Bitesize Bio is shiny!

I just discovered Bitesize Bio, an awesome site full of discussions of common molecular-bio lab questions and problems. It has an RSS feed but is also set up with categories and menus for non-blog-style browsing. The ~5 posts I've read have all been informative, well-written, and interesting. I got a couple about interesting new techniques, a couple about theoretical questions and their practical consequences, and a couple about being a good grad student or a good mentor. It's really shiny, especially for a new lab member like me who wants to know the reasoning behind the magical incantations we sometimes do. "Wash with 0.75mL Buffer PE"? What does Buffer PE even do? ...OK, that's a cheating example -- Buffer PE is a proprietary mix from a commercial kit (but I'm told that after you add ethanol to it, as you must, it's just an improvement on straight ethanol).

For example, I just read an article about touchdown PCR, a neat hack on traditional PCR.

Sometimes in a PCR reaction you'll have trouble with the primers binding in incorrect places, because there happens to be some random sequence in your sample that's sorta-kinda complementary to your primers. Then you get nonspecific amplification of random crap, which can drown the gene fragment you actually wanted to amplify. What do you do?

You can calculate the optimal annealing/melting temperature (Tm) of your primers, and make sure to do your annealing step at that temperature. But random salts and stuff in your reaction can affect the Tm, so the calculated Tm is only an approximation. And at any temperature reasonably close to the Tm, even if it's not optimum, some annealing will happen. Maybe not much, but some. That's thermodynamics for you.

The idea of touchdown PCR is that there's a sweet-spot temperature where, statistically, it's too hot for nonspecific annealing, but just cool enough that the correct annealing can happen. You can't know exactly where this temperature is -- and you wouldn't want to run your whole reaction at that temperature anyway, because you'd only get a small amount of primer annealing and your yield would be low. So instead, for your first cycles you use an annealing temperature significantly higher than the calculated Tm for your primers (about 10 C higher). Then, in subsequent cycles, you gradually lower the annealing temperature. So in early cycles, only a few primers will anneal, and they'll almost all anneal to your actual sequence of interest, and not to random other sequences that are close-but-a-little-off. By the end of the cycle, you've amplified your correct sequence by a little bit relative to incorrect sequences. Run through several more cycles, and by the time you get to a "standard" annealing temperature where nonspecific annealing can happen, you've hopefully amplified the correct sequence quite a bit already, so nonspecific annealing becomes less of a problem because there are just more copies of the correct sequence available for the primers to bind to.

When I read about that, I was blown over. It's such a clever thermodynamics hack! -- it takes advantage of the fact that chemical reactions (DNA base-pairing or anything else) have fuzzy, stochastic behavior. For a given reaction, there isn't a sharp cutoff temperature where it goes from "too hot to react" suddenly to "OK now reaction proceeds fully". It's fuzzy. If it's too hot, a few molecules will react. Get a bit closer to the optimal temperature, and more molecules go. If you have two competing reactions with slightly different optimal temperatures (like specific and nonspecific annealing!), it's like having two bell curves overlapping, centered at slightly different values. You can find a value where one bell curve is acceptably high and the other is very low -- and then once you've amplified your chosen sequence N-fold, the game changes and you don't have to worry about the incorrect sequences nearly as much. It's like magic!

References (from original post):
1. Roux KH. Genome Research. 1995. 4: S185-194.
2. Mattick JS et al. Nature Protocols. 2008. 3(9). 1452 - 1456

New Look & Feel!

So I changed the blog template.

The main thing that bothered me about the old template was that the main text column, the most important part, was of fixed width. Which is annoying if you have a wide monitor. With this new template, go ahead and change the width of your browser window, and the Dendritic Arbor will change right along with you. We strive to provide a customizable reader experience. We strive to be adaptable, plastic, and dynamic, like actual dendritic arbors.

(It also bothered me that approximately 80,000,000,000 other people are using the old template. Then again, this is Blogger, what was I expecting, hmm?)

