30 November, 2007

Tales of the Anti-Chicken

Once upon a time ago in a land not far away but farther than a snail will go for doughnuts there lived The Anti-Chicken. The Anti-Chicken had been borne of a goat and an interleukin, and as such the Anti-Chicken was very confused and clingy. It would roam the country-side in its Chicken-Head-Goat Hat and slink among the shadows. It knew that there was something wrong about it, for whenever it appeared in the daylight and among decent folk, they'd always scream and run away in fearful terrorness and screaming screaming. So the Anti-Chicken was very sad. It even tried to pass itself off as a normal chicken, but unfortunately failed (seems that explosions would occur whenever it ran into a Chicken) and was subsequently run out into the Cold Forest.

So now The Anti-Chicken roams the Cold Forest by night, looking for the Anti-Goat. One day, they may find each other, and when they do it will be the worse for everyone. Or they'll be happy and blissful together and leave everyone alone.

27 November, 2007


This is an odd photograph of bacon. Bacon usually looks much more appealing than this particular piece. It's as if this one was soaked in extra grease and barely done, like it's still all wobbly. That isn't how I like my bacon.

For approximately 3 years, I was an ovo-lacto vegetarian, induced not so much by ethical concerns as health concerns over dorm food as well as the price of meat. I stopped vegetarianism for 3 reasons (importance increasing with list decreasing):

1) Kept losing weight. At one point I found that I had a BMI of 17.1, which is apparently really bad. Now, about a year later, I'm up to a BMI of 19.6.

2) Missed fried fish.

3) Missed bacon.

At first I just started back up with the fish. And then it progressed to white meat (pork is not white meat), thus: turkey bacon! When I first had bacon again after all those long years, it was as if a long-suffering void within was suddenly filled and I became instantly happier.

So it set off the question:

What is it about bacon that makes one happier?

Is it the lipid soaked protein?

Is it the burnt crunchiness? Yes, I like my bacon slightly burnt.

Is it the salt?

It is probably a combination of all of the above. Nonetheless, bacon got me thinking a bit about how it influences science. No bacon results in crankiness and feeblemindedness. As such:

The Scientific Bacon:

1) James D. Watson - clearly his bacon consumption fell off over his lifetime. It must have been at its highest when he "co-discovered" the structure of DNA, and clearly has recently reached record lows.

2) Dr. Hwang Woo-suk - clearly a conspicuous lack of bacon led him to falsify his research results for the greater honor of South Korean science.

3) These people clearly weren't getting enough bacon.

4) This person seems to be eating bacon daily (hint: he can read his own genome).

25 November, 2007

Fundamental Paradigm

Paradigms are difficult. We live so easily within them, but then sometimes they get challenged and we have a hard time talking our way out of them. I was at a party last night talking to a chemist when a child overheard us and asked what an element is (I know, a lame kind of party). How do you explain what an element is? It’s something that has been so fundamental and easy for me for so long that I was taken aback by the question. But between the chemist and I, we managed to explain it. We explained that everything around us was made up of matter, and that that matter is made up of tiny little pieces, like little miniscule balls. And then we went on that each ball has a color, and that different colors are like different elements, because a ball of a different color acts differently than another ball of another color.

20 November, 2007

Idea Hat

This would be absolutely brilliant. To be in a class where I could participate collectively in giving the professor instant learning feedback would be truly great. Or to teach such a class. To know instantly when the "Eureka!" moment strikes, or when confusion is, would be of great advantage. A colleague of mine laughed at me and told me that the same thing can be done by reading facial expressions. She is stupid.

LEDs are cooler.

I now need to convince someone to try this.


Looking back at my last post, I can see how it may have been misconstrued that I am a cat. However, I assure that that is very much not the case. In fact, I don't much like cats, kittens, tabbies, felines, or other cat-like creatures. I prefer the canine varieties, simply because they are better. And cooler. And much, much less bitchy.

16 November, 2007

Smrt gas

Oh yeah, that's me: SMRT.

Today in the lab I was trying to turn on a Bunsen burner. I turned on the wrong side of the gas tap and vented a big old stinky stream of natural gas in the laboratory. As if that wasn't stupid enough, I wanted to know immediately if the amount of gas I'd put in the air was dangerous, so I grabbed a sparker and sparked it around me. Nothing happened. Kind of disappointed, I proceeded to correctly light the Bunsen burner, right by where I'd vented the gas, and walk away. That was stupid too.

01 November, 2007

Not-quite-right-in-the-head Syndrome (NQRITHS)

So I think I might be not quite right. In the head. In fact, I may indeed be afflicted with NQRITHS, an increasingly common disorder among scientists the world over. The symptoms:

1) Found this news story about an E. Coli breakout in frozen pizza pepperoni. My first reaction wasn't "Oh, how terrible, people are going to get sick!". No, my first reaction was "Cool! What strain? What strain!?". It was O157:H7, Biohazard Safety Level 2+. Not only does O157:H7 have cool tir ligands that lead to inflammatory effacement of the gastrointestinal epitelia (tir is secreted by a Type III secretion system [bacterial nail gun] and causes actin realignment in the cell that it effaces), but it also is an STEC, which means that it produces Shiga toxin. Shiga toxin, very deadly, has been implicated in the renal pathology (makes your kidney cells bleed) of severe E. Coli infections.

2) That I know all of the information above off the top of my head.

3) Shiny = happy.

4) That things like lactose and (1>3)-beta-D-glucan really piss me off, but for very different reasons.

19 October, 2007

Cartoons of My Creation

The words read "Like, OH MY GOD! Are those GUCCI wading boots!!??"

I know, I know, this one was a cheap joke.

This is a low-res image blown up. The thought bubble on the bacteria reads "Heh heh, I just peed."


I'm beginning to think that I should spring for a USB graph-pad so that I can more easily post the doodles and sketches that many of the concepts I write about revolve around. For example, I was thinking today and I realizes just how cool it would be to have a giant fire-breathing robotic chicken. Not for doomy purposes, but for awesomeness. I, for one, and probably the only one, find that it'd be really cool to pilot a giant fire-breathing robotic chicken down the street. And I wouldn't even have to wear shoes!

17 October, 2007


So I was wondering today about anti-chickens. Immature as it may be, I still find it funny whenever people are talking about antibodies and say things like "IL-8 goat anti-chicken". So it set me to wondering what an anti-chicken would be like. In physics, an antiparticle has exactly opposite properties of its corresponding particle, e.g., electrons and positrons. So, given that the defining properties of chickens include:

1) Feathers
2) Beak
3) Wings
4) Tastiness
5) Eggs

Then it would stand to reason that an anti-chicken would have neither feathers, beaks, nor wings, and would taste terrible (or taste so good that regular chicken would then seem to taste horrible) and definitely not lay eggs. Hence the sudden germane application of the doodle above (was drawn about a year ago on statistics notes).

