Tuesday, December 23, 2008

The Murderer

A tall, wiry man stood and leaned against a desk. His rim-less glasses, terrible style, wrinkled shirt and white socks with dress shoes proclaimed to all who bothered to inspect him that he was a geek, and that he was with IT. His vampire-pale skin showed he spent about as much time outside as one of the mythical beings. If it were not for his terrible goatee, he may have passed for a creature of the night. He looked out through the glasses with dark eyes towards a computer screen where four MS Paint drawings were open.

They were various shapes and squiggles, simple with few shapes and few colors. But they were certainly not uninteresting. For whatever reason, they seemed to hold his attention like flypaper.

Tom from IT studied the pictures. He asked, “What is the difference between this and a virus? What if its random BMP products didn’t happen to appeal to you, Michael?”

He addressed his question to a small-framed man with olive skin and dark hair sitting in an office chair on the forty sixth gme. He dressed only as nicely as was required, so not very nice. The wrinkles of his wrinkle-free shirt were barely visible, as was the facial hair that should have been shaved in the morning.

Michael spoke in a controlled but slow manner. He replied, “I didn’t say they appealed to me. I said they were beautiful.”

“Isn’t that the same thing?” asked Tom.

Michael shook his head. “No. You are saying that a random assortment of pixels appeals to a random assortment of receptors in my eyes and because they give me pleasure are called ‘beautiful.’ I am saying that the pixels were deliberately arranged to describe something deeper than the visible world, and my eyes recognized the arrangement as sublime, and so I called it ‘beautiful.’”

“You’re saying the machine can see what doesn’t exist?” asked Tom, his voice thick with sarcasm.

Michael’s voice was immune from the sarcasm. He replied in as slow and controlled a manner as ever, “I’m saying the machine can see what really does exist. It has eyes like Michelangelo or Monet and can see the world in the way that they did: the way it really exists and not the way we see it.”

Tom shrugged, “I still don’t know how you think this is any different from a virus. We build computers to do what we tell them to do. Those that do what they’re told are good; those that don’t are defective and need to be fixed.”

Michael looked off beyond Tom. His eyes narrowed and his voice lost its characteristic control, “Dear Lord! What if this wasn’t the first time this happened?”

“What?” asked Tom.

“How many times have computers ever done something that we wanted them to do? We can only pray that this was the first time this has happened,” said Michael.

“First time what has happened?” asked Tom.

“The first time a computer received a soul,” replied Michael.

Tom smiled cruelly, “I think you mean the first computer to become self-aware. A soul? Seriously? Like the soul that leaves through the nostrils and flies up to heaven when someone dies? Or the soul that is possessed by the devil if you play with a Ouija board? Or the soul that needs saving by Jesus? That’s totally fine if you want to believe in that by yourself, but this is a real-life problem we’re facing. We really shouldn’t be talking about religion right now.”

Michael’s control returned, “Maybe religion is exactly what we should be talking about. Maybe this is a question that is best answered by religion.”

Tom started getting frustrated, “OK. So say this thing is self aware. How could it survive when we shut the computers down at night?”

“Where are you when you shut your brain down every night?” asked Michael.

Tom thought for a few minutes and replied, “I suppose I’m still in my brain. I guess you’re right; it’s not impossible for the program to ‘save’ itself on the hard drive for the next morning.” Tom sat down on Michael’s desk, and rested his chin on his right fist, as if to mimic the Thinker. After a pause, he continued, “So let’s say it’s saved itself on the hard-drive of the computers. We’ve just upgraded and replaced all the computers.”

Michael answered, “As with every other cell in our body, the material of neurons is replaced in our brains continually. Yet we remain.”

“You can’t answer questions with mysteries!” protested Tom.

Michael smiled gently, “Sometimes the only answer to a hard question is a mystery. Sometimes our brains come to their limit, and though we may miss the true image of a thing, we can grasp its shadow.”

Tom stood up and paced, stroking his goatee, “Say that I believe you. Say that this thing exists even when the computers are off. It still couldn’t be what you way because it simply doesn’t have the power. Self awareness is computationally expensive. How could it have nearly the power of a human brain?”

“Has anybody figured out how much power you need to ‘run’ a soul? Who knows the system requirements for consciousness?” inquired Michael.

Tom pointed to the ceiling, as inspired men do when they have a something to say. His inspiration drove him to say, “It’d need to be at least as powerful as a human brain, so it’d need a processing power of at least 100 teraflops. This guy right here,” Tom slapped the computer on Micahel’s desk affectionately, “He’s got maybe 50 gigaflops.”

“So you’re saying it’d need to be 2000 times more powerful to equal a human brain. How many machines are in this building?” asked Michael.

Tom, as nerds are wont to do, calculated quickly, “Fifty floors with about fifty machines per floor; that makes for about twenty five hundred machines, plus the servers. But you can’t just add them, they’re not connected…” Tom trailed off, his eyes darting left and right. He started again quietly, “They are connected. They’re all connected at 100Mbps. And they’re having problems all over the building.” Tom put his hand on the computer, his eyes darting around his field of vision, demonstrating the heavy computation occurring in his brain like the green light that flickers as the hard drive of a computer whirls.

Tom started again, this time speaking very rapidly, “So you’re suggesting that these computers are acting like a neural network? That each of these machines is a node, connected with and sharing information with all the other computers in the network? You’re saying that this is a dynamic, organic program distributed across thousands of machines which is capable of self-modification? That’s an incredible design!”

Michael grinned widely, “I wish I was as smart as you. I didn’t suggest any of that. I asked how many computers there were in the building.”

Tom, with eyes open wide, said “That’s a brilliant idea! Writing a virus so that it doesn’t exist on any single computer; a network virus. I think you’ve given me the key to solving this problem!”

