Mad Scientist, Jr.

Aw, Snap! I'm back!

2011-11-13T17:46:00.002-05:00

Hallo hallo,

I've put together a new blog-device over here: http://xhonk.com/

In the time since I've last graced these pages I have left the halls of scientific research and become embroiled in programming. As such the new blog device is unlikely to really cover much molecular bio anymore, and will likely cover more of other things.

That is all,

Toaster

Onward Toaster!

2010-11-07T17:42:00.002-05:00

Every once in a while I'll get a comment that lands in one of my Toaster accounts and it reminds me that I actually do have a blog here. I come back here and I don't know what to say any more. I started this as a science blog and now that I'm not in the lab every day doing science I don't exactly know what to put here. It's become a blank, yawning chasm of as-yet-unwritten sparkliness waiting to be brought into being--but to be frank at this point it is unlikely to ever be. I've not given up on science, and nor have I stopped being a scientist, but for the past several months my life has decidedly taken me out of the scientific culture of academia and thrust me into new strange places filled with exciting ideas and motives.

The net sum of these is that I am currently in the process of starting my own company. That, coupled with the guilt I feel each time I come here for not making my own website for a blog, mean that this is probably the last post I will make here that isn't a re-direct to the new sites once I have them up.

Warm Socks

2010-09-06T19:42:00.003-04:00

At the time that the following events occurred, I couldn't recount them due to legal issues.

How I missed seeing the car remains beyond me. Sure, it was gray and bleary outside with limpid bits of snow drifting down onto ice-crusted road mush and finely aged snow. And sure, it was my everyday route where I'd practiced crossing the busy street to get to the bus stop for the past several months. I had thought I'd gotten pretty good at it. I was wrong. I missed seeing the low-slung black sedan coasting along behind the large white van, so I stepped out into the road to cross. Suddenly there was a large black mass in my peripheral vision, and I turned to acquaint myself with the contours of its hood 3m away and rapidly closing. I tried to sprint out of its way, but it was too close. The bumper caught me in mid-air and I distinctly remember the dull thwang of my skull upon its hood. I bounced off of it and over the right side of the car.

I do not remember actually falling.

The next thing I registered was how cold the asphalt was as I drew a breath face down against it. Then I made the mistake of exhaling and every neuron called in in pain. My face was oddly warm. With the next inhalation of cold, wet air, panic bloomed as I realized that I was in the middle of a lane of traffic where motorists routinely zipped past the bus around a blind curve. I was quite certain that I did not want to be hit again.

Vision unfocused, I queried the location of my hands and feet, found them, and somehow managed to maneuver myself upright. I shuffled, bent and suddenly re-learning out how my limbs functioned, the 5 feet back towards the center line, somehow objectively impressed that I'd been thrown 5 feet laterally. It took about 3 minutes for my hearing to return enough to note that the driver was frantically screaming 10 feet away, asking if I was OK. She was shaking, tears in her eyes, and I immediately felt horribly guilty. As I fumbled out words trying to assure her that I was OK, I registered the warmth trickling down my face. My right hand felt weird. I remember her eyes widening as we made eye contact, and her gasping "Oh honey, your face!". I had no clue what she was talking about. But when I took the tissues from her and applied them to the trickling on my face I was surprised to find copious amounts of blood staring back at me. My hands were shaking, my knees were unfirm, and suddenly the bus driver was there, shepherding me and the driver to the side of the road and promising to wait until the police arrived.

A cruiser pulled up within 2 minutes and the officer within persuaded me to sit down on the curb while he got the driver's information. I tried as vehemently as I was able to at the time to convince the officer that no, I was fine, I'd just walk back home and patch myself up. The officer called bullshit and informed me that an ambulance was already en route. Meanwhile, I began to get very, very, very cold. I couldn't stop shivering, couldn't stop shivering, couldn't stop shivering. I managed to fumble off my right glove to see what was up with that hand and found that the stitching on my glove had de-gloved a decent-sized patch of my right thumb.

An ambulance arrived in 10 minutes, and the EMTs insisted that I lay down in the snow so that they could check my vitals. Then they insisted to put me in a neck brace and onto a backboard. In retrospect, this wasn't nearly as much fun as one would think. After that I got trundled into the back of the ambulance like a plank of wet potatoes. They began placing diagnostics and noted that my body temperature was apparently quite low, so they packed my coat with heat packs and tried to place an IV line. Normally, I have beautifully apparent veins that make nurses cry with joy at the ease to find and draw from them. But here, I had gotten so cold that all those squiggly green lines had retreated far beneath my skin and they were unable to place an IV.

Anyhow, at the hospital there was quick admission and 2 nurses deftly managed to take my clothes off without taking me out of the neck brace. This is an impressive feat because I had on a long trenchcoat buttoned and belted up with 2 thick sweaters and a dress shirt beneath it. My pants were easy, but the armored flight boots with lots of lacing were not so easy. They managed to do all of it without having to cut anything.

After that, I got checked out by neurologists to make sure everything was still functioning, and because I was still awake, coherent, and somehow coordinated they decided that I was OK and didn't need any X-rays or CAT scans. This is when they let me out of the neck brace and sit up. It was a relief to see what was going on. Not too long thereafter, they sent over a resident with forceps and saline to dig what gravel she could out of my face. Then she patched up my hand and I was free to go. Somewhere in this, a nurse passed by and noticed that my feet were bare, so she returned with a pair of pre-warmed socks and put them on me. That was pure joy right there, and was definitely the high point of that day.

This is where a logical person would go home and seek comfort. No. I went to lab. I opened up my computer and tried my damnedest to plan an experiment, but no dice through the haze of a now-throbbing headache. So I wound up going home early and sleeping for most of the rest of that day. I couldn't shave for the next week while the fine grit healed out of my chin, and my knees are still scarred from being scraped up, but overall I made it out quite luckily.

However, I can now empirically recommend that getting hit by a car is not wise. This should be common sense, and it is, but it is nice to have data anyway.

Goggles Goggles Goggles 1

2010-05-31T07:18:00.003-04:00

Those are the beginning of my goggles. Looking back at them, I could probably have planned them out a bit better, but for what I had to work with I'm rather happy with how they're progressing. I even got out all the metal burrs out so that they don't poke little splinters into my face anymore! That being said, though, the steel is a bit uncomfortable to wear right up against my eye sockets, so I'm thinking some kind of padding is in order. I've been thinking maybe I ought to add some rolled flannel fabric around the rims, but then I'm not exactly certain how I'm going to get it to stick to the steel. Hot glue feels like cheating, but it may be my only option. The heat gun that I used to braze the steel ribbon to the steel pipe would set the fabric on fire, so unfortunately that's out.

There will be no nonfunctional gears on my goggles. Instead, I intend to add some iris mechanisms to both eyes (once I can bribe my way onto someone's CNC machine, anyone have some good cookie recipes they're willing to share?), green lenses, and at least 1 laser mounted on the side. I probably ought to also make a headband at some point.

How to make Really Heavy Glasses Frames:

1) Procure 1 3" steel pipe nipple, diameter to your specifications (I used 1.75"), with both ends threaded.

2) Sit down with calipers and devise needlessly complex formulas to make perfectly even angled cuts to get scalloped eye pieces.

3) Clamp the pipe to a firm surface.

4) Attempt to cut it with your Dremel, realize it will take about 7h to cut through it that way.

5) Get someone to teach you how to use the much more powerful angle grinder.

6) Attempt to use the angle grinder.

7) Observe that angle grinder has obliterated all planning of step 2.

8) Observe that angle grinder has kicked up a fine steel dust all over your face. Remove safety goggles and ponder your likeness to a raccoon for a couple minutes until you observe the twang that all the flying sparks left on the wall.

9) Continue angle grinding, creating several large burrs.

10) Finish cut.

11) Clamp down 1 of the eyepieces, burr side out. Change angle grinder head from cutting to grinding and apply to burrs. This may induce shrapnel. Eye protection is very important.

12) Get rid of all large burrs with angle grinder, then use Dremel to remove finer burrs.

13) Discover Dremel's polishing capabilities. This will set you back about an hour, but it won't get you much shinier.

14) Discover the 17 small burrs you missed. Go back over with a Dremel.

15) Cut slots for the 1/4" 14G steel ribbon. Thread precut lengths of steel ribbon through holes, manipulate with pliers into desired shape.

16) Rig up a vice on something fireproof.

17) Apply heatgun until goggles begin to glow, clamp down ribbon with long-handled pliers and apply some sort of binding flux*. You may have to do this sequentially, in which case it should be noted that the heatgun does not cool down rapidly.

18) Continue until all pieces are in place.

19) Be satisfied with progress for now.

20) Write self-deprecating blog post later about project.

*Yes, strangely enough this part where I was quite competent, but not with the angle grinder.

Metal

2010-05-27T17:52:00.006-04:00

When I came across this post "Medical Advice for Headbangers" on Boing Boing today, I couldn't help but click through to read the paper. What I found was a pun-fest of scholarly research, and I'm left intensely curious about who funded this research. Ironically enough, at the time I came across the post I was listening to an auto-swung version of Metallica's "Enter the Sandman" (songs run through a rather neat Python script to swing them*).

When Toaster was a young whelp in The Ozarks, it eventually came to that time in his life where he, like every young person in America, is contractually obliged to find something to annoy the hell out of their parents and stubbornly persist at it until they move out. Rather than drink illicit alcohol** and crash cars into trees, I chose to join a death metal band playing bass. As a direct result of this, I began listening to a lot more heavy metal music and going to concerts. I was never much for headbanging*** because being a wallflower is more fun, but I saw a lot of other people pursue it aggressively like a cocaine-addicted lab rat and I noted that over time these people gradually became a bit dimmer than they'd been when I met them. They were also almost always much less coordinated after they'd been to a concert.

This paper developed a mathematical model to explain why my peers were left so hammered after headbanging so much as they did. They analyzed the way people move when they headbang and developed an equation for a sinusoidal wave to describe peoples' head movements during headbanging and subsequently estimated the level of force experienced as described by the Head Injury Criterion (HIC) from the angular velocity of headbanging heads. Although the HIC projects serious injury is only likely to occur at rates of head movement/collision over 15m^2/s. However, since headbanging is a repetitive motion, they chose, with evidence, to evaluate any rate over 8m^2/s as potentially injurious. This means that the faster you headbang and the wider angle of motion your head travels through as you do so, the more likely you are to hurt your brain.

Now the methods get a bit strange. Not only did the researchers attend a couple metal concerts to observe headbangers in their natural element, but they also analyzed the way that the "legendary" headbanging duos Beavis and Butthead and Wayne and Garth headbanged. They concluded that Butthead was the one most likely to be injuring himself.

However, I drew some issue with the music they were calling metal. From the period of my youth described above, I considered such bands as In Flames, Dark Tranquility, Strapping Young Lad, and their doomy ilk to be metal. I'd never considered AC/DC or the Ramones to be music to headbang to because it was just hard rock and punk, respectively. It should be noted that metal comes in more flavors than anyone knows how to classify, but the primary ones are the American model (Static-X, Rammstein), the Scandinavian model (Hammerfall, Nightwish), and the experimental sort (Finntroll, Sleepytime Gorilla Museum).

In conclusion, they recommended that public health agencies issue headbanging warnings on headbanging-worthy CDs, issue neck braces to limit the range of neck motion, and advise that metal bands have tutorials before their concerts. This leads readers of the paper to conclude that the authors themselves have absolutely no metal cred, because everyone knows that the only way they'll ever get concert-goers to wear neck-braces is if they become a metal fashion statement.

*Swing is a musical concept that relates to the delay between upbeats and downbeats. Upbeats and downbeats refer, respectively, to beats 2+4 and 1+3 in 4/4 metered music. Much of rock has the space between all upbeats and downbeats even, but in jazz and some hiphop the space between them is staggered to create a "swing feel".
**See ***.
***OK, it was because I am and always have been a nerd and didn't want 1) to damage my brain or 2) lose my glasses. I knew what brain damage felt like, I was a clumsy kid and had been through a couple concussions--and headbanging felt far too similar to ever be enjoyable. Can't help but to feel a tinge of smug right now with science validating me choosing to almost entirely abstain from it.

Patton, D., & McIntosh, A. (2008). Head and neck injury risks in heavy metal: head bangers stuck between rock and a hard bass BMJ, 337 (dec17 2) DOI: 10.1136/bmj.a2825

T-Cell Receptors

2010-05-24T15:46:00.021-04:00

I've been thinking about T-cell receptors (TCRs) a lot lately, primarily because they're a delicious, tangled little knot of wonderful complexity. Some (Sciliz, I'm looking at you) call them fickle, but no, they're far tastier than that. Synaesthetic metaphors aside, TCRs are the gate-keepers between strong and solemn anti-pathogen protection and a raging inferno of doomy autoimmunity. More specifically, the genes that encode TCR are divided up into Lego-block-like segments [V, D, and J segments] that are sorted more-or-less-at-random*. This happens in each developing T-cell, and the genes undergo some further random mutagenesis via the RAG proteins to generate completely unique receptor specificities. In turn, this means that each TCR is unique, like a precious little snowflake or puppy nose, and it guards the body against its cognate antigen vigorously**. However, much unlike a snowflake or puppy nose, the mechanism by which TCRs generate useful signals and screen out non-specific noise is absolutely badass. In fact, rather than naming battleships after dead guys, who are no longer badass, perhaps we'd be better suited to name warships after T-cell receptor clone lines: Jurkat, D0.110,...others?

Anyway, I've been thinking a lot about the applications of network information theory to TCRs lately. But that's not what I'm going to talk about today, because in thinking about TCRs like that I've recently come to appreciate just how absolutely unrefined, perhaps even crass, my initial understanding of TCRs was.

Back when I first took an immunology course through my university's medical school extension thing, this was the impression I got of TCRs. G-protein coupled receptors (GPCRs) had been beaten into our skulls with the Alberts' Molecular Biology of the Cell text and as such I figured it worked a lot like a GPCR. This turned out to be rather incorrect. In fact, I was also under the impression that almost everything in the world was some sort of GPCR***. Fortunately, this too turned out to be incorrect.

The CD4/8 molecule pictured above is a rather handy cell-surface marker that is expressed, respectively, on CD4+ and CD8+ T-cells, which in turn respectively recognize antigen in MHC-II and MHC-I proteins. If that didn't make any sense, don't worry about it, what's important here is that CD4 or CD8 help the T-cells see the antigen that elicits a signal. CD4 and CD8 are co-stimulatory molecules without which antigen-presenting cells cannot effectively transmit information.

Anywho, as evolution would have it, there are more proteins involved in TCR signal transduction.
At the time I learned of the existence of CD3 and CD28, I had absolutely no clue what they did, so I merrily accepted that they were part of the TCR complex and moved on. Why I didn't look further into them is currently beyond me, but the most likely answer is that I was distracted at the time by free cookies. As such, I thought that signal transduction just carried on with CD3 and CD28 as handsome bookends.

Little did I know of the strange superpowers these two molecules have. Eventually, because science enjoys knocking over the obelisks of my ignorance despite how hard we've labored to keep them intact****, I gained that knowledge.
I couldn't believe it. It was like when I found out that I couldn't eat clouds. Signal transduction WITHOUT antigen stimulation? What sort of stochastic heresy was this? This shattered the beautifully deterministic world-view that my undergraduate education had instilled, that every receptor has a ligand that can be defined and that the cell is a place of beautiful complacency and order. I had known that ligands::signals weren't always 1::1, and I had accepted that, but this, this was somehow darker and more malevolent, and the knowledge that TCRs could be so deftly manipulated and easily fooled was tantalizing. This assumption, also, turned out to be wrong. TCRs are stubborn little bastards.

Nonetheless, I set aside my beloved copy of Janeway's Immunobiology and leaped into the scientific literature face first. I read cell biology papers, I read biochemistry papers, I read biophysics papers, I read autoimmune pathogenesis papers, I read genetics papers, I may have read some enzymology papers, and I know I read a bunch of computational biology papers. I emerged with a mouthful of bistable switches and nonlinear dynamics, and I believe that my understanding of molecular biology as a whole was greatly enhanced by it. Cells weren't orderly little machines, they were complex and messy tiny mechanisms that had error and chaos built in as part of their very functions. And that chaos and nonlinear responses can be harnessed by evolution to increase the sensitivity, response range, and efficiency of cells was absolutely beautiful in its inhumanity. Humans build orderly structures, boxes and flat surfaces and well-engineered machines, but cells don't given a damn! Cells get by, thrive, and capture the very entropy we try so hard to scrub out of our lives, and that, that right there was something that I didn't appreciate until I wound up climbing up atop the tallest stuff at hand one night (Halloween, exactly) and laid sprawled out on top of it watching the sky. Seeing the moon reel about the sky and the stars wheel away above it while the earth beneath me tangibly spun made me feel so very small and tiny and insignificant in the face of such a vast expanse as the universe. But then, at the same time I knew that I was composed of billions of microscopic cells to the point where we are complex molecular galaxies unto ourselves and that, too, made me feel small and insignificant. And lastly, knowing that the stars in the sky and the cells in my body will get by without giving a damn about whether I know they exist or appreciate them was a sort of beautiful thought that has remained with me, probably as the closest thing to faith that I've found.

Epic literature reading aside, the mechanisms of TCR activation as I now envision them are rather complex to draw, so I am going to use art instead.

