Gotta keep it clean.

This is what my desktop looked like on December 8, 2003. Yes, I used Kazaa, the Uber of the early 00's (see previous blog entry). Other items of note:

• Matching GUI and Winamp skin. Looks like I was listening to Hybrid - If I Survive. It was probably this remix, actually.
• Fruity Loops Studio 4, the perfect software package for the young, enterprising electronic musician on a severely limited budget.
• A Temporary Desktop Folder. Nothing temporary about it. That's where every document goes.
• Both AIM and Trillian. This version of Trillian crashed every 10 minutes or so.
• I was not as cyberpunk in real life as this desktop may imply.

Remember Napster? How about Kazaa? Do you remember how popular they were and how blatantly illegal they were? The illegality was blatant but revolutionary. It was emblematic of a myopic but resolute spirit still actively pervasive among new companies, especially those providing new mechanisms for old grey markets.

The ongoing fracas about Uber and Lyft always brings that spirit to mind. Some folks in my city are excited about its possibilities. I'm conflicted about it, honestly. Just as Napster, Kazaa, and all the other early file-sharing methods rendered music sharing painless, these new companies are simplifying ride sharing. People could and did share music before the internet made it easy and they certainly still do so. They also continue to share cars, even on an unofficial paid basis.

Here's why I'm conflicted, though:

1. Taxis are terrible but I'm glad they're regulated. I'm generally in favor of regulating services: there's always some liability issue should something go wrong during a business transaction. Uber and Lyft really need some very specific safety regulations before I'm convinced they should supplant the existing taxi system.
2. I'm increasingly worried about the distancing effect of turning human interactions into apps. Is that old-fashioned?*
3. Uber and Lyft frame their business concepts as creative destruction. I don't see anything terribly creative about it. They're organizing existing systems in a patently illegal way and discarding every logical reason why the laws exist. If that's the only way this system can be improved, then I suppose I'll get used to it. In the meantime, I'll continue to be suspicious. 

*I do really like knowing how much a taxi ride will cost up-front, though. That's a clear advantage of these new services and it's obscene that the old taxi companies couldn't provide it.

This clickbait-headlined Bloomberg article makes the claim that "The Villages", a proliferant retirement community in Florida, is the most rapidly-growing metropolitan area in the US. Something seems vaguely cyberpunk about the place, possibly because it is obscenely large and chock-full of people at the tail ends of their rich lives. That's the traditional "overbearing dystopian future society" part, at least. 

So how is The Villages different from a university of equivalent size? Ohio State (er, The Ohio State University) has about 57,000 students on one campus, making it one of the most populous universities in the nation. It's not quite the 110,000 headcount claimed for The Villages, but I'm assuming that number includes resident employees as well. If we include OSU's non-student employees, their total "resident" population is closer to 87,000, not counting commuter students. 

This is my point: the population size isn't what intrigues me about The Villages. It's not the monolithic overlord problem, either. It's having that many affluent, elderly people in one place. It's a recipe for highly-concentrated success.

Unlabeled, but not forgotten.

Today I learned about Positive-Unlabeled learning, a type of semisupervised machine learning approach. This is the general problem: if you want a machine learning method to do binary classification, you need to start with examples of items which fit into one classification or the other. This is much easier and more efficient when you can safely say that everything in Column A is not in Column B and vice-versa. That isn't the case with some data. Rather, it's either labeled (Column A) or unlabeled (maybe Column B, or maybe Column A but just unlabeled).

PU learning can be used to define negative examples for protein function prediction.  Citation below:
Youngs N, Penfold-Brown D, Bonneau R, Shasha D (2014) Negative Example Selection for Protein Function Prediction: The NoGO Database. PLoS Comput Biol 10(6): e1003644. doi:10.1371/journal.pcbi.1003644.

I had a brief look at Google's Material Design guide today after seeing it linked by Andy Baio. It's essentially a series of guidelines about how to make an interface or product look Google-y. Much of it is good design advice for other projects. The color palettes are one such example.

When future historians want to know what 2014 looked like, this will be a fairly accurate record. I hope we (or just Google, at least) can improve on a few things; their cascading menus have always looked messy and non-intuitive to me. They just pop up all over the screen.

If I had to choose the most insulting sentence currently available in the English language, it would likely be the following:

Those people are mistaken, for reasons I explained in a series of tweets.

The source is here. For more immediate context, it's in reference to people who are in favor of the Oxford comma. The referenced Twitter arguments are of the usual Twitter caliber: glib, poorly organized, and myopic. The source organization, Poynter, is intimately concerned with journalism so I can forgive their editor's concern over generally trivial grammatical squabbles. I have more difficulty with the general concept of "you're wrong because of arguments I've previously made in the worst possible format."

