13 November, 2008

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.

05 November, 2008

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...


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...

30 October, 2008


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.

16 September, 2008

Moving Forwards, Moving Backwards

ResearchBlogging.orgI 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

22 August, 2008


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.

02 July, 2008


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.

29 June, 2008


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.

26 June, 2008

Cecum II

It should be noted that, upon reflection, I have seen a bigger cecum than the one noted before, but it was in a mouse infected with cholera, and as such was mostly liquid anyway.


It's like the murine equivalent of an appendix, only with a digestive function and not just as a reservoir for normal gut flora. The jejunum feeds it and the ileum drains it, but it's pretty much a big J-shaped sack that holds digesting food. I do not know what it's contents would look like in a wild mouse with a heterogeneous diet, but in lab animals with a homogeneous diet it is uniformly brown (think pre-poop).

I bring up the cecum because I dissected out possibly the biggest cecum I have ever seen the other day. It was from a Germ-free Swiss Webster mouse, about 18 months of age, who was suffering bloat from a downstream gut twist. Ceca tend to bloat anyway in germ-free mice, and the gut twist may have backed up materials as well (although it pooped on me anyway when I picked it up), but the mouse still had retained ~3g of cecal contents (mouse weighed maybe 25g). That's incredible!

If I had the same relative mass of undigested food in me, that'd be about 9kg!

(I have a morbid tendency to calculate things upward from mice to my own mass. For example, the LD50 of Stx-2 (Shiga-like-toxin-2, produced in very virulent O157:H7 E coli strains) in mice is about 1.3E-5g/kg [if I am remembering the paper on it correctly]. Which means that the LD50 for me would be only about 3mg!).

05 June, 2008


19 May, 2008


Just got out of the lab. Spent 3 hours in the flow hood plating serial dilutions of bacteria. Tedium. Tedium in which I must remain very accurate and precise with my measurements, which had to be done a couple hundred times (the same measurements).

Sometimes I look back to the craft guilds of the 17th century prior to the Industrial Revolution. They regulated all the craftsmen and their products and what was allowable and who could sell where and what and how and for how much. But they also trained young people as apprentices, then when they became competent let them be journeymen, and finally, after their masterpiece was complete, they were masters of their trade. In some ways, becoming a research scientist recapitulates that progression.

I very recently graduated with a Bachelor of Science in Cell and Molecular Biology. As an undergraduate, I worked in labs, and on my own project, kind of like an apprentice. I learned the practical basics that they can't teach in lecture halls, such as pipetting, cell culture, operating cantankerous equipment. Now I've graduated and am working in a lab as a technician. This is like the journeyman stage. Later, when graduate school happens, it will be as if the guild has granted me permission to continue to advance my craft as a journeyman. And in graduate school, I will have to research and defend a thesis, the academic equivalent to a masterpiece.

The only problem with this is that I feel like I should have my own tools. A good set of micropipettes, maybe a pH meter, a couple sheafs of protocols. Unfortunately, micropipettes are a lot more expensive than hammers.

14 April, 2008

Office Enterprise 2007

It can really suck sometimes.

I made this really cool Powerpoint presentation that I was going to post on here. It was all about enterohemorrhagic E. coli (EHEC) and the genetics of Shiga toxin expression (which are really cool!). But Office Enterprise 2007 isn't nice enough to allow me to do so. I tried converting it to an .html file, but then Office wouldn't let me access the actual code, only look at it through my default browser. Now, yes, I could have gone and coded it all by hand, but that would have taken up much more time that I was willing to spare for this (it's finals season for me!). So you all (maybe there's one of you, but we're going to pretend that you're plural, just like we're pretending like we're plural) will just have to imagine how cool the genetics of Shiga toxin in pathogenic strains of E. coli are.

It's probably better that way anyway.

28 March, 2008

Brain Extractions

Surprisingly sticky.

I managed to decapitate the mouse well enough (it was already dead at this point, decapitation was not the primary means of euthanasia [that occurred sometime between putting it to forever sleep and exsanguinating it by means of cardiac puncture]), but skinning its head was quite difficult. Mainly because it was very slippery. You have to sort of peel the skin back (like an orange) until you can see the eyes and then fold it into a handle for yourself to cut through bones. Next you cut across the bone between the eyes, then through the ears to the back of the skull. Then it pretty much pops open once you split the skull down the middle.

But the mouse brain itself? Pale and smooth. A bit larger than I had expected for such a small mammal. Also very dense, it didn't squish very easily (I wasn't trying to squish it into paste [and I didn't], but seeing how much give it had, just gently pinching it a little).

