I don't normally feel unnerved about the omnipresent social-networking morass persistently enveloping the modern internet. It's clearly a social phenomenon and an admittedly interesting one at that. Even so, I can't help but feel a tad creeped out when. say, I edit a company's new Wikipedia page and said company's founder looks up my Linkedin profile a few hours later. He doesn't even leave any snide comments or anything, he just looks at it, a feature seemingly unique to that particular network. It's not easy to find my LI profile from my WP one without some Internet Detective work so it really just comes down to a big "why?".

Why do I care who feels like being strange on, god forbid, the internet?
Why do they go and do it anyway?

(Of course, the Wikipedia Internet Detective also felt like looking up one of my email addresses and sending me a passive-aggressive nastygram. Maybe a better question is "why do people get offended so quickly on the internet?")

Here's my glitch for the day.

We talked about the Peak-end rule in the development class this evening. It's an interesting heuristic, if perhaps an oversimplification. We discussed it in the context of giving presentations but I'm curious about how it applies to other presentation-like experiences or even whether a collective group of people tends to define the "peak" of a shared experience in an identical manner.

Thar's gels in them thar hills

Text mining is a rather unkind metaphor. In the life sciences, it refers to how we can sort through all the published data out there and extract broad conclusions from the aggregate. This does make the rhetorical assumption that most of that text is some kind of stone to be blasted away until the truth emerges, gleaming in the sun.

In practice, things are never that simple, of course. I think I've mentioned here before how some of the major science publishers have only just begun opening their archives to text mining. There's also the issue of images: current software can usually handle text without serious issues but extracting meaningful data from figures is conceptually problematic. Scientists just aren't consistent when it comes to presenting their data. That's a good thing, really, as it they often have to focus on different aspects of their results; nature (or Nature, for that matter) just isn't always as consistent as we'd like it to be.

A paper posted to arXiv recently by Kuhn et al proposes one strategy for extracting data from images in scientific papers. They focused on gel images. These kinds of figures are great because they're generally just photos with sets of horizontal bands in them.  The placement of the bands determines their relative size, so as long as a size standard is present, there's one bit of easy data already. The tricky part is knowing what's actually present on the gel. Even when we know that, the gel images are often too data-rich to tease apart every apparent result. As the authors say, "...the text rarely mentions all these relations in an explicit way, and the image is therefore the only accessible source."

These folks used a straightforward approach to break down gels into usable data - check out the paper for details. They're fond of the optical character recognition in MS Office 2003 for handling text. The gel segment recognition needed a machine learning-based approach and random-forest classifiers. Assigning relations to those gel images is much trickier so the authors had to use the ol' Human Touch in their code.

So how well does it work? Not terribly well yet, at least because it's still incomplete. The issue of inconsistent labeling remains; the authors' approach works passably as long as figures are neatly labeled with gene or protein names. This kind of approach and others like it may eventually mean authors have to consider image mining when designing figures. They could, of course, just have fun with the image mining and write out all their labels by hand.

Diners, drive-Ins, and drift

A Guy and his favorite condiment.

I recently wrote a silly little Python script which would randomly generate names of the kinds of meals one would only see in Guy Fieri's vivid, flame-scorched culinary imaginationscape. I'm not mocking the guy per se. He's clearly working with a winning formula even if it does take the lowest-common-denominator and divide it by zero. That is to say, the results fit expected parameters but aren't terribly rational.