I got married this past Saturday! Married to a lady. Photographs available on request. There's also a video on the way. Stay tuned for that.*

In other news, mice can eat a diet of bacteriophage T7 with few ill effects. Who says negative data never gets published?

*"Stay tuned", beyond being a culturally antiquated idiom, is an interesting bit of skeuomorphic language. It's a relic of a time when viewers could be asked to stay on a particular radio or TV station. Most modern radios and TVs aren't manually tuned. The audience also can and will change stations at their own volition. Asking them to remain in place is like asking them to wear the same pants for a week.

This song has been stuck in my head all morning.

I've been trying out the Android beta of Swell Radio - it's really quite nice. The basic idea is that it treats podcasts as radio shows, so you can just start the app up and it'll just keep on streaming. I had tried it on iOS a year or so ago and was disappointed to see that Android development was lagging. It looks like they're making progress now.

Its recommendation engine still needs regular maintenance. An average User Experience goes like this:

1. Swell plays hourly NPR news update
2. Swell plays a few more NPR clips
3. Swell plays a Wall Street Journal business update, or at least all of its ads 
4. User skips to next item in playlist out of irritation
5. Swell plays another NPR clip
6. Swell plays a set of Comedy Central standup clips

The issue is transitions. It wouldn't hurt for the app to announce the next item in the list so I'm not left wondering why Paul F. Tompkins is on Morning Edition. I mean, the guy loves NPR so it's not too far-fetched.

Slate apparently hasn't heard of metonymy.

In related links, @SavedYouAClick is just great. It's instant answers to all those unnecessary questions in internet news headlines. I wonder if the process could be automated.

I've been working with some very large protein-protein interaction networks lately. Many of them come out like this in Cytoscape:

An artistic re-interpretation. Not actual data. As if there was anything to find in there, anyway.

They're ominously big but still appear to be scale-free. Strict adherence to power law distributions makes me a bit suspicious even though it shows up everywhere.

Today I learned about the Girvan–Newman algorithm. It's a fairly quick way to break up networks of interacting components into clustered communities. It doesn't really join components in any way they aren't already connected. It just removes connections which don't meet betweenness requirements. If the starting network is a hairball, the final product is either distinct clusters or just a bunch of smaller hairballs (I seem to be getting the latter, for the most part, but my current networks are several thousand nodes with more than 40 thousand edges).

The clusterMaker2 plugin for Cytoscape has an implementation of this kind of community clustering. It uses GLay. The plugin hasn't been quite as fast for me as the GLay authors report but I'm content to blame that on my old* Core2 Quad 2.4GHz and/or the massive changes in Cytoscape over the last few years.


*This one came with the lab and was originally used for working with sequencing data. I'm going to use it until it dies and/or catches on fire.

I read this Nature news piece about phage therapy today. It's great that phage might finally be taken seriously as an alternative to carpet-bombing bacterial infections with antibiotics.

This sentence caught my eye: "Nature provides an almost inexhaustible supply: no two identical phages have ever been found." That claim isn't entirely true. While bacteriophage genomes are staggeringly diverse, many contain very similar conserved sequences. If we're only considering two phages to be identical if each nucleotide in one genome is present in the other, then it's very close to true. We could, of course, pick two phage out of the same culture and have a good chance of their genomes being 100% identical. Depending on the phage, we may only be talking about few thousand nucleotides (ΦX174 is only about 5 thousand base pairs, for example!). 

Let's not even start on the issue of how frequently we isolate genetically identical bacteria. We'd like to think that a culture of any one bacterial species is a monoculture, but how many cells in that culture are completely genetically identical at any one time? How about their transcriptomes? I suppose that the original idea remains true: bacteria can produce great genetic variation, so bacteriophage can do so just as well.

Bar none

"Kick the bar chart habit", they say. "Use box plots instead and you can show a distribution of your data points", they claim. They're right, of course. I suspect that most people, whether they're scientists or just members of the 24-hour-TV-news audience (there's some overlap between the two groups, of course) prefer bar charts because they're so straightforward. Higher bars are greater in value. What could be easier?

Besides scientific papers and TV news, the biggest influence on chart type is likely Excel. Hell, the newer versions let users create tiny, almost-unreadable sparkline bar charts. The only worse option may be pie charts. My introductory statistics professor was always wary of using the wrong chart at the wrong time, but he constantly warned us that there was never a right time for a pie chart. I'm usually inclined to agree.

So, bottom line: avoid using the default chart options in Excel and/or chart types which sound like desserts.

Nothing feels less productive than fighting with Git. The official documentation is the real problem: it's roughly as arcane as Norse runes.* I managed to find a few tutorials today, at least:

• Atlassian Git tutorial - just a basic rundown of the common commands.
• Try Git - I find that the Github documentation is just as bad as the Git docs: it makes the basics sound easy but doesn't provide enough detail to know what to do when things go totally wrong. This does the same thing in an interactive way. It's great for the basics but not much more than that.

