Aug 26 2015

Book Review: Stargazers–Copernicus, Galileo, the Telescope and the Church by Allan Chapman

stargazersIt’s been a while since my last book review here but I’ve just finished reading Stargazers: Copernicus, Galileo, the Telescope and the Church by Allan Chapman.

The book covers the period from the end of the 16th century, the time of Copernicus and Tycho Brahe, to the early 18th century and Bradley’s measurement of stellar aberration passing Galileo, Newton and others on the way. Conceptually this spans the full transition from a time when people believed in a Classical universe with earth at its centre, and stars and planets plastered onto crystal spheres, to the modern view of the solar system with the earth and other planets orbiting the sun.

This development parallels that in Arthur Koestler’s classic book "The Sleepwalkers”, however Chapman’s style is much more readable, his coverage is broader but not so deep. Chapman introduces a wealth of little personal anecdotes and experiments. For instance on visiting Tycho Brahe’s island observatory he recounts a meeting with a local farmer who had in his living room a marked stone from the Brahe’s observatory (which had been dismantled by the locals on Brahe’s death). Brahe was hated by his tenants for his treatment of them, a hate that was handed down through the generations. Illustrations are provided in the author’s own hand, which is surprisingly effective. He discusses his own work in reconstructing historical apparatus and observations.

Astronomy was an active field from well before the start of this period for a couple of reasons: firstly, astrology had been handed down from Classical times as a way of divining the future. To was believed that to improve the accuracy of astrological predictions better data on the locations of heavenly bodies over time was required. Similarly, the Christian Church required accurate astronomical measurement to determine when Easter fell, across increasingly large spans of the Earth.

The period covered by the book marks a time when new technology made increasingly accurate measurements of the heavens possible, and the telescope revealed features such as mountains on the moon, sunspots and the moons of Jupiter visible for the first time. Galileo was a principle protagonist in this revolution.

Amongst scientists there is something of the view that the Catholic Church suppressed scientific progress with Galileo the poster boy for the scientist’s case. Historians of science don’t share this view, and haven’t for quite some time. Looking back on Sleepwalkers, written in 1959 I noted the same thing – the historians view is generally that Galileo brought it on himself in the way he dismissed those that did not share his views in rather offensive terms. Galileo lived in a time when the well-entrenched Classical view of the universe was coming under increased pressure from new observations using new instruments. In some senses it was the collision with the long-held Classical view of the universe which led to his problems, the Church being more committed to this Classical view of the physical universe rather than to anything proposed in Scripture.

The role of the Church in promoting, and fostering science, is something Chapman returns to frequently – emphasising the scientific work that members of the Church did, and also the often good relationships that lay “scientists” of different faiths had with Church authorities.

Chapman introduces some of the lesser known English (and Welsh) contributors to the story. Harriet who made the earliest known sketches of the moon. The Lancashire astronomers, who made the first observations of the transit of Venus. John Wilkins whose meetings were to lead to the foundation of the Royal Society. He also notes the precedent of the Royal College of Physicians, formed in 1518. The novelty of the Royal Society when compared with earlier organisations of similar character was that the Fellows were responsible for new appointments, rather than them being imposed by a patron. This seems to have been an English innovation, repeated in the Oxbridge colleges, and Guilds.

Relating to these English astronomers was the development of precision instruments in England. This seems to have been spurred by the Dissolution of the monasteries. The glut of land, seized by Henry VIII, became available to purchase. The purchase of land meant a requirement for accurate surveying, and legal documents. Hence an industry was born of skilled men wielding high technology to produce maps.

I was distracted by the presence of Martin Durkin in the acknowledgements to this book, he was the architect of “polemical” Channel 4 documentary “The Great Global Warming Swindle”, so it cast doubt in my mind as to whether I should take this book seriously. On reflection Chapman’s position as presented in this book seems respectable, but it is interesting how a short statement in the acknowledgements made me consider this more deeply.

Overall, Stargazers is rather more readable than Sleepwalkers, not quite so single-tracked in it’s defence of the Catholic Church as God’s Philosophers and a different proposition to Fred Watson’s book of the same name, which is all about telescopes.

