Propping Up a Failed Enterprise

This process of Creative Destruction is the essential fact about capitalism.

— Joseph Schumpeter

Yesterday, Julia, my 18-month-old, was playing with Megablocks®. She just reached a phase where she builds — as opposed to destroying — simple structures with her toys. I wanted to play with her, giving her minimal guidance and help so she can learn to erect things and enjoy the fruits of her own labor. When she sloppily added a block, I held the entire structure in place so it doesn’t all collapse. Eventually, a marvelous piece of architecture emerged.

Megablocks, erected Take that, Frank Gehry!

But then I realized that no way in hell would she be able to erect such an elaborate structure without me stabilizing it and fixing it when she wasn’t looking. The more elaborate it got, the harder it was for me to keep it stable. And then it occurred to me. I was being the Fed! I was propping up this overly complicated monstrosity and giving her false hope that she could build anything without any downside risk. I was working against my libertarian values. So naturally, I decided to myself, Screw it! I’m going to be a libertarian dad! And I let go.

Megablocks, destroyed

Without hesitation, the entire system of interconnected plastic pieces crumbled in front of her tiny eyes. I anticipated an anguished wail. I was ready to take her into my arms and comfort her, bail her out of her tearful misery and assure her that she’ll never experience disappointment again. Instead, she looked at me and started giggling. Then, she went about building again, this time completely on her own.

Admittedly, her new creations hardly reached the same stature as our now-defunct joint venture. But she didn’t seem the worse for wear. She seemed, if anything, more eager to try different configurations without my help. Lesson learned: Megablocks megastructures, even constructed by well-intentioned and cute little girls, are not too big to fail.

Some Parting K-mers

After 12 years, today is my last day as a professional bioinformatician1. I’m not leaving because I’m fed up. I’ve just been lured away by an amazing new engineering opportunity in the financial sector.

Over my bioinformatics career, I’ve been involved in various large-scale projects, small studies, and everything in between. I’ve taken on more roles than I expected or have trained for, like systems administration, project management, grant writing, manuscript writing, logistics and operations, catering, peer mentoring and counseling, designated driving, bathroom cleaning,2 and secretarying. I’m not trying to sound derisive (ok, maybe except for the bathroom cleaning), but rather to illustrate how naive I was at the outset to expect that I’d only design and write code.

Bioinformatics is already a multidisciplinary field, drawing on expertise in computer science, biology, engineering, probability, and statistics. Also, the lack of an accepted concise definition for the term bioinformatics leads to a mismatch in expectations among biologists and bioinformaticians themselves. We are therefore often asked to perform certain tasks that we deem outside the scope of our role. I’ve ranted numerous times, mostly (but not always) privately to colleagues, about this. Tasks like writing grants were tedious and unfulfilling. Unlike code, they were outside my control and outside of my comfort zone.

But now, on the eve of my departure, having taken stock of my years as a bioinformatician, I am convinced that all that tedious overhead is an essential part of being a bioinformatician. I’ve learned a lot from writing grants and papers, managing projects, and mentoring — and being mentored by — my peers (but not so much from cleaning bathrooms). All of these tasks took me out of my element and forced me to look at the bigger picture. Even when they led to some doubt and discontent, they taught me patience and responsibility. On the whole, they made me a more effective engineer and a better colleague.

I therefore urge current and future bioinformaticians not to resent these non-bioinformatics responsibilities, but rather to embrace them as part of the core of bioinformatics. Stepping outside of our comfort zones — and outside of our job descriptions — is good for us. Some scope creep is acceptable. We can apply our unique skills in logic, reasoning, and management to make our teams and organizations more frictionless and productive. And in taking on these responsibilities, our skills will be honed further.

  1. I always preferred the word bioinformatician over bioinformaticist.
  2. Seriously: in a previous position, I was asked to clean the men’s room to make it presentable for a site visit by a VIP.

Coffee Is the New Black

(Older version of this post on CarboLog)


For the last five months I’ve been experimenting with variations of slow-carb dieting, having read several books on the subject. But if coffee were restricted from such a diet, I would not could not do it.

One of the key principles of the Slow Carb Diet is no calories from liquids. Fortunately for me, I drink coffee black: no sweetener, no creamer, nothing; just pure unadulterated java. It has negligible calories (not that it matters) and no carbohydrates of any kind (that it matters), so I can drink it until I turn into a Mexican jumping bean.

It wasn’t always this way. I used to love flavored, sugared, and well-creamed coffee. The coffee itself was just the garnish on a frothy delicious milk beverage. Over time, however — and only mildly related to weight control — I learned the intricacies and complexities of plain coffee. I read about and tasted different types of coffee beans. I’ve experimented with different brewing techniques (and have decidedly settled on the AeroPress for its perfect brewing capabilities, consistency, convenience, and affordability). It took about a year, during which I slowly reduced the sweeteners, then the creamer. I find myself savoring coffee more than I have before, studying the flavors, the acidity, even the texture.

The fact that you can’t really gulp down black coffee, particularly when it’s hot, has another benefit. It helps you manage oral boredom, that desire to do something with one’s mouth, leading to habitual snacking (plus — let’s face it — nursing a cup of black coffee signals intellectualism).

Another great thing about black coffee is that it doesn’t spoil as fast as creamed coffee. I try not to drink coffee past 4pm. If I have leftover coffee, I can pop it in the fridge, and wake up to decent, ready-to-drink iced coffee. Yes, I’ve had black coffee that has been left out — unrefrigerated — for 24 hours and it’s definitely drinkable.

