of my GPS which shows what time it thinks it is and label this “GPS”.

In fact I usually label photos after they have been geotagged: photos can be exported from Picasa as a Google Earth compatible KMZ file and then upload into Google Earth along with the GPS track in GPX format making it possible to see where you were when you took the photo, which makes labelling easier.

I use www.gpsvizualiser.com to create images of GPS tracks on top of satellite images, this is a bit more flexible than just using Google Earth, I must admit to being a bit bewildered with the range of options available here. Below is an example where height is coded with colour.

GPSTrackHinterglemm

As I go around I sometimes take sets of images to make a panorama. The final step is to stitch together these multiple images to make single, panoramic views, I now use Microsoft Image Composite Editor to do this, it preserves the EXIF data of the input image and does a nice auto-crop. My geotagging program flags up images that were taken close together in time as prospective panoramic images. The image below is a simple to image panoramic view (from Hinterglemm)

Panorama towards Schattberg West from below Schattberg Ost

I mentioned video in the title: at the moment I’m still a little bemused by video. I use the same directory structure for storing videos as I do for pictures but I haven’t found album software I’m happy with or a reliable way of labelling footage – Picasa seems promising although the playback quality is a bit poor. ffmpeg looks like a handy programming tool. Any suggestions welcome!

Monday, February 14, 2011

Book Review: For all the tea in China

ForAllTeaChinaBookI’ve been on a bit of a reading spree: next up is “For all the tea in China” by Sarah Rose. This is the story of Robert Fortune and his trips to China in the mid-nineteenth century to obtain tea plants and the secret of tea manufacture for the East India Company to use in India.

Robert Fortune (1812-1880) was a botanist with a modest background. Starting his working life at the Royal Botanic Garden Edinburgh, he later became Curator of the Chelsea Physic Garden. These were relatively poorly paid posts, however there were few such positions to support a professional botanist without their own means of support. He made several substantial visits to the Far East, funded by the Horticultural Society of London and the British East India Company. He died a wealthy man in large part through the wide range of plant introductions he had made, as well as through sales of artefacts he had acquired in the Far East. The list of introductions is well worth a skim through for the modern gardener:

The East India Company had been given a monopoly of trade to the Far East in 1600, through this monopoly they had built a lucrative trade in silk and tea from China, as well as effectively running India. The trades from China were matched with trades into China of opium from India, by the middle of the 19th century addiction to opium was a significant problem in China. The volume of trade it brought made the East India Company a very significant contributor to British government income (of order 10%). Although there are now many global corporations, the East India Company was one of the first and in many ways most powerful. The company was ultimately to lose its dominance following the Indian Mutiny in 1858, and was finally wound up in 1874. The mutiny was likely the cumulation of a long process since the monopoly that the East India Company enjoyed was not popular with free-marketeers who were starting to come to the fore.

At the time of Fortune's first trip to China in 1845 the English had long been drinking tea imported from China, in exchange for opium grown in India. The English drank both green and black teas, although unlike the Chinese they added milk and sugar (obtained from another British colonial outpost). The Chinese were keen to keep the secret of both the tea plant, and its manufacture into tea leaves for making tea. Whilst the British, in particular the East India Company were keen to get these secrets believing (correctly) that tea would grow well in Himalayan India and would make a good profit. Some tea was already being grown in the Assam district of India but is was derived from inferior Chinese plants. The tea plant is Camellia sinensis a close relative of the decorative camellias of which Fortune also introduced some species.

Before Fortune's first visit to China it had not even been established that black tea and green tea came from the same plant, but were processed differently. His trips required considerable subterfuge: Westerners had only recently been allowed into anywhere other than a limited number of ports in China, as a result of the first Opium War and Fortune's activities went considerably beyond what was allowed even under these revised regulations. One of Fortune's discoveries was that green tea had been coloured by the Chinese for the export market using Prussian Blue (which is toxic) and gypsum. Following a couple of false starts he was eventually able to transport a large number of highest quality tea plant seedlings to Darjeeling in India, as well as providing skilled tea makers and extensive notes on the tea making process.

The key to Fortune's success in shipping out tea plants from China were Wardian cases, these are essentially sealed glass environments containing soil and some water. Plants, or more importantly, troublesome seeds could be sealed into these containers and as long as they remained sealed, and given some light there would be a good chance of their biological cargo surviving a lengthy sea journey through a range of climates. Prior to this discovery long distance transplantations were tricky. Nowadays we see Kew Gardens as largely a place of leisure, but in the 19th century it was very much at the heart of the Empire in terms of facilitating the movement of plants around the world for commercial reasons. This type of activity was also an early interest of the Royal Society.

