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.

Strong in numbers

Next up on the big list of self-assessments: the Strong Interest Inventory. I remember helping to administer these tests at the university career center during my undergraduate years. The current version of the assessment hasn't changed since then. It's a series of questions of different categories relating to occupations and the kinds of activities one might do in the context of those jobs. The test is beginning to show some rust in a few areas with respect to what kinds of jobs still exist (i.e., it asks for your feelings about the job of Word Processor).

Anyway, no results yet. Will post them when I get them.

UPDATE: Results!

The Strong inventory assigns scores in six categories: Realistic (R), Investigative (I), Artistic (A), Social (S), Enterprising (E), and Conventional (C). My highest-scoring areas were I, A, and C, though R was a very close runner-up. I took this assessment a few times during the time I was administering it and always seemed to fluctuate between IAC and IAR.

So, according to the assessment, these would be my ideal jobs, plus the categories they fulfull:
1. Librarian (A)
2. Musician (A)
3. Technical Writer (AI)
4. Translator (AI)
5. Sociologist (AI)
6. Biologist (IA)
7. Computer Systems Analyst (RCI)
8. Photographer (ARE)
9. Physicist (IRA)
10. Geographer (IA)

I'm glad that Biologist is on there. Several of these jobs seem rather dull, however: I don't think I'd like the repetition inherent to being a librarian or a technical writer. Several of these occupations would be fun to do on an amateur basis (especially music, photography, or even translation) but I don't think I'd want to do them as a job. That might just take all the fun out of it.

A POSTSCRIPT-TYPE UPDATE: Talked to someone in class today (Feb 3) who essentially scored highly in every single category of the assessment. The results suggested that she'd make a good chiropractor or maybe an urban planner, but she didn't find those occupations appropriate. She mentioned that, having taken the Strong before with similar results, career advisors had informed her that her broad range of occupational interests may become a hindrance as she would be unlikely to find one job which sustained all six categories.

I was looking for some kind of utility to search for similar but not identical images in a collection today. The most helpful result was digiKam. It's pretty standard image management software, and though the GUI has a bit of that undirected feel characteristic of many open source software projects, it has a pretty decent image similarity tool. It even allows for a fine-grained control over the threshold of similarity. Very useful and very free.

Mold is vegan for some reason

It was nice to get into the flow of things today. The lab is finally looking a bit more like normal after getting flooded last week (the building is flimsy and the equipment on the roof can't handle much Winter, but at least the maintenance folks can get things under control eventually). Some of our equipment is still a little, um, musty. Hopefully that will resolve itself lest my fume hood convert itself into a mold incubator. One of the air duct vent motors also seems to have shorted out as well so I'm sure there will be something else to complain about once the warmer months arrive.

Anyway, flow. I finally got R to make me a nice heatmap today, complete with neat annotation sidebars. If you're interested (and I know you may not be, but I am, and this kind of thing is seriously more difficult than it needs to be so I intend to remember it), the smoothest implementation is a combination of heatplus.2 and the vegan package. Vegan has all kinds of useful tools in it for clustering and such. Most importantly, it's useful for dealing with dendrograms, which are kind of essential to understanding data if they're all being hierarchically clustered. Messing around with the order of leaves in dendrograms can be time consuming; vegan has tools to get that taken care of in no time. It's pretty meaty.

I've also been enjoying listening to the tasty synths of Steve Hauschildt, as below:

A pen-and-paper evaluation, now with results!

Today's psychological evaluation is the NEO-PI-3. This is a paper-based test (that is, a set of questions and a Scantron-type sheet of bubbles to fill in) which must be interpreted by someone who knows what they're doing. The questions themselves are similar in format to other personality assessments in that there are 240 statements which may be answered with strong disagreement, disagreement, neutral, agreement, or strong agreement.

I will place some results here once they're available.

UPDATE:
These results get into more psychometric material than some of the other assessments I've posted about. If you are, say, a decade in the future and reading this, please don't use the results as any kind of criterion for insurance eligibility, promotion, security clearance, marketing, poetry and/or dirty joke, drone targeting, etc. etc. Just don't do it. I'm just as paranoid about living in a Gattaca-esque social hellscape as the next reasonably educated guy.

Someone from the Dept. of Psychology at VCU came into class and went over the scoring for this test with us. I was glad to hear that she had a very low opinion of the MBTI (it's really not scientific at all and relies on the whole extrovert/introvert dichotomy too much, but some of the other assessments I've taken have been guilt of that as well). The results of the NEO-PI take the form of five category-based scores, or Domains, with six subscores, or Facets, in each domain. The primary domains are referred to as NEOAC and correspond to the following categories:
Neuroticism
Extraversion
Openness
Agreeableness
Conscientiousness

I'm not going to describe every domain in any detail - check out that wikipedia link at the top for such things. I'll just provide my domain scores:
N: 108 (High)
E: 92 (Low)
O: 158 (Very High)
A: 139 (High)
C: 109 (Low)

So what does this tell me? That high Neuroticism  - which sounds worse than it is - mostly appears to be driven by a high degree of self-consciousness. That couples with the low Extraversion score. Yes, it's true: I'm not terribly outgoing. That being said, I really do like small groups of people. It's having to deal with large groups of people who I really should know better that tends to be stressful. The high Openness and Agreeableness scores correlate with how I like to stay open to new ideas and how I try to be a good person to everybody. Nothing terribly exciting there, really.
The low Conscientiousness score is actually the result of high variability across the facets. I'm actually quite organized and confident in my abilities but I'm not really motivated by achievements for their own sake. Some of this is a result of having low self-discipline (this shows up in the results, too) but the rest is a conscious effort to avoid carrot-and-stick situations. What is the point in pursuing achievements if you don't get anything out of the process?

My overall verdict is that this test may be too limited and general for its intended purposes as a psychometric. I'm not just saying that because it seems to think I'm hopelessly self-conscious. With 40 questions per domain and 8 questions per facet, it appears all too easy for a single score to fluctuate on the basis of a single question's response. It may just come down to the limits of categorization, especially when those categories are dependent upon self-reported characteristics.

Nobody's an outlier in the Magic Kingdom

Here's an interesting piece about data tracking through transactional data, Disney World, and how gross the term "meatspace" is.

