Sunshine

This blog is about the things I find cool, the things that make me happy, the things that make me smile. The fact that there are so many is one of the reasons I have this blog in the first place, but if I were to try to write them all down, sunshine would be at the top of the list.

This is a time when sunshine makes the world a brighter place. The sun's radiance supports practically all life in some way. It's crazy awesome, and without it, this wonderful world would be a much more depressing place.

Sunshine makes trees grow and plants blossom! It spreads energy and warmth everywhere. It's like smiling, only more so; sunshine makes people happy, and compared to all the limited resources in the world, it touches everyone. 

The moments when the sun rises to the day and sets to sleep are some of the most beautiful. It paints the surface of the Earth with colors, rendering verdant trees, vibrant flowers, vivid seas and skies. It's so amazing that it's hard to imagine life without it! :D

Spring: The Most Wonderful Time Of The Year

SPRING IS GREEN!!!

NEW PLANTZ!!!

I don't care what the carols say about mistletoe-ing and hearts-a-glowing. Spring is the real hap-happiest season of all. I've already talked about why, based on purely numerical and grouping reasons, spring ought to come at the beginning of the year. But one of the most important reasons that Spring should come first is that it's simply the best.

EFFLORESCENCE!!!

1. Spring is full of sunshine.
2. Spring is optimally temperate weather, in contrast to summer hot and winter cold.
3. Spring contains the birthdays of all the coolest people.
4. Spring is a time of sex, birth, and growth of flora and fauna.
5. Spring is a beautiful contrast to lugubrious winter.
6. Spring is an exciting prelude to summer break.
7. Spring is the biggest time to sow seeds for gardeners.
8. Spring's beginning is marked by Holi, a festival of colors.
9. Spring contains Spring Weekend.
10. Spring provides life (especially plants) a vital combo of light, rain, and warmth.
11. Spring also means a source or supply, especially of water.
12. Spring also means to dart, fly, or bounce, or to be quick, resilient, or elastic.
13. Spring is prime, like the number of reasons in this list.
14. Spring is youth in a year-life metaphor.
    
15. Spring is also often metaphorical rebirth after fall's decay and winter's death.
16. Spring is green, and green is the best color.
17. Spring is a time when trees are filled with leaves, flowers, and birds.

Flame Bookmark

But don't set your book on fire.

Observations On Five Games Of Mafia

1) Observation, knowledge, and communication are all vital for success.
2) A pin in a pile of nails is hard to find.
3) Do not accuse people if you are not prepared to be accused.
4) People's educated guesses can be worse than random choices.
5) Most people are not skilled at lying.
6) People act differently in different circumstances.
7) Sound and sight are equally valuable.
8) One good public action can save one's reputation for life.
9) One suspicious public action can ruin it.
10) God can get things wrong.

A Is For Apple

What to start with? An apple, of course. Regardless of the fact that Eve's apple-eating threw mankind into sin and Eris' golden apple started a major war, apples are well-liked by most of the world. Babies eat applesauce, and apples are common and delicious (haha), so it's reasonable to start their English vocabulary with "A is for Apple." And that's besides the fact that, well, A is the first letter of the alphabet. Similarly, the apple is one of the first things novice artists typically learn to draw (or so has been my experience). So here is mine! :D

In case it isn't clear, I did not actually draw these very lines for the apple (for one, it's left and right half are perfectly symmetric, and I've never been that good at drawing). :P Instead, I drew a flame and warped it into a crescent. For the leaves, I actually drew a straight bay-like leaf and then warped it into the curves you can see above. I do feel like I'm cheating by drawing in this way, but hopefully I'll someday be able to draw something like this directly. :)

Tablet Pen or Wooden Pencil?

I love arts and crafts--drawing, coloring, painting, sculpting, the list goes on. Unfortunately, my skills at all of them haven't really grown since I was in 4th grade or so (and I'm sure I could find plenty of 4th graders far better than me).

But I still love it, even if I'm no good. As I've mentioned before, GIMP has allowed me to bypass many of the fundamentals to arrive at passably pretty abstract art ("nice" is the most appropriate adjective), mostly using tricks like gradient rendering, rotation, and symmetry. :)

Recently though, I've started to wonder whether going on this way is really acceptable to me. Making perfectly symmetric glowing flowers and vibrant colors is all well and good, but art should really be something more, some expression of an idea or memory or emotion or story. I can't do that with the skills I have now.

So it was with great pleasure that I opened a postage box on my birthday a few weeks ago and found a drawing tablet to use with my computer! It will take me a while to learn to use it well, but it's encouraging that I can already draw something I never could on my computer: the flames above, which are practically omnipresent on my class notes. And of course, now I can add in my pretty colors. :D

I don't know which comes first--learning how to draw with a tablet, or just learning to draw at all. Regardless, exciting times await!

On Uniqueness

Uniqueness is a big deal. Mathematicians are ecstatic to find that there exists a unique solution to a problem, biologists love to try finding unique pathways to various diseases, and product managers work to make their brand as unique as possible. "Of which there is only one; one and no other" is the OED's first definition, encompassing the existence and the solitary nature.

