Category: Book Reviews

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

Feb 09 2017

Book review: I contain multitudes by Ed Yong

multitudesThis book was a Christmas gift, for which I’m very grateful! I Contain Multitudes: The Microbes within us and a Grander View of Life by Ed Yong is all about bacteria.

Bacteria are somewhat neglected in the popular science literature, I think the closest I can come is The Eighth Day of Creation by Maurice Freeland Judson which is about the discovery of DNA and its role in molecular biology in which bacteria and viruses play a part.

Yong’s book is about the relationship between bacteria and other organisms, humans included. It reveals a world where bacteria are not simply passengers on oblivious hosts but are a heavily integrated part of the host’s life cycle.

The study of the “microbiome” is relatively recent. Unravelling the members of a microbial community prior to the invention of cheap, and easy, DNA sequencing was hard. Carl Woese pioneered this approach in the 1970s, and used it discover the archea, a whole knew Kingdom of life (plants and animals are two of the other Kingdoms, to give you and idea of the magnitude of this discovery). Sequencing of the bacterial inhabitants of humans gained pace in the 2000s when it was discovered that we all carry a rich community of bacteria which varies from site to site around the body, let alone from individual to individual. What is true for humans is true for other organisms.

The book continues with an overview of how important bacteria can be to an organisms life. For example choanoflagellates, typically single-celled organisms, only form colonies in the presence of certain bacteria. And bobtail squid rely on bacterial partners to provide their luminescence. The standard lab animals (mice, zebrafish, flies) have been raised in germ-free environments and whilst they do not die, they do not flourish – even in the comfortable environment of the lab. The Wolbachia bacteria interferes with the sex lives of its insect hosts, it is only passed down via the eggs of the female and so it arranges by various means that there are more eggs and females than sperm.

These partnerships are not accidental, in the sense that organisms often provide specific structures to support their bacterial partners and exchange specific molecular markers with them. In some cases the host is essential to the survival of bacteria it contains because they have given up on carrying out tasks essential to their continued existence, for example in the supply of essential nutrients. This is true on many scales, animals from termites to cows have digestive systems designed to accommodate a particular bacterial support team to enable them to digest what would otherwise be food of low nutritional value. The early years of a human infants life are shaped by its acquisition of the right microbiome to prime the immune system and aid digestion.

The reason that bacteria are so effective in providing support services to their hosts is their high rate of evolution. Not only do they replicate fast, they have a promiscuous approach to DNA they come across in their environment. This means that if any bacterial species evolves a useful trait, such as the ability to digest seaweed then its neighbours in the gut can pick up that ability via its DNA. These genes can, eventually, end up in the genome of their hosts.

Japanese people who eat nori seaweed, which contains carbohydrates which the human body can’t digest on its own, host bacteria which can. Moreover, the genes those bacteria use to carry out this digestion were acquired from marine bacteria.

Yong is not misty-eyed about his bacterial subjects, as he points out their symbiosis with other organisms is not altogether harmonious – in the end the bacteria are in it for themselves.

The book finishes with some examples of how bacteria can be used to support human health, and speculates how this approach – currently only used in curing persistent C. difficile infections – could be extended to all manner of ailments including blood pressure and mental health problems.

I’ve been following Ed Yong on twitter for quite a while, and where he found the time to write a book as well as everything else he seems to do is a mystery to me! his style, as a science journalist, can be seen in the book, both in the presentation of the story, with brief character sketches of the scientists involved and quotes from them, and in the titles of the chapters which are entertaining but not necessarily informative. The book is thick with examples which build into larger themes, turn to the back of the book and you’ll find references to the primary literature.

Bacteria deserve our attention, this book is a great introduction to how they shape the lives of “higher” organisms.

Jan 01 2017

Book review: The Headspace Guide to Mindfulness & Meditation by Andy Puddicombe

headspaceTo some degree this is a review of an app rather than a book. I started using the Headspace app a couple of months ago after a particularly trying burst of insomnia. The Headspace Guide to Mindfulness & meditation by Andy Puddicombe is the book of the app, I picked up the Kindle version for £0.99.

The mindfulness / meditation division is a bit of language engineering. Meditation is the exercise you do to achieve a state of mindfulness but also when Western medical practitioners were starting to use techniques of meditation in treating patients they found greater acceptability in the scientific community when using the newly coined term “mindfulness” rather than “meditation”.

The Headspace app costs £60 per year, more if you pay by month and less if you buy for longer. There’s much more material in the app than in the book but I find it easier to read chunks of text rather than remember the preambles to the guided meditation sessions which is where the material from the book is found in the app. I think it’s pretty much the only app I’ve bought and I had it on a free trial first – so I certainly value it.