Aug 21 2015

The London Underground – Can I walk it?

caniwalkitThere are tube strikes planned for 25th August 2015 and 28th August 2015 with disruption through the week. The nature of the London Underground means that it is not all obvious that walks between stations can be quite short. This blog post introduces a handy tool to help you work out “Can I walk it?

You can find the tool here:

To use it start by selecting the station you want to walk from, either by using the “Where am I?” dropdown or by clicking one of the coloured station symbols (or close to it). The map will then refresh, the station you selected is marked by a red disk, the stations within 1.5 miles of the starting station are marked by an orange disk and those more than 1.5 miles away are marked by a blue disk. 1.5 miles is my “walkable” threshold, it takes me about 25 minutes to walk that far. You can enter your own “walkable” threshold in the “I will walk” box and press refresh or select a new starting station to refresh the map.

The station markers will show the station names on mouseover, and the distances to the starting station once it has been selected.

This tool comes with no guarantees, the walking distances are estimated and these estimates may be faulty, particularly for river crossings. Weather conditions may make walking an unpleasant or unwise decision. The tool relies on the user to supply their own reasonable walking threshold. Your mileage may vary.

To give a little background to this project: I originally made this tool using Tableau. It was OK but tied to the Tableau Public platform. I felt it was a little slow and unresponsive. It followed some work I’d done visualising data relating to the London Underground which you can read about here.

As an exercise I thought I’d try to make a “Can I walk it?” web application, re-writing the original visualisation in JavaScript and Python. I’ve been involved with projects like this at ScraperWiki but never done the whole thing for myself. I used the leaflet.js library to provide the mapping, the Flask library in Python to serve the data, Boostrap to make it look okay and Docker containers on Digital Ocean to deploy the application.

The underlying data for this tool comes from Open Street Map, where the locations of all the London Underground stations are encoded as latitude and longitude. With this information in hand it is possible to calculate the distances between stations. Really I want the “walking distance” between stations rather than the crow flies distance which is what this data gives me. Ideally to get the walking distance I’d use Google Directions API but unfortunately this has a rate limit of 2500 calls per day and I need to make about 36000 calls to get all the data I need!

The code is open source and available in this BitBucket repository:

Comments and feedback are welcome!

Jul 05 2015

Portinscale 2015

We had an abortive trip to Portinscale in the Lake District for our summer holiday last year, ended prematurely by illness. This year we’re back and have improved greatly on last years performance! Portinscale is just outside Keswick, a small town at the head of Derwentwater. In the past we would have stayed a little further from civilisation so we could go for longish walks from the door but with 3 year old Thomas a bunch of attractions in easy distance is preferable.

Day 1 – Sunday

Rather than fit packing and driving the relatively short distance to Portinscale from Chester into a day, whilst simultaneously meeting the arrival time requirements, we travelled up on Sunday morning. In the afternoon we went to Whinlatter Forest Park, a few miles up the road. The entrance is guarded by a fine sculpture of an osprey.


It has an extensive collection of trails for pedestrians and cyclists. A Go Ape franchise for people who like swinging from trees, some Gruffalo / Superworm themed trails for children. And a wild play area featuring Thomas’ favourite thing – a pair of Archimedes Screws:


There’s also a very nice cafe. We visited Whinlatter several times of an afternoon.

Day 2 – Monday

We went to Mirehouse in the morning, a lakeside estate with a smallish garden and a rather pleasant walk down to Bassenthwaite Lake.


There’s a fine view from the lake down towards Keswick.


In the afternoon we went to the Pencil Museum in Keswick, not a large attraction but Thomas liked Drew the giant and we got 5 pencils for an outlay of £3.

Day 3 – Tuesday

In the morning we went to Threlkeld Mining Museum. Its full of cranes and various bits of mining machinery from the past 100 years or so. There is a narrow gauge railway line which runs half a mile or so to the head of the quarry from the visitor centre. Threlkeld is not a slick affair but it is great fun for a small child fond of cranes, and the volunteers are obviously enthused by what they are doing. To be honest, I’m rather fond of industrial archaeology too!

Basically, they collect cranes.


All of which are in some degree of elegant decay


For our visit they were running a little diesel train:


In the afternoon we walked down to Nichols End, a marina on Derwentwater close by our house in Portinscale.


