30 December 2011

2011 in Review

I did a bit less blogging this year, mostly because I was doing more cycling, traveling, reading, cooking, artistry, and really, just more of the things I love that are actually worth blogging about. So I would say it has been a great year.

In the spring I made the very difficult decision to leave Google, and ended up taking about six months off work. I think that taking some time off to recharge, without any plans initially, was one of the better things I've done for myself.

One of the things I had time to do was a lot of cycling. This year I logged 4,150mi of riding and 284,000 vertical feet of climb (up 54% and up 89% Y/Y, respectively). I completed a trifecta of semi- and self-supported bike tours this year: Central California (San Jose to Santa Barbara), the first tour I planned myself; the Alps (yes, again), my climbing-est tour to date; and the Pacific Coast from the top of Washington to San Jose, my first solo tour and my longest tour in total distance to date.

The Alps were, as always, stunning. And counting the Central California and the Pacific Coast tours together, I traversed over 80% of the western coast of the continental US this year. It's truly a remarkable place— it would take little convincing to get me to do any part of it again; yet, it was only passing through Big Sur in the spring that really spurred me to take the much longer Pacific Coast tour in the fall. To think, how lucky we Bay Area residents are to have Big Sur in our backyard! I met so many interesting people while on tour, and I feel like I've gotten to explore a part (however small) of America in a way that I've never gotten to do before, despite having lived here my whole life.

I guess I've raved about cycle touring enough that I also apparently convinced a few friends of mine to try it out for the first time this year. So that has been a lot of fun.

Now I'm working at DNAnexus, a software startup in Mountain View. At a high level, we're building a software platform for managing and analyzing genomic data, so researchers don't have to worry as much about the intricacies of cluster filesystems, fault tolerance, and all that other "fun" stuff. I am enjoying work at DNAnexus for a number of reasons, chief among them the tantalizing possibility that just by making computation easier to use we could help biologists and doctors take medicine to the next level, and help them to build a new kind of understanding of how living things work (and how to fix them, too).

Happy New Year, and best wishes to you all for an awesomer year 2012.

2011 Book List

I read the following 26 books this year, of which my favorites were— non-fiction: The Box, Metamagical Themas, and Sustainable Energy: Without The Hot Air; fiction: 1Q84, The Diamond Age.

Fiction Roundup

1Q84, by Haruki Murakami. As usual with Murakami's books, explaining the plot is neither necessary nor helpful. And, as usual, 1Q84 is endlessly imaginative, entertaining, and a pleasure to read. The story seems to hang together better and have more of a resolution than Murakami's others. Also, there are a number of structural symmetries that add some interesting layers. All in all, somewhat haunting, and recommended.

The Diamond Age, by Neal Stephenson. I felt a sudden urge to re-read this one while on vacation, and fortuitously, I found a copy in a used bookstore. A bespoke book-like educational device, originally commissioned for an aristocrat's daughter, instead falls into the hands of a girl who lives in the slums. One of the science fiction novels that not only presents a plausible extrapolation— a story of what we could do with technology— but is almost begging to be read (in places) as an example of what we should do with technology. Touching, and perhaps my favorite Neal Stephenson; recommended.

REAMDE, by Neal Stephenson. A computer virus triggers a chain of events in a WoW-like computer game, which causes the Russian mob to start a manhunt… and that's to say nothing of the Islamic terrorists… Stephenson's prose is characteristically fun to read at a local scale, but the world he builds here does not possess the same level of sheer awesomeness as much of his previous work. The final showdown, too, is just too long. It is, however, an enjoyable read.

A Fire Upon The Deep, by Vernor Vinge. Humans playing with fire (in the form of computer software) get burnt when they instantiate a super-intelligent entity. One expedition is forced to crash-land on a world of primitive dog-like beings. Vinge's brand of transhumanism, as well as his many inventions for this story (for example, the Tines, the dog-like creatures, which have a distributed pack mind of sorts), make for a fun read. However, I soon got tired of Vinge's flowerly and/or pretentious prose, inserted in places where human readers are meant to be incapable of actually comprehending the transcendent premise. In a way this genre seems to be a form of literary cheating. I could have forgiven that, but a book that is so epic in scope seems to me to also require a much better conclusion than this one had. It was, though, enjoyable enough that I am reading its sequel.

The Processes of Life

The Processes of Life: An Introduction to Molecular Biology was recommended to me as "Molecular Biology For Computer Scientists" (the author, Lawrence Hunter, is a Lisp hacker!), and it is a very good introduction to how living things work at the molecular level.

The text covers: the universal processes of life (and covers just enough chemistry to do so), the organization and development of living things, what goes wrong in living things e.g. cancer, and the state of the art in biotechnology. But throughout, the focus is on understanding processes as examples of regulation (i.e. modulation) and feedback, and living structures as machines or as information-bearing components; and looking at molecular evidence for certain evolutionary explanations. Therefore, engineers and others with a technical background can easily benefit from some cross-domain transfer without getting bogged down in chemistry.

Hunter's writing is lucid and engaging, and he gets to the point very quickly. (In fact, and I didn't think I would be saying this, the book is a page-turner in places.) The core of the book is just about 250 pages, and at $39, it's a great deal, too. For any non-biologist who is interested in learning about the wondrous designs that living things embody, I would recommend reading this book before delving into any introductory-level college text, which is likely to cost more, be many times longer, and contain more chemistry than you are really going to want or need to know.

Recommended.

15 October 2011

Cycling in Oregon: signage and literature

The resources that the state of Oregon provides for recreational cyclists are pretty astounding. I have never seen or heard about anything like this, anywhere.

