20 December, 2009


It's about time I reworked the blogroll on this site and prettied it up all nice-like. So who am I missing out in my blogroll, and who is sick of being affiliated here?

18 December, 2009

Upon Intelligibility

I struggle sometimes to be comprehensible. Not in text when the letters and words are nicely kerned and standardized for you to see here and let scramble into your brain, but in person, in speech, over the phone and in front of people.

It's as if I speak like:


when I know I should be speaking more intelligibly, like:

but at the same time I know I should slow down enough that I can be understood:

so that the full meaning of my words doesn't get garbled together at the back of my throat before they ever have a chance to fly to your ears.

There are always so many thoughts fighting to tumble out all at once in a spastic flood, my mind whirring several paragraphs and tangents ahead at the same time even as the words around me filter in and touch off their own cascades. I have to stop and force myself to slow down, and the entire time I'm speaking slowly I can feel my mind tugging at the reins, revving to go faster, grumbling like dropping a manual transmission into 2nd gear at 80kph. It is frustrating to not be able to just blow my mind out of my ears onto projection boards like Kleenex and show those with whom I need to communicate everything at once.

Part of this is exacerbated by having had grown up learning a lot of my English from books instead of speech and from my father, whose English is good, but still heavily accented (according to other people, I cannot hear any accent at all). Even now I'm still re-learning words that I had learned to speak improperly and had been using for years. I learned the word "jalopy" to be spoken as "yah-loupe-ooh" from my father, and until I got into an argument with a salesperson about paint I thought that the "e" in "matte" was meant to be spoken.

At the same time, there are people with whom I can blaze away at a conversation, sentences whirring past like bullets. In the last lab that I worked, one of the other staff once remarked to me that she stopped even trying to listen or comprehend when my boss and I would start slinging ultra-fast science at one another and my boss in this lab is the same way (we practice speaking slowly at one another in our meetings). Many friends can also communicate this fast, which makes it all the more frustrating when I bang up against someone in the current of my thoughts that can't listen as quickly as I can deliver.

Nonetheless, these aren't acceptable excuses. If I believe I have something worthwhile to say, then the burden to speak it intelligibly is upon me and not upon my listener.

16 December, 2009

Toaster's Stewing Stew

I woke up this morning with an iron wrench knotted around my pancreas as my bowels squirmed and writhed, desperately lamenting the mounting loss of their comfortable microbiome blankets. The peritonsillar abcess I posted about recently came back at me again, and this time after a much more painful drainage procedure I was put on a more aggressive course of antibiotics with a broader spectrum to kill off all the problematic bacteria. Problematically, however, was the addendum that this course of antibiotics was essentially going to kill off all my gut microflora at the same time and that I should expect some uncomfortable adjustments to this. This morning was an example of that, with nausea and a feeling that my upper bowels were somehow melting like Jello left outside on a hot summer day. It took me a while to get going, and the attendant headache didn't help. However, this is preferable to my tonsils being so swollen as to almost close off my throat and render speaking difficult and most eating very painful.

I am not writing this panning for sympathy or support. I find it objectively interesting even as I am subjectively very annoyed by it all. Not only that, but I'll also get to completely re-engineer the ecology of my microbial gut flora! I am aware that Bacteroides and Lactobacillus species are by far most prevalent in most cases, but I am curious what effect an equal proportion of Firmicutes species would have upon my metabolic processing. I would also really like to know how the ecological profile of my microbiome is changing as I continue to take these antibiotics, but sadly I don't have the tools readily available. Over the past several months, I am aware that I had inadvertantly shifted the profile of my ecology by switching from easy, meat-heavy and blank cooking to mostly meatless (eggs, though) cooking with lots of flash spices, hot sauce, and whiskey. I wonder if I'll be able to jump right back into burritos, cookies, orange juice, Tabasco, and Jameson being my major food groups?

Anyway, in light of this rather unpleasant digestive shift, I am going to share with you one of the recipes I have recursively crafted myself:

The Stew!

Toaster's Fast Bacon Stew

500ml volume chopped carrots
750ml volume chopped potatoes, unpeeled
250ml volume chopped green onions
250ml volume chopped celery
0.5kg chopped bacon
0.5kg can of red kidney beans, drained
Handful of noodles (optional)
Spices (see below)

1) Boil carrots in small saucepan until forky but not squishy. Fry chopped bacon in its own fat in skillet and set aside.
2) Meanwhile, combine potatoes, green onions, and celery in large saucepot and add a bit of oil.
3) Saute potato mix with continual stirring until potatoes are sweaty but not yet flaky. During this time, add generous salt, thyme, ancho chili powder, and black pepper as well as conservative coriander and basil.
4) Dump forky carrots in with potato mix. Add drained can of beans and stir in.
5) Add bacon and stir in.
6) Add in dry pasta and stir in.
7) Add just enough water to cover ingredients in pot, cover and boil hard with occasional stirring for 10min. Will still look soupy, but remove from heat and uncover and a stew will emerge in about 5min as the proteins released from boiling up the beans in the prescence of potato starch complex with excess water into a tasty sauce.
8) Subtract desired portion from pot and consume with tasty!

Note: You could add scrambled sausage or sauteed leek to this recipe and it would still be delicious.

09 December, 2009


A recent All Hands Active (the hackerspace) clean-up/reorganization night. That wall to my right is entirely covered in whiteboard, and it is awesome.

Every once in a while it's a good idea to be reminded that electricity, while awesome and good, can also be very painful. Turns out that the lamp in my left hand there had frayed and exposed wires wires up top, so when I plugged it in with the other hand it gave me a nice shock. This is not at all the first time I have been electrically shocked and it was by no means the worst, but it's still a good reminder that voltage is not just an abstract number.

I have been shocked with 120V many times. The worst was when I was in a music supply store testing out a nice little used Fender tube amp. It had nice tone, but the 2 10" speakers at 250W just didn't provide the grumble that I wanted (I later got a 400W 1 15" speaker with tweeter amp to satisfy this, which later was stolen from me and I do often miss it because that thing could roar). So I reached to the back of the unfamiliar amp to turn it off, and promptly found that the exposed vacuum tubes had been engineered right next to the on/off switch and, lucky me!, they were loose and kindly delivered a searing shock that knocked me flat on my ass and out of breath. Unfortunately, so far as I am able to discern, this did not result in the development of any superpowers. Maybe I need more volts?


06 December, 2009

Fragments of Toaster's Mind Blather 3

1) I am currently wearing a pair of suspenders. The straps keep slipping down my shoulder and have been all night. While the suspenders are very good at holding my pants up, this is really really annoying. While it is entirely possible that I'm wearing these wrong or missing some kind of special trick, I cannot help but hypothesize that I will not be able to wear suspenders until I acquire an impressive pot belly to frame with them. I think this is a shame, and not just because there exist pictures somewhere of me dancing at a string party in just suspenders and jeans, because these are some damn snazzy suspenders.

