31 May, 2009

Disjointed Mind Blather

1) I am one week away from a solid habit of being mostly drunk by 6p each Friday evening.

2) Drunk people aren't nearly as interesting as they think they are, except for me. Apparently I am fascinating (people keep talking to me). I've been partying with the other young scientists lately at bonfires, and I am quite impressed at (almost) everybody's ability to retain their scientific acumen whilst sloshed. I got into an argument last night with a plasma physicist about nuclear fusion and had to resort to using immunology jargon as an escape hatch.

3) I regret not going to ASM. I would have had to pay my own way, but now around the labs its like everyone else has seen the newest, coolest movie and I have to just nod along and pretend like I know what they're talking about. I've been poking through the literature of the talks that keep getting mentioned, but this is frustrating because the papers are always ~18 months behind the actual science that was seen at the conference.

4) Apparently I'm a good teacher in the lab. In the past week I have taught a complete lab n00b everything from how to micropipette to DNA extractions. I've also somehow become the departmental point-man on immunofluorescence, which I guess makes sense since experts are only experts because they've made and fixed all the possible mistakes and invented new ones.

5) I do not have enough projects in the laboratory. I want to be busier, or at least doing something that will turn out data. The ELISA I've been trying to develop has been a long series of failures with non-specific binding of antibodies that are supposedly specific at every turn. I've been putting a lot of time into it, but still, it requires some very long incubation times that I'd rather be doing something else useful during.

6) At this point I suspect that my wash buffer isn't washy enough (0.5% Tween-20 in 1X PBS). I'm tempted to reformulate it but haven't yet figured out what I could use that wouldn't also destroy the proteins I'm trying to get to stick together. It's also possible I'm being entirely too gentle with the plates. I've been pipetting 300ul wash buffer into each well 3X. Maybe I should be flooding a flat dish with wash buffer, plopping the plate down face first and shaking it like I'm trying to drown a Gremlin.

7) On that note, the Megablocking Buffer I made up works beautifully (for immunofluorescence at least). It contains 1% FBS, 1% BSA, 1% NGS in 1X PBS.

8) I bought a little Crassula monstrosa the other day. It's so freakishly cute! I have no idea what to name it.

9) The Dirtbombs are awesome. I have been stuck on their music for the past several months. I don't entirely know why they have 2 bass players and 2 drummers, but I don't really care either.

10) I'm really hoping that the PIs in my favorite Friday meeting decide to make another schedule and keep meeting throughout the summer because it's really my favorite meeting of the week. Vaguely: it's several PIs with tangentially similar interests coming together to float data, research proposals, and grants before each other and their labs and hash them out. It's really cool to get to see the bigger context of everyone's research and hear, and take part in, the discussion of the big ideas in the field. It's an escape from daily lab notebook tedium.

11) Speaking of which, I have really got to find a better way to keep notes in the lab. I tend to print out protocols and make notes on them as I'm doing the protocols and then collate them into binders, but then to also write down everything else on a growing stack of legal pads. So far I haven't been copying from one to the other to save paper because I feel bad using so much of it, but perhaps it's worth it. I also feel bad about printing out papers to read, but that's the only way I can make my notes in the margins and strike out what's important. Papers I read tend to have blocks and arrows and doodles going all over the place synthesizing the information (well, the good papers, at least) and until I save up enough for a nice Wacom tablet there's no other way for me to do this. Maybe there are alternatives?

30 May, 2009

Cover Meme

I've been tagged with the cover meme. The bad covers I have selected here are so cringingly horrible that I'm going to present them first.

To begin with, Marilyn Manson is a douchebag. He built his career on destroying wonderful songs by turning them into febrile little coals to warm his own ego and being the ugliest drag queen/self-injuring attention diva in the business. The bastard ruined one of my favorite songs, "Sweet Dreams" by the Eurythmics.

Compounding the douchebaggery, Universal Music Group promoted this shit actively, and has disabled embedded. You can watch 50 unnecessary costume changes and a desperate plea for attention here instead.

Secondly, Coal Chamber. Now, Coal Chamber is not an intelligent band, nor are they talented. This was evident when they released a song simply entitled "Big Truck". It's about big trucks. But then they had to go and compound their inanity by recruiting one of the most annoying voices in rock and roll, Ozzy Osbourne, to ruin a perfectly good Peter Gabriel song, "Shock the Monkey".

This was entirely unnecessary and the world would be a happier place with it. This is a band that not only shouldn't have a comeback, but should have simply never been.

And now that we're done with bad covers and you've all cleaned the vomit off of the walls, let us turn to amazing covers that stun me with their brilliance.

First, a cover of Public Enemy's* "Black Steel in a Time of Chaos" (original here). This song, in its original context, was powerful enough. But then Tricky, originally a member of Massive Attack, covered it. Embedding has been disabled by request, so the video is here.

Secondly, I'm generally impressed when someone pulls off a cover from one instrumentation to another, completely different, instrument set. For example, if someone covered a Missy Elliott (e.g., Gossip Folks) song with a trombone and xylophone, I'd be impressed enough to listen. As such, I find this excellently done cover of Pink Floyd's "Wish You Were Here" by Rasputina to be epic beautiful.

*For any that don't know Public Enemy, they also did "Fight the Power" which you might probably know.

29 May, 2009

Most Nefarious Competition

This will not do.


Some of you may have noticed a recent poll over at the cave of mein übel-(ekel)-archenemy Mein Hermitage. The poll asked: "Who's more nefarious? Toaster, Hermitage, Ninjas, or Pirates?"

This results are in, and Hermie and I have tied.


How is this even possible when I am clearly far more nefarious than her!?

So to settle this, we had a cease-fire dinner of cookies and Bento and discussed methods by which we might resolve this. Although we each generated several good ideas, from a race to discover a new metazoan species and then find a way to cook it to a giant robot battle tournament to an air guitar competition, we also found that each of these proposals lacked one critical element to ensure a fair outcome: that of transparency.

Without transparency we could each easily engage in heinous subterfuge and use our respective resources to set traps. As such, we eventually found, the fairest way to settle this matter is a Battle of Scientific Acumen and Wit!!!!!!!!!!!!

Therefore Hermie and I will be facing off in the commons of the Internet and battling through the cyber journal club format, one round only, winner takes title of Most Nefarious*.

But we need your help. Dear reader, we are surrendering the material and terms of this contest to you. Here's how it'll work:

1) Submit interesting and substantial papers to Hermitage and I. For the sake of fairness it should be something outside of our respective purviews (Hermie = Peruvian Flying Fish, Toaster = Immunology).
2) Hermitage and I will publicly deliberate upon the papers and choose one to compete upon. This part may take a while.
3) We will each post a blog entry about the paper.
4) You will judge it, and by extension, us. We understand that some of you may have mixed loyalties, so to make it fair, each reader gets 100 points that they can divide between Hermie and I as they see fit. Points can simply be assigned in comments, which will remain open for 96h following posting.
5) Winner will be chosen by who has more points.

So reach into that stack of papers you keep meaning to eventually read and send them on in. This matter MUST be settled!

*Trophy to be displayed in blog side-bar.

28 May, 2009

Toaster's Ear!

Figure A: Swab of Toaster's left ear. No visible earwax on swab after swabbing. TSAII/5%SB plate cultured ~48h at 37C, 5%CO2. Note 2 distinct colony morphologies, no hemolysis or swarming.