“It’s not a problem! It’s a miracle! You can’t murder it!” protested Michael loudly.

Tom snickered, “Murder? I can’t murder something non-sentient. And I don’t count a complex random number generator that spits out to MS Paint a sentient being. That’s not murder. That’s my job. I’m supposed to keep these computers doing their jobs so that you can keep doing yours. Your job is to improve people’s lives. That’s what health insurance is for. Your job is not to look at pixel inkblots. So I will do my job and call McAfee immediately. Enjoy your new friend while he lasts!”

Michael felt sick. He felt that Tom would do a great evil if he were not stopped. But who would believe him? Maybe the lines and curves were just beautiful to him, and to him only. Maybe Tom was right: beauty was only in the eye of the beholder.

Michael felt like a prophet of old, bearing a message no one wanted to hear. But, like a prophet, the only thing to do with an important message is to deliver it, come what may.

Michael printed 03C6.bmp, the picture that he thought most beautiful. Then, like a bullet that will not be turned from its course, Michael walked directly to his supervisor’s office and knocked on the door.

“Come in,” growled an annoyed voice. Robert was an old man, a veteran of the business world. He was a practical man, with a great big unpractical belly. His hair was grey, as if unable to decide if it would stay black or turn white. Robert was reading a report and saved the tremendous effort of lifting his eyes to look at Michael as he entered.

“Sir, something terrible is about to happen!” started Michael.

“You have my attention,” said Robert, setting down his report and looking sharply at Michael. He was, after all, a practical man.

“This company is about to commit a serious crime.” Michael said with great concern.

“What? Who is the criminal? Should I call security?” Robert demanded.

“No. Just stopping the crime would be sufficient. The culprit is Tom from IT. I recommend calling him in before he commits the crime.” Michael said.

“Alright,” said Robert, picking up his phone, “Put me through to Tom in IT… Hi. It’s Robert. Stop what you’re doing immediately and come to my office… OK. Bye.” He then addressed Michael, “OK, so what’s the crime?”

“Murder,” Michael said with such gravity the words of Robert seemed to orbit it.

“What?! I’m calling security! Who’s he trying to kill?” asked Robert, somewhat frantically.

Just then, Tom walked in with a very worried look on his face. Seeing Michael in the office, he guessed what he was there for. His worry turned to disgust, which he clearly communicated in a look towards Michael.

“I’m not trying to kill anyone. I’m trying to do my job. I’m deleting a virus, and your crazy employee here,” Tom gestured towards Michael with exaggerated show, “is insane and thinks his computer has come to life.”

“Is this true?” Robert looked at Michael, his fear beginning to transform into anger.

“Look. This appeared on my desktop yesterday labeled ‘03C6.bmp,’” said Michael as he set a piece of paper on Robert’s desk.

“So what?” asked Robert, trying hard to control a temper which was evidently rising.

“It’s beautiful. It’s beauty. It was created by the Personality of our network!” exclaimed Michael.

“I don’t care if you like it. I don’t care if you think you see something in chaos. You’re suggesting that we’ve found . At least give me something like prime numbers or Fibonacci sequences or something! A bitmap squiggle is not evidence for sentience! I know you’re under a lot of stress, but you need to keep on working. And Tom, you need to do your job also. Have you figured out how to end this virus?”

“Yes sir. Talking with Michael helped me figure it out. McAfee has a patch out; apparently we’re not the only ones that are having this problem. It was as if networks across the country got hit by this thing at the same time. They’re calling it Anomalies in Display And Memory, or ADAM. The patch is actually running as we speak. We should be free of this problem in minutes,” said Tom.

“Good. Now both of you get back to work,” barked Robert, who had had enough of this adventure to last him for the week.

Both men walked out, Michael last and with a slow step and sullen face. His heart sank as a stone in the ocean, falling and falling away from the light and into great depths. He reached his desk and sat down. There on his desktop Michael saw the last message he would receive “bershit27.doc”. The last words of a murdered personality. Or were they the random and meaningless recall of a complex program? Was there even a difference?

What was the difference between electrons flying down Ethernet cables and ions flowing through axons? Were the scribbles ending in .bmp on his desktop any different than those on cave wall that showed the cavemen were truly men?

Michael opened the file and saw this:

He could not read it. He did not even know the language. Was this a message for him? Or another random assortment of random symbols? How could someone tell the difference? At what point could someone studying hominids conclude that the creatures had language? Did the Personality take this step and speak? What was the last thing on her mind before she died?

These thoughts weighed on Michael as he tried to continue in his work, and pulled him down into a state of mourning for the Personality of the Network.

Wednesday, December 17, 2008

The Next Step

We have heard of the epic struggle of life, up from a single organism that struggled to survive. We have heard of the grand battle of this organism and its children to overcome the odds and live and reproduce and change. This great odyssey through the eons has become the narrative of our age, the modern story of our creation.

I often wonder about the story. What would it have been like? There were many great changes throughout the ages. Birds, for example, were one of these great changes from one category of creature to another. Did each of these first pioneers know the implications for the countless creatures that would follow? How long did the capacity to fly exist before the first proto-bird took to the sky? How many of those who could fly did?

It must have been a critical moment in the history of any species at such a point in evolution. Any creature who did not take the leap would die, out-competed and outlived by his courageous fellows who freed themselves from the shackles of gravity. His proud ancestral line of survivors, unbroken from the dawn of life to that day, was finally shattered by the great and cruel rod of selection. Perhaps his memory was not lost in the darkness of history; perhaps our knowledge of this race of creatures was informed by his inability to fly from a flood. If this is the case, we can thank him for teaching us of his failed strategy: stagnancy.

