Back to Writing for 'Realz'...

One of the projects that I started when I got to Stanford in October last year is finally at a stage where it's time to begin crafting it into a 'story': I've got some interesting results for which I've received a lot of feedback, and at this point figuring out what needs to be done next will best be served by trying to 'put it all together'. Therefore, I've begun writing a manuscript. Note that this doesn't mean that I'll be submitting it anytime soon - I may decide that additional, significant things need to be done - but for now I'm trying to put together a coherent draft.

I began by setting aside an entire day this past weekend to research and write the introduction. As I've mentioned before, the first advice given to me on how to write a paper (from my M.Sc. supervisor) was that a manuscript should be written in the order that it is presented. The introduction informs what results should be highlighted as significant, and the discussion should contextualize said results within the previous findings highlighted in the introduction. I'm quite certain that I'm in the minority in following this advice - in my experience most people write the results (and methods) first. The only way that I could imagine not beginning with the intro is if you're writing a paper on a specific topic upon which you know the literature inside out - something I've never really had the luxury of doing as I've explored a variety of topics in several broad fields1.

Anyways, while I think that I've begun to hit a 'stride', the first few days of laying out my thoughts and writing were tough - more difficult than I remember writing being in the past. Though disconcerting, the reason is somewhat obvious - I went from a Ph.D. wherein I was writing all of the time (if not manuscripts, then fellowship applications, committee reports, a thesis, etc.), to a postdoc where I wrote very little. In fact, the writing style of my previous lab was rather non-standard, to say the least. For starters my PI would want to see the figures that you expected to put into any draft manuscript before he was even interested in seeing any text. Unfortunately, 1) making finalized, publishable figures takes a long time, and 2) it's difficult to determine how best to present genomic data without context - something I discussed in a previous post. Thus I spent far more time agonizing over the layout of graphs and plots than I did thinking about how to construct the story.

As I'm approaching yet another new field, beginning with a thorough literature review was crucial. Now it's just about working slowly through the results, seeing where adiditional analyses are needed, reworking my current draft figures to best illustrate my points, and writing it all down such that it's comprehensible by the reader.

Oh well, like I said, it's coming back steadily. Can you believe that I actually used to be among the few people I know who actually liked writing? Crazy hunh? Gotta get myself back in the zone! 

1I am trying to narrow, rather than broaden my expertise however, on the assumption that every scientist should find an appropriate niche.  

Book Club: The Naked Ape...

Unlike some people, I haven't always known what I wanted to do with my life. Even as I finished high-school, I was still deciding between something involving computers, biochemistry, political science, and even English. In the end, I wound up in evolutionary biology, and this decision was only made during the transition between my M.Sc. and Ph.D.

Nevertheless, I do remember being interested in biology when I was young, principally because of the regular TV appearances of Canadian biochemist-turned-woo-pedling-environmentalist David Suzuki, and British anthropologist, Desmond Morris. Suzuki's particular brand of unreasonable environmentalism long ago dampened my respect for the man, and I'm sorry to say that Morris's somewhat famous book, The Naked Ape (NA; 1967; McGraw-Hill) has had a similar effect.

NA is an unfortunate work. I say this because it is clearly written for a general audience; one that may find its arguments seductive, but will lack the technical expertise required to criticize its massively overreaching use of pseudo-evolutionary arguments (specifically those of evolutionary anthropology) to explain human behaviors that cannot, in this scientist's mind, be clearly partitioned into heritable genetic components vs. 'socialization' (environment)1.

Morris argues that we are apes in flesh and blood and thus our behaviors, social organization, and life-histories bear the indelible stamp of our hominid ancestry. Clearly, it would be foolish to disagree with this. However, the problem arises when he tries to apply reductive logic to specific behaviors. What human behaviors are both general enough and free of obvious potential for purely cultural transmission such that they can be reasonably assumed to be 'hard-wired'2? Surely cogent arguments can be made for hunger, thirst, and sexual appetite, but how specific can one get?

