Rant: Replicability...

If one were to list those traits that separate 'scientific knowledge' from 'intuition' or 'revealed knowledge', one might choose traits such as a) demonstrability, b) testability, c) reproducibility, d) consistency with previous scientific knowledge, and e) subject to revision with new observations, among others1. As some scientific fields become more complex, involving highly specialized, technical analyses of ever-larger amounts of data, the question of 'reproducability' is becoming a serious concern.

One concern is practical: If I generate terabytes upon terabytes of data, I have to be able to provide said data to the community, should they want to reproduce my work. Not every lab has the expertise (nor the resources) to provide their own web-hosting of the data, therefore such data have been stored in large, public repositories such as those found at the National Center for Biotechnology Information (NCBI). However, as has been pointed out by several op-eds in the recent scientific literature, the price of data generation (mostly in the form on nucleic acid sequencing) is dropping at a rate faster than the cost of the hard-drives required to store it. Therefore, it's quickly becoming cheaper to simply store samples (and resequence them as needed) rather than store the raw data themselves2.

A second concern is more personal: Some of the analyses being done nowadays are very, very big and very, very complicated. Anyone who's ever been involved in a genome consortium paper (and I've been involved in a few now) knows that a < 10 page Nature paper may involve the work of 40+ people, each contributing significant details to an analysis. Collating all of these details together into a single story is challenging, and unfortunately, crucial details about how things were done sometimes get lost in the shuffle.

It's not only consortium papers though - anecdotally, I've heard several scientists complain upon reading new papers, that they couldn't reproduce the details of the analysis. Either the descriptions are too vague, or the available data are not in a format that makes it easy to understand where they came from, or how they were generated.

In the past month, I've come across a few papers whose details and methods I'd love to adapt to answer some of my own questions. However (and you can probably see where this is going) I can't figure out how to square the supplementary data that are provided with the details of the analysis: Why is it that the paper consistently refers to 8 classes of data, whereas the public depository entry contains 14???? Unfortunately, it's an unnecessary impediment to me getting my work done.

If scientific data are going to be held up to the somewhat lofty goals of the discipline, we need to make sure that they're well documented and reproducible3.

1The difference between 'demonstrability' and 'testability' is the subject of much debate in some scientific circles. For instance, if a theory is testable in principle (e.g., given the appropriate conditions/equipment) but not in practice (e.g., the equipment required is far beyond the scope of current knowledge), can it truly be called scientific? There are many reasonable hypotheses about things like life on other planets that just aren't testable in the foreseeable future. That's not to say that this automatically means that such fields aren't 'useful' or interesting; however, the more appropriate question may be whether funding should be prioritized towards testable hypotheses.

2There are all kinds of issues of practicality and reproducibility when we discuss such things - I'm only pointing out the details on purely economics terms.

3I have a nitpicky specific discussion point about online data depositories that I think I'm going to save for a follow-up post.

Rant: Phones both Smart and Dumb...

One of the great ironies of my life is that despite having grown up the son of the manager of a cellular phone company and having been surrounded by cellular phones since the 80s, for the longest time, I was a personal communication Luddite. I didn't get a cell phone until I was essentially forced to during my M.Sc. (I was away from home ~75% of the time and thus no one could reach me), and even then I opted for the least feature-rich, cheapest model.

I actually stuck to 'dumb phones' until a year ago, when I got aggravated that my previous postdoc wasn't allowing me to check social networking sites1. I was already stuck on a Verizon contract at the time, and therefore had to choose between their Blackberry and Android smartphone offerings. Given that the former's troubles were already quite apparent, I settled for the HTC Droid Incredible™, which had received quite positive reviews as far as I could tell. While I've certainly enjoyed many of the phones functions, I very quickly became familiar with what has affectionately been referred to in some circles as 'Android jank'.

I should mention that before I picked up the smartphone, I'd used my iPod Touch to play music. The 'iTouch' is of course an iPhone sans phone, so I was familiar with Apple's slick user-interface and design. It's difficult to overstate the difference between the 'i' devices' ease-of-use and the wild west that is the Android landscape. Whereas a premium is placed on consistency and elegance in the user interface of the former, every single app controls differently in the latter. In fact, Android apps are annoyingly constantly being updated in order to fix user interface complaints. This frequently requires 're-learning' where all of the buttons are. While it's true that many Android apps theoretically have more options than iTunes Appstore offerings, there's no guarantee that said options will not be located in tedious nested menus navigated by ludicrously small buttons.