2) It is probably bad manners to debone your dinner in front of vegetarians. However, I tried to be a vegetarian for 3 years so I do know empirically that not eating meet does not result in the development of an obstreperous sense of moral and social superiority.

3) I have taken this joke, stretched it everywhichway, smashed it, lit it afire, microwaved it, fumigated it, irradiated and blended it, grown moss upon it and then titrated it with exotic aromatic hydrocarbons and bacon, but still I find it hilarious.

4) The hackerspace is differentiating. Like how embryonic stem cells gradually specialize as they grow out in new spatial/cytokine niches, there has recently been a major explosion of stuff. New parts, tools, and supplies have been appearing daily. This is excellent as it allows us to expand beyond the range of just soldering electronics boards together. However, it contains 2 problems: A) I can't find anything anymore. I spent 40min looking for a bag of assorted resistors I'd left there and never found them, and when I found the bag of capacitors they were sitting right in front of my face on a workbench instead of in the various boxes I was hunting through. Recently someone else mislocated their fancy wire strippers and we rediscovered somebody else's big box of phototransistors and LEDs. And B) plastic chassis are bulky. We have salvaged several old Super Nintendos, tape decks, VCRs, etc and stripped them for parts and used them to teach people about electronics (including me), but the plastic cases they come in take up a lot of space and aren't nearly so useful as I'd have imagined. I am mostly convinced that the solution to this is to build a MakerBot 3D printer and grind them up to use as printy goop.

5) Speaking of 3D printers, there are several web-based businesses that will laser-cut or 3D print stuff one-at-a-time for you because the initial investment for either piece of equipment remains high. Ponoko is good for laser-cut materials and Shapeways is good for 3D printed stuff. I'm still trying to figure out what exactly I'm going to do with them, but once I do build something with them, I'll post pics.

6) I was empirically reminded tonight that it is a singularly bad strategy to play tetherball with your face.

7) I made for you a mix of music because I like blues and I like rock and roll and I especially like when they've been smashed together with a double bass.

8) There's going to be a real-life, real-time Scientists' Duel right soon where I am. I'm going up against a CMB grad student at a beer hall before a jury of my peers. Neither of us have seen the paper yet, and it's happening on Wednesday.

9) I am teaching a class in the hackerspace on quantum chemistry. I intend to discuss the VSEPR model of atomic structure through the magnety properties of the weak nuclear forces, talk about how it leads to the formation of covalent, hydrogen, and polar bonds and then tie the abstract of each of those into concrete biochemical examples. So far it looks like a dozen people may show up, which makes me somewhat nervous since my attempt to teach molecular biology a month ago quickly devolved into people asking very tangential questions that derailed the points I was trying to make. Apparently it was a bad idea to attempt to abstract the Central Dogma out past cellular anatomy. Retrospectively, I can see how that came across as nothing more than alphanumeric soup.

10) I started wearing contact lenses last summer and was amazed by the phenomenon of peripheral vision. I expected that, and it took about 3 months for me to stop habitually trying to adjust glasses that weren't there. I was not, however, expecting that the winter wind upon my eyes would induce intense watering from underneath my contacts. As it is rather inconvenient, I may have to invest in some clear goggles to keep the brunt of the wind off my eyes.

11) I have been trying, in vain, to digitally replicate the closely syncopated swing beat that appears in polka, Latin music, and blues. So far it doesn't seem that I can program it anywhere, although I have heard it done with MIDI inputs. In any event, I have realized that to make the music I hear in my head come out more effectively, I am going to need some sort of MIDI input into Reason instead of just using my keyboard and mouse pad. I would like to find some way to do this with Gak, as a squishy, oozy, sploppy interface (brightly colored, too!), but I won't be able to do this until I've gotten around to building myself an Atari Punk Circuit. In the meantime, I'm planning on routing a bunch of flex sensors through an ATMega and octocoupler to have a bendy interface. I may sew it into clothes to make a synth suit, depending on how durable I can engineer the copper foil in the flex sensors to be. However, I know myself and as such I know full well that I would be unable to resist pumping a fat fuzz bass through a synth suit most of the time.

02 December, 2009

Cookie Reviews: Erin Baker's Breakfast Cookie

It is a well established fact that Toaster likes cookies quite a bit. You may even go so far as to be able to call him a connoisseur and you'd not be inaccurate. To better guide your cookie eating through his own experience, Toaster offers the following cookie review:

The other day I had missed the bus and I was hungry, so I walked over the the nearby drive-through coffee house looking for quarters and saw that they had a sign for "breakfast cookies". Now, I eat cookies for breakfast sometimes anyways, so this was nothing novel, but the official legitimization thereof was. As the baked goods that this coffee house sells are normally excellent, I figured I'd give it a shot.

I was presented with a pre-packaged choice of Erin Baker's Peanut Butter, Oatmeal Double Chocolate, or Oatmeal Raisin Breakfast Cookie. Normally I'd go with an oatmeal raisin cookie over most anything else any day, but figured today I'd go for the double chocolate as I'd only slept 2h the night before and could use the extra sugar and chocolate-borne theobromines as stimulants.

It turns out that Erin Baker's Breakfast Cookies are edible.

The cookie itself was moist, chewy, and firm, almost everything a cookie should be (also needs crumbly), but it managed to get their respective parameters mixed up. It was too moist, too firm, and too chewy. There was no crunch to this cookie whatsoever, not even a hint of that perfect outer crustiness that I seek. It was also very dense. I had expected unusual density because it billed itself as a breakfast cookie meal replacement, but this was pumpernickel in the realm of baguettes. Furthermore, despite this being a Double Chocolate cookie, it still managed to taste like peanut butter and the chocolate chips tasted like soy carob despite the ingredients claiming real chocolate.

Examining the packaging more closely, it turns out that this was the dreaded oxymoron Healthy Cookie. No butter in it at all. Just a lot of molasses, special organic wheats, and weird juice extracts instead of sugar. Now, I can understand using raw cane juice or unrefined sugar in a cookie, but relying solely on cane sap and pear extract as sweetener is contrary to the spirit of cookiedom. And it had fiber. Lots of fiber. Toaster is fine with lots of fiber as most everything that is not a cookie, burrito, Tabasco, or whiskey that he consumes is vegetable or whole wheat, but this was like having an ingot of sawdust sitting in my belly for a few hours.

Erin Baker's Breakfast Cookie:
Texture - D
Taste - C
Idea - B+
Cookieness - D

Note - I am going to review other cookies in the future, and I will strive to only do so with brands available in most of the United States or, if homemade, only when I am also able to post the recipe.

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.