NA makes genetic arguments for many, many behaviors. Some of these are legitimately intriguing, such as how cross-cultural studies of infant drawing patterns show the same progression of angular lines to curved lines, to faces, etc. This example may have something to say about how the human brain develops, as do studies of other childhood behaviors (crying is universal and occurs before the possibility of learned transmission; however, smiling develops later).

On the other hand we're also told that human females tend to become obsessed with horses at around the age of puberty because the big strong horse galloping between their legs simulates another thrusting motion in which they're becoming interested (conveniently, this also explains why the fascination with horses dies down as they reach college age and are capable of fulfilling these needs elsewhere3). 

There are also many 'edge' cases. For instance, all human societies are similar in that they signal appeasement (submission in contests of dominance, apology, etc.) by making themselves seem smaller - ducking, bowing, etc. - and/or showing empty hands. Apparently our simian relatives do this as well, leading Morris to claim that these are hard-wired behaviors. Perhaps, but let's ask the question as to what we'd expect were these not hard-wired? It's difficult to see how one could give a more obvious, culturally derived signal than prostrating oneself before one's opponent.

And therein lies the rub to all of this. It's not that all of NA's assumptions and analyses are wrong, it's that it's incredibly difficult if not impossible to test these claims against an appropriate null hypothesis4. There's nothing particularly scientific about such 'evolutionary' claims, it's all just story-telling.

In all fairness, Morris does make some interesting and thought-provoking assertions in his book. My favorite is his point that studying obscure, stone age tribes in order to understand current human behavior is like studying extinct side branches of phylogenies in order to understand why their extant relatives are successful. The point here is that these tribes (or the extinct species) are examples of what didn't work, and we should also be focusing on what did (apparently anthropology likes to look at such tribes as models of the past).

Like I mentioned at the beginning of this post, in order to appreciate the interesting ideas made in the book, as well as ignore the flawed logic, one has to have some expertise with the material. Sadly, the contents of NA are not up to the standards expected of professional scientific scholarship. Once I'd made it fairly deep into the text, I checked some classic reviews of the work to make sure that I wasn't off base. Indeed, The Naked Ape was panned by the scientific community when it was released. Sad, but necessary given its contents.

1If you're willing to admit that the genetics of natural populations involve more detail than the additive genetic variation we routinely measure in a stable laboratory environment, then the separation between 'genes' and 'environment' is never as sharp as many would lead us to believe.

2If you want to get technical, then the concept of 'hard-wired' can be very complex. Genes can influence pre-dispositions rather then specific behaviors, for example. In this case, I mean that a human raised in isolation woud still instinctively perform these behaviors at the appropriate opportunity.

3I will never be able to look at My Little Pony in the same way again. This may also explain the overabundance of horrible furry art featuring highly sexualized 'ponies'. Wait, is there ever not an 'over' abundance of horrible furry art? I also weep for all of the frustrated young women who used to have to ride side-saddle.

4In cases like these, I like the alternative term used by economists to represent the null: the 'counterfactual'.

Monday Rant: The Modern Shopping Experience...

Over the past couple of years, I've become increasingly obsessed with preferentially purchasing from Amazon.com (or Amazon.ca, when I was still living in the Fabled Canadas), rather than frequenting local retailers. When I mentioned this to a friend, he seemed almost insulted, alleging that I'd prefer to support large, faceless, nebulous corporations rather than local businesses. My answer: Yes (with caveats as detailed below).

Let's ignore the highly consequential detail that Amazon.com is often up to 40% cheaper than local retailers1 and stick entirely to the shopping experience. I hate, hate, hate the experience that I have at most stores.

Honestly, there are only two things I need from you if you work at a retail shop: I'd like you to be available as well as knowledgeable about the products that you're selling. That's it. For some reason it seems as though many stores are trying to be annoyingly 'polite', as if this is what differentiates them from online. It drives me crazy to have people constantly asking me if I 'need help'. No, and since I'm older than six, I can be the judge of whether I need your particular brand of 'help'.