Apotheose der während des Befreiungskrieges für das Vaterland gefallenen französischen Helden, by Anne-Louis Girodet-Trioson

This isn't meant to be tongue-in-cheek about it being epic*****, but more that it is incredibly crowded and busy and spatial location matters a LOT. You see, resting T-cells have TCRs scattered across their cell surfaces more or less at random, and each of those TCRs is identical. But once 1 of those is conjugated with the triggering antigen at just the right specificity, they all suddenly (within a matter of mere minutes) condense over to the site of that triggering and form an immunological synapse.

The synapse polarizes the TCRs all to 1 side of the cell and clusters them together. Actin also gets rearranged. This provides a cell surface anchor point for intracellular proteins to begin forming a complex cascade. The TCR proteins themselves change shape and CD3's intracellular domains are released from the cellular membrane where they were held. CD3 can then serve as a scaffold for effector kinases such Lck and Fyn. Some JAK/STAT scaffolding proteins eventually transmit the signal from Lck/Fyn/Zap70 to ERK and JNK, which in turn then affect transcription of NF-kB and other response genes such as IL-1b. At the same time, there is a massive calcium flux across the cellular membrane.

Like this. I had to take considerable liberties in omitting details to make this fit on one slide.

However, the synapse is presently more interesting than its effector functions. The immunological synapse is actually composed of 2 parts, the central supramolecular activation complex (cSMAC) and the peripheral supramolecular activation complex (pSMAC). As you might have already imagined, the cSMAC is surrounded by the pSMAC. Within the synapse, many T-cell surface proteins are able to interact with their ligands on the surface of the antigen-presenting cell and vice versa. The SMAC structures are stable (relatively for T-cells) and allow the antigen-presenting cells to properly stimulate the T-cell with both its cognate antigen and some pro-proliferation cytokines such as IL-2.

Now here's where I really have no idea how to visually illustrate it. Within the cSMAC, TCRs are systematically obliterated as the activated, presumably phosphorylated?, TCRs get pulled into the cell and chewed through proteasomes to allow fresher TCRs to get at the antigen-presenting action. This degradation of activated TCRs from the cSMAC is essential for proper T-cell activation (if you block it the T-cells keel over and die, as they are wont to do). And this is what is really frackin' cool: bistable switch behavior in the activation kinetics of TCRs is mediated first by formation of the immunological synapse, and then sustained by endocytosis and degradation of activated TCRs.

Toaster, what the blugoon is a bistable switch?

Hysteresis can be found in a lot of situations, including magnetization, memristors, and a whole lot of very useful electronics and materials sciences.

A bistable switch exhibits the property of hysteresis, which is rather awesome. Hysteresis essentially means that a signal going 1 way across some response action (sensor) doesn't necessarily get the opposite response when the signal goes the other way.

Hystersis can be found in TCRs at several levels. First, it is part of the kinetic proofreading that occurs at TCRs prior to cSMAC formation. TCRs have to be extraordinarily sensitive to their cognate antigen and must be vigilant in screening out false positives. Therefore it takes a stronger signal to activate TCRs than it does to deactivate them. Second, use of hysteresis in this is an efficient way of screening out false positives; the formation of the cSMAC and subsequent degradation of activated TCRs both help to sustain hysteresis behavior. Condensation of TCRs into a cSMAC requires a stronger activating signal than deactivating signal, which means it will remain active at a signal weaker than that which activated it. Thirdly, degradation of activated TCRs helps sustain hysteresis by ensuring that the signal is propagated into the cell at a proper rate. Too fast and the T-cell's built-in anti-autoimmunity mechanisms will kill the whole cell, and too slowly risks death by anergy, while still the net signal from an antigen presenting cell must be higher to activate the T-cell than to deactivate it.

There are many finer details of TCRs that I did not cover here, and still more that I probably don't yet know about. T-cells are an essential part of the immune system, able to differentiate into several different useful phenotypes. CD8+ cytotoxic T-cells can circulate around the body and survey for viral infection or cancerous abnormalities. CD4+ Th1 cells secrete massive amounts of IFNg and help direct innate immune effector cells to combat bacterial infections. CD4+ Th2 cells secrete lots of IL-4 and are involved in battling away parasites or, more relevantly in the Western world, causing allergies and asthma. CD4+ CD25+ regulatory T-cells shut down the immune response by secreting IL-10 after the pathogens have been cleared away to prevent Th1 T-cells from tearing up the place (see: cytokine storm). Memory T-cells lurk around and provide lasting immunity to previously encountered pathogens. And Th17 T-cells do something, they seem to be involved in protection against autoimmunity but we're not quite sure yet. Each of these T-cell phenotypes relies upon the TCR to detect their cognate antigen and help defend the body against the invading microbes that find its squishy, nutrient-rich nooks so very appealing. At the population level, I sometimes think of T-cells as a library of exquisitely-finely-tuned peptide detection machinery that we all carry around with us, and I find that chaos they usefully harness in hysteresis to be beautiful and captivating. There may be other, as of yet, undiscovered T-cell phenotypes and functions despite an already broad and deep literature, and that is an exciting prospect. T-cells and the exact mechanisms of their TCRs remain a relatively open biological frontier, and the best we can do is to dive in face-first.

*Not quite, but explaining it goes beyond the scope here. Look here for more information.
**If it doesn't get killed off first, as the grand majority of developing lymphocytes do, due to anergy or too strong a reaction against self.
***I really liked imagining that there were little Ggamma subunits shuttling around everywhere, all the time, in absolutely everything making a "BlootablootalootaLOO!" burbling sound as they went, with tiny ADP bubbles behind them.
****This is an obligatory joke notification footnote.
*****Also to help break up large blocks of text.

Atari Punk Circuit

2010-05-04T11:34:00.003-04:00

The Atari Punk Circuit was designed as a beginners' project by the venerable Forrest Mims, III. I built it as a prototype of a much grander project still to come, once I get around to making those flex resistor circuits for it. The Atari Punk circuit uses 2 555 integrated circuits (or 1 556), which is a timer circuit, and slaps resistors downstream of the inputs to vary the rate at which it pulses and capacitors on the outputs to modulate that pulse into a continuous and audible waveform. In this iteration I used 2 10K Ohm linear potentiometers as resistors. The 1st one modulates the frequency of the output wave, thus changing pitch; while the 2nd one is bridged across 2 input pins to provide destructive interference and noise upon the 1st wave, thus making buzzy distortion.

Shortly after running it in the video above, I connected this circuit to a power supply without checking what it was set to first, and promptly burnt one of the 555s out. Smoke and everything. Luckily, I have a replacement and will be putting it back together once I've wired up some flex bars in the place of the current linear potentiometers, even though linear potentiometers are dead sexy.

I have no idea how this relates to molecular biology. Yet.

How to Make Carbon Nanotubes

2010-04-28T01:26:00.003-04:00

So I've been reading around, and I came across some methodology that suggested it is relatively straightforward to grow short carbon nanotubes. According to their recipe:

1) Construct vacuum chamber with heavy-duty anode and cathode within.

2) Bridge electrodes with carbon rod, evacuate atmosphere from chamber.

3) Arc 220V electricity through the carbon rod.

4) Carbon nanotubes will grow upon the anode.

5) Modulate chemical properties of carbon nanotubes by changing the atmosphere of the vacuum chamber. Apparently it's not so much important that there be no atmosphere as it is that there be no oxygen, which is fine by me as it is easier to build. Hydrogen makes sweeter nanotubes, while a nitrogen mix makes for more bitter ones.

It should probably be noted that I don't exactly yet know what it is I'm going to do with carbon nanotubes once I've grown them--in fact, that's an understatement, I have no clue--but that's not likely to stop me here. Now all I have to figure out is how to build a "vacuum" chamber. Maybe I can bribe a hacker with muffins to suck all the air out through a scuba mask regulator...

Tin Foil

2010-04-19T02:11:00.001-04:00

Telling you explicitly what this was all about would be far too easy. So what do you think it was?

Pondering #1

2010-03-23T13:00:00.003-04:00

At this point in the cycle I am going to assume that grad school is not going to work out this year, and strangely making this assumption makes me feel much better about the whole deal. There are some programs from which I've not yet heard back, but even so, they may actually not even be the best fit for me anyhow. I'm already so busy doing so many awesome things that this doesn't really set me back, it just gives me more time to better up my badness.

The more I've pondered the luster of a purely academic career, the duller its enticing sheen has become. I'm not certain that I want to spend the rest of my life trapped in an office thinking thinking writing writing chasing funds and collaborators and students. There's nothing wrong with that career, it's the endgame for many scientists and most are very effective at commanding some incredible science from their desks, but I'm just no longer sure that I want it. As the sheen of academia has faded, entrepreneurship has become more enticing. I know it would involve a lot of the same office-bound paper chasing that I mention above, but that somehow doesn't make it less appealing. I think the primary appeal of it may be that the organization I build would be a product of my own devotion and charm more than bound by the strictures of bureaucracy and tenure requirements. I am terrified of complacent mediocrity (terrified I may someday see it in myself), and I'd much rather fail spectacularly than piddle along because there's a lot more to learn in failing than in middling.

However, right now I'm just a Bachelor of Science, not even a Master thereof, so I know that founding a start-up now would be substantially more complex than doing so later after I've attained more letters behind my name and the experience (wisdom?) that goes with them*. So grad school remains as a goal, I'm just content at the moment to polish my street cred and scientific credentials to help me get in next year rather than be disappointed by this year's rejection.

*This may not stop me anyhow right now.

Video Toaster

2010-03-18T12:12:00.003-04:00

Audio quality is bad due to the room being boomy and the microphones on my camera being tiny. There ought to be Official Footage showing up soon that will likely sound much better.

I recommend listening to this on big speaker system with the EQ spiked for mids for maximum comprehensibility.

Post Ignite Talk

2010-03-04T23:50:00.013-05:00

As I mentioned somewhere down below, I was selected to give an Ignite talk about informational processing in biological systems. The talk happened tonight with an audience of about 500 people, and I completely deviated from my prepared notes and winged it very successfully (the drawing together of informational threads when I improvised was better than my notes). I even convinced my brother and sister to do an interpretive dance while I talked to illustrate the transmission of information from DNA to RNA to protein, even though one of them got dropped by the other in the middle of their big 2-person cartwheel (they made up their routine).

After the presentation, a bunch of people whose names I no longer remember shook my hand and told me that I'd given a great talk that was very interesting and many people shared their stories with me of how molecular biology has randomly affected their own lives. There were also a lot of people who knew about the Central Dogma, but had always viewed it as something to be memorized and had never considered biochemical pathways to be a form of useful, active information. Nonetheless, what people very specifically pointed out about my talk were my slides. I painted about half my slides by hand with soluble ink and watercolor. Here are many of them:

Translation.

Protein Folding.

Sonic hedgehog. It helps you tell your head from your ass.

Sonic Hedgehog talking to his buddies Smoothened and Patched.

Concentration gradient of Sonic Hedgehog helps Embryonic Pony determine anterior-posterior patterning.

Transcription. I chose to leave out semi-conservative replication to keep my talk focused.

Proteins have distinct functional motifs, like this one's tongue.

Other presentations ranged from mastodon hunting technology to home funerals to spaghetti bolognese and were overall quite excellent. A program of the evening can be found here, and I will post video of the event once my brother returns my camera. I would certainly do one of these again, and have even submitted a proposal to give a TEDxUM talk in April. I'm thinking Immunology in 15min.

Bridge Cheese!

2010-03-02T23:17:00.004-05:00

In the past couple days, my previous optimisms regarding getting into an awesome PhD program in Immunology with Computational Biology opportunities have turned to a rather danker pessimism. I rarely allow myself to be pessimistic, because when I do I start wanting to do rather illogical things to distract myself from it.

Right now I'm thinking it'd be lovely to move to Norway, somewhere up in Trollheim, and become a goatherder. Goats are nice, they'll eat pretty much anything you throw at them, and they even make milk and cheese (I believe you have to shake them to obtain the latter, though). The primary advantage of doing this in Norway instead of the Ozarks would be that I'd have no neighbors, and those that might be over the next mountain would be far too busy eating fish and enjoying socialized health care and education to care about me genetically engineering the goats.

I'd need 2 phenotypes, 1 with hooky fur and the other with loopy fur, but if I was successful, I'd have VELCRO GOATS!!! Not only could I harvest their wool for useful uses, but they've be velcro uses.

Now, what sort of uses would a velcro goat possibly have, you ask?

Well, for structural elements, of course. Specifically a bridge. A bridge over a fjord. Made out of velco goats. Sure, it'd be a loud bridge with all of the bleating and whatnot, and goats' eyes are damn creepy, but still, it would be a bridge made of goats over a fjord! Not only would it be biodegradable and able to consume the next Trollheimstadt's municipal recycling, but it would output bridge cheese!!!

Skäl!

Like this. Note that goats would be occasionally rotated to ensure an even distribution of goat happiness as I suspect the goats on the bottom of the cantilever are likely to be somewhat less happy and as such may not make quite the same quality of cheese.

Hedgehogs

2010-02-28T02:37:00.002-05:00

I found out last week that I've been chosen to give an Ignite talk about information processing in biological systems. I considered talking specifically about just 1 aspect of that processing, like receptor signaling, but found that this was far too involved for the format. Instead, I've decided to try to explain the entire Central Dogma of Molecular Biology to an audience of about 500 people in 5min with 20 slides that auto-advance every 15s. I've been working heavily on my slides, because each one has to be optimized for its content in this format.

And, because I'm ~~ornery~~ stubborn I decided to paint many of my slides by hand with watercolors. Here's Sonic Hedgehog:

This is going down this coming Thursday, March 4th, at 7p. It'll be live-streamed, so I'll post a link as soon as I have one.

Microcluster Condensation in Immunological Synapses 1

2010-02-15T02:05:00.004-05:00

I remember reading one of the popular science magazines I subscribed to back in high school, probably either Popular Science or Discovery, and coming across a brief article on the discovery of the immunological synapse. It included pretty pictures. I was intrigued by the spatial and sequential alignment of disparate signaling effectors, even though I knew absolutely nothing about the context at the time. Now, I know more about the molecules and pathways involved in dendritic cell::T-cell signaling than I am able to concisely put down here in words without rolling myself up in a cloak of jargon, and even so I barely know anything (with comparison to both the experts in the field and the scale of the unresolved questions). The immunological synapse is fascinating, and to me it is beautiful in its absolute parsimony (that's a whole other post for later).

In beginning the activation of the adaptive immune system, dendritic cells process and present sampled antigen in distinct molecules (MHC) that T-cells can recognize (via the TCR and CD4/8). Due to chunk recombination of V, D, and J regions of the TCR binding motifs and subsequent pre-programmed random mutagenesis* there is extremely high heterogeneity in the recognition cognates of the TCRs. So as dendritic cells (DCs) crawl through the thymus, lymph node, spleen, or other, they have many distinct antigens loaded into their surface display molecules, and every once in a while a TCR that has some binding affinity for that antigen will bind. What follows is the immunological synapse.

The immunological synapse starts out with the binding of the TCR and CD4/8 to the MHC, which nucleate the formation of the central supramolecular activation complex (cSMAC), when all of the TCR/MHC complexes from microclusters and merge into 1 more stable site. A lot of other things happen downstream of that, most of which are very interesting**, but what I find intriguing about this is: what sort of topology do the kinetics of microcluster condensation add up to?

All optimized networks have some sort of topology. This means the hierarchy of one node over another, because to have all nodes processing the same exact bandwidth is rather energetically inefficient. As such, there can be strictly hierarchical topologies like those found inside human corporations with management, there can be scale-free topologies in which hierarchy arises due to through-put optimization and is not strict (a good example of this is the server structure of the Internet), or others I don't know anything about yet.

Is microcluster condensation hierarchical or scale-free?

Unfortunately, it is extremely difficult to answer that question empirically because it happens so fast and because the cells involved are rather camera-shy unless given very exacting and munificent conditions. Therefore, this is more or less a thought experiment.

I posit that microcluster condensation is both hierarchical and scale-free, in turn; first, hierarchical and then, later, scale-free. Cook your noodle on that for a bit, and I'll explain my reasoning for why within the next few days.

*Not a contradiction of terms. The immune system allows for random mutagenesis of a restricted set of amino acids residues on T-cell receptors and B-cell receptors to greatly increase the range of possible binding motifs without great additional informational storage costs (DNA).
**E.g., I find the activation of such factors as NFAT, mTOR, et al to be interesting, but generally find the dynamics of histone deacetlyation to be rather dull.

Smokey Honey Chili

2010-02-13T03:07:00.004-05:00

Ingredients:
3kg ground beef
1 medium yellow onion, coarsely chopped
2 smallish yams, cut into ~5x10x7mm chunks
2 handfuls carrots, peeled and chopped like the yams above
1 large can tomatoes
1 can kidney beans
1 can black beans
4 cloves garlic, crushed
75ml whiskey
pinch lapsang souchong
25ml honey
spices

Directions:
1) Combine onion, garlic, yams, and carrots in large, deep saucepot.
2) Add generous dash of oil, salt, and black pepper.
3) Heat on high until onions are sweaty and garlic is nutty, then add whiskey and 10ml honey.
4) Stir in, continue stirring on high heat until most of alcohol smell is gone (we're after the colloidal flavors of the whiskey to caramelize them in suspension, not the ethanol itself).
5) Stir in ground beef until it is barely done.
6) Add in undrained can of diced tomatoes and tomato paste, stir.
7) Add drained cans of beans, stir.
8) Stir in remaining honey and lapsang souchong*.
9) Add generous cayenne pepper, ancho chili powder and Tabasco, moderate amount more of salt, black pepper, and file powder, and small amount of cloves and cardamom.
10) Reduce heat and let simmer, uncovered, until the protein leaking out of the beans begins to thicken the sauce to your desired consistency.