The Oregon Department of Transportation publishes a free map and guide to the Oregon Coast Bicycle Route— the recommended route when Pacific coast cycle tourists pass through Oregon. It includes (now, the first few are pretty standard, but keep reading):

  • A map of the coast
  • An elevation profile of the route
  • Suggestions for scenic detours
  • A list of state parks and cyclist amenities
  • Temperature and precipitation graphs for representative cities
  • Elevation profiles for the major roads that go between I-5 and the coast route, for your reference when you are planning the beginning and end of your trip
  • A map showing the prevailing wind direction in each part of the state
  • A graph showing the average number of cars that use each segment of the route(!) each day

This thing is practically a cyclists's almanac. And you can pick up a copy of it as you roll by the roadside kiosks they have placed, very conveniently, on the route at the northern and southern entrances to the state (Astoria and Brookings, respectively).


Picking up a map just outside Astoria, OR

As for the situation on the ground, the route is well-signed the entire way. There are bypasses that take less congested routes through major cities, and these are typically signed turn-for-turn within the city. So you don't need to pull out your map when trying to get through the cities.


For heaven's sake, even the bike shop is signed.

There are two tunnels along the Oregon coast route, and at both of them, bicyclists can press a button to activate flashing lights that warn motorists of the presence of bikes in the tunnel. (The lights stay on for a time T = [length of tunnel] / (10 mph).)


Lights in activated state

A couple of bridges have the same mechanism. In many, many other places, on bridges and otherwise, where the shoulder is inadequate, there are signs warning motorists that cyclists will be using the lane.

All in all, pretty impressive. If you're feeling inspired to ride in Oregon now, the tourism bureau maintains a website that catalogues some of the nicer bike rides in the state.

17 September 2011

Tour of the Alps 2011 Trip Report

This past June and July, I went on a bicycle tour of the Alps with Piaw Na and Xiaoqin Ma. I've now posted my trip report, which includes a map (reproduced below) and remarks and mini reviews of equipment and other things.

01 September 2011

White Noise

White Noise by Don DeLillo is (…I think…) a caricature of 1980s suburban America. The protagonist, Jack Gladney, is head of the department of Hitler Studies at his small-town college, and the book follows the misadventures of his family (Jack, his wife Babette, and their many children by previous marriages) as an "Airborne Toxic Event" forces an evacuation, and Jack tries to track down the drug that his wife is secretly taking.

What is so entertaining about White Noise is the juxtaposition of the characters' hilariously misinformed and inane dialogues, and the seriousness with which they seem to take everything, no matter how inconsequential.

Very funny, though in an unsettling way (in the year 2011): the setting of the book is by now very clearly not our generation. I feel like we can point and laugh because we left that era behind… right, guys?

Metamagical Themas

Metamagical Themas is a collection of Douglas Hofstadter's (Gödel, Escher, Bach) columns (of the same name) for Scientific American in the early 1980's.

If you enjoyed GEB I think you will really love this book. Hofstadter's favorite themes are represented here, and like GEB it is full of fascinating nuggets. But unlike in GEB Hofstadter is no longer constrained by the requirement to build a path from the starting blocks to a single central thesis. His Scientific American columns, collected, feel much more like what he really wanted to be writing.

The columns vary in quality (his comments on then-current AI projects, and on the cold war, seem of little interest today) but the best are no less than thrilling to read. Among my favorites are his columns on self-reference, language and its power to shape thought, the nature of creativity and cognition, and the genetic code. And his remarks about where AI research has to go if it is to really fulfill its charter of implementing "thinking" (here spelled out more explicitly than in GEB) are still relevant today.

Metamagical Themas is at least as good as, and possibly even better than, GEB. Recommended.

20 August 2011

Cake


Banana Nutella Cake

I have been baking cakes! The cake recipes from the Alice's Tea Cup Cookbook have served me well. In that capacity, the book comes recommended. However... I cannot yet speak to the usefulness of the chapter on how to throw a tea party.

05 August 2011

Fiction Roundup

Alice's Adventures in Wonderland

A classic, a very short read, and a lot of fun. Recommended.

The Road

The closest thing I have read in some time to poetry. In Cormac McCarthy's barren post-apocalyptic world, a father and his son are pushing their cart down the road in search of the coast, always on the brink of starvation. The setting is striking but it takes a backseat to the lyrical and poignant dialogues between father and son. These are all the more remarkable for how few words are uttered. Beautiful and haunting; recommended.

Kafka on the Shore

by Murakami. A fun read. Compared to The Wind-Up Bird Chronicle, it seemed to have more of a coherent structure and plot, but less of the wordplay (if you could call it that) that made Wind-Up Bird so hilarious.

Catching Fire / Mockingjay

The two sequels to The Hunger Games. These should be considered as a unit since Catching Fire has a cliffhanger ending. Katniss has unwittingly become a symbol of rebellion against the Capitol, but any overt action on her part would put her and her family in danger. Catching Fire was an enjoyable read, but most of Mockingjay felt uninspired, and the ending was rather unsatisfying.

Born to Run

(Of the two acquaintances who mentioned this book to me, one had started running barefoot because of it, and the other had turned vegan...)

In Born to Run, Christopher McDougall recounts his personal quest to learn to run (and learn to love running) without injury. McDougall's thesis is that the human body is purpose built for running long distances. This seems unbelievable when you realize that, in any given year, most runners will injure themselves while running. Every year. And most people find running to be a necessary evil, not something that feels good. So what is going on?

When McDougall's research led him to a band of quirky long-distance (ultramarathon) trail runners, and an elusive tribe called the Tarahumara who live in the Copper Canyons of Mexico, he sought to learn their techniques— everything from posture to diet. Perhaps the most surprising among those: Tarahumara of all ages run for hours or days on end in thin rubber sandals and sustain injuries at a rate that is close to zero. McDougall advances the case that we're built to run barefoot, not in padded shoes (which change one's running posture and provide insulation from proper ground contact).