Furthermore, there's a lack smooth elegance to the Android interface. Apps frequently have load times, which strikes me as rather insane on a portable device. It's not uncommon that that, while stopped at a red light while biking, I'll want to scrub forward to the next song or podcast in my playlist2. Unfortunately, bringing up the interface to do so takes so much time that I have to put the phone back into its holster before the deed is done. How does that make any sense? Some music programs let you switch songs without 'unlocking' the screen, while others don't - it seems that nothing is consistent in the world of Android3.

Speaking of podcasts, I recently began listening to a rather 'techy' one at tested.com (This is Only a Test), which involves discussions about the latest in gadgets, electronics, and computers. Over the few episodes that I've heard, the staff of Tested have been quite critical of Android as a platform, and one of the big reasons is this:

The original image and description are available at theunderstatement.com, and show that the majority of Android phones are a) released without the most current version of the operating system and b) receive very little if any software update support. This is in comparison to Apple products (shown at the top), which receive the newest versions of their OS as they're released, and continue to have bugs fixed and tweaks made.

The link above spells out a long list of why this is significant, but I'll throw out only two things that matter to me. 1) while some of this Android Jank is getting fixed by the OS manufacturer (Google), there's no guarantee that these fixes will ever be 'pushed' to your phone. 2) It's not surprising that Android apps are so buggy given that developers have to try to support every random version of the OS that still may be floating around out there.  

None of these details have been ruining my life or anything, but they have been annoying. When I got an email about 'upgrading' my phone at a discount, I decided that I wanted to return back to the Apple fold opting for an iPhone 4S. Coupled to my new Macbook pro, I suppose that this puts me firmly in the Applenaut camp, but that doesn't bother me. I only care that the stuff I own gets the job done. We'll see if this does the trick.

1This could be a post in and of itself: Somewhat amazingly, I didn't actually use Facebook until well into my previous postdoc. I'm not exactly sure why, but the benefits of keeping in touch with old friends and colleagues didn't occur to me, I guess. Regardless, one could ask whether being able to check Facebook during the workday really should be a personal goal in the first place. I've come to realize that social media isn't only a forum in which to 'goof off', but also tends to be the modern method by which information is disseminated quickly. I get a lot of my info about science and other important news from Facebook and Twitter, and through experimentation and self-discipline, have tried to minimize their distractive influences.

2Like in Maryland, in the great State of California, it is legal to listen to music in a single ear while biking. I've recently found that an excellent way to do this is to use an inexpensive Bluetooth headset. I recently picked up the Plantronics Marque™ M155™ Bluetooth Headset, which has shockingly good sound quality for listening to podcasts wirelessly while biking.

3A couple more criticisms of the Android platform: Compared to Apple's, the on-screen keyboard is awful (even acknowledging that Android got 'copy/paste' before Apple did). Writing texts or brief emails is a chore and the auto-correct drives me mental. Downloading a ~$3 third-party replacement called Swiftkey helps a bit, but doesn't fix the fundamental touch-screen problems. Finally, the Android's on-device directory structure is maddening, and trying to figure out where to dump music (or where it downloads from the Amazon MP3 store for that matter) is frustrating. Anyone could've figured out that letting every piece of software create its own randomly named directory in the root was a terrible idea. 

Rant: Marketing...

Been a while since my last rant; figured it was high-time.

There's nothing more annoying than receiving calls from telemarketers. Honestly, when is it ever a good time for me to listen to you tell me about some product/service in which I'm completely disinterested? Having been a telemarketer for all of 6 days, I learned a valuable lesson: cut them off right away and pleasently tell them to put your name on their 'corporate do not call list'. That company won't be calling you back. It works 'cause it's the law. Try it.

When I lived in Canada, it seemed like direct mail, credit card offers, and things like telemarketing were a background inconvenience. Here in the States, it feels like this stuff is way, way overboard.

