Dr Administrator

Author's posts

Aug 28 2021

Book review: Ancestors by Professor Alice Roberts

ancestorsSomewhat unintentionally my next book, Ancestors by Alice Roberts, follows on from Hidden Histories by Mary-Ann Ochta and The Goddess and The Bull by Michael Balter. Ancesters is an investigation of the transition from early Stone Age people in Britain through the Neolithic, to the Bronze Age finally the Iron Age through the medium of seven burials around Britain. As well as the facts of various burials Roberts talks too about in archaeological methodology over time.

The broad context of the book is a project on recording ancient DNA in which Roberts is involved, a project on hold due to covid. Motivation for this is that we can observe the movement of ancient peoples and relationships between people in burials using DNA. These techniques have not been applied extensively to Neolithic remains to date.

The first burial discussed is of the "Red Lady" in a cave in the Paviland Cliffs on the Gower in Wales. It dates back to the Paleolithic (old Stone Age), 34,000 years ago and is the oldest burial discovered in Britain, from a period before the last Ice Age. William Buckland was the first to scientifically describe the burial, and his descriptions reflect the opinions of the time. He sought to reconcile such burials with biblical knowledge, and social mores, initially describing the burial as of a "Red Lady" because of the decorative grave goods (and the body being caked in red ochre). It turns out the burial is actually of a man!

As far as we can tell deliberate burials by homo sapiens date back about 100,000 years. The evidence is mixed as to whether Neanderthals practiced burials. This rubicon is seen as important since burial rites represent a move to modern human thinking which distinguishes us from other animals (so far!). I particularly enjoyed the description of the "flower people" where, in a burial in Iraq, it has never been quite clear whether Neolithic people buried people in flowers or whether it was actually the work of gerbils that, by the way, also gnawed on the body.

Returning to UK we meet Cheddar Man, who was buried after the last Ice Age about 10,000 years ago. Incidentally we learn how to wind up an anatomist with fake skeletons: in real life the pelvis and ribcage of a skeleton collapse because the ligaments don’t hold them together after they’ve been in the ground for a bit – fake skeletons don’t show this. At 14,700 years old other skeletons in Gough’s Cave, where Cheddar man was found, are the earliest post-Ice Age human remains found in Britain.

Cheddar Man was from the Paleolithic or old Stone Age, the next burials discussed are from the Neolithic or New Stone Age. The defining feature of the New Stone Age is the move from hunter/gathering to agriculture and settlement. The key question is whether this change in behaviour was a transmission of ideas, or an influx of people with these new habits. This transition to agriculture 11,000 years ago is one of the central themes of The Goddess and The Bull, in Britain the transition takes place a later – about 6,000 years ago.

Farming arrived in Britain with people, rather than just ideas. There’s evidence of violence in some of the burials discovered (about 10% of skulls show signs of traumatic injury) but as far as can be ascertained this was farmer/farmer violence rather than hunter-gatherer/farmer violence. It seems that hunter-gathering died out with its practitioners rather than its practitioners converting to farming. Something that I hadn’t heard of before was the idea of a "house burial" – some Neolithic burial barrows are on the site of dwellings, longhouses, which have been ritually burnt. Neolithic burial sites are often reused in the Bronze and Iron Age, perhaps to maintain contact with the land. Perhaps burial becomes more important once we start to stake a claim on particular pieces of land.

There’s a small diversion at this point to discuss Pitt Rivers, a 19th century archaeologist whose methodology was beyond his times in the sense that he made meticulous records of what he had dug. He was born Augustus Lane-Fox but changed his surname to Pitt Rivers as a condition of receiving a substantial inheritance. He spent his later years in detailed excavation of his inherited Rushmore Estate which lies close to Salisbury and is incredibly rich in archaeology (or perhaps if you are rich, an archaeologist and inherited a large estate it turns out there is a lot of archaeology you can do).

Next we move to Bronze Age burials, where things get exciting in terms of grave goods. Starting gently with some arrows and so forth we move on to whole, upright chariots including the horses in the Iron Age!! The Bronze Age is also marked by an influx of people. I recall from my Seventies childhood the Beaker People (identified by a particular type of pottery).