*They all read like this.

An overly-compressed Sierpinski gasket. Say that fast enough and you sound like an irate plumber.

Fractals generally make good desktop wallpaper but viewing them as compressed bitmaps is a bit existentially disappointing. It's like going to the zoo: you know the animals you're seeing are just stand-ins for the authentic complexity of nature.

I've been awfully busy lately between planning for a wedding (well, my own wedding), trying to finish one paper in lab and analyzing the results for another, and a show I'm in this week (see below).

I get to make funny voices on-stage. It's convenient since I'd be making funny voices anyway.

It's still fun to sacrifice life-snippets to the Blog Gods (blods?) so I'll start posting some short bits more frequently. Here's one such item.

A rich stew.

This is what happens when you store rich nutrient agar in a recycling bin for a week or so. It was meant to be a temporary location for some poorly-melted yeast growth media but was forgotten. Now we have a survey of the organisms present in laboratory waste receptacles (at least, we would have if I hadn't just scraped it all out into a biohaz bag).

Today I learned about acetoin, a chemical found in many foods and fragrances. It tastes buttery.

Acetoin can be produced by some strains of bacteria, especially if they've been engineered to do so. (That's true about many, but certainly not all chemicals.) It's especially convenient to do so if you're trying to control the flavor of a fermented product like wine or soymilk.

Just don't do it.

If you're going to lie to someone about your work, don't do it in science.
If you're going to lie to someone about your scientific work, don't do it in biomedical research and especially not when researching potential gene therapies.
If you're going to lie about your gene therapy findings, don't do it repeatedly and egregiously for almost a decade and never do it to the source of your funding.

Dr. Li Chen did all that. The NIH (and by extension, the US Dept. of Health and Human Services) is not pleased with him. It's bad enough that his former lab had six retractions all around the same time in 2010. Dr. Chen was intimately involved in the whole mess.

His punishment is essentially a 3-year ban from federal funding and involvement. I'm inclined to think that the investigations and retractions are damning enough. This guy now has a smoldering crater in his CV. Even once he's eligible for federal funding again, I suspect he'll have some trouble getting his grant applications approved. That's a life-threatening condition in any field of science.

Let's see what happens when we add an extra letter to some popular web addresses.

You'd think they'd all be trying to ride on the fiber optic coattails of their more popular brethren. You may be correct in many cases.* Here are a few exceptions.**

• dreddit.com

It's an archive of the FAQ from the Usenet group alt.magic, a group for magicians to discuss their craft. The most recent updates to the FAQ are from 1998 and they're mostly listings of brick-and-mortar magic equipment suppliers. I wonder how many of them are still in business.

A choice quote from one of the supplier descriptions: "He uses a tremendous amount of hyperbola in his advertising..." Are these people magicians or mathematicians?

• twikipedia.org

An Amsterdam-based web design studio. They seem like they made a good choice.

• etwitter.com

Redirects to a site for some manner of art-printing business. The images are largely uncredited, leading me to suspect they were hijacked from Flickr. They also offer a sizable collection of Licensed Artwork From Star Wars, so if you're still looking for that finishing addition to your Boba Fett-themed living room, try Amazon because there isn't a retail frontend on this site.

*Most single-letter modifications to google.com appear to lead straight to Redirect City by way of the Download This Surreptitious Software Bypass.

**atwitter.com is for sale!

Today, I learned about the existence of RoMEO, a database used to answer a very specific but often problematic question about peer-reviewed journals. The question is "Can I store and share the work I've published in this journal with people who want to read it?" and the answer is often "No, nope, never, probably not, you don't have that right, this is ours now, bwahaha, etc. etc." RoMEO lists which publishers feel that way and which publishers have more open attitudes toward self-archiving.

StackExchange is so nice, I don't even mind spelling its name with CamelCaps. It has specialized niches like Reddit, an expert community like Quora has in its better moments, and a genuinely effective user-moderated reply system. The best part is finding new subforums: I just found one for German language questions and one for sound design. Whenever I find forums like these on Reddit, they're usually ghost towns or full of users with far more questions than answers.

I found some new tools for protein interaction alignment today. My PI forwarded me this paper:


Clark, C. & Kalita, J. A Comparison of Algorithms for the Pairwise Alignment of Biological Networks. Bioinformatics btu307- (2014). doi:10.1093/bioinformatics/btu307

Clark and Kalita seem to really like NATALIE, a tool which ignores parts of the network which don't appear to align well (Lagrangian relaxation!). It's part of the LiSA software collection and looks like it was last updated in 2012. I'll have to see how easy it is to implement - some of these kinds of tools may work really well but are just painful to get working, especially if their documentation is sparse.