It's difficult not to draw parallels between the state sanctioned opium trade which the United Kingdom used to support, and its current attitude to drug smuggling. Nor between the industrial espionage of the East India Company in the 19th century, and the current issues with the Chinese approach to intellectual property.

I found the sections of the book reporting Fortune's travels a bit unfulfilling: they seemed to be a sequence of travel anecdotes involving the mischief caused by his Chinese servants - this style does affect other parts of the books. However, more generally the book made me curious to know more about the East India Company, the Opium Wars and so forth and I felt I'd learnt something about the introduction of tea to India.

I'm tempted by Fortune's book: Three years' wanderings in the Northern Provinces of China 

Thursday, February 10, 2011

Book review: The Immortal Life of Henrietta Lacks

This post can be read in full here: http://www.ianhopkinson.org.uk/2011/02/book-review-the-immortal-life-of-henrietta-lacks/HenriettaLacks

The Immortal Life of Henrietta Lacks by Rebecca Skloot is an unusual book. It is part cell biology: the story of cell-lines kept alive perpetually in the laboratory; it is part story of Henrietta Lacks and her family from whom the first of these cell-lines (called HeLa) was derived; it is the story of how medical ethics has evolved over the last 60 years and it is part story of the story.
Henrietta Lacks’ cells were taken at the Johns Hopkins Hospital in Baltimore in 1951 and cultured by George Gey during her treatment for an aggressive cervical cancer from which she subsequently died at the age of thirty-one, later that year. Gey, with the help of Lacks’ cells, was the first person to successfully maintain a cell-line. The cells cultured are cancer cells rather than normal cells. Following his work a wide range of other cell-lines were cultured from a variety of organs and species, however it subsequently turned out that many of these were actually the HeLa cell-line which turned out to be particularly pernicious. Researchers would start with a culture of different cells, but they would die to be replaced by HeLa cell “contaminants”.
Once Gey had started the cell-line he gave them away freely to other researchers, however it was not very long before the HeLa cells were being sold commercially. An early application of the HeLa cell-line was in testing the newly developed Salk vaccine for polio, the first of many, many applications. More dubiously Chester Southam injected the cancerous cells into prisoners, and subsequently into many patients. This was with the view to seeing if they developed within the body, the problem was that the patients were not informed that the cells were cancerous. This practice ended when three young Jewish doctors aware of the Nuremburg Code, proposed as a result of post-war trials of Nazi doctors responsible for horrific human experimentation, refused to take part in the experiments.
To my mind the unique part of the book is the in depth coverage of Henrietta Lacks’ family through to the present day. Rebecca Skloot tells in detail the long persistent trail to talk to them, an African-American family who certainly have good reason to be suspicious of white people asking about Henrietta. The Lacks’ were never a model family but then there is no reason for them so to be. Race and medicine have a poor history in the US. The Tuskagee Syphilis experiments perhaps being the lowest point, in which African-Americans were denied effective treatment for the disease so the full course of its symptoms could be observed. Other racism is less direct, as relatively poor Americans the Lacks family have reduced access to the treatments arising from the cells of their ancestor. If she were a white child, Elsie Lacks, Henrietta’s mentally disabled daughter would not have died at the Crownsville State Hospital, certainly not in such terrible circumstances.
In 2011 the cell lines derived from Henrietta Lacks would not have been called HeLa. Possibly her cells would not have been collected at all, requiring full informed consent. Her name would have become known to all including the family. The family would not have learned of the gruesome details of her death at the “hands” of an aggressive cervical cancer via a book whose author had been given Henrietta Lacks medical records.
To my mind the real shortcomings of the scientists were not in what they did in the first instance but how they failed to support the Lacks’ not with money but with information. Until Skloot and Christoph Lengauer showed them and spoke to them, no-one had explained exactly what cells had been taken, what had been done with them, the significance of Henrietta Lacks to science or the specific knowledge of her condition did or did not have to their health in terms which they could understand; giving them a book on cell biology was not enough. 
Skloot relates three stories of discoveries arising from a specific persons’ cells: the Lacks story and those of Ted Slavin and John Moore. Slavin was born a haemophiliac and as a result of the blood transfusions that he had to receive as a result of his condition he contracted Hepatitis B, however he did not succumb to this disease, he was immune. His doctor told him that this made him special, and that his blood was valuable and he subsequently profited from this knowledge by selling samples of his blood. John Moore, on the other hand, had hairy-cell leukemia and only discovered his blood was valuable after his doctor had patented his cell-line, he was subsequently involved in lengthy legal action to regain some control of his cells.
As a scientist whose work once touched, peripherally on human tissue culture and who recently had surgery from which such tissue was taken this is a somewhat uncomfortable story. In the project I worked on a postdoc was tasked with organising consent forms for, I think, blood vessels removed during a procedure i.e. they were a by-product. In this instance the specifics of the cells were not important – they were destined for frequently unsuccessful experiments. From our point of view the best possible outcome would been that the materials we had synthesised proved to be a congenial home for blood vessel wall cells. In this case nothing of monetary value is derived directly from the donors cells.
For my own part: I have no problem with researchers using my medical offcuts, I do feel unhappy with the idea that my specific cells might be valuable and that I might not get a proportion of that value.