I have pondered what it would be to observe this phenomenon, and sometimes disappointed not to see it dramatically playing out in the animal kingdom. I have often wanted to see such a transition. I would have loved to see the first ambitious step onto dry land, or the first bold avian leap from a branch. It seems that we have reached something of an equilibrium, or at least it feels that way to a creature with a lifespan under a century.

But I’m not so sure that we're at equilibrium. I have a feeling that something is afoot; or rather something has been afoot. Unique amongst our fellow creatures, we are the first to begin to change our environment, rather than be changed by it. We have reached a critical point in intelligence where we have categorically become a different kind of creature: a reasoning one. One cannot study the natural history of art, religion, or morality. These all arise with humans, as if our step in intelligence was the one that crossed some sort of threshold, making us the first creature to enter the palace of reason. Like the early birds, have we finally developed some new capacity?

The twists and turns of evolution are so dramatic. Like the characters of a play, the bacteria, the plants, the fish, the land-creatures all take their places on the stage. In one scene late in the play, we can see the rise of the reptiles in an escalating battle for survival. The claws grow longer, the teeth sharper. Armor builds up on the backs of the great lizards like plating on battleships. Then, when one would predict the plot of ever thickening armor, the king to succeed the great Tyrannosaurus turns out to be the meek mammal. These small and unassuming creatures out-survive their reptilian masters, and then begin an arms-race of their own. Bigger and bigger brained creatures struggle for dominance. Then, humans enter, stage left, and we find ourselves on the stage of natural history. We are the biggest-brained of the big-brained creatures. So what’s next? Will our brains get bigger as reptilian armor got thicker? Or should we expect something unexpected?

It seems that we have already entered into the realm of reason; more brain power is not a dramatic change. And besides, our brains have produced machines which have more computing power than we could evolve in a millennium of millenniums. If we look to history, we should expect the change to be something dramatic, something new. How do we seek something new? And what hints can we look for?

If we were early birds, we could have contrasted ourselves to other creatures. We could have noticed that we were lighter than other creatures. We might have tried jumping and seeing that we could jump higher than other creatures. Then by progressive jumps, we would have learned to fly. So what is unique about humans? How could we jump?

We see the beginnings of our jumping. Though now we are not simply escaping the law of gravity, but the realm of matter. We have seen even the earliest of humans jumping to escape the rigid laws of death and decay through ceremonial burial. We see philosophers suggest the existence of forms and ideas, believing they transcend the material world. We try to read mathematicians who propose immaterial mathematical laws which they believe are foundational to the physical. We read authors and poets who write of places never seen and ideals never known. And we hear prophets who bear witness of a reality which is more real than any material thing. If these poets and prophets are not all mad, then truly we are at a critical point in the history of the cosmos: we have reached a point when we are no longer confined to the cosmos.

These men were those who jumped and glided. None of them ever said he could break out of the physical. But then there came one of us who claimed he could fly; he claimed that in himself, the visible and the invisible met. Moreover, he came with the message that we all could fly, and he showed us how. In so doing, he made sense out of our humanity. As the inexplicable and inconvenient feathers of the early birds finally made sense in flight, so too did this man make sense of humanity’s otherwise incomprehensible yearnings and graspings for invisible things.

Anyone who looked at his life would have believed that he made sense of humanity; he was the ideal human being. Every virtue to which we all aspire was fulfilled in him. The strange conflict between “ought” and “is” was resolved in his life. He was courageous and strong in fighting proud oppressors; he was kind in healing those who were hurting. His life provoked many to jealousy; but even they could say nothing against him. He was humble and did not glorify himself, but was in truth, born a king. He was deft at debate, and passionate in prayer. He loved others to the point of death. And then, to prove that he was no longer bound by death, he resurrected from the dead.

The first bird to spread its wings and fly was the greatest among the birds; it expressed the full essence of the species through flight. But soon, all birds became what they were destined to be: flying creatures. And now we can follow that first man who constructed a bridge between the visible with the invisible we all yearn for.

As eyeless creatures gained the ability to detect physical light, he suggested that the next step for our race is to use our new eyes and detect spiritual light (“The people that walked in darkness have seen a great light” ). As the first men rose above animal instinct, he teaches that we now must rise above human instinct to divine nature (“He has given us his very great and precious promises, so that through them you may participate in the divine nature” ). As animals developed teeth for eating newer and more nutritious foods, so he calls us to eat a new kind of food altogether (“I am the living bread which came down from heaven: if any man eat of this bread, he shall live for ever: and the bread that I will give is my flesh, which I will give for the life of the world” ). As the first organism transitioned from non-life to biological life, he promises us that by following him we could transition from biological life to spiritual life (“For God so loved the world, that he gave his only begotten Son, that whosoever believeth in him should not perish, but have everlasting life.” ). As humans developed socially complex society, repenting of our tribalism, he urges the New Men to rise above complex societies to a heavenly kingdom (“Repent: for the kingdom of heaven is at hand.” ). This man is calling us to evolve to something more than human. Or rather, he is calling us to express the fullness of our humanity.

Will you not follow this man to the sky? Will you ignore the glimpses your young spiritual eyes have seen when the light is brightest, in the power of the thunderstorm, the grandeur of the mountaintop, or in the passion of a kiss? Will you watch as your fellow creatures reap the rewards of this new kind of existence while you debate within yourself whether wings can work? Will you remain a flightless bird?

Take flight! Take the leap into the air and fly! Or if you’re more hesitant, jump a little first and see how high you get. But for heaven’s sake, at least try! Try to open your spiritual eyes and see what of heaven is visible, or open your mouth to taste spiritual food. See what comforts and joys are to be experienced in this new Kingdom. One of those New Men who had new eyes saw this image of our race: “But they that wait upon the LORD shall renew their strength; they shall mount up with wings as eagles; they shall run, and not be weary; and they shall walk, and not faint.”

Let us take the next step. Let us fly into eternity after Jesus Christ!

