Archive for the ‘Science/Research’ Category

… is to find the equivalent resistance starting from any vertex to the node directly across from it.

Handmade resistor buckyball by EP

Just kidding ^___^.

My girlfriend made this beautiful polyhedron for me and I’m going to hang it up soon. Isn’t it really beautiful? The graceful mathematical form, pulled down into a cloak of pragmatic engineering … . It is a world unto itself that tumbles and tumbles on its five dozen little resistor knobs …….

The human mind, like any database or encyclopedia, rapidly becomes outdated with the times — and yet one must treat the most current information as being true. So what happens to knowledge that we acquire at a young age, then never update for decades? Well, naturally, it becomes irrelevant and dusty, and yet we continue to spout it as if it were the current truth. It was once said that human beings are the collection of prejudices learned by the age of 18. While of course people can change after that age, it is true that we do a lot of our “general learning” before reaching maturity, and afterwards, we only bother to update certain portions of our knowledge. My understanding of biology and contemporary music, for example, are pretty modern and continue to be shaped and refreshed every day.

But today I was faced with a complete jolt to one of my older sectors of memory: dinosaurs. Deinonychus, when I was growing up, was the epitome of the evil dinosaur. It had that Sauron-like piercing yellow eye, dragon-like front limbs and of course its eponymous sickle-shaped toe claw that was used to tear viciously into unsuspecting herbivores. It was sleek, clean, brownish-gray, and altogether the definition of “terrible lizard.” See: http://www.ansp.org/museum/dinohall/deinonychus.php for an illustration.

And then today, I saw this: http://en.wikipedia.org/wiki/Image:Deinonychus-antirrhopus_jconway.jpg. Yes, a cute fluffy feathery friend. With the evil toe claw.

What happened in just ten years? Did the extinct creature evolve through a couple hundred years of being featured in anime?  No – it just wasn’t that big, and it had feathers, and the humongous sickle claws were probably unique to certain “well-endowed” individuals.  It was probably warm and fuzzy.  Even when in predatory mode, it looks more like a pissed-off turkey: http://en.wikipedia.org/wiki/Image:Deinonychus_BW.jpg.

And of course I cried to the gods: how could you do this?  Why would evolution select these fluffballs over my vision of giant evil bloodthirsty predators?

Brachiosaurus now has a monstrously thick neck.  It looks positively ridiculous, like a giraffe on steroids.  What happened to the slender, snakey necks?

The truth is that we all wanted dinosaurs to look like dragons.  Of course, you could take a chicken skeleton and pretend it was all scaly and thin and looked like a dragon, too – it’s not as if the feathers have bones.  But that’s just it – dragons are heavy, prone to having their necks cut off, and altogether the product of the human aesthetic, nothing more.

Dinosaurs were the product of evolution, and if you look around today, you can see that it was on the right track.  No more dragons.  Plenty of birds.

I challenge you to catch a pigeon with your bare hands.  It’s pretty tough, isn’t it?  You could probably drag down a dragon using some rope booby-trap, but you’re not going to be trapping any street-smart pigeons.

To give a creature flight, and to give it a means of keeping warm enough to be always alert and not in need to recharging with sunlight – that is pure genius.  It is no wonder that the forces that be chose the cute fluffy thing over the hunkering assassin.  It just goes to show that humans have a long way to go before they truly understand the world around them, ridding themselves of the prejudices of centuries of folklore and facing the truth that is being revealed – and that has been revealed already.  Just the other day, I saw a pigeon with that same evil claw-toe.  Okay, so I didn’t really – but you could imagine it.

Even without the legendary meteor, I bet the same evolutionary path would have occurred.  The small feathery ones would have won out against the high-maintenance classic dinosaurs, and that would have opened up the land for mammals.  Just a theory, of course, but it’s always good to rethink everything you learn in a textbook.  And especially things you learn from Jurassic Park.

Outside the Green Building, Bartlett Tree Experts are removing several sycamores and pine trees, continuing work from last year. The sycamores they’re cutting down aren’t really dead, a fact that probably no one else will notice. There are lots of little sprouts coming out from various points in the trunk, and I have no doubt that there have been for years, except that people keep pruning these little outgrowths (which come out from apical meristem left over after lower limbs are removed to give the trees the characteristic head-on-a-stick look that is among the most unnatural shapes for any tree to assume when given full sunlight and ample space). The upper branches of the sycamores all over campus have been sickly ever since I came here – perhaps it’s acid rain or something. No matter what, I’ve honestly never seen such shriveled, ghastly looking things. That’s probably why they want to get rid of them – not because they’re a risk if they fall over, but because they’re ghastly. No one wants ghastly trees on campus.

