Aside: Perl

I am trying to learn how to code in Perl. I am doing this because I find computational biology and mathematical modeling of biology to be intensely interesting. However, writing meaningful programs is currently a bit beyond my abilities. So, I submitted a variant of this as a joke to Thinkgeek. I thought I might post this for all of your enjoyments/amusements.

#!/usr/bin/perl

print "Who is awesomer (you/me)? ";
chomp($base = );

if ($base eq you) {print "Correct, you can has cookie.\n"};
if ($base eq me) {print "Fail.\n"};

If you should wish to actually run this program (for whatever bizarre reason), then:
1) Copy-paste into Notepad or a simple text editor (not MS Word).
2) Save somewhere you'll remember it at.
3) Access the folder you stashed it in from your command line using the \cd function.
4) Type "perl filename" (filename = whatever you named it) and it will run (this'll work natively in a Unix system [Mac]{I think}, might be more difficult in a Windows environment, where you'll need a Perl module installed).
5) If you want to alter it to help boost your self-confidence or momentary feelings of awesomeness, then you can alter the pieces following in bold.

#!/usr/bin/perl

print "Who is awesomer (you/me)? ";
chomp($base = );

if ($base eq you) {print "Correct, you can has cookie.\n"};
if ($base eq me) {print "Fail.\n"};

For it to work, red has to match red and blue has to match blue, letter for letter. And the space after the question mark is important, so don't delete it.

I think this qualifies me as a script kiddie. Which I don't think is too bad, considering that I'm trained as a molecular biologist and all.

Zombies #2

I drew a zombie.

Let's start with some claymation fun:

There have been several fictional interpretations of what a zombie is, how scary they are, and how they can be killed. These interpretations range from normal people unwittingly compelled to do evil at the behest of some kind of evil magic to shambling monsters with intact consumer instincts. I am not going to lie and claim that I have seen all the zombie films or media ever made, but I have seen several of them (I do still want to see this one). Therefore I am absolutely unqualified (although I assert that I don't need qualification to speculate upon fiction) to offer my commentary.

...

OK, I just started poking around the Internet and suddenly realized that I need to do more research before I can offer anything worthwhile for zombie biology. Meanwhile, I offer you my favorite short zombie comic story (the premise basically revolves around a bad-ass dentist who feels he is responsible for eradicating the undead hordes because zombies naturally rose every 100 years and dentists were the ones who made sure that most everyone in the last several decades died with intact teeth). It should be noted that the rest of the anthology is also quite good, especially "Daddy Smells Different". My favorite long zombie comic story depends on whether or not one would consider a sentient corpse-possessing squid-fighting worm to be a zombie. Actually, I guess one couldn't consider that as such because Wormwood lives on beer and not human flesh. So my favorite long zombie comic story is definitely Chris Ryall and Ashley Woods' Zombies vs. Robots (I will soon purchase Zombies vs. Robots vs. Amazons).

I don't know exactly why I shared any of that. Maybe I'm subconsciously trying to improve my geek street cred?

Anyway, for your safety I urge that you check out Max Brook's Zombie Survival Guide.

I will soon probably post more about zombie biology. To PubMed!

ZOMBIES kick Vampire ass!

Pro-feminist metaphor for daughters assuming own adult identity despite their fathers' inherent protectiveness and also about how fathers' dreams for their daughters are inherently subsumed by their daughters' own identities. From Romero's Night of the Living Dead (1968).

Once upon a time ago I think I posted something about vampires. This was a mistake only in that I did not respond to posting about vampires by also posting about zombies in proportion to the coolness that I find in each. Therefore there should have been at least 37 zombie posts to balance out that 1 vampire post. However, now I am deciding that I will assign each post now extra points for Hindsight so there should be about 3 posts total dealing with zombies until I forget about it. At the rate I post, you can expect the next post in about 4 months (I will, however, try to do better with posting more regularly).