The core of the Headspace programme is the 10 minute daily meditation. This starts with a few deep breathes to get yourself going, some scanning of the body to gain awareness of your physicality, followed by a period of focusing on your breathing and then a phase of returning to the world. Clearly, this brief description does not do the process justice. From my mechanistic point of view, the “aim” is to become a dispassionate observer of ones thoughts – mindfulness. More widely is carrying this approach in to the rest of your day.

In the app the voice of Andy is a comforting presence; perhaps more so for me because he’s from the West Country, and so makes me feel at home with his very slight Bristol accent. I found the app made it very easy for me to stick to a regular programme of daily 10 minute sessions.

I think one of the things that helped me latch on to Headspace was the exercise for insomnia, not so much the exercise itself but the fact that Andy describes exactly the form my insomnia takes (it’s also repeated in one of the case studies at the end of the book). Essentially I go to bed, and for an hour or so I fail to fall asleep. At which point I start getting stressed and frustrated at not falling asleep, and worrying about how awful the following day is going to be without any sleep. Usually the thought that set me off not sleeping is also going around and around in my head as well. At its worst this continues through the whole night.

The book is very readable much of the book is anecdotes of Andy’s time spent in monasteries, although there are some exercises and written guidance for meditation. This may seem frivolous but I found it far more interesting than dry descriptions of meditation, and as a result more likely to stick in the mind. I found these stories, and other visualisations described, very helpful.

There are frequent references to scientific research on the benefits of meditating and mindfulness through the text, as a trained scientist I muttered about the lack of in-text citations but on reaching the end I discovered the references section which, without following them up, look legitimate.

I learned a couple of things from reading the book compared to the app, it turns out my sofa is considered a bed for meditating purposes so I should be using a dining room chair. Secondly, it seemed implicit in the app that meditating was best done in the morning and the book makes this explicit.  

Strangely I find that elements of mindfulness existed in my life before I got Headspace. When I’m running (at my best) I find myself focusing on my breathing, in fact I can tell I’ve been thinking rather than focusing on breathing because I run slower when I’m thinking. I found a similar experience when we used to go walking in the countryside, the tramp of the feet acts as a good focus.

Meditation has its roots in Buddhism, and much of the experience that the author relates is from monasteries and his time as a monk, despite this the book (and the “programme”) feel like they have no religious elements to them. It has to be said adherents to meditation can sound rather evangelical – I can feel myself doing this now.

In summary, I highly recommend giving meditation, and Headspace a go. You can try the app for free for 10 days, or if you prefer the book is very cheap in its Kindle edition.  

Dec 27 2016

Book review: Elasticsearch–The Definitive Guide by Clinton Gormley & Zachary Tong

elasticsearchBack to technology with this blog post and a review of Elasticsearch – The Definitive Guide by Clinton Gormley and Zachary Tong. The book is available for free online, and probably more up to date (here), that said Elasticsearch seems to be quite stable now. I have a dead tree copy because I’m old-fashioned.

Elasticsearch is a full-text search engine based on the Apache Lucene project. I was first made aware of it when I was working at ScraperWiki where we used it for a proof of concept system for analysing legalisation from many countries (I wasn’t involved hands-on with this work). Recently, I used it to make a little auto-completion web form for company names using the Companies House dataset. From download to implementing a solution which was x1000 times faster than a naive SQL querying system took less than a day – the default configuration and system is that good!

You can treat Elasticsearch like a SQL database to a fair degree, what it refers to indexes are what would be separate databases on a SQL server. Elasticsearch refers to document types instead of tables, and what would be rows in a SQL database are called “documents”. There are no joins as such in Elasticsearch but there are a number of workarounds such as parent-child relationships, nested objects or plain old denormalisation. I suspect one needs to be a bit cautious of treating Elasticsearch as a funny looking SQL database.

The preferred way to interact with Elasticsearch is using the HTTP API, this means that once installed you can prod away at your Elasticsearch database using curl from the commandline or the  Sense plugin for Google Chrome. The book is liberally scattered with examples written as HTTP requests, and online these can be launched from the browser (given a bit of configuration). To my mind the only downside of this is that queries are written in JSON which introduces a lot of extraneous brackets and quoting. For my experiments I moved quickly to using the Python interface which seems well-supported and complete (as do other language bindings).

Elasticsearch: The Definitive Guide is divided into 7 sections: Getting started, Search in Depth, Dealing with Human Language, Aggregations, Geolocation, Modelling your data, and finishes with Administration, Monitoring and Deployment.

The Getting Started section of the book covers everything you need to get you going but no single topic in any depth. The subsequent sections are largely about filling in that detail. The query language is completely different to SQL and queries come back with results ranked by a relevance score. I suspect this is where I’ll find myself working a lot in future, currently my queries give me a set of results which I filter in Python. I suspect I could write better queries which would return relevance scores which matched my application (and that I would trust). As it stands my queries always return *something* which may or may not be what I want.