Day 4 – Wednesday

My records show that we last visited Maryport 15 years ago. It has the benefit of being close to Keswick – only half an hour or so away. We enjoyed a brief paddle in the sea, on a beach of our own before heading to the small aquarium in town.


Whinlatter Forest Park once again in the afternoon.

Day 5 – Thursday

On leaving the house we thought we would be mooching around Keswick whilst our car was being seen to for “mysterious dripping”, as it was Crosthwaite Garage instantly diagnosed an innocuous air conditioning overflow. So we headed off to Lodore Falls, alongside Derwentwater before returning to Hope Park in Keswick.

Thomas declared the gently dripping woods on the way to Lodore Falls to be “amazing”:


The falls themselves are impressive enough, although the view is a little distant when you are with a small child, who coincidently loves waterfalls and demands their presence on every walk:


Hope Park was busy, but it is a pretty lakeside area with formal gardens and golf a little back from the shore.


In the afternoon we visited Dodd Wood, which is just over the road from Mirehouse, where we did a rather steep walk.

Day 6 – Friday

On our final day we visited Allan Bank in Grasmere, this is a stealth National Trust property, formerly home to William Wordsworth and one of the founders of the National Trust, Canon Rawnsley. “Stealth” because it is barely advertised or sign posted, and is run in manner far more relaxed than any other National Trust place I’ve visited. It’s a smallish house:

Allan Bank, Grasmere

With glorious views:


The house was damaged by fire a few years ago, and has only really been refurbished in as far as making it weather proof. Teas and coffees are available on unmatching crockery for a donation (you pay for cake though), and you’re invited to take them where you please to drink. There is a playroom ideally suited to Thomas’ age group, along with rooms Wordsworth and Rawnsley occupied upstairs.


It has the air of a hippy commune, and it’s sort of glorious.


Outside the grounds are thickly wooded on a steep slope, there is a path approximately around the perimeter which takes in the wild woods, several dens and some lovely views.


We glimpsed a red squirrel in the woods.


As Thomas wrote, it was "”Fun”!


In the afternoon a final trip to Whinlatter Forest Park.

We left on Saturday amidst heavy early morning rain, the only serious daytime rain of the holiday – probably the best week of weather I’ve had in the Lake District!

Jul 05 2015

Book review: Your Inner Fish by Neil Shubin

yourinnerfishI’m holiday so I’ve managed some more reading! This time Your Inner Fish by Neil Shubin. As recommended by my colleague, David Jones, at ScraperWiki.

This is ostensibly a story of a particular distant ancestor of humans, the first to walk on land 375 million years ago, but in practice it is broader than that. It is more generally about what it is to be a modern palaeontologist and taxonomy – the classification of living organisms.

Your Inner Fish is a personal account based around the work Shubin and his colleagues did in discovering the Tiktaalik species, the first walker, in the high Canadian Arctic. It turns out the distinguishing features of such animals are the formation of shoulders and a neck, underwater a fish can easily reorient its whole body to get its head facing the right way, on land a neck to move the head independently and shoulders to mount the front legs become beneficial. Shubin hypotheses that animals such as Tiktaalik evolved to walk on dry land to evade ever larger and more aggressive aquatic predators.

Shubin recounts the process that led him to the Arctic, starting with his earlier fossil hunting in road cuts in Pennsylvania. The trick to fossil hunting being finding bedrock of the right age being exposed in moderate amounts. Road cuts are a second best in the this instance, being rather small in scale. Palaeontologists find their best hunting grounds in deserts and the barren landscape of the north. Finding the right site is a combination of identifying where rocks of the right age are likely to be exposed and knowing whether someone has looked there already.

Once you are in the field, the tricky part comes: finding the fossils. This is a skill akin to being able to resolve a magic eye puzzle. This is a skill which is learnt practically in the field rather than theoretically in the classroom. I’m struck by how small some of the most important fossil sites are, Shubin shows a photo of the Tiktaalik site where 6 people basically fill it. The Walcott Quarry in the Burgess Shale is similarly compact.