Before I start, let's have levity with this parody of Kelly's YouTube "Shoes" meme by the Living Dead Girlz (I want to know if they do birthdays):


1) Zombies are much cooler than vampires. Sure, vampires have fancy castles and tight vinyl bodysuits. And more recently they have annoying tween franchises and sexy HBO shows (warning: annoying Flash on both those last links). However, vampires are less fascinating than zombies because vampires are us, just with fangs and sun intolerance. Vampires still have families (covens?), vampires still have political struggles and human desires. Vampires also have very specific weaknesses (sun, wooden stakes, silver) just as humans have very specific weaknesses (water, bullets, piano flurries). Therefore, I posit that vampires represent a cerebral extrapolation of the human condition whereas zombies represent a base reduction of the animal instinct extant and inherent in human culture.

Zombies are walking hunger. And they're not just walking hunger, but they are exclusively hunger. Animals need water, food, sleep, and shelter from the elements. Zombies don't need food, and they do not even pursue water, sleep, or shelter unless there happens to be food (us!) inside. And zombies are terrifying, in part, because they consume and are motivated solely by the pursuit to consume human flesh. In effect, the zombies are not just consuming human flesh (cannibals can do so as well) but, because they themselves were once human, they are consuming humanity itself.

Vampires feed off of humans, zombies feed on humanity.

Zombies are pointless. They have no desires except for consuming human flesh. They have no organization (excepting Land of the Dead). They have no communication and we are left to infer from this that they have no emotion. They are the shells of humans devoid of everything that we feel makes us different from animals and therefore they hold a mirror to ourselves and our civilization, and this is largely the source of their accompanying terror. We envision ourselves as being purposeful, as being sentient and rationally separate from our base needs. We envision our civilization as being a progression from the animal state and an improvement thereupon. But zombies show us just how fragile those sentiments are and expose the deeply uncomfortable truth about just how tenuous our society is from day to day.

Furthermore, zombies are practically indestructible. In all the zombie lore, the only way to destroy a zombie is to crush its brain (tasteful Flash). Vampires can recover from such injuries if they are returned to the coffin of their original grave, but they'll also curdle if left out in the sun. Vampires are almost as fragile as humans, but zombies are much tougher. Humans do a lot to forget about or hedge their bets against their own corporal fragility. We wear seat belts and helmets and use oven mitts, etc. Zombies need none of it and perhaps this is viscerally felt by us humans as not just the consumption of humanity, but the willing abandonment thereof. And if that is so easy (just get bitten!), then what point is there to humanity?

Humankind is much more terrified by an black abyss than by a dark forest.



I was originally intending to discuss zombie biology but have gotten sidetracked. This post is already long, so I will wait for another post. I will try to get it up sooner than 3 months from now.

Flying Spaghetti Monster

Photographic proof of the Flying Spaghetti Monster. Seen here reaching out a Noodly Appendage and creating Life in the form of an indeterminate metazoan embryo.

Images of Scientists

Why is it that all popular images of science invariably involve a white dude/tte in a svelte lab coat holding up a flask of some colored liquid and gesticulating at it with gloves hands? Sure, sometimes I'll hold up a beaker of agar to make sure that it doesn't contain a lot of bubbles or burny peely stuff, but I do NOT spend my whole day filling oddly shiny beakers with food coloring and discussing them with my colleagues.

Yet, in society, these images persist. I guess, perhaps, that these images serve to differentiate us scientists from everyone else. If we were shown with hand tools, then we might actually be mechanics. If we were shown with scalpels and forceps, then we might actually be surgeons. If we were shown sitting in front of our computers crunching data, then we might actually be accountants (they're almost as sun-starved as most of us). Beakers and mysterious colored liquids are sciencely! So are lab coats and wild gesticulation!

It would be much more accurate to show biologists, molecular ones especially, wielding micropipets and microcentrifuges, perhaps even gesticulating at a hot water bath or incubator. But, now that I think about it more, it seems that a micropipet just isn't as sexy as a 2L Erlenmeyer flask filled with grape juice. Therefore, I dare a supermodel to just try to make focusing a fluorescent microscope on a single strand of rhodamine-labeled actin look sexy! If Tyra Banks can't do it, no one can (maybe Iman). Suddenly it appears that I don't tune my fiancee's TV shows out quite as well as I had believed...

