Today, I learned not to mistake Pyrex tubes for polycarbonate ones when using them in a centrifuge spinning at 12,000 x g. The polycarbonate ones are designed to not leak under these kinds of conditions. The Pyrex ones leak everywhere, in the way that liquid-containing vessels do when they disintegrate.

Within the category of "internet things I will be inordinately distracted by but will probably give hypochondriacs a case of the skin-crawlies": ProMed Health Map. I didn't realize it even existed until recently. It's a list of recent disease outbreaks plus a few poisonings and such. It's fun.

The unbearable brightness

Here are two quick, strange observations about colored light and biology:

1. A recent study in PNAS claims that exposure to orange light could have an impact on cognitive function. The MRI results certainly appear significant but I'm not familiar enough with the field to know if they're reliable. Caveats: Their sample size was 16 people, the effects of the particular light were noticeable more than an hour post-exposure, and potential participant effects (i.e., how sleepy they felt) were all self-reported, though the researchers state these reports were consistent. I'm curious to see if the results can be replicated with a different sample of volunteers.  (The paper by Chellapa et al. is here.)

2. C. elegans glows blue when it dies. Don't take my word for it. Take the word of Coburn et al. from their 2013 PLoS Biology paper, Anthranilate Fluorescence Marks a Calcium-Propagated Necrotic Wave That Promotes Organismal Death in C. elegans: "We report that organismal death is accompanied by a burst of intense blue fluorescence, generated within intestinal cells by the necrotic cell death pathway." It turns out that, at least in C. elegans, organismal death looks like a wave of necrosis as a cascade of self-destruction propagates cell death. The short story: cells burst, pH increases, things that wouldn't normally be fluorescent suddenly are. The death-glow may have been found to happen in yeast, too (Coburn et al. cite this 2007 paper by Liang et al but I couldn't find any explicit mention in it about blue fluorescence, just yellow and red).

Gen-eralizations

I'm really not fond of the term "Millenial." I didn't like the terms "Gen Y" or "Gen X" or even the whole "baby boomer" classification for the same reason: all these terms are shorthand ways to generalize entire generations of people.

It's possible that the terms were never originally intended to be pejorative. Having a shorthand way to refer to people born during certain periods of history not only provides a chronological shorthand, but it allows us to infer some cultural context. If someone's identified as a baby boomer, their childhood likely didn't include Super Soakers or AOL chat rooms. They're statistically likely to have different opinions from more recently-born folks about a number of topics. We can, of course, raise similar arguments about different racial or ethnic groups. There are objective differences in cultural context between groups, even when we ignore the obvious physical differences (i.e., baby boomers are older than Millenials, just like Native Americans have different skin tones than people with recent European ancestors).

The problems arise when the generalizations become interpretations. Any generalization of human beings is inherently dehumanizing. It's an unavoidable element of living in a modern society, though the relationship between personal identity and broader ethical concerns only really began in the mid 1600s. That's really a distinct topic -- even so, it illustrates the difficulties involved in reconciling individual identity with the identities of the Many. We can draw conclusions about one person says or does and what groups of people generally say and do, but using the group as a model for the individual is nigh-impossible when there is high variance among group members.

Really, I'm just tired of glossy stories about Millenials. I'm tired of TIME Magazine's offerings, even when they're chock-full of Joel Stein's usual everyman sarcasm. I'm tired of Atlantic pieces about how self-centered these Millenials are supposed to be (spoiler: youth is a great time for narcissism).* I'm tired of Slate articles which may be unintentional satire, as this quote may reveal:

A generation ago, my college peers and I would buy a pint of ice cream and down a shot of peach schnapps (or two) to process a breakup. Now some college students feel suicidal after the breakup of a four-month relationship. Either ice cream no longer has the same magical healing properties, or the ability to address hardships is lacking in many members of this generation.

Isn't hindsight wonderful? I'd love to be able to labor under the pretense that This Generation Is Broken, but I suspect that humanity just generally can't handle hardships well. At best, they can imagine a fantastical, pain-free past. 

I don't even identify as a Millenial. Why would I? It's certainly not going to do me any favors.

*I won't even get started on the monthly NYT articles about That Thing Gen Y Does. A slightly more acerbic Slate article than the above one may have to suffice.

Today, I learned that naked mole rats do not feel pain if they eat capsaicin. It's not that they ever have to eat chili peppers, it's just that they can't feel that kind of pain anyway.