Disney has always kind of creeped me out with their business practices. They're phenomenally good at marketing, and not even in a behemoth-tech-company, you-need-the-new-ipad kind of way. They've just mastered the concept of presenting technology in minute and frictionless ways, even when the technology isn't directly beneficial to anyone but The Mouse. They couple these technologies with brute-force strategies. The Disney Vault strategy comes to mind: I know it's not really technology per se, but it's a unique strategy that only Disney seems to have any control over.

Island of nasty cats

Also interesting, but not about me: Baker Island.

It's a tiny atoll in the South Pacific. Used as a rough airstrip by the US in WWII, it was largely abandoned after the war and is now a nature refuge. The interesting thing is that it had a feral cat population for several decades despite being almost completely devoid of fresh water or foliage. Those must have been some dangerous cats.

See also: Meyerton, a former settlement on the island.

Unnecessary! exclamation! points!

Another day, another time for a self-assessment. Today I took the VIA Me! assessment. It's much like the Clifton Strengths Finder in that it is intended to identify a set of strengths. The test itself is a series of questions with no time limit. Questions can be answered using two options each for agreement or disagreement. There is also a neutral option. Unlike the Clifton assessment, the VIA assessment places all its questions right next to each other so it's rather obvious when intentionally redundant questions arise (i.e., "I often seek vengeance" and "I seldom hold grudges").*

The assessment itself is free. The results are not, unless you just want a list of strengths. I'm not going to fork over any cash for this stuff if I can avoid it, so the list is all I got.

Here are my results:
Character Strength # 1

Creativity
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.

Character Strength # 2

Humor
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.

Character Strength # 3

Judgment
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.

Character Strength # 4

Curiosity
You are curious about everything. You are always asking questions, and you find all subjects and topics fascinating. You like exploration and discovery.

Character Strength # 5

Love
You value close relations with others, in particular those in which sharing and caring are reciprocated. The people to whom you feel most close are the same people who feel most close to you.

These results appear to correlate very well with those from the Clifton assessment. The terminology differs, but Creativity and Ideation are more or less identical while Judgment/Curiosity appear to match with Analytical/Input. These results are quite interesting in that they also include humor and love. I'd like to think that one or both of those strengths are essential to everyone to some degree, but it's interesting that the other assessments I've taken appear to completely disregard them.

Overall: Free and fairly helpful for the time it demands (roughly 10 minutes, or maybe less if you're really focused). Including humor as a strength is a critical distinction!

*I don't know if folks who design psychological assessments intend to obfuscate redundancy. The redundancy is essential to reducing error, I think, but does it impact the results if the test subject is aware of the redundancy? Do they ensure that their answers are more consistent than they would be otherwise?

It's really nice to be able to stay focused on a single task for hours. It's less nice when there are other, equally pressing tasks to pursue. I need to find a way to balance my preference to work on a single thing with my tendency to grab bits n' pieces of information from as many sources as I can find. The usual result is that, upon taking a break from whatever I've been focusing on, I tend to go looking for other information about the task (i.e. I go googling for new methods) rather than shifting focus to something else entirely. It feels inflexible.

Back when I was in a different lab and a different building, I'd try to solve this problem by climbing stairs. My building had more than ten floors so this was some fairly decent exercise. Perhaps a short walk would serve the same purpose.

On an unrelated note: Walruses.

The photo is courtesy of the US Fish and Wildlife Service.

Wikitionary suggests the plural form may be "walrus".

Shades of grey

(Or maybe shades of gray, depending on where you are in space and what you're wearing.)

Stephen Hawking has proposed that black holes may not be what we think they are. That is, they aren't black. Or maybe not holes. Either way, Hawking has long had an issue with what happens to information and energy when it enters a black hole. It's a thorny issue which the above article handles much more aptly than anything I could discuss, so here are some summary quotes:

In place of the event horizon, Hawking invokes an “apparent horizon”, a surface along which light rays attempting to rush away from the black hole’s core will be suspended. In general relativity, for an unchanging black hole, these two horizons are identical, because light trying to escape from inside a black hole can reach only as far as the event horizon and will be held there, as though stuck on a treadmill. However, the two horizons can, in principle, be distinguished. If more matter gets swallowed by the black hole, its event horizon will swell and grow larger than the apparent horizon.
Conversely, in the 1970s, Hawking also showed that black holes can slowly shrink, spewing out 'Hawking radiation'. In that case, the event horizon would, in theory, become smaller than the apparent horizon. Hawking’s new suggestion is that the apparent horizon is the real boundary. “The absence of event horizons means that there are no black holes — in the sense of regimes from which light can't escape to infinity,” Hawking writes.

This doesn't make black holes - or whatever the best term for them is - nicer places to visit. Even if energy/information entering them isn't destroyed, it's still dispersed and disrupted. Hawking ends his brief paper on the subject with

One can’t predict the weather more than a few days in advance.

Most of my day so far has been spent fighting with R. R can be very powerful when it comes to data visualization and plotting but it can also be a furious beast when it comes to parsing data. Many of its modules were written with very specific intentions and aren't quite clear about how they work under the hood.

I'm trying to make something like this, but prettier. Who doesn't like pretty colors?

Not the bees!

Been reading the following paper this evening: Li et al. (2014). Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera. mBio, 5(1), e00898–13–e00898–13. doi:10.1128/mBio.00898-13

Long story short: there's a plant virus which bees can contract by consuming it. This may not be the healthiest thing for the bees as the virus shows up all over their tiny bee bodies. The bees also have to deal with parasitic mites which may be unaffected carriers of the virus. The spread of this virus may contribute to colony collapse disorder, though it's likely not the only factor.

Update (Feb 18, 2014): Listened to an episode of This Week in Virology in which this paper was discussed. They were critical of it for a number of fully justified reasons, most notably that the authors don't show that the plant virus actually infects bees, just that some of the viral RNA can be found in bees and these bees may be less healthy as a result. The link to colony collapse disorder is the conclusion I found hardest to swallow. The TWiV guys suggested that the plant virus (if it is, in fact, even capable of infecting bees) may be one of many opportunistic infections of already weakened bees. This is true for many viral and bacterial infections of immunocompromised animals; without a sturdy immune system's protection, all kinds of otherwise benign life can become pathogens.

Is that a leopard?