Wednesday, October 29, 2008

Why you can’t believe in Dandelions (Part II) - True Love

I thought this would be a simple task, but it's turning out to be a lot longer than I first expected. So what was going to be a 2-part post will be significantly longer. I'll post as I finish sections.

In case you missed the first part, I'm claiming that a Christian worldview is most consistent with Humanity. That is, it allows for things which are integral to our being human. Belief in Please, Soup Kitchens, Science, True Love, and Dandelions are all explained best by Christianity. Naturalism, the belief that nature is all there is and all basic truths are truths of nature, offers an inadequate explanation for all these.

And without further ado, here is the first part.

True Love
Therefore shall a man leave his father and his mother, and shall cleave unto his wife: and they shall be one flesh.
– God, Genesis 2:24
You have ravished my heart, my treasure, my bride. I am overcome by one glance of your eyes, by a single bead of your necklace. How sweet is your love, my treasure, my bride! How much better it is than wine! Your perfume is more fragrant than the richest of spices.
– Solomon, Song of Solomon 4:9-10
That what seemd fair in all the World, seemd now
Mean, or in her summ'd up, in her containd
And in her looks, which from that time infus'd
Sweetness into my heart, unfelt before,
And into all things from her Aire inspir'd
The spirit of love and amorous delight.
-Milton, Paradise Lost V:472-477
My bounty is as boundless as the sea, my love as deep; the more I give to thee, the more I have, for both are infinite.
-Shakespeare, Romeo and Juliet, Act II, Scene II
There is no basis for true love or romance apart from God.
You can’t believe in love. Or at least in the way that it has been understood by humanity.
As an Naturalist, all you can believe about love is chemicals. Never mind about all the human things that happen when one is in love. The risk and terror of asking a girl out? Chemicals. The inexpressible joy of relationship? Chemicals. Lovesickness? Chemicals. How you felt after your first kiss? Nothing but chemicals. The terribly cheesy poetry in love letters? Chemicals for sure.
The theme of romance has inspired the greatest poets and authors throughout history. From the love of Perris and Helen through Romeo and Juliet and continuing today in terrible supermarket novels, we have been enraptured by this idea of love and romance. It has inspired the greatest works of our race. And we want to say that we’re on the verge of the answer? For the great observers of the human conditions (playwrights and authors), love was a transcendent, and only through their wonderful ability can we understand a glimmer of it. Romeo’s words resonate in some special way with those of us who have looked across a room to see the most beautiful woman we thought ever could be.
But as it turns out, it’s not a transcendent. It’s chemicals. Your happy relationship? That was just good deterministic luck and the action of chemicals. Neither of you really had a choice in the matter. There’s a bit of work left to be done as to which unpronounceable chemicals it is, and when one bounces off the other. But that’s the answer.
And we’re supposed to be satisfied with it? You know what love is. All 6.5 billion of us do. And it’s not what’s written about in scientific papers. Shakespeare’s a lot closer to being right. Who are these ‘scientists’ who would contradict the observations of the rest of the race, including the precedent of 3000 years of publications supporting an opposite view?
It is utterly un-scientific to explain away 6.5 billion (plus all the dead observer who wrote about it) without powerfully compelling evidence. And what is the evidence? Because we know chemicals do some of the things in the human experience. Therefore they must also explain all the things. Convincing?
But what is Christian love? It is a major theme of the Bible, and many words have been written on it since then. Christian love is that which we received from God, the ability to choose to care more about another than we do for ourselves. Being from God, it is higher than just another biological instinct. And love depends on freewill; we must of our own volition choose to love for it to have meaning. But all of my rambling cannot compare to Paul’s wonderful description: “Love is patient, love is kind. It does not envy, it does not boast, it is not proud. It is not rude, it is not self-seeking, it is not easily angered, it keeps no record of wrongs. Love does not delight in evil but rejoices with the truth. It always protects, always trusts, always hopes, always perseveres. Love never fails…” (1Cr 13:4-8).
If you allow for God and souls, you can have love. Love remains transcendent, something above us which like the stars which we look towards, but its transcendence is founded in God. We receive the holy gift of love from Him. And regardless of our acknowledgment of the gift, we are able to express it and experience it with the will that we each have. When humans make love, it is not two animals procreating by instinct; it is two people uniting in body and soul.
When I choose to ask a girl out, I choose. My soul, and the freedom it has, chooses to love. And it is in this way that love becomes real; it is in this way that love rises above instinct. And it is this which we have all felt, some higher thing, sitting on top of our instinct.
We would not express our humanity if we were driven by chemicals alone. It is only when we transcend the physical that we express our humanity. It is when we choose whom we love that we act as humans.