A new mite-mediated emaravirus may be emerging among coffee plants in Hawaii. It's too early to know whether that's a problem, but emaraviruses haven't been known to infect coffee plants before.

The most minimal bacteria

Today I learned about the existence of the bacteriome, a specialized organ found in some insect species which is just chock full of endosymbiotic bacteria. Most animals provide hosts for bacteria, but the critical part here is the endosymbiotic nature: these symbionts must live and reproduce within host cells. As a result, many insect endosymbionts are quite odd in genetic terms and have tiny genomes. They can only grow to a certain population size, too, as they're limited by the space available within those host cells.

One such example of the resulting genetic oddities is found in Hodgkinia symbionts from cicada bacteriomes. A report by McCutcheon et al in 2009 showed howHodgkinia cicadicolaappear to have re-coded their UGA codons to code for tryptophan rather than the usual Stop codon. This specific re-coding has been observed before, but only in very low-GC content species, of which Hodgkinia is not one (it has a GC% of more than 58 percent). This symbiont also has a crazy-small genome at 144 kb. That was the smallest bacterial genome yet sequenced butNasuia deltocephalinicola, another insect endosymbiont, has it beat by 22 kb.

Self-aware weddings

I first read David Marusek's The Wedding Album in 1999 in an issue of Asimov's Science Fiction. As the title implies, Marusek's novella concerns weddings and marriage, two concepts as distant to me fifteen years ago as the advent of single-serving coffee pods (I would have scoffed at the idea at the time, anyway. They're awfully wasteful, right?). It's now the future and I've had a wedding photographer booked for months. We also have the ability to read entire e-books of compiled post-cyberpunk* without digging through musty old issues of Asimov's.**

The Wedding Album begins with the premise that don't just save memories in photographs and video, they map them at the atomic level and use those maps to create virtual constructs of memorable moments on a whim. It's like a holodeck, but for notable yet trivial times like graduation ceremonies and birthdays. The killer app*** for this technology is its ability to create near-perfect AI constructs of any mapped humans. The AIs, despite their inherent humanity, are treated worse than slaves: they're as disposable as email and their re-creation could be moments away. Problems arise when folks finally have to confront the inevitable questions about whether AIs are really self-aware and whether that makes them human. Unlike in many stories, political and logistic issues also have to be addressed. Who gets to decide who's self-aware and who's just an organized bunch of electrons? If self-aware beings have the right to The Pursuit Of Happiness, where do they get to do so?

It's possible that The Wedding Album, due to its broad scope and refusal to adhere to any single post-singularity viewpoint, exudes a nearly pure cyberpunk ethos. Cyberpunk was never really about streetwise hackers and all-neon-everything any more than Tolkienesque fantasy is about forest-wise elves and rune-engraved weaponry. Cyberpunk was always about the transformative power of technology. Sometimes, it's even about how technology transforms itself (a purely metaphorical situation, at least until self-aware AIs pop up). Post-cyberpunk is cyberpunk for an age when we're both painfully aware and blissfully ignorant of technology's multitudinous effects on humanity. To that extent, The Wedding Album also sits squarely within post-cyberpunk. We may not have the ability to make perfect AI copies of ourselves yet, but we certainly have online identities and they are better reflections of ourselves than any physical mirror.

William Gibson, widely considered one of cyberpunk's Founding Fathers and credited with the term "cyberspace", began setting his works in increasingly more imminent futures more than a decade ago. His novels always had a near-future atmosphere but didn't age well as the prefix cyber- grew tired. In a 2012 interview, Gibson describes it as feeling "...haunted by a feeling that the world itself was so weird and so rich in cognitive dissonance, for me, that I had lost the capacity to measure just how weird it was." Speculation can be a gamble, but works like The Wedding Album may be just strange enough to show us how weird we've always been.****

*Rewired: The Post-Cyberpunk Anthology, edited by James Patrick Kelly and John Kessel. Kelly's quite-literally-fantastic Wildlife has always stuck with me as one of the most resonant and touching bits of transhumanist science fiction of the last few decades. He suggests in Rewired that post-cyberpunk (or in his potentially-misleading acronym, PCP) is the natural evolution of a genre so cutting-edge it ended up sliced to ribbons.