Here's a quick Excel trick for averaging duplicate values. It's the kind of simple command that I probably should have learned years ago, but it's only been available since Excel 2007 so at least there's that excuse.

Anyway, it's the AVERAGEIF function, used as follows:

=AVERAGEIF(the column with the duplicate values, a single value to get the corresponding average for, the column with the values to be averaged)

formatted so the first and last columns are static, like this:

=AVERAGEIF($A$1:$A:$1234,A1,$B$1:$B$1234)

I'm certain that something very similar can be done in a shell script based around uniq.

I’ve been taking a personal development class for the past few months (GRAD611 at Virginia Commonwealth University, part of the nascent BEST program). The class had some broad objectives: to “develop leadership and professional development opportunities for professional, graduate and post-doctoral students that will enable them to thrive in today's professional environment and empower them to make meaningful contributions to society as they realize their potential as future leaders” and to “build a network of internal and external partnerships and identify resources to support and guide leadership and professional development initiatives for professional, graduate and post-doctoral students”. Those are the course goals as they’re written on the syllabus. They’re very ambitious. When the course started a few months ago, I was very skeptical as to whether I’d gain anything from it. I tend to take most personal development strategies with a sizable grain of salt. Too often, these concepts are rife with one-size-fits-all solutions and silver-bullet problem solving strategies.

In the end, I was pleasantly surprised! I suspect that it will be difficult to tell if any new opportunities are now available to me until I can apply what I’ve learned. The second goal listed above is even trickier to address. Have I been able to access a new network of “internal and external partnerships”? Will I know when I see such opportunities in the future?

More importantly, what have I learned about myself? Let’s list a few changes:

•          I’ve noticed lately that I’m much more tolerant of how people portray themselves. I used to find it irritating that any individual would be so myopic as to define themselves in terms of an occupation or an interest. Everyone has a multifaceted personality – no exceptions. The trouble arises from trying to communicate that diverse set of personality traits to others. I can’t just introduce myself to someone and expect them to understand who I am, nor can I try to describe every aspect of my identity to them in a brief meeting. These things require time and solid relationships. It also isn’t fair for me to find others short-sighted when they try to put their identity on display. They’re human, they’re complex, and they have their own sets of strengths. These traits may be immediately obvious or they may require communication.

•          I’m not sure if I’ve identified my authentic purpose. I’m not sure if “authentic purpose” is an authentic concept. It was frequently addressed on the periphery of the class materials but rarely discussed directly. It sounds questionable to me because I don’t believe in a discrete, guiding force. Everything happens for numerous reasons but these reasons may not conspire to guide me toward a purpose. They are natural forces as much as gravity is. That force doesn’t press me to the ground because it wants me to study geology. It has that effect because I’m conveniently made out of matter. That being said, perhaps “authentic purpose” is less of a force in itself and more of a general description of how I react to forces. I have many options in life but some options do feel more “authentic” than others.

•         I’ve become more accepting of the strengths of others. It’s easy to dismiss ideas when they don’t fit into your perspective and it’s easy to dismiss others when they don’t approach problems the same way you do. I tend to approach the world in a broad but systematic way. There’s so much interesting material out there for me to absorb, but I also need to make logical sense of it all. That’s less of a priority for some people. They may be more focused on winning people over or placing information in historic context. I like to do those things as well but they’re certainly not my first impulses.

•          I’ve also become more accepting of my own strengths. It’s quite easy to lose sight of personal strengths when there’s so much to lose from having weaknesses. Spending so much time in science and academia may contribute to that phenomenon: I tend to spend a lot of time each day worrying about what could go wrong with my plans (or, even worse, if anything has already gone wrong but I haven’t noticed). It’s a habit that extends to my own self-conception. Over the last few months, I’ve been increasingly able to see my own shortcomings as lesser strengths and my more obvious strengths as foundations to build upon.

•          I’ve been attempting to use more filters when it comes to gathering sources of input. It’s quite difficult for me to separate signal from noise when I’m searching for interesting information, whether it’s research or just the daily news. The problem really comes down to how I tend to find everything interesting: even when the metaphorical signal-to-noise ratio isn’t so great, I can still get lost in the noise. Reducing the amount of input I attempt to tackle at any one point has helped with that issue.

There are changes that I’ll continue to work on:

•          I'll try to meditate more regularly, though I don't think I'll set any numerical goal on the number of times to do so. I just know that I get more done when I'm aware of my own happiness. Being productive adds to the contentedness and completes the cycle. It’s not even a matter of sitting in once place for a while and focusing on one thing. I’m glad just to notice a momentary, beautiful detail in the world around me.