Note: Eventually I intend to start doing a weekly nerd cartoon on this blog.

15 October, 2007

Pimping Music #1

So this is going to be very, very rare, only done in those cases in which music is supportive of nerdiness and science. Basically, there's this band, and they're called Pornophonique and I think that they're so nerdy it's cool. They took a guitar and an old Nintendo console and make music out of it, and they make music about nerdy things. Songs such as "Sad Robot" and "Take Me to the Bonuslevel Because I Need an Extralife" make me happy to be in the know of such nerd esoterica.
Seriously, here's their website, and here's where you can Bittorrent their music for free.

02 October, 2007


Take that, Occam!

I do believe that, by applying maximum parsimony to a massive human endeavor, I have discovered the
true nature of science of all sorts and kinds and shiny-nesses. Simply put:

Theorem: Science is the technique of sticking stuff that wasn't made to be stuck to stuff to stuff that wasn't made to have stuff stuck to it, and the art of trying to figure out why.

Now, being a scientist, I've got to go try to find some contradictions to the above postulation.

27 September, 2007


I was speaking today with a "colleague" of mine about self-experimentation, and she at one point in the conversation she remarked that she thought that "Why the hell are we becoming scientists? I mean, you and I, we are the worst people to be scientists!".

I took umbrage. Lots of umbrage. True, that I sometimes wonder what the nutritional value of my reagents are, or what it feels like for a gastrointestinal epithelial cell to be colonized aggressively by an invading and effacing pathogen. And all she did is blather on about vanillin stains smelling good.

24 September, 2007

LINK: (1>3)-B-D-glucan

Awesome summary post here at Drugs and Poisons. Take that, Charles River Endosafe!

23 September, 2007


There doesn't really seem to be much of a scientific consensus regarding self-experimentation. And when it does happen, people don't like to talk about it much, it seems, like the scientific community is mildly embarrassed by these few brave individuals who are so passionate, or nutty, about their research that they decide to become test subjects themselves. The PI of the lab I work in got really sick, with horrible gastritis a while ago, and she was excited about the whole thing because she thought that she might be the very first case of lab-transmitted H. pylori infection. Or, at least, accidental H. pylori infection. Dr. Barry Marshall once drank a culture of H. pylori to demonstrate that it did indeed cause stomach ulcers and gastritis. It did, and he got a stomach ache.

The prompt of this post is in a research article I was reading:
Relationship between Plasma Levels of Lipopolysaccharides (LPS) and LPS-Binding Proteins in Patients with Severe Sepsis and Septic Shock; Steven M. Opal, Patrick J. Scannon, et al.; The Journal of Infectious Diseases; 1999; 180:1584-1589

"Administration of endotoxin to humans in minute quantities (2-4ng/kg) precipitates typical signs and symptoms of clinical sepsis, activates the complement and coagulation systems, and triggers release of the proinflammatory cytokines. Injection of larger doses of endotoxin (~1mg) into humans has been followed by severe hypotension and multiorgan dysfunction within 2 h of intravenous administration. "

The part that caught my eye was "endotoxin into humans", and I couldn't help but wonder how the bloody hell they ever got that protocol approved, and how much did they have to pay the volunteers? So I flipped to the reference:

Brief Report: shock and multiple organ dysfunction after self administration of Salmonella endotoxin; daSilva AMT, Fromm RE, Chuidian FS; New England Journal of Medicine; 1993; 328:1457-60

The difference between a fool and a genius is slim indeed.

21 September, 2007


Germ-free organisms are, by definition and title, inherently germ-free. Absolutely squeaky clean, from their skins to their guts to every other part of their insides. Normal organisms have normal gut bacteria and normal epidermal flora. Germ-free organisms have neither. This is what makes them useful for studying bacterial pathogenesis in isolation without interference from endogenous bacteria, or to study how the immune system acts without constant bacterial presence.

Germ-free organisms are tricky to make. First, they do a vasectomy on a male and put it into a cage with a virgin female of fertile age. Then nature takes its course. Mating doesn't result in procreation, but it does result in the female releasing a crapload of eggs (superovulation). Then a hysterectomy is performed on the superovulated female, and the entire uterus is dipped in Allcide to kill anything that might be on it before removing the sterile unfertilized eggs within it. Then purified sperm is added to the eggs, embryos are allowed to form, and then they are frozen. When needed, the embryos are thawed and placed into the womb of a fertile germ-free mother. And if all goes according to plan, germ-free babies are born into a germ-free environment. And thus the germ-freeness of a population continues happily. Of course, once there are enough of both sexes within the germ-free colony, breeding more germ-free organisms becomes a lot simpler. But the whole time, they're living in plastic bubbles.

Here's the thing though, and it really really really really really bothers me: no one seems to know where the first germ-free mother came from or how she was made.

19 September, 2007


I was scrambling through the bluff forest with the dog last weekend, and on a fallen log there sat a rather square-ish Tupperware container. As I drew nearer, I saw that there was a book and a pen inside. Still nearer, and I saw the writing on top of the container:
Blog = Book on Log
Belabored groaning at the horrible pun ensued.

12 September, 2007


1) Is it wrong that every time I hear someone use the word "biogas", even in an appropriate context, I can't help but laugh?

2) First you're supposed to be minutely detailed. Then you're supposed to be concise. Finally, it's all supposed to flow nicely together. Abstracts are a bitch to write.

3) Emphatic is a funny word. So is bubbly. Try saying them repeatedly very fast and you'll understand why.

09 September, 2007


N = Xn * Ds

N is equal to the local perception of normalcy
Xn is equal to the number of nerds within that given locality
Ds is the degree of social deprivation of said nerds.

Basically, this postulates that the greater number of nerds present in a given area, the more distorted the normal-ness of the reality within that area will be. This postulate assumes no dichotomy between nerds, geeks, and dorks, but rather assumes all to be equal.

This postulate is empirical. It may be proved by gathering a massive number of nerds, all very socially deprived, into one area (must be well stocked with high-speed internet, soldering irons, and lots of chemicals) and seeing what happens.

01 September, 2007


Although I once held Parafilm to be one of mankind's greatest inventions, up there along with cookies, the wheel, and fire, it has fallen in my regard. Turns out that our sticky little friend begins to melt at 60C, which is quite inconvenient. Also inconsiderate of it.