**All my issues were recycled ages ago. They were probably musty from the beginning.

***I think the term "killer app" predates adoption of the term "app" (that is, when used to refer to any piece of software) so perhaps the true "killer app" in the information age is the ongoing concept of discrete pieces of software in an era increasingly dependent upon interdependent code, APIs, and so on. I mean, my TV has Apps. It really doesn't need them but I suppose there's an intended illusion of control that way.

****That's not to say that it's anywhere near the strangest fiction you'll ever read, or even that it's genuinely odd. It's just weird enough to provide some tantalizing reflections of What Happens Now.

This MIT Tech Review article about face verification is interesting, if only because face comparisons are one of those things that people are supposed to be ideally suited for. I'm not sure that the Facebook project presented in the article is really as good as they claim (that's a function of the training data, of course, and may not be much like real world face-matching conditions since it's, um, a Book of Faces) but it sounds like a decent start.

I'm back from Texas! Here are a few photos.

This is part of the Cibolo Creek. It's not usually this low.

The bathrooms at the Little Gretel Restaurant. It's ostensibly Czech themed but you would't know it from the facilities.

Part of the San Antonio Botanical Garden or a Park With Dinosaurs. Exact-ish location: 29.458046, -98.457146.

Can you find the cat in this lumber yard?

I'm in Texas at the moment, visiting my parents. It's not quite as warm down here as I would have liked but it's nice and sunny and I'm getting caught up on my reading. There are also many antiques (see below: an 80-dollar cookie jar in feline form).

The cookies. Place them within me. My emptiness will preserve them.

Some of what I've been reading is rehashed cyberpunk SF. It's an interesting subgenre for its supposed outcast status and heavy reliance on particular ideas and aesthetics, almost like the noir detective stories of speculative fiction, and for its stubborn refusal to admit that it may be the most prescient subgenre of fiction in general. (Except for the whole VR thing. Oculus Rift notwithstanding, virtual reality just feels like a perpetually obsolete concept, though that may be lingering cyberpunk influence again. Big black goggles can make anyone look like an amateur datajack.) Further thoughts forthcoming.

Here are three bioinformatics tools for protein structure prediction, presented without context or comparison and primarily so I don't forget they exist:

1. HHpred. Handy, fast, and the output is data-rich. 
2. RaptorX. Will do structure alignments and binding predictions, too. Servers may be sluggish sometimes.
3. I-TASSER. They've added some neat functional prediction modules (primarily based on existing structures and GO terms, I think) since I've last used the server. 

Today's paper was : 

Pernitzsch SR, Sharma CM (2012) Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori. Frontiers in cellular and infection microbiology.

It's a quick review of sRNAs in H. pylori, a species once thought to use very little RNA-based regulation (AKA riboregulation). The presumed lack was based on observations that H. pylori lacks the RNA-binding protein Hfq, generally thought to be a requirement for riboregulation. Turns out that's not the case. H. pylori may regulate plenty of cellular activities using sRNA, including the stress response and flagellum biogenesis.

A chamber, made

So, Antichamber. I finished it recently. Spoilers may follow. It's not a monumental challenge, but I'm fairly sure it's not intended to be one. It also hasn't lost much of its spark for me despite an original release date of more than a year ago. Games get spoiled so easily these days. Portal, this game's obvious inspiration in both design and technical matters (despite not sharing the same engine, but that's just a technicality in the grand scheme of things) certainly didn't have such a stable shelf life. That may just be due to cake and lies.

Yes, Antichamber. I won't describe the details and I'll assume you've either tried it out already, are planning to play it, or will never do so. It's a minimal game with an ambient background. The visuals are predominantly white or a few colors at a time. The soundtrack is a collection of chirping birds, rushing wind, and distant thunder. The goals are straightforward: go where you haven't been, open closed doors, collect new equipment and learn all the neat things you can do with it. Every stage is summarized in a tidy aphorism, the presumably obvious lesson gently restated in a single sentence and a napkin-sketch cartoon.

Antichamber is ostensibly about life. That's an ambitious goal and probably a bit too much for any one creative work to concern itself with. Instead, I think it provides an excellent example of minimal gaming. It's certainly not minimalist gaming, though that's a popular and valuable trend in and of itself.

Rather, Antichamber deconstructs modern gaming into some of its most dominant elements: confusion, movement, and surrealism. All three of these elements are particularly well suited to gaming as they benefit from interaction. A film can confuse us, make us feel like we're moving, or even present impossible images (indeed, every film is made of impossible images, or it would be theater). Only an interactive experience can make us feel like the world isn't responding to us in the way it's supposed to. It's also the only way to simulate control over one's own movement and to do it in a way that's realistic enough to be convincing and responsive but unreal enough to retain a patina of fantasy and unlimited possibilities.