But yes, the script. Here's some sample output:
Then we can start with the
Guy-talian Slammin' Bad Boy
Southern Honey Dijon Dumplings
Green Pepper Sashimi Kabobs
Pesto Baltimore Veggie Roast
Southern Johnny Garlic's Bourguignon
Bourbon Pesto Shrimp
and the
Lime Pepperoni Mashed Potatoes
then we can finish up with the
Queso Smothered Tostado Po'Boy

All the starting adjectives and nouns (that's where the meat is, this isn't any fancy code) are from the menu at Guy's own recipes, his restaurant, Applebee's, Hooters, or a competitor of these. They generally sound palatable with the possible exception of those mashed potatoes up there. That's not really the fun part, though. The fun part is that I wrote this for Python 3 though it still runs in Python 2. The output gets a bit garbled:
Then we can start with the
 Bakea  Sriracha
 Baked Potatoin'
 Kabobs Crazy
 Friestalarmesan-Crusted
 Bourguignonan
 Rings Pepperlo
and the
 HalibutSix-Cheese
then we can finish up with the
 Frittersanch

What we end up with is the logical extension of maximally-flavored American comfort-food: Guy's Impressionist Cuisine.  

The artist for today is Kate MccGwire. She makes feathery sculptures which look like they either want to eat you or want you to eat them.

Music for Programming

This mix series is wonderful. Ingredients, as per their aesthetic description:
Drones
Noise
Fuzz
Field recordings
Vagueness (Hypnagogia)
Textures without rhythm
Minor complex chords
Early music (Baroque, lute, harpsichord)
Very few drums or vocals
Synth arpeggios
Awesome
Walls of reverb

It's pretty decent background sound for programming, yes, but it's even better for an evening walk through the noisome late-February air.

Very Much Like Me

The unrelated background music for today.

Looks like it's time for another personal assessment. This is one of a series of questionnaires and inventories prepared as part of a program called Authentic Happiness. Yes, that's a name with some tall claims. The program is courtesy of the Positive Psychology Center at the University of Pennsylvania so it may have some decent, scientifically-sound psychology chops.* It's also accessible without any monetary cost.

I took the VIA Survey of Character Strengths. (I think it's a longer version of the VIA Me! survey, which I have taken previously.) It's a series of 240 statements, evaluated in much the same way as the previous strengths surveys I've described (that is, a 5-point scale from Very Much Like Me to Very Much Unlike Me). Some of the statements feel rather transparent (i.e., "I am a spiritual person.") as it's clear how they translate to results (if you say you're spiritual, the survey won't disagree). This may be by design; perhaps the best indicator of a spiritual person is that they consider themselves spiritual.

Here are my results:

Your Top Strength

Creativity, ingenuity, and originality Thinking of new ways to do things is a crucial part of who you are. You are never content with doing something the conventional way if a better way is possible.

Your Second Strength

Judgment, critical thinking, and open-mindedness Thinking things through and examining them from all sides are important aspects of who you are. You do not jump to conclusions, and you rely only on solid evidence to make your decisions. You are able to change your mind.

Your Third Strength

Appreciation of beauty and excellence You notice and appreciate beauty, excellence, and/or skilled performance in all domains of life, from nature to art to mathematics to science to everyday experience.

Your Fourth Strength

Humor and playfulness You like to laugh and tease. Bringing smiles to other people is important to you. You try to see the light side of all situations.

Your Fifth Strength

Curiosity and interest in the world You are curious about everything. You are always asking questions, and you find all subjects and topics fascinating. You like exploration and discovery. So, not too different from the short version of the inventory. As part of my personal development class, we're being assigned the task to survey other folks about what strengths they think we display. I will have to see if there is a correlation. *I tend to take just about any psychological theory or finding with a Volvo-sized grain of salt. To be fair, I don't have any formal education or experience with the actual study of psychology. My blanket judgement is largely unfounded. I've just read enough poorly-supported, statistically-unsound psychology claims to be wary.

Here's a dumb GNOME Classic interface issue that I always seem to run into: desktop elements (i.e., launcher shortcuts) aren't movable or removable by the mouse alone.* Right-clicking them brings up context menus but some options remain hidden. Holding the superkey + Alt and then right-clicking makes those options show up. This forum thread was helpful.

*This may just be a change since Ubuntu 12.04. I'm just glad to have an interface other than Unity available.