27 August, 2007

Goose Liver/Terminology Bastards #3

Note to self:

'Foie gras' is not pronounced "fooey grass", no matter how much sense it makes. Rather, it is pronounced "foy gra", with a snobby declension. I have also learned that 'matte' is not pronounced "matteh", and that people insist on saying "i-earn" when it is clearly 'iron', even though it sounds like "irun". This latter item I do no intend to compromise upon.


I dunno what they're actually called. But I don't like them. Around here they're referred to as "monkey suits", basically a one-use plastic smock with an open back panel and thumb loops. Doesn't matter if I'm sweaty or shiverring when I put one on, it only takes a couple of minutes before it is stuck to me with sweat. Yes, I know that it is to protect me from the stuff I work with, but that doesn't mean that it is pleasant to have sweat dripping down your arms and pooling in your gloves.

24 August, 2007

Terror of the Refrigerator

Och! The terror! When you walk into temp H.Q. and find a fellow lab member standing panicked before the refrigerator into which all of the lab's reagents and samples had temporarily been displaced. And when that panicked fellow lab member says to you that the outlet into which said refrigerator had been plugged had been without power, a bolt of pure terror surges through you. Luckily, though, all was fine. The lab tech's pack-rat habit of storing massive numbers of cold-packs in the refrigerator turned out to be our saving grace, and all of our reagents and samples are intact.

23 August, 2007


Sure, blame the moose. Awful easy to dump all the blame on something that can't speak up and defend itself.

22 August, 2007

1) Spam, and 2) Casserole

Not related in this post. Possibly related in a distant relative's infamous potluck dish, but not here.

1) Spam
Sometimes I get really excited about the spam I receive. My email account lies behind a really tight spam filter, so the stuff that gets through is usually really good. My favorites:

A) "Cohomology Bedspring Coronet" by Heidi Valentine:
betoken brookline concurring caspian. dither cork canadian armistice canticle
clarence. cry adsorb algonquin begrudge dart classroom b's amnesia defunct.
allotted cryostat arpa cession damascus cluck ace.

B) "Points" by Nagihan Fadum:
Proveedor local norte, sur.
According, survey released monday ea nc state engineer creates. Aviso, ofrecemos nuestras, disculpas esperando.
Explorer browser lions share. Apuroscom que la nuestros clientes. Standards believe guess texts.
Until connect postponing date as follows. Wooden crate enhances greeting invitation, youquot adventure impression. Token securable, objects registry keys. Addin attempts append, existing. Shell longer capable advisory posted turned exclusive. Music app because xmms masked, amhot cant. Xamps shrine xs aso ve! Shoes also be sure collection, unique method. Metravel homelawn videosget playgolf boat demandone schedule biggest. Santa mnica colinas valle.
Level looks senior fanatic freak, addict.
Proceso, formas pago cupones descuento.
Stateold protocols gopher telnet scriptlets xbm channels cdf dhtml. Isminie, itvar clipid title barometer cherry, blossom. Franais srpski espaol trke today wednesday march enemies.
Pleased th millionth millionen downloads mayhew reaching partners.
Process set work, me.
Acl interface isolation uipi blocks hook attach higher?

C) "
Well, the first thing you need to do is figure out whether it's a legitimate program showing traces of malicious behaviour." by Boran Juuuu
Gireiev glanced up at the wall.

These types of messages fascinate me, in some kind of odd way. How are they made? Who makes them?

2) Casserole

I think that sometime I would like to bake a casserole inside of an Erlenmeyer flask, and make it all the nastiest bacterial colors that I possibly can, just to see if people would dare eat it, even when obliged to by politeness.

13 August, 2007

LPS and Intellectual Property

No, the two titular nouns aren't related, at least in this post. Instead, they're bullet points:

1) LPS
Arg the stuff! It's everywhere. Everywhere! Even in endotoxin-free water.

2) Intellectual Property
So I wound up raising a little bit of hell the other day on an Alternet article. Basically, I asked whether or not the public should have a say in how the public funds for medical research are distributed. The responses were...interesting, and thought-provoking. It was, for one, pointed out that the public already does, theoretically at least, have a say in how funds are distributed through the voice they elect in their elected voice people. But this process is so obscure and convoluted that public funds for medical research are, fundamentally, completely in the hands of the agency that dispenses them and therefore subject to whatever dark processes or technical idiosyncrasies that the agency sees fit to impose. There is also the problem of everyday, non-nerd people understanding the highly detailed and technical knowledge needed to comprehend science itself and appraise it. This is very much exacerbated by the common inability of scientists to communicate without resorting to esoterica and jargon.

Representatives! That's what elected voice people are called...

Nonetheless, all of this also drew in the question of intellectual property and how it is defined and used. I mean, as a scientist, if I worked really hard on some kind of knowledge, quantifying, statisticifying it, etc., I'd be rather very much pissed off it someone else came and looked at my datas and scooped them and beat me to publication and got all the credit for my hard work. Publish or perish! But this is what supports the whole current structure of science, in which we guard our projects kind of closely (especially from other institutions) while closely collaborating with a select few within the same, or closely-related, institution. In addition to this, new knowledge is submitted to august journals for peer-review. While peer-review is necessary for making sure that research is kept up to quality and accurate and real, it also hinders the conversion of knowledge into practice and possibly also the rate at which science, and hence understanding, progresses as a whole.

Let us, for a moment or two before laughing at it, consider the possibility of a massive research wiki application. Scientists could got there to upload their findings and other scientists could read those findings and, as such, be up-to-date on the cutting edge continually, instead of having to rely on PubMed (not dissing PubMed, just saying that it can be a bit cumbersome at times, like a lovable fat aunt, but then, I guess that the wiki proposed above could wind up being a lot like a spastic, hyper-caffeinated troop of twinned monkey children). Would science then go faster? Would technology follow faster? And, most importantly, would improvements to the average quality of life for non-scientists and average people be faster?

But, on the other hand, how would grant funding be decided? How would the role of intellectual property change? How would scientific accreditation change? Would the profit motive (here, more academic recognition than cash) change for scientists? And in the end, would this be like changing in cookies and milk (PubMed) for Red Bull and coffee? Or does chaos theory hold that even hyper-caffeinated monkey children will eventually move together to create some kind of Electric Slide Dance order?

And I'll leave you with that, the mental image of spastic, hyper-caffeinated, twinned monkey children doing the Electric Slide.

08 August, 2007

Where Does Humanity End and Begin?

Another thing I wanna know. Let's suppose that it becomes possible for humans to integrate synthetic/mechanical machinery/technology into their very bodies and/or minds. A person with an extra mechanical arm or data storage where one of their lungs used to be would obviously still be considered to be a human. However, would a being that had modified themselves to such a point that any remaining flesh was purely vestigial and not contiguous to the continuation of their consciousness be considered a machine, human, or some other sort of being?