27 May, 2009

Your Microbiome and You

ResearchBlogging.orgYou are never alone. Not even when you might want to be. Tucked away within the ~100m2 of your bowels are ~1014 (there are ~1013 somatic and germinal cells in the human body) of your closest friends, collectively termed The Microbiota. They eat, spawn, conjugate, die, poop, fight, and secrete right there inside of you, unseen and mostly unthought of except when something is wrong. This system, the remarkably homeostatic mammalian gut, forms what is perhaps the densest and most complex microbial ecology on this planet.

These teeming microbes are not mere freeloaders living off of your access at their own convenience, they are true symbionts. In exchange for a warm, wet home and nutritional supply, they break down starches for us, metabolize complex molecules, and synthesize some key compounds, such as Vitamin K. It has been found that gnotobiotic, or germ-free, animal models require ~30% more calories to develop normally without a microbiota to help them out. In humans that have been on a broad-spectrum antibiotics, hardier inhabitants (such as Clostridium difficile) can bloom when all of their more sensitive neighbors (such as Bacteroides spp. and Bifidobacterium spp.) are killed off, which causes very unpleasant colitis and diarrhea, that can then be cured by a transplant of fresh microbiota from a healthy individual (colloquially referred to as "poop soup"). Microbiome transplants can also transfer physiological characteristics from one individual to another. For example, the microbiomes of obese individuals have been found to have reduced numbers of Bacteroidales spp., and transfer of these microbiota via poop soup into germ-free mice resulted in obese mice, theoretically because these microbiota were more efficient at releasing calories from food.

Microbes exist, or can exist, in virtually every segment of the gastrointestinal tract from mouth to anus. In the mouth, a variety of Actinomyces spp. are associated with the formation of plaque. In the forbidding and harsh environment of the stomach, only Helicobacter pylori can thrive (it does so by hiding among the mucous lining the stomach and modulating the host immune response) and it has been found to directly cause stomach ulcers and has been further implicated in the formation of gastric cancers (it's the only organism classified as a BSL 2+ carcinogen). The proximal portion of the small bowel is relatively sparsely colonized at ~104-105 microorganisms/ml lumenal contents, which contrasts sharply with the densely colonized colon (~1010-1012 microbes/ml contents).

In the human and other mammals, diverse and distinct microbial ecologies also exist in the sinuses, ears, genitourinary tract (largely Lactobacillus spp. in the vagina; the bladder is generally only colonized in disease states [long-term catherization and/or pyelonephritis] by uropathogenic Escherichia coli, Proteus mirabalis, et al), and on the skin as a whole (mostly Staphylococcus spp.). These others will, however, be excluded from the present discussion.

However, what's very puzzling about all of this is: how does the mammalian immune system manage to differentiate from the massive basal antigenic signals coming from the microbiome from pathogenic antigens? In other words, why isn't the immune system raging against the huge number of microbial signals in the gut?

One of the exquisitely elegant features of normal gut physiology is that gut-associated lymphatic tissues (GALTs) mediate fine-tuned hyporesponsiveness to commensal microbiota while remaining responsive to pathogenic microbes. This flies directly in the face of most immunology, which holds that microbial antigens will always provoke a stimulatory response when ligated to TLRs, CLRs, or NODs (conserved receptors of the immune system that bind conserved molecular patterns associated with pathogens). In vitro data support this. Physiology doesn't.

Physiologically, the germ-free mouse is weird. A germ-free animal is one that has been reared in an environment completely free of all microbes, fungi, and exogenous viruses and as such they have no native intestinal microbiota. Not only do they require more calories and vitamin supplementation, but they also tend to accumulate undigested fibrotic material in their ceca, which predisposes them to gut twists and bloat. Additionally, they feature underdeveloped Peyer's patches (distinct GALT sites on the gastric mucosa), altered CD4+ T-cell and IgA-producing B-cell population profiles, and the follicles in the spleen and lymph nodes where T- and B-cells mature are poorly formed. All of these abnormalities can be rescued by adding back microbial signals such as LPS, even without the microbes themselves. Due to these alterations, it is becoming accepted that the microbiome plays a crucial role in the normal development of the immune system. But to reconcile this with the dogma of microbial signal + PRR ---> inflammatory immune reaction is somewhat difficult, or at the very least complex.

Immune cells that reside in the lamina propria underneath the gastric epithelium generally show signs of recent activation and a particular subset of dendritic cells (CX3CR1+) has been found to extend dendritic processes up through the tight junctions binding gastric columnar epithelial cells together to directly sample the lumenal contents. M cells that cap the Peyer's patches have been found to shuttle lumenal contents, and any antigens contained therein, to the dendritic cells and lymphocytes underneath. These pathways of antigen exposure are thought to be involved in the induction of immunological tolerance to microbiotal antigens, which could explain why the immune system does not attack the commensal microbiota. However, it does not explain how pathogen antigens processed by the same pathways are recognized as pathogenic and stimulate the immune system to attack.

Recent evidence strongly suggests that the intestinal epithelium itself is responsible for the differentiation of nonpathogenic microbiota from pathogens. Canonically, the intestinal epithelium is thought of as a simple barrier that is involved in the absorption and transcytosis of metabolites and nutrients. But it seems that it is much more involved that we had previously believed.

It turns out that intestinal epithelial cells (IECs) express TLRs and directly modulate the composition of the microbiome itself as well as the responsiveness of immune cells. This ranges from TLR expression on Paneth cells in the small intestine that secrete potent antimicrobial molecules (RegIIIg) when ligated [Dr. Lora Hooper, in seminar given 11/19/08] to actual expression of MHCII and direct antigen presentation. It was previously believed that MHCII expression was restricted to antigen presentation by dendritic cells.

When investigators deleted TLR4, NOD1, or MyD88 (an adapter protein involved in many TLR-mediated NF-kB inflammatory pathways) in murine IECs they found that the mice were more susceptible to bacterial infections, which implies that the TLR signalling on the IECs is essentially to the development of normal protective immunity. A second feature of this is that IEC TLRs and NODs are located intracellularly, instead of on the cell surface as in immune cells, which means that they'd only be ligated and activated when an invasive pathogenic microbe breaks into the IECs themselves (e.g., Salmonella typhimurium, Vibrio cholerae) as opposed to the more peaceful commensals. It may be that noninvasive gastrointestinal pathogens are recognized by the proteins that they shoot into IECs via Type IV secretions systems (e.g., Tir and Escherichia coli O157:H7) in the same manner.

The commensal microbiota is also at work on the IECs themselves, actively acting against IEC-mediated inflammation. Bacteroides thetaiotaomicron has been found to induce the PPARg anti-inflammatory (acts by increasing cytoplasmic shuttling of pro-inflammatory NF-kB away from the nucleus) mechanism in vitro. Commensal-derived metabolites such as butyrate (a short-chain fatty acid) have been found to inhibit expression of pro-inflammatory cytokines and increase expression of anti-inflammatory cytokines in IECs.