•          I’ll think more critically about what I consider failure. In a world without failure, I would become very confused and suspicious as to why I wasn’t failing at anything. Failure is a natural part of life and an educational one. Much of what people refer to as failure may just be evidence of authentic challenge.

The GRAD611 course was genuinely one of the more unusual yet useful courses I’ve taken during my graduate career. It’s provided me with a wealth of material to think about. I've listed some fairly abstract observations, but the lessons about time management and conflict resolution have already proved valuable as well. I’ll have to see what kind of lasting effect all this material may have in six months or a year from now.

"...every one of them is slowly going mad."

I found this blog entry about how much programming sucks though Lifehacker today. If you were to ask me what the top problem with programming is, I'd say something to the effect of "programs are written for computers rather than for people" or "code is like a hammer you have to read" and so on. (You didn't ask me about programming but I'm going to tell you anyway.) I'd suspect that most of what makes code "bad" comes down to the inherent differences between computers and human beings. Humans tend to freak out without context while computers don't need reasons to get things done. Humans see value in hard work, so they'll hammer away at the same problem for weeks or years; a computer will do the same but we don't see any value in its long-term labor unless there really isn't a faster way to do it.

So, I think I interpreted the blog post differently than Lifehacker did. Their idea was "The good news, if you're learning to code, is you don't have to worry (too much) if your code is bad." The impression I get is that you just can't write good code unless you're also doing good writing. That means you're simultaneously writing for an audience with perfect comprehension and no consciousness (computers, that is) and for human beings with plenty of consciousness but far from perfect comprehension. That doesn't sound fun at all. The solution most programmers use is to not even bother.

A few choice quotes from the post echo these sentiments:

Not a single living person knows how everything in your five-year-old MacBook actually works. Why do we tell you to turn it off and on again? Because we don't have the slightest clue what's wrong with it, and it's really easy to induce coma in computers and have their built-in team of automatic doctors try to figure it out for us. The only reason coders' computers work better than non-coders' computers is coders know computers are schizophrenic little children with auto-immune diseases and we don't beat them when they're bad.

The human brain isn't particularly good at basic logic and now there's a whole career in doing nothing but really, really complex logic. Vast chains of abstract conditions and requirements have to be picked through to discover things like missing commas. Doing this all day leaves you in a state of mild aphasia as you look at people's faces while they're speaking and you don't know they've finished because there's no semicolon. You immerse yourself in a world of total meaninglessness where all that matters is a little series of numbers went into a giant labyrinth of symbols and a different series of numbers or a picture of a kitten came out the other end.

It's a good post. It's very cathartic.

Today's paper is: 

Legrain, P. & Rain, J.-C. Twenty years of protein interaction studies for biological function deciphering. Journal of proteomics (2014). doi:10.1016/j.jprot.2014.03.038.

I keep changing the reference format. This really shouldn't bother anyone but me.

The take-home message: There's a lot of protein interaction data out there! Contrary to popular belief, most of it isn't just false positives. Rather, most of this data reveals actual biological complexity. Proteins may just interact with more binding partners than we originally thought.

A few awkward points:

• Both of the authors are experts in the field but are also employed by Hybrigenetics, a company providing protein interaction screen services. They don't advertise the company's services specifically so I suppose it isn't really a conflict of interest. I still grow concerned about such things.
• The title sounds odd. Couldn't it have been "Twenty years of biological function deciphering by protein interaction studies"? I think it's the word "deciphering", mostly.
• The entire review sounds a bit strange, actually. I assume it's a result of English as a second language. It does make some conclusions hard to understand, i.e. "Almost 2000 different proteins were analyzed over six time points, covering four orders of magnitude in terms of protein abundance. In those papers, the aim of the purification process is no more the isolation of a protein complex but just a way to zoom in a specific part of the proteome", which sounds dismissive.
• More specific references to recent interactome-dependent functional studies would have been nice. As they mention, there have been thousands, but it continues to be an active research venue. It looks like the authors just forgot to add some references in other sections: i.e., "..in different cellular contexts (for review on affinity-purification coupled to mass spectrometry, see)".

These guys made an early protein interactome of Helicobacter pylori so I can't complain too much.

I never seem to remember the name of the film Mafioso. It's the one with the Italian guy who gets shipped to NYC by the mob. It comes up in conversation every so often but its title is just so generic that it's hard to recall.

Here's a neat little story about frozen frogs. The basic idea is this: wood frogs freeze solid over the winter, though that's not a problem since they can keep ice out of their cells (otherwise, all those ice crystals can really mess up those frog tissues). They do it by using glucose as a cryoprotectant and a specialized glycolipid as an antifreeze.

The paper in the Journal of Experimental Biology is here.