A few days after my one year anniversary of being in the US, I started receiving credit card offers - a lot of credit card offers. In fact, there are at least 5 different companies offering me credit cards, some of them mailing me TWICE A WEEK. I swear, I'm getting ~100 packages a year from Capital One alone that I tear up and dump into the recycling bin. Oh, I also get coupon books and flyers pretty much every day. I also have received GQ, Cycling magazine, and some running mag all without having actually signed up for anything. I empty my paper recycling bin weekly because it's full of junk mail.

How about emails? Any company from which I've ever ordered anything online emails me DAILY. That's right, I get 1-2 emails per day from Newegg, Amazon, Barnes & Noble, etc. I know that I can block them (and have), but does this make sense? How much stuff can I possibly buy? I've heard that the idea here isn't to actually advertise anything, it's simply to keep the names of these companies on the tip of your tongue. I'd like to see a serious study just looking into whether this constant deluge of shit just pisses people off about these companies.

Here's another one. CVS, the big pharmacy chain in the US, calls me frequently with an automated message, asking me to 1) confirm my name, then 2) enter my date of birth before helpfully reminding me that it's allergy/sunburn/flu season and that I should stock up on some particular product. Thanks for calling me at 2 in the afternoon, while I'm in a meeting at work to remind me of this garbage. What in the hell are they thinking?

Oh, here's my big pet-peeve. Why is it that every frickin' store is trying to get me to sign up for their particular meaningless 'reward' card? Why can't I just bring my stuff to the counter, pay, and leave? I shouldn't have to take off my headphones at every single store so that I can say 'No, I'm not interested' or 'Can we please skip the part where I give you my whole address and/or email address?'. Just let me pay and walk out - aren't you getting my money? Why are you still not satisfied?

 I'm sure that some research firm presented some talk at a marketing meeting, showing a 4% increase in quarterly revenue from some obscure company when they started harrassing the hell out of their customers. Rationality would argue that companies wouldn't do this if it didn't work. However, I wonder if anyone ever gets so annoyed by this junk that they actually stop doing business with particular companies? We can't always choose the stores nearest to where we live, but I've certainly stopped using some websites because of the constant email spam I get from them... something to think about.

Rant: Institutional Email...

As I prepare to leave my current postdoctoral position and embark on a new chapter of my career, I'm again faced with going through the process of changing my 'institutional email address'. This is to say that the email address given to me by my current employer will be shut down and I'll have to obtain yet another one at my new place of work. I've gone through the following institutional suffixes in the last decade: '@dal.ca', '@sfu.ca', '@mcmaster.ca', and finally '@mail.nih.gov'. At this point, I consider myself somewhat of a 'professional' and find it very annoying that, yet again, I'll have to send out a blanket email telling a variety of people to 'please update their address books'. No doubt, I've lost contact with prior acquaintances solely because my email addresses have constantly been changing.

It would be far more useful both career and personal-wise if I had a functionally-permanent, independent email address, wouldn't it? The obvious solution would therefore be to either a) use my gmail address, or b) pay for a professional 3rd party email box. However, there's a big catch: many professional activities require 'institutional email addresses'. For instance, I've had calls for manuscript review that required an institutional address, people wanting letters of reference from me requiring an institutional address, and various campus organizations that refused to send information to any other email address. Great.

It would be wrong to say that the impermanence of institutional addresses for non-faculty is their only weakness. In fact, I'm often surprised by how unfriendly most of these email servers have been as compared to the free, ad-supported gmail1. For instance, all of my institutional email servers have had tiny maximum attachment sizes and ludicrously small maximum storage capacities - without exaggeration, I've hit max capacity (from a fresh clean) on my current professional email address in an afternoon of being sent powerpoint slides. Gmail's capacity is > 36 times the capacity of my institutional mailbox. Yet another problem is that these mailboxes are difficult to access. Obviously, this is partly due to security reasons, but I'm also talking about terrible, slow web interfaces as well. Don't even get me started about what a chore it is to search through my mail, or how tedious it is to set up any kind of address book.