This was absolutely delicious, and it made enough to feed me for 2-3d. It was at once spicy and savory, but not sweet as one might expect from the ingredients because the low-weight sugars from the honey, cardamom and whiskey caramelized and added depth to the smoke of the lapsang souchong, ancho chili powder and cayenne. There was a faint hint of a mellow, orange sweet echo on the top of the palette, but this was largely obscured by the very well-complexed clay and blue flavors below it.

I set out in inventing this spice combination to get the mild tones of traditional chili while using sweet potatoes as the base. I succeeded on both accounts, I believe, and I really do recommend giving this one a try. I know I will be making it again sometime soon.

*Lapsang souchong is a Chinese tea that's much better at cooking than being drunk. It's a black tea that is dry-roasted over a fire of dry pine needles, and a hot cup of it tastes like literally drinking smoke. So I just added a very small amount this time to get the smokiness without resorting to liquid smoke. The tea leaves steep in the tomato juice, and they're completely edible.

Album

2010-02-08T10:56:00.004-05:00

In those restless gaps in the middle of the night*, washed in the faint glow of my screen, I make music. I produce a lot of bad music that should never be heard by others' ears, but some of it turns out to be fairly decent. When all I had was an analog bass guitar and guitar, I was frequently frustrated by my inability to record and multitrack, but once I procured a virtual synthesizer suite, I was suddenly freed of this constraint. The immediate consequence was a lot of noise and I produced such tracks as "Sneeze Bucket Hat", "Los Pantalones Brillante" and "Pomegranite Ballet". But time progressed and my skills improved and I eventually found that I have 3+ hours worth of music that I think is good enough that I don't mind other people hearing it. This music tends to fall into 2 categories: crunchy, fast electronica smashing subgenres from 8-bit to breakcore jazz together and a smoother music of mostly classical instrumentation running over hip hop/industrial types of backgrounds. I could probably pull 3 full-length albums out of everything, but it is only recently that I finally decided to make an album out of the latter genre.

Toaster Sunshine - "Arc"
1. Oxidative Periphery
2. A Retrospective Abnegation of the Postmodernist Solipism
3. Swiftly Daftly Boom Boom Doom
4. Density Earache
5. Dishware Flossery
6. Additivity (Damitol)
7. Suburban Dirge
8. Erosion
9. Thermal Counterpart
10. Thunder Melted Your Words
11. Läpikuultava Syndan**
12. Aftermath
13. The Nineteen Shades of Concrete Unbeknownst to Sunlight
14. Saccharine Nocturne
15. Somewhere the Magic Happy

This is just a working title, and all the songs are in rough draft form. I think "Retrospective Abnegation of the Postmodernist" needs some more slices mixed in to make it more interesting (it was composed entirely out of about a dozen samples from Shostakovich and Bartoks' string quartets), "Suburban Dirge"'s violins need EQ tweaking, and I have noticed that there is a high pitched percussive artifact in "Thermal Counterpart" that needs to be found and dealt with. Also, something weird happened with "Saccharine Nocturne" upon conversion to an .mp3 that I'll have to track down.

Anyway, if you'd like to listen to the raw tracks in all their muddy glory, you can download a zipped version of the above album at: http://drop.io/ji4trez#. If you do so, please, by all means, criticize it as bluntly as you'd like.

*Notwithstanding the background music I tend to produce whenever there's a guitar handy, despite whatever else is going on around me.
**This translates to 'translucent heart'.

Passionate N00bity

2010-02-03T22:58:00.003-05:00

I was somewhat disappointed when I first started attending non-class seminars for my projects in the lab and my interests to find that there wasn't much rambunctious cheering or passionate cheering. Sure, everyone is very polite and asks Very Intelligent Questions and I understand that much of this is due to an inherent respect for the speaker's effort in gathering and interpreting their data and an abstract need for civility. However, if we're doing science because we love the intellectual challenge, why don't we get more worked up about it and express that excitement? I know that science is not the same thing as sports, but why can we not get up the same passionate lather as sports fans in our arenas of data and theoretical abstraction?

Part of this is due to my dream of one day delivering a data talk in the form of a power ballad, but it's also due to confusion as to when I may break down the barrier of formality and ask a douchey question within the cloak of excited admiration? I recently saw a speaker present some really awesome new biotechnology she had developed in the course of her project and its applications. The tangibility of the data (real-time fluorescent tracking of cells in a living matrice by 2-photon microscopy; which basically meant actually seeing immunotyped immune cells crawling around and interacting with each other) was surreal and exhilarating, but when she talked about her methodologies I was left wanting. I don't want to out the speaker, so I cannot say exactly what my beef was, but it had to do with the algorithms by which she chose to quantify her data. I refrained from asking this question in the Q&A session because of the very civility I mention above, it just seemed like too rude a question to ask in such a polite intellectual subculture as an academic presentation. Of course, on the other hand, there was also the possibility that my question would have revealed my ignorant n00bity, and to be honest that also played a part in me not asking.

Nonetheless, when can we whup it up and get excited about the science all around us? Can I ever high-five or fist-bump a speaker when they've shown me something awesome or would doing so break down this fifth wall academic politeness has surrounded us with?

Old-School Anti-Woo

2010-01-28T00:24:00.003-05:00

I came across the following letter on BoingBoing.

Nov. 20. 1905
J. H. Todd
1212 Webster St.
San Francisco, Cal.
Dear Sir,
Your letter is an insoluble puzzle to me. The handwriting is good and exhibits considerable character, and there are even traces of intelligence in what you say, yet the letter and the accompanying advertisements profess to be the work of the same hand. The person who wrote the advertisements is without doubt the most ignorant person now alive on the planet; also without doubt he is an idiot, an idiot of the 33rd degree, and scion of an ancestral procession of idiots stretching back to the Missing Link. It puzzles me to make out how the same hand could have constructed your letter and your advertisements. Puzzles fret me, puzzles annoy me, puzzles exasperate me; and always, for a moment, they arouse in me an unkind state of mind toward the person who has puzzled me. A few moments from now my resentment will have faded and passed and I shall probably even be praying for you; but while there is yet time I hasten to wish that you may take a dose of your own poison by mistake, and enter swiftly into the damnation which you and all other patent medicine assassins have so remorselessly earned and do so richly deserve.
Adieu, adieu, adieu!
Mark Twain

This was a response to an advertisement from a patent medicine salesman, apparently seeking endorsement. I hope to remember in the future to slam the proponents of alt-med woo with such grace and wit, for at the very least it is more elegantly entertaining. In the meantime, my respect for Mark Twain* has only increased.

*Sooooooo much better than Kierkegaard.

City of Loathing

2010-01-18T11:01:00.003-05:00

I'm just a scrawny cracker, and as such I don't exactly have much gravitas when it comes to commentary on things such as Martin Luther King, Jr. Day. But I have something to say anyway.

I grew up in an area of the country where racism is everyday and accepted. African-Americans lived on Grand Blvd., Benton Park, Boonslick, Blanchette and in East St. Louis. Koreans lived down Manchester Blvd., Serbians lived through the worse ends of Kingshighway, Italians lived on The Hill, Irish lived in Dogtown, French lived in Soulard, Jewish people lived in Tower Grove and University City while Hispanics were practically invisible. Generic white people lived anywhere they damn well pleased, but were especially adamant in Florissant, Chesterfield, Hazelwood, Maryland Heights, Forest Park, and the Central West End. Saint Louis is a city of several million people that has been standing for more than 200y, and these divisions remain, perpetuated by infrastructure and class. The neighborhoods around the dying industrial zones just west of downtown are crumbling and so are the schools within them, and this just sets the stage for a cyclic repetition of the same social injustice. Meanwhile the office towers of Clayton feed the vibrant school discticts of Forest Park and the Central West End as well as luxury shopping villas like the Galleria.

But in all of this, it was the Page Avenue Extension project that most clearly illustrated the dystopic undercurrent of casual racism in the city. This project built another bridge west across the Missouri River, providing a direct line of transit from Page Avenue, which runs from downtown St. Louis all the way through to Maryland Heights, out to suburban St. Peters now. The largely white denizens of St. Peters nearly shat themselves in consternation, and the reason I kept overhearing was that now "black people could move in" and apparently would ruin everything. This highway project shaved about 30min of driving time off of getting from St. Peters to downtown, and I found it absolutely ridiculous to suppose that 30min by car would have effectively stopped African-Americans who wanted to move in from doing so. But that's what people were nonetheless afraid of.

And what disturbed me most about the whole thing was that the same people who had problems with the highway project were those who frequently also had tactical armories in the basements of their homes. That venal and irrational hatred, coupled with such easy access to powerful firearms, never sat well with me. This is the same city that sees the homes of interracial couples defaced with defamatory graffiti and witnessed the firebombing of the only Muslim mosque in the city with nary a murmur after 9/11. With Obama being elected, I would like to believe that racism has gone away, but I'm not so naive as that. Racism persists not because powerful people wish to keep oppressed minorities explicity repressed, but rather because those that have "made it" are desperately afraid of having to share their slice of pie with a strange group they perceive as not being of themselves.

Well, I cannot morally identify with those who cower in their suburban homes with semi-automatic assault rifles and hollow-tipped bullets in their basements for fear of simple progress. I reject their fear, I reject their hatred, and I condemn them for their prideful ignorance.

I left St. Louis in 2004. It had already left me much earlier.

*I can understand hunting guns and have no problems with them, but there is a massive difference between a single-shot hunting rifle and a semi-automatic tactical assault rifle loaded with bullets designed to inflict maximal harm.

Scalpel in My Head, Wielded by Mine Own Hand

2010-01-15T17:37:00.004-05:00

I am an imbecile.

I am also a genius.

How do I manage to operate simultaneously at both extremes of intelligence? It's not as simple as a statistical mean, but rather a wild and exhausting oscillation between them, careening from high level metacognition to struggling to tap out a single important word that I can see in my posterior inferior frontal gyrus, stubbornly not moving despite my need of it.

Simply put, I wouldn't have the slightest clue that I am intelligent if not for others around me reinforcing their perception of my intelligence upon me. This isn't to say that differences in processing speed, retention of information, or synthesis of broad principles would not have eventually become apparent to me, but they would have taken quite a while as I, and others, have found myself to be profoundly dense when it comes to the nuances of human emotional social behavior. Basically, this stems from the contrast between feeling my sentience buzz with tantalizing data and sometimes feeling remarkably stupid.

I am aware that feeling stupid or feeling smart is an entirely subjective internal experience. Furthermore, it is likely that feeling remarkably stupid is actually due to being able to perceive my mistakes and/or shortcomings in their full implications and on (perhaps too) many scales. I am not writing this to polish my own ego here, this is speculation. I have been very frequently puzzled by other peoples' behaviors, and this is not the pleasant, relaxing kind of puzzled where there is some verifiable formulation of the question to begin with*, but the kind of maddeningly unquantifiable mystery that follows no logic except self-interest.

I don't understand most people. I believe I understand a large aspect of them, but I don't understand why. I have met so many people who seem content to live in the shallow end of the pool, who have never regarded information as anything other than temporary and fleeting, and I cannot help but wonder why they are content with it. Sure, everyone becomes a philosopher on their deathbeds, but what of the rest of their time before it? I cannot relate my frame of experience to theirs. I make no claim that my mode of thought is superior. I cannot comprehend satisfaction without questioning the vast beauty and complexity of the world sparking all around me.

On the other hand, nerds and scientists are comprehensible people. They operate on the same strong currency of curiosity and wonder that I do, and as such I find them much much much more relatable than most "normal" folks. Sometimes I amuse myself by trying to view the nerd/hacker/scientist cultures of which I am a part like I am an outsider to it, and the way that we interact with one another is in many ways fundamentally different. We are scientists, nerds, or hackers because we love what we do and are deeply emotionally vested in the outcome of our clever work. We question the world around us and reinvent our relationship to our understanding thereof frequently, and that, more than anything, is what sets intelligent people aside from others.

*E.g., a jigsaw puzzle has a solution if the complete set of pieces are placed in the correct spatial sequence, or the structure of a protein may be hacked to test its function in measurable environments.

Food Hacking 1

2010-01-10T18:31:00.003-05:00

Unfortunately these were so delicious that I forgot to take a picture and by the time I did remember they were all gone. This is a recipe for Advanced Cooking Idiots that I invented yesterday, and I hope you find it as tasty as I and my guests did.

Cinnamon Radishes

Ingredients:
1kg radishes
1 bag cinnamon chips
3 eggs
1 glop of breadcrumbs
oil

1) Wash radishes thoroughly.
2) Boil radishes until slightly soft. Drain and let cool.
3) Cut off top sprout of each radish and use end of a potato peeler to excavate a narrow cavity.
4) Stuff as many cinnamon chips into that cavity as will stay.
5) Roll around in beaten eggs.
6) Roll around in breadcrumbs until well-coated.
7) Fry in 4cm hot oil, turning as needed, until evenly golden-brown.
8) Remove from oil with slotted spoon, shake off excess oil.
9) Serve.

Not too complicated, but sort of laborious. These will be crunchy on the outside, and the tart starchiness of the radish will both offset and complement the sweet kick of the cinnamon melted inside. Best served with a dollop of Sour Pepper Sauce on top.

Sour Pepper Sauce*

Ingredients:
500ml ketchup
2 fat limes
100ml soy sauce
100ml Thai pepper sauce
2g tumeric
1.5g coriander
3g ancho chili powder
2g ginger
1.5g salt
1.5g black pepper
1g cardamom

1) Stir all wet ingredients and powder together. Bring to an vituperous boil.
2) Squeeze in all juice from limes.
3) Continue stirring intermittently at a high boil until the sugars in the ketchup begin to carmelize and turn the whole sauce a ruddy brown.
4) Cover and simmer for 30min.
5) Remove from heat and refrigerate overnight.
6) Serve cold.

This will be both hot and smooth with a nose tingle. It's is highly acidic, so exercise caution and titrate with base in such a case as indigestion develops. Pepto-Bismol may be used as a base.

*Also an effective way to clear one's sinuses.

Dinosaur Scientists

2010-01-08T02:13:00.005-05:00

HD isn't doing me any kindnesses, but I stand by my thesis: we need more dinosaurs! Or robots!!! Or robot dinosaurs. Just something more charismatic than "Scientists have discovered..." in media reports as though we're all faceless data drones. I mean, if sports teams can have mascots, why can't we have them too?

Consultant Toaster

2010-01-07T17:52:00.003-05:00

I have decided to do some consulting on the side to bring in some extra dough. And by dough, yes, I do mean that I will accept payment in cookie dough, but it better not be peanut butter cookie dough or I will cut someone*. Seriously, peanut butter belongs with jelly on bread, NOT IN MY COOKIES!

Anyway, I have noticed a large number of people who complain about the greater-than-desired circumference of their waistlines very often. I cannot force these people to do sensible things such as eat better or exercise more regularly, and I am wholly unqualified to perform bariatric surgery. Therefore, I will help motivate them to exercise more intensely.

For just $20/session, Toaster will chase you full-speed with a pointy stick. You supply the pointy stick! Each time you slow down or stop fearing the stick, Toaster will give you a gentle jab with the stick to re-motivate you.

And for just $50/session, Toaster will come to your house in the morning and ambush you with not just one, but TWO pointy sticks as you walk to your car and chase you all the way to the nearest health food store, lurk ominously until you have purchased low-calorie, high-fiber foods, and then chase you back to your home screaming obscenities in a foreign language of your choosing!

Toaster is offering this service for a limited time only because he is well aware of the rate at which people lose their convictions to stick to their New Year's Resolutions. So don't delay, email Toaster now to schedule your first one-on-one personal weight-loss consulting session!!!

*Even if that means drawing a hotsauce face on a block of tofu and slashing at it.

Worms in My Data

2010-01-06T00:53:00.003-05:00

This is real flow cytometry data I collected. The terraced blotches represent different populations of cells as differentiated by staining their surfaces with fluorescent antibodies, as such the axes represent 2 different fluorophores' distinct staining intensity. Non-floaty blobs like the sandworm blob are common because primary cell populations are always somewhat heterogeneous and as such will rarely stain in perfectly discrete pots. I couldn't look at this plot and not see a sandworm, so I made it better.

Muffin Ravioli

2010-01-04T17:49:00.005-05:00

In theory, ravioli are watertight. So maybe this will work. But I'm not certain.

Background:
I like food. I like science and the engineering/hacking methodologies. But I know it's not a good idea to eat off of labware, so the natural solution is to hack food. To this end, I am hosting a food hacking potluck with many of the local hackers this coming weekend*, and I've been trying to figure out what to make.

Experimental Aim:
Essentially, I want to make blueberry muffin ravioli. I will serve it in a mango avocado basil reduction. Now, making either raviolis from scratch or muffins from scratch is relatively straightforward, but combining them so that the ravioli is still pasta-ey and the muffin is still muffiny is an issue. Will pasta cook if I just bake it in the oven? Or do I have to boil it first? I know from literature research that lasagna noodles must be boiled before being baked. It is possible that I could blanch the muffin batter-filled raviolis in boiling water and then bake them, but I am concerned that this would lead to leathery pasta shells. I mean, honestly, I think my best bet is to cook the ravioli squares first without muffin batter, fill them, seal them, and then bake them moist.

What do more experienced cooks think?

If this falls flat, I have a backup plan: caramel-filled radishes breaded, fried and then served with a sour pepper sauce.

*I will be posting pictures and recipes of the things that turn out tasty.

Science Isn't a Job

2010-01-03T20:38:00.000-05:00

I am not suited to have a job.

