The following are mini-reviews of books I read in 2012.
Also see the full index of books I've read.

Little Dorrit

As was the case with Nicholas Nickleby, I was channel-surfing one day and happened upon a movie adaptation of Little Dorrit. It looked interesting, so I decided to read the book. (I've only seen about 5 minutes of each movie.)

William Dorrit had been in Marshalsea debtors' prison for over 20 years. His youngest daughter, Amy, a seemingly frail young woman, was born and lived in the prison. From an early age, she took tender care of her father, even to the extreme of forgoing food so that he might eat. She also made every effort to help her brother and sister get on in life, efforts that were largely unappreciated by her two elder siblings who, in fact, looked down upon her for having been born in prison. (The family was free to come and go; only the father was confined to the prison.) The other protagonist of the story, Arthur Clennam, called her Little Dorrit, the name given to her by his mother's housekeeper. Arthur attempted to help the Dorrit family because (i) he was just that type of guy and (ii) he had a nagging feeling - but no evidence - that his father's business was in some way involved with Mr. Dorrit's downfall. Although admirable in all other respects, Arthur had one shortcoming: he failed to realize that Amy was in love with him and he, subconsciously, was in love with her.

Prominent in the novel are parodies of the upper class in the form of various characters and parodies of the government in the form of the Circumlocution Office. The purpose of the latter was to ensure the primacy of the "How Not to Do It" philosophy over the counter-philosophy, "How to Do It". Dickens is long-winded in these passages, which is unfortunate since he has a perfectly good story to tell otherwise. The parody of the government didn't sit well with me given that, at the present time in the United States, politicians in the federal and state governments are attacking public-sector employees as being unworthy to worship the ground upon which private-sector employees walk. Not surpisingly, many of the most vociferous critics, primarily Republicans, have sucked at the government teat most of their lives and show little evidence of familiarity with the private sector and its foibles. It reminds me of a fellow contractor at NASA, a Rush Limbaugh dittohead, who crowed about the Republican-engineered government shutdown in 1995. I began to list the government employees in our department, beginning with his beloved mentor (a very talented individual) and continuing with all the rest who were equally capable, and asked him one-by-one whom he would fire. End of conversation after a lot of sputtering on his part.

There are a number of parallel story lines progressing simultaneously; consequently, there are so many characters that you sometimes lose track of who's who. Midway through the book, Mrs. Merdle made a second appearance and I couldn't place her. I then made the mistake of searching for "Merdle" in the Wikipedia entry for Little Dorrit - the sentence I found reminded me of who she was, but the following sentence, which I couldn't help but notice, gave away some important parts of the end of the story!

Little Dorrit seemed to be a more awkward read than the other novels by Dickens I've read. I can't quite put my finger on why. Early in the book, he often uses the literary trick of repeating a word or phrase throughout a paragraph for emphasis. Then there's Flora's stream-of-consciousness dialog. And, of course, there are the flowery parodies. Perhaps he was trying to be too clever by half. Regardless, the writing style does not overpower the interesting story. I found the denouement to be somewhat confusing; the recounted story involved many people not mentioned by name and the relationships between them were hard to follow. Even one of the characters yelled out "Names!" in an attempt to remedy this deficiency.

Project Gutenberg eBook: Little Dorrit

Eloquent JavaScript: A Modern Introduction to Programming

1995 - Brendan Eich reads up on every mistake ever made in designing a programming language, invents a few more, and creates LiveScript. Later, in an effort to cash in on the popularity of Java the language is renamed JavaScript. Later still, in an effort to cash in on the popularity of skin diseases the language is renamed ECMAScript.
    - "A Brief, Incomplete, and Mostly Wrong History of Programming Languages" by James Iry.

My son was about to take a "Web Development Using JavaScript" course, so I decided to learn the rudiments of the language in case he had any questions. (I did a little bit of JavaScript programming back around 2000, but not enough to still remember it.) At under 200 pages, this book is a concise introduction to JavaScript. The example code gets longer the further into the book you read and, consequently, I became less inclined to study the code line by line; knowing the concepts, I can always research them in detail on-line when necessary. The language impresses one as a hodge-podge of features, duct-taped together; James Iry's quote above is apt.

