Thursday, April 1, 2010

The Intron--Nature's April Fools Joke?

So in the last post I indicated that I wouldn't be posting for a while. I suppose that wasn't true--I just hate wasting my time, and at this moment I am rather restricted in what productive operations my excited fingers can bring forth.

Let us cozy up in a tree outside your dorm room and discuss DNA, that vast library that determines what you are and some believe, to some extent, who you are. Such a vast, vast library--if one of the haploid chromosomes within your cells, one of the "stacks" if you will of the library, were to be laid out end to end, the resulting string would be taller than you (unless you're more than 2 meters tall). We call the books, the instructions for the proteins that arduously manage your entire existence, exons. Strangely enough, only about one percent of the pages in your library are books--exons. They are buried within long chains of non-coding sections, and then even within and between all the books lies shelves and shelves of gooblygunk.

These gooblygunks, seemingly random strings of letters, are called introns. I have heard people say they are evidence of species-to-species evolution because they are useless. Since they do not code for anything, they must be left-overs from our distant past, before all the mutations that made us human, that haven't been deleted yet. I had the pleasure recently of discovering that introns actually serve a legitimate purpose.

Your genes are intensely regulated to ensure that you only read and copy ("transcribe") the "books" that you need for each moment. It would be silly and possibly dangerous if you JUST needed an organic chemistry book, but someone threw the entire physics section at you, too. To prevent this, your genes have switches that turn reading on and off for each exon. You have switches to modulate HOW MUCH you read, too. They even have switches that send messengers to flip switches to turn reading on or off. It turns out that a lot of your switches that are controlled by other switches are written into the introns.

Let me just take a moment to totally praise God for this. He is so clearly showing us that just because you don't see use for something doesn't mean it doesn't have a purpose. I will go farther and say that many times, things that are useless are absolutely bursting with infinite purpose. So judge not, for "whatever you do, whether you eat or drink, do it all for the Lord Jesus Christ." Remember that verse? All things can be a glorious expression of worship...all introns may hold a deep message that we have simply overlooked.

Intron/Exon information from my BME 2104 class at UVA, taught by William Guilford

Wednesday, March 31, 2010

Agh my brain hurts

And unfortunately I will have to make an admission.

I can't update each week. I can't even update biweekly. Heck, there are things I'm supposed to update monthly that I can't keep up with.

This will change after the MCAT. This will change. But I cannot keep pretending that I have time, when I do not.

Please pray for me, because it is so hard to focus on that which matters. It's a lot more fun to focus on nothing at all.

God bless,

Wednesday, March 17, 2010

Prometheus Studies: Orgo Chem Video Series

A'ight people, so in addition to commenting on sci fi that no one cares about, over the weekend I did a few quick "Jesus Geek" videos. Check 'em out.

While you're at it, stop by my other Prometheus Studies vids on youtube. If anything interests you, be sure to subscribe so I can try to throw you more.

Who are you? Who am I talking to? Well, I don't know! But I hope whoever "you" are that you enjoy what you see.

Hopefully you're not me. 0_0

Monday, March 15, 2010

God and...Cartoon Network!

SO it's been a while, but if you check the dates, you'll notice I'm doin' a once a week thang, and I'm sticking to it! So don't be judging me y'all...and broadjam is about to take my primo membership away, so if you want my music, you better get it now.

OKAY so time for a little sci fi. Hopefully you don't know me, but if you do, you know that this new children's sci fi has completely captured my heart. Why the crazy over Ben 10 and its sequel, Alien Force? Well, let's start with the sci fi.

Admittedly, the "science" part of this kid's show is somewhat lacking at times. The producers expect that throwing out the word "DNA" every few minutes and mixing it up with "turbo" will impress their audience, and since it's made up of ten-year-olds, they're probably right. The Omnitrix, the alien watch that melds itself irreversibly with the child protagonist's DNA, stores genetic information from all over the universe and then mutates the wearer into one of "ten super cool alien dudes," as Ben says. How is not explained, but the awesome transformations Ben undergoes takes our nine-year-old minds out of the realm of magic and into that elusive imaginative world of the possibilities of science. What if genetic instability and the universally horrible effect of mutation on the human body could be REVERSED? What if, in the light of the progression of gene therapy, in vitro gene transformation could go BACK AND FORTH? And, more importantly for the target audience, what if a ten year old boy can be a superhero? THAT kind of question, the wonderful what if, is why science fiction is a good thing for kids, and why it didn't hurt to throw a little more science into Ben 10.

