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?

Oh say say say: treemaps in R

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.

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?