I'm glad to live in a place where I can walk to most of my destinations. This benefit becomes readily apparent whenever I look at real estate listings. There are so many homes out there which are either landlocked by suburban sprawl or are smack dab in the middle of Bumpass, metaphorically. I'm in a preferable situation as I can get to a grocery store or restaurant in minutes without even burning any oil. It's really just about the groceries, really.

Speaking of real estate listings, check this one out. I will not comment on the decor beyond the single descriptor "questionable".

You're a Libra, aren't ya darlin?

Time for another personal assessment! This one is the Clifton Strengths Finder, provided by Gallup. I got a code through the class I am participating in so I suspect this test requires a monetary cost. Let's see if that extra bit of investment leads to any valuable insights.

The assessment asks a series of timed questions with paired answers. One of the two answers in each pair can be answered with "Strongly Agree" or "Agree". There's also the option to answer neutrally. Because each question is timed and only allows about 20 seconds to answer, the assessment appears to encourage answering based on initial impressions. I found this to be challenging as many of the questions aren't clear-cut dichotomies: one option may read "I think all people would steal if they had the chance" while the other option reads "People who steal should be punished." In some instances, the options diverge more in tone (i.e., one option sounds optimistic while another sounds pessimistic, or one concerns the past while the other discusses the future) than in content or conclusion. I really couldn't agree with either of the options for some question pairs and had to seek refuge in the Neutral Zone.

As per the name, the results of the Strengths Finder are a list of strengths. These are mine:
1    Analytical
2    Learner
3    Ideation
4    Input
5    Self-Assurance

There's also an expanded list for a total of 34 strength categories. Each category has accompanying explanatory material.
It's interesting to see how all the test results are framed as strengths rather than strength/weakness dichotomies like the Igniter tests I took. While I appreciate the positivist attitude and reduced reliance on binary choices, the resulting lack of resolution in the results diminishes the "yes that certainly sounds like me" factor. In the end, that may be a preferable result as it encourages self-discovery rather than reliance on pre-conceived identity.  

So what can I learn or apply from these results? I can't deny being an analytical person and I do actively enjoy learning. The Ideation category is a little more general but the corresponding material describes people with strong Ideation as  being "...fascinated by new ideas and concepts, which come to them easily." OK, that sounds accurate as well. Input and Self-Assurance roughly translate as "thirst for knowledge" and "confidence in one's judgement". Once again, doesn't seem inaccurate.

Interestingly, my lowest-scoring strength was Harmony, which the material frames as "natural practicality and preference for emotional balance". I find most conflict unproductive and generally avoid it, so I'm surprised this one is at the bottom of the list. The text explains: "building consensus and ensuring people get along are not likely your top priorities".

A few bon-mot suggestions from the results material:

• "Accept that at times you will need to move before all the facts are in place."
• "Be a catalyst for change. Others might be intimidated by new rules, new skills, or new circumstances. Your willingness to soak up this “newness” can calm their fears and spur them to engage. Take this responsibility seriously." 
• "You get bored quickly, so make small changes in your work or home life. Experiment. Play mental games with yourself. All of these will help keep you stimulated."
• "Deliberately increase your vocabulary. Intentionally collect new words and learn their meanings."
• "Seek start-up situations for which no rule book exists. You will be at your best when you are asked to make many decisions."

Overall: not a bad assessment and potentially even useful. It does feel like reading a horoscope but that may just come with the territory.

Analyze This (1999)

The personal development course I am in recently discussed an online set of personality tests by a group called Values Based Leader. Personality tests of any stripe really start ringing my skepticism alarms, especially having worked with the MBTI assessment in the past and finding it misleading. The tests I took are here. Results are below; comments follow.

First is a personality test of 22 questions over 4 minutes, rated on a 4-point scale from Strongly Disagree to Strongly Agree.

I started becoming skeptical about this one as soon as it started asking questions about small talk (that is, in the first question). The whole introvert vs. extrovert dichotomy has always felt like such an artificial construct. People already tend to identify as one or the other based on what they tend to do or what they try to avoid. Is it really helpful to define people with such binary categories, or are we doing them a disservice by bundling so many potentially unrelated tendencies together?

Anyway, these are my results. Very little is terribly surprising and it corresponds well with my MBTI results: I'm usually an INTP or INTJ. The bottom line here is what these results tell me and how well they correlate with existing observations. Clearly I can't take anything here at face value. It's true that I tend to be a logical, critical thinker who needs time to contemplate ideas and prefers efficiency. It's difficult to evaluate any of those blindspots, though, without input from living human beings. A personality test isn't and can't be emotional or empathetic, so how can it declare anyone unemotional? (For the record, the "fear of being wrong" is pretty spot-on, but who actually likes being wrong?)


The next bit is an exercise in which words representing Core Values must be dragged n' dropped into bins from Most to Least important. Only the Most Important values appear to be saved. Here are mine:

I had the most trouble deciding which values were least important or unimportant to me. Is Competition really not important? What about Results, whatever that means? Everything is important to me in the right context. Sometimes Results are what I want more than anything else, but I certainly won't get them without the Top Values listed above. Once again, not quite enlightening but I suppose that isn't the point. This stem seems designed to help with isolating values which you'd be willing to make sacrifices for, should it be necessary. 

Is there a way to discuss self-improvement and self-awareness without the breathless enthusiasm of a grade-school art teacher? Enthusiasm is refreshing but it should never oversimplify complex systems. That's how people crash economies. It's also how conspiracy theories become common knowledge. 

The biggest heart

I'm grateful that my parents took me to so many museums when I was growing up. We'd go to the Franklin Institute maybe once or twice a year until I was a bit too old to really get anything out of it. Even traveling into Philly for the day was exciting: it was like the infinite highway would suddenly drop us into a noisy, smoky City. I live in a fairly dense metropolitan area now but I still don't consider it a capital-C City. Then on to the FI, and the following attractions:

• The giant heart, of course. 
• A Rube Goldberg-esque mechanical sculpture which moved some kind of wooden balls around ad infinitum.
• Video demonstrations about antibodies.
• The Omnimax, which I guess is called IMAX Dome now

I'm really not doing these memories justice. There's a particular childlike joy only found in memories of science museums. I remember visiting the FI again sometime in the early undergraduate years and finding it underwhelming. I was older, certainly, but the exhibits also seemed to gloss over most scientific explanations for phenomena in favor of snappy little demonstrations without much rationale behind them. It was less of "this is why things happen like they do" and more of "hey look at this happening! That's because of Science!" Plus, a good quarter of the exhibits were broken or damaged from use.