It is now thought that IECs regulate dendritic cell function through secretion of thymic stromal lymphopoietin (TSLP) and modulate T-cell activity through expression of MHCII in the abscence of costimulatory molecules. TLSP acts directly on dendritic cells and inhibits their production of pro-inflammatory cytokines (such as IL-12), which in turn promotes dendritic-cell-mediated activation of regulatory T-cells. TSLP is also implicated in skewing the immune response to a TH2-type T-cell response, which is implicated in both response to metazoan parasites and pulmonary atopy. If naive T-cells are being exposed to MHCII on IECs without co-stimulatory molecules, then the T-cells will either kill themselves off (anergy) or mature into tolerogenic T-cells that limit the immune response to those given antigens. This, combined with widespread TGFb secretion by IECs, directly indicates an active role for IECs in promoting immune system hyporesponsiveness to the antigens present in the gastrointestinal system. Without this direct suppression of active, inflammatory immune responses, the immune system would be in a continual inflammation state due to not knowing what to do with a safe commensal antigen vs. a dangerous pathogenic antigen. Indeed, emerging research indicates that dysregulation of this process may underlie the pathophysiologies of inflammatory bowel disease and Crohn's disease.

It'll be interesting to see what's found next.

Artis, D. (2008). Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut Nature Reviews Immunology, 8 (6), 411-420 DOI: 10.1038/nri2316

25 May, 2009

Loyalty vs. Opportunity

So about a month ago my boss told me I should probably start looking for other jobs because the only grant funding we had left was due to expire this coming Sunday. I went home and sent out a flurry of graceful applications to as many jobs as I could find posted in the area. Since then the lab has been rescued by an ARRA-funded challenge grant. Now, though, I'm beginning to hear back from the positions I applied to.

The new grant in my current lab presents me with new opportunities to expand upon techniques I've already learned and finally generate some real data. But at the same time, these other positions potentially represent very real opportunities to sink my teeth into an entirely new system and expand my skill set. My current position is applied immunology/microbiology, the potential positions are more basic immunology.

I find myself caught between loyalty to my current boss--who has taught me quite a lot but at the same time also left me alone in the lab and expected me to move mountains with chopsticks (and no glue to make a bigger lever)--and feeling that moving into another lab with another PI and even broader immunological focus would make my application to graduate school this fall stronger. However, this premise itself could be false. I know that in looking for a job, it's a major black mark to have drifted among several labs for short periods of times; but is the same true for graduate schools? I've spent 2 years in the current lab, if you combine the time I have spent here as an undergraduate student, temp, and staff. Would the grad school admission committee see my moving into another lab shortly before applying as a negative quality?

I'm tempted to send out the information requested and attend any interviews I am offered. If they wish to follow up my references, of which my boss is one, I will let her know that she may be getting some calls. Yet I worry that doing so will endanger a good recommendation letter from her.

Therefore I find myself at somewhat of an impasse.

UPDATE: I went ahead and sent out the requested information and affirmed my interest in the position. It's not even an interview yet, so maybe I'm making chromosomes out of oligomers. But still, it's a research assistantship instead of tech position, so I feel it is wisest to pursue it and see what may come of it.

24 May, 2009

Toaster vs. Bobbin

Please place your bets now before reading further.

So Toaster has been in an unproductive funk lately that he has been filling with video games and whiskey. This happens from time to time, usually when I'm low on Cookie Power and I'm used to it; it always passes fairly soon. Maybe these periods are just subconscious protective mechanisms to keep me from overclocking too often and burning out. Or perhaps its a visceral reaction whenever I look at the towering stack of papers I mean to read and blog, eventually. Either way, it's no big deal, although it is interesting that, with the help of whiskey, I've entered a stable biphasic sleep schedule where I take a nap of ~2 sleep cycles in the late evening then remain up most of the night, only laying back down at dawn for ~3 sleep cycles before awaking completely refreshed and ready to go. I spent most of last night with my sketchbook trying to break out of this creative ennui and failed to do so, although now my desk is covered in a lovely sheen of eraser shreds.

Anyway, given this state of affairs, I've been trying to get around and finally do some of the chores that I've been putting off. One of these chores is sewing. A particularly irritating consequence of my lanky stature is that clothes very rarely fit me right off of the rack. If I want a shirt that has long enough sleeves, I must buy something that hangs about my torso like a tent while if I want a shirt that doesn't flap about in the wind it is usually far too short. I've even tried those "athletic fit" and "trim fit" shirts and they're almost as bad, just very slightly less so. Dress shirts are especially bad about this. To remedy this, I learned how to sew so that I could take in the excess fabric on the sides of the shirts. I can usually cut out 8" of material and the shirt is still loose. I have several shirts that don't fit well at all and the novelty of flapping them about like I'm a flying squirrel has lost its appeal.

Enter the bobbin.

I had* an old sewing machine from an aunt. I used to know how to use it. Apparently I haven't used it so long that I've completely forgotten the basics of setting it up. I started out with the machine set up completely backwards and then noticed that the bobbin was not threaded through the needle plunger hole thingy. Sewing machines are not meant for large clumsy man hands, so I was sitting there trying to guide the bobbin thread into what I thought was the proper channel with two straight pins. I thought I had it right, and tried starting the machine up only to have a large knot form instantaneously. About a half hour of cleaning knots up and trying to fix things to prevent them from happening ensued. Finally, I RTFMed and in the process managed to slam my thumb in the sewing machine case with the entire weight of the the bastard crashing down on it. RTFMing didn't help much because even after that, even after I'd managed to thread the bobbin and pull the threat through the right part of the machine, the thread started falling off of the needle. I would have the needle threaded, then it would go into the machine and disappear into a lovely new knot, somehow remaining connected to the spool while getting out of the eye of the needle and the other end of the thread in my other hand. Magic shit.

I am ashamed to say that I gave up because it was going nowhere slowly. I mean, who designed this? Even FACSDiva is more intuitive! And then the bobbin ran out of thread, and I didn't want to try to reload it and risk injuring myself in the process. So I wound up hand-stitching shut some of the holes in other shirts (armpit holes, so not worth throwing away yet).

Yeah, the bobbin won.


*Yep: past tense.
**For the noobs among us, RTFM refers to "read the fucking manual" and is commonly used when noobs go to free tech support forums and ask inane questions that could easily be answered if they'd looked in the ware's documentation first.

P.S. - Arikia, you are correct: armwarmers do indeed increase one's typing speed.

22 May, 2009

Toaster Revealed

Oh noes!

Arikia Millikan done blogged me!

The invasion was surprisingly easy, I'd expected greater resistance from the native population. Instead the soldiers manning the defenses left their posts to join the streaming crowds basking in the glow of our wonderous glory and welcomed us as their new overlords.

Phase I of Plan Lunar Domination* complete!

Extra special post-script note thingy: Hermitage is trying to prove who's more nefarious by polling. Options are Toaster, Hermitage, Ninjas, and Pirates. Dear readers, you all know who is far more nefarious. So please, be true to that knowledge and go crash that poll!

Post-post script: I may or may not still be drunkish from myself and Arikias' wonderous invasion, and I don't know whether it's from the smoke of ten thousand votive incenses burning or the power. This is the state of Schroedinger's Sobriety.

*Better suggestions for a lunar domination plan (because earthly world domination has too many people to govern and control) are being crowdsourced, so send in your suggestions today! The winner will receive a free caricature of their choosing (Toaster and Arikia excluded from choosingnessability).

