30 November, 2009

Power Tools

Just when I begin to believe that maybe I am wise enough to use power tools.

28 November, 2009

Cloudy With a Chance of Meatballs

I make no secret of the fact that I still really like cartoons and comic books. Entertainment material written for children is frequently far more interesting, imaginative, and deep than the endlessly recycled fodder that keeps getting repackaged for grown-ups to consume. So I continue to watch them. In fact, the last time I went on a date-like date I went with Prime to see "Shorts" in Boston.

Anyway, last night I watched "Cloudy With a Chance of Meatballs" long-distance with Prime, and the movie almost got it. I am all for kids' movies that hype the coolness of science, such as "Meet the Robinsons" or "Dexter's Lab" and Cloudy tried really hard to do so. It accomplished the hype, but unfortunately it did so so well that it completely rolled right over a potentially great sub-story that could have brought the science hype to a perfect boil. In the movie, Flint is the errant mad scientist son trying to save his sardine town and inadvertantly makes food weather while Sandy is the weather channel intern who gets sent to the island right as the weird food weather starts happening. It turns out that Sandy, who was sent for being so very perky and nice, was actually a meteorology nerd growing up and that she chose to stop wearing her glasses and let her hair down to become socially accepted. Flint puts her glasses back on and likes her as a fellow hot science nerd, but then makes the mistake of ignoring the warnings of her science when his own mad science begins to roll out of control, thereby stunting her nerd-ful self-actualization. And even though Sandy goes on to help save the day with Flint, she still winds up in a backseat role and is never redeemed by her science in the face of those who made fun of her.

The film could have been a much more positive role for all young people seeing science if it had not just shown science as the province of a crazy dude and rather shown the benefit of including the female nerd's scientific expertise as equally valuable. That being said, Flint's habit of narrating his actions ("Planning! Welding! Wiring!") was pretty awesome, and it does not detract from my urge to wear a full-length cape at the lab bench sometimes.

26 November, 2009

Peritonsillar Abcess

On Monday night, while I was showering I began to feel dizzy and nauseous, so I reached for the wall of the tub to steady myself and instead abruptly found myself face-first on the floor outside the tub with no recollection of falling. So I picked myself up from my elbows and forehead and tried to figure out why I still had the shower in my hand. Logically the best thing to do was to get out of the shower and lie down somewhere with more padding as I was still rather dizzy and was entirely unsure of where my feet were. So I rinsed off the suds, turned the water off, reached for my towel, and promptly found the floor on the other side of it. Somehow this got me angry enough to stop feeling dizzy and I managed to make it into my room to dry off and put on pajamas. I set my alarm to wake me up in 1.5h and kept doing so throughout the night as a concussion watch. It didn't feel like a concussion so much as a bruise, but I wasn't going to take any chances.

Ordinarily, this kind of thing would prompt one to go see a doctor the next day. Not so much for me. I had lost my voice and was having great difficulty swallowing food and liquids 1.5d before, so I figured by that point that I was rather dehydrated and as such the hot shower steam simply got to me. No, it took another night where I couldn't tell the fever sweats from the drool and not even being able to comfortably drink water around the bellicose pin cushion that had taken up residence at the back of my throat to get me to seek medical attention.

By this point I could barely even manage a hoarse whisper, so after I'd managed to phone in an appointment at the student/staff clinic that afternoon I tried to legibly write down the timecourse that symptoms had emerged on. It helped. The doctor at the clinic looked into my throat and saw the same thing I had for the past few days, the right side of my throat swollen so much that my tonsils were stuck to it. I had attributed it to weird strep throat and expected it to start improving any time, maybe I'd leave with cyclosporin antibiotics and an analgesic gargle. She recognized it as a peritonsillar abcess, which is basically a very acute infection in a very limited site that gets massive neutrophilic infiltration and subsequent inflammation (pain and pus) and that if it was left untreated it could wind up occluding my trachea. So I was sent off to the ER at the university's hospital, trying to figure out how they were going to drain an abcess at the back of my throat.