I'd still take kids to museums now. There must be ways to cultivate wonder and the search for meaning concurrently.  

Home taping is killing home taping

This is a post-audio-scarcity world and I am grateful for it.

It's not too difficult to remember a time when music had to be purchased and lectures only happened once. Recording was trivial to begin but laborious to maintain. Don't forget to turn those tapes over so you can use the other side, as space is precious! The same was true of buying music: with the right resources, you could certainly have bought every album in existence, but who wants to deal with all those discrete physical objects sitting around?

So now the audio is everywhere. Yes, internet connectivity is a limiting factor. Yes, the DRM can be both obtrusive and intrusive. I don't care anymore. I can download all the podcasts* I could ever want without having to walk through the door of some specialty store. I can turn the music on and never hear the same track more than once. The biggest limiting factor is now time. That, and a willingness to be advertised to.


*Isn't there a better term for these yet? The whole pod- prefix should have gone the way of cyber-, though I suppose that my-**, e-, and i- are enjoying pleasant undead lives in the vernacular.  

**Would you believe that mySimon is still online?

3 reasons this pile of kittens will make you believe in ghosts

It's helpful to be aware of the day's minor irritants. We're at least partially aware of them when they occur, so why not anticipate them appearing again the next day? For me, three of these irritants are as follows.

1. Online news and literature. It's not just the overwhelming nature of having to realize how I will never and should never read every bit of content I could be interested in. It's not even just because I will never have access to every piece of potentially amusing or interesting information. (Feedly handles much of that issue for me, while the more academic material is deftly provided by Mendeley, Google Scholar, and PubMed). The stressful part is the signal to noise ratio. There is just so much noise inherent to any one content source that it's a strain to determine if there's any signal at all. Much of the noise is certainly content I'm not interested in at all, but increasingly there's also rehashed blandness masquerading as content, whether it's linkbait headlines or poorly-written journal abstracts. I find all this irritating because I really don't like having to multitask, but I also don't want to get stuck in an information bubble. There has to be a balance between being open-minded and focused.
2. Stacks. They're acceptable for data typing but not for physical objects. If I look around my house or lab and see a pile of anything, I find it incrementally more difficult to focus on anything else. I can't remember where I read it, but someone with a similar problem explained the issue as less of a direct response to the current disorganization and more of a response to the memory of a recent period in life when order had to become a lesser priority. That's a fairly satisfying explanation as I don't tend to find it stressful to deal with others' clutter unless I could have had a chance to prevent it from becoming that way.
3. A lack of integration with my department. The whole "introvert vs. extrovert" dichotomy is an oversimplification. I don't feel uncomfortable being around people at all. Being in grad school actually makes me feel very outgoing on occasions when my colleagues are playing the "let's see how many times I can check my email during this meeting" game. Even so, I pass people in the hallways all the time who I really should get to know better, if only because they're my neighbors and I may need their help (and vice-versa, of course). That's the issue, though: I'm quite poor at building and maintaining relationships. Or, maybe I'm about as unskilled in it as everyone else is. There's a great potential for confirmation bias as I compare all the people I should communicate with more often with those who I even see regularly. It might just come down to networking, but that term has always evoked the image of a Dark-Suited Business-Person yelling into an early Motorola cell about a need to "touch base" or some other baseball metaphor.

What I'm saying is that I wish I was distracted by other people as much as I was distracted by content and clutter. People are much more useful and interesting. 

I will have more mail tomorrow.

Ah, the sublime lightness of Inbox Zero. A task as trivial as sorting electronic mail really shouldn't feel so satisfying to complete. Perhaps it's simply symbolic of a romanticized Luddite-like existence, just like how people love zombie movies because the undead don't care if you follow them on Twitter.  Or, perhaps it's more like the inverse of First World Problems; we have these First World Joys because we can't imagine being elated by anything other than every detail coming together at the right time.

following on

My favorite word today is "tractable", meaning obedient, flexible, pliable, easily molded, or in some cases, just useful or optimal. Here's an example from a recent Nature piece about science during WWII:

Elegant derivations from first principles — which often proved tractable only when applied to idealized situations — were of little value to the many colleagues who needed to fine-tune electronics components for maximum efficiency.

 It translates to German as "folgsam". A related adjective is "folgend" which is an adjective meaning "following" or "according to" as in "according to plan" (or, in German, "dem Plan folgend").

I also mention here the the German word "Entwickler", or "developer" in English. I only mention it because it's fun to say.

lifting a fat broth

Was reading Carl Sandburg's Smoke and Steel again this morning. "Soup" will be my favorite forever, but the following is a close second.

Hats
Hats, where do you belong?
 what is under you?

On the rim of a skyscraper’s forehead
I looked down and saw: hats: fifty thousand hats:
Swarming with a noise of bees and sheep, cattle and waterfalls,
Stopping with a silence of sea grass, a silence of prairie corn.
 Hats: tell me your high hopes.

People don't really wear hats quite so much anymore. This is fine as we have plenty of other accessories to worry about. Feel free to replace "hats" with "phones" if you must.

A bloody resistor

This Intel announcement is interesting - in short, they're trying to phase out use of raw materials (in this case, rare metals like tantalum) sourced from conflict regions in Africa. This is certainly one of the human rights bottlenecks for the information age. It's really difficult to enjoy cheap, bleeding-edge consumer technology without getting a child, a soldier, or a child soldier involved at some stage of the process.

I'm generally skeptical of corporate announcements but I genuinely hope this Intel thing isn't just the human rights equivalent of greenwashing.  It would be insulting to see the consumer electronics market fragmented into "cheap n' bloody" vs. "conflict-free" products like what happened with diamonds. The problem with diamonds is that they're still valuable no matter who is buying or selling them. Perhaps the inherent brief period between release and obsolescence can enable consumer electronics to avoid that issue, at least.

Alma Mater

How many altars does this school have?

On the continuing subject of Old School Papers, that's my high school anthem up there. As far as I am concerned, a school's Fight Song, Alma Mater, anthem, official cheer, et al. are really all the same set of Mad Libs. The Downingtown High School Alumni Association claims to be the "Oldest Continuously Meeting Public High School Alumni Association" in the US, so this song may originate with them and their older times. 