The science in Born to Run is somewhat sparse, and the writing can be overdramatic and incoherent. At times the book feels like a way-too-long magazine article. But it is nothing if not entertaining, and the conclusions are eye-opening. Mildly recommended.

04 August 2011

Peach iced tea

I have been making my own iced tea this summer. Prototypical recipe:

3 quarts water
6 tea bags
1/2 cup (100g) sugar
2 cans (11.5oz ea) peach nectar (e.g. Kern's brand)
Juice from 1 lemon

Brew the tea. Mix with remaining ingredients. Chill.

This recipe makes about 3.5L of tea and is much less sweet than the typical bottled stuff. I poked around to compute the sugar concentration for some representative iced teas:

Sugar concentration*
Peach iced tea (above)54g/L
Trader Joe's Pomegranate Green Tea63g/L
McDonald's Sweet Tea73g/L
Snapple Peach Iced Tea97g/L

By the way, iced tea as Americans know it (the unsweetened tea that is ubiquitous in restaurants) is, as far as I can tell, nowhere to be found in Europe. Quelle horreur!

* As I understand it, different sugars have different taste and nutritional properties, so these numbers don't tell the whole story.

The Story of the Tour de France, Volume 1

Bill and Carol McGann's The Story of the Tour De France, Volume 1 is a fairly comprehensive history of the Tour from its inception in 1903 to 1964.

The book takes the form of a play-by-play for the significant stages of each year's Tour, and discusses how the rules of the Tour evolved to adapt to the changing times. The creator of the Tour, Henri Desgranges, was quite the character. He wanted the Tour to be a show of the individual cyclist's strength and cunning, but he was in the end unable to keep the team element out of the sport.

The main takeaway from this volume, for me, is that the Tour de France used to have a lot more badassery than it does today. Consider, for example, Stage 2 of the 1909 Tour, 398 kilometers (247 mi) long and run entirely in freezing rain, in which François Faber broke away for the entire second half of the stage. Or the story of Eugène Christophe in the 1913 tour, in which he broke his fork on a descent during Stage 6. There were no follow cars back then; under the rules of the time, riders had to make their own repairs. Christophe carried his broken bike down the hill, walking 10 kilometers to the next town. Here he found a blacksmith, who was able to talk him through what he would need to do to repair his fork (this was as much as was permissible under the rules). Christophe worked at the forge for 3 hours. But at some point, he ran out of hands. He asked a little boy to work the bellows for him. For this the Tour referees gave him a 10-minute penalty. Eventually Christophe finished the repair and kept on riding. He finished the stage 29th— still ahead of 15 other riders.

If you are interested in the history of the Tour de France, there is probably not a better book. The Story of the Tour de France gave me some perspective about how competitive cycling works and about the historical evolution of the sport, but at times it seemed to me to be little more than so many names and numbers.

Sustainable Energy: Without The Hot Air

You can get a digital copy of this book for free. Or get a paper copy on amazon.com.

Reading this book should be a prerequisite for having a conversation about energy policy. Like balancing the budget, the question of how we make the transition from fossil fuels to sustainable power sources requires a quantitative approach with quantitative questions. And, like in the discourse around balancing the budget, people regularly make insane, impossible, or useless proposals because they don't know any better (or they think they can get away with it).

Sustainable Energy, by David JC MacKay, tries to establish a solid numerical foundation for such discussion. At its heart is the question: Is it possible to switch all our energy production from fossil fuels to sustainable sources? And this is more or less an arithmetic question. Either the supply of energy available (given technological projections) can meet demand, or it can't.

MacKay lays out the numbers for various classes of energy consumption and energy production. It turns out that you can reach some nontrivial conclusions just based on very crude lower and upper bounds. For example, what are major uses of energy? MacKay estimates that the typical Briton, who makes a transatlantic plane flight once a year, has a carbon footprint on that single flight of approximately the same as his carbon footprint due to driving during the remainder of the year. And we are not going to make planes that are substantially (say, more than 2x) more efficient than they are today; physics provides a pretty clear lower bound there on the amount of energy that is needed to fly people around. In total, transport (planes plus ground transport) accounts for about a third of total energy usage in developed countries. So to make a dent in total energy usage, we are likely to have to either dramatically cut the amount we fly, or make ground transport much more efficient. (MacKay advocates the electrification of cars as one of the most significant things we can do.)

Conversely, it's also important to know what classes of energy usage account for only small portions of total usage. Lighting in homes and businesses? Around 5% of total usage. Vampire wall warts (like cell phone chargers)? Around one quarter of one percent. Now, some people will insist that "every little bit helps". While this is true in a superficial sense, we can't delude ourselves into thinking that we can, say, halve our energy consumption by implementing ten (or 200) "tiny" interventions like replacing incandescent bulbs or unplugging cell phone chargers when they're not in use. They won't add up. It just can't be done unless you touch the heavy hitters: transport and heating (together, about two-thirds of energy usage). You have something like the equivalent of Amdahl's law here, which upper bounds the total savings even if you were to optimize one class of usage completely away. To think that you can somehow dance around this mathematical constraint is madness.

MacKay reaches a sobering conclusion: for developed countries, making the switch away from coal will require industrialization of vast amounts of land. Whether it's designated for tide power, solar farms, wind farms, biofuel farms, geothermal installations, or something else, we're going to need a hell of a lot of it. (If you find this unpalatable, have we mentioned nuclear power?)

We have been implored at one time or another to try and reduce carbon emissions by carpooling, installing LED lights, eating less meat, not using plastic bags, turning down the volume on the television, breathing more slowly, etc. But we have to pick our battles, and that requires a cost/benefit analysis. I always get annoyed when I hear on the radio a useless and impossible-to-evaluate comparison of the form, "If we all just [made some change], it would be like {taking [large number of] cars off the road, planting [large number of] trees, heating [large number of] homes for free, etc}." Sustainable Energy convinced me that there is a response superior to smashing the radio with my hands, namely, doing some back-of-the-envelope math.

