Category: Book Reviews

Reviews of books featuring a summary of the book and links to related material

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.

Jun 15 2015

Book review: Mastering Gephi Network Visualisation by Ken Cherven

1994_7344OS_Mastering Gephi Network Visualization

This review was first posted at ScraperWiki.

A little while ago I reviewed Ken Cherven’s book Network Graph Analysis and Visualisation with Gephi, it’s fair to say I was not very complementary about it. It was rather short, and had quite a lot of screenshots. It’s strength was in introducing every single element of the Gephi interface. This book, Mastering Gephi Network Visualisation by Ken Cherven is a different, and better, book.

Networks in this context are collections of nodes connected by edges, networks are ubiquitous. The nodes may be people in a social network, and the edges their friendships. Or the nodes might be proteins and metabolic products and the edges the reaction pathways between them. Or any other of a multitude of systems. I’ve reviewed a couple of other books in this area including Barabási’s popular account of the pervasiveness of networks, Linked, and van Steen’s undergraduate textbook, Graph Theory and Complex Networks, which cover the maths of network (or graph) theory in some detail.

Mastering Gephi is a practical guide to using the Gephi Network visualisation software, it covers the more theoretical material regarding networks in a peripheral fashion. Gephi is the most popular open source network visualisation system of which I’m aware, it is well-featured and under active development. Many of the network visualisations you see of, for example, twitter social networks, will have been generated using Gephi. It is a pretty complex piece of software, and if you don’t want to rely on information on the web, or taught courses then Cherven’s books are pretty much your only alternative.

The core chapters are on layouts, filters, statistics, segmenting and partitioning, and dynamic networks. Outside this there are some more general chapters, including one on exporting visualisations and an odd one on “network patterns” which introduced diffusion and contagion in networks but then didn’t go much further.

I found the layouts chapter particularly useful, it’s a review of the various layout algorithms available. In most cases there is no “correct” way of drawing a network on a 2D canvas, layout algorithms are designed to distribute nodes and edges on a canvas to enable the viewer to gain understanding of the network they represent.  From this chapter I discovered the directed acyclic graph (DAG) layout which can be downloaded as a Gephi plugin. Tip: I had to go search this plugin out manually in the Gephi Marketplace, it didn’t get installed when I indiscriminately tried to install all plugins. The DAG layout is good for showing tree structures such as organisational diagrams.

I learnt of the “Chinese Whispers” and “Markov clustering” algorithms for identifying clusters within a network in the chapter on segmenting and partitioning. These algorithms are not covered in detail but sufficient information is provided that you can try them out on a network of your choice, and go look up more information on their implementation if desired. The filtering chapter is very much about the mechanics of how to do a thing in Gephi (filter a network to show a subset of nodes), whilst the statistics chapter is more about the range of network statistical measures known in the literature.

I was aware of the ability of Gephi to show dynamic networks, ones that evolved over time, but had never experimented with this functionality. Cherven’s book provides an overview of this functionality using data from baseball as an example. The example datasets are quite appealing, they include social networks in schools, baseball, and jazz musicians. I suspect they are standard examples in the network literature, but this is no bad thing.

The book follows the advice that my old PhD supervisor gave me on giving presentations: tell the audience what you are go to tell them, tell them and then tell them what you told them. This works well for the limited time available in a spoken presentation, repetition helps the audience remember, but it feels a bit like overkill in a book. In a book we can flick back to remind us what was written earlier.

It’s a bit frustrating that the book is printed in black and white, particularly at the point where we are asked to admire the blue and yellow parts of a network visualisation! The referencing is a little erratic with a list of books appearing in the bibliography but references to some of the detail of algorithms only found in the text.

I’m happy to recommend this book as a solid overview of Gephi for those that prefer to learn from dead tree, such as myself. It has good coverage of Gephi features, and some interesting examples. In places it is a little shallow and repetitive.

The publisher sent me this book, free of charge, for review.