Beats!

Music for today - like many on Youtube, this guy does very high-quality song covers. The difference here is that he covers electronic-heavy songs that would be impossible for anyone to cover without a finely-trained ear, perfect timing, and just the right batch of equipment. I usually prefer covers to move in entirely new directions (the lady and I have been musing about what a female-fronted cover of December, 1963 would sound like*) but these are impressive on a more technical level.  Here are a couple.

A cover of Lovely Bloodflow by Baths. That whole album is wonderful.

A cover of Windowlicker by Aphex Twin. He doesn't quite capture as much of the original's classically weird atmosphere but that may be impossible.

A cover of Lost and Found by Amon Tobin. This is the live version, for reference.

Courtesy of this Metafilter post.

*A good cover. There are some on Youtube but this is the best one I could find, if that tells you anything.

Hello there! You may have noticed this blog transitioning to more of an electronic portfolio. This means that it will be less of a collection of musings and more of a collection of musings with a good bit of Context included. The rambling journal entries are still a primary focus. Now, however, you can learn about me in the "About" tab up there. I've included my personal mission and Curriculum Vitae. There's also a tab for Research: this page describes my current area of study. More material is on the way.

On networks of the social variety

It's a strange time when I'm feeling better about Facebook and more uncertain about more specific social networks. In theory, the Book of Faces really is the internet's Walmart: it's a place to get all your social interaction needs as long as your needs aren't too specific. It's great for small talk but actually quite inefficient for any kind of extensive dialogue (to see what I mean, try picturing your next Facebook comment thread as a real-life conversation. It gets pretty difficult in those 10+ comment rigmaroles). The same goes for Twitter.* Even so, there's something to be said for small talk. It's better than no talk at all.

The constant level of background chatter is also preferable to noise with a perceived sense of urgency. In real-life terms, I'm talking about ringing phones, ambulance sirens, or other warning klaxons. These are notifications designed to get your intention; they signal immediacy and the need for rapid action. That phone isn't going to ring all day and that ambulance may need the road you're on. A bit of that urgency shows up in email and social networking messages. In each case, we see a tally indicating how many new requests for our attention there are today. Most of those cases aren't even as urgent as a ringing phone. We can ignore most of what happens on Facebook without any cost.

I've been trying out Researchgate over the past few weeks. It's one of the smaller, more specific social networks I alluded to above. It came strongly recommended by folks in my personal development class. Researchgate is essentially a social network specifically for scientists. Each user has a profile as with other sites, but the focus is less on their biographic details and more on their scientific accomplishments (read: publications). The site is well-designed and leverages a more natural approach to networking than sites like Linkedin do. Connection suggestions are frequent but appear to be weighted in favor of real-world contexts (i.e., colleagues in your department, people in your field, or authors you've cited) rather than a largely generic network structure.

The mildly irritating part about Researchgate is the question-and-answer portion. Much like Stackoverflow, it's a forum for technical questions sorted by method or scientific topic. Unlike Stackoverflow (or even Reddit, for that matter), the moderation is minimal. Many questions are hardly questions at all. I can excuse the lack of English proficiency in many cases but it renders many questions impossible to interpret. In other cases, the phrasing is nearly perfect but the question asker fails to provide anything but the most basic details. The worst part may be the sense of urgency: these questions give the impression that entire careers are on the line. A wrong answer, employed in earnest, may waste weeks or even months of valuable research time. I know it isn't my fault if people don't know how to ask helpful questions or how to take advice from internet strangers.** Social networks are just enough of a potential waste of time as it is.


*I'd suggest that Twitter is the Starbucks of social interaction. It's ubiquitous, frequently noisy, and redolent with fashionable credibility, yet even the people who use it often don't seem to devote much mindspace to it. It's usually pleasant yet generally forgettable.

**This is the way.


Additional note to self: don't forget that Biostars exists. It's Stackoverflow for bioinformatics.

Today I found out about the grid.arrange function for R (it's in the gridExtra package). It's one of those things which would have been useful to know about years ago. I just found it on a Stackoverflow answer today. The function just takes plots and squishes them together into a single canvas. It's easy, too: just enter

grid.arrange(p1, p2, nrow=2)

and you have everything in one place. The results look great with ggplot's faceting, too!
The extensive package library is absolutely one of the nicest things about R.

Despite the absolutely ideal weather this past weekend*, I spent a small chunk of time beginning to learn Ruby. The programming language itself seems fun and friendly; it's billed as a conceptual hybrid of Perl and Python with the object-oriented nature of something like Java. There are a few reasons why I'd like to learn the language:

1. Learning new programming languages enhances understanding of the others. My Perl and Python can always be improved.
2. I've seen a few bioinformatics-related job postings lately which specifically mention the desirability of Ruby experience. They're usually talking about Ruby on Rails and its use in web development. 
3. It's either that or go back to learning Haskell. As far as learning a new language goes, most programmers seem to take Ruby seriously, at least.