But I don't know. It was sort of profound. There I was, sitting in the lab with another creature's brain in the palm of my hand. As if there was some kind of phylogenetic resonance recapitulating my evolution of my own brain from one similar to that in my hand. Like saying hello to a baby. I would even have to admit that it was kind of cute, so grayish pink, almost like a newborn mouse pup (but less wrinkly). I sat there and looked at it, thinking to myself: "So this is what propelled the little creatures in their cage to climb over each other and twitch their whiskers in alarm each time we manipulated their cage." It was cool.

Perhaps I'll post some sketches of the procedure if I ever remember to draw them.

Although it may appear otherwise, I am not a sick fuck. I respect the animals that we use in science and always feel regret when I am required to euthanize them. But in seeing how they are put together and how all of the organs and systems are connected to one another: that is undeniably cool. And while it is important to remember that laboratory mice are living things that must be treated as such, it is also important that we as scientists be able to speak of them frankly and with all the delighted curiosity that (hopefully) brought us to science in the first place.

06 March, 2008


Gotta start remembering that I have one of these blog things. I got some new software (Propellerhead Reason) and I've been neglecting everything else just to play with it.

Although maybe it would be cool for me to speculate to the molecular biology of vampires, that's not what I'm doing. Instead, this is a short commentary on the morbid-ness of scientists. For example, one of the lab techs told me at lunch that now we were taking brain samples for histology and that it was gross. My immediate response was "Cool! How do we do that?", which led to an explanation of splitting the scalp open, rolling it down off the head, and then cracking the skull and peeling it like an orange. I must learn how to do this myself.

Or, as another example, I just sent an email to the germ-free animal manager asking if we had any uninfected mice that needed culling. Not because I want to go over and slaughter hapless mice, but because I could make good use of their serum for my project and I might as well get it anyway if they're slated to die.

Just saying.

05 February, 2008

Why Flow Cytometry Is Cool

It has lasers!

(insert awesome laser picture here)

And it shoots lasers at cells!

Cells and lasers are cool!

Therefore, flow cytometry is double-cool! Maybe even Gigacool!

And, furthermore, that the physics of how it works and its optics aren't too convoluted to understand! Woo! And it calls groups of different cells pots! Pots! How absurd is that? Would you like a pot of cells? Why yes, sir, thank you very much, but may I have some PE-A and CD3 with them? Ah yes, very tasty. Lasers!

23 January, 2008


So the cart in my lab is probably about as old as I am. It's made entirely of metal, made for a much shorter person than ever uses it, and rattles so much that you can't even hear your own footsteps when you're stomping. No, we don't have a nice new cart made of HDPE that doesn't rattle or anything. Ours is like an angry dinosaur in desperate need of new ball bearings.

Why do I mention the cart?

Because it occurs to me that I should stop running down the hallways with it, loaded with biohazard waste, before I knock one of the old tenured PIs over and have to wear a Crystal Violet "U" (for Unfit Scientist). But there are some PIs who'd be funny to chase...

07 January, 2008

Still Alive

Been in a quasi-hibernation in this quasi-kaamos.

So I'm trying to reconcile 2 statements the professor of my Microbial Genetics course made in class last Thursday.

1) There are approximately 100 bacteria to every 1 cell in the human body.

2) It is estimated that only 1% of bacteria in any given sample of anything can be cultured and identified.

Each statement could be taken as true in its own context, at least if you ignore questions as to how such statements were formulated*, but together they don't make a lot of sense. Yes, there are ~3kg of bacteria in the human digestive tract alone (thinking of this ensures that I never feel lonely--I've always got a couple trillion close friends at hand). Nonetheless, if only 1% of the bacteria, even in a gut lumen sample, can be cultured and quantified, then how do we know how many were there to begin with? And as such, then how can we know what the ratio of bacterial cells to human cells is?

And as for the first statement, how does that work spatially? Bacteria range in size from 0.5-5.0 micrometers, and eukaryotic cells (e.g., human cells) are 10X as large. If these figures can be taken as directly proportional to volume and not just length, then there should be at most 10 bacteria to each human cell, and even then the total size and mass of those bacterial cells would be the same as the size and mass of the human. But if they are not directly proportional, then maybe it could work, although I still have a hard time imaging those volumes working out.

*Seriously though, how the hell did they get this figure? Did they take a whole healthy human and fractionate the entire body into its cellular components, then centrifuge everything and run it through flow cytometry to get the ratios? Or did they just take a liver biopsy and count that? But that would be inaccurate...