Toaster Ventures Outside

So Toaster summoned up the courage to leave the comfy Internet and Hyrule* last night to venture out into the real world. I went to a local metal concert with a group of assorted scientists. The headlining band was fucking awesome, and I have nothing but deep respect for a bass player who rocks out on a home-made upright electric flying V and uses walking bass-lines and 4-finger syncopated picking in progressive instrumental metal: you are 1337. HOWEVER, the other bands' bass players lead me to a question that, as a Mad Scientist who also plays bass guitar, is important to me: why is the bass player in 95% of all rock bands the dorkiest person on stage? Is this some requirement that I was never told about? Because 1) I think I'm far too pretty handsome to be that awkward when I'm having fun and 2) I couldn't even look that dorky if I tried.

Maybe I'd be less critical if the music your band had played had been more interesting, but really you weren't interesting enough to be an instrumental metal band, and ripping off of Chevelle, poorly, barely qualifies you as metal. Wearing a lounge shirt, driver's cap, and red pants was not helping your case. And seriously, did you polish your instruments before you got on stage!? Mr. Dorky Bass Player, your lead guitarist was playing the flame-top maple semi-hollow body Gibson Les Paul that every whiny bastard whinges for Christmas, the rhythm guitarist (was he even awake?) was playing a shiny new red Gibson SG**, and you yourself were playing a through-body high-model Ibanez. Which brings me to another point: you played an Ibanez, yet you didn't even slap bass once! WHAT THE FUCK!? That bass was made for that kind of playing, and you completely ignored it. And don't even get me started on your dubious choice of amplifiers.

And yeah, I saw you all get upset and sour when the lead band came on, turning away with feigned indifference trying to cover up your wounded egoes. Next to them you looked like slime mold on the ass of Aphrodite. Maybe I'm also upset at you for playing crappy music while they were doing their pre-show yoga. At least your set was short. For that much, I thank you.

*Spending an evening slashing away at Bulbins and Bokoblins usually seems simpler than interacting with people.
**Disclosure: I have a red Gibson SG sitting in my instrument rack, but mine is old and chipped. I traded my old Yamaha bass guitar for it from Pikkuveli. It can be heard in "Mad Scientist Personal Ad" here.

21 May, 2009

Story of Toaster: Self Experimentation #2

[Neither Toaster nor Hammer endorse trying this at home.]

Looking back at this, I can fully admit how absolutely stupid it was to try. This stupidity was compounded by collaboration with my good friend, whom we shall here refer to as Hammer Fishplate, that endangered both of our lives. In our defense, it should be noted that we were 16-year-old boys with a car, so perhaps stupidity was entirely unavoidable. But at least it was stupidity in the Name of Science!

Our hometown was completely dominated by aviation, and as such we grew up well aware of the principles of Bernoulli and aerodynamics (our middle school even had a wind tunnel). So one night after having lost the competition to see who could push my car the fastest, I proposed that we try steering said car by altering its aerodynamic profile by using the car doors as ailerons*.

So we got some tacos and thought about it.

Since we couldn't come up with any good reasons not to try this, we conducted the experiment. We rolled up all the windows in my car and went to the straightest, widest stretch of local branch of the interstate highway. It was well past midnight so there was absolutely no traffic. Hammer was in the passenger seat while I drove. I floored the car and got it up to 38m/s (since we had reasoned the effects would be negligible at lower velocities). Then Hammer pushed his car door open while I held the steering wheel straight. The car veered gently left! SUCCESS! So then he let his door get slammed shut by the wind and leaned over to grab the wheel while I pushed my own door open (this is difficult to do at 38m/s). Sure enough, the car veered right! DOUBLE SUCCESS!!!

The natural extension of this was to see if we could steer the car productively by this method. There was a large bend coming up in the highway branch, so we gamely took it on and sure enough: it's manageable, if difficult. We wound up drifting across several empty lanes and coming rather close to the concrete median, but we made it nonetheless.

Later on we tried a negative control and repeated the experiment at a much lower velocity (8m/s). It didn't work at all and I'm fairly sure the gas station attendant didn't much appreciate our quest for Science.

Conclusion: yes, car doors may be used as ailerons, but only at sufficiently high velocities.

[Neither Toaster nor Hammer endorse trying this at home.]

Relevant: Story of Toaster: Self Experimentation #1

19 May, 2009


For no apparent reason I find myself absolutely fascinated by these.

Why is the man in a bikini? There's nothing wrong with it, but why?

18 May, 2009

Introducing The Millikan Daily

One of the titans that rules the Internet from the murky shadows has chosen to come forth and write a blog for all of us pathetic plebians whom she allows to tread her realm, perhaps that we might tremble in fear more appropriately when we gnats dare cross her wishes.

Ladies, gentlemen, and assorted others, I introduce to you The Eleventy Cat Herder, Kickballertress Extraordinaire, and Power DJ: Arikia Millikan and her shiny new blog The Millikan Daily. She alone among the Internet Sirens possesses the power to divide the Internet by 0, but will generally restrict her fury to hacking your homepage to 4chan and cutting you off from all unicorn chasers.

Head over and check it out; it still has that acetoney new-blog smell.

Disgusting Misogyny

[No science in this post.]

This is disgusting, even for the Huffington Post*.

Guess The Celebrity Breast Implants (PHOTOS)

What happened to egalitarianism? Why is this acceptable?

This kind of shit:
1) objectifies women for their bodies and in doing so denigrates their intellectual self-worth by making them seem like nothing more than a collection of parts to be groped and drooled upon;
2) legitimizes my fellow mens' too-often outright skeevy objectification of said women when this appears in "respectable" publications. If it belongs anywhere, it belongs in Playboy or Hustler;
3) oppresses all women everywhere;
4) perpetuates stereotypes;
5) gives assholes and douchebags an excuse to be assholes and douchebags in public (in the comments).

You know, the 1950s may have been a period with some serious social inequalities and major hypocrisies built into its zeitgeist, but at the very least the adults of that time would have had the decency and sense to label this kind of B.S. as rude, objectionable, and crass. I am not advocating a return to the '50s values, but maybe that sense of decency wasn't such a bad thing.

I think about the sacrifices my grandmother and mother have made in their lives, the uphill battles they had to fight to see the world become what it is today and I appreciate them for it because greater gender equality isn't just good for women, it's good for everyone. I even think back to my great-grandmother and how she was perceived as daring simply for having a job outside of the home. We have come so far, that we can live in a world where it is seen as perfectly OK that our grandfather could teach my brother and I how to feed ourselves with nothing more than a fishing pole and at the same time our grandmother could teach us how to clothe ourselves with nothing more than a needle and a bolt of fabric and NO ONE GIVES A SHIT. We have come so far that my cousin can be good at volleyball, make-up, texting, AND math and NO ONE GIVES A SHIT. We have come so far that my mother can walk down the streets holding her partner's hand and NO ONE GIVES A SHIT.

But then at the same time we have this kind of utter hogwash plastered through the news, these regressive pop stars selling their KY-fit leather jeans and plastic surgeries over their opinions and intellects. We have so many wonderful and intelligent women out there in the world making differences and kicking ass, but all we seem to pay attention to is fashion and cleavage and who's fucking whom in Hollywood. This is an injustice, a gross disservice to the women reclaiming their intellectual heritage as people from crusty old men who can't see out of their pants scared of competition and unfortunately NO ONE GIVES A SHIT...