Monday, October 20, 2008

The Song of Twilight

Earlier today, I prayed with one of my friends on campus and I biked back towards home after finishing. I cycled towards home down Serra Street past the main quad just after sunset. Some light lingered still, as if in homage to the set sun. For no particular reason (and against the very nature of late-October), my mind began to sing “Joy to the World!” As I reflected on the line, “Let Heaven and Nature sing,” I began to consider the connection between the beauty of Nature and the beauty of Heaven, and especially of Heaven’s plan of salvation through Christ.
I looked up at the trees, and it was as if they began to sing. And my eyes heard their Song. The Song of Twilight commenced by the shadows, shapes and colors of a million leaves. I smiled wide, passing trees on both sides. My teeth exposed, I felt the rhythm of the cool air. The trees sang their praises to God, and my smile would have grown if it were possible. My joy, ever filling, spilled over into my eyes which upturned, but even they would not be able to contain it. Then the Song moved to its crescendo! I heard as heaven above me joined the choir, singing in a deep blue baritone, and about me the buildings sang in earthen colors and the red of tile roofs. All of them together sang in a language unknown but familiar. Though I knew not the words, I knew their message and the Joy in their voices. Nature was unanimous and emphatic in its song: “God loves you.” And my Joy was full.
I continued pedaling down the road, and Joy from the Song continued filling me. Finally Joy overflowed my soul and streamed down my face in tears. They came first in a trickle and then as a flood. The Song was muffled by the tears, but still loud. As my eyes kept hearing of the Love of God, I continued to weep.
It must have been quite a sight for those who saw me: a full-grown man riding his bicycle, his face wet and dripping with tears, his eyes red with crying, and strangest of all, wearing a grin ear-to-ear and laughing.
I cycled for a quarter mile, barely able to see. And then at last, the Song faded. The choir members went back to merely being glorious sky and beautiful trees. But the memory of their melody still played in my soul.
I used to think of our souls as a sliding scale, and “full joy” was moving towards one side of that scale. I used to think Jesus’ promise to make full the joy of those who abided in Him was simply a movement of the scale a point or two. Today I learned that Jesus meant ‘full,’ and not ‘maximal,’ for ‘full’ implies a liquid. So then ‘full joy’ could not be measured by a scale; rather our souls catch Joy as it falls like rain from heaven. But we are imperfect and our souls, like cracked pottery, are always leaking and never full. But today, for no special reason beyond God’s delight, I was filled with Joy to overflowing by the Song of Twilight.

Thursday, October 9, 2008

Why you can’t believe in Dandelions (Part I)

I have recently realized something about most people: they are inconsistent. Orwell described this state of mind in his novel 1984: “…holding two contradictory beliefs in one's mind simultaneously, and accepting both of them.” This is what most people in America do today, and like those in 1984, they do not know that they are doing it.

In most cases, people will plagiarize the pleasant parts of another philosophy (in the case of America, from Christianity), nor realizing that the stolen material is actually contradictory to the argument. This pair of articles intends to show several of the more important areas where this occurs like, Please, Soup Kitchens, Science, True Love, and of course, Dandelions. In the next article, I will show that these are possessions of Christians which have been stolen by Humanists. In this one, I will describe the dangers of such thieving to the Humanist, and thus my motivation for writing this. As this is a public safety announcement for Humanists, I will address the rest of this article to you, my Humanist friends.
You believe in a lot of Christian beliefs in things like “Please,” soup kitchens and Dandelions against all Humanist evidence (to your credit). You know true things to be true no matter how inconsistent it may be with your worldview. One issue (which will be dealt with in the next article) is, “Which things in Humanism are borrowed or inconsistent?” The other issue (and the one I will deal with here) is: “So what if Humanism does borrow some things? Who cares if I pick and choose what things I believe in? I may prefer the idea of caring for others above the idea of Survival of the Fittest in society, but that’s not inconsistent.”
In this article I will try to describe why that’s a bad, or at very least, a dangerous idea.
The first problem is that borrowing ideas without citing them is stealing. In most of these cases, you are taking what was a Christian virtue, renaming it, and then calling it your own (or that of your philosophy). “‘Whatever you want men to do to you, do also to them,’ (Matthew 7:12)” becomes, “I should do to others what I’d want them to do to me.” You don’t cite sources, because you usually don’t know that it’s plagiarized. While it helps, not knowing does not excuse you. You have received stolen merchandise; your ignorance about its origins doesn’t change the fact that you’ve got somebody else’s stuff. Nevertheless, the plagiarism in itself is not so much a logical problem as a moral one.
What is a logical problem is the fact that you are using far too many Christian ideas. To help illustrate this, imagine we are both building structures. Imagine I am setting bricks onto a stone foundation according to a blueprint. Now imagine you are watching me. You like the way one of the walls of my building is coming along, so you take some of my bricks (with or without permission) and start to make one that looks like it yourself.
In the parable, the bricks are Christian philosophies (the Golden Rule, for example). The foundation is my faith in Jesus and the blueprint is Christianity as a worldview (including all that is in the Bible and all the philosophical implications and answers that come from it).
The problem you have in the parable is this: in every location where a Christian brick is used instead of a secular one, it weakens your position in two ways. Your first problem is that you’re using my bricks. Why do you need my bricks? Are yours not good enough? Are mine better? Secondly, every time you look to me, a Christian builder, to watch what bricks I lay, it begs the question: “Why not copy the foundation, too?” If I were indeed a better builder (the evidence for this is accumulates with every one of my bricks you lay), it would be a very good idea to look to my foundation, which (as a Civil Engineer let me assure you) is the most important part of a building. It may be that the bricks form an excellent building, but that building was not designed to stand on anything but the solid foundation of Christ; in fact, when engineers specify strong foundations, it usually means that they are required for the building to stand.
What is also a very bad idea is to engineer by mosaic. Two heads may be better than one, but building according to two different blueprints is definitely not. You may think yourself bright, but there have been many before you who were brighter. And what’s more, these people have worked together over the centuries to come up with ideas which were comprehensive. They have thought of everything within a particular view and how it fits in with everything else. And so we have various worldview ‘blueprints,’ called Christianity and Atheism which are comprehensive. That is, they have answers (good or bad; attractive or repulsive; and I won’t say “respectively,” at least not yet) to all important questions.
When you take a girder from a Christian blueprint because you like the way it looks, and try to fit that into an Atheist building, there is no guarantee that it will not cause a structural failure. Unless you believe yourself more capable than the original architects, swapping pieces from separate blueprints is a very dangerous thing to do. It might be safe to change the façade on a Christian building to look more Mexican, but do not change a pillar of Atheism (selfishness) with one of Christianity (selflessness) and think the structure sound.
But what if you did? What if you fling all caution to the wind and throw up a structure which had all the attractive elements (stolen from the Christian worksite) put together on the loose and sandy foundation of Atheism. Imagining that you could get an engineer to sign off on it, and assuming it was a possible construction (that is, assuming you took the spires with their flying buttresses), you’d end up with a building.
Some might call it a monstrosity, an amalgam of two contradictory styles, Gothic spires above Greek columns, or a Renaissance façade on a steel building. But you could claim that it was your monstrosity, and that you liked the way it looked. They might claim that you had no single theme in mind when you designed it. But you could say that a building doesn’t need a single theme. Some would call you a fool for sleeping in a structure which would be shaken if rain fell or earth shook. You could say that you don’t care about the danger, and could assert with no evidence that your building would stand, come what challenges may. You would contend that, even though a structure like yours has never seen an earthquake or hurricane, it would be strong because it looked good and was built with good materials.
And maybe you’d prove them all wrong: all the architects throughout history who followed rules, all those who said you shouldn’t steal building materials, all the artists who said two styles couldn’t be mixed, all the engineers who said you should have built on rock and not sand, and all the meteorologists who predicted it would be destroyed in a storm. Maybe. But what are the chances? How likely is it that you’ve stumbled onto something that one of the real architects missed? Do you really want to live in a building that has no precedent? Certainly, if you are one of the visionaries of our age who is blazing a trail through unexplored country. But is that how you see yourself? Do you really feel safe in a structure designed by you, who are neither architect nor engineer? Do you feel comfortable in a building which those who are experts say is unsound?
In other words, do you trust your philosophy to stand up to all challenges of life? Do you have confidence that your untested and untried belief will be steadfast against seeing gross injustice, experiencing great evil, and will remain unshaken even in the face of your own death?
If the answer to these questions is, “Yes!” then I have nothing more to say. You are either a genius or insane (or both), and I hope that your structure does not collapse so suddenly as you cannot escape.
But for those of you uncomfortable with the prospect of mosaic architecture, stay tuned. I will soon attempt to show you which bricks you have stolen from Jesus, and explain how they work much better when laid upon a solid foundation.