I found the material regarding analyzers (which are applied to searchable fields and, symmetrically, search terms) very interesting and applicable to wider search problems where Elasticsearch is not necessarily the technology to be used. There is an overlap here with natural language processing in the sense that analyzers can include tokenizers, stemmers, and synonym lookups which are all part of the NLP domain. This is expanded on further in the “Dealing with human language” section.

The section on aggregations explains Elasticsearch’s “group by”-like functionality, and that on geolocation touches on spatial extension-like behaviour. Elasticsearch handles geohashes which are a relatively recent innovation in encoding spatial coordinates.

The book mentions very briefly the ELK stack which is Elasticsearch, Logstash and Kibana (all available from the elastic website). This is used to analyse log files, logstash funnels the log data into elasticsearch where it is visualised using Kibana. I tried out kibana briefly, its an easy to use visualising frontend.

Elasticsearch is a Big Data technology from the start which means it supports sharding, replication and distribution over nodes out of the box but it runs fine on a simple single node such as my laptop.

Elasticsearch is a pretty big book but the individual chapters are pretty short and to the point. As I’d expect from O’Reilly Elasticsearch is well-edited, and readable. I found it great for working out what all the parts of Elasticsearch are and now know what exists when it comes to solving live problems. The book is pretty good at telling you which things you can do, and which things you should do.

Dec 24 2016

Book review: Roman Chester by David J.P. Mason

roman_chesterI recently realised that I live in a city with rather remarkable Roman roots. Having read Mary Beard’s book, SPQR, about the Roman’s in Rome, I turn now to Roman Chester: Fortress at the Edge of the World by David J.P. Mason.

The book starts with a chapter on the origins of the study of the Roman origins of Chester, and some background on Roman activities in Britain. The study of the Roman history of Chester begin back in the 18th century, with the hypocaust under the old Feathers Inn on Bridge Street a feature promoted by its owner. The Spud-u-like on the site now similarly boasts of its Roman remains. The original Roman east gate was still standing in the 18th century, and there exist several drawings of it from that period. The Victorians were keen excavators of the Roman archaeology, and formed the Chester Archaeological Society in 1849, and built the Grosvenor Museum in 1883.

A recurring theme of the book is the rather wilful destruction of substantial remains in the 1960s to build a couple of shopping centres. The Roman remains on the current Forum Shopping Centre site were destroyed after the rather fine Old Market Hall had been knocked down.

The core Roman activity in Chester was the fortress, established in 75AD under the reign of Vespasian. The fort is somewhat larger than other similar forts in England and the author suggests this was because it was, at one time, intended as the provincial governors base. Vespasian died shortly after the building of the Chester fortress started and the work paused. At the time of its Roman occupation Chester had a very fine harbour, the local sandstone was suitable for building, a brickworks was setup at Holt, further up the River Dee, and there was metal mining in North Wales and there was salt sourced from Northwich – all very important resource at the time.

Standing on the river Dee meant Chester could serve as a base for the further conquest of Britain and Ireland – although these plans did not come to fruition.  The evidence for this is some unusual buildings in the centre of the old fortress, and the rather more impressive nature of the original walls than the average Roman fort, and the discovery of rather classier than usual lead piping.

The book continues with a detailed examination of the various parts of the Roman fortress and the buildings it contained: the public baths, granaries and barracks. This is followed by a discussion of the surrounding canabae legionis, including the amphitheatre, the supporting Roman settlement and the more detached vicus. This includes the settlement at Heronbridge which was excavated relatively recently.

The third part of the book travels through time, looking at the periods c90-c120 in which the fortress was rebuilt, c120-c210 when the legion stationed at Chester was sent elsewhere to fight leaving the fortress to decline significantly. c210-c260 when the original impressive buildings at the heart of the fortress, not initially completed, were finally built. c260-c350 when the fortress fell and rose again. To finish in the period c350-c650 when Britain became detached from Rome, and fell into decline. The Roman fortress was robbed to provide building stone for the medieval walls and other structures including the cathedral.

Roman remains are visible throughout modern Chester. The north and east parts of the modern city walls follow the line of the walls of the Roman fortress. Some pillars are on display in front of the library, the hypocaust found under the Grosvenor shopping centre can now be found in the Roman Gardens, the amphitheatre is half exposed, parts of the walls particularly near Northgate and parallel to Frodsham street are contain Roman elements, the mysterious “quay wall” can be found down by the racecourse.

The book finishes with some comments on the general character of the investigations of Roman remains in Chester, and suggestions for further investigations and how to better exploit Chester’s Roman history. On the whole Chester has done moderately well in its treatment of the past, study started relatively early but much material has not been published. These days archaeology is mandated for new developments in the city but these tend to be rapid, keyhole operations with little coherent design.