It's not so much indecency as it is injustice. The men-children who run amok on campus and embarrass me deeply use feminism as an excuse to be lazy douchebags or subtextual misogynists. That because women are liberated they shouldn't be given "special-treatment" and forgetting that respect and "special-treatment" are very different things. These assholes who whine that feminists are too complex and man-haters when it really is just as simple as respecting women. Failure to show respect to a person for being a person regardless of their whatever whatever is a form of injustice. And that, fundamentally, is why I am pissed off about this piece in the Huffington Post, because it is deeply disrespectful, regressive, and bullshit...and I really thought we, in 2009, were better than this.

*Not that I had high expectations anyway.

15 May, 2009

Breast Milk Transfer of Antigens Establishes Anti-Allergenic Tolerance to Those Antigens

ResearchBlogging.orgMilk isn't just milk. The pasteurized cow milk that we can purchase in the grocery store has been cleaned, processed, and in many cases chemically scrubbed of fat. Unique among mammals, we Western humans stubbornly persist in our consumption of dairy products well into adulthood regardless of whether or not our guts like it. But the cow milk in the store is very different from the fresh milk humans nurse their newborns with. Fresh human milk contains growth factors, vitamins, an astounding density of calories, IgA antibodies, and also antigen. Disregarding the controversial and impassioned debate surrounding breast milk vs. infant formula, research has found that the immunological molecules secreted in breast milk are important for the developing immune system of the infant.

Verhasselt and Julia et al have demonstrated that antigen secreted in a mother's breast milk significantly impacts the later development of allergic asthma in her infants. In effect, this is immunological programming.

They used an elegant experimental system wherein they took nursing dams (mouse mother) and exposed them to antigens (OVA) without their pups, then placed them back with their pups to nurse. Later on when the pups had reached adulthood, they sensitized the mice per the immunology canon and tested their allergic asthmatic (hereafter refered to as atopic) response. In mice breastfed by OVA-exposed dams it was found that, in comparison to those breastfed by non-exposed dams, airway hyperreactivity, pulmonary eosinophilia, cellular infiltrate, and mucus deposition were all decreased towards mice not challenged with OVA (normal, negative controls). Moreover, the classical TH2 cytokines (IL-4, IL-5, IL-10, and IL-13) that have been associated widely with atopic responses were decreased in OVA-breastfed mice, as were the frequencies of the lung CD4+ T-cells that secrete them. Overall, this points to OVA-breastfed mice having a significantly weakened allergenic response to an allergen, or put another way, these mice tolerated the prescence of the allergen much better.

As an aside, OVA is an abbreviation for ovalbumin, which is a key molecule in eggs and is a very sticky molecule. In every study of allergy or asthma that I can remember reading, OVA was used to sensitize mice and produce an allergic response to it. This is done by injecting a solution of OVA into the peritoneal cavity of the mice, waiting 2 weeks to let OVA-specific CD4+ T-cells develop, and then challenging the mice by squirting an OVA aerosol up their noses. This model has proven to reliably produce a strong and specific allergenic response.

But how did the authors determine that it was secreted antigen itself that was inducing the tolerance?

To address this, they took normal, wild-type C57 mouse pups and gave them to lactating uMT and RAG-2 transgenic dams*. Both these transgenic strains of mice are completely unable to mount an adaptive immune response to anything; they do not and cannot make antibodies. When these mice were exposed to OVA and then nursed the wild-type pups, the same effects of the OVA-breastfeeding inducing allergen tolerance were observed. This was also replicated with Balb/c mice (which is important because the C57 strain is known to skew towards a TH1 response phenotype while Balb/c skews more to TH2, which is better characterized in the pathophysiology of atopy).

But then Verhasselt and Julia took a look at some important and specific immunoregulatory molecules: TGFb and IL-10. Both of these molecules are broad suppresors of inflammatory immune responses regardless of that response's cellular phenotype. IL-10 transgenic dams did not alter observed results when exposed to OVA, but TGFb knockdown dams did in that the pups they nursed were reactive to OVA. This strongly suggests that TGFb must accompany antigen in the breast milk in order for the infants' immune systems to recognize that antigen as a harmless allergen and, in effect, program itself not to react against it. Luckily for human mothers, though, breast milk already contains TGFb.

At a wider level, this suggests that mothers who are exposed to many allergens will pass on tolerance to those allergens to any breast-feeding infants they may have. Perhaps this, coupled with the hygiene hypothesis, is a call for more moms to teach their infants how to make mud pies even earlier.

*I can't help but wonder how many times they did this and found all the pups had been killed off by their adoptive mothers, as this is what stressed out rodent dams tend to do.

Verhasselt, V., Milcent, V., Cazareth, J., Kanda, A., Fleury, S., Dombrowicz, D., Glaichenhaus, N., & Julia, V. (2008). Breast milk–mediated transfer of an antigen induces tolerance and protection from allergic asthma Nature Medicine, 14 (2), 170-175 DOI: 10.1038/nm1718

12 May, 2009

How Vaccines Work: An Immunological Primer

Vaccines prevent disease. They do so by causing you to develop immunity against an infectious organism before it gets a chance to infect you and cause disease. In essence, vaccines teach your immune system how to recognize infectious organisms and fight them off much faster. Without vaccination, exposure to an infectious organism is like being thrown into the deep end of a pool without water wings where your immune system thrashes around desperately trying to save you. But vaccines are like the shallow kiddie pool where you touch the bottom and your immune system gets acquainted with the water so that it will have a better idea how to handle it later on when you can't touch the bottom. Vaccines do this by exposing the immune system to dead, weakened, or pieces of infectious organisms, usually along with a signal molecule called an adjuvant, so that it can learn that the molecules associated with the infectious organism are bad and should be attacked if they're ever seen again. The adjuvant acts like a wake-up call to the immune system to make sure it takes a look and does what it's supposed to.

Vaccines are education for the immune system.

The human body has 2 different immune systems: the innate immune system and the adaptive immune system, and they talk to each other quite a bit. The innate immune system is the infantry of the immune system; it reacts rapidly to invading pathogens and can destroy most of them, but it can have a hard time telling exactly who to kill and when and how much firepower to use. Meanwhile, the adaptive immune system is more like a laser-guided cruise missile from a fighter jet that very specifically takes out invading pathogens and tags the enemies that the innate immune system should kill off. However, just like it takes time for jets to get to where they need to go, the adaptive immune system takes several days to warm up and start fighting.

The innate immune system is scattered throughout the body in circulating white blood cells, in the mucous membranes, in the skin, and in the gut; all places where invading pathogens are likely to try to enter. The adaptive immune system, when there's no infection present, generally hangs out in the bone marrow, thymus, and lymph nodes; but when there is an infection some of them will go out to the site of infection to join the battle while others will stay behind and direct subsequent reinforcements.

In an infection where there is no prior vaccination present, say S. aureus in a pimple, the innate immune system quickly (in minutes) recognizes many of the molecular patterns that are generally associated with all bacteria, including S. aureus. These patterns are signals for the innate immune system to kill and also go talk to the adaptive immune system. So the innate system goes to work blasting away as well as it can at the S. aureus, but it's good at hiding so the innate system doesn't see all of it and S. aureus is able to establish an infection.

So meanwhile, the innate immune system has gone off to the adaptive immune system and handed it the information it has gathered about the infection. The adaptive system examines it and then begins to multiply and specialize. Some of the multiplying cells get out to the site of infection and join the battle. Other cells make antibody against the S. aureus, which is then secreted into the blood and binds the bacteria, lighting them up brightly and saying "Destroy this now!" to the innate and adaptive system cells that are already there.