27 October, 2009

Language Blathering

I posit that language acquisition is driven less by intellectualism than daily utility. A recent post over at Greg Laden's Blog got me to wondering why Anglophones remain so stubbornly monolingual when so much of the world speaks a couple different languages fluently. Upon ponderation, I believe that Anglophones don't learn second or third languages because we don't need to, not really anyway. This isn't to say that this attitude is right, nor that I condone it, but from England on outward to the United States of America to Austrailia, English-speakers have been very successful at ensconcing themselves in geographical isolation, cultural imperialism, and economic massiveness underwritten by strategic military stubbornness. These three conditions having combined to make English the predominant formal language in the world despite its sillinesses.

We dumb Americans don't learn French, Spanish, Hindi, or other non-English languages because we have no daily use for them. We may take a few semesters of a foreign European language in high school, but because we don't have a need to use them, nor a community, space, or occasion to trot them out, we largely forget them. And when we go to other countries we have the privilege borne out of economic massiveness that leads us to expect, and even demand, that our hosts speak our language even as we remain entirely ignorant of theirs.

This isn't necessarily a good thing, but maybe this is why it is the way it is.

For the record, I speak and read German fluently enough to also make out written Dutch and Swedish and can stammer out just enough Spanish to keep myself fed and housed. I intend to learn French if I ever find time because I think it sounds funny, and Mandarin if I can.

18 October, 2009

Marathon Science

My boss told me that I should factor in that everything will take much longer when I have many samples and that I should plan my time accordingly.

She was very right.

In fact, she was so correct that I wound up pulling 29h in the lab, and 14h the day before, to get Experiment done. There weren't that many samples to begin with, but by the time that I split those samples into cell culture under different conditions and then stained each of those conditions for different sets, I had a couple hundred samples to run on my hands (or, rather, in a tray because I couldn't carry them all at once).

What I found most interesting about this (aside from the Science of it that I can't blog yet), was how all-night science affected me. The entire night was an odd rollercoaster of exuberancy and despondency.

11a - Got to lab, felt guilty about being late but vindicated by 14h there yesterday.
12p - Relieved to see that samples had not drowned in melting ice bath overnight, put into refrigerator to finish staining later because Machine was scheduled out into early evening.
1p - Indian food buffet!
2p - Talk to visiting scientist, then journal club.
3p - Journal club.
4p - Realized that I didn't have enough Enzyme, so I went to go get more from our super-convenient on-site Enzyme Store.
5p - Started finishing staining.
8p - Finished finishing staining, Machine time.
10p - Done with Machine for now.
11p - Pulling cell culture.
12p - Plating for staining, blocking, singing deliberately off-key.
1a - Sandwich and caffeine time.
2a - Primary stains, dancing around laboratory to punk music.
3a - Washes. Laboratory is very cold. Sweater not helping. Note that this parallels drop in body temperature that occurs when sleeping. Turn up lab thermostat just a little bit. At least it's warmer in the cell culture room.
4a - Fixation. I could have gone home and slept at this point, but didn't want to have to come back in later. Arikia and I discuss what we carry around in our backpacks/bags, she rightly points out that the contents of mine would have me on a terror watch list in no time flat. I have my laptop, a zombie comic book anthology, lots of heavily annotated biology papers, a screw driver with a full tip set (even hex wrenches!), a digital multimeter, wire strippers, a soldering gun, needle-nose pliers, gloves, fisticuffs, a gigantic rubber band, a set of Exacto knife scalpels, some faded index cards, cufflinks, a bunch of batteries, and Pepto Bismol. I do not know how old that Pepto Bismol is. Might need to add a crowbar.
5a - My pellets have disappeared. I have become paranoid and cynically convinced that all I'm doing is spending lots of time moving small bits of liquid around even though I know from doing this before that fixation can cause a change in their color.
6a - I found enough change in my pockets for a vending machine Snickers bar. It's dawn and I am shivering even with my sweater on.
7a - Still washing and enzyming, other people start to filter back in (this is Saturday now, right?).
8a - More washes and a brief 30min nap on the couch in the departmental library, which is surprisingly comfortable. Glad my phone can be used as an alarm clock, also glad that protocol has 40min incubation periods.
9a - Still can't see any pellets. Morose about prospects for data. Still washing.
10a - Final stain!!! Just one more wash...the sound that the suction makes when washing no longer amuses me...
11a - Machine time! Crap, gotta restart the machine. Fairly certain that I dozed off waiting for the machine to start up all its pumps and stuff, woke back up when I started to fall out of chair.
12p - Staining controls calibrated.
1p - Running samples, strangely extremely alert, become completely attuned to Machine such that I am already fixing a problem before it pops up a problem-prompt.
4p - Finished running samples, Machine no longer talking to me.
4.5p - Promptly miss only bus home for next hour, decide to walk instead.
5p - I am lost. I know by dead reckoning exactly where my apartment is, but there are all these inconvenient streets and houses in the way.
5.5p - Home.

Truth be told, I still didn't go to sleep until 1a. First I ate a lot of food, drank a lot of drink, and played with the new power tool that finally came in the mail even though I didn't have anything on hand that expressly needed it. I need to find space in my backpack to add this tool. And to top it all off, I even had trouble falling asleep.

UPDATE - Dremel is now in my backpack. Also found bag of 15 2" 30-Ohm speakers in there.

26 September, 2009

7 Kinds of Awesome Busy

I have been 7 different kinds of awesome busy lately, although at the moment exhaustion is chipping away at the thick layer of exuberance I've been smearing across my forehead lately. Please do not expect this post to be in chronological order.

Last Tuesday the flow cytometer I needed to get data was broken. So instead I went to Chicago and Milwaukee and drove back in the same night for the Two Hands Project. I also went to Boston for a week at the beginning of the month with absolutely no hotel reservations, just friends of my brotherfriend to stay with. There I met Prime*, who is awesome in 17-8,597 different ways and I'm 97% certain that I'm in love with her now and I can't help it and don't care except that there's a rather inconveniently large physical space between us (1Mm, too big for catapults!). We're trying to figure out how to fold the space between us into technical nothingness, so if you live between Michigan and Boston please be aware that there may soon be a sudden extreme change in the topography of your region. I'm sorry, Cleveland, but Prime sends me cookies and cookies > Cleveland, although it should be noted that I can be bribed with plane tickets now.

I did many other things in Boston, some of them rather unbloggable** now that I know my boss reads this site, but they include surviving biking through downtown Boston traffic with several kgs of computing and goggles and letting complete strangers surprise-dye my hair however they wanted to. They're not strangers anymore and my hair was a very lovely bright pink for about a week when it faded to a strawberry blonde. However, the purple sides did not fade nearly so quickly and now, even after buzzing away the unruly mop that needed trimming anyway, I have a subtle bright yellow blotch on one side of my head.

Regarding blog-reading bosses, I changed laboratories shortly before going to Boston and am quite pleased with the change. In Immunolab, I read papers to actually apply them to the science I'm doing and planning instead of just reading because I'm bored, and doing so matters(!) and this is also awesome even though it has also resulted in a drastic cut in how many PLoS Computational Biology articles I have time to read. I expect to find an equilibrium again sometime as I climb the learning curve.