Eloquent JavaScript is extremely well-written, but it is not for beginning programmers. The chapter on functional programming in JavaScript is likely to fly over the heads of programmers not familiar with functional programming. I'm not sure how programmers who have solely used class-based object-oriented languages such as C++ will adapt to JavaScript's prototype-based object mechanism. I used to read the ACM's OOPSLA proceedings in the early 1990s (back before they became largely composed of Java-related research papers) and had been exposed to various OO systems, so object-oriented programming in JavaScript was no surprise. Inheritance using vanilla JavaScript techniques is rather tedious, so different programmers have taken different approaches to writing helper functions to simplify the process, which can be somewhat confusing if you maintain other people's code or use existing libraries.

There were a couple of historical inaccuracies in the book. The common use of i, j, k, etc. as loop indices probably arose because of their use in mathematical notation, not because programmers are lazy, as the author suggests. Also, not all programming languages begin array indices at 0; C was the first mainstream language I knew that followed that convention. Other languages used 1 as the first index or allowed the programmer to specify an arbitrary range of indices for an array.

Haverbeke offers some practical advice on programming throughout the book, mostly good advice. However, I did take issue with his recommendation concerning documentation: write the documentation after you've coded and tested the software. He seems to envision programming as a give-and-take puzzle process such that the public interfaces to function packages and objects are likely to change as coding progresses. My feeling is that a programmer with sufficient experience should, with rare exceptions, be able to correctly specify public interfaces before writing code and that the documentation of those interfaces should serve as a design document for coding purposes. Regarding comments on code fragments, why risk the chance of forgetting to go back and comment on a particularly complex piece of code?

One minor complaint. My daughter and I have noticed the increasing frequency with which people in entertainment and the media use what my daughter calls "OCD as an adjective"; e.g., someone is OCDish about one thing or another. Haverbeke calls for adopting an "obsessive-compulsive mind-set" when faced with browser-specific JavaScript quirks. Throwing the OCD term around so freely in popular culture tends to trivialize the actual disorder, a disorder which is very serious for those who suffer from it. I'm sure Haverbeke meant no offense, but I wish he'd used different wording.

Also see:

• The book's web site, Eloquent JavaScript. The site includes an HTML variation (i.e., it's not identical) of the book and a code sandbox in which you can run examples from the book or type in your own JavaScript code.
• Mozilla's JavaScript Programming Guide and Reference Manual.

The Theory That Would Not Die: How Bayes' Rule Cracked the Enigma Code, Hunted Down Russian Submarines, and Emerged Triumphant from Two Centuries of Controversy

I seem to remember learning about Bayes' rule in a statistics class I took (in the Economics department; I was at least smart enough not to attempt the more rigorous course in the Math department) or when I worked as a student programmer for the Pattern Recognition lab at the University of Maryland. Having forgetten whatever I learned, I hoped that McGrayne's book would provide some insight into the rule. She tried, but that was not the main focus of the book. As I understand it, you guess or estimate the prior probability of an event (and the prior probabilities of related events) and, using Bayes' rule, calculate the future probability of the event. In an iterative process, as new data becomes available you update the prior probabilities and calculate a refined future probability.

As I said above, the focus of the book is not so much on Bayes' rule itself, but on the history of the rule. In particular, the author covers:

• The long-running battle between Bayesians and "frequentists", the latter being statisticians who believe future probabilities can only be computed based on past data samples, not on "guesstimates". (My simplification!)
• The applications of Bayesian inference in a multitude of fields.

The academic battles are quite interesting, but I found the many applications of Bayes' rule to be fascinating. Of particular note were the use of Bayes' rule in decrypting German communications during World War II and the sad story of a key player, Alan Turing, whose name is well-known among computer scientists for the notion of "Turing-complete" programming languages and the "Turing Test".

Coincidentally, the book spends some time on John Tukey, a brilliant man who, like many post-war scholars, was recruited for and worked on national security research. He was also hired by NBC to predict election results, to which end he used Bayesian methods, but, oddly, never "confessed" to using Bayes' rule; McGrayne speculates that this reticence might have had something to do with his classified work. Anyway, the professor in charge of the Pattern Recognition lab at the University of Maryland taught a course, "Exploratory Data Analysis", based on Tukey's book of the same name. Prior to the course, I was assigned the task of adding some features to the interactive data analysis program (received on magnetic tape) to be used by the students. From the Wikipedia article, I'm guessing it was the Carnegie-Mellon University Data Analysis Package (CMU-DAP). Being the days of teletypes and DECwriters, the program was interactive in the sense that you would enter data points and the program would generate the famed box-and-whisker diagrams using typewriter symbols. (Graduate students - and programmers working for professors! - had access to a motley assortment of CRTs.)