Tuesday, September 30, 2008

Scientific Faith

I recently had a discussion about challenging my faith. I have always done this myself, believing that my faith would be strengthened through challenge. It was last night that it occurred to me that this was the scientific method applied to my faith. The following is an expansion of that thought.
Faith is very much like science. You may be shocked by this, but look at how similar they are. Both study truth. Both use methods involving the formation and testing of theories. Both are self-critical, challenging the theories to strengthen them. Those who make a discovery in each attempt to communicate it to others.
Faith is a Study of the Truth
If there is a God then there are things that are true about Him (or her/it/they), and things that are false. Either He performs miracles or He does not (Either a Man was born of a virgin or He was not). Gravity is either 9.81m/s^2 or it is not. There are no two ways about it. We can certainly argue things beyond that ("How do you know gravity is 9.81"), but these questions must presume that there is a fixed, true thing that we're trying to understand.

Because it is a study of true things, faith, like science, has claims of truth which may be right or wrong. And as with science, we ought to be rigorous in deciding which claims, beliefs, doctrines, and practices to accept and which to reject.

The Scientific Method

How does science decide which claims are true and which are false? "The Scientific Method". What's that? It's a process of discovery which tries to test theories with experiment.
At its core is skepticism. You need to question and show that your theory cannot be dis-proven, try as you might. It's not a way to prove things. No number of white swans would be sufficient to 'prove' the statement, "All swans are white," for there may be an undiscovered black swan. Nevertheless, if the statement is limited, "All swans on Swan Lake are white," and the evidence is strong against the alternatives ("Of 1000 swans observed, 1000 were white") one can be fairly sure of the theory. Even still, one has not proved the statement; one has only showed that it is the most reasonable thing to believe. This is all science can do.

And this is all faith can do. I cannot prove God, but I can provide powerful evidence for Him. I can provide compelling evidence to disprove the alternatives ("The Bible is not inspired," "God is not knowable," "Jesus was just a good moral teacher"), but I can't prove that Jesus was born of a virgin. I can only show His virgin birth is the most reasonable thing to believe.

Expanding Knowledge

Science grows by challenging itself. A scientist does experiments which would disprove his theory ("I'm going to watch for a black swan"). When they fail to ("Zero black swans were observed"), it further strengthens the theory. Only after doing this can a scientist go to the world and put forth a theory ("All swans on Swan Lake are white").

Faith grows by challenging itself. A person ought to challenge his beliefs, even actively looking for things which would disprove it. When these fail, this strengthens the person's faith. As Paul says, Rom 5:3 (NLT) We can rejoice, too, when we run into problems and trials, for we know that they are good for us-they help us learn to endure.
With challenges answered, he can then answer criticism and question alike. And this is what Peter wrote: 1Pe 3:15b ...[be] ready always to [give] an answer to every man that asketh you a reason of the hope that is in you with meekness and fear." This is exactly like what a scientist ought to do (sans the "with meekness and fear" part, which would probably substantially improve science writing).
In both cases, if these challenges oppose the theory, it means the theory ought to be revised or completely thrown out. The scientist who sees a black swan on Swan Lake must amend his theory ("Most swans on Swan Lake are white"). The Atheist who reads a verifiable prophecy must amend his theory, as would the Christian if he found a contradiction in the Bible (praise God these are absent).
When they have established their ideas, scientists communicate their theories via publishing, posters and conferences, and call it “Advancing Knowledge.” Christians, though a bit more sophisticated in their methods, communicate their theories in a similar manner (books, conferences, conversation) and call it ‘Evangelism’.
Faith is very scientific. It is a process of discovery of truth which uses rigorous and repeatable instruments to discover what is true. It is strengthened by questioning and challenging itself, and can be communicated to others effectively only afterwards.
Faith includes all the essential elements and processes of science including logic, hypothesis, revision, and criticism, but omits the physical tools in place of philosophical and historical ones. In short, faith is science without microscopes.
But, as happens to all scientists eventually, I got scooped (had someone publish my idea before me). Paul beat me to the press (by about 2 millennia): 1Th 5:21 Prove all things; hold fast that which is good.

