Figures...

I think that I've begun classifying different sub-disciplines within the biological sciences based on how obsessed they are with manuscript figures. An oversimplified continuum may place 'figures are the only thing that matters' on one end, versus 'actually some things are better explained by tables and text' on the other1. Geneticists? Very far on the figures side. Evolutionary biologists? Text-of-center. Population geneticists? I suppose that a plot will illustrate the power of my math to the savages. And so on...

In all seriousness; coming from a population genetics/evolutionary biology background, I certainly recognize the value of illustrative figures in conveying a point. However, I have noticed that there is a massive difference between my field and the more figure-obsessed disciplines: In genetics (for example), the figures are the paper's story, and the text is written in order to explain them. In evolutionary biology/population genetics, the figures are produced in order to illustrate the results of an often computationally complex analysis of multi-dimensional data.

While there are a few tweaks that you can pull in terms of how to best present a western blot, there are often many, many different ways to present the results of a clustering algorithm, or to represent a gene expression profile among other examples. Perhaps I'm just not very good at this stuff, but I've found that it's incredibly difficult to choose the most appropriate representation of the data a priori. Rather, I find it necessary to flesh out the overall thrust of a manuscript using place-holder representations, and then choose the best way to represent the data once it has all come together. 

This is why it was a major sticking-point for me when a former boss used to say that he wasn't interested in seeing any manuscript text until he'd seen the finished, publication-ready figures. I wouldn't subscribe to this approach in general, but I can see how this would be much more 'do-able' in certain fields as compared to others. In my case, it was rather paralyzing.

Here's another thinking point: I've also learned that some figure-focused people only look at the pictures when they read manuscripts. I'm not entirely sure that this is a good idea in any field, but it seems especially potentially misleading in large-scale datasets: Before I accept the validity of an analysis, I want to know that the sample sizes were appropriate, the null hypothesis was warranted, the statistics employed fit the data, etc. In evolutionary biology, these factors can change a solidly supported model to pure hand waiving speculation. If you only look at the figures, you'll rarely be able to distinguish one from the other. 

1Alright, a more 'extreme' continuum may end with, 'I'll just crap the figures out in MS Paint the morning that the paper is submitted'. However, while I have actually witnessed the 'FIGURES ARE EVERYTHING' school, I haven't seen anyone who didn't care about them.

Point Reyes National Seashore...

Point Reyes is a cape that juts out into the Pacific, approximately 30 miles north west of San Francisco (as the crow flies - it takes roughly ~2 hours to get there by car):

The entire northern half of Point Reyes National Seashore (as the actual park is called) is seperated from the rest of the continent by Tomales Bay. The famous San Andreas Fault runs directly under said bay, and if you extrapolate it south, through the Bolinas lagoon, you can see how the fault basically runs into San Francisco proper (or at least along SF's Pacific coast). Hence the frequent earthquakes in the area.

Though Point Reyes actually encompases a decent sized park with quite a few camping and hiking trails - its most famous attraction is the lighthouse on the tip of the cape (marked 'B' on the map above), which is built on the edge of a long granite cliff that can only be accessed by a few hundred stairs built into the rock:

It's quite impressive that the lighthouse was finished in 1870 and is still intact today. It must've been horrible to carry all of the building materials way out onto this bluff. The main light, while no longer operational, is still completely intact and viewable by tourists. Apparently the several hundred individual mirrors that compose the light were shipped from France, without spares, and arrived undamaged!

Here's a panorama of the view from the lighthouse itself, capturing the Pacific westward as well as the northward cliffs and the station.

We did do a bit of hiking along the Chimney Rock Trail, which lies on the southern tip of the same peninsula where lies the lighthouse. It's a short, easy trail that follows the top of the granite cliffs, with gorgeous view of the Pacific Ocean on one side as well as Drake's Bay (that's Sir Francis Drake, of course, who 'may have' landed here) on the other:

 Here's a shot of Drake's Bay, with its much more gentle sloping hills leading to the water than the Pacific side.

And here's a shot of the Pacific side. We saw an elephant seal on the beach below.

Finally, I took a 360° Panorama from the middle of the Chimney Rock trail:

For those interested, there are some pretty good photos (I think) in a Picasa Web Album that I've created. Point Reyes may be a bit too out of the way for a visit if you're only in the Bay Area for a few days, but if you've got the time, I highly reccomend it!

Twin Peaks, San Francisco...

Unfortunately, I'm not planning to discuss David Lynch's classic, short-lived, ahead-of-its-time TV series in this post. Rather, this past weekend I made the trek to Twin Peaks San Francisco, which are a pair of ~900 ft tall hills, pretty much in the center of the city:

The Twin Peaks (indicated by the red dot) are located roughly a 40 minute (uphill) walk from the Mission District.