At this point, in the late Iron Age we transition from prehistory to history with Roman writings on Britain. Such records need to be treated with a little care since they are often second hand and are the viewpoint of a conqueror. It is interesting to see the names of Iron Age tribes carried forward to the present day, for example in the Parisi in Northern France (turning into Paris) and Durotriges turning into Dorset.

Roberts notes at the end of the book that burial practices don’t have to be universal across a period we consider to be discrete such as the Bronze Age, to the people living at the time they were not "Bronze Age" they were people of a much narrower place and time. Large changes in burial practices are not necessarily indicative of religious changes – Britain shifted from burial to cremation from the end of the 19th century to the Sixties with no change in religion.

The writing of the book stretched into the covid pandemic, it is an interesting mix of topics written in an engaging style. There are a couple of places where the editing slips a bit. Overall I found it an engaging read.

Jul 24 2021

Book review: The Code Breaker by Walter Isaacson

code_breakerFor my summer holiday reading I have The Code Breaker by Walter Isaacson, the author was recommended by a friend. It is the story of CRISPR gene editing, and Jennifer Doudna, one of the central characters in the development of this system and winner of the Nobel Prize for Chemistry in 2020 with Emmanuelle Charpentier for this work.

CRISPR is an acronym for "clustered regularly interspaced short palindromic repeats", a name derived from the DNA sequences that prompted its discovery. CRISPR are the basis of a type of immune system for bacteria against viruses. The CRISPR repeats form a fingerprint which matches the viral DNA and the associated system of enzymes allows a bacteria to snip out viral DNA which matches this sequence.

Whilst CRISPR is interesting in itself, it has applications in gene editing as a cure for disease in humans. CRISPR simply requires a short piece of RNA to match the target DNA in a gene to carry out its editing job. Short RNA sequences are easy to synthesise making CRISPR superior to earlier gene editing techniques. In addition there is potential to use CRISPR as a diagnostic tool for identifying infections such as covid and even as a cure for viral diseases. The Code Breaker does a good job of explaining CRISPR to a fair depth.

There is a section of the book on gene editing in humans and the moral issues this raises. Perhaps central to this is the story of He Jiankui, the Chinese scientist who led the work to carry out germ line edits to add a gene protective against HIV. Germ line gene edits mean editing the genes in an early stage embryo which means that all the cells in the child it gives rise to have the edit, including reproductive cells, hence the gene edit will be passed on to descendants. This is considered more radical than somatic cell gene editing where the changes stop with the person treated. I must admit to having some sympathy for He Jianku. Principally Western scientists had made a great show of considering the moral issues in germ line editing eventually deciding that the time was not yet right, but going against a moratorium or regulation in the area. This seems an ambiguous position to me, and the associated comments that Jiankui had done his work for publicity is a bit rich from a group of scientists who have been so competitive in the research over CRISPR. Jiankui conducted his research with the approval of his local ethics board but was subsequently disavowed by the Chinese authorities and then convicted.

Coronavirus is woven through the book because the work on CRISPR is very relevant here from a scientific point of view, and the key characters including the author are involved, as we all are! As far as I can tell Doudna et al have been involved heavily in conventional covid19 testing and have done research on CRISPR-based diagnostic tests which have great potential for the future – essentially they would allow any viral illness to be definitively tested at home (rather than a sample being sent off to do PCR test) – but are not yet used in production. Similarly there is the potential for CRISPR-based vaccines but these are not yet been deployed in anger. The Pfizer and Moderna vaccines are based on RNA but use older technology.

A chunk of the book covers the patent battles over CRISPR principally involving Doudna and her co-workers and Feng Zheng, scientist at the Broad Institute. The core of the patent dispute is how obvious the step from understanding the operation of the CRISPR system (which Doudna’s team demonstrated first) to applying it to human cells (which Zhang did first) is. I think my key learning from this part of the book is that I’m not very interested in patent battles! Tied up with the patent issue is the question of the great science Prizes which similarly give a winner takes all reward to a small group. The Nobel Prizes have a limit of three on the number of winners, so do more recently instituted prizes. Science simply isn’t done this way, and hasn’t been for a long time. There’s a group of at least a dozen scientist at the core of the CRISPR story and probably more, singling out a couple of people for a reward is invidious. It made me wonder whether the big science prizes are really about the prize giver rather than the winner.