So, for furtherance of one of the things that keeps me awake at night wondering about things (see below), I think that mitochondria would sound something like a washing machine filled with Jello and power tools on the wash part of the cycle. Maybe throw a hedgehog in there too to make it sound right.

The 3 membranes makes imagining their sound difficult.

The washing machine wash cycle "chug, chug, churn, churn, chug" would be more or less the continual flux of electrons through the electron transport chain. The Jello only makes sense because the mitochondria do, after all, contain cytosol-like stuff. The power tools for the shunting of materials and supplies across the membranes, including the spinning off of ATP (that'd be the buzzsaw). And the hedgehog to introduce a dimension of chaos (yo biology!) that would otherwise not be present.

05 August, 2007


While I am still very much pissed off about the House of Representative's failure to take meaningful action on CAFE standards for the auto industry, I would like to, in the meanwhile, suggest that auto makers try a different tack. For the past several years, Detroit has been focused on making cooler-looking cars with cooler gadgets and more cupholders. Instead, why not add actual content-based value to a car?

For example, I would very much like my car to be more like my dog. I would like to be able to walk outside and call for my car "Here, Betty!" and have it come to me, like a good dog. I would like to be able to tell my car "Fetch groceries!" and have it go do that for me. I wouldn't even mind if the car insisted on cleaning itself, although rolling over would present a bit of a problem.

04 August, 2007


* from the previous post

* = thought of in the course of writing the post

Things I Want to Know

These are the kinds of things that keep me awake at night, pondering and pondering.

1) My parents had a pool installed in the back yard when I was a teenager. Soon after, I found myself wondering how much Jello mix it would take to fill the pool with Jello (answer: about $1,200 worth, given Jello at $0.30/pack). I figured that in the fall, there'd be a day when the temperature would be at around 40 degrees, and the pool had a heater, so I could mix in all the Jello mix as directed. Unfortunately, I was never able to put this experiment into practice, so the question still plaguing me is: If I were to belly-flop in to a pool of Jello, would I a) bounce back, b) land flat, or c) sink into the Jello?
I even tried using physics for this. I mass about 60 kilos (z) and have a ventral surface area of approximately .66 square meters (y). If Jello has a surface resiliency of x, then so long as I zy doesn't exceed xy, I shouldn't sink in. But that still doesn't tell me whether or not I'd bounce or land flat.

2) Do M.D.s actually use the term 'booger', or do they have some kind of complex fancy term for them, like 'congealed mucus globule'? Doctors are strangely unwilling to answer this question when you ask them.

3) If one were in incredibly dire straights, could one survive on pure high fructose corn syrup? Or would its osmolarity spell doom (although neither HFCS nor osmolarity actually spell D-O-O-M or can be reconfigured to say so)?

4) What are the ethics of android sex? I mean, eventually technology is going to produce rather sentient and human-like machineries, so will it be ethical to also give those androids sex drives even though they would, at a nominal assumption, be unable to procreate thereof (that's a whole other issue)? And if so, would they discriminate from one another on a basis of voltage? And, furthermore, would gender differences arise in androids? If so, would they be the result of different programming structures or of socialization?*

5) What if there's another Earth the same size and composition of ours orbiting exactly 6 months ahead/behind us? It'd be always hidden on the other side of the sun so we'd never be able to see it with our telescopes.*

6) What kind of sounds to mitochondria make? Or, for that matter, chloroplasts?

7) Wouldn't it be cool to build a gigantic (e.g., 15m high) mechanical chicken and pilot it to work everyday? And while at it, why not install some fire-breathing apparatus?

8) While I am relieved that terrestrial bacteria are microscopic, I can't help but wonder if, somewhere in the universe, there are massive, planet-sized Ur-bacteria? And wouldn't it be ironic if multicellular organisms lived on or in them?*

9) Would perchloric acid be spicy or sour?*

10) Let's pretend that there's a giant catapult, say, with the fulcrum in Hawaii and the launch arm ending somewhere in California. If one were to get into the basket at the end and launch themselves, would a) they launch themselves into orbit, b) fall off due to inherent structure instabilities that are inescapable at such large scales with present construction technology, or c) be crushed by G-forces and/or fried crispy by friction from air?

01 August, 2007

Philosophicality #1

I can wield a micropipettor.

I can wield a cello bow.

But what lies betwixt?

This is a question that often occupies my mind: wondering about the relationship between science and art. At the moment, the most obvious answer seems to be my fingers, without which I could not wield a micropipettor, cello bow, or toothbrush.

More upon this later...

27 July, 2007


I about freaked out majorly this morning as I was getting dressed and wasn't able to find my lab T-shirt. I was standing there pawing desperately through my closet, getting frustrated, because I had to go through a lot to get that T-shirt, and because it actually says "M.S., Jr." on the front of it, which is (obviously), so awesome I went and named my blog after it. But then I remembered that I accidentally left a load of laundry with some relatives (way too far away to conveniently drop by to pick it up, unfortunately [oh, why do I have such a hard time remembering how to spell unforetuneately?), about a month ago. And now I am hoping quietly that, when that laundry arrives, it shall also contain my lab T-shirt. Not the least because it'd be really awkward if there were to be some kind of laboratory activity (sunlight!) and I didn't have my shirt...

25 July, 2007

Practical Oddness

It seemed entirely practical to me.

Today I was in the lab, doing a crapload of serial dilutions of bits of murine gastric epithelia to culture the stuff growing on them and, as such, I was suited up in a big sweaty rubber lab coat and double gloved. In doing this, I had to maintain sterile technique at all times.

Problem: My glasses started slipping down my nose.

Dilemma: Neither my gloved hands nor my glasses could be assumed to be sterile. My hands might have been contaminated with pathogens, and my glasses might have been carrying crud in the first place. As such, I could not use my hands to push my glasses back up my nose. Nor could I use my shoulder as I do when I'm only wearing gloves because of the big lab coat.

Solution: Take off gloves, go find a piece of tape. Attach tape to bridge of nose and run it upwards to attach to the nose-piece of my glasses and then to my forehead. Then go back to work with glasses firmly in place.

However, my fellow lab workers found this immensely amusing. Maybe it was that the tape was neon teal. Or perhaps it was that I did it without any fan-fare and quietly returned to the procedure, such that they didn't notice it but through a double-take.

23 July, 2007

Statistics / Politicalish Rant

Mark Twain once wrote something about statistics being worse than lies. I guess that makes sense, given that statistics are like Play-doh, easily manipulatable, colorful, and not very tasty. Statistics have their uses, especially in science, for how else am I to determine whether or not the differences observed in optical density for different stuffs is significantly different or not, were it not for the Student's t-Test?