Notwithstanding my circadian malfeasance, I can't just have a job. A job is something you go to for 8h a day and detach yourself from coming home, something that pays the bills and fits in a big chunk of your daily routine. Something that weekends are an escape from.

Science isn't just a job. Science isn't just a career. Doing science is a mode of being, a way of thinking and a pervasive outlook that permeates all aspects of life. To be sure, there are people doing science to whom science is nothing more than a job, but to the scientists, doing science is a passionate outpouring of their innate internal curiosity and excitement at the sheer wonder and awesomeness of the reality around them.

As I said, I can't just have a job, I need the storm and flow of science's complex funneling of my creativity, cleverness, and joie de vivre. Even as I define the parameters of my experiments, science, in many ways, defines me. My education in science has sharpened my inquisitive and skeptical predispositions to become useful tools and not just the occupation of idle daydreams. This utility of my innate urge to create new stuff, to explore and discover are why science isn't just a job for me, it's awesome.

There are times that I get frustrated with my benchwork. Recently I had a long series of experiments not work properly for a couple months, and tearing through my methodology to try to find where I'd gone wrong, trying to plot out possible sources of error and chafing at the bit as each of these experiments took several days to validate was draining and discouraging. There are times that the poor quality of my data, such as getting a higher event count from bleach than my sample on the flow cytometer, makes me question my scientific aptitude in the first place. How could I ever expect to succeed in this experimental endeavor when I wasn't smart enough to begin with?

But it is this that is also valuable. Science forces us to question ourselves. We wrap up our self-esteem in our experimental results and we take rebukes from reviewers personally. We chase windmills of perfect data and push the capabilities of our minds ever further seeking to integrate our data into a new story the world has never seen before. This is important. By being both scientists and science, by loving what we do and the delightful but exhausting challenges it confronts us with, we are pushed not only to improve the quality, scope and ambition of our experiments themselves, but also to become better, savvier scientists and humans as well.

As a science, biology is weird. It's messy, it's frequently stubborn, it's complex and chaotic and these are what attracted me to studying it. And then into more complexity I realized how awesome immunology is. But it's not so much the complexity itself that draws me back into the lab, it's that with molecular biology I am literally peeling back levels of reality with my mind through the careful design of experiments with cells and reagents that I cannot see, feel, or taste. It could not be cooler, unless I had more lasers, but I digress:

Science ain't a job so much as it is riding an angry horse through a buffet of cookies and ice cream.

Caricatures

2010-01-02T06:41:00.004-05:00

Somewhere over the course of an incorrigible doodling habit, I got to a point where I could draw kind of decently. If I sit down and make the formal effort I am able to bang out a pretty good approximation of what I see in front of me. But life drawing has never satisfied me. It's as if the point of life drawing is to cast reality in cold marble, and to me this loses a great deal of the vitality of real-time, unfiltered visual perception. Instead, I like caricatures, those potemkin representations of people that take an aspect of their physiognomy and amplify it, draw it out like a good cook brings a subtle flavor simmering to the surface and celebrate it. I find that these more daring 2D casts of faces and people and things and places capture more of the realness than a photograph because it is filtered through the unique wrinkles of the drawing hand's mind.

And I like drawing caricatures.

So, dear readers, would you like a Toaster-drawn caricature of yourself? Email me* a picture you want drawn through my distorting parameterization and I will send you back a quick caricature, with no guarantees as to humility or reverence. It should be noted that I will also post them here, but will not append your name and/or pseudonym if that is your wish.

*Toaster DOT Sunshine AT gmail DOT com

Theory vs. Practice

2010-01-01T04:26:00.002-05:00

In theory, a flex sensor is simple. It is just a bit of resistive material, like anti-static plastic sheeting, sandwiched between 2 bits of copper laminate and squished inside some heat-shrink tubing. There are many things that I would like to build of of this. First up as a prototype is building flexible antennae for an Atari Punk Circuit to modulate the sound based on how they are moved about. Then I want to make a suit out of them at all my major bendy points and route them through a Freeduino into a MIDI to have an instrument suit. I think it'll be neat to be able to make roaring bass lines just by waving my arms about wildly, which is how I normally dance anyhow.

In practice, however, securing the copper laminate has been more difficult than expected. Turns out there are a lot more different types of copper foils than I had ever expected and I'm not sure exactly which one would suit my purposes best. And while we're on practice vs. theory, it turns out that Ethernet cables are much easier to make into complex braids than 16G aluminum wire. While a 4² braid of Ethernet does look cool, it is not a torc.

Upon Intelligibility

2009-12-18T15:31:00.005-05:00

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:

or

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.

Toaster's Stewing Stew

2009-12-16T14:53:00.003-05:00

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

Ingredients
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)

Directions
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.

Electricity

2009-12-09T13:36:00.003-05:00

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?

Voltage!!!

Fragments of Toaster's Mind Blather 3

2009-12-06T04:21:00.003-05:00

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.

Cookie Reviews: Erin Baker's Breakfast Cookie

2009-12-02T13:11:00.003-05:00

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.

Power Tools

2009-11-30T17:47:00.001-05:00

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

Cloudy With a Chance of Meatballs

2009-11-28T00:00:00.002-05:00

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.

Peritonsillar Abcess

2009-11-26T00:48:00.007-05:00

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.

With a What?

2009-11-21T06:58:00.006-05:00

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.

Sound:
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.

Toaster the Psychic Organ Builder

2009-11-18T19:07:00.004-05:00

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.

We Need a Verb!

2009-11-15T03:39:00.002-05:00

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...

On Recognizance of Competence

2009-11-04T14:39:00.004-05:00

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.

Language Blathering

2009-10-27T17:00:00.004-04:00

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.

Marathon Science

2009-10-18T20:46:00.004-04:00

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.

7 Kinds of Awesome Busy

2009-09-26T02:58:00.006-04:00

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.

E-mail Quandary

2009-09-09T15:10:00.004-04:00

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:

HEY DR. DOOD!
ZOMGFLUFFLES UR RESEARCH IS, LIKE, SO HAWT!!!!11!1! U R TEH AWESOMES!!!!!!!!!!!!!!!!!!! :) HAZ U ROOMZ IN UR LAB FOR ME!?
SQUEE!,
TOASTER

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?]

[Respect]
[Word.]

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!?

Tactile Ostrich

2009-08-25T14:55:00.000-04:00

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.

Dear Reader

2009-08-22T23:58:00.004-04:00

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,
Toaster

Blathering on Hunger

2009-08-18T16:22:00.004-04:00

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.

MAGIC!!!

2009-08-12T21:01:00.004-04:00

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

WHY

IF

HOW

IMAGINE

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?

How to Explain the Senses?

2009-08-10T23:21:00.006-04:00

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.

Hat

2009-08-10T13:19:00.000-04:00

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

Night Owls

2009-08-10T01:18:00.003-04:00

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.

How To Make Greens

2009-08-07T18:15:00.006-04:00

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

2009-08-07T12:50:00.002-04:00

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.

Why Science Needs Dinosaurs

2009-08-05T00:43:00.008-04:00

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?

The Culture of the Internet is Permeating Science (TRANSLATION)

2009-08-03T17:20:00.004-04:00

[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.”

Blather Fragments

2009-08-02T14:09:00.010-04:00

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.

Keywords

2009-07-31T15:32:00.005-04:00

For the first time in a long time, I looked at the Google Keywords that are leading people to this site. I was very amused. In fact, I'm still amused, and also bewildered. Since this is a happy state of being, I thought it might be polite of me to share it with you.

fire breathing chicken
mass haul optimization algorithm
belgian blues
20 flirty questions for scientists
a scientist and makeup blog
adiponectin the scientist
bass player scientist
bigger cecum
can bacteria grow on oreos
cartoon word
do llamas have breasts?
ear toasters
friends flirting bad side
fucking awesome toasters
guild of mad scientists
hats that a scientist would wear
hungry leptin
igf-1 before after pics
in vitro system to create apoptotic cells
invader zim gir mens sneakers
luciferin problem
mad to breast
moshing as a woman
picture of a mad scientist
pipette tips in nostril funny
read the fucking manual cartoon
silk muscle
tesla jr
there's a llama
vampire ass
was i flirting
weakness of a men to a woman
zombies cooler than vampires
leptin ghrelin adiponectin resistin milk

Of all these terms, it's "there's a llama" that worries me the most. I picture someone nervously googling that term while an angry llama stares inside their bedroom window, chewing oh-so-patiently whilst waiting for the full moon to rise! Because that's what llamas do, right?

Also, I do not recommend ear toasters. Use muffins instead; they are thermally dense and edible!

On Animal Research

2009-07-30T11:24:00.005-04:00

The recent venal response to Dr. Isis' very reasonable worry regarding animal-rights activists posing as university inspectors to gain access to her lab and wreak harm upon herself, her employees, her research, or her livelihood. In response, implied threats against her family were made.

Let's be clear: Toaster supports animal research. I do not support inhumane treatment of animals or unnecessary cruelty, but I will defend the necessity of animal research whenever it called into doubt. I do not undertake animal research lightly, and I seek to treat the rodents I use as humanely as possible. Some persistently argue that animal research is inherently inhumane and cruel, but I find that it is far more cruel to perpetuate human suffering that may be preventable due to animal research by sitting back and doing nothing.

Nonetheless, the recent debate got me wondering how far I would be willing to go to further research that alleviates human suffering. Adult humans aside, I suspect that if taking on a silverback gorilla armed with nothing more than a 22-blade scalpel was guaranteed to save a stranger's child, I would do so. And if that child were family, I'd forfeit the scalpel for a potato.

Dueling Clarification/FAQs

2009-07-29T14:20:00.002-04:00

What is a Scientists' Duel?

As opposed to a traditional gentlemens' duel in which the participants try very hard to wound or kill each other, a Scientists' Duel is a rather gentler sport. In this, 2 scientists agree upon a paper to read and publicly explain (e.g., through research blogging). The public then gets 100 points to divide between the participating scientists as they see fit based upon the quality of their explanations. After a set time period of voting, points are added up and a winner is declared.

How do the participating scientists choose a paper?

However they wish to and feel it fair, but it must be mutually agreed upon. In my duel with Hermitage, we chose the brain-machine interface paper because it is far outside each of our respective expertise, which we felt would make the competition fair. At the same time, a duel between scientists within closely related expertise upon a paper from their field would also be fair.

How do readers judge the Dueling Scientists?

However they want to. But generally comprehension, intelligibility, and accessibility are good benchmarks.

What benefits are there to Scientists' Duels?

Not only do these duels get more than 1 interpretation of otherwise unpublicized research out into the ether for knowledge and consumption, but it also adds a fun element of competition. Concurrently, Scientists' Duels accord an inherent worth upon a scientist's ability to concisely and clearly explain complicated research, which is a win for both their readers and the scientist's skills.

I want to Duel a Scientist. How do I do so?

Contact the scientist in question, let them know what you're about and see if they're up for it. This would be where you challenge them. At that point you can invite submissions for dueling material from your readers or work it out with the scientist you challenged. Either way, for the duel to be fair, the material must be mutually agreed upon. Then you read the paper, write about it, and post that. Let your readers know it's part of a duel and provide a link to your opponent's entry. It would also help to aggregate it into Research Blogging. Then sit back and let your readers vote.

Add other unclear questions in comments and I shall amend this post to include them.

Let's Have a Duel!

2009-07-28T22:46:00.004-04:00

I would like to see more Scientists' Duels.

Kinda like that, but sciencier. Maybe they have rancors attached to the end of those ropes.

Sure, dueling was widely regarded as a vile gentlemen's sport in the 19th century, but that, I suspect, was primarily because it involved rather a lot of pistols, sabres, death, and fluffy shirts*. Nonetheless, dueling was a visceral bloodsport that involved honor and competition. I'm not advocating that we turn to scientific bloodsport** for amusement and funding, but rather that we start competing intellectually. Yes, we as scientists already compete upon the scientific edge, trying desperately sometimes not to be scooped as we race to publish data and inadvertantly grind graduate students' free will*** to dust in the process. But at the same time, friendly, rigorous competition is a good thing as it raises standards and adds a slight sheen of adrenalin to even the most esoteric of topics.

If future Scientists' Duels were to take place in the form of competing research blogging, the benefits would be manifold. Namely:

1) Intellectual competition is fun.
2) Important research is disseminated.
3) An inherent value in explaining complicated science for uninvested audiences emerges.
4) More scientists communicate outside of their fields, thereby increasing their explanatory flexibility.
5) Research gets explained more than one way in each Duel, which would allow those with different knowledge-absorbing patterns to more effectively learn what it means.

I am not explicitly saying that I will take on any and all comers in challenging me to a Scientists' Duel, but I am implying it while trying to encourage others to square off and Duel for themselves.

Thoughts, ideas, encomium, and/or**** excoriation?

*Which I do believe I could pull off admirably, the shirts, I mean, not the pistols. Anyone up for a bout with quarterstaves?
**Like writing grants, but with sharp, pointy things. Come to think of it, an actual duel may be easier, and preferable for both parties, than endless traction of 2 closely scored grants in study section. But I digress.
***That's a joke, I think...
****The English language really needs an "and/or" functionality. "Else" is inexact. Therefore I propse "twick" and/or "andort". The added "t" makes it cooler.

Scientists' Duel Outcome

2009-07-28T17:11:00.004-04:00

Hermie won*.

The final score was 205 Hermitage, 195 Toaster.

Poop.

But at least I only lost by 10 points instead of only getting 10 points!!! She graciously extended the offer to me to not count the midnight dark horse Erk, which would have resulted in me winning, but as I am a Mad Scientist with integrity, I decided that responsibility to the rules was more important than my own ego and we counted their votes anyway.

However, let it be known that this is far from my last duel!

*Gloating can be found here.

Optimizing Algorithms for Brain-Machine Interfaces

2009-07-24T00:00:00.004-04:00

Imagine waking up trapped in a prison of your own flesh, blinking awake in the dull glow of a softly bleached hospital room. Your arms and legs are unresponsive to the will to move them, to the simple desire to reach up and scratch the itchiness of morphine from your eyes. Nothing happens, nothing responds, nothing moves, nothing feels. You are an immobile head trapped on an unresponsive body, and no matter how loudly you scream against the walls of your confinement from inside your head, nothing happens.

Luckily many quadriplegics retain the ability of speech and independent respiration. However, their quality of life, and that of the more unfortunate patients who are fully lucid but cannot communicate with the outside world by anything more than eye-blinking Morse code, remains severely compromised due to poor rehabilitation prospects and dependency upon caretakers. Perhaps one day we'll be able to repair injured nerves and restore connectivity with the rest of the body, but for now we're beginning to work out how to directly interface the brain with mechanical actuators. The goal is to develop an interface through which a paralyzed patient could control a machine that would augment their standard of living using nothing more than their mind and some technology.

Nerves and computers and both conveniently electrical. The problem is that they each operate on very different electrical schema. With computers we more or less know which transistor is storing which bit of information and have discrete units of conductors, resistors, capacitors and such. But it is very difficult to isolate the behavior of a single neuron in situ, so instead we use mass behavior of relatively large numbers of neurons to try to approximate functional firing chains. To translate the chaotic, non-discrete signal from neurons into discrete signals for machines, we need an algorithm. And to develop that algorithm, we need electrode-implanted animal models (unrestrained monkeys in this case) and scientists who can do math.

Li and Nicolesis et al have developed a novel modification of pre-existing brain-machine interface algorithms in "Unscented Kalman Filter for Brain-Machine Interfaces". Previous brain-machine interface algorithms were either linear approximations or non-linear particle filters. Linear filters (such as the Wiener and standard Kalman filters) didn't do as well approximating the behavior of neurons as particle filters, but they were much faster and computationally cheap enough that they could be used in real time. In general, particle filters (such as SSPPF) were very good at modeling the behavioral input of neurons, but they were so cumbersome that each iterative point required computing time that put it outside the range of useful real-time applications. Li and Nicolesis et al have modified a Kalman filter such that it uses a nonlinear tuning method (a quadratic model instead) and adds historical regression with multiple time offsets to help predict future behavior patterns. The quadratic tuning model integrates previous neural activity to arm movement models (the cosine tuning model, tuning to speed, tuning to distance of reach) into one cohesive and flexible equation. The historical regression with time offsets gives the model a short memory that allows it to quickly predict possible future states of neural activity to arm movement correlates and optimize them based on current neural activity input.

Implementing the quadratic neural tuning model greatly improved the accuracy of predicted neuron firing behavior, which means that the algorithm was better at interpreting the noisy signals from the neurons. At the same time, the historical regression made brain-activity-guided movement of the prosthetic hand* smoother and also helped to tune the monkeys' training on the algorithm by operating as a sort of continuous optimization that kicked out inefficient processes to improve overall performance. This quadratic model also significantly improved the reconstruction of the monkeys' desired hand movements during real-time tests in comparison to standard Kalman and Wiener filters.

In effect, this new algorithm construction allows for more accurate control of a prosthesis, with low tuning demands and progressive learning of efficient movement correlates. Ideally, this will one day allow paralyzed patients to accurately control mouse cursors (better than existing technology, anyway) or robotic prostheses that will greatly improve their quality of life. This technology may still be crude, but it is progressing rapidly and with great potential. I, for one, welcome the prospect of an auxiliary robotic arm. It would be great for my benchwork productivity.

*In this case, a cursor on a computer screen.