But as for equilibria, that's been thrown even further off balance by trying to organize a local hackerspace. And that brings me back to the Two Hands Project, but only in a moment. A hackerspace is a place where creative awesome people can come to build their ideas, talk technical shop, imagine, invent, innovate, destroy and re-create whatever they want to. It's essentially a community in a common shared working space with shared tools and parts, and maybe even eventually club-like membership to buy those parts, that fosters creative productivity by pitting like-minded people of completely different backgrounds into their own creative passions. These emerging spaces have the potential to remodel the entire American economy by shifting innovation from closed-source company driven patents to fast and flexible open-source crowdsourced invention. So far we have computer programmers, musicians, roboticists, artists, biotechnologists, cooks, textilers, and other crazily awesome people coming to meetings and generating large numbers of incredible project ideas. However, forming this group involves a lot of email management, community outreach, calender planning, part sourcing, charter writing, agenda creating, etc etc etc and I for that I am grateful that I can rely on most of my friendfamily, who're also all embroiled in this.

And yes, I have a friendfamily that has coalesced. Sister Doom, Brother Discord, Brother Deliverance, and myself, Brother Destruction. These are people whom I can completely count upon to have my back, whom I can trust and who know that they can depend upon me as needed. Sometimes I want to kick Brother Discord in the face, but that's probably because he's also my roommate. Sister Doom and I drove to Chicago and back last Friday to pick up a stranded Brother Deliverance.

But The Two Hands Project is also awesome. As I understand it, Brother Deliverance first came up with the project when he found out that JetBlue was offering a $600 ticket that lets you fly as much as you want from September 8th to October 8th. So he put out a call for donations at http://www.twohandsproject.com and raised enough money for a ticket and people donated equipment, and 2 have even joined him on his bad dash from coast to coast. It was with him and his crew that I (politely and enthusiastically) stormed Pumping Station One in Chicago, went on to interview James Carlson (director of Bucketworks in Milwaukee), and then drove from Milwaukee back to Ann Arbor so I could be back in lab by 10am. Because Brother Deliverance et al are too busy recording footage, flying, and meeting awesome people across the country to keep up the blog at Two Hands Project, they've enlisted me to do it for them remotely. I posted the first semi-polished video from San Francisco's Noisebridge and The Internet Archive*** today here and will be posting a string of profiles of hackers/makers soon.

There're some sweet experiments coming up that I am very excited about, and I just realized that I forgot the slip of paper that has the part name of the low-voltage audio amplifier I wanted to buy from RadioShack tomorrow on my desk in the lab.

I'm not quite sure what to do with Atomic Pudding. On the one hand, I could just use it like I've used this venue and let my awesome shine through, but on the other hand I liked what I was doing with open-access research and interviews, but it was just getting absolute crap page views and as such I'm not sure I was doing very well with it. Thoughts?

I also went out to visit i3 Detroit recently (Wednesday night, I think?) and had mjaddra before that (I think?) after a local maker/hackerspace meeting that Brother Deliverance recorded for the Two Hands Project (I had a lapel-mic, but was probably still unintelligible) and invited them to the free Drupal Web Development class that our as-yet-unnamed space**** is holding this coming Wednesday. And somewhere in here I know I made some really awesome live music with a fellow maker/hacker at a meeting sometime that may have been last night but I can't be certain. Wasn't I in Boston last night?

*Whose intellectual and physical hotness are mutually inclusive and inseparable properties! In testiment to her awesomeness, note that she was the first person to ever convince me of the functional utility of buying clothes that don't need to be modded to fit and has even inspired me to replace the whiskey in my burritos-cookies-and-whiskey diet with vegetables!
**Get your mind out of the gutter!
***Technically not a maker/hackerspace.
****We're working on it!

P.S. - I don't recommend prying all the keys up off your keyboard and rearranging them from QWERTY to DVORAK before you know DVORAK very well. Makes passwords very difficult.

09 September, 2009

E-mail Quandary

I find myself facing a bit of a quandary.

I need to send out emails to professors at places I would like to attend graduate school, but I am not sure how to write these emails. I want to write:


When I know that it wouldn't do to do so. I know that perhaps 3 professors might appreciate getting such an email, but in the vast majority of cases I am aware that to do this would be folly and most likely leave an irreparably bad impression. So I'm left with:

[Banal Salutations],

[Bland Statement 1] [Who I Am] [Something Vaguely Intelligent] [I Read Your Paper, By Which I Really Mean I Read the Abstract] [Bland Statement 2] [Something Trying To Be Intelligent] [Bland Statement 3] [Might There Be Room In Your Lab For Me?]


And this just seems so damn contrived and passionless that I don't know what to really do with it. It's so boring and flat and it communicates none of the enthusiasm or intelligence I may be able to bring to bear on their research focus. But it's what's right, kinda. If I try to inject personality by dressing up words just a little, I'm liable to come across as a sophist jackass or, as is more likely in my case, as a crazy person not to be trusted with pencils.

So this is my quandary, and I don't really see any good ways around it. How do I balance my enthusiasm with the need for propriety/formality? Suggestions!?

25 August, 2009

Tactile Ostrich

If we have Wiimotes that make little blurtles and blops when you past them over an icon or button or pick up a sword within a game, making it feel more as if you're actually touching those items and increasing engagement with the medium, then why do we not also have computer mice that do the same for icons and links?

Someone fix that, please.

22 August, 2009

Dear Reader

Dear Readers,

You may have noticed I'm not as engaged as I used to be, that I'm not hanging out on your blogs like I used to, or updating nearly as much. Yes, I have been busy, true, I have not had much time, and yes, also correct that my Internet access has been spotty at best lately. However, none of those are the reason for my scant attention. Dear reader, let me blunt: there's another blog in my life.

It's not you, dear reader, it's me. I've changed. My ambitions have grown larger in proportion with my happiness, and through some persistence I have procured a spot for myself over at True/Slant called Atomic Pudding. Over there I'm going to be writing about science and health and kicking ass, and due to the time it is requiring out of the increasingly rare free time I do have this blog, our special place, has fallen to inattention.

Also, dear reader, I've not been entirely forthcoming with you. I've told you that my name is Toaster Sunshine. My real name can be found here. I am not posting it here because I do not want it to show up in search engine results.

I intend to keep posting here, but my posts will be less frequent, and at least until I get regular Internet back in my life I will not be so active as before on your blogs. In the meantime, however, my good Brother Discord has sworn upon his first child's foreskin that he shall help with the posting here.