But statistics also have a dark side. A very, very dark side. Especially in the hands of those gifted with more loud words than brains to use them. Lately here in America, a bunch of Republican morons have been yammering on about how the solution to the so-called "immigration crisis" is to overturn Roe v. Wade, because those darned immigrants are taking the jobs that all those aborted fetuses would otherwise have taken.

1) The "Immigration Crisis"

Point blank, this is a bunch of bullshit. Furthermore, it's a bunch of racist, xenophobic bullshit. Those who spew this bullshit are inevitably assholes (pun intended), usually conservative. All of them claim that they are not racist, yet they continue to rail against how the "tide of immigration" is "ruining this great country".

Do these people forget every morning when they look in the mirror that they're pasty? More importantly, do they forget that pasty people come from Europe? Their ancestors were an "immigration crisis" for the Native Americans. Also, their ancestors participated in the wholesale slaughter (read: genocide) and disenfranchisement of Native Americans, all while oppressing an "inferior" race of people (who only counted as 3/5 of a person anyway).

Umm...last time I checked, Latin immigrants aren't rounding up pasty people and shooting them for being white and in their way. White people even catechized their weak moral justification for the genocide they perpetuated for their own narrow economic interests by calling what they were doing "Manifest Destiny" and "Westward Expansion". Well, Latin Americans aren't coming up here spouting out crap about "Northward Expansion" and how claiming "our" land as theirs is their destiny. So, either anti-immigration white people are suffering from a severe case of whitewashed historical amnesia or are participating in wholesale hypocrisy...

Frankly, I believe that the root of the anti-immigration rhetoric is a very basic fear of white people being numerically forced to assume minority status in this country. I posit that the gross majority of white Americans are fully aware of the extent to which minorities are marginalized, disenfranchised, and stigmatized in this country. As such, white Americans fear being forced into the very conditions that they helped create and perpetuate.

Disclosure: I am one of the pasty people.

2) Jobs

I find it safe to posit that the predominant stereotype of a white American in the workforce is of a white-collar worker in the information industries who sits in a cubicle and commutes to work from a suburban home every day. Now, I have gathered that the typical stereotype for a Latin American in this country is to be either bound by linguistic narrow-mindedness into low-wage manual labor, or as being lazy and welfare-dependent. How does one reconcile these two stereotypes with the oft-repeated claim that "Mexicans are coming here to take our jobs"?

Let's be honest here, this is scape-goating, and that's all it is. The economy, for average people, blows horse chunks, so average people find solace in blaming their economic problems on a subset of the population without a strong voice of their own: immigrant laborers. By all normal measurements, the economy is booming (didn't the Dow Jones just set some kind of new record the other day or something?), but the predominantly white middle class of America is finding itself increasingly squeezed by shifty financial circumstances. I guess it is far easier to blame the "lowly" immigrant than the government that allows the companies in this country to relocate labor as they please, hide their finances, and benefit from tax break upon tax break. After all, the immigrants are automatically assigned outsider status, whereas we don't entirely want to face the possibility that our own kindred elected are cheating us hand over fist.

3) Roe v. Wade

I feel like there's a certain odd moral arrogance to this part of the argument. But who's making this argument?

a. Promulgator of Anti-Immigration Rhetoric
- white
- upper-middle class
- well-educated (often by their parent's money), but this point may have been lost upon them
- suburban
- white collar
- conservative
- religious

Such a type of person often argues that the type of person to have an abortion is 1) immoral, 2) poor, and 3) likely to remain poor. Therefore, it seems that there is a tacit assumption in this argument that we wouldn't have immigration if we didn't have legal abortion and that those fetuses who were aborted would have been born into low-class families and subsequently forced into low-wage, manual labor, which it seems are the jobs that are currently primarily filled by seasonal immigrants. But who is to say that all of those aborted fetuses, born to families that didn't necessarily want them, wouldn't turn out to be criminals that would, in turn, prey upon the suburbs? Or, even worse, aspire towards higher education and the liberal ideals that it often fosters?

As a closing aside, doesn't it make a lot more sense to try to reduce the need for abortion, by increasing the availability of contraception and comprehensive sex education, than to ban it outright?

17 July, 2007

Lunch with Microbiologists

The general populance needs to grow up.

Organisms get sick. Sometimes they die. And most are filled with mushy networks of organs and other various liquids and goos.

But the general, non-biologically-inclined, public seems hellbent on ignoring the most basic aspects of their own constitutions. In general, people wait until something is wrong and then go to a doctor and treat them like a plumber for a quick fix, like some lug nuts and a prescription can cure anything. It seems to me that it would be much wiser to go ahead and learn about the workings of one's own body in the first place so that the states of health, disease, and the various shades between can be better recognized and dealt with.

But maybe that's unreasonable, that'd require comprehensive and well-funded science education, as well as curiosity and a willingness to learn.

Or at least to be less squeamish. I've found that people in general really hate it when they're reminded that the meat on their plate came from a living animal, as if it reminds them on their own animal-ness somehow, or their responsibility in the death of another living organism despite their vaunted culture and whatnot.

So basically, I was at a joint lab lunch today with a bunch of animal researchers and microbiologists. Didn't happen today, because the restaurant was kind of empty and our table was kind of isolated. But to hear these more experienced scientists recount the disgust with which non-scientist people greet their work-related discussions kind of bothers me. I could understand a table of non-scientists getting up and walking away if we were gleefully debating the best ways to exsanguinate a mouse or to homogenize a tissue as though they were activities we look forward to as if they were cookies. However, in general, scientists discuss their research in respectful tones, and obfuscate their topics with jargon. But as soon as some soccer mom hears about taking fecal samples or sections of the anthrum for histology, she suddenly loses her appetite. Is it really so disgusting to be reminded that living things poop?

I guess that is one of the "greatest" talents of the human animal:

Collectively, we dupe ourselves into believing that we are beyond biology simply by grace of being human. Somehow, being human means trying really hard to ignore poop, pee, sweat, smegma, snot, puke, spit, and any of the various fluids produced by our genitalia. And we take it even further with our obsessions over clothing and shaving and hair styles.

A dog simply doesn't care if its hair is fashionably stylized so long as its not uncomfortable. Most bodily secretions provide very useful information to most animals. But we hide all of ours away to the point where we have deluded ourselves to the point where we think we are completely separate and above nature. How convenient it is to forget that the food on our plate, be it flesh or vegetable, was grown out in a field somewhere, nourished by the sun and soil! I guess that doesn't much matter though, when >50% of our body mass came from high fructose corn syrup...