Once the infection is cleared, many cells of the adaptive immune system specialize again and become memory cells that wait out in the body, able to specifically recognize the same infection they just fought off. This means that if S. aureus tries to come back, the memory cells will see it very specifically and very quickly and they can then jump-start the rest of the adaptive immune system and mount a very rapid lethal attack against it.

The problem is that many infections are strong enough to kill, or do serious and permanent damage to, a human before the adaptive immune system is strong enough to fight it off. Although the innate immune system starts fighting quickly, it takes the adaptive immune system about 4 days to start responding very much and a full 7 days to really get into swing. Memory immune cells can bypass that waiting period and kick both immune systems into battle mode right away.

Vaccines are designed to skip the infection part and go directly to teaching the adaptive immune system to recognize the infectious organism and then form the memory immune cells that will kill the pathogen before it even has a chance to cause infection.

This is why vaccines are effective, useful, and necessary. They also happen to be quite safe*.

NOTE: This was largely inspired by Abel Pharmboy's guest post over at Dr. Isis' place. I left a long comment there and then realized that it wouldn't do very well for me to be a hypocrite. If you feel I've left anything out, or if there's anything you want to know more about please let me know. I tried to keep it simple because even the basics of how the immune system functions could keep me busy with posts for the rest of the year.

*Bears, however, are something you should worry about. Bears are crazy dangerous.

11 May, 2009

Trepanation 2.0

Figure A: Trepanation. I almost laughed at the expressions on their faces, until I realized that these grimaces were likely due to strokes, hematomas, or hydrocephaly.

So I asked how you all perceive yourselves, your mental selves, and promised my own response later. This is that.

As far back as I am able to remember, I have had difficulty thinking in a linear fashion. My mind has always seemed to move in more of a swarm, thinking several thoughts and juggling lots and lots of things at the same time. This isn't to say that I cannot focus upon one consideration, but that absolute concentration is rather rare* and there are usually several things going on in the back on my mind at any given point. However, this doesn't usually prevent me from entering the flow state of creativity and/or knowledge synthesis.

I have not been able to fathom the shape of a container for my mind because that would give it a finite volume (and Klein bottles aren't big enough). But I do think of it on an x-y-z axis plan with core autonomic functions at the origin (e.g., my hypothalamus shouting "Feed me, you bastard!" would be at [0,0,0]) in a sort of "tip of the tongue" vs. "back of my mind" vs. "top of my head" dialectic gadget. In practice, this translates to the wheeling jabber of the swarm occupying the backchannels of my mind while I speak, write, and am generally intelligible at the front of my mind as a sort of command line function. Memories seem to be stored farther back, behind the swarming backchannels but these also frequently interact. I perceive short-term thoughts and memories as being stuck to the "ceiling" as it were where I can conveniently access them.

From what little I've read, it seems that I dwell more or less continuously within a cognitive map of my own devising and frequent editting. From what I understand, cognitive mapping can be consciously learned and taught.

I asked the question because I am curious as to how others experience their mental selves.

*Needs very powerful or engaging stimuli to happen.

10 May, 2009


Figure A: Up Toaster's nose. I thought about getting some LEDs and shining them out of my nostrils (see post below) to better illustrate my point, but since I'd been awake for 21h at the time and didn't have any batteries small enough immediately enough on hand I figured my judgment may be better when I was better rested. Nonetheless, this pathetic fuzz isn't going to be getting me aboard any technopirate ships anytime soon. At least this particular angle makes my head look less gargantuan.

OK, so this is as far as I got. I know I said below that I was going to try to grow a beard, and that's all I could manage before I got too annoyed by my face continually being itchy. That 5'0'clock shadow was about 7.5d of growth. Now I'm going to see if I can manage sideburns. I'm not entirely clear on why I feel the need to do this, but perhaps I associate inappropriate hair with rocking out and my hair is still too short and doofy to get into a proper Mad Scientist pompadour. But that hasn't stopped me from rocking out although my neighbors might intervene soon, especially if I keep wailing away at bass with the window open.

I apologize for the recent complete lack of science. It's just that every paper I've read recently is just too vague, too rote, or too scattered to research blog. However, this could also be due to reading papers primarily during Happy Hour and washing them down with the darkest, most evil-smelling beer I can find. But this, in turn, has led me to the discovery that not only is gold eyeshadow available, but also that cracker girls are blind/vain/self-delusional enough to wear it. It makes their eyelids look crusty.

I am currently listening to "Happy Fcuking Birthday" by Combichrist and for some odd reason that reminded me that I am trying to decide whether or not to maintain the "Sunshine" part of "Toaster Sunshine" because I took it on in the context of my recently dissolved relationship. My Guitar Hero band's name is "Toaster Doomly", but that doesn't seem right. I do, however, like "Toaster Tron", just because it is a lot of fun to say and because Megatron is a badass. But "bubbles" is also a fun word to say, and that doesn't mean I want to be "Toaster Bubbles". I may retain the original anyway.

Crusty golden eyelids!

07 May, 2009


I am curious about this, but to try to answer this one with a scalpel or welding torch would be deeply unethical and terribly illegal. I mean, unless you like trepanation...

How do you perceive yourself?

Not you yourself your physical self and fleshy presence. I mean, how do you perceive of your own consciousness(and/or/)sentience? Not so much in the sense of "I think, therefore I am", but more of where your thoughts are thought and your memories are stored, how the stream of your consciousness moves, if it moves, or the shape of the container thereof.

I've given a lot of thought to this, but I'm not going to reveal how I perceive myself right now lest I bias your responses.


Figure A: Toaster had a spare TSAII/5%SB plate. This is 48h normal atmosphere growth of a sterile swab of Toaster's right nostril on 5.4.09. There are just 2 different colony morphologies, which seems too few. Maybe next time sneezing on the plate will be more efficacious.

05 May, 2009

Moving Forward List of Things to Make Done and Do

Thank you all for your kind words and support. I appreciate it. Toaster is tungsten alloy in more properties than just density. Last night I took me my sledgehammer and hewed away mightily at an undisclosed object (5th Amendment of the U.S.A. Constitution) until the following plan to keep my hands busy and mind occupied had formed.

1) Make food:
  • Bake cookies. Perhaps cayenne pepper, cinnamon, Tobasco, dark chocolate cookies would be tasty. Note: first learn how to bake.
  • Make and consume these.
  • Cook something more than pizza and frozen burritos*.
2) Purchase soldering gun and solder stuff:
  • Take apart defunct laptop, fix, and reassemble.
  • Construct tiny vacuum cleaner to get cookie crumbs and charcoal shavings out of my computer keyboard.
  • Build computer speakers. Not sure whether to use this or that as a chassis.
4) Read more papers.

5) Rock the fuck out:
  • Begin each morning by rocking out.
  • End each night by rocking out.
  • Rock out in the lab.
6) Kick Zant and Bowsers' asses** all over the TV screen and finally beat the games.