May 22 2015

Book review: Cryptocurrency by Paul Vigna and Michael J. Casey

 

cryptocurrencyThis review was first posted at ScraperWiki.

Amongst hipster start ups in the tech industry Bitcoin has been a thing for a while. As one of the more elderly members of this community I wanted to understand a bit more about it. Cryptocurrency: How Bitcoin and Digital Money are Challenging the Global Economic Order by Paul Vigna and Michael Casey fits this bill.

Bitcoin is a digital currency: the Bitcoin has a value which can be exchanged against other currencies but it has no physical manifestation. The really interesting thing is how Bitcoins move around without any central authority, there is no Bitcoin equivalent of the Visa or BACS payment systems with their attendant organisations or central back as in the case of a normal currency. This division between Bitcoin as currency and Bitcoin as decentralised exchange mechanism is really important.

Conventional payment systems like Visa have a central organisation which charges retailers a percentage on every payment made using their system. This is exceedingly lucrative. Bitcoin replaces this with the blockchain – a distributed ledger in which transactions are encrypted. The validation is carried out by so-called ‘miners’ who are paid in Bitcoin for carrying out a computationally intensive encryption task which ensures the scarcity of Bitcoin and helps maintain its value. In principle anybody can be a Bitcoin miner, all they need is the required free software and the ability to run the software. The generation of new Bitcoin is strictly controlled by the fundamental underpinnings of the blockchain software. Bitcoin miners are engaged in a hardware arms race with each other as they compete to complete units on the blockchain, more processing power equals more chances to complete blocks ahead of the competition and hence win more Bitcoin. In practice mining meaningful quantities these days requires significant, highly specialised hardware.

Vigna and Casey provide a history of Bitcoin starting with a bit of background as to how economists see currency, this amounts to the familiar division between the Austrian school and the Keynesians. The Austrians are interested in currency as gold, whilst the Keynesians are interested in Bitcoin as a medium for exchange. As a currency Bitcoin doesn’t appeal to Keysians since there is no “quantitative easing” in Bitcoin, the government can’t print money.

Bitcoin did not appear from nowhere, during the late 90s and early years of the 20th century there were corporate attempts at building digital currencies. These died away, they had the air of lone wolf operations hidden within corporate structures which met their end perhaps when they filtered up to a certain level and their threat to the current business model was revealed. Or perhaps in the chaos of the financial collapse.

More pertinently there were the cypherpunks, a group interested in cryptography operating on the non-governmental, non-corporate side of the community. This group was also experimenting with ideas around digital currencies. This culminated in 2008 with the launch of Bitcoin, by the elusive Satoshi Nakamoto, to a cryptography mailing list. Nakamoto has since disappeared, no one has ever met him, no one knows whether he is the pseudonym of one of the cypherpunks, and if so, which one.

Following its release Bitcoin experienced a period of organic growth with cryptography enthusiasts and the technically curious. With the Bitcoin currency growing an ecosystem started to grow around it beginning with more user-friendly routes to accessing the blockchain – wallets to hold your Bitcoins, digital currency exchanges and tools to inspect the transactions on the blockchain.

Bitcoin has suffered reverses, most notoriously the collapse of the Mt Gox currency exchange and its use in the Silk Road market, which specialised in illegal merchandise. The Mt Gox collapse demonstrated both flaws in the underlying protocol and its vulnerability to poorly managed components in the ecosystem. Alongside this has been the wildly fluctuating value of the Bitcoin against other conventional currencies.

One of the early case studies in Cryptocurrency is of women in Afghanistan, forbidden by social pressure if not actual law from owning private bank accounts. Bitcoin provides them with a means for gaining independence and control over at least some financial resources. There is the prospect of it becoming the basis of a currency exchange system for the developing world where transferring money within a country or sending money home from the developed world are as yet unsolved problems, beset both with uncertainty and high costs.