However, after doggedly tracking Ben 10's spin-off, Ben 10 Alien Force, I have discovered why it is a good thing the original series did NOT delve TOO much into the science. Sometimes Man of Action, bless his soul, does not merely offend the intelligence of children: he stomps on the beauty of science fiction itself. I made sure to go back and put in the word "sometimes", because sometimes Man of Action very nicely hints at how the Omnitrix works by relating it to topics he/they know about, such as Wi Fi. The diverse alien creatures themselves really do form the backbone of the show, making for some terribly interesting daydreaming, especially in the first series. The danger lies in easily obvious scientific fallacies. The moment any sixth-grader with a periodic table realizes that there cannot be a Uranium isotope with as many neutrons as posited in season 3's "Fool's Gold," the flaw rips attention away from the fiction. Add to that injury the insult of watching a character bounce on Uranium deposit explosions--an absolute impossibility-- and people like this critic show up. Fiction is great, and fantasy is great, but when you're making science fiction, vague is better than pure WRONG, because it allows us, the viewers, to come up with our own explanations. Vague spurs our imaginations; wrong limits them and turns us into critics.

So what is it about this show that makes it somehow awesome, and why am I about to tell you that Christians should enjoy it? Is it the way Ben often learns how he should have listened to his grandfather? Not really. Don't get me wrong: the idea that a child should listen to an adult's loving advice is a refreshing breath of life amidst all the stale, putridly justified rebellion in children's films today. It does bother me that Ben's constant bickering with his cousin Gwen and the tone of voice Gwen uses when addressing her elders (I'm not a parent, but she really makes me cringe) counteract the entire premise of kindness and respect; parents should understand that this show, like any other, is probably not for the littlest ones who are still learning about obedience unless parents are willing to sit down and discuss things with their kids. I do adore the didactic way the bad guys' mental states are extrapolations of common childhood "badnesses", but my satisfaction with the show does not come from knowing that Dr. Animo's mutant guinea pig is showing kids how easily "I've earned it, I deserve it" goes too far.

So, if it's not in the episode I simply love the plot? I do admit that I am a biased sucker for kids defeating the same bad guys over and over and over, and will never tire of the old squid-faced supervillian revenge spiel. This may not be your thing. The sci fi aspect of each story, however, makes it an intriguing watch for kids, and despite my harping on Uranium isotopes, I really have to hand it to these guys for talking easily with preteens about carbon dioxide exchange and cell immunity. Each episode leaves us wondering what the heck kind of demented and freaky bad guy they will come up with next and how an ordinary kid will have to deal with it.

Therein lies part of the illusive attraction. Unlike most superheroes, Ben Tennyson does not hail from a troubled childhood filled with science experiments or depressing manipulations that turned him somehow into the hero he is today. No matter how many times he violates the "10" part of the show title's as he collects over 20 new aliens to turn into, he will always be the normal kid who just happens to wear a weird watch. In the original series, Ben often ultimately defeats the "bad guy" by coming up with something clever as an ordinary kid. His powers are a tool, not who he is, and Man of Action tells us over and over that normal Ben is awesome. Christians should be all over this. The idea that every special ability is part of a gift we use to bless others, rather than part of some the search for self-expression: doesn't this sound like Jesus' tale of the talents? Jesus made a point of explaining with his parable of the widow that what you have does not matter half as much as what you do with it, and unlike Ben's genetically gifted sidekicks, Ben is a hero because he does his best with what he's given. The producers did even better when they made a hero in the audience's age range, subtly standing against the cultural obsession with Teen heroes for NON-teen kids. Like Paul to Timothy, rather than saying, "look up to the hip kids older than you," Ben Ten says, "Be someone worth looking up to."

