Favorite Books Read 2012

General Non-fiction

I jumped on the bandwagon that is John Jeremiah Sullivan's "Pulphead". These are rightly considered to be some fucking great essays. I reread some of them recently and was struck by how clean the prose was. Nothing particularly fancy, but it is the authorial stance that is breath-taking. His approaches to his subjects come askance, exposing some unexpected facet of his own life, which oftentimes succeeds in illiminating a shared humanity. In one brilliant biographical essay, Sullivan was able to turn Axl Rose into a tragic figure. In another, he gazes straight into the maelstorm that is Michael Jackson, and manages to hold onto the music as the heroic center of genius. Indeed, the music essays in this book comes as closes to anything in modern journalism to explicate why music is so utterly essential to this modern life.

Like most Australians, I passed through the Australian school system and failed to learn any passable history of our nation of any consequence. I feel some shame in knowing more about the US presedential elections than our own political system. And so, it is with some relief that I read journalist George Megalogenis' rather compact history "The Australian Moment". The Moment which the book refers to was the economic jujitsu move that Australian prime minister Kevin Rudd did on the GFC, which smacked it so hard, that the Australian was able bounce from recession, and off onto the billowing safety of the onrushing Chinese mining boom. But really, the gimmick of the Moment is really just a hook into nothing less than a readable and authoritative history of 20th century Australian politics. It's clearly a labor of love as the source material includes in-depth interviews with all the surviving prime ministers of Australia conducted over many years.

This year I read yet another translation of "Mumon's Gateless Gate" by Koun Yamada, the central book of koans in the Zen canon. My favorite before this was Robert Aitken's folksy American translation, which dissolved a lot of the weird mystical interprations in other translations. What is great about Yamada's version is that it puts in a lot more context of each of the koans so much so that I could figure out some of the more obscure koans that had stumped me on previous translations. Yamada is also much more patient in laying out the logic of each koan. I also got a chance this year of reading different collections of essays by Dogen, the great medieval Japanese Zen master. Dogen is a minefield for the aspiring translator as he is one of the hardest writers to translate in what is an already difficult to translate genre. He invents terms out of whole cloth and is linguistically playful with his explanation of the dharma. With Dogen you can get a precise but pedantic and clumsy translation like Cleary's translation. But you can also get a fluid translation such as Bob Myers' "First Dogen Book". In Myers' translation, he makes many surprising and pleasing word choices that ripple through the whole texts. Getting these just right requires years of study and practice. Without this level of translation, it's very hard to appreciate the true beauty of Dogen's Zen.

Cities are the greatest creation of humanity. Well at least according to some, which include myself, and also P. D. Smith, who has written one of the best books on the city yet "Cities: A Guide for the Urban Age". What is it exactly? It's like a little encyclopedia, a collection of short essays, each devoted to one aspect of the city, or city life. This book has no particular agenda, it just wants to celebrate this most human of inventions and so, the topics range far and wide, from city gates to marathons. Of course, this book would not be noteworthy if not for the quality of the writing. And Smith is incredibly well-read and erudite. His tone is somewhat elegiac and I think this book will stand the test of time, providing as much intellectual sustenance for future lovers of the city.

Peter Watson's "The German Genius" is one very long book. It's dense, and it has nazis in it. Or rather Watson's main contention is that the recent history of nazi Germany has unfortunately obscured the vast intellectual contribution that German culture has made on the modern world. This book aims to demonstrate, and I believe it does so in ample measure, that the culture of the modern world is Germanic in origin. How did a bunch of illiterate barbarians on the edge of the Roman Empire reinvent themselves into the most sophisticated society Europe had ever seen? Watson traces the influence of the Pietist branch of the protestant revolution in the development of German culture, from philology to philosophy, music, science, engineering and the arts. I've studied my fair share of physics and philosophy and I was constantly surprised by just how much Watson had absorbed. His thumbnail sketches of seemingly every significant German intellectual are astonishing. But more importantly I got to see how the development of German ideas went hand-in-hand with the political development of the German political state. What is disturbing though, as highlighted by Watson, is that the heights of German culture developed specifically at the expense of the development of their political system. There was a perverse parasitic relationship between the two, a relationship that would uncoil in the twentieth century in the worst possible book. This is an exhausting book, but the chance to see so many ideas tied together by a sure hand is rare to see indeed, and if you are a lover of the history of ideas, this is an absolute must.

Fiction

2012 restored my faith in fiction. I read so many brilliant novels, phatagasmorphic books that dissolves reality and makes one ache for the pain of living. There was Kate Grenville's "A Secret River", a book that digs into the collective consciousness of the Australian psyche. It's a richly imagined period piece of a man straddling the squalor of Victorian England and the prison colony of early white Australia. It's an unbelievably tense collision of worlds, English, colonial Australia, and the indigenous world, with a ferocious climax that shook me up something wicked.

A page-turning juggernaut, "Hunger Games" is the first book in years that made me stay up till 3 in the morning to finish. Merely young adult fiction? Of course not, it is simply one of the greatest adventures ever written, right up there with Dumas' "Man in the Iron Mask". Suzanne Collins has given us one of the vivid heroines in literature. The arrow-slinging, steely-minded Kadniss Evergreen can prick the prissiness of every treacly Jane Austen archetype ever written.

Then there was Hilary Mantel's "Bring Up The Bodies", the continuation of one of my all-time favorite novels "Wolf Hall". "Bring Up the Bodies" is every bit as bloody and visceral as its predecessor. But it is the voice of Thomas Cromwell that I crave, he is more real to me than friends I have known for years. This is a man as cultured as he is brutal, but pragmatic, and even generous when he can afford to be. I love the way Mantel captures the mind of a man who has deftly moved into the world of the Enlightenment and trying to drag the rest of England with him.