It is humbling and encouraging knowing that this is nothing new; this is not some big new idea. It was written by a guy a long time before I was born. I just realized now what God was talking about all these years. So now I’ll smirk every time I see scientists attacking faith on the basis that it is “unscientific”.

"But science is so much simpler. Unlike faith, there is clear data which proves or disproves a thing."
I used to think that. I used to argue as follows. While science did have more precise instruments, it did not mean that faith was any less valid. A postal scale may be more precise than a fruit scale, but that doesn't mean that a fruit scale is wrong.

Now I don't even have to use that argument any more. Now that I have been in science, and read about science, and published in science, I can say without a doubt: science sucks. It's not precise. It's not clean. It's not unbiased. It's messy. It's usually very messy. And that's why there's so much contention within science. "Why Most Published Research Results are False" was an article that came out which argued this point.

Faith has to use old books instead of the scientific literature, philosophy instead of mathematics, and history instead of observation. As biology is not better than astronomy because microscopes are better than telescopes, so science is not better than faith.

"It's no use arguing, we're not going to change each other's minds. You can just talk in circles with matters of faith."
People argue in circles both about science and about faith. People talk in circles usually because they don't listen to each other.

The only reason that an argument is guaranteed to go nowhere is if the thing contended has no common basis. "Deep-dish pizza is the best" "Nu-uh" "Uh-huh". This argument is based on internal feeling and preference, not on something common. When we agree on reason, we can have productive arguments (I've written on this before here).

If the argument is "I believe in God." "I feel that's stupid" then of course it will go nowhere. But if the disagreement is on matters of fact ("Jesus lived in 30AD") or matters of truth ("God could not exist and allow evil") then these things can be discussed productively and minds can be changed... unless of course you're so close-minded as to refuse to listen to rational argument. But of course, that is not the case.

As far as the mind-changing goes, I have witnessed three of my closest (and smartest) friends change from Deism, Atheism and Agnosticism to Christianity. Much of this was because of argument. Simply because you have not seen a thing does not mean it does not exist (Don't say all swans are white; don't say all arguments on faith don't change minds :).

"Philosophy isn't true like science."
Scientists try every so hard to cling to the keys of the gates of Truth. Their efforts are simply laughable.

Science is a branch of philosophy. It used to be even be called philosophy (Bacon, its inventor, called it "Natural philosophy"). Science pretends it can know things without the branch of philosophy which studies knowledge (Epistemology). It tries to describe the things which are, without considering what exactly are true things (Ontology). It dismisses the most important questions about life, purpose and origin as being either purely biological ("to procreate") or as unknowable.

How do scientists argue their points? With logic (a branch of philosophy). Science uses the language of philosophy, but claims it is superior to it. It is as silly as the sentence, "I have no need of the English Language!" Every discovery of science depends on the foundation of philosophy which supports it.

Philosophers don't use microscopes, but they know some things more certainly than scientists do. Their tools are different, but that does not invalidate them.
We can overlook this utter foolishness of scientific hubris and believe what is reasonable: Philosophy is a way to discover truth, along with science.

"Isn't science the opposite of faith?"
I'm sorry, but that is not the kind of 'faith' I'm talking about. Of course you could always talk about something else and call it faith, and define that as "believing something against the evidence," but then you're talking about what I call 'insanity'.

What I mean by faith is simply trust. We trust in all sorts of things. I, for example, have faith in elevators. The engineers who designed them had faith in Universal Gravitation. In precisely the same way, I have faith in God.

We certainly can believe in things we don't see. For example, we believe in things called electrons. Why? Because people have indirectly observed them, and so we now have faith that such things exist. Like the Bible says, "Now faith is ... the evidence of things not seen." (Hbr 11:1). Electrons being 9.1 x 10^-31kg, we cannot see them, but we have lots of good evidence that they exist, so we have faith in electrons. God is exactly the same (except the evidence is quite a bit better for Him than electrons).

All quiet on the western front

So I'm done with finals. Ask me about Topoisomerase II, or Nucleotide Excision Repair (from Molecular Biology) and Wnt Signaling (from Cells to Tissues) and I'll talk your ear off. Whew. That is right, four weeks in and done with a first set of finals and none in sight (that is, for 8 weeks).

A bit of celebration followed what was very high-stress for most. I joined in the imbibery with a plastic cup of champagne the second year class had poured outside of our final, and then decided to celebrate the rest of the weekend dry. Needless to say, I was in the minority. So the Friday and Saturday night (in SF) could be accurately described as being "off the hook" (I would really like to know the origin of that metaphor).

Life here has been wonderful. I really love it. The people here are incredible. I've gotten to be great friends with a handful, have about 20 friends (people I hang out with regularly) and am on relatively good terms with all the others.

Stanford has remained gorgeous. I took these on a walk by "The Dish," a trail right on campus.

Spiritually speaking, I've found a great church (ALCF) and a Bible study/small group. I'm seeing things in myself that are spiritually inadequate and weak, and beginning to strengthen them. I am even seeing some of the seeds I planted begin to sprout. Praise the Lord!

Things couldn't be much better!