Li, Z., O'Doherty, J., Hanson, T., Lebedev, M., Henriquez, C., & Nicolelis, M. (2009). Unscented Kalman Filter for Brain-Machine Interfaces PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006243

___________________________________________________

This is my entry in the Scientists' Duel that Hermitage and I are fighting for the title of Most Nefarious. Her entry is here. You, dear reader, will decide who wins. As of 12:00AM, 7/24/09, you have 72h to vote. You get 100 points to divide between Hermitage and I as you see fit. Report your scoring in comments. At the end of 72h we will tally up the points and determine the winner.

BATTLE BATTER ANNOUNCEMENT!

2009-07-21T23:10:00.007-04:00

This Thursday a 5pm EST a mighty and fierce battle will break out in the sciencey blogosphere. I know this because I will be one of the combatants, and I intend to kick some serious arch-nemesis ass! This will not be any ordinary flame-war or troll-con, no, this will be far more violent, far more bruising, and inflict far more collateral damage on the surrounding countryside.

This will be the duel for the TITLE OF MOST NEFARIOUS!!!

Hermitage and I dispute and have fought at great length to determine which of us is more nefarious. Indeed, entire dinosaur armies (my shock troops) have been obliterated into smushiness by her trout-gore spewing bento cannons (her favorite weapon) and I have fried literally tons of her self-replicating bunny robots with the stabby teeth with my mighty Tesla coil cannons! The countryside can not support such vicious and scientific warfare for too much longer, so Hermitage and I agreed to settle this dispute like proper scientists: a paper duel.

Because each of us is rather fond of all of you, we chose an open-source PLoS ONE paper upon which to wage war: Unscented Kalman Sensor for Brain-Machine Interfaces. This way each of you can see the original source.

The battle will not be over the paper itself, but rather for your hearts and minds. Hermitage and I are each going to blog about the paper cited above. Then you, our lovely readers, will each get 100 points to assign between us as you see fit. Whomever has more points after 72h for voting will be declared the winner.

I tap out this announcement in order to give you fair warning. Shore up the walls of your own individual Internet homesteads, put the fine china in the cellar, and get yourself a hammer to beat at us if we encroach too closely to your territory in the blushing heat of the battle.

Watch out, it's coming!

Also:
Dear Hermitage,

Sincerely,
Toaster

Book Meme

2009-07-20T23:23:00.000-04:00

DuWayne Brayton has tagged me with the book meme. I didn't follow the rules precisely. There are probably more than 15 books below, and I took something like 20odd minutes to write and hyperlink all this together. The books that follow are in no particular order of favor. I don't necessarily agree with the viewpoints espoused in all of these books, but they nonetheless seem to be persistent sticks in the mud of my mind.

In the Name of Science: A History of Secret Programs, Medical Research, and Human Experimentation , Andrew Goliszek
Mutants : On Genetic Variety and the Human Body, Armand Marie Leroi
The Language of Life: How Cells Communicate in Health and Disease, Debra Niehoff
Janeway's Immunobiology
Neuromancer, William Gibson
The Complete Essays of Mark Twain
Maus I + II, Art Spiegelman
Percy Gloom, Cathy Malkasian
The Brief and Wondrous Life of Oscar Wao, Junot Diaz
One Hundred Years of Solitude, Gabriel Marcia Marquez
American Psycho, Bret Easton Ellis
Ender's Game, Orson Scott Card
Green Eggs and Ham, Dr. Seuss
Stiff: The Curious Lives of Human Cadavers, Mary Roach
Sex, Time and Power: How Women's Sexuality Shaped Human Evolution, Leonhard Shlain
Grimm's Fairy Tales
A Scanner Darkly, Phillip K. Dick
American Pastoral, Philip Roth
Catharsis, Andrzej Szczeklik
Lord of the Rings trilogy, J.R.R. Tolkien
Amor y Cohetes (Love and Rockets), the Hernandez Bros.
The Jungle, Upton Sinclair
1984, George Orwell
The Grapes of Wrath, John Steinbeck
Alice in Wonderland, Lewis Carroll
The Futurological Congress: From the Memoirs of Ijon Tichy, Stanislaw Lem
Frankenstein, Mary Shelley
Watchmen, Alan Moore and Dave Gibbons
The Portrait of Dorian Gray, Oscar Wilde
James and the Giant Peach, Roald Dahl

Now then, I tag Arikia Millikan, Hermitage, Science Bear, Hexadecimal, Tig, Stephanie Zvan, Ktbug Ladydid, Lost Marbles, and Quietandsmall. Let's see what all of you have!

AHAA Addiction

2009-07-20T22:36:00.006-04:00

Every day we labor in the lab, hoping to build knowledge into a coherent and publishable narrative, pursuing understanding. Often I have heard scientists speak of the "A-HAAAA!!!!!" moment where months' worth of laborious experiments snap into place and reveal a new bit of truth, and how addicting that moment is, how it is akin to pure joy or The Perfect Cookie. This is a wonderful goal, and somehow it keeps us working long hours for little pay and even less respect. But, admittedly, it's hard work.

I have found that every once in a while, as I'm reading along through some papers, I come across a well-supported point or elegant experiment that is just SO DAMN AWESOME that my mind has to stretch a little farther to accommodate the new view of the Entire Frickin' Universe that that paper has just jammed into my eye sockets. It's like licking lightning*, but less painful. And these papers don't have to be recognized across the scientific sea as revolutionary to make that difference. I still know approximately nothing, inasmuch as my scientific knowledge is but a 5uL drop in a 3L pond of ignorance. And as such, papers that fasten together what were previously disparate informations (for me, although that may have already been old hat to the greybeards) can be just as mind-boggling.

Apparently I have a knack for finding these papers. The other day in the lab after his committee meeting, the grad student turns to me and sez, "You failed me there! You're my Master Downloader, and you didn't catch the paper that completely changes 1/5th of my thesis!". He was kidding, I think. I have yet to read the paper in question. From the abstract, it's been recently found that IL-12Rp35 doesn't just participate in IL-12 signaling, but also in IL-35 signaling, which has an antagonistic effector function against IL-12 (IL-12 is pro-T_H1 T-cell response, IL-35 is pro-Treg T-cell response). This is on top of previous knowledge that the IL-12Rp40 subunit is also part of the IL-23R complex (IL-23 is involved in T_H17 T-cell differentiation and function).

These frequent revolutions of our understanding are unequivocally Good Things. Sure, it makes our lives difficult and increases the range of possibilities in which we make asses of ourselves in front of our colleagues, but at the same time it's the very stuff Science is made of. If we cling to out-dated theories and disproven information, we will not produce accurate new information and we will fail as scientists. This necessary nimblemindedness is sometimes frustrating, but at the same time it allows us to have those A-HAAA!!!!! moments all the more often without doing all the benchwork ourselves.

To date, there are 3 papers that stick out in my mind as having been particularly eye opening:

1) Käfer J, Hogeweg P, Marée AFM (2006) Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences. PLoS Comput Biol 2(6): e56. doi:10.1371/journal.pcbi.0020056

I didn't see this when it first came out, but when I finally read it and worked through the differential equations it really made a huge difference in how I view organogenesis. I wasn't much interested in the functional dynamics of Dictyostellium morphology, but the work on cell sorting and migration based entirely on size and net kinetic energy was really really really cool. Blogged here.

2) Venegas J, Winkler T, Musch G, Vidal Melo M, Layfield D, Tgavalekos N, Fischman A, Callahan R, Bellani G, Harris R (2005) Self-organized patchiness in asthma as a prelude to catastrophic shifts. Letters to Nature. doi: 10.1038/nature03490

This was some major computational sweetness wrapped up in massive physiological awesomeness. It integrated all the separate physical forces at work on individual alveoli to integrate them into a model of whole-lung pathology. This was tight work, very well-done, and immediately relevant to clinical practice as their model revealed that inhaled anti-asthma drugs would likely affect only the non-spasming portions of the lung airways, although it also didn't exactly make an alternative recommendation. Anyway, still relevant. Blogged here.

3) Artis D. Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat Rev Immunol. 2008 Jun;8(6):411-20. doi: 10.1038/nri2316

This paper assembled a major heap of evidence and thoroughly blasted the simple view of intestinal epithelial cells as humble nutrient transporters that I had been taught to ragged shreds. Intestinal epithelial cells aren't just lining for the gut, they actively interact with the massive volume of microorganisms inhabiting our guts and modulate both the ecology thereof as well as the responsiveness of the innate and adaptive immune systems. Intestinal epithelial cells even express MHCII! As far as I can discern, this paper has helped to provoke a flurry of gastroenterology papers that discuss the rapidly evolving view of the microbiome, even going so far as to label our intestinal microbiome another metabolic organ**. Blogged here.

So, dear reader, what papers have changed your world-view and why?

*Don't try that at home. It tastes terrible.
**If you want to look smart to a gastroenterologist, drop "TSLP" casually into conversation. TLSP = thymic stromal lymphopoeitin, it's secreted by intestinal epithelial cells to attenuate inflammatory T_H1-type immune responses to the bacterial antigenic signal from the gut microbiota. It kinda skews the response towards T_H2 effectors instead.

Of Superheroes and Pirates

2009-07-19T04:44:00.010-04:00

Each summer, Ann Arbor, Michigan subjects itself to a massive art fair that usually draws 350-500,000 people into town to view and buy stuff. Naturally, since it was a crowded environment with delicate and expensive stuff crammed tightly together, Toaster thought it'd be an excellent idea to get a large-ish group together to dress up as charmingly pathetic superheroes and play Tag. So we did.

Toaster, The Superhero, having a blissfully unaware Spiderman 3 moment.

Left to right: P-par, Tie Fighter, The Cloaked Librarian, Punkupine, Zebragirl, Toaster, Hufu Transformer, and Skrull. It may dismay (or delight) you to know that 5 of the people present here are actually scientists by day. If it dismays you, dismiss us as Mad Scientists.

Left to right: The Cloaked Librarian, Toaster, and Hufu Transformer. We know we're badass.

Childrens' reactions to seeing us (excitedly jumping up and down, staring and grinning, asking their parents whether we could really fly) just reaffirmed my empirical knowledge that too many adults are stuffy dunderheads. Sure, be responsible and stuff, but it's silly--very silly--to be so full of yourself, and so vain, that you deny yourself fun for fear of looking like an ass. Or maybe we're just weird.

And then tonight there was a concert with a pirate song band followed by a burlesque show, which had a Star Trek-in-the-ocean theme. I watched Dr. Spock get mobbed by stingrays in pasties, and the ribbon encircling my hat (because, of course, I was also dressed as a pirate*) was part of the North Pacific Trash Gyre's costume that she abandoned throughout the course of her routine. This was all followed by a massive dance party that had us dodging glitterbombs and slipping on bubbles.

*You may wonder what kind of pirate wears a top hat. Well, to put it simply, fancy motherfucking pirates wear fancy motherfucking hats.

In Defense of Cliches

2009-07-18T17:14:00.007-04:00

Bora Zivkovic of A Blog Around the Clock and Ed Yong of Not Exactly Rocket Science alerted me via Twitter to an article in Wired Science by Betsy Mason entitled "5 Atrocious Science Cliches to Throw Down a Black Hole". In short, the article claims that "Holy Grail", "Silver Bullet", "Shedding Light", "Missing Link", and "Paradigm Shift" are overplayed, tired terms that should be banned from scientific reportage.

Betsy Mason is wrong.

We need cliches. We depend upon cliches, and cliches are quite useful in the proper context. While it may be true that the above terms do get thrown about quite a bit, they're still quite useful. Science journalism is already a convoluted field that must continually walk the line between being too esoteric for its mainstream, non-scientist audience and maintaining proper accuracy to satisfy its scientific constituents, which keeps information flowing. Banning the use of any widely understood vehicles for explanation just raises the barrier to effective communication between science and the public. And when we, as a scientific community, have already made it clear that we're not usually pleased by the transmission of our findings to the public through the prism of science journalism, do we really need to throw in even more barriers?

This article indulges in a great deal of unfortunate professional myopia. From the perspective of a scientist, calling research, such as active in vivo RNAi therapy, the Holy Grail of cancer research will seem inaccurate given the breadth of other therapies being developed to combat cancer. It may be more accurate to place RNAi therapy in the context of all the other therapies, from advanced laser ablation at the level of individual cells to cytolethal fusion proteins, but with this accuracy comes a great sacrifice in public comprehensibility. Science is detailed, science is convoluted, and science is very nuanced. But unless we're willing to write and peer-review multi-chapter articles for the popular press, if those outlets would even carry the required tomes, we must tell a complex story simply and linearly in order for anyone but the most educated and avidly interested members of the public to understand it. Using widely understood cliches as vehicles to convey that comprehension is not just necessary, it's laudable.

I do not mean to impugn the intelligence of the general population. Perhaps naively, I still believe that the public is usually smarter than we give them credit for. But at the same time, scientific communication is a form of technical communication with clearly defined words and standards. We use "attenuated", "potentiated", "significantly", "stochastically", "sufficient", and "necessary" in very specific ways that don't necessarily* translate into normal, everyday public usage. We can't well use these standards to communicate effectively to the public, instead we must speak to the public on the public's terms, which by and large will involve either sports analogies or cliches. The above maligned cliches are here to stay, and they remain quite useful. If they continue to help convey broad understanding of scientific concepts, then I will continue to welcome them and their use.

*Like that.

UPDATE (tweets):
[@ToasterSunshine] @BoraZ @edyong209 | In defense of the "5 atrocious science cliches": http://bit.ly/15vgZL | Must speak to the public on the public's terms.

edyong209@ToasterSunshine You present false choice between cliches and jargon. Entirely possible to write lay-friendly copy w/o cliches.
edyong209@ToasterSunshine Or at the very least, without seriously misleading cliches.

ToasterSunshine@edyong209 Yes, sometimes cliches may be overused/misleading. But to call for a ban takes tools away from communicating scientists.
ToasterSunshine@edyong209 Scientists get jargon + don't need cliches or analogous metaphors as vehicles for understanding research. Public probably does.

edyong209@ToasterSunshine If tools are crap, they won't be missed. Good writers/communicators ought not to rely on cliches *anyway*.
edyong209@ToasterSunshine Neither article nor I calling for end to analogy/metaphor but end to MISLEADING ones.
edyong209@ToasterSunshine Again, I think you're presenting false choice between jargon and cliches. Metaphors are good but we can do better.

betsymason@toastersunshine I don't advocate a ban on metaphors for science, just the most overused, hyperbolic & annoying cliches. We can do better.

ToasterSunshine@edyong209 @betsymason I don't dispute that "paradigm shift" is overplayed. I do stand firmly against anything that attenuates science comm.

edyong209@ToasterSunshine Not attenuation. Sci-com benefits if misleading terms are lost, writers forced to think creatively. Atten'g BAD comm= good.

ToasterSunshine@edyong209 Agreed less bad comm good, but cliches not always misleading/bad. Cliches often help capture interest and sustain story reading.
ToasterSunshine@edyong209 See rec Herceptin research: "Herceptin magic bullet against breast cancer stem cells" vs. "Herceptin inhibits even HER2- tumors".
ToasterSunshine@edyong209 HER2 = jargon, but HER2 also absolute key to story. Accurate inclusion in headline turns general audience away. Need interest.

Reading

2009-07-17T15:38:00.002-04:00

Aside from scientific papers and comic books*, I don't do much reading any more. I can't remember the last new thing I read for fun. Maybe it was World War Z by Max Brooks, and that was well over a year ago. I mean, I have read Neuromancer by William Gibson since then, but I tend to do that annually, so it doesn't really count.

The problem is that whenever I sit down to read anything, even a comic book, which is quick and awesome, I feel guilty that I'm not off reading scientific literature instead. I've got a stack of unread papers rapidly approaching the thickness of my head, and I have a large noggin. I see something that looks really interesting, read the abstract, and print it off to read later. Problem is that all too often it doesn't actually get read later, it just gets buried under everything else I've been meaning to analyze and forgotten.

But at the same time I really miss curling up with a good book and reading away.

So, dear reader, what do you recommend? Any great books you've recently parsed?

*Although I am also reading "Makers" by Cory Doctorow as it comes out, serializedy, on Tor's website. It's what made me realize I miss reading stories.

The Invisible Hand

2009-07-16T10:39:00.003-04:00

The current global recession notwithstanding*, I have some major beef with economics in general. Economics exists to describe, regulate, and predict the markets, yet it inevitably fails to recognize reality and only perpetuates an unfortunately narrow self-interest in the majority of its participants. I posit:

1) The self-regulating "invisible hand" of the markets that supposedly guides consumers en masse to the best possible outcomes is nothing more than a foolish myth.

2) Economics pretends that it is uniquely exempt** from basic thermodynamic principles.

The invisible guiding hand is a convenient white lie that humanizes the volatility of markets, which amplify human indecisiveness and greed, and makes them seem comprehensible. This is pure fluffery at its least ingenious. The invisible hand's actions throughout history have, by and large, only served to increase the wealth of those who could afford to speculate within the markets, those who had money to risk and milk. It is entirely true that the invisible hand will guide consumers to purchase equivalent goods at lower costs and thereby benefit the producer who is able to manufacture those goods at the lowest marginal cost. But the same time this effect will not increase the purchasing parity or real wealth of the consumers themselves unless we insist on qualifying wealth by measurement of cheap plastic tchotkes. The invisible hand excludes benefit to the poor by marginalizing their purchasing to the necessities and using them as labor. The latter effect is especially apparent in third-world sweat shops churning out luxury items for industrialized nations' consumption. This disparity between benefit to the rich and cost to the poor is starkly visible in material trade and manufacturing between wealthy consumer nations and poor producer nations.