To my mind Bitcoin is an interesting idea, as a traditional currency it feels like a non-starter but as a decentralized transaction mechanism it looks very promising. The problem with decentralisation is: who do you hold accountable? In two senses, firstly the technical sense – what if the software is flawed? Secondly, conventional currencies are backed by countries not software, a country has a stake in the success of a currency and the means to execute strategies to protect it. Bitcoin has the original vision of a vanished creator, and a very small team of core developers. As an aside Vigna and Casey point out there is a limit within Bitcoin of 7 transactions per second which compares with 10,000 transactions per second handled by the Visa network.

It’s difficult to see what the future holds for Bitcoin, Vigna and Casey run through some plausible scenarios. Cryptocurrency is well-written, comprehensive and pitched at the right technical level.

May 02 2015

Book review: The Information Capital by James Cheshire and Oliver Uberti

Today I review TheInformationCapitalThe Information Capital by James Cheshire and Oliver Uberti – a birthday present. This is something of a coffee table book containing a range of visualisations pertaining to data about London. The book has a website where you can see what I’m talking about (here) and many of the visualisations can be found on James Cheshire’s mappinglondon.co.uk website.

This type of book is very much after my own heart, see for example my visualisation of the London Underground. The Information Capital isn’t just pretty, the text is sufficient to tell you what’s going on and find out more.

The book is divided into five broad themes “Where We Are”, “Who We Are”, “Where We Go”, “How We’re Doing” and “What We Like”. Inevitably the majority of the visualisations are variants on a coloured map but that’s no issue to my mind (I like maps!).

Aesthetically I liked the pointillist plots of the trees in Southwark, each tree gets a dot, coloured by species and the collection of points marks out the roads and green spaces of the borough. The twitter map of the city with the dots coloured by the country of origin of the tweeter is in similar style with a great horde evident around the heart of London in Soho.

The visualisations of commuting look like thistledown, white on a dark blue background, and as a bonus you can see all of southern England, not just London. You can see it on the website (here). A Voroni tessellation showing the capital divided up by the area of influence (or at least the distance to) different brands of supermarket is very striking. To the non-scientist this visualisation probably has a Cubist feel to it.

Some of the charts are a bit bewildering, for instance a tree diagram linking wards by the prevalent profession is confusing and the colouring doesn’t help. The mood of Londoners is shown using Chernoff faces, this is based on data from the ONS who have been asking questions on life satisfaction, purpose, happiness and anxiety since 2011. On first glance this chart is difficult to read but the legend clarifies for us to discover that people are stressed, anxious and unhappy in Islington but perky in Bromley. You can see this visualisation on the web site of the book (here).

The London Guilds as app icons is rather nice, there’s not a huge amount of data in the chart but I was intrigued to learn that guilds are still being created, the most recent being the Art Scholars created in February 2014. Similarly the protected views of London chart is simply a collection of water-colour vistas.

I have mixed feelings about London, it is packed with interesting things and has a long and rich history. There are even islands of tranquillity, I enjoyed glorious breakfasts on the terrace of Somerset House last summer and lunches in Lincoln’s Inn Fields.  But I’ve no desire to live there. London sucks everything in from the rest of the country, government sits there and siting civic projects outside London seems a great and special effort for them. There is an assumption that you will come to London to serve. The inhabitants seem to live miserable lives with overpriced property and hideous commutes, these things are reflected in some of the visualisations in this book. My second London Underground visualisation measured the walking time between Tube station stops, mainly to help me avoid that hellish place at rush hour. There is a version of such a map in The Information Capital.

For those living outside London, The Information Capital is something we can think about implementing in our own area. For some charts this is quite feasible based, as they are, on government data which covers the nation such as the census or GP prescribing data. Visualisations based on social media are likely also doable although will lack weight of numbers. The visualisations harking back to classics such as John Snow’s cholera map or Charles Booth’s poverty maps of are more difficult since there is no comparison to be made in other parts of the country. And other regions of the UK don’t have Boris Bikes (or Boris, for that matter) or the Millennium Wheel.

