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.