Counselors often say "everyone is unique" as though it ought to make someone feel better about themselves; interestingly, it usually does. Somehow, the very thought of being different is highly gratifying to the self-esteem, in spite of all the effort we put in to be just like everyone else.

It's certainly true, of course, that no two people are exactly the same, but why is this inherently a good thing? I believe it stems from people substituting another definition of unique: irreplaceable. That is, "everyone is unique" translates to "every person has special talents or qualities unlike any other."

The subtle problem is that those qualities may or may not be positive. Taking the edge case, if a person A is absolutely talentless at any and every non-basic activity, the fact that A is unique is not any reasonable cause for comfort.

However, such an edge case is non-existent, and given the vast number of possible talents and the combinatorially explosive number of sets of talents, it is pretty rare to for some person A to encounter a person B whose positive talents are a superset of A's. But in such an instance, should A feel any rational solace in the fact that he is unique, but in a strictly inferior way? Should B feel pride in achieving all that A has, and more? What is each of them justified in thinking?

Birthday a la Duck and Bunny

Scones! With jam and theoretical Devonshire cream!

For once, we celebrated my friend's birthday this year at the Duck and Bunny rather than the Cheesecake Factory. I'd never been, but it definitely earns its self-title of "snuggery." A cozy place with warm and bright decor, it seems like a bunny's version of the Cheesecake Factory, specializing in crepes rather than cheesecakes. :)

A crepe masquerading as a burrito! o_O

I only had the bean dip and the Creperrito, but I would heartily recommend both. The former blew all of our minds with its surprising depth of flavor, and the latter had all the right touches for a satisfying meal--lightly dressed greens, rich crepe and beans, and touches of guacamole, tomato, and sour cream. NOM!

Newton on Graduation

As I was strolling through the CIT today, these three pieces of paper on a professor's door caught my eye.
Thirty seconds later, I was laughing out loud, and I hope that you are too. =D Enjoy!

Apparently, credit should be given to the PHD program at Stanford University. Yay Stanford!

And So I Declared.

Last week, I formally submitted my declaration for computational biology. I've been flip-flopping since the start of freshman year, and I'm still not convinced that I've made the right choice, but I have made one, for whatever it is worth.

Applying to and arriving at Brown, I was confident that I would leave with a degree in neuroscience. The brain was the most fascinating object I had ever considered; as V.S. Ramachandran once said, “It can contemplate the meaning of infinity, and it can contemplate itself contemplating on the meaning of infinity.” It truly is a remarkably plastic, self-regulating, parallel-processing biological computational machine, and I wanted to find out how it works. I still do, of course, but I have since gained a profound appreciation for computation itself, as well as the systems and algorithms humanity has developed to assist in solving more and more complex problems.

Yet I am, now and forever, a biologist at heart, and the problems I am most excited about solving are biological ones. How are gene expression and translation regulated? Why do proteins fold the way they do? What are the protein networks and pathways in any given cell? How do they interact to perform a distinct function (or malfunction, say cancer, when an error is introduced)? Returning to neuroscience, how does the complex circuitry of the brain generate its fantastic abilities? The answers to these questions lie in the realm of computational biology.

Food, Glorious Food

Sometimes, the Ratty has really, really awesome food. Those days are happy days.

I'm talking about crusty, chewy sourdough and a variety of crackers
topped with bright brie and gouda with a side of succulent strawberries. NOM!

Bio-Hardware: Patterns

Fractals are generated by repeating a pattern--over and over and over and...

From the smallest toddler to the oldest senior, we all love patterns. Even if you think you don't like patterns, your brain does. Patterns are not just the spice but the life itself. Associations, fractals, habits, cycles, noun-verb syntax, symmetry--they are all just examples of patterns: things that repeat in a predictable manner.

One of my flower fountains: symmetry in action!

We are evolutionarily hardwired to find patterns. If you eat a certain berry and get sick, you had better learn to associate that berry with sickness. If you walk into a cave and it turned out to be a snake retirement home, you had better not walk back in there again. 

"A for apple"?

In essence, learning itself is biochemical pattern-finding. A parent shows a baby girl a picture of an apple 10 times and says the word "apple," and she learns to associate the two. "Clearly," her brain thinks, "there's a pattern there." A rat presses a lever and receives a tasty morsel. "Aha! Lever --> NOM!" 

"Neurons that fire together, wire together."

On a molecular scale, synapses between neurons that fire together are strengthened by NMDA receptors, which are aptly called "coincidence detectors." Not a "lucky coincidence" kind of coincidence, but a "two-things-happened-together" kind. Co...incidence.

Hint: What do preschoolers learn about?

Personally, I really really really love patterns. They are everywhere, they are mentally and even almost emotionally satisfying, and the act of finding a pattern is often inherent in all kinds of puzzles and problems that I enjoy. Besides which, I like learning, and learning is patterns, after all. :D

Nuclear Catastrophe: When Life Goes Wrong

Nothing in life is perfect. Nothing in biology is either. As DNA replicates inside the nucleus, errors happen--a deletion, an insertion, a duplication, maybe an inversion of a couple bases. DNA polymerase, which copies out a new strand, is pretty good- only one in 10⁷ bases are wrong, and with the built-in proof-reader in the very same protein, that goes down to one in 10⁹. Not bad, not bad at all! On top of this, there are even more DNA repair proteins that routinely scan for bumps or nicks to make sure that everything is as it should be.