Monday, February 07, 2011

Hinterglemm

CIMG1253
A view up the Saalbach-Hinterglemm valley, Hinterglemm is in the distance
Mrs SomeBeans and I have been skiing again, staying in Hinterglemm in the SkiCircus area of Austria. Hinterglemm is the upper of the two main villages in a valley running east-west, Saalbach is the larger village and gets more sun but the lifts are spread out around the village. We went with Inghams, flying from Manchester to Salzburg, the transfer time is about 2 hours, with a stops at Zell am See and Saalbach which are both relatively close. Salzburg airport can’t really cope with the number of package tour flights it gets in a short period.

Conditions last week were fantastic, for the first four days of our holiday we didn’t see a single cloud, temperatures were fairly low but there was no new snow during the week. Skiing was best between about 8:30am-10am before most people, other than the locals, had got out on the slopes. I suspect getting up at 7:30 every morning is not most people’s idea of a holiday.

Hinterglemm has a lot of lift capacity out of the village, a short gondola ride takes you to a set of four chairlifts on the south-facing side of the valley and two longer gondolas take you to summits on the north facing side of the valley. The link to Saalbach on the south side of the valley is a bit odd: from Saalbach it an an old 3-seater chair lift, followed by a long t-bar drag lift and an old 2-seater chair lift. The return from Hinterglemm the link is a bit easier but still involves a short t-bar. A nice range of skiing with some big wide pistes, pistes through trees and a few long black runs on the north-facing side of the valley which we didn’t try out. The area is pretty well linked up with some circular routes, and the ability to get to pretty much anywhere in the linked are in a couple of hours at most.

We stayed at the Hotel Glemmtalerhof in a large north-facing room looking towards the Reiterkogelbahn which could have accommodated 5 people. The hotel is right in the middle of the village with only a short (~200m) walk to either the Reiterkogelbahn taking you onto the south-facing slopes or the Unterschwarzachbahn taking you to the north-facing slopes. Food was fabulous and overall a good hotel. Drawbacks were that is was a bit noisy, since it sat on the middle of the village and there seemed to be an awful lot of smoking being done in the reception, cafe and bar area. Across the valley, right next to the Reiterkogelbahn, was the Hotel Alpine Palace Wolf which looked very posh and maybe worth a go in future.

Some of the other guests were a little odd: Sunday night as Gala dinner night featured a dessert buffet, which they ate from copiously pretty much all the way through the meal. Mrs SomeBeans, qualified to teach food hygiene, observed sufficient prodding and sniffing of the desserts that she preferred not to partake.

Once again we were plagued by “other people”. This time the party who didn’t realise that “Boarding at gate 7” meant: “get on the plane”, and one of whose children spent the flight gently pummelling my back through the seat back – I was calm since I decided to treat it as a free massage!

Overall a very good holiday with some fabulous skiing: this trip was unusual in that we were able to travel in term time – normally we are restricted to school holidays. I suspect the lift system in SkiCircus copes fairly well with February half-term, so might give it a go then next year.

A selection of photos:

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This is "twinkly snow", as you ski past it the ice crystals twinkle.

CIMG1233
Mrs SomeBeans and I on a chairlift, we're a bit camera shy

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Great snowfields near the top of a mountain
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The Leoganger Steinberge, a panoramic view from Wildenkarkogel

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Looking towards Hinterglemm,invisible over the edge, with pretty clouds and icicles
GPSTrackHinterglemm
Obviously I captured GPS data, we covered about 180 miles in 7 days including uplift

More photos here, along with captions.