I don't really have any special attachment to this high school in particular. It's not a bad institution by any means and is scholastically superior to many in the surrounding area (a claim I'm not going to bother proving). Most of my fond memories are just about the people and events during high school rather than as part of the good ol' laudable High School Noble Deeds Experience. I am occasionally curious about what it would be like to own a pair of rose-tinted specs. Perhaps they would allow me to use the word "specs" un-ironically. 

Disclaimer: I'm taking a personal development course

Some comments on an IEP from the 3rd grade.

The internet is a strange place in that I've grown so used to it actively promoting anonymity even when recent trends on social networks and the like champion having a public face for the meatspace self. It's nice to be able to present content devoid of personal context or at least pretend that my online self is somehow independent of the remainder of my personality. That may just be escapism.

What I really want to talk about is the 3rd grade.

I'm not in elementary school anymore so my 3rd grade identity sits in the same shadow as all other personal histories, fictional or otherwise. That's my Individualized Educational Program up there. It says I was on or above grade level but I can't take that too personally: a latent sense of over-achievement tells me that it really should say "...may be far above grade level as our current metrics are unprepared for his intellectual might" while the pragmatic cynicism pipes suggests, "that's just a boilerplate response and you should focus on the details". This is the usual sensation I get when reading over old school materials. I wasn't really an overachiever in school at all but looking back causes me to feel like I really should have tried harder. That would have been difficult, of course, as I'm still not really sure what the behavior of trying hard looks like.

I still pride myself in my ability to pick apart the complexity inherent to cause and effect. How about all those other traits? Maybe a checklist would help:

• Generates many ideas/solutions to problems: Maybe too many?
• Able to apply critical thinking skills appropriately: Not entirely sure what this means. When is critical thinking inappropriate?
• Seems to have a flair for the dramatics: Yeah, that one shows up on every IEP after 2nd grade or so. Yeah, it's still true. No, I can't tell if that's a backhanded compliment.
• Needs a stimulating environment: Still true. I can't really tolerate the idea of thinking about the same few issues every day. Pure office jobs are rather hellish.
• Needs to work on strengthening group skills: This has improved substantially! I can't believe that any school kid is actually skilled at working in a group. Doing theatre in college probably helped more than any class project ever did, even in high school.
• Frustration, failure to understand, etc.: This may still be the case, but my daily routine is now so overstuffed with things I don't understand that I have to take a more Zen-like, let-the-river-flow-around-me type of approach.

Overall: Not the same person I was in the 3rd grade. It's for the best.

éventer

I'd like to think I was an introspective child. I certainly tend to be introspective now, so that hasn't changed too much. What has changed is the subject of the introspection and the potential role.

As a child, I didn't have to concern myself with why I was concerned about the future. It's just a natural element of being young. Kids don't have the background knowledge necessary to make rational predictions about the directions they're heading, so they're left with nothing but imagination. A bit of creative thought tends to push introspection toward the fantastical, of course, so it's difficult to even begin to consider such mundane concepts as "where will I be living a decade from now". None of those thought processes really mattered, though! They didn't need to resolve any issues and were really just fun.

That's potentially the greatest loss inflicted by adulthood: the inability to think without purpose or intent. Maturity brings so many issues to face each day that any choice which doesn't work to solve such issues resembles avoidance. I genuinely miss the opportunities to be purely creative. Sure, it's easier to realize your influences as youthful naïveté erodes, but at least a portion of that childish imagination is the sincere willingness to disregard intent, at least briefly. I can never get that back.

Here in my car, I am safest of all

I don't really like being in cars. Having the freedom to drive virtually anywhere is always nice, as is the convenience of having a full HVAC system and an array of entertainment options at arm's reach. The problem is all the liability: one misplaced curb and/or young child is all it takes for the mobile pleasure palace to become a bringer o' death and chaos. Aside from a few fender-benders, I haven't really had to worry about much of that. It's also not a new subject for any driver. We know these machines are dangerous.

What's been more bothersome lately is how the steady march of feature creep impacts driving. GM and AT&T recently announced a small partnership. Chevrolets will get wireless data connectivity, while AT&T gets sweet, delicious money. It's a natural step as most new cars now have some kind of connection to a data source, whether it's to a phone or a satellite. The difference here would be the lack of carrier choice (because everyone loves those folks, right?) and, er, the fact that streaming content is a great way to eat up even the most generous data plan in very little time. The issue here isn't what should or shouldn't be a feature in cars, but rather why wireless providers are still such a tight bottleneck for delivering wireless data. Is this another problem with a Google-based solution, or is that a more dangerous path to wander down?

A related note about corpses.

Today I learned about the story of Elmer McCurdy:

In December 1976, during filming at Queens Park (A.K.A. The Pike), of the television show The Six Million Dollar Man episode "Carnival of Spies" (#4.17) (1977), a crew member was moving what was thought to be a wax mannequin that was hanging from a gallows. When the mannequin's arm (some accounts say finger) broke off, it was discovered that it was in fact embalmed and mummified human remains. Later, when medical examiner Thomas Noguchi opened the mummy's mouth for other clues, he was surprised to find a 1924 penny and a ticket from Sonney Amusement's Museum of Crime in Los Angeles.

Long story short: the guy got shot in 1911, got mummified, got turned into a sideshow attraction, and somehow became a prop on a California boardwalk.

"the corpse progresses through several forensically recognized stages of decomposition, including Fresh (before decomposition begins), Active Decay, which includes Bloating and Rupture, and Advanced Decay"

Creepy-spooky microbiology fact: Grave soil differs in biochemical composition from other soils. It's probably due to the action of microbial communities. Along the same rapidly-decomposing lines, forensic investigators may be able to use microbes to estimate a corpse's time of death in much the same way they may use insects.

Salt of the earth

The word of the day is 'saltern'. That's a place where salt is made. We've been doing that (making salt, that is) since prehistoric times, but what's even more interesting about salterns is how rich they are in salt-loving microorganisms. One such group is the Ectothiorhodospiraceae, or purple sulfur bacteria. They just love salt. That, and sulfur. 

There's no conclusion here. I just really enjoy microorganisms with exotic lifestyles.