This is a very important book. Did I mention it's free to download? Highly recommended.

03 August 2011

The Year of Magical Thinking

Joan Didion's The Year of Magical Thinking is a memoir of the year in her life after her husband of 40 years (fellow writer John Gregory Dunne) died of sudden cardiac death. During the months surrounding John's death, their only daughter, Quintana, was in a hospital, in a coma, suffering from septic shock.

Grief is common, but Didion has the uncommon trait of being detached enough that she could dissect her grief and commit it to paper. So she was able to pick apart the state of derangement that she found herself in. When people think about loss and the prospect of grieving, they expect to be inconsolable, perhaps unable to function, unreachable in a way. They do not expect to be "literally crazy," as Didion characterized her own mental state when she realized she was unable to throw out John's shoes, because, well, how would he get around when he came back? That is the sort of thing that (if you were in Didion's shoes) would seem to clearly indicate that part of you had abandoned rationality and taken up "magical thinking", and yet, remarkably, it would go unchallenged and possibly unrecognized unless you had explicitly articulated it!

There is little inspirational advice for coping here; just Didion's bare and unfiltered retelling of the event, its fallout, and the strange ideas that her derangement led her to. A very personal account, and a sad but satisfying read (especially if you recognize bits and pieces of Didion's derangement in yourself); recommended.

The Box

The author is Marc Levinson and the subtitle is How the Shipping Container Made the World Smaller and the World Economy Bigger.

Ships, trains, trucks. Giant computer-controlled cranes. Operations research. This book is pure nerd porn.

Marc Levinson documents the history and the rise of standardized shipping containers in this astonishingly interesting book. Today, 40-foot shipping containers full of stuff are routinely sent from factories to warehouses without being opened in transit, even as they are loaded from truck to train to ship and back to train to truck. Before the 1950's, no one implemented seamless intermodal transport: at a dock, for example, longshoremen would unload cargo from a truck or train, piece by piece, and put it in a warehouse, then repack it again into the hold of a ship. This process was slow, labor-intensive, liable to be interrupted by strikes, and made the goods prone to damage and theft. A 1959 report estimated that the cost of shipping some commodities accounted for 25%(!) of the sticker price. Shipping containers and integrated shipping changed all this. You ever wonder why you don't hear much about dockworkers and longshoremen these days? It's because docks don't actually need very many of them anymore.

Levinson covers the complex web of economic, regulatory, and standardization challenges that faced shipping container proponents. But he only hints at the real shipping revolution: manufacturers that adopted shipping containers actually didn't obtain substantial savings until they also retooled their businesses to use containers end-to-end and to think of fast and reliable shipping as something they could count on. Hence developments like just-in-time (JIT) manufacturing and reduced inventory costs (I am now on the hunt for some reading material on these subjects).

Recommended.

02 August 2011

Hackers

Hackers is Steven Levy's classic social-anthropological account of software pioneers and the computer revolution.

Levy's history takes us from the birth of the hacker culture and the hacker ethic, hammered out in Building 26 at MIT, to the commercialization of software, exemplified by On-Line Systems (better known by its later name, Sierra On-Line) and its seminal series of computer games, and the creation of GNU by Richard Stallman.

(It is strange, to me, now, to think that hacker culture was born out of a subgroup of MIT's Tech Model Railroad Club [TMRC].)

Levy introduces us to a large cast of characters from different generations, from the 1950's to the 1980's. And while the history as Levy tells it— recounting all their intertwined stories— is intriguing, Hackers also serves to document the hacker culture and the hacker ethic.

The software pioneers were always trying to push the limits of what computers could do. Still it seems strange to speak of a singular ("the") hacker ethic or hacker culture, since their motivations and their worldviews (while all idealistic in some way) were so different. Some viewed hacking as a search for ever more elegant programs, eternal discoveries of a nearly mathematical nature. Others viewed the computer as a tool for the empowerment of individuals. (This was a tough sell in Berkeley, where computer software, which at one time was in large part the product of (D)ARPA funded research, was viewed with skepticism.) Moreover, each generation's version of hacker culture was shaped by the technological and commercial environment of its time. The MIT hackers were concerned with ensuring that they had unfettered access to the extremely valuable hardware on their hands. But by the 1980's, when inexpensive computers were widely available, what seemed more important was bringing the fruits of computing to the masses.

When Hackers was first published in 1983, it seemed as if it could merely be a chronicle of a little-known and dying subculture. (At the time, Stallman referred to himself as the "last survivor" of the hacker culture.) But today the hacker ethic has permeated society and popular discourse in a way that few might have imagined then, and Hackers is the definitive account of its birth.

Recommended.

By the way, in 1983, at a panel at the first Hackers Conference in Marin County, CA, Stewart Brand made an utterance which is widely quoted out of context as "Information wants to be free". It is worthwhile to read his original comment, which is substantially less normative and more interesting than it is often made to sound:

On one hand, information wants to be expensive, because it's so valuable. The right information in the right place just changes your life. On the other hand, information wants to be free, because the cost of getting it out is getting lower and lower all the time. So you have these two fighting against each other.

Brain Rules

Brain Rules: 12 Principles for Surviving and Thriving at Work, Home, and School is John Medina's guide to some of the principles that underlie how the brain works and how we can best take advantage of those principles when living out our lives.

Even though I've read plenty of popular psychology books, I found a lot of interesting nuggets here, including:

  • How exercise boosts cognitive performance (exercise stimulates, among other things, generation of new blood vessels in the brain)
  • The mechanisms by which prolonged stress breaks down our bodies (we're evolutionarily adapted to respond to threats on timescales of seconds to minutes, not months to years)
  • The importance of the sense of vision: some years ago, brain researchers gave white wine tinted with red dye to a bunch of wine-tasting professionals and found that they described the taste and smell of the wines using the vocabulary usually reserved exclusively for red wines. The outcome of this study is frequently cited as evidence that wine connoisseurs are full of it, but Medina's (more charitable) explanation is that the way our brains are wired, the sense of sight is so compelling that vision input preempts all our other senses.