The book is written in the more journalistic style that has arisen in scientific biography relatively recently, that’s to say there is a lot of incidental detail about where Isaacson met people and their demeanour than in older scientific biographies. I must admit I find this a bit grating, I’ve tended towards collective biographies recently rather than single person biographies which have a bit of a "great man" feel to them. However, I’m starting to make my peace with this new style – it makes science feel like a more human process, and makes for a more readable book. It’s fair to say that this is in no way a "great man" biography, although Doudna and her life and personality are a recurring theme other people get a similar treatment.

Jun 26 2021

Book review: Guitar Looping – The Creative Guide by Kristof Neyens

creative_loopingFor completeness I include my review of Guitar Looping: The Creative Guide by Kristof Neyens. This is in the same series as Guitar Pedals by Rob Thorpe. These are both quite short books but I’ve found them useful.

A looper pedal is a simple recording device which is started and stopped using a footswitch. A loop can be built up by making successive recordings, or layers, one on top of another. Typically loops are only a few bars long at most but modern looper pedals can record for tens of minutes.

I bought a looper pedal a year or so ago (reviewed here) and, to be honest, it has languished a bit on my pedalboard. I think the problem is a lack of education in the right format. Also I probably should have started with the simplest looper available, the author uses a tc electronic ditto rather than a step up (my Boss RC-3).

In common with Guitar Pedals, Guitar Looping contains lots (117) of short examples annotated in normal musical notation and guitar tab notation with accompanying audio files downloadable from the website. There is a brief text introduction to each example. I find these nice exercises in ear training, it’s good to be able to follow along with the tune.

The author is quite fond of the volume swell as part of a loop, this has got me thinking I need a volume pedal – previously I couldn’t see the point of them. This presents a problem because I’ve run out of space on my pedalboard!

Aside from the technical skill of starting and stopping loops at the appropriate point, there is also the skill of controlling the volume of your play within a layer and also getting the volume of different layers right. The loops illustrated often contain a percussive layer made by playing with strings muted, a rhythm/bass layer and a melodic layer which may be single notes or simple chords. Neyens talks about providing both harmonic space and dynamic space in layers. That’s to say there is no point in recording a layer loud and filled with sound because there is nowhere to put additional layers. This means that individual layers can sound quite simple and sparse. To get harmonic space you might play low notes with an octave pedal, on the lower three strings and melodies on the higher three strings, further up the neck.

The other useful piece of information I picked up was how to make your guitar sound like a clarinet! You pick the string 12 frets from where you are fretting – so if you are holding down the low E string on the third fret you need to pluck it and see. Try it and see.

After reading this book I’m using my looper pedal a bit more, there’s a lot of ideas in here and perhaps the most important thing is a stimulus to play around a bit – it doesn’t cost anything!

Jun 20 2021

Book review: Data Pipelines with Apache Airflow by Bas P Harenslak and Julian R De Ruiter

data-pipelinesMy next review is on Data Pipelines with Apache Airflow by Bas P Harenslak and Julian R De Ruiter. The book was published in 2021, and is compatible with Airflow 2.0 which was released at the end of 2020.

Airflow is all about orchestrating the movement of data from sources such as APIs and so forth into other places, it originated in Airbnb. It is designed for batch processing, rather than streaming data, and for pipelines that do not change much.

Data pipelines in Airflow are represented as "directed acyclic graphs" or DAGs which are defined in Python code using "Operators" which carry out tasks. A graph is a collection of nodes (tasks in this case) with "edges" between them. The "directed acyclic" bit means tasks have a definite order, the edges between them are "directed", and the graph cannot have loops or cycles because that would imply having to finish a set of tasks before you could start them. Simple data pipelines would just be a linear set of tasks that always follow one from another, a more complicated pipeline might bring in data from several sources before combining them to produce a final data product.