The help thing is a mild annoyance compared to something that I touched on last year: paying for products has become the most obnoxious process in the world - so much so that I can become very frustrated and testy when dealing with checkout clerks. "No, I don't want your 'savings' card", "I'm not interested in an extended warranty", "I don't want to pre-order anything," "I don't want to give you my phone #/ email / zip code", and so on. I'm giving you my money, leave me alone!

I've also noticed a disturbing trend among specialty retailers (particularly in electronics) where the staff just isn't knowledgeable about the products that they sell. They offer poor, often self-serving advice, to the point of outright lying in order to make a sale. If all you do is sell audio/video equipment, the least you should know is whether product X is compatible with product Y, no?

I've heard some scuttlebutt suggesting that big-box retailers largely shifted business models in the 90s. Instead of hiring career clerks as they did in the past, they focused on young, cheap, less-knowledgeable labor. To this they added a massive push towards service-based 'products' such as extended warranties, service contracts, and the like. It seems to be the hindsight narrative of the 90s, but everything seemed to move towards cutting costs and boosting profits, which isn't necessarily 'bad' per se. In this case it seems to have had a negative impact on the customer experience. Nation-wide and international chains seem to be going under left and right these days.

In all honesty, who cares2? When I shop online, I'm more likely to find the product I want, reviews give me the ability to get a diversity of opinions, and best of all, it's shipped right to my door. I don't have to put up with lines, useless offers, or any of the other headaches of 'shopping'.

In all fairness, there are some types of retailers that will likely resist the move to online for a long time (if not indefinitely?). I'm still not comfortable buying most clothes through cyberspace, nor would I purchase quality furniture without giving it a try in the store. And of course there are some types of stores whose products are available online, but for whom I'd like to support the 'local guys'. This happens when the retailer provides a service that I can't get elsewhere (a music shop where I'm always discovering new artists, or a gaming store that offers play space and the ability to demo products, are a few examples). 

However, as Sartre said: "Hell is other people", and I'm certain that he intended a special focus on those who work at retail.   

1We're ignoring it despite this alone being argument enough to shop online.

2Who indeed? I've heard all of the arguments against shopping online and find them unconvincing. Am I really costing local people 'jobs'? Any job that's so volatile probably wasn't a good 'career choice' in the first place. Furthermore, we're just getting into a classic argument as to who should be responsible for your livelihood: Why should I sacrifice my hard-earned money to keep you afloat? A more interesting argument is an environmental one: Local is better because it involves less transportation. Unfortunately, this is often false: It's much more fuel efficient for a delivery truck to deliver Amazon goods to each of us, rather than for us to get into our own cars and drive around picking up the stuff locally (this week's Econtalk podcast is all about the unintended consequences for the environment of 'common-sense' environmental thinking).Save & Close

San Francisco Chinese New Year Parade...

It is my understanding that the Chinese New Year (CNY) was actually on January 23. Nevertheless, the City of San Francisco chose to hold their CNY parade this past weekend, on Saturday February 11th. Having cancelled more elaborate plans due to the possibility of poor whether, I decided to travel to Chinatown and witness the New Year festivities.

In full disclosure, I must admit that I have somewhat mixed feelings about SF's Chinatown. It's certainly worth walking down Grant st. to witness the cultural history of the city. At the same time, I find the place to be a) very 'touristy' and b) quite dirty. If you tell me that the most authentic Chinese food in the city can be found here, that's great, but you may want to go to the restroom before going out... just saying1.

Anyways, Chinatown was ridiculously packed, to the point where getting around took some effort. 

I'm tempted to make some kind of remark about how I figure busy Chinese cities look just like this... I guess I just did.

On the way to the parade, we saw many people waiting in really long line-ups in order to get free samples of things that they could easily get from any convenience store. Call me crazy but I think that waiting 30 minutes in line to get a sample of Coke isn't worth my time.