14 July, 2007

Sprachliche Herrschaft (Lingual Dominance)

Manchmal muss ich bedenken, die Herrschaft von der englischen Sprache ueber Wissenschaft. Und nicht nur Wissenschaft, sondern ueber die Weltwirtschaft und Weltpolitik auch. Warum ist die herrschenden Sprache Englisch anstatt einer anderen Sprache? Ja, stimmt, dass Grossbritannien fast die ganzen Welt erorberte, und sie sprachen ja Englisch.

Aber ich will nicht die Geschichte der Herrschaft nicht untersuchen, sondern die Erfolgen. Gibt es eine eigenen Beschraenkung, wenn eine Sprache alle andere Sprachen uebernimmt? In Wissenschaft? Waeren wir alle besser mitteilen, wenn es eine Sprache fuer Wissenschaft gaebe? Wie Esperanto? Waere das eigentlich besser, oder haben wir solche Umstaende schon mit die Herrschaft der englischen Sprache?

Und ich koennte noch weitere Fragen nach diesem Problem werfen, aber ich kann keine davon antworten, nur retten...

Sometimes I have to ponder the dominance of the English language over science. And not only science, but all of the world-wide economy and world-politics as well. Why is it that the ruling language is English instead of another language? Yes, it is true, though, that Great Britain conquered almost the whole world and that they spoke English.

But I don't want to examine the history of this dominance, but the consequences. Is there an inherent limitation when one language overtakes all other languages? In science? Would we all communicate better if there was a single language for science? Such as Esperanto? Would it be actually better, or do we already have such a situation already with the dominance of the English langauge?

And I could throw further questions at this problem, but I can't answer any of them, only guess...

Und ja, ich weiss schon gut, dass meines Deutsch sehr schlecht ist, aber ich will mich nicht nur zu einer Sprache einschraenken. Und hier muss ich mich wundern, ob es eines wirklichen Ziel dazu gibt. Fast die ganzen Welt spricht Englisch schon, so warum soll ich mich besorgen, um eine anderen Sprache zu lernen? Aber ich glaube mir, dass solch einen Blickwinkel nichtwissentlich ist und die Welt gar nicht und wird nie helfen. Und das, dort, kehrt mich sehr oft. Wie koennen wir, als Menschheit, zur Frieden arbeiten, wenn wir auf allen Linien und Massstaben verteilt sind, und dort sturr bleiben wollen?

And yes, I know very well, that my German is very bad, but I don't want to limit myself to one language. And here I have to wonder, whether or not there is a real goal in doing so. Almost the entire world already speaks English, so why should I go to the trouble to learn another language? But I believe that such a viewpoint is ignorant and does not and will not help the world. And that, there, bothers me very often. How can we, as humanity, work towards peace when we are divided on all lines and measurements and want to stay as such stubbornly?

Und dort steht es, klar und dunkel, eine die haupten philosophischen Problemen, mit denen ich strafen:
Wie kann ich, persoenlich, Wissenschaft nuetzen, die Welt zu verbessern? Wie kann ich anderen beeinfluessen, ihre Wissenschaft fuer Weltverbesserung zu nuetzen?

And there is stands, clear and dark, one of the primary philosophical problems with which I fight:
How can I, personally, use science to better the world? How can I influence others to use their science for world-improvement?

Es ist wahrscheinlich nicht viel, aber ich glaube mir, dass es, am wenigstens, ein bisschen helfen kann. Jeder soll eine anderen Sprache lernen, sprechen, und nuetzen. Dadurch koennen wir als Menschheit vielleicht sich einanderen besser verstehen, und durch diese Verstehung kann eine groessere Zufriedenheit entstehen...

It probably isn't much, but I believe that it could at least help a little bit. Everyone should learn, speak, and use another language. Through this it is possible that we as mankind could understand each other better, and through this understanding a greater happiness could come into existence...

(note: this post was written piecemeal extemporaneously in German and translated freestyle, but accurately)

07 July, 2007


While driving through northern Chicago the other day, there was a traffic jam. We made literally 2.5 miles in 2 hours. The reason behind this traffic jam was that a truck laden with pig offal had spilled, and they were trying to clean up the mess while diverting traffic around it. So the highway was strewn with pig grease, pig snouts, tails, and hooves. And if only lightning had struck in the right way, there'd have been an undead army of reanimated pig conglomerates shuffling around Chicago right now. Or it would have caught on fire, and that would have been even more nasty...

26 June, 2007

Necropsy Practice

This is a rather smelly organ. I managed to puncture one today while practicing necropsies on mice and it oozed out of the too-deep cut I'd made into the peritoneum, sloshed down the side of the mouse and pooled in the Petri dish beneath. I've observed dissections of pathogen infected mice, and it seems that Vibrio cholerae kind of turns it into a watery, even fouler-smelling mush.

Enjoy your dinner.

23 June, 2007


I wish there were more robots in science. Growing up, I was inundated with tales of robots sealed in sterile rooms doing dangerous science experiments hundreds of times faster than a human could do. Multi-pipetting robot arms. Media making thingamazoos and other cool machines. But, working in science as an apprentice mad scientist, I find myself disappointed. Where are all the big shiny robots, just anthropomorphic enough to remind us of our own fragility? Where are all the fancy humming machines with levers and swirly-gigs and doo-dads, lights and pinging noises and lots and lots of brightly colored, even backlit, buttons?

Simply put, what is it about the commercial nature of science today that standardizes it so much that scientists don't get to feel as special and smrt?

More on this later...

22 June, 2007

Terminology Bastards #1&2

1) Shiga toxin
Make up your minds, microbiologists!  First you're calling it Shiga toxin and abbreviating it Stx.  That was fine.  So was the classification of Stx-1 and Stx-2.  These are structurally different, and as such, that's cool with me.  But then came along such terms as verotoxin, which is apparently the same thing, and SLTs.  SLTs are Shiga-like toxins, but when these terms are used, the scientists writing these invariably fail to adequately differentiate them from Stx.

2) APC
Here's one that the whole world needs to agree on.  APC stands for WAY too many things.  Antigen presenting cell.  Adenomatous polyposis coli.  Anaphase promoting complex.  Activated protein C.  Armed Proletarians for Communism.  A Perfect Cirlce.  Association for Progressive Communications.  American Plastics Council.  American Pie Council.  Attoparsec.  Automatic performance control. Adaptive predictive coding. Advanced process control. Alternative PHP cache.  Armored personnel carrier.  Average propensity to consume.

21 June, 2007

Funny Word #1

Avail is a funny word. So is aardvark.