Thank you for your understanding,

18 August, 2009

Blathering on Hunger

As I was fumbling contacts into bleary eyes this morning, my stomach untied itself from the knot I had been unaware of and startled me with the ferociousness of its growl. I was hungry. I am often hungry as I tend to skip meals to do more interesting things and frequently go 12 or more hours without any food*. This is a long-tailed habit rooted back 8 years, and it is not likely to change. I don't mind being hungry. I relish it, because it reminds me of the sheer vitality of the human body, its metabolic resilience, and it makes my next meal taste that much sweeter. I sincerely believe that food would not be nearly so appealing if I didn't occasionally let myself get so hungry that the reptilian brain underneath my consciousness begins to wonder how squirrels taste. That being said, this morning's hunger was somehow different. Normally hunger pangs are diffuse, a distant inconvenience upon the sphere of my awareness, but this was sharp and intense and immediate like a rattlesnake uncoiling.

And my hunger made me feel guilty.

I had oatmeal in the pantry and a stove to cook it on. This is a privilege, and it is one that I do not take lightly or for granted. So many people in the world are hungry, even in the West, and we simply don't see them. Sure, we admonish children to finish their peas because a kid in Poor Country X doesn't even have peas, but this nicety conceals an ugly truth: that the kid in Poor Country X really exists, and actually is hungry.

Wrapped up within this is the disgust that the phrase "I'm starving!" evokes from me. It is a terrible hyperbole, and I find it cruel and inappropriate to use when you merely want lunch while someone else in the world may not have lunch, or have had breakfast, dinner, or lunch the day before. Americans claim to be starving at the slightest hint of hunger, but maybe that is just the uniquely privileged perspective that we as a nation have, when we live in a country that has so much food that many are obese even on top of all the food we simply throw out. I suspect that the majority of the people who use this phrase so callously have never really been hungry and I wonder what they would do in a hard situation. So much of our Western society is carried upon the backs of titans treading on toothpick bridges, tenuous and fragile. Entirely dependent upon fossil fuels, yet still incredibly wasteful. The food we, as a country, throw away before even opening the package could probably feed a great many people. Yet somehow, just as the hyperbole of "I'm starving!" or the "Eat your peas because a child in Poor Country X doesn't have them" is part of our culture, food waste is also deeply ingrained upon our national consciousness.

I'm debating whether or not I am too proud to reclaim some of the unspoilt food that gets thrown away. On the one hand, it is there, free to take and perfectly edible, but on the other hand I feel that it is somewhat gross to eat dumpster chicken (if found still cold in an unopened package). I am fairly certain that many of those who are relatively well-fed yet claim to be starving would find it disgusting, but what are your thoughts?

*It should probably be noted that when I do eat, I try to eat 1Mcal+ at a time.

12 August, 2009


The 4 GREATEST words in human language are, undoubtably and irrefutably:





So much of our daily tedious lives are consumed so much by the "what", the where we're going and what we've gotten done and what we've yet to do in any given day. We rush and we careen through each day, blindly numb to the absolute wonder that simply being alive allows us to experience! So many of us fumble through every day, finding nothing but monotony when all around us there are secret lives of insects and rodents playing out tragedies that the Greeks couldn't've even begun to fathom. Each day the grass bending under the weight of a squirrel and ruffling in the new nuances of a fresh breeze is different!

And all so many of us do is go home to bask in the banal glow of the television, consuming aspartame shovelware with no analysis or reflection thereof. To me, this is a catastrophe! Sure, we've dissociated ourselves from the intricate and minute rhythms of nature and congregated in cities, but that nature still flourishes underfoot whether we want it to or not. The stubborn tufts of grass clawing out of the asphalt, the clever raccoons who persist amid our concrete monuments to our own aggrandized sense of self-worth*. Nonetheless, there is wonder bursting all around us, and all we have to do is notice it!

Too often, we're too breathless, too tired, too distracted, to find the simple awe that is captured in every bubble that the dish soap sprouts. And at the same time, we're not asking why, we're not wondering if, we're not trying to figure out how, and we're not imagining. If we let ourselves fall into this shallow pattern, then we fail the full realization of our evolutionary endowment and I wonder if we can truly say we have lived and not just merely existed.

This is all born out of the manic and inescapable conviction that if I could just crack open my mind and let you see inside, let you peer into the window of my imagination, you might understand, you might realize just how absolutely wonderful the feeling of midnight rain and the lovely contrast to a warm pillow at night is, how exquisite the sharp pang of a bit of hunger and how it sweetens one's meal may be, and just how much MAGIC exists in the world. As if I could shake you laughing like Jello until your spine was marshmallow and your mind was flooded with the brilliance of what the world is and how it came to be and how it works and what it might be someday if suchandsuch does thisorthat.

This is also wrapped up in my frustration with the limitations of language itself. I could shout "IMAGINE IT!" at you until my vocal cords tried to strangle me in protest and it would do nothing to help you realize the pure depth of the inner vision I am trying to communicate to you. There exists SO MUCH potential in the world, so much burgeoning awe that it stings to know that so many people prefer to wrap themselves up in soporific entertainment, hate, or blind ignorance.

I know that there's no such thing as ooga-booga-hocus-pocus magic, but I remain convinced that the world is thoroughly magical. All we need to do is see it.

So, tomorrow, go outside, or stay inside, or fall asleep with a tea cup over your eyes, and look in the corners of the world and of your mind. Instead of waiting to see a Wunderkammer, find your own instantly and for free. Seek out the dust bunny that reminds you of your Aunt Matry, find the chord that rings back the sweetest memory to roar back through your senses clearer than the moments it happened. Notice the glinting halo of light around the glimmering rain as it splatters across the pavement in aggregated fluid dynamics (that you're observing almost in REAL TIME!) and sing a song that only you know but will not remember in 5 minutes! Ask WHY, let yourself IMAGINE, question HOW, and wonder IF!!! And, most of all, teach it to others and spread this joy of wonder!

*That isn't a condemnation of the human ego. We have, collectively, wrought great, terrible, and beautiful things upon the face of the Earth. The decaying industrial rust towers of Detroit are exquisite in their intricacy! The rudely squatting chemical factories of Saint Louis are brilliant works of art in the loaming glint of the fading sun piercing through foggy humid air! The oil refineries of Toldeo and Maumee bellow upon the horizons, belching red underglow into Cheerio snowstorms (I once lived in Toledo across US-23 from a cereal factory), give the entire short little city a Monet-like quality! The sheer patched-togetherness of Gary, Indiana is an awe-inspiring exercise in ret-conning! And all of this has been wrought by human hands and human minds, to bend the Earth itself to our will! How is that not marvelous?

10 August, 2009

How to Explain the Senses?

Crowdsourcing: to open up the development process of any given project to the public in a meaningful way that allows the public to impact the course of that project's development.
Ann Arbor, Michigan is about to have a mini-Makers' Faire (as opposed to a Gigantic Makers' Faire). This entails a large gathering of creative people showing off the products of their creativity and ingenuity in a public forum. Typically there are demonstrations, learning, and sharing as most everything is open access. Basically, it is a gathering of nerds who like to make stuff teaching other nerds of similar aptitude, and the curious public, about the stuff they made. The purpose is to share, awe, inspire, educate, elucidate, demonstrate, and possibly also confuse.

