Sep 11 2021

Book review: Precolonial Black Africa by Cheikh Anta Diop

diopMy next book follows on from reading Black and British by David Olusoga. It is Precolonial Black Africa by Cheikh Anta Diop. I was looking for an overview of African history from an African perspective. Diop’s relatively short book focuses on West Africa. It turns out he is a very interesting figure in himself, building several political parties, doing research in history as well as physics and chemistry and having a university named after him. Some of his ideas on African history are controversial (you can see the wikipedia page relating to him here).

The core of the controversy is two fold, one is his claim that ancient Egyptians were black, and the second is that there is a historical unity in West Africa civilisation with migration from the east of Africa populating the continent. The basis for this thesis relies quite heavily on similarities in totemic names across the region as well as cultural similarities. These days there is some support for the migration of populations out of the Nile basin to West Africa from DNA evidence.

Most of the discussion in this book is oriented around the area of West Africa where Diop grew up, in Senegal, with some mentions of Eygypt and Sudan. Diop draws parallels in the internal organisations across the empires of Ghana, Mossi, Mali and Songhai. The Empire of Ghana stretched beyond the boundaries of the modern country, and stood for 1250 years. Mossi was to the east and south, in the area of modern Burkino Faso, Mali and Songhai were a little to the north encompassing the modern Timbucktu. Looking at wikipedia these empires appear to have overlapped to a degree both in time and space. Precolonial Black Africa covers the period from about 300AD to the 17th century although it does not make much reference to dates.

There is almost no mention even of the area of Nigeria, a little to the east, or Southern Africa. I was nearly half way through the book before I realised that Sudan referred to two different places: Sudan the modern state in North East Africa, and the Sudan Empire which stretches across the southern margin of the Sahara in the West of Africa.

The books starts with a description of the caste system, emphasising the two-way nature of the system and contrasting it to a degree with the caste system in India.

Precolonial Black Africa contrasts Africa with Europe, in the period covered by the book Europe was based on city-states which evolved into feudal structures, with Roman geographical divisions, where defence from marauders by the lord in the castle was important. Land ownership was core of this political system whereas Africa evolved more along Egyptian lines which saw countries divided into regions with regional governance and no tradition of land ownership.

These empires were led by kings with a small cabinet of advisors who had both a regional responsibility and a specialism (like a minister for finance, or the army). Although not republics, nor democratic in the modern Western sense, Diop claims that these governments were more representative than their Western European equivalents of the time.

The technological expertise of the ancient Romans and Greeks was carried through the Middle Ages by the Arab world. It is no coincidence that Spain was once a technology leader, given the Muslim rule of Spain. Islamization of West Africa is a recurring theme of the book, and Arab writers feature regularly in the lists of sources for the early history of Africa. Islam was important in education through to the present day, this is in part responsible for slowed technological progress in the region. Islamic schools did not place a great emphasis on what they consider pagan history, nor so much on modern science.

Precolonial Black Africa covers technology relatively briefly, mentioning architecture and the Great Zimbabwe – a significant stone-built city in present day Zimbabwe whose early excavation was plagued by the then Rhodesian governments view that it could not be constructed by Black Africans. Coins, and metalworking are also mentioned – West Africa made relatively little use of the familiar coinage of European. Gold dust was used as currency, as were Cowrie shells. The Benin Bronzes dating from the 13th century demonstrate there was significant metalworking skill in West Africa (the Bronzes are currently in the news as the UK refuses to return them to Benin). Little of technology and writing seems to have survived from precolonial times, I suspect this is a combination of the environment which is not conducive to the preservation of paper (or even metal), successive colonisations by Islam and then Europeans and relatively little archaeological activity.Trade seemed quite significant across West Africa, even in the absence of conventional coinage.

The interesting thing reading this book is the contrast with flaws that Western history has had in the past, being focussed on great men, the idea of the natural superiority of the white man, and leaning heavily on Classical heritage for legitimacy. I suspect these points of view are generally not prevalent in modern academic history but they certainly hold sway with the current UK government and a coterie of right-wing historians. To a degree Diop suffers the same types of prejudices but from a different perspective – the superiority of the Black African. My view of African history is still heavily influenced by those old Western European foundations.  

After a rocky start I came to enjoy this book, I found the book alien in a couple of respects firstly in its discussion of history from an African perspective, and also simply that it is African history. What I know of Africa is largely through a colonial lens. 

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