The smallest of the small

The topic of a "minimal bacteriophage" came up in conservation with my lab's PI and postdoc yesterday. I got philosophical about it: what is a phage other than a genome, some structural proteins, and the means to enter bacterial cells? If we began removing items from a phage genome piece-by-piece, at what point would the genome cease to code for a phage? The questions really seem to concern how much genetic information is really necessary to self-propagate. 

There are some incredibly small phages out there, of course. Phage MS2 is a single-stranded RNA phage which infects E. coli and similar species. Its genome is just under 3600 nucleotides and contains just four genes. It was the first full genome to be sequenced - that small size made it a great candidate. It also seems to be used as a model for viruses in water quality studies.

So is MS2 a minimal bacteriophage? At the very least, its single capsid protein self-assembles into capsids and can even be used to encapsulate a protein of choice. If a phage needs to have a capsid then MS2 certainly passes the test. The other MS2 genes also provide basic functions: attachment, replication, and lysis. I'm guessing that the only way to get smaller would be to optimize or completely lose one of those functions (except for attachment, as it still needs to stick to something on its host surface), but would it still be a virus?

Today's music is one of the TMBG songs which has stuck in my mind for the longest (that is, for at least 15 years):

It's one of those mornings when I have to start the day with TMBG and cleaning out my desk. It's comforting.

Oh say say say.

R provides a seemingly endless toolbox of data visualization options. As a quick example, I was trying to find a way to create a treemap yesterday and a Flowingdata post provided the ideal R solution. It requires the portfolio package. Here's a test with some randomized data:

> testdata = data.frame(replicate(4,sample(0:1000,150,rep=FALSE)))
> map.market(id=testdata$X1, area=testdata$X2, group=testdata$X4, color=testdata$X3, main="Random Map")

The result looks like this:

Ignore the color key - there are no negative values here.

True, this example defeats one aspect of the purpose of a treemap. There's usually a hierarchy directed by qualitative variables. There is, in fact, room for two different quantitative variables and one category for each item in the data. We can certainly add a category to the data as it is:
> testdata$category <- ifelse(testdata$X4 > 800,"Large", "Small")

Now, every item with an X4 value greater than 800 will be in one category and everything smaller will be in the other. The output:

Neatly-organized boxes.

As expected, the smaller category ("Large") gets squished into one size of the figure and its contents get resized to fit. I miss the individual data labels though they got a bit dense.

The remaining issue is one of colors. The map.markey function allows for different scales but doesn't appear to provide many customization options. This blog post describes an alternate implementation which is RColorBrewer-friendly. Once installing and loading RColorBrewer (it's essential code, but it never seems to be installed when I need it), the newer treemap method is handled like this:
> treemap(testdata$X1, testdata$X2, testdata$category, testdata$X3, main="Random Map with Categories", pal="Reds", textcol="black")

From Sunset Snowbank to Waxy Red Delicious.

A treemap like this is likely a bit overkill for most applications, especially if there are too many categories or data items to be informative. A figure like this treemap of Vietnam's industrial exports provides an example: the smaller items are all unlabeled, so why include them? As always, results will vary and depend upon both data and conclusions.

What is the worst job in life?

(Like the personal development class I took this past Spring, I am taking another course from which I will be mirroring writing assignments here. This course is about career options so the writing pieces will have a relevant focus. They will remain introspective.)

The worst job I can imagine is a dull one.

To be fair, when I talk about a dull job, I'm not talking excluding unpleasant jobs. It's possible that many of the jobs out there are painful, dangerous, morally questionable, or even just repulsive in a sensory way. We hear about Mike Rowe-caliber dirty jobs all the time. They run the gamut from cleaning out septic tanks to cleaning the decks of fishing boats to castrating sheep. These unquestionably difficult jobs frequently couple manual labor with personal danger. They're often smelly or require interacting with substances most reasonable people would choose to avoid.

That being said, I imagine that these kinds of jobs have been romanticized just as difficult jobs throughout history have been. Few people can genuinely say they would want to clean out septic tanks but it remains a genuinely unique occupation. Someone has to have the job - and they may not even enjoy it - but its offensive tendencies lend it notability. We could look at high-seas piracy the same way. For centuries, piracy has meant living in cramped, disease-ridden places along with murderous co-workers, all at risk of grievous personal harm. It's not an ideal job for most people but it's great for billion-dollar movie franchises.

I don't find dirty jobs attractive. Rather, I'm willing to believe that there are worse options, if only because there is clear evidence that they exist.

What's worse than cleaning sewage? Let's imagine a job with the following responsibilities: arrive at workplace, sit at desk, place headphones on ears, and listen to the sounds of human suffering for eight hours. The reason for the suffering and the reason for the listening are both unclear. Requests to management for context are met with friendly, illegible Post-it notes left by unseen managers. You may take a break (in fact, it's mandatory to do so every few hours) but it will hurt your chances of promotion. It's unclear how often promotions occur yet every employee at this company fights for them. The sounds coming over the headphones are muffled but seem to mix urgent requests for help with personal insults. The insults are surprisingly specific and include personal details you've never made public. The job is the same every day and never requires more or less effort than that required to stay awake.