Wading through the throngs of people wasn't a complete waste, however, because I got my hands on this (I HIGHLY recommend reading the whole thing, but allow me to quote Nietzsche so that you know what you're getting into: "[I]f you gaze for long into an abyss, the abyss gazes also into you."):

 This is one of the craziest things I've ever read. Really? Side note: My gf asked me why I don't just grab every piece of paper that random people on the street try to hand to me. Why not just take it and make them happy? I'll tell you why: The majority of stuff people hand to me makes me mad. Forgive me, but I'm not going out of my way to piss myself off. 

We eventually got to the metal fence indicating that the parade would be passing by and waited in the cold for the floats to appear. It took a while, but eventually we saw the dragons interspersed with a lot of public officials and too many school marching bands and cheerleading squads.

On top of it being the Year of the Dragon, dragons are the most iconic things about Chinese New Year parades, aren't they?

Speaking of school marching bands and cheerleaders, I took a video of a bunch of them, which I've uploaded to YouTube. I'd ask that you please pay attention to the Tourette's-like motion of the cheerleaders' heads. We were trying to figure out what was up with that (all the schools were doing it). If anyone has any info, please drop me a line. 

As usual, I've created a Picasa Web Album for anyone who'd like to see a few more photos from the area. It got dark quick, and many of the pics are more blurry than I'd like. I'm glad I saw the parade, the best parts of which involved Asian cultural centers and the like putting on big, entertaining displays. Seeing politicians drive by in convertibles just doesn't compare (oh look, it's the District Attorney!). 

Oh, and one last thing: school marching bands playing glockenspiel remixes of some kind of Lady GaGa songs doesn't scream 'Chinese New Year!' to me...

1The food at the Chinese restaurant we frequented was great, but the lavatory left much to be desired. The men's washroom was stacked to the ceiling with boxes, which had to be circumvented/avoided in order to use the dirty toilet. I don't think that any of the boxes contained foodstuffs, but they certainly did hold the napkins that were being used at the tables... Eww.

Baker's Beach and Land's End, SF, CA...

Forgive me for the lack of posts dear readers, but things have been very busy since the beginning of 2012. Thankfully, this is the 'good' variety of busyness, where my work is proceeding apace, and I feel like I'm making great progress on my projects. Hopefully, I'll be able to talk more science in the near future.

Today however, I've decided to post some photos taken during a recent excursion to Baker's Beach and Land's End, both located on the North Western shore of San Francisco:

Baker's Beach and Land's End are unfortunately not indicated on this map of San Francisco. However, they're located in the area bounded by the red box, so you can get an idea of where they are in the city.

The previous weekend featured a depressing cold drizzle, so many people were out-and-about taking advantage of Sunday's beautiful weather. There were people on the beach in swimwear, but I've been told that it's never really appropriate 'beach weather' here in the Bay Area, and the water is always very cold.

Here's a shot that capture's the entire beach. As you can see, the Golden Gate Bridge is off in the distance. People have assured me that this area offers the best views of the bridge in the city.

From Baker's Beach, it's a fairly straightforward walk along some streets to reach the Land's End park, where the cliffside trail offers some very nice views of Marin County to the north. The houses built on the aforementioned streets have the same spectacular views, and I cannot imagine that they're anywhere near 'reasonably priced'.

Here's a view looking east from the cliffside trail. You can see some of the houses that you have to pass in order to get from the beach in the distance to here. Very, very nice houses.

Finally, wanting to use the features of my iPhone, I took a panoramic shot of the Sutro Baths, the cliffs, and the rocks out in the water (heading westward, this is the end of the trail, just before you reach Ocean Beach).

The Sutro Baths are kinda weird. They have this 'faux Roman ruins' look to them, but they're actually the foundation of an old public pool the burned down in the 60s. This is prime real-estate, and while I understand the desire to preserve the area as a park, it seems like there's a lot that could be done with the land for public purposes.

As is typically the case, I've generated a Picasa Web Album here for people who would like to see more photos of the area. It's a fairly nice walk with only a few odd hills to navigate, and I'd recommend it to any SF tourists, if only for the excellent views!