OK, forget about it. This is the point at which I am abandoning the old template of this blog. I could write lots and lots of molecular bioanthropomorphisms, but at some point they'd all begin to start sounding the same. This is only to be expected, and in retrospect, I should have seen it coming, because the principles governing life at a molecular level are few, basic, and more or less universal. There're just millions upon millions of alterations to an over-arching and evolutionary-conserved rubrics.
So, this now becomes a blog about other stuff. Most likely thoughts and rantings about science in general, but we shall see as time progresses whether or not that remains true. However, it is safest to assume that the null hypothesis is true.

26 April, 2007

Metaphorical Molecular Riddle

The trapeze artists are at war, yet the net result is peace.

They cry at each other, 120 times over, "NACTI! NACTI! TINAC! NACTI!"

Individual soldiers came and went, more remain than gone.

While their weapons repeat beyond their shield 5 to 6 times.

Their weakness lies in the happy 2 plus upon which all depend.

What system is this?

25 April, 2007


It's like one of those old Popeye cartoons.

Popeye and Bluto are fighting. p53 and Mdm2 are fighting.

Popeye and Bluto are fighting for Olive Oyl.

p53 and Mdm2 are fighting for the fate of the cell. It is an epic battle played out daily all over the world, being won and lost every single moment. p53's purpose is to make sure that all of a cell's DNA is properly replicated and not mutated before cell division may proceed. Mdm2 opposes p53 to keep it from clamping down too tightly upon cell division.

Although it may seem that p53 is antagonistic to life by opposing cell division, it is essential for our survival. In multicellular eukaryotic organisms such as we usually are, cell division is tightly regulated. Too little cell division and the organism doesn't work whereas too much cell division results in uncontrolled cell proliferation (also called cancer). So thank your p53. And Mdm2.

22 April, 2007

Multiple Sclerosis

On any other day one would find them standing close by, snug up against each other and glued in place to create an impenetrable wall. But today something is odd. As blood pulses, pushing at them from one side, they begin to lose grip, just a little bit, but it's enough. The endothelial cells panic. Normally it is their given purpose to protect the precious brain matter on the other side of the capillary, and they are failing. Collectively, they don't know what is going on, so they signal for help individually. Cell surface proteins are changed from cadherins to integrins and cytokines are wafted out into the blood, calling for macrophages to come and see what is wrong.

That was their first mistake.

As they always do, the macrophages quickly come sailing down the bloodstream, slowing down and rolling along the sides of the capillary until they reach the distressed endothelial cells, where they squeeze themselves between the loosened cells. Normally, macrophages cannot penetrate the tight barrier presented by the endothelial cells in the blood-brain barrier, but this is different.

Letting them cross was their second mistake, but it was one they could hardly help since something seems to be wrong with their adhesion factors in the first place.

Inside the densely packed brain matter, the macrophages are confused. This is tissue they've never seen before, it is strange and alien to them, usually closed off but suddenly opened wide for them to see. The macrophages know that that which is strange and alien means danger to the organism, and as such, they mount their normal innate immune response. The funny-tasting brain matter is blasted with oxidative chemicals as yet more cytokines are wafted out through the bloodstream.

Soon the side of the weakened capillary is crawling with immune cells. In addition to macrophages, there are now monocytes, neutrophils, natural killer cells, and dendritic cells. All that the former can do is blast the weird tissue with yet more chemicals and try to eat it, but it is the latter cells, the dendritic cells, whose appearance is most ominous.

The dendritic cells busily set up shop, ingesting pieces of the brain matter and swooping back out in the bloodstream. There they sneak out of postcapillary venules into lymph nodes and other lymphatic organs and, like mother birds regurgitating food for their young, spit those pieces of brain matter back up so that the developing, naive T cells and B cells can see and and feel it and memorize one simple fact: THIS IS OUR ENEMY!

The T cells and B cells go wild and proliferate all over the place. The B cells swell with antigens against the brain matter, and so does the blood serum. The T cells migrate to the site of weakened blood-brain barrier and join the macrophages and others in bombarding the brain matter with pro-inflammatory chemicals in a concerted effort to destroy it. The B cells' antigens mark the brain matter for destruction, and phagocytosis sets in.

The oligodendrocytes of the brain matter are confused, hurt, and reeling from the sudden onslaught of the immune system. Collectively, they teeter on the edge between survival and apoptosis, and unfortunately many of them fall to apoptosis, disrupting the normal course of electrical signalling in that part of the brain.

Eventually, the endothelial cells of the blood-brain barrier recover and rejoin to once again deny the immune system access to the brain matter. So the immune system lurks outside, ready and muttering to itself, while the brain matter inside ineffectually tries to heal itself, recovering to some degree, but nonetheless still bearing deep scars.

13 April, 2007

Cubitus Interruptus

Pity poor Cubitus interruptus. If you are here, and reading something such as these words, then you can identify with poor, scrawny Cubitus. Every day Cubitus was held down by the other big kids, like Fused, and backed up against a microtubule as he was beaten again and again, degraded time after time. All that Cubitus ever wanted to do was run away to the nucleus to play with his imaginary friend, CSL, but alas, Fused kept him away every time.

The all-seeing Patched saw all that happened to poor Cubitus, every time, and did nothing. Patched only sat there imperiously, watching with a cold hard and an even colder grip on Smoothened's shoulder. You see, Smoothened had a kind heart, and would gladly have gone to help poor Cubitus by disrupting the bullying actions of Fused, but Patched restrained her.

Then one day Hedgehog came along. Hedgehog snuck up alongside Patched and all of a sudden sank his spines into Patched.

No one knows why Hedgehog did it.

Nonetheless, it gave Smoothened that one opportunity she needed, and she darted away and shoved Fused off of little Cubitus. Cubitus, finally free of Fused's blows, immediately darted away to the nucleus to frolic with his imaginary friend and was happy ever after.

Moral: Smoothened is nicer than you think. Patched is a bitch.

02 April, 2007

Signalling Poem 1

A steroid receptor receives
A protease cleaves

A ribosome makes
A proteasome breaks

GPCRs stimulate
Within the cAMP appelate
Although PDE hates
What adenylyl cyclase makes
Together they speak
In a molecular feat
Signals from outside to in

When one shoves the other
The other shoves back
Although the cAMP'd druther
Avoid the PDE hack
But a balance is made
And a signal is sent
Action potentials laid
Or secretory granules rent
And communication is.

20 March, 2007

Bad Dog

It was a bad dog. An unruly one, to say the least. No matter how the scientists tried, IGFBP-5 just wouldn't behave properly. They tried gene knock-outs, knock-downs, and morphelino-RNA. But to no avail. First IGFBP-5 wouldn't stop carrying insulin around. And then it wouldn't pick it back up, unless it wanted to. IGFBP-5 never followed any commands. One moment it would be bound to the extracellular matrix, the next it would be bound to cell-surface integrins or in the nucleoplasm.
And the mess it left behind! In some places it would stimulate cell proliferation, in others cell motility. And then in yet other places it would inhibit those very same things!
Ultimately, researchers concluded that IGFBP-5 wasn't a dog, but a mule.