Rumor has it that the peaks offer the best view of the city, and in this I was not disappointed. I downloaded a panorama photo app for my iPhone (DerManDar) and snapped a few cool shots from the top of the mountain:

The fact that doing this with a cell phone is even possible still kind of blows my mind. The quality of the image produced by the panorama software is slightly lower than that produced by default images on the phone, but it's still pretty awesome.

This one's a complete 360° panorama. There were a lot of people on the hill moving around, and thus there are some artifacts in the shot.

You really can see the entire city from the 'summit', from the Bay Bridge to the east, to the Golden Gate bridge to the north, all the way out to the ocean out west. 

 The peaks are separated by ~200 m. The North one definitely seemed to be the more popular. Only a single solitary photographer stood atop the southern peak.

The sun may rise in the East but at least it settles in the final location.

I took a few more photos and have placed them in a Picasa Web Album for anyone who's interested in seeing some photos of the lead up to the hill and its environs. This is definitely a must-see for any SF tourists!

Book Club: Keynes Hayek: The Clash that Defined Modern Economics, Part 1...

Many of my recent book selections have come from listening to author interviews on podcasts. In the case of Nicholas Wapshott's Keynes Hayek: The Clash that Defined Modern Economics (2011; W. W. Norton & Co.), I heard the author interviewed both on NPR's Planet Money and Russ Robert's EconTalk. The discussion on both shows was great, and prompted me to learn more about the history of two fascinating characters.

I'd like to open this post with a disclaimer: Much of the focus of Wapshott's book is on the personality and lives of Keynes and Hayek while they both lived, taught, and argued incessantly in England from the 1920s to the 1940s. While it makes for a fascinating read, I'd rather focus here on an overview of the two men themselves, with an amateur focus on the legacy of their theories. JM Keynes so thoroughly trounced FA Hayek in terms of popular perception while he was alive that I felt that it was ok to write a first post focusing only the former. Hayek's popular rise to prominence came later in the 20th century (with the exception of his popular 1944 book The Road to Serfdom) and will be the focus of a subsequent post.

The British-born John Maynard Keynes (1883-1946) (pronounced 'KAYNES') was arguably the most famous public intellectual in the English-speaking world during the first half of the 20th century. His initial professional fame as an economist came from working for Britain's Office of the Treasury during the First World War where he shrewdly negotiated the borrowing of vast sums from America in order to finance the country's war effort. His public fame, however, came from his vocal opposition to the Allies' behavior during the negotiations at the Treaty of Versailles (1919).

In his book, The Economic Consequences of the Peace (1919), Keynes argued that the hatred-fueled, unreasonable sanctions and war reparations being demanded by the Allies against Germany and the Austro-Hungarian Empire would beggar and destroy the lives of the citizens of two modern, powerful nations. In time, this would foster political radicalism and likely plunge Europe into a second great conflict. The book was an incredible success in both Europe and America and with the rise of the Nazi party in Germany in the early 30s, Keynes was proven correct. The argument expounded in the book is now regarded as one of the more prescient works of classic non-fiction.

There were consequences, however, to his criticism of the British government, and Keynes was largely excluded from his previous employment, instead taking up a post as a professor of economics at Cambridge. Initially Keynes continued to criticise the misguided policies of the post-war UK government, all the while developing what would become the field of macroeconomics and the particular theory that would come to be known as Keynesianism1: That the government could spend its way out of recessions using borrowed money to fund public works projects, boosting aggregate demand and employment. It's important to note that in order to understand the crux of an economic theory, it's often useful to find out what the theory is specifically trying to address. For Keynes, it was trying to curb what he saw as unnecessary and wasteful unemployment in the lead up to the great depression (Hayek's focus, however, was on minimizing inflation and later unintended consequences of collectivist market control).

Keynesianism was initially met with resistance - it was a rather unorthodox theory in what was an almost entirely microeconomic field. However, after the stock market crash of 1929 and ensuing depression, the demand for government to 'do something' about the crisis was so great that Keyne's theories swept to the fore and became enshrined as economic law for the next ~40 years.

While highly contested today, the observation that massive government spending brought the world out of recession during the Second World War was seen as a startling confirmation of the theory. Massive public spending ensued, and the rolling out of constant, new governmental programs became politically desirable. In hindsight, 2.5 decades that followed the Second World War were a massive boom period in general, and it's difficult to separate the effect of deficit-funded government spending from the general 'boom' period in which the West found itself.

The Keynesian 'revolution' came to a grinding halt during the OPEC Crisis of 1972-73, during which fuel prices quadrupled overnight killing economic growth. Despite the stagnant economy, inflation spiraled out of control - something that was considered impossible according to then Keynesian economic theories. In America, economic policy quickly shifted from from unbridled spending in order to boost employment to curbing inflation which was quickly inching into the double digits. It was during this time that Hayek's work was popularly 'rediscovered' and rose to the popular fore...  