7) Grow stuff.
  • Try to grow a beard, just to see if anyone notices***.
  • Grow something edible.
  • Grow my hair back out of this stupid, doofy haircut I mistakenly went and got. With this, I look more like a normal scientist than a Mad Scientist, and this displeases me. To the credit of my scalp, however, it is forming multiple cowlicks despite the shortness.
  • Continue growing muscles to become less scrawny. Having the approximate physique of a stick figure and the disproportionate head of an anime character has lost its novelty.
8) Get business cards.
  • "Toaster Sunshine; (contact info); Lisenced Zombie Hunter; Professional Mad Scientist."
  • Resist urge to get "Pardon me, sir/ma'am (circle one), I couldn't help but notice you're a douchebag" cards and hand them out as needed.
9) Be more social.
  • Force myself out of my lair and interact with humans in their natural habitats.
  • Leave phrenology calipers at home as these will probably not endear me to anyone.
  • Don't talk about Mad Science when first meeting someone to avoid scaring them away.
  • Suppress Mad Scientist Laugh in public.
  • Do not wear top hat to happy hour, as this might be construed as rude.
  • Quantify human body language. May need calipers for this.
  • Drink more? My liver has gotten pathetically complacent.
10) Finish out cartoon commissions.

11) Gather data around hypothesis that "charm" is just "normal social graces" integrated over a power law with range 5 to infinity (Blogger interprets proper mathematical notation as an in-line html style tag).

*The 4 Food Groups of Toaster: frozen burritos, sushi, cookies, and orange juice.
**For non-nerds, that corresponds to Legend of Zelda: Twilight Princess and Super Mario Galaxy, respectively.
***Last time Toaster tried to grow facial hair no one noticed for weeks, likely because it is blond and therefore only visible in limited lighting contexts.


More Incoherent Blather!!!

[WARNING: There is absolutely no science in this post, just bullshit. Please be polite: don't point and laugh, for Toaster is unaccustomed to being this exposed regarding the mechanics of his life. If you insist on pointing and laughing Toaster will have no choice but to use you for spare parts.]

I can't help but find it odd to note that now, after everything, all I've got is a lovely little knot of rage warming my spleen. And the thing is, I'm not even angry at anyone or anything. So maybe it's not rage, but that's simply the best name I've got for it; perhaps sisu reawakened would fit better.

As it is, a great deal has changed in The Life of Toaster in the last year. One year ago I was sitting on The Diag with my fiancee, exhilarated in my cap and gown, full of idealism and hope and thinking I was ready to take on the world and win. Now I am suddenly single, although that's been coming for quite a while, for the first time in 4 years. Effectively, for a long time we were two single people poking along the rotting zombie corpse of the relationship we used to know, but who each have changed too much to fall back into those too simple roles and syrupy love. I'm still ready to take on the world, but instead of idealism and hope like a fool, I am instead full of piss, vinegar, and perchloric acid. Instead of wanting to take on the world with grace and charm I find myself wanting to take it on with a motherfucking sledgehammer. Uncle Thor would be proud.

I knew this was coming. I may be tungsten when it comes to social interactions, but even as such I could see the signs of disintegration. Looking at the past 8 months, it's somewhat amazing that I was able to pull enough hopeful fluff out of my ears to blindfold myself for so long. But in the end, all either of us had left of what we had once sought to be together was a handful of bittersweet hope, and that's not enough to sate. We began avoiding each other, withdrawing into our respective spheres. Slowly, I began to ease out of the yoke of her expectations, becoming less (Toaster)monochrome and more (Toaster)eleventy!. In idealizing my love for her, I allowed too much of myself to be subsumed by her expectations. I gave and gave and gave and gave and gave and rarely ever received and in the end began to feel more like a hollow toaster than Toaster himself, exhausted and frayed and, kind of, used like I was an appliance. She told me that this or that was wrong and that it was something I needed to change, and I made the colossal error of turning my analytic lenses around onto myself, thinking that if I could just figure out what was wrong with me and fix it then maybe she'd reciprocate my love for her. I was foolhardy. In dissecting myself, I began to question absolutely everything and quickly found myself caught in a viscous resurgence of the OCD tendencies I have struggled with my entire life and wrapped my daily routine up in comforting, but obsessive, rituals. I stopped drinking because I wanted to drink, to seal myself in a bottle of whisky to break the anxiety. But in the end the thing that defanged it was to reclaim myself from what our relationship had been, regaining the things that make Toaster Toaster instead of who I was expected to be. She always thought they were silly and annoying and items to be corrected, but doing things like playing music too loud and singing deliberately off key while dancing around in my leprechaun socks and underclothes make me happy even though I don't exactly understand why. Cookies also make me happy (there are going to be more cookies in my near future). At the same time as I was emerging from all the anxiety, stress, and expectations, I began to blog more heavily. I'd been blogging anemically for years, at first as a way to synthesize what I was trying to learn in my cell bio class, but getting into science blogging and discovering that there are other unabashed science nerds out there perfectly happy to be their nerdy selves allowed me a space* to be Toaster as Toaster is in his natural habitat instead of suppressing Toaster whenever she was around.

The feeble illusion we'd been maintaining came crashing down last night. True, I'd asked for her ring back months ago when we had a fight that exactly echoed how my parents fought when they were still together. But we'd poked along some kind of odd hope, even though we both knew that we were each essentially alone anyway, or at least I did (I can't really speak for her). Afterwards, I retreated back into the comfortable world between my headphones and forced myself to listen to the music I had composed 3 years ago for our wedding. I was OK until the violin solo halfway through it, the most beautiful melody that my clumsy hands have ever crafted, and then I folded, all the self-incrimination from the past 2 years flooding back all at once and squeezing my lungs like a shivering asthma attack. So I opened up a program and awkwardly poured it all into my laptop in words; not a way in which I am accustomed to expressing my inner milieau, but my hands were shaking too badly to take up charcoal and graphite at the moment. The important thing is that the blood-letting seems to have gotten it all out and even though I only got perhaps 3h of sleep last night I feel somehow relieved and lighter despite all of it.

I had decided back near the start of the new year that I was too stubborn to walk away immediately is spite of all of the bullshit and toxicity that had built up and that I'd give it until June, one last little reservoir of hope. Close enough, I guess. Now, though, I can't bring myself to be angry about any of it, nor to feel that I've wasted 4 years. All I have is this hungry knot of sisu smoldering. For the first 1.5 or so years I was very happy, and I was absolutely, completely in love and I'd rush home with a grin stretched across my face and my heart in my mouth. That was good. The next 1.odd years were middling and it's really only been the last many months that sucked, but all of this has taught me so much about myself and what I really want out of life. I suppose I have to appreciate at least that much. And now, of course with the clarity of retrospection and deep maturity of 23**, I can see that maybe my family was correct in supposing that at 19 we were too young to know ourselves well enough to imagine the rest of our lives together. The thing that I do, however, regret is allowing her expectations to drive away most of my friends. I'm going to be busy repairing bridges here in real life for a while.

The thing is, is that Toaster is not a simpering romantic and never has been***. This isn't going to stop me or set me back in the slightest, because I refuse to allow it. I will heed its lessons, but I will move on. I'm not the type to languish about in grief for months, and the absolute last thing I will ever allow myself is the indulgence of pity. She may have never realized it, but I am much stronger than this: I've survived and thrived through worse. Today my head is clearer than it has been in months, there's no longer that frustrating swirl of self-doubting seeking and feeble hope constantly chattering up the backchannels of my mind. Today I'm going to pick up my sledgehammer and take on the motherfucking world. My sisu is fucking hungry.