The North American Free Trade Agreement (NAFTA) effectively removed all barriers to trade between the United States of America, Canada, and Mexico. Large businesses in the USA and Canada have benefited from the cheaper labor available from Mexico even as their own working classes have suffered. Consumption intensive (defined as consumption relative to income) middle class families have certainly benefited from this with the rise of Walmart-type stores. But at the same time, large agricultural businesses, through chemical-heavy agricultural practices, can produce more corn per acre and do so more cheaply than Mexican farmers, and as such cheap USA grain flooded the North American market and dropped the bottom out of the smaller local markets that Mexican farmers depended upon. This bankrupted Mexican farmers, which in turn benefited large USA and Canadian businesses by providing hungry labor and mass immigration to urban centers (e.g., maquiladoras). Ironically enough, this has greatly increased the benefit to risk ratio of illegal immigration into the USA or Canada, something that the very politicians who championed NAFTA are now bemoaning and demonizing.

The invisible hand also fails to take into account individual greed. For the most part, most people will always hew true to one law and one law only: serve thy immediate needs! It is very difficult, sometimes even nigh impossible, to convince people to care about anything beyond their own immediate surroundings and even then it has to have a benefit to them. This is especially true in the relationship of the economy to the environment, and by proxy, peoples' apathy to caring about anything to do with the environment (or people far away, for that matter).

This brings me to my second point: economics acts as though it is independent of the physical laws that govern all things and organizations. The economy treats the environment, and the mineral, biological, and human resources contained therein, as infinite. Our entire global economic system is predicated on the assumption that infinite growth is posssible, practical, and inevitable. Barring the development of cost-effective space colonization and mineral extraction, this is only absolute madness! The Earth has a finite mass and a finite chemical composition and as such there is an absolute limit to the volume of materials we can extract and use. We can only move so much, and at that relatively little, amounts of stuff around before we start to poision our own garden. We've been quite tidily moving the carbon in fossil fuels to carbon dioxide in the atmosphere for the past 2 centuries, which is now incontrovertibly linked to global warming and ocean acidification.

Economics also ignores the very real and deadly costs of waste products. Manufacturing waste, whether steel slag, arsenic extractant for gold, or simple office paper trash, take up space and, because its toxic more often than not, poisons its immediate environment. Waste represents an energy sink, a huge cost that is magicked away from the accounting sheets because it is long-term and distant and will be someone else's problem before we are willing to take responsibility for it. Economics treats waste as just another commodity, pretending that the Earth contains infinite space for landfills, infinite fresh water to pollute, and infinite poor nations to dump toxic waste upon. While this does indeed maximize profits for the already-affluent shareholders, it does nothing to increase the average standard of living for the human race. If anything, it just makes it worse.

If nothing else, we can at least conclude that the invisible hand is not only invisible, but also blind, venal, and utterly unwilling to acknowledge its limitations. Funny how an invisible hand can look so hard at itself preening in the mirror.

*Seriously, who thought it'd be a good idea to sell debt around? That's like selling someone a cookie before the flour has even been ground, and if you sold me a cookie before you so much as even had the ingredients you'd have a very unhappy and possibly angry Toaster on your hands.
**Politics, however, does operate independently of thermodynamic principles.

On Apoptosis in Development

2009-07-13T22:46:00.001-04:00

Apoptosis means doom for an individual cell. As such we tend to automatically assume that apoptosis is a Bad Thing, but in reality apoptosis often is quite necessary for normal physiological function at the organism level. In order for our bodies to maintain the homeostasis that defines so many of our cellular processes, we have to sacrifice some cells. As it turns out, we actually wind up sacrificing enormous numbers of cells every day. Worn out red blood cells, dangerously self-reactive lymphocytes, individual columnar epithelial cells and others. These processes are tightly regulated, so much so that most cell types actually require biochemical signals from neighboring cells, tissues, or even distant organs just to tell them to keep living. The anti-apoptotic survival signals can fall below a threshhold value and/or be overridden by pro-apoptotic stimuli, which normally results in swift induction of the apoptotic program. When individual cells develop mutations that deafen them to these signals, they become dangerous proliferation-happy pre-cancerous cells more interested in their own survival than that of their constituent organism.

Figure A: TUNEL histochemical staining in murine liver, brown cell is apoptotic.

The apoptotic program ultimately results in highly oxidative and degradative enzymes (such as proteases) hidden away in the mitochondria being released into the cytoplasm to wreak havoc. Usually the raw material of a dying cell is tidily absorbed by its neighbors to be recycled. I've always imagined mitochondria as pulsing with a low, gentle buzz in normal cellular physiology with occassional metallic pings as statistical flucuations in the net free energy of electrons falling down the electron transport chain is captured in ATP. Following this, I think the sound of caspase-8 et al slicing open the mitochondria would be like the initial panicked braking shriek of a train loaded with Furbies who are quickly drowned out in the self-amplifying roar like a tornado grinding through a gravel pit as the apoptotic effector enzymes set to work dissolving the cell from within.

Apoptosis is absolutely essential not just to adult homeostasis, but also to normal ontogeny. Without apoptosis organs would fail to separate, fingers would remain stuck together, and many other things would go very, very wrong. There are 2 families of intracellular proteins that battle to determine whether or not a cell will become apoptotic: the (generally) pro-apoptotic Bcl-2 family and the (generally) anti-apoptotic IAP family. Conveniently, IAP stands for Inhibitor of Apoptosis Protein. A recent review by Dr. O'Riordan et al discussed the diverse and essential roles for IAP proteins in normal tissue development across a wide range of model organisms. From ablated organ development in the absence of Diap1 in Drosophila larvae to stunted hematopoeitic developmental repertoire in the abscence of Survivin in mice, IAPs seem to be evolutionarily conserved signal transducers that integrate diverse extracellular signals into a coherent cellular action. Developmentally, the IAP proteins seem to be involved in everything from proper vascularization to chromosome stability, although it is important to note that direct modulation of apoptosis in developmental processes has only been established in invertebrates. Lack of any one of several IAPs in higher chordates has not been directly linked to developmental apoptosis, but several abnormal embryonic phenotypes and attenuated adult functional capacities have been demonstrated.

IAPs are grouped by the prescence of BIRs (baculovirus IAP repeats) and many also have RING domains. Both motifs have been found to have zinc-finger conformations and the interaction of different sections of adjacent BIR motifs in some proteins, such as direct inhibition of pro-apoptotic caspases-3 and -7 by BIR2 of XIAP (X-linked inhibitor of apoptosis protein), has been found to modulate a number of diverse effects. These diverse effects are potentiated by the ubiquitin ligase activity that some RING domains have demonstrated. IAPs help the organism balance necessary apoptosis and unnecessary apoptosis, and because apoptosis is required for the homeostasis of most tissues the IAP family has been evolutionarily conserved and biochemically diversified. IAPs remain an active and engaging area of research that holds great promise in the treatment of pathologies from cancer to intracellular bacterial infections and underscore how a little sacrifice for the team by one cell can make a massive impact on the constituent organism's overall fitness.

IAPs have also been found to modulate innate immunity, which will be discussed in another post.

ORIORDAN, M., BAULER, L., SCOTT, F., & DUCKETT, C. (2008). Inhibitor of Apoptosis Proteins in Eukaryotic Evolution and Development: A Model of Thematic Conservation Developmental Cell, 15 (4), 497-508 DOI: 10.1016/j.devcel.2008.09.012

Additional Source: Molecular Biology of the Cell; Alberts et al; 4th ed.; pages 1010-1014

Against Megalomania

2009-07-11T17:54:00.003-04:00

The public has an odd image of scientists are reclusive loners with deep eclectic streaks and megalomaniacal tendencies. Eclecticism aside, it should most vehemently noted that megalomaniacs are, by their very nature, doomed to failure, so as a scientist you shouldn't even try. Yes, it may be tempting to ponder as you blearily load Blue Juice into agarose wells and wonder why you bothered to crawl out of bed. And yes, you may know, in your data-ey heart of hearts that the world would be a better place if it was ruled by a rational scientist*, but the truth is that each and every megalomaniac aspirant begins their path to conquering the world with grand visions of uniting the world as one cohesive and peaceful society. Then they inevitably make 2 mistakes:

1) Try to invade Russia.
2) Fail to take into account that people actually live in the world.

First of all, it should be noted that unless you've found a way to animate snow men as soldiers, you will never successfully conquer a very cold, wintery Northern country (except maybe Canada). The people that live there are used to the staggeringly brutal winters and know how to use it as an advantage against you. To understand that this is true, you only have to look to the historical examples (of which there are relatively few) where one Northern country tried to whup another militarily instead of just economically. In the Winter War of 1942, Finland and Russia fought a nasty border war. The Russians attacked on snow mobiles, and the native Finns who knew the land ambushed them, guerilla-style, on skis. Russia tried to use tanks, but really should have known better: they got stuck in freezing mud. Moscow may be flat, but Karelia and Finland are full of lakes, and what looks like dry ground between lakes is usually actually a swamp. Finland eventually lost this battle because they didn't have the supplies to keep fighting, and they wound up losing a substantial amount of territory in Karelia and also lost the important industrial city of Viipuri (now Vyborg).

Secondly, in almost everywhere on the planet, in every little nook and cranny where you'd least expect to find them, are people. Living there. With histories, and traditions, and individual languages and land rights that make the task of being their benevolent ruler aggravatingly complex and bureaucratic. You're stuck with them. You have to deal with them, regardless of whether or not you want to because, if you're in charge and decide to ignore them and focus elsewhere, you'll have a steaming pile of rebellion dropped right into your fancy oatmeal. And let's face it: rebellions are an expensive pain in the ass. You've got to send soldiers to keep them from taking it out on any vulnerable scapegoats, you've got to rebuild whatever they manage to destroy (never underestimate the sheer raw power of 10,000 angry people with hammers), and then you've got to figure out whatever the hell it was they wanted in the first place. Pain. In. The. Ass. Instead of eating exquisite grapes off the juicy bodies of your servants and having your wine washed in fancy feet, you've got to rule the people.

Alternatively, you could conquer the world and set up a Parliament so that the people you now have to rule would feel like they had some say in things, but then you'd also have to deal with Parliament interfering in your wishes. And if you decide to go even further and let Parliament actually rule and be a figurehead emporer instead, well, let's just say you're setting yourself up for a coup d'etat, and once the whole world is pissed off at you there's no where for you to flee to.

Isn't this sounding like a massive bother? Wouldn't a nice cup of tea and a cookie be better instead? I mean, if you're going to rule something absolutely, start somewhere where you can decide who gets to live there. Like the Moon. If anyone tries to rebel you can politely tell them to go walk it off outside.

*Because if we let an engineer run the world everything would suddenly have 3X as many buttons, 1/2 as many useful functions, and nothing would be properly labeled.

Ready For Conference

2009-07-10T00:35:00.003-04:00

Disclosure:

Toaster is ready for the conference. Are you?

Notes From The Sprawl #5

2009-07-08T00:28:00.005-04:00

A song, entitled "Suburban Dirge 1", may be found here. Maybe not so much Notes From The Sprawl as Excoriation Thereof. This one is from my archives, and I think it illustrates the topic at hand quite well.

A Proposal

2009-07-06T23:19:00.005-04:00

PROBLEM: At conferences and meetings of scientists, it is difficult to differentiate the academic ranks of the various attendees. This greatly complicates politeness and increases the risk of disrespecting a big shot who will then sabotage the entire rest of your career for your unwitting slight.

SOLUTION: Conference attendees shall wear hats, with the fanciness of said hats increasing as their academic rank increases.

SCHEMATIC:

Undergrads = berets of various colors (by lab or school)
Grad students, pre quals = Fezs
Grad students, post quals = bowlers
Post-docs = tri-corner hats, add 1 feather to hat/successive post-doc
Profs w/out tenure = princess cone hats, add 1 sequin per publication
Profs w/ tenure = princess cone hats w/ gauze streamers, add 1 sequin/publication
Departmental chairs = fruit baskets with real fruit
Journal editors = appropriate hat + bling
Techs = top hats, fancier ribbons indicating greater experience
Lab managers = fedoras
Core facility staff = cowboy hats
Journalists = cat-earred head bands

And Now For Something Unrelated

2009-07-06T00:06:00.003-04:00

For anyone who believes classical music is outdated and boring, or that it's an antiquated and dead genre that is not relevant to modern times, I present this rebuttal:

Notes From The Sprawl #4

2009-07-04T17:18:00.000-04:00

The acrid stench of bleach kept the bristling green riot at bay behind the well-polished kitchen windows. She sniffed, momentarily satisfied, and rubbed blearily at the caffeinated caverns stretching beneath her itchy eyes. A sudden twitch brought her shoulders about her ears as a birdsong clarion echoed faintly through the vinyl siding. With a moist sigh, she turned to rummage through her obese bag for the earbuds that made her daily penance upon the treadmill more bearable and shuffled away on the fresh linoleum.

Later that day, after she’d bit her tongue while he complained about his boss—forgetting, as always, to remember to ask how her presentation that morning had gone—over a skillet-warmed stir fry with no monosodium glutamate, she curled into the squeaky couch and nursed a gingerly spiked cranberry juice as a dull parade of local news and commercials marched past her flickering thoughts. There was a knot somewhere, something not quite right, but she thumbed a pregnant sniffle away from her nose and lost the mustering concentration to put her finger on it.

The next morning, bleary from being woken at dawn by seven friendly sparrows and one erstwhile loon (which she thought was an owl), groping for her probiotic yogurt breakfast as she backed her sedan out of the oil-smelling garage, she suddenly stopped. Two of the dozen mole traps scattered about her patchy front yard had been sprung. Knowing that he would leave 5 minutes too late to bother noticing or doing anything about, she jammed the car into neutral and clattered out into the yard, cursing the tiny stones that persisted amid the rooting sod. With a fragrant mixture of revulsion and curiosity, she reached down to pull the first sprung trap out of the proud mole hill he’d punched it into.

It wouldn’t budge.

She pulled.

It resisted.

So she pulled harder, kneeling down in her favorite floating yoga position to grasp and tug with both hands. With an organic wet suck, the trap abruptly came free of the dew-drenched earth and she reeled backwards, crashing onto the thick sod with a disgruntled thud. The trap was empty. Snarling invectives against the undeveloped patch of forest that hemmed in her orderly cul-de-sac, she lunged forward and peered into the hole she’d just opened up, just in enough time to see the hairy, tapered rear end of something brown retreating down into the wormy murk. With a cavalcade of searing oaths, she stomped back into the gingerbread house to change her newly grass-stained blouse.

Now she was going to be late, and she was pissed.

Notes From The Sprawl #3

2009-07-03T23:27:00.007-04:00

I am back in Michigan. I have nothing particularly profound or insightful to say regarding my week-long trip back to my Ozarkian whelping grounds, except that it became painfully, perhaps even absurdly, obvious just how pale I have become since moving to Teh North. I am delighted to report that the cliffs of the Meramac River do indeed amplify one mightily, especially when one sneezes whilst floating below them in a kayak. I thought I was being shot at.

This little series, "Notes From The Sprawl", will continue a little while longer until it dries up. I go back to the place that I used to call home, that I fought so hard to get out of, and I see how much has changed. Not for the better, just more of the same. It seems like almost every single fucking one of the wild places I inhabited growing up has been plowed over for more bland tract homes or been walled away behind fanciful shrubbery. The fingers of wilderness that the developers couldn't profit from are being razed anyway, plowed under for more vacuous consumption as new construction techniques are magicked into thin air. I still think it's stupid to try to build houses in a swamp.

But it remains gut-wrenching to behold. The swampy forest with the deep ravines that I used to carry my bike across a fallen tree to get to, where I could ride wherever and however I wanted, every green tree blurring past my handlebars climbable, has been felled, filled in, and paved over. I wonder where the salamanders I used to chase down the streams have gone now that those same streams are heavy and swollen with the mud running off of the clear-cut land while small-minded box homes are put up in their place. The ponds I used to chase tadpoles in have been fenced off and labeled as dangerous. The hollers are being swept away underneath the bluffs being rudely shoved into them by bulldozer armies, replaced by pesticide lawns and asphalt parking lots that ooze malodorously in the summertime heat. Every piece of the wild, every part of the real, is being torn apart or boxed away. The proud old oaks with their gnarled roots hiding years' of birdsong are being pulled down to make way for plastic ficus trees and cheap lawn frappery. The birches, the elms, the hickorys, the careful slow dogwood and the stodgy firs: my friends, our family.

Sure, maybe it's the American Dream to own your own piece and house and fill it with whatever you like; but at the same time, we're doing so en masse and completely losing the authenticity of the red clay earth that holds that land up, losing reality when we truck in manufactured top soil and sod instead. I wonder, perhaps cynically, how many of the people who dwell in these cookie cutter houses have ever actually dug in the earth, gotten the lovely reek of it up to their elbows and ingrained its grit in every tiny whorl of their fingertips. I wonder who among them has ever tried to jump a creek and failed laughing among the startled turtles. I wonder whether any of them have ever looked down and seen the tiny, ancient shells that run through the area's red flint stones like fire through our veins and felt small and insignificant in the sheer scope of what the earth is and has been and will continue to be long after they've ceased to be, and just wondered at the sheer marvel of it all.

We're rushing to trade this*:
For this:

What are we losing?

Damn near everything that matters.

*Yeah, it's blurry. I apologize, but I was rolling backwards when I took it.