Medina's writing is occasionally a bit too cute and circuitous for my taste, and, annoyingly, some of the connections appear to be based on little more than wild extrapolation (e.g. the parts about the student-teacher relationship, or the significance of synesthesia). But for the most part the book is easily digestible and appears to be based on solid research. Medina also proposes many interesting ideas— not just suggestions about how in our lives we can better accommodate the natural limits of our brains, but also ideas for experiments that could shed further light on things.

Mildly recommended.

19 June 2011

Congratulations, Ed and Sue!

Live long and prosper!

For our part we made some small mementos. Thanks a million to Shapeways, whose service and support greatly outshines my rectilinear design skills.


Magnet pairs

18 June 2011

Google Image Search

Google's new search by image feature produces uncannily specific and accurate identifications. I spent a bit more time than I should have, plugging in some of my own photos:


"Best guess for this image: munchen hbf"


"Best guess for this image: upenn fine arts library"


"Best guess for this image: kleine scheidegg"


"Best guess for this image: harry potter"

13 June 2011

The Wind-Up Bird Chronicle

The Wind-Up Bird Chronicle (paperback, Kindle) is classic Murakami: bizarre and beautiful.

The cast of absurd characters (juxtaposed with the brooding and passive narrator) is fun, but the real star of the book is Murakami's prose (translated by Jay Rubin). The everyday blends seamlessly with the bizarre. Even the mundane is unmistakably sinister. And fairly regularly there is a metaphor or an aside that completely throws you for a loop.

I won't pretend to be able to comment coherently about the plot or what it means. (I'm not sure anyone can. But I certainly can't.) This story is like a dream committed to paper, one of those books that is about the ride rather than the conclusion. A fun read (and I usually stay far away from contemporary fiction). Recommended.

The Seven Sins of Memory

In The Seven Sins of Memory (paperback, Kindle), psychologist Daniel Schachter attempts to characterize the failure modes of human memory. Schachter enumerates seven "sins" of memory: transience, absent-mindedness, blocking, misattribution, suggestibility, bias, and persistence. At a high level, these failures include not being able to recall things when desired, recalling things when not desired, and recalling things incorrectly.

I suppose most of us are keenly aware of the first and second categories of memory errors, because at the time we experience any such failure it is very obvious that such a thing has happened. The last category, recalling things incorrectly, represents the "silent failure" mode of memory, and is rather more pernicious (and less well understood). The sin of bias, for example, reflects the fact that recalling is an active process. One manifestation of bias is that recollections of the past are suspiciously similar to conditions in the present. For example, "[people] whose views on political issues have changed over time often recall incorrectly past attitudes as highly similar to present ones." Another sin, suggestibility, has major consequences for how we should interpret the testimony of witnesses in court.

Schachter explains in detail each sin, and mentions relevant literature that sheds light on the specifics of each failure mode. Frequently, understanding these specifics suggests useful tips and techniques that can be used to counteract or "work around" the failure. (The tips are also simple— very little is said of memory palaces, Mega Memory, and other very tiring techniques.) These days, the portable electronic devices we carry around are also useful tools for augmenting our memories.

In the last part of the book Schachter speculates on why memory evolved this way.

For example, forgetting the details of events gradually over time (transience of memory) is clearly economical, since we have a greater need for recalling things in the immediate past. So it appears that the brain initially encodes detailed records in memory ("We started the morning with continental breakfast at the hotel...") but gradually replaces the detailed record with the gist of what happened ("I had a great time"). When you are trying to recall an event from long ago, you use the gist of the memory and other techniques (inference, your knowledge of what usually happens under similar circumstances, a wild-ass guess, etc.) to reconstruct the event rather than recalling it directly. The brain uses lossy compression, and for events further in the past it dials up the lossiness! Some sins, like transience, appear to be evolutionary adaptations (i.e. actually useful behaviors), but others are the byproducts of evolutionary design trade-offs. All told, memory is not a poorly implemented and unreliable hack, but rather a pretty decent system given the hardware constraints.

This book is ostensibly about memory but, memory being such an integral part of our awareness, there is also plenty about attention, learning, and cognitive biases. This book is chock-full of useful information about one's mind and how to use it just a bit more effectively. Recommended.

The Man Who Tasted Shapes

The Man Who Tasted Shapes (paperback, Kindle), by Richard Cytowic, is the story of one of the neurologists who brought synesthesia back into the field of view of psychologists. Synesthesia is a neurological condition in which stimulation in one sense leads to involuntary (and consistent) experiences in another sense. (Famous artists believed to be synesthetes include Billy Joel, David Hockney, and Itzhak Perlman.) In some of the more common variants of synesthesia, individual letters on a printed page, or individual musical notes, are involuntarily experienced as having colors. While synesthesia was known and widely studied even in the 19th century, by the mid 20th century the predominant view was that synesthesia was not really interesting to investigate and that the phenomena that synesthetes experienced were just "in their heads". Unfortunately, before long, few doctors were even aware that synesthesia existed, despite the fact that estimates of its prevalance are generally agreed to be at least 1 in 2000. Thanks to the work of Cytowic and others, synesthesia is now something that gets covered in an intro psychology course (the one I took, anyway).

The first part of the book is sort of a memoir and a medical detective story, in which Cytowic— working with a couple of patients over a period of years— assembles clues about synesthesia, digs deep into the literature, and begins to conduct experiments to learn more about its genesis. While the dialogues do seem a bit overdramatized and redundant at times, it is a good portrait of how science is done. Not the technology part— the fMRI and other imaging devices are only incidental to the plot— but rather the imaginative part of science: synthesizing theories based on the mass of available evidence.