Check it off

As part of my quest to find ever duller subjects to blog about, I will now briefly discuss web-based task managers. These are bits of software (let's avoid that badly-abused term 'app', shall we?) designed to replace all the usefulness of a pen and pad of paper, at least when they're used for keeping track of lists. Electronic solutions offer benefits like sorting, accessibility, and categorization, all of which can be performed on paper with the right combination of tabs and color-coding. Even so, no notebook matches the Internet's ability to make the same bits of information available everywhere, all the time. The end goal is to decrease the amount of friction between conceptualizing a task and actually completing it.

So here's a bit of pro and con:

• Pen and paper. It's easy, requires no power or data connection and looks great in a Lisa Frank Trapper Keeper.* It also cannot exist in more than one place at once. That may be a feature rather than a bug if security is a concern.
• A text file. The digital equivalent of pen n' paper, this option is cheap and flexible. It does require access to wherever the file happens to be, though placing it in a Dropbox solves that issue handily. Even so, mobile devices find editing text files challenging. I'm not sure why. Text editors also aren't ideal environments for sorting tasks though they are great for searching, especially when regular expressions are involved.
• Remember The Milk.  I used this for a while last year after migrating from the maddeningly minimal Google Tasks. It's free-ish, plays well with Google Apps of various sorts, and parses natural language very smoothly (i.e., you can enter a task as "eat ham on Wednesday" and it will understand when the task should happen). The -ish is an issue as the web interface is free but the mobile version won't sync tasks more than once a day without a $25/year pro account. The interface used to be genuinely ugly on all platforms but appears to have improved recently. It has plenty of features and active support. That added cost is really the only downside but it's a notable one.
• Astrid. This isn't even a real option any longer as the Astrid team got bought out (read: consumed and digested) by Yahoo** a few months back. It's sad. Astrid ran smoothly on all kinds of platforms, looked great, and allowed for shared lists. Now it's all gone.
• Wunderlist. This option may, in fact, be on its second iteration (Wunderlist2) and is primarily a mobile application. At least, I had daily problems with its interface: tasks would disapper, buttons would become invisible, and most recently I couldn't even log in to my account. The entire project has a Web 2.5 sheen which is attractive until the point at which it works slowly. Even worse, there is no option to export tasks to anything other than a bloated, difficult-to-import-with-other-software JSON file. I used Wunderlist for about six months and just couldn't tolerate all the bugs.
• Toodledo. Just started using this one. It's rich in features but I'll have to use it a while to see if they're useful. The desktop web interface has some really basic usability issues, but hey, it's all free.

Next week, I plan to discuss the care and handling of airborne sawdust. Stay tuned, kids!

*I was blissfully immune from the Trapper Keeper trend when it was endemic. Have students ever been so excited about personal organization since that time?

**Or, more officially, YAHOO!

Yes, that is correct, more dumb Excel tricks

For personal future reference and otherwise: how to hide text in Excel but retain the formatting. Just change the Format to ;;;. That's all it takes.

See also: this blog post.

Learning to love mothballs

Today, I learned about the existence of a bacterial species named Polaromonas naphthalenivorans. This lil' guy* fits into the mysterious, often baffling category of extremophile bacteria - that is, species capable of living in environments we normally wouldn't consider habitable. Originally isolated from a coal-tar-contaminated aquifer somewhere in the northeastern US,** P. naphthalenivorans can grow using naphthalene as its only carbon source. It's not terribly surprising, as naphthalene is a major component of coal tar (and was originally isolated from coal tar, in fact), so this species is just working with what it has. It's still rather odd as naphthalene is toxic and a suspected carcinogen. Those kind of rules don't always apply to bacteria.

Dividing P. naphthalenivorans cells. Micrograph is from the Joint Genome Institute (JGI). See this page for more details.

Most people are familiar with naphthalene as a component of mothballs. This paper suggests that a whole metabolic community could subsist on naphthalene, or at least could adapt to its presence. Evolution is great that way!

*Literary anthropomorphism is a constant danger when discussing animals and especially when discussing microbes since it's difficult to understand why they do what they do. I will rarely, however, avoid an opportunity to make bacteria seem cute. They're already tiny, and tiny things are cute, right?

**A paper describing the aquifer describes it using little more detail than "A single truckload of coal tar was buried in a forested area in the northeastern United States." This MicrobeWiki page says it's in South Glens Falls, New York. There's a lab at Cornell that likes to work there. As far as they know, the local drinking water isn't contaminated with coal tar or anything like that.

Goofy Excel tricks episode #1048577

Just a quick trick I learned today about how to make Excel search a series of values and return one or more corresponding adjacent values for each. I'd normally use VLOOKUP for such a thing but the function only returns the first match it finds. How about situations when I have more than one match, like this one:
A   elephant
B   truck
C   large rock
D   pudding
B   gopher

in which I want to know which values are adjacent to value 'B'?

Googling a bit provided this convenient and non-obvious answer. The general function is:
=INDEX([the values you want to return], SMALL(INDEX(([the search value]=[the values being searched])*(MATCH(ROW([the values being searched]), ROW([the values being searched])))+([the search value]<>[the values being searched])*1048577, 0, 0), COLUMN(A1)))


The function will return one matched value at a time, so to get the other matched values to appear in the same row just copy it over to the adjacent cells in the row. It will return #REF! if the search value isn't found.


Don't forget to make references static as needed, i.e. $A$4:$A$979. The 1048577 is to convert the function from an array function into a normal one, I think. Not really sure what that COLUMN(A1) part is doing. Maybe it's just to establish where the upper-leftmost cell is.


This post is mostly for my own edification but I hope it was helpful. To me. Most people don't use Excel arrays for things that are better suited to a bit of SQL, right?

For future reference: to remove bromophenol blue stains from clothing, soak with ethanol, dry with paper towel, then spray with Windex or something similar and dry again. It's not just the isopropanol in the Windex - I think the surfactants help, too.

For future reference: the Excel escape character is not a slash. It is a tilde, i.e. searching for ? performs a wildcard search but ~? will return question marks.

No big deal. Just some big viruses.

Searching PubMed for the keyword "giant virus" always provides some fun results. That's not what I did today - though I do recommend trying it sometime - as the recent reports about oversized viruses have been spreading like some kind of very small causative agent of infectious disease.