I've gotten in on this, and a project is rapidly coalescing. In the Sensory Augmentation Devices booth, we're trying to demonstrate the electrical properties of nerves. However, to do this live and in real time, we must also tread carefully to avoid disgusting the public. Listed below are the ideas so far, and they are open to your comments and criticism.

1) Brain-ablated Xenopus (frog*) with thoracic cavity open connected to electrical leads at each limb in a physiological solution of potassium chloride. Each electrical lead will be run by a robotic sensor glove such that movement of the glove will induce neuromuscular contraction in the frog limbs. In effect, this is a frog puppet. We hope that the physiological potassion chloride solution will allow passive diffusion of ions back into nerve cells and allow for repeated contractions.

2) Similarly, brain-ablated Xenopus with thoracic cavity open and heart connected to an LED through a tranformer. The blinking LED will demonstrate to observers that the heart does indeed contract due to pulsed electrical impulses.

3) Petri dishes of rat or mouse neurons with silica implants connected to a computerized output to show random electrical activity of cultured neurons. We have a source of cultured neurons, but we still need a way to get a signal amplified out of them.

4) Brain model, either preserved real or plastic so that we can get the neuroscientists among us to explain the structural functionality of the brain and how it relates to neonatal development in humans, as well as anatomical siting of neural pathologies.

5) Setting up some of the basic sensory tricks, such as the Wet Illusion. In the Wet Illusion you place 2 cold metal bars against someone's bare skin with a warm bar sandwiched between them. Although all bars are quite dry, the brain registers the unusual temperature gradient as wetness. If you have other sensory tricks to use, let us know.

6) Electrode-based EEG interfaces hooked up to a sound synthesizer to allow the audience to "hear" the wearer's "thoughts". Getting the EEG output to interface with the sound synthesizer is the easy part, but getting a hold of the EEG/electrodes will be difficult.

7) 8-bit imager, where the audience may flip any of 64 switches to light up one of 64 LEDs in a board to explain how rhodopsin in the eye's cone cells converts light (the audience's hand) into an electical signal (the LED) by way of altering its molecular conformation (the state of the switch).

Any and all of this is completely open for your comment, criticism, and input. In fact, all 3 of those things are explicitly welcome! New demos may also be suggested, but the general theme of this is simply that we show how nerves and sense work.

*We figured that frogs are uncharismatic enough that no one, save the hard-core animal rights' activists, will have a major problem with using them for education purposes.


I am unsure about the structural stability of this hat, but I do not doubt its awesomeness.

Night Owls

The world begins at midnight. As the stroke of midnight is called out from bells, we herald the dawning of a new dusk even as most others melt away to wrap themselves in the comfort of their beds and late night television. At 1a the people stop leaving and the rushing cars become more sparse. The streets empty of people and the ranks of the half-sloshed bar-dwellers dwindle just a little more. Underneath the frowning street lights, we emerge, fresh-faced and laughing, full of energy, piss, and vinegar. At 2a we stand laughing delighted in our odd suits at the ashen-faced last call stragglers as they come creeping out of their dens, just drunk enough to question whether we are real. By 3a the streets are mostly clear, populated only by a lone bicycle wending its tired way home or a tight knot of quietly moving people with shoes in hand. We remain alert, alive, forming circles around fires, computers, in the cracks of the world that most people that don't even notice. 4a rolls around on the dour clock faces and we launch new adventures, setting out into the clean, abandoned parks, reveling in the crisp thunderstorms roiling along the rivers and the sheer scope of the wonder in the world. When the cities are crowded, they seem mundane due to everpresent companionship, but in the night each and every one of us could well be the last person alive, the lone witness to the absolute joy of the moon gliding from clouds to shine down on vociferous arguments and manic productivity. By 5a we begin to wonder whether our wakeful watching through the march of dusk has percolated into the snoring minds of those who comfortably slumber around us. At 6a, the Eastern sky begins to wash away into the first barren hints of the coming day, and we realize that the dread Morning People will soon awaken and disturb our revelry. So we end our projects, dry our war paints and clean our tools, then wend our ways homeward, hissing over dew-drenched asphalts for one last snack before drawing the heavy curtains and rolling ourselves into the brilliance of our dreams. We are night owls, and we are watching.

We try to be polite.

07 August, 2009

How To Make Greens

I have been missing Southern cooking rather sharply as of late. I need a massive Southern feast to recharge. Fried catfish or chicken, okra (fried or gumbo), home-made macaroni and cheese, cornbread, green beans, greens, field-fresh sweet corn, wild rice with bacon, biscuits, yams, and a side of Jello. Maybe peach cobbler with walnut ice cream and watermelon for dessert. I would eat enough to distend my stomach* and then some. Crap, now I'm drooling...

Anyway, of all the delectables that I list above, it has been greens that has drawn the greatest consternation from the Northerners I now live among: "What are greens? What do they taste like!?"

Well, dear culinary n00bs, allow me to explain:

1) Greens are indeed green.
2) Greens are leaves and stems of leafy edible plants.
3) Greens are simmered down for at least an hour in broth and spices until they are delicious.
4) Greens go well with anything.
5) Greens are a recycling dish.

I now impart unto you my recipe for greens.

Toaster's Greens:
1. 1 large potful mixed greens, washed. This typically includes collard greens and mustard greens, but can also use common lettuce (if you must, but I do not recommend this), beet greens, even dandelion or nettle leaves (be sure to blanch the nettles first!).
2. Broth. I like to use chicken, but you can use whatever stock broth you'd like.
3. Mustard.
4. Hot sauce (smoky hot sauce better).
5. Seasoning salt.
6. Black pepper.
7. Bacon grease.
8. Ham hock.
1. Wash greens, dice coarsely if needed, and load into pot.
2. Pour in broth to 1/3 the volume of greens.
3. Turn heat on low, cover.
4. Add bacon grease and ham hock (these are optional, but very useful for recycling leftovers).
5. As greens begin to wilt, add spices. 1 tbsp mustard, generous hot sauce and black pepper to taste, light on seasoning salt.
6. Simmer at least 1h, covered, until you are left with a delicious mass of wilted greenery and spice. Add broth as needed for desired soupiness.
7. Serve with cornbread and a side of awesomeness, garnish with bacon.

You will enjoy this! Greens can be had very cheaply at local farmers' markets, and Trader Joe's even sells them, pre-mixed and pre-cut, by the pound.

*This isn't uncommon. When you're as scrawny as Toaster, any food in your stomach is visually apparent.

New Moral Compass

I think I have decided that this song is my new moral compass:

If ever I find myself questioning whether a given action is correct, moral, or ethical, I will play this song in the back of my head. It'll be like a Magic 8 Ball, not even I will know the mechanism of how exactly it works, but the answers it gives will just magically be correct.