Uh...

Anyway, there are stereotypes about scientists that can sometimes be kind of accurate, at least part of the time. Let's examine them a bit:

1) Scientists wear glasses. This is frequently true, and perhaps even observed at a greater frequency than the general population outside the lab. However, it could also be true that those outside the lab are more likely to wear contacts to correct their vision.

2) Scientists have wild hair. This depends on what you could call wild. Most men in science maintain either conservative short hair or let it grow very long. I have yet to observe any hairstyle trends (beyond low-maitenance) among female scientists. It is possible that scientists are more likely to avoid going to go get hair cuts when they need one. It is also possible that scientists are less likely to brush out the bedhead in the morning.

3) Scientists are nerds. This is true. Mostly (there are always a couple of exceptions). Otherwise we wouldn't be scientists in the first place.

4) Scientists are all anti-social deviants who universally aspire to mad, crazed experiments. This may be true. We all have our moments where we indulge ourselves in a cinematic mad scientist trope. But by in large, scientists are just dangerous people who are better kept busy in the lab than bored on the street (consider: since scientists are generally inclined to want to know how things work, how safe would it be if all scientists were working from non-standardized improvised laboratories?).

5) Scientists have bad hygiene. This is only true if we have a shitton of data that needs to be crunched into a grant application or presentation by tomorrow. Therefore, this is always true because there is always a shitton of data to go through. However, it is not true so long as one does not consider the standard of hygiene to include several daily facial scrubs, moisturizers, daily shaving, perfume, and ironed clothing. In conclusion, our bad hygiene isn't nearly so bad as it is often made out to be.



Huh. I started this post out with a point in mind. And then somewhere I lost it. As such, I apologize for rambling.

Typical scientist pictures!!!!1!:
Oh, wait, they uploaded to the top...

Ruminations

I've always found it odd that humans can ruminate upon some kind of thought, and thereby produce ruminations in spite of humans being non-ruminant mammals, yet when a cow ruminates its ruminations are manure.

Anyway, that is not the point of this blogpost.

There exist jokes as part of the human condition that I find very interesting. Some jokes are just plain funny no matter what, but others create a group and then make fun of it to the out-group's humor. Specifically, I am referring to redneck jokes that follow the form "You might be a redneck if...X, Y or Z."

Why aren't there "You might be a nerd if...X, Y or Z." Or "You might be a scientist if...X, Y or Z." From personal experience, I put forth the following:

You might be a scientist if you notice mechanical squeaking while walking and your first assumption is that your parents must have forgotten to tell you you're an android.

But maybe that's not a funny joke, because it really happened to me. My belt buckle was squeaky. Surely you can do better than this.

Moving Forwards, Moving Backwards

I read the above paper. Re-read several parts of it, actually. It may be that this was the first modeling paper I read to discuss pattern formation in cell masses (I've got a couple more waiting in my stacks now), but I found the principles and mechanisms laid out in this paper to be both profound and eye-opening. I didn't care much about how cyclical chemotactic signaling in Dictyostelium affects its cell differentiation, but it was still interesting in light of everything that had been previously discussed (I probably wouldn't have read the paper if it was only about Dictyostellium).

Normally we think about squishiness and stickiness as being separate properties of a material. For example, ice cream is both squishy and sticky but Jello is only squishy. Compared to Teflon, wood is sticky but not squishy. This paper integrated squishiness and stickiness on the cellular levels as the net effective surface energy of a given cell through the lens of physics models of foams. While it is possible that I was just being unobservant, this seems like a major intuitive leap forward. We know that cells interact with one another through various chemical interactions, whether it is simple polar interactions as lipid-rich plasma membrane innately repel each other or more complex composite polar interactions as the proteins embedded in those membranes are differentially attracted to each other. This paper summarized this as sticky cells have a high effective surface energy tied up in interactions with neighboring cells (or media/substrate) that holds them together while squishy cells have a lower effective surface energy and are therefore deformable because there is a lower entropy cost to do so. Essentially, it is easier to fall when you're only held up by a couple of thin supports (a late stage of a Jenga game), but much more difficult to do so when there are lots of solid supports (new Jenga game).