Here's the first one: the isolation of a Mimivirus from a patient with pneumonia. The particular viral isolate is more than 550 nanometers wide and has a 1.23 megabase genome. For reference, that's huge. For a better reference, that's about the width of an average E. coli cell and a genome in the same size range as many of the more genetically streamlined bacteria (it's more than twice as large as the tiny Mycoplasma genitalium genome, though that's about as minimal as known bacterial genomes get). Most viruses we know of aren't quite this massive, though Mimiviruses and other record-holders for viral size share the characteristic of infecting Acanthamoeba polyphaga amoebae. So if this new mimivirus infects amoebae, is it pathogenic to humans as well? The authors of this paper seem to think so. As always, further viral isolates will be necessary. (The actual paper is right on the other side of this concrete paywall.) 

If you thought that mimivirus was big and/or had a silly name, check out the Pandoraviruses. These viral isolates average more than 700 nanometers in diameter and bear genomes of, in at least one case, more than 2 megabases. They were found in sediments and mud where amoebae are plentiful. There are some hyperbolic news reports out there about these new viruses already so I'll just pick some interesting bits out of the paper itself:

Unlike eukaryotic DNA viruses and phages, which first synthesize and then fill their capsids, the tegument and internal compartment of the Pandoravirus particles are synthesized simultaneously, in a manner suggestive of knitting, until the particles are fully formed and closed.

Knitting viruses. Don't tell Pinterest. Not yet.

The high percentage (93%) of CDSs without recognizable homolog (ORFans), the alien morphological features displayed by P. salinus, and its atypical replication process raised the concern that the translation of its genes into proteins might not obey the standard genetic code, hence obscuring potential sequence similarities.

The authors are trying to say that these viruses are almost suspiciously strange. It's not uncommon to see large chunks of viral genome sequences that don't look like any known sequence, but when you're talking about genomes larger than many bacterial ones then this becomes a sizable reservoir of new, uncharacterized genes and proteins. They may be more familiar than we can initially tell.

...their DNA polymerase does cluster with those of other giant DNA viruses, suggesting the controversial existence of a fourth domain of life ... The absence of Pandoravirus-like sequences from the rapidly growing environmental metagenomic databases suggests either that they are rare or that their ecological niche has never been prospected. However, the screening of the literature on Acanthamoeba parasites does reveal that Pandoravirus-like particles had been observed 13 years ago ... although not interpreted as viruses. 

So these viruses aren't totally alien. They've been around for at least 13 years! Probably even longer,* though exactly how much longer may determine how controversial that claim about the "fourth domain of life" becomes.

Citations follow.

Saadi, H., Pagnier, I., Colson, P., Cherif, J. K., Beji, M., Boughalmi, M., … Raoult, D. (2013). First Isolation of Mimivirus in a Patient With Pneumonia. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. doi:10.1093/cid/cit354.

Philippe, N., Legendre, M., Doutre, G., Coute, Y., Poirot, O., Lescot, M., … Abergel, C. (2013). Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes. Science, 341(6143), 281–286. doi:10.1126/science.1239181.

* Some varieties of amoebae may have been around as long ago as the Neoproterozoic Era, or between 1,000 and 541 million years ago. If there were amoebae then viruses with amoebic hosts may have also been present.

New job, same as the old job

I'm finding this report on the growth of temporary work in the US quite interesting. It's at least partially because I've worked temp jobs before, even immediately after finishing the undergraduate stages of my ongoing academic career. The unnerving thing about each job wasn't the uncertainty, the mediocre pay or the lack of decent benefits. Rather, it was the sense that you could serve as a critical element of a larger whole yet retain absolutely no role in your long-term fate with the company. Anyway, here are some bits from the report I found especially damning:

Every year, a tenth of all U.S. workers finds a job at a staffing agency.

That's both temporary and contract workers. The American Staffing Association states that staffing agencies employ more than 2.9 million people in the US every day. That time factor is the critical element here -- these may not be the same 2.9 million employees from one day to the next.

“We’re seeing just more and more industries using business models that attempt to change the employment relationship or obscure the employment relationship,” said Mary Beth Maxwell, a top official in the Labor Department’s Wage and Hour Division. 

Obscuring the employment relationship doesn't initially seem like an ideal goal but it certainly looks like an effective way to turn formerly long-term employment into a more commitment-free model.

“I think our industry has been good for North America, as far as keeping people working,” said Randall Hatcher, president of MAU Workforce Solutions, which supplies temps to BMW. “I get laid off by Employer A and go over here to Employer B, and maybe they have a job for me. People get a lot of different experiences. An employee can work at four to five different companies and then maybe decide this is what I want to do.”

This kind of attitude reminds me of the whole "self-deportation" idea. Nothing with that much uncertainty can be a solid long-term solution. There will always be enough work for everyone but not at the same time. Traditionally, this problem was alleviated by unions, though clearly they come with their own issues. Aren't they worth a try for temp workers?

A 2004 order by the National Labor Relations Board barred temp workers from joining with permanent workers for collective bargaining unless both the temp agency and the host company agree to the arrangement.

Oops, maybe not.

Only 8 percent get health insurance from their employers, compared with 56 percent of permanent workers. What employers don’t provide, workers get from the social safety net, i.e., taxpayers.

And don’t look for Obamacare to fix it. Under the law, employers must provide health coverage only to employees who average 30 hours a week or more. After pressure from the temp industry and others, the IRS ruled that companies have up to a year to determine if workers qualify. 

Health care, or the lack thereof, may be the most worrisome element of the growth of temp work. If most of the temp job growth is in industrial jobs, more people will continue to be at risk of experiencing injuries they will never be able to afford. Many of them may not even work for a single employer more than a year, or when they do, they still won't be able to afford the plans the employers offer (in my experience, the plan wasn't exactly cost-competitive).

This whole problem is genuinely worrisome from numerous perspectives. It's yet another economic maelstrom waiting to happen, with the added stench of Industrial Age exploitation swirling throughout.

Time to BRCA the habit

The US Supreme Court has ruled that human genes cannot be patented. That's great news until we stop to consider what a human gene includes. The ruling bars patents on original human DNA, presumably in any variation of its sequence. That is, I couldn't file a patent for the sequence of my favorite human gene or of any of its alleles. The ruling does specifically permit any implementation or subsequent product made using that sequence, up to and including synthesis of cDNA. By means of awkward simile, that's like prohibiting patents on maple trees (or, at least, the concept and structure of a maple tree) but permitting patents on maples grown in a tree farm. There's still plenty of room for perfectly legitimate patents to be granted and for new products to be protected. I'm just concerned that this ruling stops well short of actually resolving the issue of what kinds of biological material can or can't be patented.