They’ll probably attempt to replace the trees, but if the pine project is any indication, they’ll screw it right up. Besides the fact that a baby sycamore will take our lifetimes to grow into the ones they’re cutting down, they also seem to have little understanding of tree species in general.  Indeed, I would not be surprised if they planted a few red maples or perhaps some tulip trees by mistake.  Instead of replacing the dead red pines with more red pines (2-leaf bundles), they replaced them with Eastern white pines (5-leaf bundles).  The two trees look nothing alike, and the wispy, dense, straight-as-a-needle white pines will never look like the sparse, shaggy, almost Asian-looking red pines.  While this is more of a landscaping issue than anything else, I think it reveals a great deficiency in basic tree training.  Perhaps I shall write a more extensive entry about species of trees in New England.

I’m learning how to make red bean (hong dou, or azuki) soup today, and it’s a rather simple recipe that follows the main principles of bean-cooking.  What struck me first was advice from my girlfriend’s mom to soak the beans for 2-3 hours in water prior to cooking.  Then I read online to soak the beans overnight.  I talked to my dad this morning about it, and he said, “[We] never soak the beans, but we boil them and let them cook for a long, long time. [. . .] Do NOT add the sugar to the soup until the very end, or they will stop cooking.”  At this point, I suddenly remembered the lab I had just done on Friday, where we pushed cell solution at 1x PBS into a microfluidic PDMS trap and replaced the liquid with 0.1x PBS.  The cells bloated and bordered on exploding, with a 1.5-fold increase in diameter (coinciding with approximately a 3-fold increase in volume).  Yet another recipe I just came across warns you not to add any salt whatsoever to the soaking water – hard evidence that maintaining a strong concentration gradient is the key to cooking red beans.

Just as making crunchy Chinese pickles must be done by patting the cucumbers with loads of salt in order to coax the water out, to bloat and explode the beans so that they form that characteristic grainy red soup, one must only use pure, solute-free water.  Because the sugar (carbohydrate) concentration of in beans in extraordinarily high, adding sugar too early to the soup would be deadly – something that seeing the ingredients list off-hand would not convey.

Wouldn’t it be fun to compare the osmotically-driven expansion curve of the white blood cells in dilute saline solution (or even ddH2O) to the expansion curve of red beans in soup solution?

I am trying to logically plan the next experiment, to build a protocol and set of controls that will have the highest chance of yielding a success.

And yet, there is this overwhelming desperation and sense of helplessness and hopelessness that fogs the clear view of logic, and I feel that at any moment, I might succumb to tears, even as my spirit claims that it doesn’t want to give up, and it feebly tries to think of yet another protocol, yet another way to spend the rest of my hours, withering away …

Two years

without success

is too much for my soul to handle

I am already crying on the inside

I never thought about non-lab solutions this way, but grape juice is about 1.03 M sugar, and seawater is ~0.88 M salt.  I mean, can you imagine how big a lump 44 grams of sugar per 8 ounces is?

Today, James and I gave Sukant a crash course in genetics as preparation for his journal club presentation tomorrow.  During this “course,” James was explaining how we know certain genes (e.g. p53) are essential:

“We know certain genes are essential when the test animals die with the gene knocked out.  Think about how we know if a file is essential for your computer – if you delete ‘autoexec.bat,’ you notice that your computer doesn’t boot up anymore.  It’s an essential file.  However, if you delete ‘Shakira – Hips Don’t Lie.mp3,’ your computer runs just fine.  It’s not an essential file.  Genes are the same way.”

=)

include doing a literature search on your first day of real work and finding out that the project you’ve been given has already been done.  Blah!  It’s not like I never did a literature search on it before … where the heck did this paper suddenly pop out from?

After eating lunch today, I noticed a green thing moving below my plastic box. This was on a table inside the student center, mind you, so the moving part was a bit strange, although I was so out of it (from exhaustion and melancholy) that it took a long time to register, and even then I didn’t so much as glare at the mobile lettuce.

It turned out to be an inchworm, probably startled at being smacked by the clear lid from above. It had a small narrow head, elastic body, and two stubby prolegs in the back that sort of grappled rather than walked. It was a strange little fellow, being green and all (we know that it isn’t easy being green ..). What really struck my attention, though, was this thin channel traversing the entire dorsal side of the geometer moth caterpillar. At a rhythm of maybe one per second, a dark green fluid would build up in the hinder regions and then pulsate through towards the head. It was subtle but definitely real, and definitely consistent over several minutes as I watched it crawl. Was this an inchworm heart? Does an inchworm even have a heart?

Note: the inchworm was subsequently safely deposited beside a tall tree next to Kresge Oval.

Gratuitous picture of a disciplined caterpillar army: http://en.wikipedia.org/wiki/Image:Processional_caterpillar.JPG

Dumbo octopus.