Roman Chester is a rather a dry read, it is written much I would expect an article in a specialist archaeology journal to be written. The book could have done with a full double page map of modern, central Chester with the archaeological sites marked on it. As it was I was flicking between text descriptions and Google Maps to work out where everything was. Perhaps a project for the Christmas holiday!

If you are a resident of Chester then the book is absolutely fascinating.

Update

I’ve started making a map of Roman Chester on Google Maps.

Nov 17 2016

Book review: The Invention of Science by David Wootton

inventionofscienceBack to the history of science with The Invention of Science by David Wootton which covers the period of the Scientific Revolution.

Wootton’s central theme is how language tracked the arrival of what we see as modern science in a period from about 1500 to 1700, and how this modern science was an important thing that has persisted to the present day. I believe he is a little controversial in denying the ubiquity of the Kuhnian paradigm shift and in his dismissal of what he refers to as the postmodern, “word-games” approach to the history of science which sees scientific statements as entirely equivalent to statements of beliefs.This approach is exemplified by Leviathan and the air-pump by Steven Shapin and Simon Schaffer which gets several mentions.

Wootton argues contrary to Kuhn that sometimes “paradigm shifts” happen almost silently. He also points out that Kuhn’s science is post-Scientific Revolution. One of the silent revolutions that he cites is the model of the world. “Flat-earth” in no way describes the pre-Colombus model of the world which originated from classical Greek scholarship. In this theoretical context the sphere is revered and the universe is built from the four elements: earth, wind, fire and water. The model for the “earth” is therefore a variety of uncomfortable attempts to superimpose spheres of water and earth. The Ancients got away with this because in Classical times the known world did not cover enough of the earth’s sphere to reveal embarrassing discrepancies between theory and actuality. With Colombus’s “discovery” of America and other expeditions crossing the equator and reaching The Far East over land these elemental sphere models were no longer viable. The new model of the earth which we hold to today entered quietly over the period 1475 to 1550. 

Colombus’s “discovery” also marks one of the key themes for the book, the development of new language to describe the fruits of scientific investigation. Prior to Colombus the idea of an original discovery was poorly expressed in Western European languages, writers had to specifically emphasise that they were the first to find something or somewhere out rather than a having a word to hand that expressed this. Prior to this time, Western European scholarship was very much focused on the “re-discovery” and re-interpretation of the lost wisdom of the Ancients. Words like “fact”,”laws” (of nature), “theories”, “hypotheses”, “experiment” and “evidence” also evolved over this period. This happened because the the world was changing, the printing press had arrived (which changed communication and collaboration entirely). Machines and instruments were being invented, and the application of maths was widening from early forms of banking to surveying and perspective drawing. These words morphed to their modern meanings across the European languages in a loosely coupled manner.

Experimentation is about more than just the crude mechanics of doing the experiment, it is about reporting that work to others so that they can replicate and extend the work. The invention of printing is important in this reporting process. This is why alchemy dies out sometime around the end of the 17th century. Although alchemy has experiments, clearly communicating your experiments to others is not part of the game. Alchemy is not a science, it is mysticism with scientific trappings.

As a sometime practising scientist all of these elements of discovery, facts, evidence, laws, hypotheses and theories are things whose definitions I take for granted. They are very clear to me now, and I know they are shared with other working scientists. What The Invention of Science highlights was that there was a time when these things were not true.

The central section of the book finishes with some thoughts on whether the Industrial Revolution required the Scientific Revolution on which to build. The answer is ultimately “yes”, although the time it takes is considerable. It flows from the work of Denis Papin on a steam digester in the late 17th century to Newcomen’s invention of the steam engine in the early 18th century. Steam engines don’t become ubiquitous until much later in the 18th century. The point here is that Papin’s work is very much in the spirit of a “academic” scientist (he had worked with Robert Boyle), whereas Newcomen sits in the world of industrial engineering and commerce.

I’ve not seen such an analysis of language in the study of the Scientific Revolution before, the author notes that much of this study is made possible by the internet. 

The editor clearly had a permissive view of footnotes, since almost every page has a footnote and more than a few pages are half footnote. The book also has endnotes, and some “afterthoughts”. Initially I found this a bit irritating but some of the footnotes are quite interesting. For example, the Matses tribe in the Amazon include provenance in their verb forms, using the incorrect verb form is seen as a lie. In my day to day work with data this “provenance required” approach is very appealing.

The Invention of Science is very rich, and thought provoking and presents a thesis which I had not seen presented before, although the “facts” of the Scientific Revolution are well known. I’m off to read Leviathan and the air-pump partly on the recommendation of the author of this book.