It’s completely unsurprising to see Tufte credited in the end papers of The Information Capital. There are also some good references there for the history of London, places to get data and data visualisation.

I loved this book, its full of interesting and creative visualisations, an inspiration!

Apr 14 2015

Book review: How Linux works by Brian Ward

 

hlw2e_cover-new_webThis review was first published at ScraperWiki.

A break since my last book review since I’ve been coding, rather than reading, on the commute into the ScraperWiki offices in Liverpool. Next up is How Linux Works by Brian Ward. In some senses this book follows on from Data Science at the Command Line by Jeroen Janssens. Data Science was about doing analysis with command line incantations, How Linux Works tells us about the system in which that command line exists and makes the incantations less mysterious.

I’ve had long experience with doing analysis on Windows machines, typically using Matlab, but over many years I have also dabbled with Unix systems including Silicon Graphics workstations, DEC Alphas and, more recently, Linux. These days I use Ubuntu to ensure compatibility with my colleagues and the systems we deploy to the internet. Increasingly I need to know more about the underlying operating system.

I’m looking to monitor system resources, manage devices and configure my environment. I’m not looking for a list of recipes, I’m looking for a mindset. How Linux Works is pretty good in this respect. I had a fair understanding of pipes in *nix operating systems before reading the book, another fundamental I learnt from How Linux Works was understanding that files are used to represent processes and memory. The book is also good on where these files live – although this varies a bit with distribution and time. Files are used liberally to provide configuration.

The book has 17 chapters covering the basics of Linux and the directory hierarchy, devices and disks, booting the kernel and user space, logging and user management, monitoring resource usage, networking and aspects of shell scripting and developing on Linux systems. They vary considerably in length with those on developing relatively short. There is an odd chapter on rsync.

I got a bit bogged down in the chapters on disks, how the kernel boots, how user space boots and networking. These chapters covered their topics in excruciating detail, much more than required for day to day operations. The user startup chapter tells us about systemd, Upstart and System V init – three alternative mechanisms for booting user space. Systemd is the way of the future, in case you were worried. Similarly, the chapters on booting the kernel and managing disks at a very low level provide more detail than you are ever likely to need. The author does suggest the more casual reader skip through the more advanced areas but frankly this is not a directive I can follow. I start at the beginning of a book and read through to the end, none of this “skipping bits” for me!

The user environments chapter has a nice section explaining clearly the sequence of files accessed for profile information when a terminal window is opened, or other login-like activity. Similarly the chapters on monitoring resources seem to be pitched at just the right level.

Ward’s task is made difficult by the complexity of the underlying system. Linux has an air of “If it’s broke, fix it and if ain’t broke, fix it anyway”. Ward mentions at one point that a service in Linux had not changed for a while therefore it was ripe for replacement! Each new distribution appears to have heard about standardisation (i.e. where to put config files) but has chosen to ignore it. And if there is consistency in the options to Linux commands it is purely co-incidental. I think this is my biggest bugbear in Linux, I know which command to use but the right option flags are more just blindly remembered.

The more Linux-oriented faction of ScraperWiki seemed impressed by the coverage of the book. The chapter on shell scripting is enlightening, providing the mindset rather than the detail, so that you can solve your own problems. It’s also pragmatic in highlighting where to to step in shell scripting and move to another language. I was disturbed to discover that the open-square bracket character in shell script is actually a command. This “explain the big picture rather than trying to answer a load of little questions”, is a mark of a good technical book.  The detail you can find on Stackoverflow or other Googling.

How Linux Works has a good bibliography, it could do with a glossary of commands and an appendix of the more in depth material. That said it’s exactly the book I was looking for, and the writing style is just right. For my next task I will be filleting it for useful commands, and if someone could see their way to giving me a Dell XPS Developer Edition for “review”, I’ll be made up.