There are so many ways this show could go wrong, but honestly, as long as Ben remains a normally growing kid and the aliens stay fresh foreign aliens, people will probably keep on watching. Writing science fiction shows for young minds is a challenge, and anyone who airs beautifully colored, decently drawn characters on a channel that has begun to produce badly animated crap like "Chowder" and "Total Drama Island" should receive support simply as a matter of artistic principle. In the name of art, God, and all that is sci fi, get with your ten-year-old in front of the TV at 8:30 Friday evenings, because as a Christian parent you can get one heck of a teaching opportunity out of that show! If you don't talk to your child about aliens, who will?

Unless, of course, you planned to go star-gazing or to valiantly defend planet earth from a giant tick--those really are better family activities than TV.

Saturday, March 6, 2010

The God of the Endosperm

Two candidates wait, crouched eagerly for discovery within their dark hovel, both of them equally gifted--they are sisters, from the same cell--both poised to burst forth into glorious flowering purpose. Only one of them, however, will usher herself into colorful notoriety. The other, we will call, the endosperm.

HUH, you say? Well, when the megasporocyte (cool name, huh?) inside a seed-bearing plant divides, she produces two megaspores, one of which dies, the other of which divides again three times to make eight cells. Each of these cells is "equally gifted" with the same genetic material, but out of each three, one is chosen to become an egg, and the other two become "polar nuclei." These cells all wait patiently inside the pistil, the female part in the center of a flower, until a pollen grain lands on the pistil and sends a long tube of sperm down to them. The egg, when fertilized by pollen, grows into the embryo that grows into the main body of the beautiful flower. The two polar nuclei, when fertilized, fuse together in obscurity and form the endosperm, the triploid freak with three copies of genetic instructions instead of the customary two. Flowers are the subjects of poems, treatises, research, and poetry from every civilization. The endosperm? Not so much. We shall call it the historical loser.

Much like many biblical characters, actually. Abraham, Isaac, and Jacob, Jesus' ancestors, failed miserably over and over and over again. And again. Abraham, an unloved nobody in a strange land, repeatedly sold out on his wife to save his own skin; Isaac treated one of his sons better than the other so that they nearly killed each other out of jealousy; Jacob not only followed in his father's favoritist footsteps, but also lied to his brother, cheated his uncle, and proved helpless against the rape of his daughter, loss of his son, or the slaughter of an innocent town. Successful guys? Not so much. Each of them lived in sorrow in their old age, not only because of their own failures, but also because of the trickery of others. Classic losers. Classic endosperm.

Yet it is the endosperm that is most crucial to the survival of a plant. A seed would have no purpose, and in fact no body, without the endosperm, for it is this strange entity that feeds, protects, and provides the living foundation for the plant before it fully sprouts. The endosperm really lives on in the spirit of the flower itself, for while the endosperm doesn't need the embryo, the embryo desperately needs the endosperm.

Sometimes our lives, like that of the endosperm, seem to us like pointless failures. We assume that because we aren't rich, or popular, or right all the time, or fit, or A plus students, or ________, we aren't serving our purpose in life. However, over and over in the Bible God refers to himself as the God of Abraham, Isaac, and Jacob, and they certainly didn't have it all together. So why would God essentially call himself "the God of the Losers?" Because just as he builds a flower on the foundation of the endosperm, he builds his kingdom on a foundation of losers who can testify to the power of love and sacrifice. So don't give in to the lie of pointlessness--if you are His, you are NOT a failure. In the words of two lovely songs, "Little is much, when God's in it," and "there's nothing about you that's plain."

I know it sounds funny to say, "I am precious endosperm in God's sight," but hey, I say it, and the laughter makes me live longer anyway. We have a tremendous God. Never forget that.

Information gathered from my Bio 2040 Lab at University of Virginia. Music linked to: Little is much, by downhere, and Plain, by Zoegirl.