I chose this particular theme via the complex and deliberate heuristic of seeing which one looked the most like the one Larry Moran picked for Sandwalk. I've been reading his series on protein structure and admiring Sandwalk's look-and-feel. I guess this is the exact same theme as Sandwalk has, just with different colors.

By the way, the protein structure series is excellent and here are links to all its items. There isn't really a 'best' order to read them in, but I've put them in an order that sort of makes sense.

Evolution and Variation in Folded Proteins
Levels of Protein Structure
The Alpha Helix
Beta Strands and Beta Sheets
Loops and Turns
Examples of Protein Structure

Why I am a hard agnostic

I believe that the nature of deity is both unknown and unknowable (by humans).

As I understand it, "the nature of deity is unknown (and may or may not be knowable)" equals 'soft' or 'weak' agnosticism, and my position is 'hard' or 'strong' agnosticism. I was a soft agnostic up until relatively recently.

(Quick aside: that terminology bothers me because it's possible to be a strong weak agnostic -- i.e. you believe very strongly in the soft-agnostic position -- or a hard soft agnostic, or also a soft hard agnostic ("I'm pretty sure the nature of deity is unknowable as well as unknown"). Not sure what would be good alternative terms, though. Also, hard agnosticsim != militant atheism.)

I've been fairly sure for many years that the nature of deity is unknown, what with implausible theologies and the power of science, etc etc, blah blah woof woof -- this argument has been made, and people have responded to it, a million times.

There are two possible arguments, I think, for why we cannot know the nature of deity (as opposed to merely "we don't know it, but we might figure it out"). One is the "perverse liar god" argument, and it's sort of tongue-in-cheek. If there's an omnipotent deity, then it could make itself unknowable, never mind why it would want to. It could even put on an understandable mask while leaving its true nature hidden.

The other possible argument is "fundamental limits of human understanding". The human brain may be the most amazingly complex awesome thing in the universe, capable of conceiving arbitrarily complex and abstract ideas... but is it capable of understanding something omnipotent, omnipresent, omni-everything, possibly vaster than the universe? I highly doubt it, given how hard it is to truly grasp (say) the sheer size of a galaxy. (And I do mean truly grasp. Saying "oh, it's so many frillion light years across" does not count.) A galaxy has got to be a lot smaller than an omni-deity.

You'll note I said "fundamental limits of human understanding", not "fundamental limits of any understanding". I don't doubt that an omnipotent deity could understand itself perfectly well. It's perfectly possible that there are forms of understanding out there that are orders of magnitude more powerful than our piddling little thoughts, or maybe even have a completely different basis -- call them "super-understanding". But given that humans are limited to human understanding, can we understand super-understanding? I doubt it.

(For a very readable, math-flavored analogy to the topic of super-understanding, see Scott Aaronson's fabulous essay Who Can Name the Bigger Number?, which you should read anyway. He discusses Turing machines and Super-(Super-Super-...)Turing machines, among many other fascinating topics.)

And by the way, I have high standards for what I'm willing to call understanding deity. I'm not willing to settle for a grammatical string of English words, or a bunch of math, or whatever, that describes deity perfectly. I am perfectly capable of 'understanding' (sneer quotes!) a sentence like "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, and truth", in that I know what all its words mean and I can parse the sentence, because that is perfectly fine English. But can I fully appreciate the impact of a spirit, infinite, eternal and unchangeable, in its being, wisdom, power, etc? Can my body generate a sufficiently large visceral/emotional reaction to the import of that idea, or will it run out of neurotransmitters first? Can my humble heart and mind contain the infinite? I think not.

Now, since I'm feeling a bit Hofstadterian, try this one on for size: "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, truth, abstraction, recursion, subtlety, and inscrutability." Can this new, improved sentence give us a true, visceral understanding of an omni-deity? It's certainly an improvement.


(God-sentence is from Chapter 7 of Anne of Green Gables. I love that book.)