The central theme of the book is the one-ness of life, in the sense that humans share a huge amount of machinery with all living things to do with the business of building a body. These days the focus of such interest is on DNA, and the similarity of genes and the proteins they encode across huge spans of the tree of life. In earlier times these similarities were identified in developmental processes and anatomy. It is significant that researchers such as Shubin span the fossil, development and genetic domains.

Anatomically fish, lizards, mammals and birds represent the reshuffling of the same components. The multiple jaw bones found in sharks and skates turn into the bones of the inner ear in mammals. The arches which form gills in fish morph and adapt in mammals to leave a weird layout of nerves in the face and skull. These similarities in gross anatomical features are reflected in the molecular machinery which drives development, the formation of complex bodies from a single fertilised cell. Organiser molecules are common across vertebrates.

It’s worth noting the contribution of Hilde Mangold to the development story, her supervisor Hans Spemann won the 1935 Nobel Prize for medicine based in part on the work differentiation in amphibian embryos she had presented in her 1923 thesis. She died at the age of 26 in 1924 as the result of an explosion in her apartment building. Nobel Prizes are only awarded to the living.

Why study this taxonomy? The reasons are two-fold, there is the purely intellectual argument of “because it is there”. The shared features of life are one of the pieces of evidence underpinning the theory of evolution. The second reason is utilitarian, linking all of life into a coherent structure gives us a better understanding of our own bodies, and how to fix them if they go wrong.

As examples of our faulty body Shubin highlights hiccups and hernias. Hiccups because the reflexes leading to hiccups are the descendants of the reflexes of tadpoles which allowed them to breathe through gills as well as lungs. Hernias because the placement of the testes outside the abdomen is an evolution from our fish ancestors who kept gonads internally – external placement is a botched job which leads to a weakness in the abdomen wall, particularly in men.

This book is shorter and more personal than Richard Dawkins’ and Stephen Jay Gould’s work in similar vein.

I liked it.

Jun 29 2015

Book review: Gut by Giulia Enders

Gut-by-giulia-endersIt seems a while since I last reviewed a book here. Today I bring you Gut: The Inside Story of our Body’s Most Underrated Organ by Giulia Enders.

The book does exactly what it says on the tin: tell us about the gut. This is divided into three broad sections. Firstly the mechanics of it all, including going to the toilet and how to do it better. Secondly, the nervous system and the gut, and finally the bacterial flora that help the gut do its stuff.

The writing style seems to be directed at the early to mid-teenager which gets a bit grating in places. Sometimes things end up outright surreal, salmonella wear hats and I still don’t quite understand why. The text is illustrated with jaunty little illustrations.

From the mechanical point of view several things were novel to me: the presence of an involuntary internal sphincter shortly before the well-known external one. The internal sphincter allows “sampling” of what is heading for the outside world giving the owner the opportunity to decide what to do with their external sphincter.

The immune tissue in the tonsillar ring was also a new to me, its job is to sample anything heading towards the gut. This is most important in young children before their immune systems are fully trained. Related to the tonsils, the appendix also contain much immune tissue and has a role in repopulating the bacteria in the large intestine with more friendly sorts of bacteria following a bout of diarrhoea.

The second section, on the nervous system of the gut covers things such as vomiting, constipation and the links between the gut and depression. 

The section on the bacterial flora of the gut gathers together some of the stories you may have already heard. For example, the work by Marshall on Helicobactor Pylori and its role in formation of stomach ulcers. What I hadn’t realised is that H. Pylori  is not thought to be all bad. Its benefits are in providing some defence against asthma and autoimmune diseases. Also in this section is toxoplasmosis, the cat-born parasite which can effect rats and humans, making them more prone to risk-taking behaviour.

I was delighted to discover the use to which sellotape is put in the detection of threadworms – potential sufferers are asked to collect threadworm eggs from around the anus using sellotape. I can imagine this is an unusual experience which I don’t intend to try without good reason.

There is a small amount of evangelism for breast-feeding and organic food which I found a little bit grating.

As usual with electronic books I hit the references section somewhat sooner than I expected, and here there is a clash with the casual style of the body of the book. Essentially, it is referenced as a scientific paper would be – to papers in the primary literature.

I don’t feel this book has left me with any great and abiding thoughts but on the other hand learning more about the crude mechanics of my body is at least a bit useful.

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