One case recounted by McGrayne is the 1966 mid-air collision of a refueling tanker and a B-52 bomber carrying 4 hydrogen bombs over the small village of Palomares, Spain. Debris and 3 of the bombs rained down on the village, contaminating the soil; the fourth bomb dropped into the sea. Months were spent on a Bayesian-guided search for the fourth bomb. A grid was laid out on the sea and probabilities were calculated for each cell in the grid. The cells were then searched in order of probability, with search results used to update the probabilities of the remaining cells. Finally, two sailors grabbed a Spanish fisherman who had witnessed the bomb falling into the water (but whose account had been deemed unreliable) and got him to show them where the bomb had dropped. The bomb was found in short order. The formal search was hampered by the primitive technology of the underwater sensors at the time and the lack of readily-available computing power. McGrayne tells the stories of several other cases in which Bayesian-guided searches were cut short by actual pre-search sightings. Carl Brashear, the first African-American Navy diver, lost his leg in the Palomares incident, an event dramatized in the movie, Men of Honor, starring Cuba Gooding, Jr.

The last chapter is a lengthy (!) whirlwind (!) overview of the application of Bayes' rule over the past 20 years in an extraordinary number of fields. It seems as if there isn't a field of inquiry that hasn't been touched by Bayes' rule.

One thing that surprised me was that the advent of computers in the 1940s seemed to do nothing to promote the use of Bayes' rule. In fact, it wasn't until around 1990, nearly 45 years later, that Bayes' rule came into its own, thanks to (i) more powerful computers and (ii) the adoption by Bayesians of Markov chain Monte Carlo (MCMC) methods. Apparently MCMC greatly reduces the computational intensity of practical applications of Bayes' rule.

Also see:

• Bayes' Theorem at Wikipedia, suitably flagged as "This article may be too technical for most readers to understand"! (Naive Bayes Classifier used in pattern recognition.)
• Eliezer S. Yudkowsky's widely referenced article, "An Intuitive Explanation of Bayes' Theorem. This is a long paper, as the author ackowledges in the subtitle: "Bayes' Theorem for the curious and bewildered; an excruciatingly gentle introduction."
• Some visual tutorials on Bayes' rule: Oscar Bonilla's "Visualizing Bayes' Theorem" and Komponisto's "Bayes' Theorem Illustrated (My Way)".
• James V. Stone's concise "Bayes Rule: A Tutorial Introduction".

River of Darkness: Francisco Orellana's Legendary Voyage of Death and Discovery Down the Amazon

In 1541, Gonzalo Pizarro, a younger and even more ruthless half-brother of Francisco Pizarro, conqueror of the Incas, set out from Quito in search of the "Lost City of Gold", El Dorado. (Quito, later to become the capital of Ecuador, was then part of the Inca Empire.) Francisco Orellana joined him shortly afterwards as his second-in-command. According to Wikipedia, the freezing trek across the Andes Mountains resulted in the deaths and desertions of about 3,000 virtually unclothed native porters and about 140 Spanish soldiers. (Oddly, the book mentions the severe conditions of this part of the trip, but not the loss of manpower.)

Getting through the dense jungle was difficult and slow. On the Coca River, a boat was built to transport sick and injured soldiers. More men became sick and weak from hunger and a halt was finally called. Orellana suggested to Pizarro that he (Orellana) and a group of about 50 men take the boat, scout downriver for food, and then return to the encampment. Pizarro agreed, the boat set off, and that was the last Pizarro saw of Orellana. After floating downriver for a few days, Orellana's men found the current too strong to make rowing back upriver feasible, so they had to continue on. Pizarro, eventually realizing Orellana wouldn't be returning, led his remaining men on an alternate route back to Quito.

That's the beginning of the story. In the remainder of the story, Orellano and his men descended the Coca River to the Napo River, then on to the Amazon River, and finally out to the Atlantic Ocean. The full length of the voyage is unclear; different articles on the Internet give distances between 2,000 and 3,000 miles. (Once in the Atlantic Ocean, the men had to travel an additional 1,400 miles north to reach Spanish-occupied islands.)

Levy keeps the story interesting and moving along at a good pace. Which is surprising since the story is somewhat repetitive from here on out: land at a friendly village and fill up on supplies, land at an unfriendly village and fight to escape with your life, land at a friendly village, etc., etc. Somehow the trip was made with minimal loss of life despite frequent battles against overwhelming odds; this fact was reminiscent of Francisco Pizarro's conquering of the Incas despite being vastly outnumbered.