I'm essentially describing a hellish variation on working in a call center, with a few admittedly hyperbolic additions. The last detail I've included is truly the most discouraging part of this fictional job. Having to repeat the same types of actions on a daily basis is bad enough, but doing so without any chance to improve a skill or address a challenge is essentially prison. An individual with this job may work for years and gain in nothing but age.

The remaining details in the job description have more to do with relationships. There are always relationships between individuals at any organization. It's a function of living in human society. Companies and organizations are founded by humans, staffed by humans, and managed by humans. Any effort which renders the experience dehumanizing is coercive and psychologically harmful. Having to perform unpleasant work (in this case, listening to suffering and insults) fits the bill and is dehumanizing because it's not clear why it's necessary or what it's all a part of. In this example, I've included instances where the company culture favors misinformation and confusion. I'd like to think that this type of culture, whether accidental or by design, may contribute the most to feelings of dehumanization. It's easy to feel less than human when you're not treated with respect and when you don't know how to earn respect.

I've never worked in a job as bad as the one I've described. I've come close and I know people who have come closer. Monotony and dehumanization will repel me from a job faster than any other offense but I've been very lucky to have avoided them when I can. 

Two audiovisual Internet Things which have caught my eye and ear lately:

See Hear Party

Provide some keywords for visuals and music. The site returns a stew of animated gifs at a frequency roughly corresponding to the music's rhythm. It's a neat project and plays well with the modern derivations of the glitch aesthetic (I still see the term seapunk from time to time though that's likely archaic now, too). 

The intended result seems to be something like this, though there are other ways to play the game.

tildemash

Youtube contains a wealth of isolated tracks (i.e., just the vocals or the drums) from classic songs. What would they sound like if you picked a few at random and mashed them up? That's how new classics get made, right?

It's Amsterdam Again

The vacation photos continue! There are no more after this, at least as far as this trip goes.

Before returning to Amsterdam, we visited an event called Parkleuchten with our Germany friends. Essentially, the entire little town of Metelen gets turned into a mystical land of colored lights. My photos do not do it justice, primarily due to the torrential rain and flooding which began soon after we got to town.

It's blurry, but I'm sure you get the idea.

Follow the flames to escape this backyard without falling into the pool.

Let us hide in the Heimatverein.

They're proud of their vintage machinery.

Colored spotlights and water don't mix well. We spent some time hiding from the storm before escaping back to the car. I have to assume that Metelen is now a small lake.

The next morning, we hopped on an early train back to the Netherlands.

The train tracks in Ochtrup. Not shown: trains.

Ah, there they are. Hello, trains.

Finally, the hotel. I think three stars is code for "our hallways are fashionably dark but our front desk service is sufficiently friendly".

It was time to return to Canal Town. It was much more humid this time.

This car is a bit like Amsterdam itself: exposed to more moisture than it probably should be but it remains a charming and colorful patchwork. (That sentence is best read in the voice of Rick Steves.)

It's the Royal Palace of Amsterdam. The royal folks don't live there but they visit on occasion.

The building is opulent by design. It's what you get to build when you're everyone's favorite merchant society.

This flooring stays shiny because it only gets used for state functions. 

Many of the rooms are still in use by state visitors but were traditionally offices and lodging for government VIPs. This is the Insurance Chamber. It's where the guy in charge of insurance lived.

The Palace hallways are rather dark, both in lighting and in atmosphere. Many of its doorways are decorated with scenes of death and execution.

In this case, it's horrified children instead of skulls.

Having had our fill of 17th century royal excess, we proceeded to the Kattenkabinet. It's a museum of cat art. That is, it doesn't appear to contain any art by cats but it features paintings, sculptures, and advertisements featuring cats. The collection is all nestled into a set of apartments in a very catlike way: unassuming, offering limited context, but undeniably unique. 

I don't recall the cat in this film ever wearing a helmet. Perhaps the Italian version is different.

That's a real cat rather than a sculpture, but who am I to say what isn't art?

Elsewhere in the city (specifically, the Rembrandtplein), Rembrandt stands alone. The lady remembers seeing a full collection of additional statues around him before but they appear to have been moved.

A brief stop in the flower market.

Time for a waffle. It's not a Stroopwafel but we had plenty of those, too.

Goodbye, Amsterdam! Tot ziens.

Lists of other peoples' words

I mentioned the book list meme a few posts back, so here's mine. I posted it to Facebook already but it offers more posterity here, plus a chance for context.

1. Herb Seasoning by Julian F. Thompson

This is a Scholastic young adult novel. It sticks with me because it's about the impact of major life choices but it's also notable in a "how did this get published" kind of way. Its storyline is decidedly PG-13 and much more explicit than one might expect from an admittedly surreal coming-of-age story. I think I found it in a library sale during my earliest teen years. The last YA novel I read was the final Harry Potter text so perhaps more modern youth fiction trends towards the surreal as well. 