And lastly, did I mention that a Venti® Pike Place® is about a third the price of some fancy Starbucks drinks of the same size?

So to summarize, the benefits of black coffee are that

  • it won’t fatten you up
  • it replaces potentially fattening snacks
  • it’s cheap
  • it stays relatively fresh
  • it makes you look smart

Like many other habits, it’s hard to shift to drink black coffee if you routinely drink coffee-flavored smoothies, but there are ways to scale into it: incorporating one black cup every week, phasing out sweeteners and creamer slowly, or replacing refined sugar with artificial sweeteners. And don’t only think of restricting the types of coffee you drink. Think instead about the world of possibilities that drinking black coffee opens.

Gingi, Interrupted, Interrupted

I came up with a new title for my rarely-updated blog. I decided to rename it for two reasons. The first is that the previous title, Gingi, Interrupted, inspired by the memoir, Girl, Interrupted, was misleading. Unlike some of the characters in the story, I am not suicidal and I don’t have borderline personality disorder I don’t think. So to all my loyal readers, particularly those that recommended that I seek psychiatric consultations, I apologize if I gave the wrong impression and thank you for your unexpressed concern.

The second primary reason for renaming the blog is primarily motivated by the ongoing presidential primaries. I will make a small political disclosure. I am registered here in New York as Independent, and therefore cannot vote in the primaries. It’s okay because votes tend to count less in polarized states like New York. Still, I get criticized regularly for being a spineless moderate. I’m not a moderate, and I have a spine (yup, I just checked).

I tend to have fairly strong opinions, and I am not ashamed of them. But I cannot align myself with a singular political party or belief system. My Venn diagram just cannot be contained within another Venn diagram. But my Venn diagram does intersect somewhat with other Venn diagrams. There are many ideas in various ideologies that I embrace, but there are often some that I reject. Excuse the cliché, but I will not be defined by any one ideology.

To put it in lexical terms, some of these ideologies apply to me as uncapitalized adjectives (get it?), but not as capitalized nouns. I am libertarian, but I’m not a Libertarian. I am independent, but I’m not an Independent. And so on. (I am almost tempted to use an OOP metaphor that illustrates the benefit of interfaces over class inheritance — the GoF would be proud.) After much contemplation, I think the new title captures my superficial defiance of institutionalized over-categorization.

One last note. I am not generally opposed to the pigeonhole principle.

Desperately Seeking a Personal Backup Scheme

I’ve already had two hard disk failures on my work Mac. The first time was on a PowerBook, but my home directory was recovered after about 2 weeks. The second time was on a new MacBook Pro that replaced the PowerBook as a result of the first failure. It contained much of the data from the first failure, and took about 6 weeks to recover most of my home directory as well as some applications. I think I learned my lesson!

Yesterday, I finally got a nice, 500 GB, FireWire external hard disk so that I can begin to back up both of my Macs. Lovely. But now what? I am researching the best engineering solution to meet my requirements, listed below:

  1. Back up of both hard disks

    I have a personal PowerBook and a work MacBook Pro. I’d like to back up both hard disks on a regular basis.

  2. Consolidate data libraries

    I have an iPhoto and iTunes libraries on both machines. Both started from the same copy but have since diverged significantly. I would like to use the external hard disk to keep the libraries synchronized.

  3. Granular File Restoration

    I would like to have the ability to synchronize, if I wish, a unique set of files to my local machine. For example, I’d rather keep my entire music library on the hard disk and only download a set of playlists that I want to listen to.

  4. Sharing Data Between Macs

    I want to easily access data that originated from the other Mac. Say I have a license for an application on my PowerBook that I’d like to copy over to the MacBook. I know that I can do it over the network or BlueTooth, but is it possible to use the external HD as an intermediary?

I think that these four requirements pretty much sum it up concisely. Here are various solutions that I am contemplating:

  • WD Backup
    The software that comes packaged with the hard disk. It seems pretty feature-laden, and I think it will meet Requirement 1, but I’m not entirely sure about the other requirements.
  • SuperDuper!
    A widely-acclaimed disk recovery program. Uses sparse disk images to maintain active backups. It might be able to meet Requirement 2 by the creation of a separate disk image for specific libraries.
  • unison
    An open-source tool for synchronizing multiple file systems. Combines functionality of rsync with SCM features. It seems that with some effort I’ll be able to meet all of the requirements.
  • In-House Solution with SCM
    Write my own backup system that leverages a revision control system to meet all the requirements. I would probably start out with a golden disk that will contain a merge from both hard disks. I would then use some versioning features, such as branching and local checkouts, for granular control (Requirement 3). I would probably use Subversion or Perforce. But then I’d have to deal with scheduling. Besides the fact that this will probably be a pretty involved undertaking.

Some other considerations involve handling of the raw 500 GB of storage. I need to figure out whether I should go with a single partition or multiple partitions. I am considering reserving part of the disk to save movies from my DVR. Also, I’m thinking of setting up a RAID scheme, but that may be overkill.

So does anyone out there have any other suggestions or feedback about how I should go about doing this? I hope that I’ll be able to implement a solution before my hard disk crashes yet a third time!

[tags]mac, external hard disk, unison, perforce, subversion, backup[/tags]