Also see:

• Francisco de Orellana (Wikipedia)
• "Orellana and the Amazons" (Athena Review, Vol. 1, No. 3)
• Gonzalo Pizarro (Wikipedia)
• Amazon River (Wikipedia)
• Ed Stafford (Wikipedia) and Gadiel "Cho" Sanchez Rivera walked the full length of the Amazon River in a trip that began in April 2008 and ended in August 2010. I saw a program on a science cable channel that appeared to be a compilation of these videos filmed during the trip. The program gave a good idea of the difficulties in traversing the jungle, which, along certain stretches of the river, were compounded by the seasonal overflow of the river which flooded large areas of the jungle and the subsequent withdrawal of the flood waters which left the jungle bone dry.

Epidemiology: A Very Short Introduction

... currently reading ...

The God Species: Saving the Planet in the Age of Humans

In 2009, a group of scientists under the aegis of the Stockholm Resilience Centre drew up a list of nine planetary boundaries - limits on aspects of the earth system that, if exceeded, would cause harmful, possibly irreparable, effects to the human species and the environment. The nine boundaries (Wikipedia) are:

1. Climate change
2. Biodiversity loss
3. Biogeochemical (human-caused conversion of stable nitrogen from the atmosphere into reactive nitrogen in the atmosphere, on land, and in the oceans; human-caused dumping of phosphorus into the oceans)
4. Ocean acidification
5. Land use (especially the amount of land devoted to agriculture)
6. Freshwater
7. Ozone depletion (once exceeded, but now expected to recover by 2100)
8. Atmospheric aerosols
9. Chemical pollution

Limits have not been established for several of the boundaries and the remaining limits were set assuming no interactions among the categories. Of course, there are interactions, but trying to determine limits while taking the interactions into account would have resulted in variable limits that probably wouldn't have been useful as guidelines. (Also, a boundary is actually the low point of a range of values; the midpoint of the range is called the threshold.)

Lynas begins in a breathless rush to expound on his subject. He eventually either slowed down to a normal pace or I just got used to it. The book provides a good description of each planetary boundary, the history behind the boundary, and the potential futures if the boundary is or is not exceeded. All very interesting and informative.

There are some problems, however. Lynas comes across as pursuing a vendetta against environmentalists, or "Greens" as he calls them. The rare compliment paid to the Greens is always followed by "but". While I see and agree with some of his differences with the environmentalists, his attacks on them in the book seem excessive.

Lynas believes strongly in technological solutions to the problems facing us. His most controversial stance is advocating for nuclear power plants. I'm not sure how I feel about this. It's true that accidents in the fossil fuel industry have killed more people than in the nuclear power industry, but the nuclear power industry is still subject to the possibility that an unlikely disaster could be catastrophic. Lynas downplays the Fukushima incident in Japan in March 2011, rightly pointing out the widespread non-nuclear contamination caused by the spillage of industrial storage and waste in the tsunami. However, as I write this a year later, it has been reported that Japan has shut down 52 of its 54 reactors nation-wide for safety reasons. This may be an irrational response as many have suggested, but the reactor accident in Fukushima and the shady practices of the power company (TEPCO) that have come to light as a result are causes for concern. In fairness, Lynas urges the construction of new types of reactors designed more recently than the 40-year-old reactors commonly in use at Fukushima and elsewhere.

To promote nuclear power, Lynas brings up Einstein's equation, E = mc², where c is the speed of light (300 million meters per second): "Clearly even with a very small amount of fissionable material, multiplying it by the square of 300 million yields a very big number." While this statement sounds impressive, the equation applies to any type of energy, including that generated by fossil fuels. The enormous energy produced in a nuclear reaction actually comes from breaking the strong force holding together the particles in an atomic nucleus (Wikipedia).

The author's also believes that we are smart enough now that the technological fixes we devise won't have unforeseen consequences. I don't buy that and two examples he gives in the book belie his point. First, the invention of fertilizer in the early 1900s had two effects, one good and one bad: (i) it has enabled us to feed the rapidly expanding population and (ii) it led us down the road to exceeding the nitrogen (biogeochemical) boundary. Second, the invention of freon in the 1920s also had two effects, good and bad: (i) it made safe refrigeration and air conditioning possible and (ii) it led to the depletion of the ozone layer. The bad effects only became apparent many decades later.

The use of fertilizer is an interesting issue. The alternative, organic farming, has a lower yield (persons fed per acre farmed). Consequently, reducing or eliminating the use of fertilizer would require increased land use (probably achieved by deforestation), thus resulting in exceeding the land use boundary, losses in biodiversity, and further aggravating climate change. On the other hand, I'm not optimistic about the development of genetically-modified, self-fertilizing grains, a feat which Lynas foresees happening within 10 years. (The roots of naturally self-fertilizing grains provide an oxygen-free environment for microbes which produce nitrogen.)