Notes From the Sprawl #2

2009-07-02T20:19:00.002-04:00

The Sprawl is the flabbiest of all civil structures. It represents the ultimate in chaotic decentralization driven entirely by the profit motive of land developers who raze forest and farm alike to plane the earth and replace them with rows of standard plan houses and pear trees*. Cloned subdivisions with timber frames and false brick facades spring up from the Caterpillar wreckage of the land. Many have argued that decentralization increases resilience of almost any system, including the suburbs, but I strongly disagree with this. In order for decentralization to have a net positive effect upon the structure in question, adequate infrastructure must first be in place. Suburbs are spawned on old county roads that once only served farms and light traffic, suddenly jammed full of SUVs and minivans as people wend about on their daily multitudinous commutes. Developers benefit from this tangibly, consumers nominally, and society pays the remaining negative balance through the continual development of catch-up infrastructure: new roads and new schools, new strip malls and parks to accommodate the shifting needs of an ever-pancaking population. Fundamentally, barring the development and implementation of efficient and unlimited energy, The Sprawl is entirely unsustainable.

Living in The Sprawl, one must drive everywhere. There are no other options. Sidewalks and bike lanes are rare; the logistics and cost of trying to implement mass transit in the landscape of streets designed to maximize profit through over-indulgence in cul-de-sacs and curving lanes is an absolutely Sisyphean nightmare. The creation of this curiously inefficient arrangement of society has been enabled and perpetuated by the development of the personal automobile. Without dependable, affordable personal transportation, people would never have been able to sever their dependency upon centralized mass transit in the more densely populated cities and begin to commute. Without relatively cheap energy, the absolutely massive scale of material trafficking required to sustain suburban patterns of consumption would be untenable. Even with cheap energy from gasoline, the traffic of the wheat from field to factory to face is fragile and easily disrupted. This is not resilience, this is absurdity!

With a city, the population is concentrated, and so are the infrastructures that distribute solutions to their needs. The environmental footprint, as quantized in gross inputs and outputs, is easily measured and containable. Suburbia spreads out over the farmland that once fed the city it is creeping out of, over the forest that once purified that city’s waste. Suburbia replaces these with new needs, spread thinner and spread farther. And through it all, the personal automobile reigns supreme. We’ve come to view driving as a right, and not an economic privilege. The reality of it is that driving is massively subsidized by the public through the creation and maintenance of roads, and this is one of the truthisms that lies sharp behind the seductive veil of the American Dream. It ain’t nearly so cheap as we’d like to believe, not for our wallets our the surrounding environment.

*Pear trees seem to be a favorite in the Midwest because they grow quickly and make a nice, dense shape. However, the most popular variety planted doesn’t even bear fruit and has a common habit of falling apart in a strong storm. It also doesn’t even have the decency to smell nice.

How Not to Flirt #4

2009-07-02T10:00:00.000-04:00

If you are going to take the risk of consuming food in the presence of the object of your affection, it is recommended that you take care not to place a volume of food larger than that of your mouth into said mouth, regardless of whether or not you also try to continue speaking through it.

Llamas Against Breast Cancer

2009-07-01T16:00:00.001-04:00

We all knew llamas were kind of weird. They're fluffy. They're smelly. They spit. They're like Sanrio (the Hello Kitty company) tried to make over a camel. But that's not all. Llamas are also immunologically strange. Whereas most all other organisms with a humoral immune system produce large, multi-domain antibodies with several distinct genetic and structural motifs, llamas instead make nanobodies. Nanobodies are, basically, tiny little antibodies. Normal antibodies contain 2 heavy chains and 2 light chains, which each have V (variable, where the epitope binds) and J (joining) regions; and the heavy chains also have C (constant, these make up the Fc fragment) regions. All of those chains are bound together by disulfide bonds and the resulting antibody typically has 2 binding sites, each at the tip of the Y shape. Nanobodies dispense with all of that and only retain a functional binding site with a single variable light chain domain. As a result, nanobodies are much much smaller and can access and bind to sequestered epitopes or complex 3D epitopes that may otherwise be hidden inside a molecular cleft.

Figure A: Structual phylogenetic picture, much like a family picture. This is only an approximation as Good Images are copyrighted and Photoshopping ribbon-style molecules is difficult.

The point of this study is not that nanobodies are weird and cool. Instead, Alvarez-Rueda et al harnessed the complex 3D structural variability of nanobodies to mimic the immunogenic structure of HER2. HER2 is a surface protein normally only expressed in fetal development that is reexpressed in 20-40% of breast cancers and 30% of ovarian cancers. It is a member of the epidermal growth factor (EGF) family and is suspected to help cancerous cells proliferate more rapidly and aggressively. Tumor expression of HER2 correlates strongly with increased metastatisis and decreased survival. We've known about HER2 for a while now and it has been a target of intense research. There are now genetic tests available for HER2 alleles that correlate with increased morbidity from breast cancer. There was also a passive immunotherapeutic treatment against HER2 approved for use in combination with chemotherapy in 1998 called Trastuzumab (marketed as Herceptin(R) and manufactured by Roche). Trastumuzab is a humanized antibody therapy that targets HER2 directly; it is thought that it mimics the natural humoral immune response to HER2, which is observed to slow down tumor growth in early tumors but unfortunately sometimes fails to stop it. The primary problem with Trastuzumab is that it must be repeatedly administered over the course of cancer treatment to have any effect. While Trastumuzab is an invaluable tool in the fight against these cancers, it has long been recognized that inducing a robust host immune response would help to combat the tumor itself, and subsequent induction of a host immune memory against HER2 would help to prevent relapse of the cancer.

The best way to do this is with a vaccine.

Simply injecting HER2 with an adjuvant could produce a strong immune response, but the HER2 itself could make the cancer worse meanwhile. The ideal vaccine would be a molecule that mimics the structure of HER2 closely enough to induce cross-reactive immunity but that doesn't have the biological activity of HER2.

Enter the llama and its nanobodies.

Alvarez-Rueda et al injected Trastuzumab into a llama and the llama kindly produced nanobodies. Because Trastuzumab is an antibody against HER2, the llama's immune system produced a molecule against it that is somewhat structurally similar to HER2. When this nanobody molecule was isolated and expressed via transgenic clone library, it was found to strongly bind both Trastuzumab as well as isolated human anti-HER2 antibodies. So they then took the nanobody (called 1HE) and injected it into mice (along with Freund's adjuvant). As expected, the mice produced antibodies against the nanobody. These antibodies then, in turn, bound strongly to both 1HE and the HER2 protein. This strongly implies that immunization of a human with the 1HE nanobody and adjuvant would induce a strong anti-HER2 antibody response, effectively immunizing them against HER2-expressing breast or ovarian cancers or arresting the growth of existing tumors as part of chemotherapy*. Additionally, the polyclonal antibodies produced by the mice in response to the nanobody were found to inhibit growth of HER2-expressing carcinoma cell lines. The data have not yet been validated in vivo.

Either way, this is a cool advance in the fight against breast cancer, and I sincerely hope that something therapeutically useful in humans will soon come out of this. Thank you, llamas.

*This is technically known as an anti-idiopathic vaccine.

Alvarez-Rueda, N., Ladjemi, M., Béhar, G., Corgnac, S., Pugnière, M., Roquet, F., Bascoul-Mollevi, C., Baty, D., Pèlegrin, A., & Navarro-Teulon, I. (2009). A llama single domain anti-idiotypic antibody mimicking HER2 as a vaccine: Immunogenicity and efficacy Vaccine DOI: 10.1016/j.vaccine.2009.05.067

Notes From the Sprawl #1

2009-06-29T21:59:00.001-04:00

I’m sitting in the Sprawl. Endless tract homes outside, old forests fell to birth new frame-house clones. Green lawns sprinkled with new trees, small trickles of Ozarkian forest running through the places where developers can’t profitably reshape the land. The deep ravines, heavy bluffs, and holler creeks preserve what this land used to hold. This Sprawl is not unique. There are many thousands of other subdivisions just like it scattered in traffic jammed rings growing out from wheezing city cores. The houses, the cars, the flabby pink people, these same exact forms have become ubiquitous elements of the American landscape. I posit that this landscape fosters, exacerbates, and breeds ignorance. Like the soft and flabby bodies that automobile dependency and the “American diet” create, so too does the mind wither away in the suburbs. The American Dream may have directly led to the genesis of this massive Sprawl, this gross misallocation of resources, but it is here, in the Sprawl, that individuals’ dreams come to die.

We’re told that we should aspire to a tract home with a 2-car garage and enough bedrooms to raise our own brood. We’re sold the idea that we need to fill these thin-walled homes, new and insecure in the earth, with the latest LCD TVs, computers, fancy textiles and leather couches. We’re instructed to raise children like we maintain our houses: superficially beautiful and nice, but without depth or lasting permanence. These homes are not built to last. They are cheap opportunism, dry-walled profiteering. Just like the media we consume, the entertainment we float in.

Once we have achieved the perfect suburban house, what’s left? To climb the corporate ladder? To acquire a pool? A perfect vacation? These are small goals, individually oriented. These small goals constrain the empathetic powers of the mind, reduce it to baby steps and the politics of the immediate cul-de-sac. Housing associations enforcing false aesthetics, prime-time TV, faraway libraries; all combine to stifle the intrinsic human urges to curiosity and adventure. What more is there to know when all your immediate needs are immediately met?

This environment implicitly allows the ignorance that politicians and demagogues can prey upon. This is the danger of the uninformed, where grown adults cannot help their children with their homework because they have never, nor have ever even tried, to learn more than was simply required of them. This is most relevant to us, as scientists trying to improve science’s relationship with the public, because we fundamentally cannot convince adults deadened to novelty, wonder, or curiosity, to suddenly wake up and engage us. We can push the spark, but we cannot create it.

This is also entirely relevant to our discussions of gender roles, politics, religion, etc. We rant and rail against how society currently operates, we question how it can even be this way when it is so clearly repressive or illogical, we even offer solutions; yet the truth of the matter is that these discussions take place in a rarified atmosphere. We live in intellectual townships, on or near university campuses, and these places just aren’t like the rest of the country. Our discussions still are useful, they still have meaning, but the simple fact of the matter is that most people will not and cannot care until they perceive a direct benefit to them in the form of an infotainmented soundbyte. It ain’t necessarily the best or right, but it is how things currently work.

Silky Muscles

2009-06-27T06:00:00.001-04:00

You're running through the cool woods on a hot day, barefoot as dead leaves rustle underfoot and the cold flint tickles beneath. The green leaves and kudzu blur past as you dodge beaming shafts of sunlight and the hot ground they illuminate. You scan the earth ahead for sinkholes and patches of poison ivy, but still, the chilled, humid air coiled around the trees flowing in your ears feels joyous in comparison to the sauna of the open field. You dart between two trees, then suddenly stop and gyrate wildly, windmilling arms about your face as you splutter and ick; swiping instinctually at your face to pull away the clinging threads of a spider web.

To many of us, spiders are mostly nuisances, either by dangling from a single invisible thread in the most inconvenient places or by stumbling into webs and getting their sticky strands stuck in our eyebrows such that we look like a surprised Gandalf. However, a recent publication suggests that spider silk, the material they spin webs and drag lines out of, may turn out to be much more useful that we previously thought.

Compared to contractile biological muscles, mechanical rotary motors are rather inefficient. Getting a micro-servo to function correctly in a robot arm is a difficult art of soldering and fine-tuning. In prosthetic limbs, robots, and industrial applications, there is a current need for a small, reliable, lightweight, and dependable actuator. It turns out that when spider silk is exposed to alternating extremes of ambient humidity*, it contracts much like a biological muscle and does so repeatedly. Many biological fibers (cotton, wool, etc.) can also contract in high humidity, but they can only do so once before becoming inert. This occurs because different fibers are composed of repetitive hydrophilic materials that suck up water and collapse into lower net energetic states when the water is available, as it is during humid conditions.

The really cool part of this research was the force generated by the spider silk. On a basis of equivalent mass, spider silk was found to be capable of doing 500X the work of a human biological muscle. Agnarsson et al calculated that, based on their scaling experiments with combining individual silk fibers, a 2cm diameter strand of spider silk would be capable of lifting 2tons of mass! Similar, though weaker, effects were observed in silkworm silk (which is already commercially availble).

The caveat to this, because there's always a caveat, is the degree to which the spider silk contracts. Human muscle is capable of elastic modulus (how much it can bunch up without breaking) of 30-40%, while spider sillk was found to be capable of a modulus of only ~2%. This is considerably less useful, but still cool. The researchers noted that this was all done in one particular species of spider, Nephila clavipes, and that the silk of other spider species may turn out to have more useful modulus while preserving greater scaling strength and simple humidity switch.

Let's hope that these tests are done and something found, because robots everywhere are itching for a change.

*Steps of 10% differences. Contraction was found to be irreversible after exposure to <70%>

Agnarsson, I., Dhinojwala, A., Sahni, V., & Blackledge, T. (2009). Spider silk as a novel high performance biomimetic muscle driven by humidity Journal of Experimental Biology, 212 (13), 1990-1994 DOI: 10.1242/jeb.028282

How Not to Flirt #3

2009-06-25T23:28:00.006-04:00

Leave the calipers at home. Although it may seem that measuring the ratio of her shoulders to her brain pan volume is an easier and more direct way of assessing her intelligence, it actually turns out that most women prefer you speak with them and use conversation as a gauge. Needless to say, this is messy, but it is not only expected, it's required. It should also be noted that normalizing the least squares average of you and hers' combined brain pan volumes to the width of her hips as an approximate function of successful procreation is a very large and inexcusable mistake.

______________________________________________________________

Cheese Poll.

No doubt you've noticed it's done and the poll is now closed. I have to say that I'm somewhat intrigued by the results. I had not anticipated that Stilton would be so popular; it almost beat Gouda. Honestly, I expected Gouda to win, and it did, because everyone seems to think it's a fancy, lovely cheese.

Now, perhaps you're wondering: what cheese would Toaster be? Well, I think I would be one of the least popular cheeses in the poll, the Double Gloucester.

Also, I had thought that the possible list of cheeses was rather comprehensive, so for those of you who marked others: what did you have in mind?

______________________________________________________________

Toaster is going on vacation in a place that does not guarantee Internet access, and as such does not guarantee your regularly scheduled blogging. I will, however, still be active on Twitter (@ToasterSunshine). Nonetheless, I have prepared a couple of posts that are scheduled to publish while I am away to tide you over.

Take care of the Internet in my absence. I'm going to be mightily pissed if I come back and find it overrun by LOLcats.

Cultural Possession Post Script

2009-06-25T15:53:00.007-04:00

The Western male presumption of ownership over women is particularly evident in the social treatment of women who dare to deviate from prescribed gender roles and expectations.

As a society, we castigate ambitious women as being cold harpies and equate them managing men in a brusque manner with castration (whereas the same managerial style from a male leader is expected; it's as if subordinate men expect a compassionate mother figure instead of a boss). We traditionally celebrate homemakers as the epitome of woman-hood, and this is wrong. Although I am not suggesting that all homemakers are unhappy, it does seem that it would present a life of social isolation, financial dependence, menial tedium, and absolute boredom. However, with recent modern revolutions, homemaker women have, to a degree, come to be both looked down upon and become a source of envy (because they don't really work, but if it's a stay-at-home father, he's a martyred hero).

But the most glaringly obvious cases arise when men interact with out lesbians. If the man* interacting with them finds them attractive, there are culturally approved denigrating tropes to fall back upon that always involve him getting involved in her sexual life or at least watching. And if that same man finds the lesbian with whom he is interacting unattractive, he will commonly write her off as a misguided woman who just hasn't had the "right man" yet (to put it politely). Both cases invoke explicit assumption of ownership by the man over that woman's sexuality.

Here there is a substantial level of cognitive dissonance. On the individual level, women completely own their sexuality and control when, how, and with whom they choose to have sex. Often, men inappropriately perceive this as women "holding out" or having an undue control over them when in reality it has absolutely nothing to do with them. But on the societal level, men implicitly control women's sexuality. Through cultural invocations of idealized beauty, through cosmetics, through lingerie, clothing, make-up, hair styles, shoes, and pornography. Although cultural conditioning allows individual women to find empowerment in their femininity, the social machine sets and enforces the standards of "beautiful" femininity and is driven entirely by men's desire and lust. Through dissemination of culture in pictoral advertising, men express their idealized desires and women strive to meet what they are told is beautiful. This leads to insecure, depressed women and demanding men in a self-amplifying feedback loop, which furthers neithers' cause nor equity.

To move forward, we need to dissociate our individual images of ourselves from those idealized images we see in the media-driven world around us. It is far more constructive to look to a loved one for a compliment on one's appearance than to try to use a fashion magazine as a mirror. In effect, if we continue to do the latter, unwittingly or not, we are allowing cultural standards to own all of us. Men become owned by the standardized ideal femininity and pursue it to the exclusion of everything else, and this reinforces the male privilege of owning females' sexuality. Women become owned by the same standards and torture themselves trying to meet them because the advertised message that beauty = happiness has been so deeply ingrained by Western media that it is now unavoidable and pervasively subconscious.

Maybe it's time Western ideals were broadened, both to increase the happiness of women as well as to dilute the male sense of cultural ownership over women.

*Singular term used generally, not specifically.

How Not to Flirt #2

2009-06-23T16:00:00.001-04:00

Good Hygiene is important. Failure to bathe will result in rejection, although it is important to note that the object of your affection being kind enough to Febreeze you does not count as reciprocation of that affection. They're merely quarantining your stench.

Muscle Hypertrophy (Dynamics Addendum)

2009-06-22T21:48:00.004-04:00

A while back I wrote a post about the interactions of IGF-1 and MGF on muscle hypertrophy following mechanical stress (exercise). From that post, it could be assumed that it's all about IGF-1 and MGF, but the reality is considerably more complex than that.