The Operators are strung together using expressions of the form "operator 1 >> operator 2" or even "[operator 1, operator 2] >> operator 3". 

Operators do not have to use Python, they can invoke code in other languages such as the BashOperator, or interact with other systems such as databases or storage systems such as S3. It is relatively easy to write your own operators. Alongside operators that do stuff there are branch operators which select one or other path in the DAG, and there are also sensors which detect changes in filesystems and trigger work and hooks which form connections with external services. Dummy operators can be used to simplify the appearance of DAGs.

As an orchestration system the intention of operators is that they should not contain a great deal of code to process data, that function should be off-loaded to libraries or systems elsehwhere.

The Airflow system is comprised of a web server which allows you to observe / trigger execution of DAGs, a scheduler which is responsible for the scheduled running of DAGs and workers which do the actual work of the DAG. The Airflow system loops over the tasks defined in a DAG, and tries to execute tasks which depends on the tasks upstream of the task in question, if they have been successfully completed then a task can execute.

A basic implementation runs DAGs locally using a simple queue to schedule work, and a sqlite database to store metadata. A production implementation would use something like Postgres or Amazon RDS as the metadata store, schedule work using Celery and run tasks in Docker containers marshalled using Kubernetes.

For some reason reading this I was reminded that big projects like Airflow are just other people’s code, and if you look too carefully you’ll find something nasty. This is both comforting and mildly scary. I think the issue was that Airflow uses jinja templating to inject parameters into code which feels wrong but is probably a pragmatic and safe why to do it, these shenanigans are not required for Python operators. Also discussed are issues with code dependencies, which the authors suggest are best eliminated by putting operators into Docker containers each of which contain their own code dependencies – allowing otherwise dependency incompatible libraries to work together. 

Alongside the material on Airflow there are moderate chunks on Python modules, testing, Docker and Kubernetes and logging so you get a well rounded view not only of Airflow but also of the ecosystem it sits in. The book finishes with deployment into various Cloud environments. I found these parts quite useful since the most complicated work I do in my role is trying to get things to work in AWS! The data science part is easy…

The book finishes with some short chapters on Cloud deployments, mentioning first fully managed services such as astronomer.io, Amazon MWAA and Google Cloud Composer before going on to talking about implementation of one of the demos in the book on AWS, Azure and Google cloud services. I considered skipping these chapters but they turned out be quite interesting in highlighting the differences between services and perhaps the preferences of the authors of both the book and of Airflow.

I found this a readable introduction to Airflow with some nice examples, and interesting additional material. Useful if you are thinking about using Airflow, or even if you are working on data pipelines without Airflow since it provides a good description of the moving parts required.

The code repository for the book is here: https://github.com/BasPH/data-pipelines-with-apache-airflow

Jun 03 2021

Book review: Guitar Pedals by Rob Thorpe

guitar_pedalsAnother brief sojourn with a guitar related book, this time Guitar Pedals by Rob Thorpe. It has the lengthy subtitle "Discover How to Use Pedals and Chain Effects to Get The Ultimate Guitar Tone", and the front cover continues with a range of other promises as to content. This isn’t intended as a criticism, it just struck me as an usual stylistic effect.

For those not familiar with electric guitars, an guitar effect pedal is a little box of electronics, around the size of a cigarette packet but rather thicker, with a socket on one side to take input from a lead from your guitar and a socket on the other side to send the modified signal out to your amplifier. On the top face of the pedal is a switch to turn the effect on and off, and one or more knobs to configure it. Guitar pedals are usually grouped together on a pedalboard which will hold up to 10 or so of them, chaining their effects together. They introduce effects such as distortion, reverb, delay and so forth.

If you watch videos of live music you’ll most likely notice the guitarist and bass player with a pedalboard on the floor at their feet, occasionally poking it with a foot to change the sound of their guitar.

Guitar pedals are a cheap and easy way of changing the way your guitar, I have a couple of more expensive Boss pedals which cost about £100 and a couple of Donner pedals which were under £40.