23 February, 2007


Trouble was afoot in the sticky wastelands of the cytosol. The plasma membrane sky was turbulent overhead, sphingomyelin rafts swirling faster than normal as ear-splitting explosions rattled down the signal transduction cascades, amplifying as they arced off towards to distant mass hovering on the horizon. Something wasn't right there, either. The nucleus had been hurt badly in the last infection. It's latticed double envelope still bore the oxidative scars of the inflammatory reaction, the translocons feebly trying to properly refold with half of their functional domains blasted away. The mitochondria were rumbling, louder than normal, but perhaps they only seemed the louder because the endoplasmic reticulum and Golgi stacks were uncharacteristically quiet.

It was dark. Almost all the ATP had been hydrolyzed in the Inflammation, and now the mitochondria weren't producing any more--glucose and lipid transport had all but ceased. Even though they were still rumbling away...

This city was in trouble, and it knew it. The nation's dark Bim messengers were gathering quickly, clustering in ominous clouds with their Smacs while the wounded Bcl-ws could only drift aimlessly amid the sticky desert, observing.

Another explosion rattled down the signal transduction cascades, and with it phospolipid translocases began to fall in slow-motion, plunging into the boiling recesses of the peroxisomes. But this explosion didn't head towards the beaten nucleus; instead it flashed right into the hovering Bim/Smac clouds. A critical threshold had been reached...

The gloomy flocks rapidly dispersed and swarmed the mitochondria, diving into their wrinkled surfaces and rending their membranes. The mitochondrial rumbling rose in pitch, becoming a tortured kind of scream as the oxidative hellions broke loose of their matrix prison. Capsase and cytochome c erupted into the cell, colliding chaotically with everything else inside the cell, shattering the fragile secondary structures and motifs with their destructive oxidations.

The city was awash with the death-cries of the wounded. The nucleus gradually imploded, caving inwards and collapsing into the flailing centrioles and endoplasmic reticulum. The integral proteins of the plasma membrane sky plummeted further downward, rending the sticky desert with their cries as massive holes opened up in the sky and neighboring cities began to suck up the rubble, even before the city had been completely destroyed.

Within minutes, it was all over. Everything was gone, and it was as though the city had never existed in the first place...

19 February, 2007

Endocrine Stuff

While pondering a post up at Alternet about how widespread endocrine disruptors are in modern society, I wrote the following in response:

Humans are, more or less, nothing more than tottering sacks of chemicals in the first place, so it is only natural that we would seek to augment the messiness of our own chemical nature with chemicals of our own making.

But in the meantime, take some more chemicals!

Are you concerned that your little boy is too full of antiandrogenic chemicals to become virilized to the full extent that he otherwise would? Then shoot the kid up with some extra testosterone (warning: acne, aggressiveness, shrinking testicles), aromatase inhibitor (warning: not guaranteed to work), or luteinizing hormone (warning: may exacerbate effect)!

Think that your breasts haven't developed to their fullest capacity? Then shoot up some human chorionic gonadotropin (warning: may induce nausea), prolactin (warning: may stimulate lactation in addition to breast growth), or oxytocin (warning: addictive)!

Do you suspect that your metabolism is too slow? Then take some extra thyroxine (warning: may cause eyes to bulge out, irritability, shakiness, persistent feeling of cold, and trouble sleeping)!

Do you feel fat? Then perhaps some extra glucagon (warning: may mimic and/or cause diabetes) is right for you! Shed those pounds away as the breakdown of glycogen, lipids, and proteins is stimulated and converted to energy!

17 February, 2007

Multicellularity and Cytoskeleton

It was a curious city, to be sure. No one knew quite why, but for some arcane reason the entire city had been built upon wheels and stilts. To be sure, this city-wide mobility had its advantages, as it could always migrate with the weather and in search of food. The only problem with this design was that the designers hadn't had any clue as to how to keep a city from wobbling and shaking and to keep all the parts staying in place in the same place all the time. And as a result, a good many of the townsfolk of this city spent most of their time running around from one part of the city to another, building ladders and struts and wheels where needed and disassembling them where they were no longer needed. On top of this, a good 2/3 of the city was constantly occupied with throwing things over the city walls and hauling other stuff in. As such, the entire city was in a continual state of rushing movement, although it was also peaceful.

So the city rolled along across the landscape with its attendant army of scaffold engineers. Often the watchguards would see something on the horizon and yell back to the entire town that food was near. And the cry of food would travel on down the chain of communication until even the scaffolders heard. And they'd turn the entire city around, and shamble off in the direction of food.

This arrangement of a moving city was all good and well until one day the moving city ran into another city on wheels. Suddenly there was competition, as more and more of the ground-dwellers up and built themselves rolling cities. Soon the field grew so crowded that some of the cities began to band together and pool their cities, although they kept their individual walls intact. The newer, bigger cities were more efficient, although subject to frequent subterfuge by single cities. Nonetheless, they prospered and grew larger and larger as more multi-cities fused together and began to stretch farther than any of the inhabitants had dared to dream. However, the sprawl had a limit as to the benefits it offered every city. Soon, a trade-off between size and efficiency had to be made, and so each city began to specialize.

Eventually this led to the emergence of nations, and since then the world has never been the same.

15 February, 2007

Clathrin-Coated Vesicle Formation

Once there was a nice neighborhood, it had abundant nutrients and metabolites, and all was well.

That is, until one ominous day something happened outside of the neighborhood wall. That day a signal slammed into the wall and caused one of the wall's embedded signal detectors to start blinking ominously.

And then it happened again, and again.

And soon there was a whole row of ominously blinking signal detectors, screaming to the inhabitants of the quiet neighborhood: "HEY! SOMETHING IS HAPPENING HERE!", and of course the inhabitants quickly sat up and took notice. So they sent their clathrin pets to investigate the disturbance, and they quickly removed that portion of the wall, and packed it up nicely so that none of the disturbance could leak out and disturb the otherwise undisturbed neighborhood.

The wall quietly sealed behind the clathrin pets as they clung to the blinking signal detectors and fetched them for their owners.

Once inside the neighborhood, the pets, being forgetful, as is their wont, quickly became distracted by other shiny things and dropped the package and left it up to the inhabitants of the neighborhood. They gathered around and thoughtfully thought about what to do, and then some of the inhabitants realized that they had equipment was of the right configuration of deal with the disturbance, so they quickly hauled it off to their neighborhoods and took care of it.

And then the neighborhood lived quietly ever after...

That is, until the next time.