The Right Way to Respond to Getting Hacked / Cracked

Wired: Boston Subway Officials Sue to Stop DefCon Talk on Fare Card Hacks

Three MIT students have figured out how to hack the fare card system used on the Boston-area public transit ("the T"), to ride for free, add money to a stored-value card, and other such things. They cracked both the RFID card and the magnetic-stripe card. Here is a PDF of their presentation.

They were planning to give a talk on their discoveries at DefCon, the big annual hacker/cracker convention. The Massachusetts Bay Transit Authority (MBTA), which runs the T, sued them to prevent them from giving the talk. The talk will not be given. The students' faculty advisor, Dr. Ron Rivest, is being given a hard time.

The MBTA are going about this exactly the wrong way! (Although their response is understandable.)

Security systems are only trustable if they are thoroughly tested in actual use -- including normal users, hackers, and crackers. No matter how hard the MBTA try to hush up their security flaw, it will not make their security flaw magically go away. They should fix the flaw. Yes, it will cost money, but my sympathy is limited.

It is basically a given that many people will hear about this security flaw, whether or not there is a DefCon talk about it. Hello, Internet. But if people hear about this flaw only through underground/unofficial channels, what impression does that give them of the MBTA? It gives the impression that they either don't know about the flaw, or know about it and aren't doing anything about it. It gives the impression that the people who run all of Boston's public transit are a bunch of incompetents.

Moreover, by stage-whispering "Shh! Don't tell anyone about this!", they're also saying "Hey, this is significant! And leaves us very vulnerable!"

(By the way, if their goal is to decrease the number of people who hear about their security flaw, they have failed dramatically, because it's getting all over the news now. For example, I don't know anything about the presentations at DefCon, but now I know there's a security flaw in the subway system I use all the time, precisely because they're suing my classmates over it.)

What should the MBTA be doing? Shouting this as loudly as possible: "Yes, we have a security flaw! Thank you guys so much for pointing it out! We're working around the clock to fix it!" This would give the impression that the MBTA is run by intelligent people who can face reality instead of frantically trying to make it magically disappear. People would realize that the MBTA is serious about fare security.

The "Fare Security: SERIOUS BUSINESS" attitude would help decrease all kinds of subway sleaziness, including people who break fare security by the super-advanced hack of jumping over the fare gates. Not to mention things like littering, graffiti, and panhandling (none of which are huge problems on the T, I'm glad to say!). If I see someone fare-jumping, it makes me think the subway system is for shit anyway, so what does it matter if I stick gum to my seat?

And besides, the MBTA's anti-hacker attitude will just annoy crackers and make them more inclined to crack the T fares. Being realistic, and trumpeting increased security, will make crackers less inclined to attack the T.

Come on, MBTA. Have the grace to admit you've been hacked, instead of going into denial. Fix the vulnerability. Show us all you're serious about fare security. In fact, why don't you talk civilly to the people who hacked you? I'm sure they could help you build a better system.


...And, because I need some levity, here's a related episode in the adventures of Domo-kun. Hooray, cute pictures.

Some programming resource reviews

Since I've been teaching myself, and especially since I've been flirting with several different sources rather than settling into a steady relationship with any particular one, I thought I'd share my impressions.

So you know where I'm coming from: I took AP Computer Science AB (Java) in junior year of high school. Then in senior year we had a semi-experimental Scheme class based on the classic SICP (see below), but nowhere near as hardcore. Because Java and Scheme are so different, and because I forgot a lot of Java over the intervening summer, this amounted to me learning to program two separate times with very little cross-contamination.

After that, I didn't write so much as a line of code for my whole first year at MIT. (Yeah, I know -- how could I?!?, etc.) But somehow a lot of vague programming ideas seem to have stuck in my brain, making it much easier to (1) learn a new language, and (2) re-learn programming in general. So I'm somewhere between 'rank beginner' and 'person who wants to pick up a second language after their first CS class'. This will affect my assessment of resources.