Fields of gold

The only truly wasted parts of my day are those spent on hold, waiting to speak to customer service. You'd think, at the very least, that there would be numerous alternatives to this phone-queuing. You would be absolutely right because you are aware of the internet. You may have even sent an Instant Message at some point! Barring any of that potential experience, though, I'm sure there are better phone-based alternatives. Could I just have a call back when a human is willing and able to speak to me rather than having to wait while the entire Sting catalog floats through my senses at 8 kHz?

On a directly related note, I learned today that some Cisco call-processing software had some pretty nice default hold music. It had some kind of mention in This American Life a few weeks back. I didn't hear that episode but the little tune is preferable to, er, just about anything else. It makes me nostalgic for all that great mid-90's tracker music. Even kinda terrible MODs would be just fine.

Nothing but flow-ers

I had a fair amount of trouble getting into anything like a flow state this week. It's not normally so difficult: I tend to stay focused on anything repetitive or anything involving researching a topic. The former situation isn't really ideal as I don't actually like those kinds of tasks. I just have to treat them as a kind of meditative exercise to even want to do them at all. The second situation is more enjoyable. It's really nice to sit back and query the total of human knowledge about a subject, whether it's the function of a particular protein complex or the discovery of phosphorus. This is the kind of flow state I can get into at work and at home.

Unfortunately, I find it very easy to get knocked out of a flow state. The most trivial email can do it in seconds. This week presented all manner of distractions and the inclement weather became just one of them. 

Messages in the ether

Just finished up two things yesterday: Greg Bear's Hull Zero Three and my Twitter account. The former took much less time; it's a quick read in a genre of science fiction known for its long-winded exposition and overwhelmingly massive scales. The novel benefits from a brisk pace despite leaving its plot obscured until the last quarter.* The Twitter account, however, was hampered by the network's breakneck pace. I never really felt compelled to post anything but the most sarcastic thought morsels there, at least partially because those were the kinds of tweets I actually found funny. The rest was largely dispensable.

Twitter just doesn't seem like an efficient way to convey any kind of idea except for the most urgent or expendable ones.


*I give it 3 out of 4 possible Oort clouds. I'm not going to explain the plot or setting or even note when it was written. I just didn't find it that notable.

A drug for when myosin starts actin up

Here's the slightly overstated science headline of the day: "Protein folding: Bringing dead proteins back to life". This is actually an overview of a larger scientific paper in one of my favorite newer life science publications, eLife.

The hyperbole isn't entirely undeserved as this is some pretty neat stuff. Myosin, famous for its role of moving things about inside cells, appears to gain efficiency and stability when a small molecule called EMD 57033 is around. This small molecule isn't a new discovery and has been studied for at least twenty years. What's new is its potential role as a pharmacological chaperone. Cells produce classes of proteins known as chaperones to keep proteins from misbehaving, especially when these proteins are being assembled and often after stressful circumstances (i.e., heat shock). EMD 57033 isn't naturally occurring in cells but it may serve a similar function as a drug.

Transmutation

Urine luck.

Today's artwork is The Alchemist Discovering Phosphorus, also known as The Alchymist, in Search of the Philosopher's Stone, Discovers Phosphorus, and prays for the successful Conclusion of his operation, as was the custom of the Ancient Chymical Astrologers. It is by English painter Joseph Wright, also known as Wright of Derby. The painting may or may not be about the historical discovery of phosphorus, a process which involved the reduction of urine, a fluid rich in phosphates.

William Gibson Describes the Attractions at Colonial Williamsburg.

The "Great Authors" bits at Something Awful are easily some of the best content-morsels to ever emerge from the site. The shtick itself is very McSweeney's but it really toes that line between parody and detachment. (All of this is a good, enjoyable thing.)

I'm actually rather surprised as to how Something Awful keeps on truckin' otherwise.

Today I learned about laser guide stars.

I don't think I misjudged my planned career path and I don't think I'd ever want to be an astronomer. That being said, space is neat!