The Last Speakers: The Quest to Save the World's Most Endangered Languages

"Saddened, we departed Nersa, village of mostly forgotten stories." This is the primary theme of Last Speakers, as author David Harrison travels around the world to villages where languages are dying. When the last remaining speakers of a language "go berry-picking" (to use a Tofa metaphor), the cultural, environmental, and historical knowledge encoded in their language and embodied in their culture is lost.

Last Speakers was a slow read for me - I was having trouble concentrating and the many languages covered tended to blur together as a result. Regardless, nuggets of information were frequent enough to keep me going and I came away with a respectable amount of food for thought.

Harrison warns against "exoticizing" these dwindling societies, but falls prey to romanticizing them himself at times, perhaps out of exuberance at gaining new knowledge. The Chaco region that reaches into Paraguay, Bolivia, and Argentina is characterized by a harsh environment and, despite a limited population, is a linguistic "hotspot" (i.e., many languages are found there). When a group of natives would get too large to sustain itself, it would break into smaller groups that would go their separate ways; this might explain the divergent languages that evolved over time. I'm reminded of a book I read years ago by a paleontologist hunting for dinosaur fossils in Africa. He remarked on the fact that the local natives, while very friendly and apt to break into smiles, daily walked a thin line between life and death by starvation or disease. Harrison is well aware of and describes the difficult lives lead by many of the groups he studies, but he naturally focuses on the groups' languages, which is, after all, the subject of the book.

Also see:

• Living Tongues Institute for Endangered Languages and its Enduring Voices Project.
• Enduring Voices Project YouTube channel.

Mary Barton: A Tale of Manchester Life

Elizabeth Gaskell was a contemporary of Charles Dickens and addressed many of the same social issues in her novels that Dickens did. Trying to describe the plot of Mary Barton risks giving the ending away, so suffice it to say that Mary Barton was a poor young lady who planned on becoming a rich young lady by marrying a rich young man. She was quite beautiful, so her intention was not out of the realm of impossibility. Aside from telling a romantic story, the novel also had the purpose of portraying the plight of the poor, both in terms of being poor in and of itself and of being poor in the industrial milieu of early 19th-century Manchester, England. The storyline is tied to some actual historical events in the late 1830s and early 1840s. One of the most poignant moments breezes by when Mrs. Wilson mentions in passing that she began working in a factory at the age of 5.

Mary Barton is almost a treasure trove for English-language linguists. Many times, oddities of spoken English are flagged with footnotes defining the terms and/or giving examples of their use in prior literature. It must have required an extraordinary effort by Mrs. Gaskell to track down the citations, especially in a pre-Internet age! (Let me amend what I've just written. The footnotes get fewer and fewer as you get further into the book. This is unfortunate. For example, upon encountering the word "moider" in dialog, you might think of it as an attempt to reproduce the pronunciation of "murder", thereby missing the fact that "moider" is a perfectly good British word meaning "to bother or bewilder".)

The New Bailey (Prison) of Manchester is not to be confused with the Old Bailey (Court) of London.

A quotable quote about fetching a "physic" for the dying Ben Davenport (Chapter VI, "Poverty and death"):

They are the mysterious problem of life to more than [John Barton]. He wondered if any in all the hurrying crowd had come from such a house of mourning. He thought they all looked joyous, and he was angry with them. But he could not, you cannot, read the lot of those who daily pass you by in the street. How do you know the wild romances of their lives; the trials, the temptations they are even now enduring, resisting, sinking under? You may be elbowed one instant by the girl desperate in her abandonment, laughing in mad merriment with her outward gesture, while her soul is longing for the rest of the dead, and bringing itself to think of the cold flowing river as the only mercy of God remaining to her here. You may pass the criminal, meditating crimes at which you will tomorrow shudder with horror as you read them. You may push against one, humble and unnoticed, the last upon earth, who in heaven will for ever be in the immediate light of God's countenance. Errands of mercy — errands of sin — did you ever think where all the thousands of people you daily meet are bound? Barton's was an errand of mercy; but the thoughts of his heart were touched by sin, by bitter hatred of the happy, whom he, for the time, confounded with the selfish.

Project Gutenberg eBook: Mary Barton

The Ghost Map: The Story of London's Most Terrifying Epidemic - and How It Changed Science, Cities, and the Modern World

... currently reading ...

Also see the book's website, The Ghost Map.