>> Learning Python, Mark Lutz & David Ascher

...Comprehensive, I suppose. It's the O'Reilly book, which gives it lots of reputation points. It goes into a lot of detail about basically everything (I'm reading it online, but the dead-tree edition is quite hefty). Tables of built-in integer and string functions, that sort of thing. Even -- get this -- more than one chapter on getting Python to run on your system, choice of IDE, and how to run programs you write from a variety of situations. This makes it surprisingly useful as a reference, for a book with the word "Learning" in its title.

The thing that bothers me about this book is that it can't seem to decide where it's aiming. It's definitely a programming book, not a computer science book; but it's in between "dense comprehensive tutorial/reference for people who already know what they're doing" and "learn programming from scratch using Python". For example, it explains the ideas of iteration and recursion, gives very basic examples, and discusses the general sort of situation in which you might want to use them -- and then a minute later it hits you with a lot of jargon and dense stuff. Curious approach.

Perhaps some of the confusion is because the authors are trying to take a "quick survey first, then dig into the details" approach on each section, and their definition of "section" is too short, leading to a confusing rapid alternation between the high view and the details.

I'm only up to the section on classes and OOP so far, because I've started to run into stuff I never learned or have forgotten; so I can't comment on the GUI section or anything like that, but I'm sure everything else is quite comprehensive.

>> Structure and Interpretation of Computer Programs, Abelson & Sussman

Ahh, the classics. Especially the classics that are available online, for free, in full, under Creative Commons, and not in a really irritating interface!

This is a hardcore nerdy book. It doesn't teach you computer science, it ties you down and throws computer science at you thick and fast, but in a totally awesome, non-evil way. It's really not a programming book, either -- the authors go out of their way to teach you the absolute bare minimum of Scheme syntax to handle the concepts they're presenting. This is kind of irritating if your goal is to be able to do practical things quickly (ha). But if your goal is to achieve nirvana, you could do a lot worse than this book.

Read the footnotes. They are snarky, and competently so, unlike the lame attempts at humor you see in most textbooks.

>> Teach Yourself Scheme in Fixnum Days, Dorai Sitaram

This is a straight-up no-frills tutorial for people who already know how to program, more or less. Reading this after having taken a SICP class was pretty interesting: I kept going "Hey! That piece of syntax makes it really easy to do X thing we were always beating our heads over in class, because SICP HATES SYNTAX OR SOMETHING." Hooray for actually doing things with Scheme. I'd gotten the (not entirely wrong) impression that Scheme was good for nothing but theoretical interest and formalism with a dash of AI.

I'm not sure whether to recommend reading this along with SICP. On the one hand, I tried it and got really confused. Part of the charm of SICP's syntax starvation is that it actually helps you figure out how to do things; they simply refrain from teaching you the four other ways to do it. On the other hand, Scheme can actually do stuff that's not all abstract and theoretical and weird, and this teaches you how to do that.

>> [pdf] How To Think Like A Computer Scientist: Learning with Python, Downey, Elkner, and Myers.

This, I think, would be a good book for a (dedicated) beginner. It starts right at the beginning with the very fundamentals, and keeps a great balance between new concepts and new syntax. I haven't gotten very far at all in this book, mostly because I've spent so much time on the O'Reilly Learning Python book, but I like it very much so far.

Plus, how can you say no to a book that's written in LaTeX? Seriously, now.

>> Project Euler

Oddly enough, none of the above books have enough exercises in them. Teach Yourself Scheme has none at all. Learning Python only has a few, once every five chapters or so, and they're all about catching tiny nitpicks that trip you up. SICP has plenty but they're geared toward teaching CS principles, not coding practice. How To Think Like A Computer Scientist has good ones but not many of them. I googled around but the only thing I found that wasn't too advanced was FizzBuzz, which wasn't enough.

Enter Project Euler. It's a site full of math puzzles, varying in difficulty from "ludicrously easy" to "frackin' impossible", and set up such that you basically have to solve them by programming. Things like "find the ten-thousandth prime number", too big to be solved by hand. Excellent!

The site is obviously run by people who know what they're doing -- all the problems are very unambiguously stated, with examples, and the site keeps your score for you. Once you've solved a problem, you can look at the discussion thread where other people post their code and discuss alternative methods. The other people, by the way, are brilliant, and come up with all these elegant methods and neat optimizations for you to imitate.