Saturday, February 27, 2010

The Pest Quest

Remember the old Sun and the Moon metaphor? The Moon's light, as you know, is merely a reflection of the Sun. When the earth comes between it and the Sun, it has no light--in the same way, for someone pursuing a relationship with God, when you let something get between you and that relationship, you dim your light. As you know, I hope for you to view some of the unknown features of the scientific world in the same metaphorical light with which so many of us view the Sun, Moon, flowers, and open horizons. Enter the Gypsy Moth, a fat little insect in a wedding dress of fluffy wings.

You know the larvae as "tent caterpillars", I believe. Maybe you don't. Either way, they're huge pests, plant vampires that suck the nutrients out of backyard trees. From their point of view, however, perhaps they are peaceful, idyllic teenagers, children who live together in huge utopias built of a softer version of silk. Their silk first brought them to the Americas, because a foolish scientist wanted to see if he could breed them to produce it commercially. They escaped from his evil slavery designs, and today most young Gypsies live together until the age comes and each must leave the Community tents to take on the Quest.

When a caterpillar youth comes of age, he or she enters a deep meditation state within a pure, simple hermitage. He leaves the comforts of the mobile, spacious life and pledges to develop himself into something greater in his self-made coffin. As we all know, through the miracle of sleep, he undergoes his first trial, the Opening, and emerges as a moth, resurrected like Christ himself, or sometimes, like you. He begins the glory and the challenge of the Flight, and begins to seek the Mate.

During her deep meditation, the Mate has mastered the subconscious art of producing pheromones to draw her Questor Mate to herself. She is his everything, and he is her everything, and their union, like your union with God, fulfills the Quest.

Those outside the Community, the Humans, do not understand, and in evil futility design poisons to shrivel the Communities, de-flight the Mates, or otherwise destroy the Youth, their real enemy. In their giant dark laboratories, through unspeakable tortures worked upon Mates and complex chemistry, they have devised a simple ruse to prevent the creation of the Youth--in short, to prevent the Quest from fulfillment.

The Humans spread pheromones EVERYWHERE. The world may do this to you. The Questor Mates now follow any number of useless signals, and die frustrated or deluded in their old age, never having found true happiness and fulfilled their Quest.

Don't let anyone do this to you. The world will throw things everywhere, things that are often good, that despite all their beauty and wonder, should never get in the way of your Quest. Remember who you are, and the Community you came from, and the re-birth you claimed, and never lose sight of the One Being who is your ultimate goal.

Friday, February 26, 2010

Lessons from my Tarantula

This morning from atop my slowly stiffening mattress I noticed an odd movement from the tarantula tank on my bedside desk. My chilean rose hair tarantula stood on her tip toes, oscillating her abdomen like a paintbrush as she drew web over the doorway to her log home. Her spinnerets (the sticks on her rear from which web emanates) stretched out in two different directions as she gracefully wove her acrobatic form up to the top of her little castle and down to the floor. I wish I were that limber.

This is the most work I have ever seen her do, I think. Her webbing seems to be some form of decoration, for she has never used it to actually catch anything or even to hide herself. Remember Jesus' "Do not worry about tomorrow" spiel, where he compared the flowers to Solomon and the birds to farmers? The birds do not sow or reap, he said, and yet they have food. The flowers don't stress out making themselves beautiful, and yet they will continue for all history to be the very emblem and metaphor for beauty itself. If he had come through a Latina in Chile instead of an Israeli girl in Bethlehem, perhaps he would have spoken about the tarantula. Perhaps.

My tarantula, tastefully christened Mary Jane, can go for two months without eating. (Talk about "waiting on the Lord" to renew your strength!) I feed her every two weeks, and expected that by the time two weeks completes she would begin prowling throughout the tank like a wolf spider, stalking her prey. At the very least I expected MJ to construct some sort of trap.

These tarantulas do not eat that way, however. They wait. Literally, this week from the moment I journeyed to Pete's Pet Forum to obtain the succulent crickets, to the moment the crickets entered the tank, to an hour afterward, she did not move. She did not worry--she trusted the very stupid crickets to come to her, and they did. One cricket actually LICKED HER FOOT. When the crickets completely trust her, then she strikes, putting them to rest in one quick, painless efficient blow before liquefying their innards into a delicious smoothie.