Some examples of DNA mutation

But sometimes, much bigger changes can happen. Deletions of entire genes, inversions of regions on the scale of kilobases (kb), translocations that cause one chromosome to attach to another! These larger structural errors are called, unsurprisingly, structural variants. As you might imagine, these are somewhat more likely to be serious enough to impair cell function, though several point mutations can be deadly as well.

But wait! Sometimes, something even worse happens: a really catastrophic nuclear event. These are called complex events (and at the far end, chromothripsis). Just look at these graphs! Each of the outer colored segments is a chromosome. One of the curves inside connects two breakpoints, where the chromosome broke and then reconnected to a different spot. In these cases, you can even see many with multiple breakpoints at multiple chromosomes!

We used to just say, "Oh, these are just one mutation happening after another, collectively creating this scrambling." But with this new data and visualization, it's clear that the breakpoints are often clustered around particular areas, which suggests a shattering of the chromosome around that point and then scrambled rearrangement. We're still not sure how this happens though.

In particular, such a catastrophic event should definitely just kill the cell, right? So why do we ever see these? The answer is that we usually don't. These are from three cancerous tumors, and tumors are where we are increasingly finding these complex variants. Do these crazy rearrangements cause cancer? Or do some cancer pathways enable the dramatic events to occur? These are the kinds of questions that some computational biologists are working to answer. 

Hot Tails

No, really. Hot tails. In 2007, researchers discovered that when ground squirrels and rattlesnakes face off, the squirrels heat up their tails. We already knew that rattlesnakes have infrared(IR) sensors (heat vision), and we knew that squirrels wave their tails at snakes, but this was the first time scientists had detected such a vivid heat-mediated signalling mechanism. Scientists built a robo-squirrel to confirm the deterring effect of the heat shift, but for some reason news sources are getting excited about it all over again lately. Robo-animal fan clubs, I assume.

Presumably, heating up their big, bushy tails either serves to make the squirrel look bigger and more intimidating, or just to make its warning more noticeable. ("Warning?" you ask? Adults are largely immune to the venom, and can therefore harass and fight the snake fairly well. Mostly rattlers favor surprise attacks, and the tail-waving warns it that it's been seen.) As far as I know, we're still not sure which. Either way, it's pretty cool, especially considering that squirrels themselves can't see IR. o_O

This reminds us of some important lessons. To well-analyze a particular species, we have to think about the other organisms it interacts with in addition to the species itself. Squirrels can't see IR, so if we hadn't been focusing on the snake-squirrel interaction, we never would have found this cool example of evolution. Moreover, another reason this took us so long to find out is that we can't see IR either. It's important to break out of our human-centered box, because the world is full of things we can't see, hear, smell, or detect, and we'll never know about them if we don't think to look.

Hi Qu

A feathery fire

Struggles to stay dry and fly

In shimmering sheets

In times of trouble,

Strengthen or weaken your limbs:

Fight or drop away.

Where dragons burrow,

Worms will always find their place,

Like bees in a hive.

Fortune will find you,

A strange truth will confuse you,

A lie will blind you. 

Lugubrious shell,

Once occupied, now empty,

Awkward no longer.

The Twelvefold Way

1...2...3.

The triple gems (Ratnatraya) in Jainism are Right Vision, Right Knowledge, Right Conduct. The first involves belief and conviction, the second clarity and reality, and the third action and application. This is similar to the eightfold path of Buddhism, which can be broken down into Wisdom (right view and intention), Conduct (right speech, action, and livelihood), and Concentration (right effort, mindfulness, and concentration).

As you might expect, the twelvefold way is also a paradigm with great power and application. However, it has absolutely nothing to do with ethics, and instead is used to count! I know what you're thinking: "Look, I know how to count. Why on Earth would you need a twelvefold way to do something as simple as counting?" The short answer is that life is full of things that are too complicated or too large to enumerate easily, and so we need combinatorics, the art of counting. Plus, if you can count something in general, you don't have to count it again. :)

So what is the twelvefold way? It is a classification of 12 commonly occurring counting problems, based on functions from a set to another set. This creates a useful simplification of larger or more abstract problems, making them easier to count. For example, how many ways are there to distribute 6 distinct candies to 3 kids? This is the same as:

• The number of ways to put 6 items into 3 boxes, which is the same as 
• The number of ways to line up 6 dots and 2 bars, which is the same as 
• The number of ways to get 2 heads on 8 coin flips, which is the same as
• The number of bit strings of size 8 with exactly 2 ones, which is the same as 
• The number of ways to choose 2 things from 8 things.

All of these can be simplified into the same category in the twelvefold way, so once we've found the answer to that, we know the answer for all of them! Which is 28, by the way. 2 and 8, see? :D