I've had an abcess before. I developed a topical abcess on my chest one season where I was playing cello for Bach's "Double Violin Concerto in D Minor - Vivace" and practiced so much that the contact point for the cello on my chest developed into an abcess. But they're easy to deal with on the skin surface, even if it did open back up after draining right as I arrived at my stats class.

I arrived at the ER and was fairly quickly seen, and within about 1.5h they determined that I could have IV fluids, a dose of antiinflammatories, a round of cyclosporins, and morphine. They pushed all of these at once and the nurse wrapped me in warm blankets and suddenly I was a sublime cloud. The clot of burrs at the back of my throat was gone, and I was simply at absolute peace in a way that I have not been since last I saw Prime. I sat somewhere between wakefulness and dozing and I have no idea how much time passed in this state.

Then a resident walked me (I denied the use of a wheelchair because I wanted to see what it would be like to try to walk on morphine [not easy]) up to the otolaryngology clinic and sat me in a procedures room. A nurse bustled about and laid out far more surgical instruments than could possibly, POSSIBLY, be used at once, right? Once I realized that there was absolutely no way topographically that all of those pointy and sharp objects could be applied to the back of my throat simultaneously, I was greatly reassured.

Eventually, one doctor did the procedure and I got to help. First he sprayed the back of my throat with Lidocaine, which does not taste good but thankfully numbs that which tastes and followed it up with an injection of Lidocaine into the abcess. Next came a 10ml evacuation syringe, which drew out about 7ml of pus. Then there was a tiny little scalpel blade to widen the incision and another evacuation of a similar volume, and then I sat there dutifully holding the suction hose drawing away the remaining blood and pus into a bucket on the wall (no appreciable further volume). I'm now on a course of major cyclosporin antibiotics (more than 1.0g/d!), a course of antiinflammatory steroids, and some painkillers, and there will be a follow-up appointment to make sure the abcess hasn't reconsolidated and needs further drainage. It was also mentioned that there is a risk for repetitive abcesses here now and that I should consider getting my tonsils out to stop them from happening. On the last point, I'm not yet sure.

Abcess pus. Pic taken while doctor wasn't looking. I could make several inappropriate and disgusting Thanksgiving food references here, but I shall refrain for your sake.

UPDATE: Culture of above pus showed that the cause of the peritonsillar abcess was clindamycin-sensitive Fusobacterium necrophorum, which is apparently a normal microbial resident of the mouth (no satisfactory reference found for this yet save one that cites isolation of it from canker sores), but apparently it causes a hoof disease in sheep called scald and it survives in the soil of sheep pastures for years.

21 November, 2009

With a What?

For the hackerspace, I send out a lot of emails. Most of them get ignored, but some of them stick. One of the ones that got a reply was a request to tour a museum collection of rare and antique musical instruments that the university's music school owns. In one of the conversations we had with the outreach director of the collection, we decided that co-hosting an educational event that melds technology and music into a workshop for kids and their parents would be an excellent idea. This is what is referred to as a Make and Take, particpants register, pay a fee for parts, come and get taught how to make stuff, and then get to take it home with them afterwards.

So, like a good engineer scientist (hacker?), I started thinking about what kinds of musical/technology projects we could conceivably build in a few hours. A while ago, Abel Pharmboy, a fellow science blogger, scientist, and musician linked me to the trailer of "It Might Get Loud" which showed Jack White of The White Stripes making a primitive electric instrument out of a 2x4 plank. This got me thinking about what sort of materials an instrument pickup could be made out of with the eventual thought of making a plank guitar. The potential for a Make and Take with the music museum gave that notion impetus, so tonight I built a 2 string electric slide guitar.

Figure 1: It's not exactly science, but it does make noise!

I used a 1"x4" plank, the voice coil of an old telephone (has lots of 42G copper wire), some nails, a set of nickelwound guitar strings, 6 screws, and a glass bottle of Nantucket Nectar juice which was quite tasty.

Humbucker construction:
A humbucker is a type of electric guitar pickup that transforms the vibrations in the strings into an electronic signal. It is an electromagnet that projects a magnetic field perpendicular to axis through which the guitar strings vibrate when plucked, which induces a current. Some commerical pickups have a separate magnet for each string, and some have 1 rectangular magnet stretching under all the strings at once. I chose the latter option, and since most commercially used hardware is ferromagnetic, I figured I could use the dry-wall screws as the core of my pickup.