*If I forgot anyone I apologize: t'wasn't intentional.
**OK, yeah, I heard you snorting at that. Shaddup.

***It should be that reports of Toaster being an irredeemable asshole are largely conflated with his unredeeming bluntness.

[Cultural Note: Sisu is a Finnish word and concept translating roughly as stubborn perserverance and courage. It's similar to "having the guts" to do something, but in a more sustained sense. It can also be understood as sustained toughness and from what I remember it is said that with enough sisu one can even go through the grey stone (meaning granite in Finland).]

04 May, 2009

5.4 #2: In Which Toaster Is Mostly Incoherent and Unintelligible

1) I think I've found a new favorite word: "der Unfug". Short, simple, sweet, and too the point. It's a synonym of "der Blödsinn" meaning 'nonsense' or 'mischief'. I mean, you can't invent such a great word out of the air, and even better that the opposite of Unfug exists only as an idiosyncronism "mit Fug und Recht" meaning 'with order and justice'. Sometimes I really do wish English were as silly as German, it'd make speaking a lot more fun.

2) An diesem Punkt soll ich es verkünden, dass jetzt meine lieber, aber unheilvolle und finstere Schwester Verhängnis, und ich einander mit "Zum Unfug!" grüssen soellen. Wenn ihr alle es woellt, koennen wir auch diese Begrüssung als verborgene Meldung nützen, um zu zeigen, dass wir (verrückte) Wissenschaftlern und Wissenschaftlerinnen sind. Manche von euch schriebt, dass ihr die Lust zu einem Ehrfurchtgebietenden Wissenschaftlersverein schaffen haben. Veilleicht koennen wir hier anfangen. [Für einer geheime Grund arbeitet meine "oe" Täste nicht...]

3) Presentation went OK today. I presented, for really real journal-club kung-fu style, the paper that I research bloggered here. I included about a dozen slides of immunology run-down for the people in my lab group meeting that don't know much about it, and then ran through the paper itself for another 15 slides. I was told that I'd done a very good job breaking down a very large and complex paper, and best of all neither my boss nor TechnoGrad, who've been drinking the Immunology Champagne for far longer than I, disputed my immunology run-down! This must mean I am finally getting somewhere with that whole learning thing, which is somewhat relieving. Getting into immunology is awesome, but it's so deep and complex and chaotic and, most of all, dependent upon very finely detailed contexts that at first I felt like I was drowning in a slurry of cytokines, cellular determinants, and maturation dynamics.

But it was due to my inexperience with immunology that I didn't catch the many problems with the paper that TechnoGrad and my boss did in just their cursory examination. For example, the Ohnmacht et al 2009 paper had a flow cytometry figure showing increased CD4+ T-cell infiltration into different tissues (axes were stained for CD4 and CD8) that showed massive increase (21%) CD4+ T-cells in kidneys of mice without dendritic cells and they explained this as autoreactive T-cells surviving without tolerogenic dendritic cells. But the control kidney had 5% CD4+ T-cells, which apparently is really really unusually high. Materials and methods said that these were obtained by collagenase digestion of whole tissues into single cell suspensions, but then they didn't mention whether the 21% and 5% were of total cells isolated or just total lymphocytes isolated and didn't even mention or show their side- or forward-scatter gating. I had no idea that 5% CD4+ T-cells in the kidney was unusual as the papers I've been reading about lymphocyte dynamics in peripheral tissues make it sound like we're crawling with lymphocytes all the time. So it didn't set off a flag and I'm kind of left feeling like I should have caught it.

But I guess that's what journal club stuff is for, to teach us all how to read papers more critically and extract useful information.

Bloggable Science-Like Paste

I did a little quasi-scientific quasi-experiment for your entertainment. I'm curious to see how quickly all of you can poke holes in it.

Informal Background:
So, the other day I found a sleeve of plates in the fridge that were rather old and on the verge of becoming trash. My boss has told us that if we need to keep our work sterile but can't fit it in the flow hood (or someone else is in the flow hood already), we can just light a Bunsen burner and it'll create an updraft that sweeps all the microbes away from our work. I don't trust my cell culture media with this, but I am willing to use this for bacteria work. However, I haven't seen this qualitatively proven with my own eyes or in the literature so I figured I should test this.

A burning Bunsen burner is sufficient to keep your work sterile within 1m.

Materials and methods:
Set up line of split TSAII/5%SB and MacConkey agar plates from BD. Lit Bunsen burner and allowed to burn freely for 5min. Then turned over plates and removed lids from closest to farthest. Plates were then left uncovered for 5min and re-covered while the Bunsen burner burned. Plates were incubated 48h at 37C, high humidity, 10% CO2 in a water-jacketed incubator. After 48h, bacterial growth was assessed.

Figure A: Toaster's benches showing experimental setup. My benches are particularly messy here because I was also running an ELISA at the same time and did this during an incubation period.

8 out of 10 plates remained sterile. The 2 plates that did not remain sterile were plates 1 and 3 (numbered going out from Bunsen burner). Growth on both of these plates was a single large colony of yellowishness on the blood agar side.

Inconclusive. Growth on plates did not follow distance as one would logicaly expect if the Bunsen burner does indeed create an updraft. Growth that was observed was likely Gram positive (because it didn't grow on MacConkey agar, which contains bile salts that inhibit Gram positive organisms' growth).

02 May, 2009

It's a Holiday! Where's Toaster?

As the higher-ranking nerds among you may know, today is a Very Special Holiday in The Nerdness. For the rest of you more sensible people, it should be clarified that today, May 2nd, is Free Comic Book Day.

Free Comic Book Day began in 2002 as an effort by all the major North American comic book publishers to introduce comics to new markets, promote new titles that we otherwise wouldn't hear about*, and thank the die-hard comic book readers. It falls on the first Saturday of May after the release of a major film adaptation of a comic book (this year's being the Wolverine** X-Men movie) to ride with the heavy film marketing. It is currently being celebrated at Toaster's awesome local comic book shop (they're by the robot part supply store downtown), and Toaster is not there.

Why not?

Because upon every occasion that I go to the comic book store I wind up spending more money than I should. And even though today is Free Comic Book Day, that doesn't mean that every comic is free or reduced in price. I'd wind up walking in, being disappointed with the free comics (usually 8-page promos from Marvel, DC, Dark Horse, and IDW; not much of substance or maybe I've always gotten there too late), picking up my subscriptions (Hoxford and Wormwood: Gentleman Corpse [below]), and then wind up buying TPBs and HCs trying in vain to complete the Hellboy, Fell: Feral City, and Neil Gaiman's Sandman series as well as resisting the urge to begin collecting The Walking Dead, Y: The Last Man, or Frank Miller stuff.

This would not be conducive to paying other things, such as rent. And high-ranking nerds, lest ye deem me of lesser street cred because of my non-attendance, let it be noted that without paying rent Toaster would have no shelter and therefore all of the comics and video games he has collected would ruin out in the rain. Also, dearest Amazon, could you please possibly hurry up and ship me the copy of Zombies vs. Robots vs. Amazons that I bought back in February? Zombies vs. Robots is looking kind of lonely.

*Contrary to what one might expect, Battlepope is actually a well-established title.
**On this note: if any of you lived in the X-Men universe (any of them), which character would you want to be? You may not choose a Skrull.