Sunday, February 06, 2011

Book review: Lives of the Engineers

blucher_killingworth_1814Reading the biography of Isambard Kingdom Brunel got me interested in engineers; Rolt, the author of the Brunel biography, mentioned the biographical writings of Samuel Smiles: in particular his “Lives of the Engineers”. This post is about one part of the full work: ”The Locomotive. George and Robert Stephenson” this edition was published in 1879 although the original was written in the years following George Stephenson’s death, around 1860. The title describes its contents. George Stephenson, although not the inventor of the first locomotive, was instrumental in making it a workable proposition and his son (Robert) continued in his fathers line of work, although died quite young.

George Stephenson (1781-1848) was born and grew up around Newcastle-upon Tyne, at the time the area was riddled with coal workings. His father was employed as a fireman working on the pumping engine at Wylam colliery.

George is described as an inquisitive child very interested in nature, and constructing models of the machines he saw around him. He started working with the engines at the colliery as a child progressing to ever more responsible jobs at a range of collieries. Alongside this he did various bits of other work, such as shoe-last making and clock and watch repairs to bring more money in; paying to be taught to read and do arithmetic as he entered his late teens. I can’t help making a parallel with Joseph Banks who benefited from a more prosperous upbringing. It’s worth noting here that Samuel Smiles also wrote a book called “Self-help”, it’s clear he’s very much taken with George Stephenson as a self-made man, he is also very much taken with the entirely private nature of the enterprises he undertook.

Steam engines had been used to pump water out of mineworkings since around 1710 with the invention of the steam engine by Thomas Newcomen. These were large, inefficient engines. The first attempts at making a traveling engine seemed to take place around 1769 by Cugnot in France with the first practical moving steam engines due to Richard Trevithick around the turn of the century (1800). In the meantime various miner owners were experimenting with modified roadways to ease the movement of large amounts of heavy stuff (ores, coal) from mine-head to waterway for onward transport. This started with the laying down of wooden roads, followed by metal plates (1738) and finally rails (1776). It’s intriguing to see how the coalescence of these elements around mineworkings led naturally to the invention of the locomotive. For the early railroads, such as the Manchester-Liverpool there was a very real question as to whether locomotives or horses should be used as moving force.

The Manchester-Liverpool line really is key here: it was built out of desperate need for better commercial communication between Liverpool (port) and Manchester (manufacturing centre). In common with many lines there was enormous opposition on the ground from landowners and canal owners. It is also here that the modern locomotive comes into being in the form of the “Rocket”, reliability and commercial viability being absolutely key. In common with Brunel, Stephenson also faced parliamentary committees scrutinising the appropriate railway bill. In early discussions Stephenson argued that the locomotives would not exceed a speed of 12 miles an hour, so as not to scare the parliamentarians. Early railway lines were built with goods in mind, but turned out to be immensely, surprisingly popular for the carrying of passengers. The alternative being slower, less comfortable horse-drawn carriages of much lower capacity. George Stephenson was also responsible for at least some of the initial surveying of routes.

The rate at which the rail network came into being is truly astounding. The Manchester–Liverpool was opened in late 1830 by 1843 there were lines linking London to Birmingham, Southampton, Bristol, Brighton and Dover. There were also lines from Liverpool to Manchester and Leeds and onwards to York and Middlesborough, there was also a line between Newcastle and Carlisle. Follow this there was a wild burst of speculative activity, with several hundred proposals to parliament for new lines in 1845 (maps here).

Also covered in this book is Robert Stephenson (1803-1859), George Stephenson’s son. George gave Robert the education that he wished for himself. Although Robert started his engineering career working in the Stephensons’ locomotive workshop, set up in Newcastle, prior to the building of the Manchester-Liverpool he went on to be involved in the surveying and planning of new railway lines. Most notably bridges such as the Britannia Bridge across the Menai Straits, the Victoria Bridge across the Lawrence Seaway and the High Level Bridge in Newcastle. These first two were both originally “tube” design but were modified in the case of the Victoria bridge to a trestle design and the Britannia bridge was destroyed by fire in 1970. The building of the railways necessitated a huge expansion in bridge building: big, strong, well-built bridges.

Overall an enjoyable read although I suspect Samuel Smiles does not comply with modern historical best practice, with his enthusiasm for self-help, and anecdotes shining through in a number of places. Nevertheless, I feel motivated to read some more of his biographical work of the engineers of the 18th and 19th century.

References

Full text of a number of Samuel Smiles books available here.