This paper didn't stop there though. It kept going.

Then they discussed chemotactic dynamics when there are 2 types of cells in a confined volume and the differences that may arise:
1) Pressure gradient: with Big cells and Small cells responding equally (to same degree and direction of chemotaxsis) to a given uni-directional chemotactic signal, the Big cells will get pushed in a direction opposite to the chemotactic signal. This occurs because Small cells form a pressure gradient that acts upon the larger surface area of the Big cells to accumulate a pressure differential between the leading and trailing edges (anisotropy). Small cells have a smaller effective surface area per given volume and can therefore tie more energy up in bonds with neighbors in a given volume than large cells, allowing them to cluster together more efficiently and form the pressure gradient.
2) Minority sorting: for this to occur, there must be a difference in the interactions of the 2 cells types such that the energy of interaction of like + like (of either cell type) is greater than the energy of interaction of like + different (also known as differential adhesion). Therefore, if there are fewer Jelly cells than Jam cells, more Jelly cells will have lower surface energy because they will numerically be bordered by more Jam cells and will thus have an entropic incentive to migrate together and get clumpy (although clumps can act like big cells within the pressure gradient). Furthermore, this doesn't just work with unequal cell populations, it'll also work with equal so long as the difference in energy of interactions is large enough.
3) Probability of moving: is energy of new conformation lower than energy of present conformation? If so, the probability that a cell will move to that conformation is greater. This is a lot like chemistry and orbital excitation, but cooler.

So, I thought that the paper was well-written, concise, and very interesting. Read it!

Käfer, J., Hogeweg, P., & Marée, A. (2006). Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences PLoS Computational Biology, 2 (6) DOI: 10.1371/journal.pcbi.0020056

Face

I have a face!

I mean, I had a face before, of course, but now that face is here where you can see it and not just me when I look in the mirror or when another person who is really there uses their eyes to see the light reflecting off of it (yep, I'm shiny) and thusly sees my face. You see, when their eyes see my face in real life, the light hits molecules inside their eyes that are also inside cells. And light is both a wave and a particle, so not only does it carry energy but it also can exert a force. Enough force from enough light quanta push on the molecules in the eye cells and make then change shape on a molecular hinge that acts like a switch. Like a light switch. But not. More like a pump because that switch makes little holes on the outsides of the eye cells open up and let charged particles enter. Enough charged particles get inside the cell that it accumulates a charge relative to the outside of the cell that is called the action potential. At a certain magnitude of action potential the eye cell fires off an electrical signal to the neuron that connects it to the brain that interprets the signal as seeing the light that is reflecting from my shiny face. If my face were not shiny at all it would be invisible.

And now you can see my face because I posted a picture.

Nerd

Those who know me in person harbor no doubts as to me being a complete and total nerd. Although my nerdiness stops short of D&D, I do play things like Laser Chess and Zombies. However, once in a while, I do something that I later notice as being particularly nerdy or indicative of my nerdiness. I was composing a hip-hop/dance anthem on my computer and built it all up to a very intense drum and bass breakdown. The nerdiness struck when it occurred to me to insert an accordian-driven breakdown into the other breakdown and I thought it sounds awesome. I'm leaving it in there.

Security

I think I'm going to begin wearing the maximum amount of PPE we have on the weekends and late nights in the lab to keep security from barging in and demanding to see my ID. PPE = personal protective equipment. I suspect that opening the door to the lab and seeing me working in the biosafety cabinet with a gas mask-style respirator, chemical splash goggles, 3 pairs of different gloves, and one of our big blue plastic suits would deter them from bothering me. Maybe I could use the head lamp with magnifying eyepieces, too.

Of course, now I'm going to have to put all of this on and get someone to take a picture of me in it.