Look Mom, Tags! And a Coding Trance!

[Before I start, let me admit that I am still very much a programming n00b. Everything that excites me is probably old hat to the majority of the coding population.]

I like tags very much. They are a million times better than folders. 'nuff said.

I've been writing a tagging system. It's nothing special -- just something that pairs up items and tags, and can do some of the same kinds of lookup that the tagging systems on blogs can do. Have been wanting to do this for quite some time, so now I feel all accomplished :D

I haven't finished testing the thing yet, so there are probably a lot more mistakes hiding in there, but most of the ones I've caught so far have been pretty similar. I tend to confuse the actual tag object with the tag's name, and refer to one when I should refer to the other -- kinda like confusing the phrase "scientists are people too" with the tool that lets you do this. Same thing with confusing tagged items and the objects they contain. These are pretty easy to fix.

There are a couple more functions I want to write -- eg, I haven't got a thing that lets you organize the tags in order of frequency of usage (as they are in the sidebar). But I've got the majority of what I wanted. (And no, that doesn't include a GUI. This is strictly text-based, Python-command-line stuff.)

I guess I'm kind of excited because, back when I was thinking about teaching myself to program again, a tagging system seemed like kind of a big challenge -- one I could do relatively quickly, but a challenge nonetheless. And now I'm about 90% of the way there. It's astonishing how fast you can learn to program when you've already learned to program twice before! ^^

This is also the longest block of sitting-and-writing-code time that I've spent in quite a while. I seemed to fall into a sort of trance -- very focused, very losing-track-of-time. This is an interesting mindstate (not to mention a very productive one!), and I'd like to get into it more often. (It helped that some people over on the XKCD forum turned me on to the streaming lyricless music from Blue Mars, which bills itself as "music for space travelers". Despite the word "mars" in their title, I think they really mean "music for headspace travelers". I find it quite relaxing and focusing.)

Perverse, Ugly, Terrible Beauty

Neurophilosophy writes about amyloid plaques and Alzheimer's, showcasing this really interesting 3D rendering of the plaque's constituent protein fibrils -- larger picture with the original article at Discover. The article and the post are really informative and you should go read them because I'm not going to address their content. (Gasp!)

My first reaction on seeing the image was, "How strangely beautiful". Even though this is a picture of a prime suspect in an absolutely horrific disease. Even though it's got a rather menacing fire-and-brimstone color scheme. Even though I shudder at the idea of these nasty little fibrils snaking their way through my brain, withering neurons like the Goo of Death from Princess Mononoke.

It's well established that good, hardworking, well-oiled biology is a joy to behold (if you have the right mindset). Listen to PZ Myers rhapsodize about the time he got a close-up look inside his hand. Read Dr. Sidney Schwab's eulogies to the body unmarred, and to the regal liver and warm, welcoming intestine. You've all seen The Inner Life of the Cell; watch it again and marvel.

It's also pretty well established that diseased, shattered, out-of-control biology is ugly, ugly, ugly. Hear Dr. Schwab, again, on how injuries and cancer ravage and ruin the anatomy that was so lovely. And who hasn't shuddered (inwardly) at the sight of scabs and puckered scars?

But somehow, I find there's a genuine (albeit perverse, ugly, terrible) beauty to diseases and such evil things. In the same way that it's interesting to watch flames blacken and consume a sheet of paper, it's interesting to imagine a cancer burning its way through a tissue. There's an elegance to the way viruses hijack and pervert cells to their own nefarious ends. And so on. I'm not saying that I think diseases are a good thing, or anything that causes pain/death is "nice" or "pretty"; far from it. But can't you see the grace, the sweeping lines, the eye-drawing colors, of those evil amyloid fibrils?


(Having thus far skirted the edge of hell, with these paragraphs I commit my soul to the inferno.)