I do have a few concerns.

1. Is Ruby (or Rails) becoming obsolete? There's clearly room for a great diversity of frameworks in the scope of web application development. I'm also not qualified to answer such a question. Programming is just one of those areas where a newly-learned language or skill can quickly become a dusty relic. Every framework might as well be Esperanto in the long run: they all have their strengths, even if the only strength is facilitating communication between the right people.
2. Will I ever really need to know Ruby (or Rails)? This question is even more difficult to answer, but I'll give it a try: "probably not." There will always be someone with better code than mine and it may even be in a different language or even an entirely different framework (for all I know, even scientific applications will be most frequently run in a mobile OS in a decade from now). 

Learning for fun seems like the best plan of attack. I can do it at my own pace without worrying about how applicable it is to Doing Bioinformatics. I'll just have the background to know it when I see it. 

*Here's a shot of the grounds at the University of Virginia.

Brooks Hall.

I've been enjoying the short "Futures" science fiction stories in Nature since they started. They tend to be concise, punchy, taut, and perfectly suited for the science-savvy audience. The most recent entry, "How Kameron Layas rode out the crash", is an ideal example. It breezes through some post-cyberpunk hallmarks without getting bogged down in anything but the most critical details, yet hints at a fully-fleshed periphery. It might even make a nice novella.

The author is Rahul Kanakia. The guy studied economics at Stanford but now writes SF. It's a natural progression but not a common one. He's also just a tad older than I am, a sure fire trigger for the "what are you doing with your life when this guy has already written a bunch of novels" effect.  This is alleviated somewhat by his great blog.  It's very analytical and unpretentious. If I ever decide to give up science for science fiction, I'll have to follow some of his examples. He's not big on advice, though.

This is the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto.

That's a nice-looking building. It was built in 2006 and really captures a particularly minimalist glass-and-color-burst aesthetic (the building reminds me of a larger, more technical Pompidou Center at least, and that building has been around since 1977). I'm curious about how energy-efficient all that glass is.

I think I just like labs with plenty of window space. It may be that the natural light cycles provide a constant reminder of the power of omnipresent natural processes. Or, it may be symbolic of the open exchange and transparent review characteristic of an ideal scientific process. The colors are nice, too. They're always a great way to find your way around a building and orient yourself.* Little details like that can really make the process of science much more enjoyable and efficient.


*In the absence of colorblindness, of course. Perhaps each area of a building could have a corresponding color and pattern.

I felt very caffeinated today. For me, the line between "fairly awake" and "very caffeine-stimulated" mostly appears to be a function of when I'm drinking it rather than a function of coffee volume consumed. Late afternoon seems like the time when caffeine is most effective (or maybe a little too effective, depending upon the level of focus the day requires). A few recent papers and at least one science blogger explain this effect in terms of cortisol levels and the circadian rhythm. See also: the concept of the zeitgeber.

I'm also reducing the level of anonymity for this blog, as you may have already noticed. This trend will continue. The person writing this is the same person who does everything else that person does every day.

Distant roses and yoga poses

Today I read about Sarcopoterium spinosum, a species of flowering plant common to the Mediterranean and Middle East. It's not an especially interesting plant - at least not to me. I'm not entirely certain why I focused on it. Perhaps it was the idea that this plant is quite common in some areas yet poorly studies. Some folks seem to think it's a potential source for an antidiabetic agent (but that's in the Journal of Ethnopharmacology; I neither have access to this journal nor can read the linked abstract without raising an eyebrow to the point of strain).

Unrelated: I'm been trying to take moments to be present lately, i.e. stopping to breathe and focus. I'm skeptical of most things which would look ideal on pamphlets for yoga classes but hey, meditating is really nice and much-maligned. Most notably, it pays to notice what's going on around you or perhaps even because of you. It's nice to notice when you're happy, too. Somehow that often appears to be treated as a separate idea (noticing you're happy, that is).

Dang, that guy is quotable.

I was trying to batch-rotate a whole bunch of photos today in Ubuntu 12.04 (it's 2014; maybe it's time to try out Trusty Tahr) but my usual solutions just weren't cutting it. Shotwell doesn't even have batch options, as far as I can tell. I've used digiKam before for batch editing but it doesn't even appear to import files anymore. Luckily, I found the Nautilus Image Converter. It can rotate and resize images right from the file manager, just like in, um, most recent versions of Windows. Anyway, problem solved.

Music for today is Solyaris - Achieving Sky True through Vertigo Vortexes.

Have a listen. It's spacey.