Guitar Pedals runs through chapters describing a bunch of distinct effects, talking first about the background of the effect before going through some short examples of the effect in different contexts with different configurations (these appear as written guitar tabs, and accompanying downloadable audio files), and finishing with some examples in real music.

Since reading "The Birth of Loud" by Ian S. Port it struck me that much of the development of the electric guitar and its ecosystem has been the story of electrical equipment abused. Particularly so with distortion /overdrive pedals described in the first chapter – the original distortion pedal made by Gibson in 1962 (the Maestro FZ-1) attempted to replicate the effect Link Wray achieved in Rumble by stabbing his speakers with a screwdriver! Jimi Hendrix was a fan of the Arbiter Fuzz Face but quality control was so poor he would buy a bunch of them and pick the best (or even get his guitar tech to cobble together a pedal from the parts of multiple examples). Purple Haze is an example of Fuzz Face in action. Overdrive is what you get when you turn the volume of your amplifier right up – pedals can achieve the same effect without making a really loud noise.

Next up is a chapter on delay – essentially an echo effect which was originally implemented on tape. I’ve always thought of delay effects and reverb being related with reverb the more important of the two. Reverb and compressor effects each get their own chapter but Thorpe sees them as more production effects than pedal effects per se. Tracks like Beautiful Day by U2, King of Zion Dub by King Tubby and Country Boy by Albert Lee use delay.

The chapter on modulation effects covers phasor and flanger effects, where part of the signal is phase shifted and mixed with the original signal. Shine on you crazy diamonds by Pink Floyd is an example of a phaser in use, and Barracuda by Heart uses a flanger. Also included are chorus effects (where part of the signal is delayed) and tremolo (where the volume is modulated). The first chorus pedal, the Roland CE-1 started life in Roland’s Jazz-Chorus 120 Amplifier. A background in physics is quite handy here, vibrations and waves are at the heart of any physics degree, as are operational amplifiers – pedal effects are these things in action! Come as you are by Nirvana is a good example of the chorus effect, and How soon is now by The Smiths demonstrates the tremolo effect (for this performance the tremolo effect comes from the amplifier rather than a pedal).

My wah pedal is my favourite, and it gets a chapter largely of its own. Think Voodoo Child by Jimi Hendrix (watch his left foot at the start of this video) or the theme from Shaft by Isaac Hayes. A wah pedal is an adjustable band pass filter, in the same why that the tone knob on any manner of audio equipment is an adjustable low-pass filter. The wah pedal is unusual in that you adjust it during play – the position of the pedal controls where the band pass sits, other pedals have their configuration set before hand and are simply switched on and off. All I can say is it’s great fun to play with!

Next up are octave pedals and other pitch shifters and harmonisers, I’d assumed the point of an octave pedal (which plays a note one octave above or below the note you are playing) was to emulate a bass guitar, but it seems not.Jimi Hendrix’s Octavia pedal added a tone an octave above what he was playing, on tracks like Fire and Purple Haze. Jack White of The White Stripes uses octave effects to add notes both an octave above and below the played note to give a "thicker" tone – try tracks like Ball and a biscuit and Blue orchid.

Originally effect pedals contained simple analog electronic circuits (or even liquids) which did one job, now with digital processing a single pedal can emulate many different effects. I must admit I find multi-effects pedals a bit overwhelming – it’s no fun trying to navigate 50 or so effects, and their configuration on a one inch display with a couple of buttons.

The book finishes with a chapter on ordering of guitar pedals, and how this can change the sound made and finally there are some interviews with professional guitarists, and how they arrange their pedals. A point that both Thorpe and one of his interviewees makes is that tone, the sound of the guitar, depends a lot on the player and how they play. Chasing after a tone by buying the same pedals as your heroes is a losing game.

Guitar Pedals is a short book, it doesn’t have the high production values of the Rikky Rooksby but it carries much of the style – embedding the example riffs in the chapters works really well for this book. Online guitar courses tend not to cover effects pedals, this book fills the gap pretty well.