I'm quite the Douglas Hofstadter fan, and I'm right in the middle of rereading his book Le Ton beau de Marot: In Praise of the Music of Language. In the introduction, Hofstadter dedicates the book to his wife, Carol, who was "hit from out of left field by a strange and eerie malady with the disgusting name of glioblastoma multiforme... vanishing from our midst almost as suddenly as if she had in fact been hit by a bus, with so much of life still left in her... all cut short by some cell gone wrong." Le Ton beau de Marot is in large part a commitment of their shared soul to paper. The book is stimulating, beautiful, and moving; I cried when I read of her death and his grief. I don't mean to minimize any of that. But I have to disagree with Hofstadter on one point. I don't think the name glioblastoma multiforme is "disgusting". "Strange and eerie", yes, and awful and dreadful (in the sense of inspiring awe and dread). But not disgusting. There's even some euphony, some beauty in the sound of the term.

Of course, I say this as someone who has never lost a close and treasured friend or family member to cancer (and I'm very grateful for that!); I certainly don't blame Hofstadter for describing as "disgusting" a name associated with so much pain and grief. His reaction is completely natural; in fact there would probably be something wrong with him if he didn't react that way. You could as well say that I am incapable of tasting all the bitterness as that Hofstadter is incapable of seeing any of the beauty. Nothing wrong with that.

Gallery of nudibranchs!

Check this out: National Geographic nudibranch photo gallery. It's absolutely amazing.

I've seen a couple of nudibranchs underwater, scuba diving in Hawaii. It's neat to see them live and in context, but it being underwater, it's kind of dim and the colors are washed out. Seeing them in optimal photography conditions like this is really cool.

[h/t Pharyngula]

It makes a fella proud to be a scientist

Pharyngula linked to this amazing video that "compares creationism and science". Really, it's no comparison. [3:54]



You could watch it without the music -- none of the strictly visual beauty would be lost -- but instead, I highly recommend turning your speakers up to eleven, putting the video on fullscreen, and inviting all your officemates to come watch. Better yet, invade a conference room or a lecture hall for five minutes. It'll be worth it.

I found it incredibly affecting. Some parts had me cheering and yelling "SCIENCE: IT WORKS, BITCHES!". And some had me tearing up. I felt like a little kid again, all "when I grow up I wanna be a scientist!" I'm damn proud to be a part of it (or at least to be on track to become part of it).

Blogroll!

You might have noticed the shiny new section in the sidebar. Yes, I finally got around to making a blogroll.

...Well, more like a catalog of the RSS feeds I follow. Everything in that list is something I read religiously (which, given Google Homepage, is a much weaker statement than it used to be). I've seen blogrolls that have hundreds of links to blogs whose names start to seem awfully similar, and which sound like they cover mostly the same content -- so, more of a "recommended reading" list than a reflection of what the blogger actually reads on a regular basis.

Eventually, I'll flesh it out into a proper blogroll, but for now, I'm not experienced enough to evaluate a blog without following it for quite a while.

Edit: Also, I would have included my brother over at Mage's Plane, but he's just gotten started, so I'll give him a little time to build up steam. Right now what he gets is a tongue-in-cheek for using the same Blogger template as me, right down to the color choice. *shrug* Yes, this is a very common template.

What's This `Conlangery' Business? [Linguists and Conlangers, part 1]

[This will be part of a series of posts about conlanging and its interaction with academic linguistics.]

So, what is conlangery? It's not a popularly known art, so here's a primer for y'all who haven't ever heard of it.

The word conlang is short for "constructed language". Well-known conlangers include Ludwig Zamenhof (Esperanto), Marc Okrand (Klingon), and the revered JRR Tolkien (who once wrote that he invented Middle-Earth largely in order to give his beloved Elvish languages a place to live). We invent languages: spoken languages, signed languages, artificial siblings and alternative scripts for natural languages, artistic languages, logical languages, international auxiliary languages, mind-extending languages, you name it.