The conclusion of the "mystery" is a bit anticlimactic, since we still don't have a complete understanding of what mechanism is responsible for synesthesia, just a few tantalizing clues. Cross-talk between regions of the brain responsible for processing different senses has been implicated. In fact, all newborns are born synesthetic but lose that ability over time as connections in the brain are pruned. Interestingly, though, a substantial fraction of people appear to have latent synesthetic abilities. Studies have shown that the incidence of synesthesia among trained meditators is about one hundred times higher than the baseline prevalence! So it appears that synesthesia represents a natural background process of the brain that is simply unavailable to conscious view in a select few people.

This observation is a springboard for the second part of the book, which is a series of essays on "the primacy of emotion". Synesthesia is not an isolated phenomenon in the respect I mentioned: much of what goes on in our brains is not accessible to self-awareness except possibly under extraordinary circumstances. It now seems that the conscious mind is in fact not even in the driver's seat when it comes to planning and execution. (See: Bereitschaftspotential) The essays in this section are a reflection on the implications of this somewhat unsettling model of mind. I enjoyed some of the essays but found just as many of them to be completely opaque.

Despite its flaws I found this to be an enjoyable and eye-opening read. Recommended.

08 June 2011

The Hunger Games

The Hunger Games (paperback, Kindle), by Suzanne Collins, is a novel set in a future North America. Each year twenty-four teenagers are selected from the twelve Districts and thrown into a wilderness arena to fight each other to the death in a televised event. The Hunger Games are the Capitol's way of demonstrating its absolute power and humiliating the districts. The heroine, Katniss, volunteers to enter The Hunger Games in her sister's stead. Katniss is very clever and quickly figures out what she is going to have to do (and how to play everyone— including but not limited to the other contestants) in order to win.

(Yes, the premise is a lot like Battle Royale; or "Survivor", with killing.)

This is a fun and not-very-long read. It is well paced and there are hardly any lulls in the action. I had trouble putting down this book. Recommended.

Looking forward to reading the sequels and watching the movie.

The Lifecycle of Software Objects

The Lifecycle of Software Objects, by Ted Chiang, is a novella centering around sophisticated virtual pets— "digital entities" ("digients") that are positioned as somewhere between pets and children.

The story follows the rise and fall of the startup that creates the digients, as well as some of the programmers and "owners", who become increasingly attached to them.

The storyline and the implications of the technology are well thought out, and you could see it unfolding the way it's described. But as a whole the story just seemed kind of empty. Nothing really happens to any of the story threads at the end, which I would be willing to forgive if the premise of the story were thought-provoking. But I felt like I had seen enough pieces of the plot before that I did not find the questions Chiang raises to be particularly interesting. Perhaps I am just AI jaded. Decent airplane reading but little more than that.

The Birth of Plenty

In The Birth of Plenty (paperback, Kindle), William Bernstein proposes a framework to help make sense of how civilizations get on the treadmill of sustained economic growth that has only been attained in the last 200 years. Why was it the English who managed it first, and not, say, the Chinese, or Muslims, both of whom had a tradition of scientific discovery and mathematical inquiry going back a thousand years or more?

Bernstein argues that four factors are necessary for nations to break out of stagnancy:

  • Property rights, including protection both from the government (i.e. rule of law) and from others (robbers, highwaymen, etc.)
  • Scientific rationality
  • Efficient capital markets (easy access to capital)
  • Useful power (for work and transport) and communications

The core of the book is case studies of the four factors and how they were (or weren't) implemented in various countries. It's history and politics and economics but Bernstein makes it very interesting and explains the relationships between the relevant threads of history.

The last part of the book concerns the modern era and the future. It would be really interesting to be able to use this sort of analysis in order to direct policy decisions, but it seems to me that the four-factor story has become, at least in part, a just-so story. After all, one can read about the tenets and method of science anywhere; capital is easy to come by (if not in your home country, you can obtain it from abroad); machines for work, transport, and communications can be shipped to anywhere in the world. With respect to the latter three factors, the cat is out of the bag. The only place in the modern world where any of those are not readily available is, possibly, North Korea. So it may be that no future natural experiment could assign any explanatory role to factors two, three, and four.

Instead, the first factor plays a key role: if we would merely supply the rule of law, says Bernstein— if people believed that they were not in mortal danger and that the fruits of their labor were safe from seizure— then people would have the motive to innovate (with the other three factors guaranteeing the means and opportunity). Not a new idea, but there is a twist. The four factors are logically independent of democracy; they can be present even under totalitarian regimes. And Bernstein cites some evidence that suggests that it's prosperity, borne of the four factors, that makes people ready for democracy. The causality between prosperity and democracy goes the way opposite to what many people assume.

Now, if we take this narrative seriously, then we really have to rethink the way we approach foreign aid and humanitarianism. Promoting (or installing) democracy in a country won't, by itself, lead to prosperity. And just giving money to poor countries is no help at all, if not worse. In both cases the change amounts to planting a seed in infertile soil. What's needed to bootstrap third-world countries today is, almost invariably, the first factor: property rights, considered very broadly. People need to believe that they and their possessions are secure; they need judges and lawyers. The absence of the requisite social institutions is so corrosive that economies cannot thrive without it, no matter how the political leaders are chosen or how much money there is lying around. Conversely, Bernstein suggests that once people have attained some critical level of prosperity they tend to lean towards democracy anyway. But that can lag economic prosperity by years if not decades.

This book is well worth reading, even you take issue with some of Bernstein's analysis. People are becoming increasingly mindful, and they want to know what they can do to make the world a more decent place to live; but no one (except ideologues, I suppose) is so committed to a particular means towards that end that they would persist in advocating something that demonstrably didn't work.

Economic history is complicated, and the scope of this book is very ambitious, but Bernstein manages to make it an easy (and even engrossing at times) read. Recommended.