2. Wildlife by James Patrick Kelly

This one is essentially a collection of cyberpunk musings. I read a fair amount of Asimov's Science Fiction as a youth so I was used to the novella format; it works well for cyberpunk. A short story can introduce just enough new ideas to dismantle them all in short order. The whole cyberpunk aesthetic and ethos was so good at deconstruction that the genre rapidly dismantled itself. Wildlife is a great example of the poignancy of such a phenomenon as I see echoes of its ideas in every other headline. A gaggle of apathetically-wealthy teens hold parties themed around destroying priceless museum pieces. Children almost literally become their own parents, if they ever grow up at all. Others grow out instead of growing up.

3. Equus by Peter Shaffer

I don't like to deal in superlatives so I won't call this "the best play ever written". If anything, it's an exercise in balancing restraint and exuberance. I can't remember if I read Equus in high school or college but it was in a setting where most readings are rich in meaning but low in significance. This one startled me. It was significant to me, at least, as a recent adolescent. I couldn't understand the factors necessary to transform a horse into a god (even now, I haven't been on a horse in decades). It truly seems like madness.
4. Cat's Cradle by Kurt Vonnegut

A classic. It sticks with me as a feeling rather than a discrete set of details.
5. The Life and Opinions of the Tomcat Murr by E. T. A. Hoffmann

OK, I'll confess. I haven't read more than thirty pages of this one yet. It still manages to stick with me by virtue of sheer, inexplicable weirdness. It's ostensibly a cat's biography
6. The Three Stigmata of Palmer Eldritch by Philip K. Dick

Potentially just as critical to the genre of end-times spiritualism in science fiction as Cat's Cradle, Three Stigmata is one of Dick's more obviously paranoid works of fiction, though that may depend upon your opinion of VALIS. It sticks with me for many of the same reasons as Cat's Cradle does. The entire idea of drug-mediated collective hallucination is, in itself, philosophically challenging.
7. The Bridge Trilogy by William Gibson

I could also include his Sprawl and Blue Ant trilogies here, though the latter novels lack the breathless futurism of classics like Neuromancer or All Tomorrow's Parties. Gibson defined concepts like cyberspace and that prescience remains present in my mind. It pops up frequently: one of Idoru's core plots involves a convenience store chain installing 3D printers (minor spoiler - a rouge AI takes control of them). Self-aware computers aside, 7-11 could roll out such a service in the next few years and it wouldn't be unexpected. Beyond specific bits of futurism, Gibson was responsible for the whole cyberpunk aesthetic. It's about as dead now as a genre can be but it reappears everywhere from glitch music to failed TV series.
8. 3500 Good Jokes for Speakers by Gerald F. Lieberman

It's an ancient joke book! That is, it's a book of jokes published in the 70's but more appropriate to the 50's or 60's. When I read it in the early 2000's, it was an alien, nearly indecipherable thing full of obscure cultural references lost to the ages. It's also chock-full of racism, sexism, homophobia, and just about any other -phobia you can imagine. Because of all that, it's a great example of the plasticity of humor over time. It's an authentic time capsule.
9. The Incredible Machine by Robert M. Poole (1994 ed.)

I read this one for the pictures and the pictures are what stick with me, along with an appreciation for biological complexity.
10. CLOSURE by _why

Here's a modern story: a young programmer anonymously contributes code for years. He's knowledgable about the language and frequently implements ways to make it more useful, not only to experienced programmers but to beginners. He produces instruction manuals unlike any other, soaked with surreal cartoons and stories. His personal details escape into the Internet and he leaves every online community he's been part of. The only certain detail is that he needs anonymity. 

He may have been suffering from burnout. That's what CLOSURE seems to be about, at least. It's not entirely clear where everything in the collection came from or even who made it. The title was assigned after its initial release. Much like any complex code, it's a dense stew with many cooks.

Burnout isn't exclusive to coding. It can happen in any field, especially when it's not clear what your contributions mean to society. Do they have to mean anything? If so, how long should they remain relevant? Who decides what stays relevant? I wrestle with these questions on a near-daily basis but they haven't won yet.

There's a transition here with regards to why books stick around in my mind. The first three books in this list involve fairly nontraditional coming-of-age stories. Life offers multitudinous possibilities and these options appear inconceivably extensive during youth. The possibilities only narrow as we grow older and begin to comprehend where our limitations lie. That being said, we also grow slightly more able to predict future events. We begin to see long-term patterns, even in chaotic situations. Items four through seven on this list fit that latter category: they're all either science fiction or magical realism and they concern massive disasters. In the case of Hoffmann's Tomcat Murr, the disaster is literary. The other stories concern societal collapse and its metaphysical ramifications.

The metaphysical aspect is one which I was surprised to find in this list. Equus, Cat's Cradle, and Palmer Eldritch specifically include folk religions and emergent spiritualism. I'm not entirely sure why this concept is so interesting to me. It appears in some of my other interests; I have been collecting religious literature for several years simply because it's varied and interesting. The idea of the "emerging church" is an interesting one in itself. I'm an outsider to that movement, though, so I'm still trying to understand why I find it so alluring.