(I should warn you that conlangers, being naturally fond of playing with words, habitually `overgeneralize' and apply all kinds of grammatical forms to the word `conlang'. Just for starters, it's both a noun and a verb. A conlanger is someone who conlangs, what they create is a conlang, and the art in general is conlanging or conlangery. On top of that, the con- prefix has become productive, meaning it can apply to all kinds of invented/imagined things: conlangs, conworlds, conscripts (meaning writing systems, not military draftees), conreligions, consolarsystems, conbiology...the list goes on.)

The earliest known conlanger is Hildegard von Bingen, a 12th century German abbess. She's best known for her gorgeous music, but she also invented a language called Lingua Ignota ("unknown language"), which supposedly came to her by divine inspiration.

The best known conlanger...well, it depends who you talk to, but most people will name either Zamenhof or Tolkien, and here we come to a major split in the world of conlangery: that between auxlangers and everybody else. Auxlang is short for "international auxiliary language", and not to make any sweeping generalizations here, but the sort of people who make auxlangs are also the sort of people who have fiery and/or highly unconventional political agendas, and a lot of them are also shamelessly self-promoting. Unfortunately, if you're auxlanging in earnest, this isn't really fixable. You have to want the entire world unified, in some sense, by your language. And you have to think your language is not only `good' enough for everyone in the world to speak, it's `better' than the dozens and dozens of old failed auxlangs. A certain amount of crankery is inherent to the practice of serious auxlanging.

(Quite apart from the above, the vast majority of linguists and conlangers have a horrible visceral reaction to the thought of losing most -- if not all -- of the world's linguistic diversity. Who wants to replace all that culture, knowledge, and sheer beauty with something necessarily bland?)

(Yeah, and, in case you couldn't tell, I'm totally biased, and I freely admit it. Auxlangs are not all bad; any conlangery effort bears some useful fruit.)

So what about the `rest' of the conlangers? People conlang for all sorts of reasons, but the one that really unites us is, trite as it sounds, is love: love of language, its beauties, its intricacies, its elegances; and love of playing around with that in systems of our own creation.

This is not to say that there aren't divisions within the body of non-auxlangers. Probably the biggest group is the artlangers, like Tolkien, who conlang for aesthetics and elegance. (This is not to say that all artlangs end up looking like Tolkien's Elvish languages, all full of L and R and vowels everywhere with nary a `guttural' consonant. Conlangers have as much variation in taste as the general population. Plus, for example, there's a lot to be said for a language in which you can swear effectively. Imagine trying to shit-talk someone in Quenya or Sindarin.) At the very least, many hundreds of artlangs have been made, or at least started. My own language Tlharithad is a young artlang, though I sadly haven't had time to work on it since the beginning of the semester. You can find quite a few well-developed artlangs, associated with the fantastic conworld of Verduria, at Virtual Verduria, made by Zompist. I have to apologize to the many, many, very worthy artlangers that I haven't linked to, but for non-conlangers, Zompist's work makes a good place to start.

On the flip side of the same coin, you have the engelangers -- engelang is short for "engineered language" -- who design their languages to achieve a particular goal. There are logical languages, like Lojban, which are designed to eliminate ambiguity. And there are other engelangs, whose design goals don't really fall naturally into groups. A seminal example is Ithkuil, which has about five times the information content per syllable of natural languages. In the words of its creator, John Quijada, Ithkuil is "systematically designed to blend a high degree of communication of cognitive intent and meaning with a high degree of efficiency, i.e., to allow speakers to say a lot in as few syllables as possible." While I'm not intimately familiar with the language, I know the making of Ithkuil involved a lot of mindbending reorganization of cognitive concepts. For example, if you're indoors, the spatial axes around which you organize your speech are placed with respect to the long axis of the room! (Of course, JohnQ freely admits that Ithkuil is extraordinarily difficult to learn, and has in fact created a somewhat simplified version, called Ilaksh, for those of us without superhuman vocal tracts.)