This strikes me as a particularly good idea.

However, that could also be due to 3h of sleep from having to change a blown-out tire at 2am*, not arriving back at home until 4am, and trying to wash all of that down with vodka. I did, however, procure a large tube of industrial-strength epoxy and a ball of string last night, so that makes me happy. Dear readers, I am curious now what you think of me in the regard of: which do you think I will wind up getting into more trouble with? The epoxy or the string?

My new roommate also bought epoxy, although instead of string he opted for a lot of fake shrubbery. You can count on some guest blogging from him in the near future.

Roommate (left) and Toaster (right, wrapped in cape). Trust us, we know what we're doing: WE'RE SCIENTISTS!

*Yes, Roommate helped. Toaster tried to repay him with an apple fritter today, but he wasn't in his lab, so Sister Doom got it instead.

05 August, 2009

Why Science Needs Dinosaurs

1) Dinosaurs are cool.
2) Little kids (and adults) think dinosaurs are cool.
3) If we use dinosaurs as a vehicle for communicating science, more children become interested in science at an earlier age, which is a net win for both science and the kids.

The first time I heard about deoxyribonucleic acid, it was from a film within a film, enthusiastically described and explained by an animated firefly that the lead character scientist grudgingly sat through. I was 7 years old at the time, and I had to forfeit a loose but stubborn milk tooth in order to get to go see it at the local AMC theater. I'm fairly certain that my mother quickly regretted taking me to see it at all as the proportion of sentences involving dinosaurs that poured from me in an unstoppable flood increased dramatically. I'd been previously building wooden models of dinosaur skeletons, and I had several inflatable dinosaurs in my room. I knew many of the dinosaur species by name, although I've now forgotten, and I was fascinated by the sheer scale of them. When I was 4 and again at 5, I'd gotten to see a fully articulated Brontosaurus skeleton in the Smithsonian, and even been allowed to revertentially touch a real dinosaur bone that they had on display. When my mother tried to tell or read me bedtime stories, I firmly rejected any story that didn't involve a dinosaur of some kind. In fact, I was so utterly obsessed with dinosaurs that my little brother, who became self-aware just at the peak of my obsession when I got Jurassic Park on VHS and as a game for the Sega Genesis, later developed a crippling phobia of dinosaurs. He was sincerely terrified that a Tyrannosaurus rex was going to come back to life in the middle of the night, sneak between the houses, break into his 2nd story room, and summarily eat him. He was not reassured when I pointed out that the Ozarks had been an ocean at the time such dinosaurs roamed. Come to think of it, he also was not convinced when I showed him the coral, sea shell, and worm trail fossils that the local stream beds were chock-full of.

As an adult, my obsession with dinosaurs is gone because immunology is much more complex and chaotic and therefore much more interesting to me. The evolutionary dynamics of bone morphology are still damn cool, though, and the prospect that we might one day recreate an extinct species through the Dark Arts of our biological sciences is absolutely captivating.

But that's not my point.

Imagine if this creepy, feel-good hippy marshmallow fluff excuse for a dinosaur

Had instead been a smart, endearingly disheveled scientist dinosaur instead?

Even if he was incredibly annoying, Barney was also incredibly popular and he taught an entire generation of American children...something. He did teach stuff, right? Nonetheless, the fact of the matter is that the singing purple dinosaur generated huge viewership and made a tremendous impression upon young children as well as some deep product marketing for PBS. Imagine if instead of peddling self-esteem, there had been a relatable dinosaur mascot dishing out some awesome, intelligible science! Consider the depth of the impact that that might have had! Instead of a smarmy self-confident generation of young adults now, we'd have a science-literate generation of young adults who found self-confidence through knowledge and understanding instead of songs and dancing! And that would be incredible! Not just for us as scientists, but for society as a whole because even some basic familiarity with the principles of scientific thinking and research structure can make tremendous impacts upon the operations of very diverse fields.

And yes, Bill Nye the Science Guy was indeed on simultaneously as the blobby excuse for a dinosaur, but he never got the kind of veneration that the dinosaur did, even though he did have a talking rat for an assistant. Dinosaurs are alien enough to children that they hold a distinct appeal, while children already know that rats are bad.

So why couldn't we have a talking dinosaur educating youngsters about science now? I can't think of any reason we cannot, even if cartoons in general have been shifting in favor of robots and monkeys. Maybe if the dinosaur professor had a robot monkey assitant we could grab both demographics in one fell swoop?

03 August, 2009

The Culture of the Internet is Permeating Science (TRANSLATION)

[Recently, Spektrum der Wissenschaft published an article (Die Internet-Kultur sickert in die Wissenschaft ein) citing Dr. Bora Zivkovic of PLoS and A Blog Around the Clock. I found the article by Lars Fischer, of Fisch-Blog, to be quite interesting, so with permission I have translated the article and am posting it here. UPDATE: Lars Fischer has posted the original English-language transcripts of the interview with Dr. Zivkovic.]

The Culture of the Internet is Permeating Science
by Lars Fischer
translated by Toaster Sunshine

Open Access is changing scientific communication through both online periodicals such as the successful PLoS ONE or the increasing diversity of classical publishers’ online offerings.

“Open Access”, says Bora Zivkovic, “is just a stage of the process through which scientific communication will change as a whole.” He should know, because as Community Manager for PLoS ONE, currently the most successful Open Access journal, he is directly involved in this change. PLoS, founded in 2001 as the Public Library of Science, is financed by money from an endowment and authors’ dues, and makes all articles it publishes available on the Internet for free.

While the copyright of published works in Germany is still debated philosophically, international publishers are preparing themselves for the time after their abolishment. “The next step is that the journals abandon printing their articles on paper,” said Zivkovic. As a result they would be compelled to conform to economic reality: “Because the biggest costs in publication houses have nothing to do with their content. The preparation for printing, the printing itself, the paper, the ink, the truck and driver, the distribution system, all these are enormous costs.”

Pioneering in the Industry

That’s why even scientific publishers are working diligently to cooperate with the new digital world. Elsevier, with headquarters in Amsterdam, is currently developing a far-reaching, paper-free publication model. The “Article of the Future”, as the project is called, is strongly organized around the technical opportunities and demands of the Internet: individual article sections are laid out next to each other in the same page view, with valuable video and audio data embedded and all bound up in links. Naturally, readers’ comments also receive their own section.

Other industry leaders, such as the Nature Publishing Group in Britain, are going even farther. Admittedly, their journals continue to be available on paper. However, Nature has also already established a broad spectrum of online communities and services tailored to scientists, which is ground-breaking in the publication industry.

All of this does not signal the end of published articles. “The printing process simply shifts itself from producers to consumers”, says Zivkovic. This is a pattern seen across many industries: “It is like a supermarket, where one places what they want into their cart and take it to the cash register. For the past 50 years we’ve had someone putting the products onto the shelves for us.”