Social animals

This editorial in Nature makes some very definitive claims about what should and shouldn't be done about addiction research. That isn't really my field - I don't work with any organism capable of addiction as we understand it - but the steadfast stance is a worrisome one. Without quoting anything, here's the TL;DR: "Animal-rights protesters claim addiction is a social problem and use that to support how we shouldn't use animals in addiction research. Scientists have shown addiction is a disease so we need to keep using animals in addiction research."

The stance is myopic at best and logically erratic at worst. The dichotomy of "disease vs. social problem" really doesn't do anything toward understanding or treating addiction. Neither does banning animal research, whether wholesale or specifically in the context of addiction research. Equating animal research directly with physical disease paradigms is little more than a knee-jerk reaction to the similarly over-reactive policies promoted by the animal-rights folks. There is unquestionably a social component and ignoring this component should not be sacrificed in favor of a hard-line stance on animal model use.

On a related note, this history of opiod addiction treatment is interesting.

I've always liked this view of Richmond. I never really want to do much cityscape photography in the winter, though.

Emotional Quotients

It's Tuesday, so that must mean it's time for another personal assessment! (This is not specifically due to Tuesday but rather because Tuesday is a discrete period of time.)

I'm taking the Talentsmart Emotional Intelligence Appraisal. It's billed as the "#1 measure of emotional intelligence (EQ)." You'd think that would mean something about how many emotional intelligence tests there are out there or even why people keep framing intelligence tests in the context of IQ, but there are in fact similar tests out there, including this one by a group at UC Berkeley and this one used by Yale. The Talentsmart test is intended to be bundled with the book Emotional Intelligence 2.0 by Bradberry and Greaves.* 

Judging by the introductory demographics questions, this test has been designed with fairly traditional career ladders in mind; one of the questions is "What type of score did you receive on your last job
performance evaluation (performance review)?" The test itself is very short, including only 20 questions or so about how often you are able to do things like handle stress or read the mood of a room. I'm always suspicious whenever an assessment tries to draw conclusions based on limited data. In this case, the assessment appears designed to simply identify emotional or social areas and skillsets in which you may feel lacking. This suggests that the assessment may not be misleading, but it may not provide much insight, either.

The results confirmed my suspicions and are copied below. Scores are from 0 to 100, though anything below 59 is "a concern you must address." Scores in the 70s and 80s indicate areas which can be improved, while higher scores than that are definite strengths which should be employed often. I don't have to worry about that last category. My social competence is evidently lower than my personal competence, which is to be expected, but I'm having trouble gleaning any useful material from these scores since I know they're based on just a few questions. Self-reporting is bad enough as it is, but with this assessment they practically just asked "are you socially aware?" and then mirrored the provided answer.

 

Your Overall Emotional Intelligence Score: 75

Personal Competence: 80 The collective power of your self-awareness and self-management skills. It's how you use emotional intelligence in situations that are more about you privately.

Self-Awareness 75 Your ability to accurately perceive your emotions and stay aware of them as they happen. This includes keeping on top of how you tend to respond to specific situations and certain people.

Self-Management 85 Your ability to use awareness of your emotions to stay flexible and positively direct your behavior. This means managing your emotional reactions to all situations and people.

Social Competence: 69 The combination of your social awareness and relationship management skills. It's more about how you are with other people.

Social Awareness 67 Your ability to accurately pick up on emotions in other people and get what is really going on. This often means understanding what other people are thinking and feeling, even if you don't feel the same way.

Relationship Management 71 Your ability to use awareness of your emotions and the emotions of others to manage interactions successfully. Letting emotional awareness guide clear communication and effective handling of conflict.

Verdict: Little insight to be gained. I'll give the accompanying book a fair shake eventually.

*The course gave us a copy of this book. I've only read one page out of the middle of it so far. The page told me I should stop taking notes at meetings lest I miss out on the emotional states of others.  Still a bit split about that advice.

New toys!

The lab got one of these guys today. I'm excited to try it out and even more excited to have a piece of new lab equipment that actually works and isn't a fridge or a water bath.

Unrelated music for tonight is the following.