We've reached the point at which the whole "natural" vs. "artificial" dichotomy just doesn't pass muster anymore. Advancements in synthetic biology promise to blur a line that wasn't especially crisp to begin with, especially when discussing raw DNA sequences. The SCOTUS ruling states "cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments...creation of a cDNA sequence from mRNA results in an exons-only molecule that is not naturally occurring." The issue here really shouldn't be whether cDNA of a patented sequence could be found in a human (that is, without influence by outside factors like viruses), but rather that the cDNA still bears exactly the same protein-coding message as the RNA transcript does, just in an edited format.

We can, of course, get more philosophical about the issue and debate what constitutes a "human" gene. At least eight percent of the sequenced human genome is made up of retroviral sequences. Some of them even code for things in active use. There have also been suspected instances of bacterial sequences jumping into the genome of their human host. I suppose each of these issues will create their own legal issues when the time comes, i.e. the next time a biomedical company gets overzealous about their intellectual property. In the meantime, this new ruling will have to suffice.

Update: I like the 2010 district court ruling. It went farther than today's SCOTUS ruling.

"We shot lightning"

Hello! Here is a neat timelapse of a particularly large and impressive storm. Not anywhere near me, and not my video, but quite striking nonetheless. That's it for now!

Golden eggs

I just got back from visiting my lovely lady counterpart in Germany. In lieu of describing the whole trip, here is a photo of a gold-plated silver chicken.

Click here and see if you can find this guy. Hint: he's smaller than the average rooster.

Many, many more photos, presented with no context at all, are present here.  Nope, that link is no longer operational. Photos available upon request.

Do you have a second?

Every 15 minutes, someone averages a sum of events over an arbitrary period of time. No, I don't have a citation for that. It's standard practice to assume that frequencies are infrequently constant yet are much easier to understand if we can apply some kind of linear assumptions to them. That's perfectly fine, especially when we don't really know when the event in question is more or less likely to happen. This approach is used in science and medical journalism with the intent of breaking down impossibly huge numbers (i.e., 50 thousand deaths due to Ocelot Fever) into something more human-readable.

The problem arises when the level of granularity imposed by averaging over time obfuscates the reasons why the events happen at all. If MADD tells us that "In 2011, 9,878 people died in drunk driving crashes - one every 53 minutes", what do we really learn? That single number, (9,878 deaths / 53 minutes) is so specific that it disregards critical time-related factors like the weekend.*

I was planning to do an XKCD-inspired bit of Googling** and search for results of a few arbitrary frequencies to find out what happens at those times, every time. The results are too ghastly to share as most of the assumed events involve death, dismemberment, or assault. So, for the sake of diversity, I'll pull a few numbers from everysecond.info instead:

• Every second, Johnny Depp makes $2.92. The guy makes $92 million a year. Economists do use hourly pay or yearly salary to estimate how much an individual's time is worth, such that any period of time is "worth" however much they would have earned had they spent it working for pay. This can lead to some rather ludicrous estimates when inappropriately applied. We know Johnny Depp isn't actually working continuously despite his numerous sources of income. Even so, a number like $2.92/sec doesn't really provide us with any context to Mr. Depp's economic situation.
• Every second, 194 videos are watched on Myspace. What a perfect example! The statistic is from 2009. Some big changes have happened since then. Even so, it's fun to imagine Myspace users draining what's left of their attenuated attention spans on single-second videos. Hundreds of them every second!
• Every second, cows emit 250 kgs of methane in the United States. It's already difficult to imagine what a single kilogram of methane looks like,*** much less how what happens to it when the next second's round of methane arrives. Even so, cows don't continuously emit methane and they may emit more or less of it depending on what they're eating. Those factors can't even be considered when we break things down into seconds or even hours. If I observe a cow swish its tail three hundred times in an hour, perhaps I can safely claim 5 tail swishes per minute. Expanding the observation to a thousand cows over the course of months or years would render per-minute or per-second estimates useless without a greater knowledge of the relationship between cow tails and time.

All I'm saying is that averaging massive numbers over time is misleading at best and dangerously myopic at worst. These are situations best handled by probabilities, not solid quantities and linear relationships. Averaging such an immense quantity over such a small period of time distorts our understanding of both quantities.


*This paper's thesis in brief: young people like to drink for fun on the weekends. To be fair, the study subjects were Swiss rather than the usual Americans. I'll refrain from griping about social science research for now.

**I have this nagging suspicion that this actually was an XKCD piece at some point. If so, go read that again too. It was probably pretty entertaining.

***250 kg of methane is 375 thousand liters, if that helps.

Get well soon

Here is a use for one of the strange but inevitable results of modern society: singing greeting cards. The materials in one of those cards, plus a cheap resistor and capacitor, are enough to assemble a perfectly usable pulse sensor. The original paper suggests that this off-the-shelf solution could be used in an educational setting. 

A little Googling shows that a number of pulse sensors are available or can be made for all kinds of platforms.

• This one is intended for use with Arduino. Total cost is ~$25, not counting whatever it's attached to.
• For comparison, this one is a more clinical model. I can only imagine how much it costs.
• This setup uses an optical approach instead of a piezoelectric one. It seems like overkill, possibly because the signal requires a lot of amplification.

I'm imagining an art project in which a viewer's heart rate changes the intensity of lights in a room or turns certain appliances (i.e., a fan or a radio) on or off at certain rate thresholds. Even something like a cheap knock-off of this bike helmet seems entirely feasible. 

More like "Nope! Share, Fool!"

It's worrisome to see politics bleed into science. It's even more alarming to see sources of scientific funding dry up because they don't fit a specific agenda. The National Science Foundation, under directive from Congress, recently cut off funding for political science research except for that "promoting national security or the economic interests of the United States." It's a rather general guideline for a specific field. It also reveals how legislators feel about the role of any science and when it deserves to be funded: we want results, we want them now, and we want we certainly don't need any context.


The NSF spent more than $7 billion last year. It's where 20 percent of the money for federally-funded research in the US comes from. That total goes a long way and contributes to numerous fields, from engineering to education. It's only a matter of time before some Congressman decides an entire field of research doesn't need federal funding at all.