28 May 2011

People who are not in our league VII

Jin8 plays tetris. So fast is he that being able to see the blocks already on the board appears to be just extraneous. That hypothesis is confirmed when the blocks turn invisible (at 5 minutes in) and he just keeps on playing.

People who are not in our league VI

Fabrice Bellard wrote jslinux, Javascript that emulates an x86 processor and boots a working Linux kernel.

As if that weren't impressive enough, the hosted filesystem includes a C compiler... that he wrote himself... and a partial emacs clone... that he wrote himself.

Bellard was also responsible for ffmpeg, QEMU, and what was (at the time that it was released) the fastest known algorithm for computing digits of pi.

Movie roundup

Recent movies, in descending order of enjoyableness:

Ip Man. Semi-biographical account of the life of Ip Man, the grandmaster of the Wing Chun form of martial arts who taught Bruce Lee. Donnie Yen is pretty much the embodiment of unadulterated badassery. Excellent fight scenes. Recommended.

Source Code. Not only an entertaining thriller but also somewhat moving (which I did not expect). Don't take the science seriously and you will enjoy the movie a lot more for it. It's well executed and the characters and their interplay are very likable. Recommended.

In The Shadow of the Moon. Documentary about the Apollo missions, as told by the Apollo astronauts. Really brings to life the political and social climate of the time. I watched the JFK footage and I could not tell if he was a visionary, or insane. Also, sometimes we forget that, yes, some astronauts did die so that we could go to the moon. Recommended.

The Rock. Classic action movie, and one with heart.

Contact. It does have its moments of awe, but the cheesiness is way overdone.

Con Air. Everyone in this movie seems to play a caricature of himself, which gets tiring very quickly.

District 13: Ultimatum. I enjoyed the original District 13 (the parkour scenes are something to behold), and had been looking forward to the sequel. Unfortunately Ultimatum is just ridiculous and nonsensical in alternation.

The Taking of Pelham 123 (2009). Empty and unexciting.

27 May 2011

The Immortal Life of Henrietta Lacks

The Immortal Life of Henrietta Lacks, by Rebecca Skloot, is the biography of the poor black woman whose cancerous cells were taken from her (without her knowledge or permission) and which subsequently became the first line of human cells to be successfully grown in vitro. Lacks died in 1951 but the HeLa line of cells, descended from the cancerous cells in her cervix, live on in labs around the world.

There is some science background/history in this book, but it is primarily the story of Lacks and her family as well as a story of the history of medical ethics. Shockingly, as recently as the 1950s, doctors frequently withheld critical information (such as, oh, a diagnosis) from their patients, for fear of upsetting them. Black patients like Lacks were the least likely to be given all the facts. Given the lack of respect in the doctor-patient relationship then, it does not seem quite so surprising that when Lacks went to Johns Hopkins for cancer treatment, doctors dared to take and store samples from her tumor for use in experiments without even asking for her consent.

The discovery that HeLa cells were actually capable of reproducing in culture medium (outside of the body) sparked a revolution in medicine. Suddenly you could perform experiments on human cells without having to perform experiments on a human. HeLa became part of the standard arsenal for research studies involving human cells. HeLa cells were used to test the first polio vaccine; they have been used to test the effects of carcinogens, drugs, zero-g environments, and more on human cells. By 2009, research done on HeLa had led to the publication of some 60,000 research articles.

And yet, for about twenty years after Lacks's cells were taken from her, by which time they were already routinely in use in labs around the world, Lacks's children had no idea that any of that was happening. Understandably, they became quite upset and paranoid when they finally learned what was going on. The irony of this story is that while Henrietta Lacks's cells have produced scientific research of untold aggregate value, her descendants are still too poor to afford decent health care.

In researching for this book, Skloot definitely crossed the traditional boundary between author and subject. She worked closely with Henrietta's youngest daughter, Deborah, and helped her to learn about her family's history, unravel what it was that had actually happened to her "mother cells," and assuage many of her concerns. Lacks's descendants were relatively poor and uneducated, and this book could easily have crossed the line into sounding patronizing, but it doesn't. Skloot has done an admirable job in not just identifying but creating the human story here.

This book is both thought-provoking and captivating; recommended.

Review ends here; only moderately thought-out speculation begins. IANA doctor or medical researcher.

Reading The Immortal Life of Henrietta Lacks, you can see that the medical institution has come a long way since the 1950s, but as a society we still don't have a lot of the answers for how to deal with the use of donated human biological products (tissue, usually) in medical research. One positive change is that the idea of requiring "informed consent" is now widely recognized and standardized. But patients do not have a great incentive to actually donate their biological products to research, because the vast majority of samples are worth approximately nothing, except as part of a larger collection, and donors receive no other benefits. (It doesn't help that in Moore v. Regents of the University of California the Supreme Court of California ruled that once a biological product is taken from your body, it is no longer yours; therefore, in order to profit from its use you would have to have the extraordinary foresight to come to some agreement with the hospitals/researchers before you donated the sample.)

There are a number of proposals to compensate donors of biological products, e.g. with reduced health care costs, or money paid out of a pool funded by pharmaceutical companies. I think some of those are good ideas. But what may be interesting to try here is some sort of analogue to a Creative Commons license: something drafted by lawyers, similar to all the pre-written legal documents or software licenses you can get today, that would provide various stipulations that ensure that research and IP derived from a patient's particular biological sample meet some standard of public accessibility. As Skloot points out, what many donors really want is not remuneration (especially since only an exceedingly small fraction of single biological samples are worth anything anyway) but the knowledge that the fruits of research done on their donations are available to the public and to other researchers, rather than staying in some freezer because no one is going to pay some exorbitant fee for an unknown sample. HeLa itself revolutionized medicine because it was widely distributed, and that only happened because it hadn't occurred to anyone to patent cell lines in the 1950s.