I began by trying to solder the 4 screws together. Turns out that silver-core solder doesn't stick very well to cold hard metal alloys regardless of how much I'd have liked it to. So I used some 20G copper wire on hand in the hackerspace to bundle the screws together. Next I tried to solder (stubborn-ness) the bundle of screws to an improvised Dremel bit to help me wind the 42G copper wire from the telephone voice coil around my ferromagnetic core more easily. This also didn't work. I wound up making a handle out of hemostats and hanging the voice coil like a spool from my soldering helping hands and winding it by hand. I got sick of this after 2h and decided the thick belt of copper wire now girdling the screws would suffice. Finally I soldered leads to the ends of copper wire (the trailing end and the beginning end that I left sticking out) and soldered that to the leads on a 1/4" audio jack someone gave to me. When I plugged it into my amp, it made clicking buzzy sounds, but this was expected since there weren't any vibrating metal objects nearby. I tried to simulate one by banging a stainless steel bowl around near it, but this doesn't work as stainless steel is a crappy magnet and it was annoying the other people present.

The guitar:
When I embarked on this phase of the project, I immediately regretted that the hackerspace doesn't have a T-square yet so I don't know if my lines are even close to even. Nonetheless, I began by plotting out a point near one end of the plank and nailing an E and D string through their winding holes to the board with skinny nails. Then I played with the placement of the glass juice bottle as an acoustic resonator and bridge and decided that about 4.5" was good for tension. I used 4 nails to create a little cradle/fence that keeps the bottle in place while also laying it flush against the plank.

Creating functional tuners was more difficult. I found 2 wood screws and tried to tie the strings around them to no success, hoping to be able to tune the guitar with a screwdriver. None of the knots stuck, they just rotated. I had expected about as much. So I hauled out the metal cutting bit of my Dremel and deepened one of the notches on the screw's head to be flush (made lots of pretty sparks that didn't start any fires). Then I filled the screw hole with molten solder and poked the end of the string into it and held it steady until it cooled, then used needlenose pliers to bend the string down to loop around the screw. This worked well, but since I had filled the screwdriver holes with solder, I had to use the needlenose pliers to tune, but tune I eventually did, with the supposed E string winding up tuned to a D2 and the supposed D string winding up as a C3.

The humbucker is stood up near the tuning pegs by 2 small nails.

It's quiet. At least, it's quiet when it's plugged in inasmuch as it has a very low signal to noise ratio. Acoustically, it is surprisingly loud and was causing loose screws and nails to bounce about on the table surface when laid flat. I had to run it through a pre-amp with the volume boosts, EQ boost, and gain all the way up to get an appreciable signal out of it. But once I did it was loud and gritty with a very steely twang. It is a bit awkward to play, but that's part of what makes it cool. I quickly found the sweet tonal spots on the neck of the guitar and began to bang out simple rock and roll chord processions.

The signal is loaded with tones of natural distortion, so much so that hooking up my Boss Bass Distortion pedal didn't impact the tone or intelligibility of its done much at all.

What I Would Do Differently Next Time:
1) Use an actual magnet for the pickup core.
2) Find a way to wind the copper wire around the core mechanically instead of by hand.
3) Wax the wound wire around the pickup to give it some insulation from outside interference.
4) Mill tuner screws with holes through them to thread the strings through. Find a kind-of-flattened bottle to use for the resonator to decrease the necessary height of the strings from the board so I can also make a flatter pickup.