It can be argued that artlangers are just engelangers whose design goal is that of beauty, rather that something more conventionally associated with the words "design goal". It's a little like the distinction between architects and sculptors: you have people who are clearly one or the other, people who are mostly one with a little of the other, and people like Michelangelo or Maya Lin who straddle the boundary so well that no one ever finishes arguing about which category they fall into. (And, as good linguists, we have no problem with this, knowing that strict definitions are artificial constructions, and everything is better described in terms of generalizations from prototypes.)

Next up: the enmity, such as it is, between conlangs/conlangers and professional linguists / linguistics research.

Another essay on killing lab mice

Ran across this essay, which aired on NPR's All Things Considered five years ago. I especially liked this bit:

When I started, sometimes I had to go walk around the lab building afterwards to take a breath and gather myself. Now it still upsets me whenever I have to kill mice, but I'm used to it. I think that probably some scientists do get over it completely; the mice become tools. Other scientists hire technicians to handle and kill the mice. The researcher works with the cells of the mouse once it's killed, but never encounters the living mouse.

But that's not how we do things where I work. In fact, the people I get along with best in my lab sometimes even talk to their mice. While we're herding a mouse towards one side of a cage or another we might say, "Come on, sweetie." Maybe if we're injecting a mouse with something and it squirms, we say, "OK, OK. It's going to be just a second." When we put it back in its cage, we might say, "There you go." And while the mouse is sniffing and inspecting its cage mates, we say, "There's your buddies." I was in the mouse room with a colleague of mine and I noticed her doing this. And I said, "You talk to your mice, too." She said, "Doesn't everybody?"

It really captures the tension between mouse-as-tool and mouse-as-animal. And the -- well, I don't want to call it a happy medium, but the medium that most good scientists find. I dare say that working exclusively with cells, and never encountering the organisms they come from, has got to be dissociative. Seems like it'd be a good idea to keep that perspective in the back of your head, that these little spots in a dish came from a living animal, and serve multifarious purposes in that animal, and do things besides sit in culture and express your marker protein or what have you. They grow, they thrive, and above all, they are more complicated than they seem, even when you take that last into account.

A scientist who gets too debilitatingly upset over the death of a mouse will never get anything done, and a scientist who doesn't care about the mice as living creatures will have less perspective and, in all likelihood, get worse results for not being personally involved with their care.

I don't recall ever talking to the mice, but I didn't handle them all that much. Pretty much all I did was scruff and snip, and then they couldn't listen anymore. If I have to do more involved mouse procedures in the future, I probably will get in the habit of talking to the mice, especially given that I already even talk to inanimate objects when I'm working on them.

Stir-fried wikipedia, anyone?

The highly estimable Language Log points out yet another instance of Chinese menu translator ingenuity. Wikipedia: now with even more uses!

For more on this phenomenon, see Engrish.com (marginally NSFW), which is devoted to collecting this sort of unintentionally hilarious bad English, mostly from Japan. Aside from just giggling at the bad translations, it's interesting to occasionally catch a nugget of linguistic insight. Well, I mean, the fine folks at Language Log can catch them all the time, but I'm an amateur, so I have to take what I can get.

A while ago, Engrish.com featured a shirt (which I unfortunately can't seem to find now), bearing the sentence "We are dumb and haven't intelligence apes." And I jumped out of my seat, because it made perfect sense to me. In English, that sentence means "we are dumb and do not possess apes of intelligence." Presumably the shirt-writers meant "we are apes who are dumb and do not possess intelligence." (Perhaps dumb here means mute rather than unintelligent -- a relatively subtle distinction, but I've seen Japanese<==>English dictionaries that do very well at this. Or, y'know, maybe it's just redundant.)

What English handles as a relative clause, "apes who do not possess intelligence", Japanese handles by effectively turning the verb "not possess intelligence" into an adjective. To say "we are apes who are dumb and do not possess intelligence" in Japanese, you say something along the lines of "we are dumb and non-intelligence-possessing apes", which is clearly the origin of the T-shirt.

Of course, there's also the complete nonsense, e.g. "I smell the smelly smell of something that smells smell", and the grammatically-correct-but-thematically-inappropriate text, a la this classic example.