Unfortunately, all of this belies the greatest travesty underlying institutional email addresses: The insane amount of 'legitimate junk mail' one receives on a daily basis. Consider the following: I have no problem giving out my gmail account to every ridiculous online marketing scheme in existence. The very first email they send me goes into a filter (they take roughly 10 seconds to set up) and I never hear from said company again. I get surprisingly little junk mail to my free, ad-supported email account.

On the flipside, I receive multiple dozens of emails per day to my institutional account from various sources because I am automatically associated with a bunch of 'distribution lists'. It actually drives me crazy to think that part of the cost of running various institutions goes to paying the salaries of people who send out inane email 'reminders' about upcoming flu season/performance by X at local venue/inspirational message from program chair/etc. At my current institution, I get tons of emails that have absolutely nothing to do with me but are sent to everyone by default.

The tragedy of this is that I and others regularly miss emails about legitimate issues such as documents that need to be filled out and signed or training that needs to be complete because we don't want to waste time reading every random message that hits our inbox. All of this junk is a waste of time and money for the person writing it, and a larger waste of time and money for all of the people who then have to read it. Think about this: If I'm right, it would actually be better to pay a person to write the inane email and send it to their own trash folder than to mail it to everyone in terms of net productivity. 

There's a substantial literature on the 'information overload' effect of email (for example, see here). It's ease-of-use as compared to traditional 'snail mail' has led to its overuse, forcing us all to waste time on reading meaningless trivialities that accomplish little if anything2. Even ignoring all of the earlier complaints, if using my gmail account allowed me to get off of all of these distribution lists so that I receive only messages directed to me, that alone would be a massively welcome change. Oh well. 

1I have no idea how some people can still use Hotmail, however. Unless they've changed radically in the past few years, I've always found their servers to be incredibly slow and tedious.

2I'm open to be proven wrong on this one, but my hypothesis is that sending me some ridiculous clip art about allergy season does nothing to reduce the very real irritation that my allergies cause.

Rant: Amateur Public Performance...

Given the rough week I've been having1, it is high time that I bring back the venerable tradition of the online rant. Here it goes: There are a crazy number of people near my current home who like to either: 1) sing, 2) rap, 3) proselytize, or 4) listen to music without earphones in public places, particularly at bus stops and subway stations. I guess I've seen this stuff before - there are rude and/or crazy people everywhere you go, of course. However, the big difference between the places I've been and where I am now is the frequency of these occurrences: I'd estimate that I have to listen to someone's awful performance(s) ~2-3 times a week nowadays.

I really don't get it. Most of these people don't seem as though they're suffering from mental disabilities or anything like that. It's not people that are babbling to themselves about the apocalypse or begging for change. Instead, some normal-looking guy will walk onto the Metro train platform, stand around for a few seconds, and then break into a loud impromptu freestyle rap featuring all kinds of profanity. I've also heard little old ladies start belting out gospel at bus stops. One time, a rather large man began a completely undesired, one-sided loud conversation with another person waiting for the bus about how his faith in Jesus Christ was the only reason he wasn't out there killing people right now. As he explained it, Jesus was the only thing holding back the 'anger in his soul'.

Okay, I admit that that last one was 'hella' disturbing, and if I wasn't way out in the middle of nowhere setting up utilities for my apartment, I would've moved to another bus stop. But again, if most of these folks are sane, I can only assume that they're also incredibly rude. I don't care if you're an excellent singer, or if the music you're blasting out of your cell phone is great (occasionally it is something I legitimately enjoy), it's no cause to bother everyone around you. It also violates the first rule of public transportation: Keep quiet. There's a certain amount of ambient noise that's to be expected - conversations, traffic, etc. - but there's something especially aggravating about someone standing next to you shouting out some random off key tune.

And if anyone still thinks that this isn't annoying enough to warrant a rant, allow me to present exhibit A: The isolated vocal track of David Lee Roth singing Running with the Devil (1978). No seriously, compare it to the original Van Halen track. SEE?!?!?!?

1Every once in a while, you have one of those weeks where the work piles up faster than you can deal with it and nothing seems to work. Oh, I was also expecting this to be the first weekend I'd able to go biking in 3 months, but after spending an hour tuning up my bike, a spoke snapped the second I jumped on it. I brought it into the shop where I was informed that their work backlog is so big that I won't get it back for 2 weeks... Ungh.