P.S. I cannot end any discussion of Keynesian or Hayekian economics without linking to the awesome 'Fear the Boom and Bust' rap video made by econstories.tv:

1Wapshott is quick to point out (and even some of Keynes' opponents such as Hayek himself, noted) that some of the aspects of modern Keynesianism were introduced by Keynes' disciples, such as the Canadian-American John Kenneth Galbraith, and not the man himself. Keynes' was not anti-capitalist and was highly critical of socialism. Furthermore, though his writings aren't always clear, Keynes focused more on how government can work to exit recessions rather than how to manage the economy during the 'boom' cycle. Modern Keynesianism is sometimes equated with 'social planning', which Keynes discussed a bit late in his life but wasn't the focus of his prescriptions.

The Future is Now...

As mentioned in a previous post, I've been listening to some 'tech' podcasts recently. It on these podcasts that I first heard about 'Siri', the cloud-based voice recognition software that Apple acquired a few years ago and made available in its current incarnation on the iPhone 4S (Apple's official perhaps somewhat idealized advertisement video can be found here). Having been very disappointed with previous voice recognition software1, I didn't really pay much attention to it.

Then I ws biking home from work, listening to some music through my bluetooth headset, and thought I'd give the system a try. My phone sits in a pocket on my biking jacket, and activating Siri requires only holding down the iPhone's 'home' button for a few seconds. I tried a bunch of different ways of saying things, and while I got some odd results at first, I began to figure out things that work consistently.

For example, I can say 'shuffle playlist jogging' and it'll start playing that particular playlist. 'Next song' skips ahead, 'pause/resume music' do just that, etc. You can actually say things like 'Play album Thank You' or 'Play podcast Giant bomb' and it'll actually do it. Furthermore, if I get a notification tone while biking I can say 'Notifications' and it'll read off any new emails, txt messages, tweets, etc. I've received. Maybe I'm easily impressed, but this is pretty Star Trek to me2. Oh, and is there anything better than a lab timer that you can talk to? ('Set timer, 45 minutes').

The one area where Siri isn't so great, at least so far, is in taking dictation. That's not exactly fair - it's quite accurate if you stick to common, well-defined words. However, as a scientist who uses a lot of non-standard verbiage, Siri's not particularly useful; it does incorporate some good ideas though. For one, it highlights all of the words that it detects as ambiguous - this includes both misunderstood words and homonyms. You can then click on them and select from a list of best guesses or edit them yourself. This is not particularly useful as a hands-free feature, though. I can see some utility in being able to fire off quick acknowledgement replies to emails or text messages, but I doubt that many screenplays will be written by dictation.

It's not clear from the Apple website, nor the dreaded Wikipedia how Siri works, but according to the Tested.com podcast, the system actually offloads data-processing to Apple's 'cloud' servers where the heavy crunching is done. The results are then sent back as text to your phone (in practice this takes a matter of seconds)3. If this is the case, it's an interesting glimpse into the future of processing, where your PC will be naught more than a box connected to the internet and the heavy lifting will all be done on servers.

Stuff like this makes me think that current/future generations take technological progress for granted. In our parent's first 30 years of life, they went from what: AM to FM radio? Teletype to fax machine? Mimeograph to photocopier? Frustrating wheels to power steering? I'm exaggerating a bit, but it's difficult to understate that we've gone from the Sears Wishbook of my youth to buying stuff on Amazon.com over 3G Wireless internet on our cell phones, or looking up stuff in a 12 volume encyclopedia to searching libraries of text on Google.

I challenge you to go back and read sci-fi books from the 70s. In much of the imagination of those authors, we're already living hundreds of years into the future4.

1Did anyone ever try Dragon Naturally Speaking back in the day? This was a piece of sofware that would allegedly allow you to dictate Microsoft Word documents. I tried demos of a few versions and remember being stunned by how poorly the software worked - It's not exactly useful if I have to go back and correct the dictation by hand every 5 or 6 words.

2Incidentally, the pocket I use for my phone happens to be on the upper-left side of my chest. Thus activating Siri basically involves me 'tapping' a virtual communicator badge thingie...

3This explanation seems a bit weird as it means that you require an active data connection to tell the phone to play music. It may, however, only do such cloud processing for internet related searches and not for on device lookups. This cloud thing also may explain why the system doesn't work on previous iPhones, even when 'hacked in' - Apple can tell the phone's model when the servers are accessed and thus it can reject the data.

4For instance, in the classic sci-fi book The Mote in God's Eye (1974), the authors, Larry Niven and Jerry Pournelle, predict that by the year 3,000 we'd have invented faster-than-light travel. Yet we'd still lack wireless networking as well as contemporary laptop computers. The sci-fi novels that impress me are the rare ones that really 'nail' it. I'd still rank Neuromancer (1984) among the finest in this tradition, as well as the odd, yet interesting, Snow Crash (1992). This being said, I'm not the most well-versed in classic sci-fi. I'm always looking for recommendations though!