18 November, 2009

Toaster the Psychic Organ Builder

So the other day I was standing inside of a 4-story pneumatic pipe organ while it was being played thinking to myself: "Holy crap I'm inside of a 4-story pneumatic pipe organ while it is being played!" when it occurred to me that maybe I might actually know something. For a while I've been feeling like I have spent so much time and effort learning about molecular biology that I no longer know anything actually useful outside of the laboratory. This feeling was jade creeping into the awesomeness of science, and I found it best to promptly shake it off like a dog after a bath and go roll around on the floor joyously with all my legs in the air. I mean, sure this science sometimes appears to be nothing more than moving tiny amounts of expensive liquids around while muttering vague incantations about hypotheses and replicability. But what it is, what molecular biology fundamental is, is me dissecting LIFE ITSELF with my MIND!!! I could have all the fancy tools an R01 can buy at my disposal and a hammock above my bench, but those things wouldn't mean crap for meaningful, insightful science if I didn't start by designing an elegant, productive experiment. It's like I'm telekinetic at the molecular level, because I have to imagine the true nature of all these stochastically interacting proteins, genetic elements, or other molecules and their aggregate behavior clearly, I have to fix it in my mind and strip away the limitations of my vision to harness the quiet power of chemical reactions and hydrogen dipoles to prove the accuracy or folly of what I have captured with my mind.

Sure, this science doesn't have the immediate satisfaction of swinging a hammer and building a chair, the delay to sate the fundamental human need to create and explore burns on a longer fuse, but oh, when it connects it is all the more beautiful. I may not be building a pipe organ, but I am reverse-engineering something many more times intricate when I can't even see it with my naked eyes. That. Is. Awesome.

15 November, 2009

We Need a Verb!

You know that thing that sometimes crazy people, or parents, do where they put their mouth on another's belly and then exhale forcibly, making a very loud and ticklish THWBBT!!! noise?

Why doesn't the English language have a verb for that, or at least a name!? Really, it'd only be decent and all...

04 November, 2009

On Recognizance of Competence

Recently I had some business cards with my personal contact information printed up to help me network more effectively and remain in touch with the awesome people involved in science and technology that I've been meeting. As these aren't for work, per se, they have a picture of a Velociraptor skeleton, a quote from Mark Twain ("The more you explain it the more I don't understand it." A good reminder to keep things simple and short, I think), and "Awesome Scientist #17" as my job title, even though it doesn't signify exactly where I work. I'm not sure exactly who the other 16 are. About this time, I realized something: people think I'm smart. This is strange.

I don't know that I'm smart. I don't feel any differently and I cannot imagine being any other way. Frankly, most of the time I feel stupid because there is so much that I do not know and that which I have captured in my mind is so insignificant compared to how much awesome there is to learn. I only know that I am smart by interacting with other people and seeing the reflection thereof. I used to be more reclusive and introverted, counting bacteria by day (doing science) and making music alone at night, but now I have been forcing myself out of that bubble and taking on challenges and actually talking to real people*, doing SCIENCE in the new lab job, and dropping awesomeness and scientific knowledge through the informal molecular biology classes I've been teaching in the Makerspace (Youtube soon). Through all of this, I have come to realize that people actually value my knowledge, experience, perspective, and opinion. I have more opinions than anything else, but it's still a bit strange because I still feel as though I haven't done anything truly awesome that deserves any respect yet.

I probably never will. I realize this, because I know that my ambitions and analytical nature will never let me rest because there will always be more science and/or awesome always going up or something else shiny will captivate my interest. The positive side of this, I think (self-delude?) is that it'll keep me busy, and that's a very good thing as a bored Toaster digs out his backpack of tools and starts taking things apart. The other positive of this is that by taking on more, I hold myself to doing more and am forced to learn how to synthesize all the enzymes to help masticate all that I've bitten off. I used to read scientific papers for fun, but now my boss sends me papers faster than I can read them. I used to make music just for my own enjoyment, but after doing in impromptu live set I have been volunteered to make live music at an art show in 10 days (and all I have prepped are 2 remixes of the Leekspin song). I used to tinker using just my own limited tools and experience, but now that I've helped create a cooperative makerspace I have access to a much wider range of tinkerables and tools (I even coined a new term last week; making a silly, simple mistake now has the swear word: "BLOOTLELOOT!" attached to it after I mistook a diode for a resistor and soldered it to an LED). I used to play with data for weeks just out of curiosity, long after the main aim of the experiment had been answered, just to see what I could draw out of it, but now I have so many data sets to mine that pure play has transmuted into teasing the data for the prettiest results.

These are good changes. It was silly of me to ever think I should first know what I was doing before trying. This is much more informative.

*Not that bloggers aren't real people, but Internet-based communication is easier because it has a backspace key.