So to take a page out of Jesus' parable book--if God takes such good care of MJ, who does not hunt, fish, or even get out a blender to make a milkshake, will he not much more see to your every need, if you trust him?

Isaiah 40:31, Matthew 5,6

Thursday, February 25, 2010

New Header: Introduction and Pilobilus

This blog is going to take on a little new flavor. I am slightly uncertain about this, but I figure that since I am so reluctant to completely throw away the "How Not To Blog" and since I really believe the Jesus Geek thing actually matters more in the scheme of things, I am going to marry the two together, that the perversion they create may open gaps between the Netherworld and this one, ripping holes in space and time that destroy the fabric of the human PSYCHE! This child of their scandalous elopement shall be named Prometheus Studies.


World-ending aspirations aside, I want to establish a basic guiderule here. First of all, I am not really here to discuss Creationism and Evolution. I am here to point out the illusive and intricate God-given metaphors that exist in science and occasionally science fiction, and although I am perfectly willing to address the subject of macro-Evolution on request, it's something I have studied all my life and quite frankly become bored with. Some people will never accept evidence, and I say that to people on both sides of that argument. Secondly, please do not sue me if I forget to cite a source. I want to say right now: unless otherwise stated, none of the scientific information that I vomit here comes from my own creation or study, for no one ultimately creates the food that becomes their barf.

I think that metaphor there at the end failed so epically it won. ALRIGHT let me show you something less fail.

Imagine walking through an alien forest. Above you rise crystal clear stalks, pliable trunks if you will, made of nearly translucent strands called hyphae. The outside of these hyphae bears an armor-like material akin to that of an insect, called chitin, and inside the cells are nearly continuous. You, of course, cannot see that, but you can see the bulbs up at the top of the see-through trees, each one capped with plate of bright orange or smooth, reflective black.

Suddenly the tree-like creature above you rears back, nearly crushing you as the kickback of an explosion drives that head almost to the ground as a black plate bursts off. The force of the stream of liquid firing the plate off into the distance accelerates the alien trees backwards so quickly that they completely smash, bursting with their whole being into nature's fastest action. I hope you leapt out of the way in time, but I sincerely doubt it.

These spore-bearing reproductive structures, sporangia, belong to the Pilobilus fungus. Imagine if your mother shot you out of a cannon like this as a newborn! This dispersion technique allows the fungus to maximize its spread, prevent competition between the young spores and the original fungus, and give them the hope of a better life farther away.

I believe that desperation often drives people simply to wilt. A frustrated desire builds up over time, and social fear or a troubled past or uncertainty or what have you pushes you down on top of it until that desire becomes a haunting and you being to hate it. Perhaps you dream of an illustrious career or perhaps you want to do well on your football team or your English paper, or maybe you're "saving it" for the right person. What happens when that person doesn't seem to exist, or your grades come back Cs and Ds again and again? In the words of Langston Hughes, what happens to a dream deferred? Many people cannot take the pressure and wilt into discouragement as the dream lingers in their mind but they no longer strive to take hold of it. Although they may not have given up, they let off a little pressure, hanging in the middle with a shriveled dream.

Maybe, if you clicked on the link and read the poem, you see where I'm going with this. The Pilobilus builds up incredible pressure over time in that tiny head as it continues to soak up fluid like you soak up ideas and dreams. To let off the pressure is to decrease the incredible potency of the glorious burst. The Pilobilus waits until the push is much more than too much to bear, until the dream of fulfilling its natural purpose spurts forth of its own accord and the world of fungi is made better for it. Not every dream is worth a wait that kills you, but every dream is worth a wait until suddenly success comes not in the way you had imagined it, but with an eerie power that far overshadows anything you could have done had you given up or let off the pressure.

So keep working on that novel, sending it to agents, and waiting for an answer. Work smart, but work hard, and don't let off the pressure by backing out the easy way (or selling the story off to a "preditor"). Realize that this "novel" is a metaphor within a metaphor for anyone waiting for love, and love the wait knowing how unique and beautiful you are, no matter how drab or humble your surroundings.

Thanks to BIOL 2040 at UVA, and Marciel Garcia, who provided the videos on Collab.