Donors are going to have to be the ones to fight for the public interest, but they don't really have any leverage unless they show strength in numbers.

24 May 2011

Mastering Regular Expressions (O'Reilly)

Many programmers use regular expressions frequently, but most of us can go for months, if not more, between the occasions when we really need to understand what the heck the regex implementation is doing.

For those times when you actually need to know, Mastering Regular Expressions, by Jeffrey Friedl (ebook version available on O'Reilly) is the book you want to have read. It does discuss various regex features, but you can usually find the same info in the API docs for the language bindings you're using; the real meat of this book is its clear discussion of regex engine implementations.

When you want to answer such questions as "Why is the regex engine matching the string P, and not the different-but-equally-valid match Q?" or "How can I make this regex code faster?", then it really helps to understand what's going on under the hood. NFAs, DFAs, state machines, and all that good stuff are covered here, but with many more practical notes than appear in your college compilers textbook.

Recommended... if you're into this sort of thing.

05 May 2011

20 April 2011

Bike Tour of the California Coast

I just returned from leading a bicycle tour of the central California coast. Yoyo Zhou, Ed Lee, Sue-Ting Chene, Kalvin Wang, and I spent six days biking from Saratoga to Goleta (near Santa Barbara), a total of about 340 miles. Highlights included biking down Big Sur and eating lots of great food.

You can read more in my trip report.

18 April 2011

Bicycling the Pacific Coast, by Vicky Spring

I just returned from leading a cycle tour down the California coast from the San Francisco Bay Area to Santa Barbara. The classic Bicycling The Pacific Coast, by Vicky Spring, was an indispensable reference and a major part of my trip planning process.

For the section of interest to us (central coast of California), Bicycling the Pacific Coast routes you down Highway 1 (California State Route 1, a.k.a. the Pacific Coast Highway) nearly the entire way. The book provides turn-by-turn instructions that explain when it is advisable to deviate from Hwy 1 (either when bikes are not allowed on the highway, when there is a scenic detour with less car traffic, or when there are specific points of interest), and exactly how to do so. It explains when food, water, restrooms, and lodging are present along certain segments, as well as when they aren't. These elements are (understandably) missing from guidebooks that assume you are traveling by car.

Elevation profiles of each day's ride are also given, which was handy for mentally preparing my travel-mates for each segment. Points of interest and other considerations for cyclists (such as when there is a wide shoulder, and which segments get really hot in the summer) are noted.

Although the book is oriented towards expedition cyclists (i.e. cyclists who carry a tent with them and stop at a campsite each night), and our group was doing credit-card touring, I had little difficulty adapting the suggested routes to stop each night at a city rather than a campsite. It is also straightforward to follow the suggested route but lengthen or shorten each day's ride, depending on your taste.

I purchased a copy of the book on Google eBooks and loaded it onto my phone, so I was able to consult it on the road as well. You can do something similar with the Amazon Kindle edition.

Route planning for a cycle tour of the coast is an optimization problem in many dimensions, and you will need to consult maps and references other than Bicycling the Pacific Coast, but this book helps to pare down the search space considerably and make it much more manageable. Highly recommended.

06 April 2011

Tron: Legacy followup


Look, it's eshell!

Josh Nimoy wrote about his special effects contributions, among others, to Tron: Legacy:

I spent a half year writing software art to generate special effects for Tron Legacy, working at Digital Domain with Bradley "GMUNK" Munkowitz, Jake Sargeant, and David "dlew" Lewandowski. [...]

In addition to visual effects, I was asked to record myself using a unix terminal doing technologically feasible things. I took extra care in babysitting the elements through to final composite to ensure that the content would not be artistically altered beyond that feasibility. I take representing digital culture in film very seriously in lieu of having grown up in a world of very badly researched user interface greeble. [...] In Tron, the hacker was not supposed to be snooping around on a network; he was supposed to kill a process. So we went with posix kill and also had him pipe ps into grep. I also ended up using emacs eshell to make the terminal more l33t. The team was delighted to see my emacs performance -- splitting the editor into nested panes and running different modes. I was tickled that I got emacs into a block buster movie.

I previously wrote that

the filmmakers should win some sort of award for Not Totally Outrageous Use Of Unix In A Hollywood Movie. Whoever is responsible, I salute you.

So I guess we now know how that transpired and who is responsible for (part of) it.

(via Romain Francoise)

30 January 2011

"Seinfeld" in economics

Princeton econ prof Avinash Dixit's paper "An Option Value Problem from Seinfeld" is a treatment of Elaine's quandary in Episode 119 ("The Sponge") as an option pricing problem. When Elaine's contraceptive of choice goes off the market, she has only a finite supply remaining and she has to become much more, uh, judicious in her use of them. It's a case of "Investment Under Uncertainty" (Dixit's much more voluminous work on the subject).

There's a WSJ article about the paper. If you like this kind of stuff, there's a bit more in the same vein (though with less in-depth discussion) at Yada Yada Yada Econ (The Economics of Seinfeld).

I consider "Seinfeld" to be one of the better products of the 1990s, so it's awesome that it still gets talked about. Moreover it doesn't surprise me at all that there is so much econ content in a show that is ostensibly about "nothing". Econ is everywhere.

03 January 2011

Giant Plush Tux Penguin

or, What Happens When Engineers Learn to Sew

Encouraged by how well the plush (Linux) Tux penguins turned out, Santhosh, Samson, and I spent a couple of afternoons over the holiday making a Giant Plush Tux in honor of our favorite kernel. It was a lot of fun and I got to practice skills that I usually neglect (such as hand-eye coordination).

Giant Tux is 3'8" tall, weighs 24 lbs, is made out of fleece and reappropriated stuffing, and really likes to hog the couch.

You can read more about how Giant Tux was made and see more pictures here.