The paths in Antichamber are circuitous but eventually require pursuit of a floating, dark, ghostly mass. The mass sounds like strangers congregating in an art museum lobby* and looks like a glitch.** By the end of the game, it's fully within the players control, ready for release until just the last few moments. Before that point, the ghost does many of the same things the player does as far as opening doors and wandering around an illogical maze goes. We could almost recursively view this black mass as the game's player or even just the concept of a player. Players make games what they are, but they'll all have different experiences in the process.



*Or, um, maybe an antechamber. Anterooms are pretty critical to congregating and to the hanging of coats, though neither happens in Antichamber.

**It's kind of like this recent art project.

A brief, hopeful rant about Powerpoint

The "tools of the trade" are little more than iconography for most trades. In science, no matter the field, one of those tools is usually Powerpoint. It doesn't look as good on a flag as a hammer or sickle or even a cutlass* but it's still the reliable sidearm of any scientist with conclusions to present and an audience to hear about them. Despite -- or perhaps because of -- its popularity, Powerpoint is widely abused. It's less of a tool and more of a drug. Many scientists just can't get through a presentation without loading up a stack of slides and letting 'em fly.

Lets break the cycle, folks. Some physicists are abandoning the slides in favor of whiteboards and direct conversation. Even better, we can avoid the bullet-point habit entirely and adapt to specific audiences. Presentations should be about expanding upon ideas, not glossing them over! I can't claim to be a presenting expert and certainly haven't had a long career. Even so, I can hope for numerous chances to present my research outside the bounds of Microsoft's glowing rectangles.


*I once saw a version of the University of Virginia logo specially prepared for their department of Biology. The sabres had been replaced by micropipettes, the actual tools of the molecular biology trade.

It's tough to stay focused. There's always something requiring more attention than it's ever going to get, and in the odd times when it gets nearly the required amount, it's probably due to the sacrifice of some limited resource. Time is a limiting factor, certainly. Motivation is another one. If the end result of a project looks dim and distant, I can only imagine how it will look when it's within reach.

I suppose there's a lot to be said for having a concrete idea of presumed context. I've often found this to be an irritant in fiction: the author provides just enough detail for me to get a good mental image of the characters and their context, but just when it's relevant, new details emerge. This isn't along the lines of "she saw the reflection of her blue eyes in the pooling rainwater" when all along I had thought the character had brown eyes. It's more like having the rainwater appear in the first place when I had understood the weather to be clear. Is this the fault of my own assumptions, or can I reasonably expect authors to provide me with enough detail to minimize assumptions?

The same issue is true with writing scientific manuscripts. That's what I'm doing now. It's a collaborative job, so at any point a fellow author may add or remove details and data. The collaboration is helpful when it works toward the same goal but that goal often remains blurry, a granite crag looming in the distant hills.

Dysfunctional uncles and luminous oncology

I've been trying to remember a particular film all afternoon and was totally stumped about it. I knew it was from the 90's and involved someone dying of cancer, but beyond that, all I could remember was finding it inordinately sad -- a real heartstring-gripping jerker-of-tears. I remembered that and the keywords "Jewish packrat uncle." Those three words were enough for Google identify the film: 1995's Unstrung Heroes. This was a validating result as I had already tried searching for "Unsung Heroes", though this is actually a North Korean spy film series and an unrelated short mockumentary about superheroes.

Andie McDowell looks awfully cheery on that movie cover for somebody dying of cancer. Franz Lidz, whose memoir was the distant base material for Unstrung Heroes, later wrote about the subject, finding that "...the terminal sappiness of cancer movies is probably beyond remedy."

I had a weekend full of mind-flexing! It's enough for a whole bunch of meditative blog-postery so that is what it will be. Just not yet.

In short, though: the lady's university had a departmental conference which she had helped to organize. I presented a general overview of my work at said conference; this is especially notable as I am a student of the Life Sciences and this was a conference of German language and literature. It was, however, intended to be interdisciplinary by design. It succeeded quite well and I have some fresh ideas to think about. There was an especially nice talk about repetition in music. See the following example, Steve Reich's It's Gonna Rain:

I've also been trying out a few artsy games: Antichamber and Starseed Pilgrim. They're elderly in internet years but young n' fresh to me. Thoughts later.