It's tempting, and easy, to think of our bodies as constant and that growth is only occuring when we can see it. However, the body is continually tearing itself down and building itself back up. The entire intestinal epithelium regenerates completely, a couple cells at a time, over the course of 4 days to 1 week. Our skin is continually growing outwards and being worn away. Some organ systems, such as skeletal bone, rebuild themselves at a much slower rate while others, such as the central nervous system, are essentially immutable over the entire course of our lives. Most of the molecules that make up the body are in a continual state of flux as metabolism breaks down cellular products in adipocytes and delivers free fatty acids to the liver for oxidation into pyruvate, phosphocreatinine, or glycogen for use by skeletal muscle to do work, although this is not the only direction or only pathway in which such conversions constantly take place.

Colonic smooth muscle actin (red). The bright red strand is the smooth muscle lining the columnar epithelium of the colon (fainter chambered red). The really bright red strand is the musclaris mucosa that helps to drive peristalsis, or the sequential movement of intestinal smooth muscles to drive lumenal contents (food being digested) along the length of the gastrointestinal tract. 40X magnification, bar is 200um.

Muscles are made up of highly-organized fibers, such as the actin in the picture above. These fibers are organized into bundles that are studded with molecular motors known as kinesins that effectively run along parallel fibers. When you contract a muscle and tense it up, the fibers are dragged past each other by the kinesins to make the effective length of the muscle shorter and producing work in the form of moving whatever the muscle is attached to. In the process of this, the molecular motors burn cellular energy in the form of adenosine triphosphate (ATP) that the body makes from pyruvate molecules.

Over time as the muscle fibers get used they start to breakdown due to mechanical wear and tear (the initial burn from a workout is due to accumulation of calcium from anaerobic respiration; the soreness the next day is due to injured muscle fibers). The order of the molecules in the fibers starts to break down, and it's much cheaper in terms of energy used for the body to break down the worn-out muscle fibers and replace them with new fibers than it is to just repair them. As such, skeletal muscles are in a continual flux of breakdown and new fiber synthesis. This dynamic process that continually renews our muscles is not only completely normal, it's advantageous. Genetic experiments with mice have shown that deleting the gene that encodes myostatin, a protein strongly implicated in muscle breakdown, results in massively muscled mice who aren't any stronger than their scrawny companions that still have myostatin. Deletion of myostatin arrests muscle breakdown, but also leads to hypertrophy of those muscles primarily through retention of damaged and useless muscle fibers that add absolutely nothing to the ability of the muscles to perform work (strength).

In relation to food, the breakdown and building of muscles, which are really just facets of the catabolic and anabolic states of metabolism, can be classified more simply as muscle protein breakdown (MPB) and muscle protein synthesis (MPS). Put simply, muscles will shrink when the rate of MPB exceeds that of MPS and vice versa. The body increases MPB when blood sugar and insulin levels are low and the bodily stores of glycogen in liver and skeletal muscle have been depleted. Although fatty acids are also mobilized for energy from fat tissues, the net effect of this is that the body begins to slowly eat at its skeletal muscles to keep going. The body also pulls acidic or basic amino acids out of muscle proteins as needed to help regulate blood pH, which has to remain within a narrow range for us to survive. After eating, and for 4-6h afterwards, the body decreases MPB and increases MPS such that new muscle fibers are built. How we work out, the spacing of our meals, and even the composition of those meals all influence the efficiency with which muscle protein synthesis occurs. For what it's worth, branched amino acids such as valine, leucine, and isoleucine are absorbed across the brush border of the duodenum and into the blood stream at a faster rate than other free amino acids.

The primary lesson of all of this is that bodily flux is entirely normal. I know that when I first started trying to gain weight I obsessively checked the scale everyday and would be disappointed when it registered a 2kg loss over the course of a day, and astounded when it would suddenly report a 4kg increase in 1 day. The reality is that one's immediate weight, and muscle mass, are determined by a large number of factors and unless we are trying to be super-athletes we shouldn't sweat them too much. Variation is normal. The body already has flux down and we don't even have to think about it for it to occur.

P.S. - Scicurious of Neurotopia has published an excellent introduction to the mechanics of neurotransmission, which are quite relevant to how nerve signals are transduced to musclar action through neuromusclar junctions.

[Sources for this post included what I remember from a few old textbooks (primarily Griffin and Ojedas' "Textbook of Endocrine Physiology", Vander, Sherman, and Lucianos' "Human Physiology", maybe some Alberts et als' "Molecular Biology of the Cell", and a wide scattering of abstracts I remember reading, but not saving.]

How Not to Flirt #1

2009-06-22T00:44:00.004-04:00

Failing to wear pants will likely result in an eyeful of mace or a police report.

Isänpäivä Tuuman

2009-06-21T16:32:00.005-04:00

Looking back, I suspect that throughout my childhood and adolescence my father waged a covert campaign to ensure I would not want to become a physician through over-exposure. When I was young he'd take me with him to the hospital on the weekends when he got called in to do an emergency CAT scan, and subsequently film and video game gore seems poorly contrived. Too gushy. Instead of having water guns, I had 500ml syringes to play with and I'm still not convinced that a Super Soaker is any better, and syringes don't have to be pressurized to work. I grew up with scrubs for pajamas. He took the X-rays whenever I broke a bone, and he always assumed it was a sprain unless my joints were visibly distorted. And he fixed everything, and I mean everything, with hemostats. Cars, lamps, light sockets, locks, fans, clothes. I had to turn a pair of hemostats to turn on the lights in my room.

Well, his campaign worked. Although I can still carve poetry with a scalpel when needed, I was one of maybe 7 students in my molecular biology program that weren't pre-med. Instead I am a scientist, and my father is just glad that I'm not trying to pay rent by playing bass guitar. Because if I'd managed to succeed already at the latter he'd have to admit that he was wrong to groan each time I happily hauled a new bass guitar, effects pedal, or amp into the house. This way he can just be confused about what I do and that's easier.

Hyvä Isänpäivä, Isä!

Happy Father's Day, Dad!

Cultural Possession

2009-06-20T00:57:00.005-04:00

Cultural overtones of male possession of women are prevalent throughout Western society. Institutionalized inequalities continue to demonstrate that men are expected to be allowed to own a greater share of society without complaint.

Not only is it completely socially acceptable for a man to name his most prized possession (lawn tractor, mid-age crisis sports car, guitar, boat, computer, etc.) a feminine name and refer to it in the feminine sense, but it is also expected among many men that a man in a committed relationship fulfill a given quorum of complaining about it to retain the status of his manhood[1]. The former creates a sense of entitled ownership of the feminine while the latter represents the opposite side of this in which men must frequently repudiate any claims of ownership from a woman to retain his sense of masculinity. This bizarre dialectic creates and perpetuates the prevailing Western attitude of women being worth less than men, and by proxy male desires being generally worth more than female autonomy.

Granted, things are better now in Western cultures than they used to be. Marriages used to be formed on the basis of dowries[2] and young women maintained hope chests for their future expectations. The culture of my ancestors even has oral traditions that tell of young men literally stealing their wives from neighboring villages and running off with them into the night to evade capture by their angry families. In these traditions, women were more objects to be bought, sold, and haggled over than human beings with whom to develop deep intimacy and strong relationships. Nonetheless, many men still see most women as little more than fleshy collections of orifices for them to use at will or expectation regardless of how the woman in question may feel.

Cultural Evidence[3]:

1) The Wage Gap.
Per the last statistics on the issue that I have read, women continue to make, on average, just $0.77 for every $1.00 that men earn. This implies that the work men do is ~30% more worthy than equivalent work and work-hours produced by women. This is patronizing bullshit, and when it's combined with hostile and sexist workplaces that continue to exist despite anti-sexual harassment policies it becomes indicative of a subtly expressed but pervasively held belief that men own the economy, and therefore the world, more than women because they "do more"[4]. That the leaders of top companies and political bodies are overwhelmingly male just makes that attitude all the more visible.

Believing that men should earn more[5] because they "do more" makes women into second-class workers. This, in turn, leads all too easily to believing that women are second class people, period, and can be used as such. This is very apparent in the stud vs. slut paradox that Ktbug Ladydid has aptly dissected here.

2) Protectionism
Many men conflate the societal expectation that they protect the women around them with a naive assumption that they, by extension, also know what is best for those women (mentioned in a post below). And all too often and far too easily men confuse their own immediate desires and gratification with what they think would be best for the women around them. This also represents an inaccurate conflation of (comparatively) diminutive physique with assumed mental prowess.

3) Dating
In a typical Western date[6], the guy takes the woman out for dinner and a movie and pays for both. If it was a nice place for dinner the guy can wind up spending a rather large amount of cash. The problem here is that the more money a guy spends on the date, the more he expects that she reciprocate his investment in the night by putting out. In effect, this reduces the date to the guy paying an entry fee to his desires being met, regardless of her desires. This is the milieu in which date rape flourishes.

The key difference here is expectation vs. hope. When a guy goes out on a date expecting that she follow up by allowing physical intimacy to proceed to some vaguely defined "base"[7], it is wrong because it reduces the woman's boundaries, desires, and autonomy to mere conditions, confounding factors, of the the guy's expectations. At the same time, it is perfectly OK for a man to go out on the same date hoping that the relationship will get to the next "base" because simple hope is couched in his respect for the woman and does not in any way conflict with her autonomy.

Nonetheless, the current[6] culture of dating seems to thrive much more on expectation than hope. Expectations also create entitlement in that the societal expectation of reciprocation from the woman creates the popular illusion that that (very uneven) reciprocation is the way things should be, and it is from this narrow vantage point that guys try to justify date rape. If the woman isn't meeting their expectations, they become the victim and once they believe themselves oppressed or treated unfairly it becomes all too easy for them to transmute that into coercive or violent behavior. The entitlement that stems from expectation also serves to diminish the woman's voice and reinforces her standing as a second-class party.

/Cultural Evidence

Date rape and sexual coercion[8] continue to exist because men are socially allowed to view women, and women's autonomy, as less than their own. By feminizing owned things (symptom) and attempting to own women (pathology), men do both genders a gross disservice by deepening the too-wide gap in understanding and social valuation between sexes. In my cohort of 20somethings and younger, the extant traditions mentioned above are slowly eroding and as such I do hope that the next generation will come up even more equitable in general, although unfortunately there're always a couple of jackasses in any given population. Hopefully their behavior will come to be increasingly stigmatized.

[1]E.g., "pussy whipped", "grow a pair and go out tonight", "where does your wife keep your balls?"
[2]Additional evidence that Western culture thinks less of women than men, because the males' families literally had to be paid to accept the bride in the first place.
[3]If you know of additional evidence that I have missed, please add it in comments.
[4]Today's doubty quotation marks generously provided by Büllshyte Incorporated, LLC.
[5]Silence here amounts to tacit endorsement.
[6]So far as Toaster's field research has yet been able to determine. The data are, however, inconsistent.
[7]In lieu of a more elegant term that must exist somewhere.
[8]Infantile posturing, pouting, guilt trips, put-downs, pleading, begging, pestering, insinuations, and innuendo.

Ambiguity in Flirting

2009-06-19T01:45:00.006-04:00

Stephanie Zvan of Almost Diamonds has ~~called me out in the mini-series going on below for having not~~ aptly noted that I have not yet discussed how women socially condition men. I have discussed how men are failing their brothers and sons and how men acting in society perpetuate, unwilling or not, gender inequality. She's quite correct in that I have so far left out a very important part of the dialectic, but honestly I haven't yet done so because how men and women interact and shape each other in society is even more complex than the differentiation pathways of dendritic cells, and I still don't feel like I know enough about the latter in the first place, let alone the former.

For example, I was walking home from the lab the other day, still in my lab clothes (dress shirt tucked into Dickies with sneakers and a jacket), lost in the depths of my head as I often am. I noted that there were 2 casually dressed women approaching me from the opposite direct walking side by side, so I politely stepped to the edge of the sidewalk so they could pass and fixed my gaze somewhere oblique. Then, as they approached, one said loudly to the other "That's a GREAT IDEA, NAME!" and then she turned to me as they passed and told me so as well. I stammered back "Good, I'm glad to hear it!" and turned away to walk away and hide my blushing. I still have no fucking clue what any of that was about.

But the thing is, is I immediately wondered if they'd been playing a joke on me because my nerdness is apparent from 50m distance or if it was some odd form of flirting. I suspect that the ambiguity of flirting shapes a lot of how men perceive women's cues and accordingly react. Men grow up exposed to women in films and other popular media who very often say the opposite of what they really want, who are coy, or who are fufilled by a the acquisition of a strong protective man. This, in turn, leads men to believe that in order to ~~possess~~ win over a woman they must be strong and protective, and this is all too frequently transmuted into a smothering sense of entitled control and possession.

Although, in rational terms, it seems a wide and ridiculous leap from a protective attitude to a possessive attitude, the emotional space is actually rather small. It is all too easy for one to go "I protect them when they need it" to "I protect them therefore I know what is best for them". This kind of thing perpetuates the patriarchal attitudes of society just by itself and was especially evident in the historical argument against women's suffrage that they'd just vote how their husbands told them to.

Nonetheless, men believing that they must be strong, aloof*, and shallow to gain access to a relationship with a woman hurts both men and women in the long run. Men hide their emotions from women, and then from themselves, and as such carry around a knot of confusion that too easily erupts into rage and violence. And when many men may perceive the women in their lives (or lack thereof) as the source of their stress (which is a socially encouraged scapegoat**), they lash out at them, emotionally conflating their own misunderstood hurt with the "fight" response of flight-or-fight.

That society tells men they must be strong for women and to get women creates a strong impetus for men to not show weakness around women, especially those they are in relationships with. A woman may push very hard on the man in her life to open up to her emotionally, but when he does so she may very well never be able to see him as she used to want to perceive him, and at some level many men know this and as such it is an additional incentive to remain closed off. Perhaps women could help men here by signaling that they will not judge them poorly if they open up, as this clarity could help a lot of men to become more confident simply with feeling their emotions and not dangerously bottling them up.

I know I'd sure appreciate it if flirting were clearer.

(UPDATE: I just noticed that it doesn't say so anywhere here, but this video is "Closer" by Suffrajett. Citation citations!)

*Toaster has frequently been described as aloof. This is inaccurate. Toaster is simply oblivious.
**Bachelor Pad vs. Ball and Chain.

On Weakness

2009-06-16T21:31:00.004-04:00

Western* men are not to be weak; we are expected to always be strong. A moment of public weakness is considered humiliating, and an inability to deeply cage one's less acceptable emotions (sadness, hurt, depression, fear, anxiety) is an inexorable mark of heavy shame. As noted in my previous post, we're allowed jocularity, enthusiasm (for sports, money, and women), and stoicism. Deviation from these acceptable expressions is socially punished by labeling an offending man as effeminate or weak and successively isolating him from the in group.

Consider the case of an uncontrollably sobbing man vs. that of an uncontrollably sobbing woman. In the woman's case most everyone's first instinct, regardless of whether it is expressed or not, is empathy and compassion. But if we see a man on the sidewalk sobbing uncontrollably with his head and shoulders bent to his chest in defeat, we first look away and walk by pretending not to notice, wondering if it would wound the man even more if we were to offer a word of kindness (because to recognize his pain is also to recognize his weakness).

It's a simple rule: those who play by the rules may continue playing while those who do not are cast aside and marked as other.

Some societal circles are substantially more insulated from the consequences of not exactly following that rule. Academia is considerably more tolerant of expressional deviation in men than, say, construction. Even so, in academia we are apt to write off a man who is expressing his emotions outside of prescribed means as either eccentric or poorly socialized. Over time, it seems that these men take those labels unto themselves and perpetuate themselves as cover for their (subconscious?) rebellion against the rule. Perhaps it eases their cognitive dissonance.

In order to follow the rule, Western men have to become accustomed to, or at least numb from, cognitive dissonance between what they actually feel and the means with which they are allowed to express it. This is most evident in father-son relationships, especially after the son has grown and struck out on his own. The son may desperately want his father's approval, to hear that his father is proud of him, but he isn't allowed to come right out and say so because it would expose him as insecure and seeking attention to fill that. Meanwhile, the father may very well be proud of his son, but he is discouraged from expressing that for fear that his son will see him, the role model, as weak.

Within popular culture, this tension is evident in the common, and somewhat true, trope of the a woman battling her boyfriend to open up more and share his feelings with her. Often we try to deflect these uncomfortable requests by claiming to not actually feel nearly so much as women**, and this may be partly true because we're socialized not to really examine our own feelings or consider what they may mean. Once again, the reason is because we have been taught that acknowledging weak emotions, admitting that we have been hurt or that we feel something more than our next goal, is itself weak. In effect, vulnerability itself is weakness, and this perpetuates entire populations of men who don't really know what they're feeling or why. And if we as men cannot understand our own emotional selves, how can we accurately consider those of women?

Here as well, advancement in considerate and respectful treatment of women is contingent upon men coming to better understand themselves. Only when we are able to be truthful with ourselves about what we are really feeling can we hope to begin to understand the casually oppressive world we have been taught to create for women. Only then can we begin to help effect change.

We can start by helping to remove the social stigma attached to perceptions of weakness.

*I qualify this with "Western" because I lack knowledge of male, or even female (although for what it's worth, female behaviors seem to be more universal), behavioral expectations in other cultural milieus and as such I don't claim that what I say here applies to them in any way at all.
**Admittedly, there are some women who seem to feel an amazingly large number of different things in astoundingly short periods of time, but perhaps these few are 1) compulsively emotive or 2) exceptions to prove the rule.