“A doctor in Chad cannot afford to purchase research”

Zivkovic is convinced that current developments in Open Access will eventually prevail in scientific publishing. “If everything online is available, then it is only natural that everything will somehow also be free. A doctor in Chad who wants to learn more about the symptoms of his patients and potential therapies cannot afford to pay $60 per article when he finally find what he was looking for. The pressure of consumers on journals to open their content for free access will grow strongly.”

As demand increases, publishers will have to greatly alter their business models. Through digitization, printing and distribution costs, which make up the lion’s share of the journals’ prices, fall sharply. Accordingly, remaining costs must be covered by other sources of income. “Open Access journals have diverse opportunities to cover their costs and simultaneously utilize others.” Currently the most widely known opportunity is that the authors themselves pay for the publication of their work, which constitutes only a small portion of the hosting costs under PLoS.

When applicable by individual circumstances, PLoS also waives author’s fees to reduce the hurdles faced by less cash-flush researchers and institutions. However, this raises the possibility that, barring conflicts of interest, editors and reviewers will perceive articles for which no fees were paid as being of poorer quality. To protect against this, Zivkovic is strenuous on the rule: “As to what was paid for, only the accountant knows.”

In any case, Open Access has established itself in the publication scene. For example, the Open Access model is apparent when scientific articles are published traditionally and later made freely accessible on the homepage of the journal. In the meantime this “Green Path” has also received official sanction: the NIH now stipulates that all research works produced from NIH funding must be made openly available within 12 months of publication. Despite this regulation, “golden” Open Access has also grown: approximately 4000 journal titles are now freely available online, the trend is increasing and demand is also growing. This is certainly due to practical reasons: “The culture of the Internet is permeating science”, says Zivkovic. Many also push for the free posting of their research on the Internet as a political and ideological action. It also applies, that: “They who pay for something on the Internet expect that it is absolutely fantastic, absolutely necessary, and absolutely inimitable.”

Publication determines who may ultimately consume data

In the long term the practical reasons for Open Access easily outweigh any costs. Many fields of research are already relying upon widespread sharing of digital data. “Publishing makes examples of those, the physical chemists or bioinfomaticists who are unfortunate that their search mechanisms and data crawlers cannot fully utilize the data on the Internet. In bioinformatics this stymies the development of new medicines, when their search mechanisms cannot access the necessary databases and calculations of other researchers.”

The trend to Open Access will take on classical publishers themselves. The subscription costs of journals in particular have increased immensely in the last few years. “That has nothing more to do with supply and demand,” grouses Zivkovic, “it’s a pure rip-off.” In 2007, Norwegian scientific libraries and the German Max-Planck-Gesellschaft threatened to boycott certain journals for this very reason.

Naturally the problem with high subscription costs has yet to be resolved. Because of this “the libraries [are] important patrons of Open Access. Because of the enormously increased prices they are able to afford ever fewer journals, which further hampers the researchers and their institutions.” Open Access journals demonstrate that it can be done differently, yet established print journals have not entirely committed. At least not all publishers raise their prices so casually: “On the other end of the scale are journals such as Nature, which are not nearly so expensive and are consequently prepared for the new, digital world.”

02 August, 2009

Blather Fragments

1) Has any research been done on the viscoelastic properties of instant mashed potatoes? I cannot help but wonder if they'd undergo wave-form or blunt deformation from wind resistance at high velocities. At the same time, could you efficiently pump mashed potatoes through a tube at similarly high velocities or would such an endeavor necessitate the use of gravy to reduce the frictional coefficient? Dr. Isis has already told me how to get the mashed potatoes into a balloon, but it remains to be seen whether those balloons are efficient projectiles. I am concerned that the deformability of mashed potatoes may inherently make mashed potato ballistics very difficult to aim. And if anyone knows where I could get 20kg of instant mashed potatoes, please let me know.

2) I think I truly need one of these, although I'm not sure what for. Anti-bear defense?

3) I have recently found that when you say to someone, "Yeah, I can fix that, just let me go get my gun," it is best to clarify that you mean a soldering gun first.

4) Volleybadminton is a most excellent game. Volleybadminton is, essentially, badminton played with volleyball rules. There are no back-bounds to the court so you can hit the birdie as far away as you'd like and laugh as the other team sprints backwards to try to get it, but beyond the sides of the net remain out-of-bounds. You may pass up to 3 times on one team to get the birdie back over the net, and if you're venal you may spike. Volleybadminton is best played at dusk when it is difficult to see where the birdie is. I play volleybadminton with more grace than skill. Credit for its invention goes to this deranged old professor.

5) What do you suppose the volume of a shopping cart is?

6) In the course of the Scientists' Duel that Hermie and I fought, we have tied to win PLoS Blog Pick of the Month when Coturnix's attention fell upon us. I wonder if he would have noticed our scrap without Twitter? Anyway, we get T-shirts (one each, luckily we do not have to share)! Unfortunately, they do not say "AWESOME BADASS SCIENTIST!" They do, however, say "PLoS", which is just as good. Those two terms are practically synonymous.

7) In a recent local Mad Scientist meeting*, which involved a Godzilla costume, it came up in discussion that I was the least massy of everyone in attendance, weighing even less than Sister Doom. This makes me sad because I'm 10cm taller than everyone there. I have been trying to gain weight for the past year, and although I've had some limited success it is also really difficult to eat 2.5-3Mcals/day without resorting to cake. The problem is that I don't particularly care for cake.

8) Ever since I bought a cape and awesome goggles to play Superhero Tag, I have been having a difficult time resisting the temptation to wear them everywhere (I am using the goggles as sunglasses, though)! I know it isn't entirely rational, but I cannot help but to feel that my experiments would just work so much better if I wore a cape while doing them. In reality, though, it'd probably mean I'd just spend 3X as much time walking to where I need to go because I'd wind up optimizing my routes based on the prevailing wind direction so that I'd always have a head wind. I'm not sure if this would increase or decrease my scientific credibility. I suspect I need tenure before I'm allowed to be eccentric.

9) I've not been cursing as much here as I usually do lately, so instead I'll post something a little bit racy to make up for it (NSFW, contains pasties):

10) I'm very intrigued by the answers that are coming in to the poll on the left of your screen. I hadn't figured that anyone would pick psychologists as holding their own in a fight against molecular biologists. I mean, what would they use as weapons? Therapy couches and hurtled copies of the DSM-IV?

11) This is something well worth reading, if you read German. Spektrum der Wissenschaft interviewed Bora Zivkovic of PLoS and A Blog Around the Clock notoreity fame and did a very thorough job explaining the breadth and relevance of the Open Access publishing movement. For those of you who don't read German, let it be known that I am waiting for permission from Spektrum to post a translation.

*Yes, for reals. We meet monthly.