I didn't get to read too much french this year, but I did get my hands on the latest from Justine Levy in "Mauvaise Fille". It's a short read but packs a double-handed whopper of plot: her mother dies of cancer as she gives birth to her first. It would be pure melodrama were it not for that hypnotic voice, wry and cerebral, but always on the verge of a meltdown. Sure it's semi-autobiographic, but that makes it all the more entertaining.

Capping off a superb year, I was fortunate to read Junot Diaz' "This is How You Lose Her". The prose crackles off the page and the stories run the gamut of human of experience. I did not want this book to end; I wanted the stories to spin forever and forever. Diaz has managed the godly feat of creating a character that walks the poignant line between deplorable and incandescent. Oh Yunior, I hardly knew you. Diaz' ability to conjure up the world of the Dominican Republican through a supple play of patois, over-sized characters and fatalistic myths remind me very much of the ferocity of Rushdie's Booker-of-Booker "Midnight Children". Yes, "This is How You Lose Her" is that good.

Science non-fiction

After a barren few years for popular science books, I stumbled onto several good ones this year.

I first encountered evolutionary psychology about a decade ago in its former incarnation as social biology but was rather put off by it then, when it was rather short on data and long on theorizing, inevitably becoming a mirror for the writer's political ideology. The field of evolutionary psychology has since progressed in leaps and bounds, and one of the glittering lights of the field is Jonathan Haidt, who also happens to be a gifted writer. His "The Righteous Mind" outlines a persuasive case that there are several underlying psychological modules that define human moral thinking, which to rattle them off carelessly are: care/harm, fairness/cheating, loyalty/betrayal, authority/subversion, liberty/oppression and the most interesting to me, sanctity/degradation. This theory is backed by oodles of cross-cultural research and steeped in careful evolutionary thinking. I think combining these insights with the work in evolutionary religion (David Sloan Wilson) will provide a doorway into 21st century religion.

As a scientist working in biology, looking for a connection to medicine is an important skill to improving one's grant-baiting ability. Sadly, this does not mean I actually know anything about medicine; my knowledge of the history of medicine is rather meagre. I fortunately got a chance to fix this when I stumbled onto James Le Fanu's "The Rise and Fall of Modern Medicine", filling a rather surprising gap in the literature. It does this through a rather provocative hypothesis – that there was a golden age of medicine, and it has already passed. The first half of the book provides an extremely readable history of modern medicine, mainly over the course of the 20th century, structured in terms of 11 pivotal breakthoughs. This half of the book is wonderful and has definitely enriched my understanding of modern biology. The second half, where Le Fanu rails against modern day medical research, is rather uneven, and can be safely skipped.

In biology, two of hottest areas are neuroscience and developmental biology. In Rob DeSalle and Ian Tattersall's "The Brain" we have a exposition that beautifully syntheses the two. This book explores,not just the brain, but the whole notion of a nervous system in terms of developmental biology. To do this the book reaches right back into the tree of life to trace the evolution of organic life, and at each stage of development, feeling out the functional requirements of a working nervous system, culminating into the nervous system of the human brain. Unlike other lesser books on the brain, the brain doesn't even make an entry until 2/3 of the way into the book. More that the generally breezy quality of the writing, what impressed me most was how clued these guys were into the cutting edge of biology – they write about the fascinating world of non-coding RNA, transposonic elements, and the even more mysterious process of RNA editing. These are findings I've found to be still outside the mainstream (see for example many bioinformatician's resistance to the idea that transposonic elements have any biological function at all).

I have had a hole in my technical education, ever since I skipped second-year Linear Algebra for what I thought would be the sexier subeject of Introductory Philosophy. It's been a problem ever since as standard linear algebra theorems are often invoked to explain higher level physics. I've tried to rectify this over the years, but each time I'd try a new linear algebra text book, I died a little. The difficulty with teaching Linear Algebra is that there are no really overarching equations that binds it all together, instead there is a forest of numerical techniques to master, as well as a bunch of disconnected abstract algebraic theorems. As a consequence, half the linear algebra textbooks soar into abstractions which obscures the messiness of practical techniques, whilst the other textbooks dive into the nitty-gritty algorithms, but get lost in the ability to make sense of all the different techniques. Gilbert Strang's "Linear Algebra" is that rare Linear Algebra textbook which perfectly straddles the two. It got me interested to learn all the theorems, which were presented in a way that handily motivates all the key techniques. You will learn how to reduce matrices into various canonical forms, but also how to use the abstract theorems to grasp the meaning of the solutions. As a result, I can now plow through some machine-learning papers in bioinformatics that has had me stumped for a while.

This was also the year that after many aborted attempts, I finally got my head around information theory. I settled on David MacKay's "Information Theory, Inference and Learning Algorithms" because it was the only one that was willing to motivate all the theorems of information theory for a rank beginner. Before every theorem, MacKay patiently describes in elaborate and necessary detail the kind of problems each theorem would solve. Information Theory can be a beautifully abstract theory, but its power is in its ability to illuminate very specific computation problems. I loved the focus on practical consequences such as the explanation of how the gzip algorithm works as an elaboration of the use of entropy in encoding files. But more importantly, MacKay has taken the idiosyncratic (but ultimately correct) approach of teaching information theory as a branch of bayesian inference. The information theory then becomes a launching pad into machine learning. Thanks to this, I also got to learn the basics of machine learning for free. Booyah.