Anonymity, the Web, and whether people still use the term "the Web" in conversation

My Wikipedia username used to be a fiction. I changed it recently: it was time to cease being anonymous in that forum.* I didn't do it because of other Wikipedia users. If anything, I've always been a bit worried about the prospect that today's editor, blindingly-furious with me for my edits to their favorite page but completely incapable of actually communicating with anyone about it, will be tomorrow's supervisor. Academics can be tricky that way. By that same token, however, I changed my Wikipedia name so people begin to see my name attached to their favorite subjects.

I spend a fair amount of time writing about microbiology, whether it's online or for some kind of eventual peer-reviewed research**. The chances still seem pretty slim that academics will ever take Wikipedia seriously (and that's fine! It's just an encyclopedia, right?). Many of these researchers are unfortunately intent on citing Wikipedia in their articles. It's still pretty neat to think that the first words someone may read after googling the name of some bacterial species may be mine. Er, partially mine.

Maybe that whole shared-content aspect is the real stumbling block. Academics love the peer review process because it lets People Who Know What They're Doing evaluate People Who Are Doing Something Similar Yet Different. The process works just fine when it's partially anonymous; most people are kind in their everyday interactions but have a license to be critical when their identity is hidden. Pseudo-anonymity doesn't provide the same kind of protective shroud. It's really more of a dissociation effect in which a distinct aspect of one's personality is brought to the forefront.

I'm certainly not an expert in the field of anonymity. It doesn't matter because this is a place where I can write about things I may know very little about. I can do that more easily because my Real Name doesn't have to be responsible for it.  


*Not this one, though! If you're reading this, you already know who I am. It's the internet equivalent of wearing a false mustache.***

**That's all online now, too. I've done much more writing under a pseudonym than under my Real Name if you don't count classwork.

***The meatspace equivalent of wearing a false mustache on the internet is probably something like "breathing" or "eating lunch" or "sinking into a creative morass."

Today's paper is: 

Bansal-Mutalik, R. & Nikaido, H. Mycobacterial outer membrane is a lipid bilayer and the inner membrane is unusually rich in diacyl phosphatidylinositol dimannosides. PNAS 111, 4958-4963 (2014).

The shortest-possible summary: Mycobacteria like M. tuberculosis have cell walls but they have nice, thick lipid membranes, too. All these layers add up to protection from antimicrobial compounds: the bacteria won't get killed if antimicrobials can't even get inside them.

Today, I read the following paper: 

Yurlova, L. et al. The Fluorescent Two-Hybrid Assay to Screen for Protein-Protein Interaction Inhibitors in Live Cells: Targeting the Interaction of p53 with Mdm2 and Mdm4. Journal of biomolecular screening 19, 516-25 (2014).

This one is really just about a fairly simple method to assay protein-protein interactions. It's an advertisement: the method was developed commercially by ChromoTek Gmbh and is sold as a kit. The basic idea is that proteins are expressed in Baby Hamster Kidney* cells as GFP and RFP fusions. The GFP-fusion baits also have LacI, so they'll end up bound to lac in the nucleus no matter what happens. The RFP-fusion preys should just float around the cell unless they interact with the baits, at which point they'll also be present at the same spot as the GFP. The process is reversible, so an interaction can be observed in real-time as it is disrupted, i.e. by some variety of specific protein binding inhibitor.

I probably won't use this method much myself, but it's quite simple and looks like it could be convenient for screening potentially therapeutic small molecules or peptides. It would be nice to see a paper published about the method's applications by groups other than ChromoTek employees.

*There's something about the word "baby" that makes it difficult to take seriously. This is an established cell line and has been in use since the 60's.

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.

I don't normally feel unnerved about the omnipresent social-networking morass persistently enveloping the modern internet. It's clearly a social phenomenon and an admittedly interesting one at that. Even so, I can't help but feel a tad creeped out when. say, I edit a company's new Wikipedia page and said company's founder looks up my Linkedin profile a few hours later. He doesn't even leave any snide comments or anything, he just looks at it, a feature seemingly unique to that particular network. It's not easy to find my LI profile from my WP one without some Internet Detective work so it really just comes down to a big "why?".

Why do I care who feels like being strange on, god forbid, the internet?
Why do they go and do it anyway?

(Of course, the Wikipedia Internet Detective also felt like looking up one of my email addresses and sending me a passive-aggressive nastygram. Maybe a better question is "why do people get offended so quickly on the internet?")

Here's my glitch for the day.

We talked about the Peak-end rule in the development class this evening. It's an interesting heuristic, if perhaps an oversimplification. We discussed it in the context of giving presentations but I'm curious about how it applies to other presentation-like experiences or even whether a collective group of people tends to define the "peak" of a shared experience in an identical manner.