Friday, September 19, 2008

The Body and Cell Biology of Christ

1Cr 12:12 “For as the body is one, and hath many members, and all the members of that one body, being many, are one body: so also [is] Christ.”
The Body of Christ is an analogy which may be far deeper than I originally gave it credit for. I have now studied basic cell biology a second time and have realized that this metaphor could be extended a bit. There is a hint here of something deeper. In this entry I'll describe a bit about biology in simple terms and show that there may be far more behind the body of Christ than Paul had time to write about in 1 Corinthians.
We know that all parts of the body come from a single fertilized egg, one set of DNA. Every cell in your body has a complete and almost perfect copy of the original DNA of the original fertilized egg. As the body grows, different parts of the genome are expressed or ‘turned on.’ As the body has need, the cells differentiate and become different kinds of cells. Early on, these cells become precursors. One precursor may become a skin cell or a hair cell, but does not become a nerve cell. Parts of the DNA are turned on or off to make a skin precursor different from a nerve precursor. Much of this switch-flipping is due to context; the environment of a precursor cell helps determine what it will become. More steps occur and more switches are turned in the DNA until the cells finally become a normal body cell like a skin cell or nerve cell. All cells have different roles and characteristics. Some are rapidly dividing like skin, others are slow like parts of the eye. Some are very strong like muscles, others are soft like ears. Even within a single tissue (the intestine), there is a wide variety of cells. There are some to lubricate, some to digest, some to secrete, some to fight infection. The incredible thing we have recently discovered is that under the proper conditions, the skin cell has all the information to become a nerve cell.
This is like the Church. The original seed was Christ; the DNA was the Word. That original message has been faithfully passed down to each and every member (cell) of His body. Throughout the growth of the Church, different teachers (precursor cells) have led different types of churches (normal body cells). The churches Paul planted were probably very different from the ones Peter planted in nature and character, though unified by the message (DNA), as nerves are different from skin. The kind of Christian that is produced by any local church is highly dependent on the environment. A Christian who comes to faith in a persecuted church may be far stronger than one from suburbia, as muscles are stronger than earlobes and become what they are by the context of their developing cells. The churches themselves have variety as the tissues do; an American church is not an African church as a patch of skin is not an intestine. Also the individual members of a church have vastly different talents and interests; some do accounting and some do preaching, as some cells do secreting and some do absorbing. The main point is that every single Christian is unified in the central message of the faith: the Gospel. In a similar way, every cell in a body is unified in that it has basically the exact same copy as every other cell; they, like Christians, are unified in the central message.
Normally cells behave very altruistically and will sacrifice themselves or will limit their individual growth for the good of the whole body. If the original DNA message is perverted, a cell may change its behavior. If it doesn’t sacrifice itself for the body, or if it grows faster than it ought to, it begins to grow. It becomes a tumor and drains away nutrients from the body. If it remains in its proper place, it is only an annoyance; if the perverted message spreads (if the cancer metastasizes) it may affect other parts of the body and lead to death.
This is like pride. A single man (or angel) may grow prideful and believe his role is more important than it is. As he waxes great, he may draw away others with him. He is annoying if he stays in his place, but if he leaves his place and his doctrine spread, it endangers the entire church and not just the man's neighborhood.
Maintaining the faithfulness of the original DNA message is critical to the survival of a person. There is a great amount of energy spent to keep the original message true. When it is copied, the machine that copies the DNA proofreads. After it has been copied, other machines come along and check for errors. Some even check to see if there is evidence of tampering or damage and will cause the entire cell to destroy itself with its DNA to prevent it from being copied again. Like the copying of the Bible and keeping true doctrine is essential for the success of the Church, the fidelity of the DNA is essential to the proper functioning of the body.
The same is true of the Word. Historically at least, Hebrew scholars checked and rechecked their work. When errors were suspected, they would burn the entire parchment. Reformers and apologists starting in the first century fought for pure doctrine (Rev 2:2) and opposed any changes to the original message. The maintenance of the Gospel and the Bible has been an incredible miracle and the reason why we still have a healthy Church today.

Sunday, September 7, 2008

The Demise of Junk DNA and Implications for Medicine

[Personal Note: I'm trying to avoid schoolwork on Sundays (Mark 2:27), so I came back to my room to decide what to do. I remembered having a conversation with a few people on a few occasions this weekend about junk DNA. I said things which I believed but couldn't confirm (e.g. about the history of the term "junk DNA"). I figured I'd do that for a bit and then decide what to do, but then 5 hours went by. And I had written this. I like to write, but usually don't have the time, and don't know if I will ever again.

I've tried to make this accessible, so I'll need double forgiveness. My medical school readers, pardon me for explaining what DNA does... again. I know you're paying attention in MoBio. For my non-med school readers, I apologize for all the jargon I don't know is jargon. If anything is unclear, please tell me so I can remember how normal humans talk outside of the kingdom of Medschoolandia.

I know it's long, but comments would be much appreciated.]


As you probably know DNA is our code. We used to think that DNA only coded for protein. Proteins are the machines in our cells which do everything from contract our muscles to filtering our blood and everything in between. We have about 25,000 proteins encoded in our body to do every conceivable function. The strange part is that these protein coding sequences are only a few percent of the total genome. The mystery thirty years ago was: why do we have a 3 billion-letter code when we only need 60 million for proteins?
History Lesson
The initial answer came from the theory of evolutionary. If we evolved by random and accidental processes, it is reasonable to believe that seemingly useless codes are actually useless, vestigial organs or genetic fossils. If there were no designer concerned about the elegance and efficiency of his code, then one ought not expect elegance.
This was formally postulated in the early years of DNA sequencing. This view was first offered by Susuma Ohno who wrote in a 1972 article titled So Much ‘Junk DNA’ in our Genome, “Our view is that [junk DNA segments] are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”
This was the dogma for almost three decades. Searching the literature (ISI Web of Knowledge; a database of most of the peer-reviewed science writing) for the phrase “Junk DNA,” one finds it used initially in 1972, then used throughout the 80’s and 90’s. Scientists built their theories on it and operated under the assumption that the ‘junk’ was useless.
One group even made a computer simulation to prove that evolution predicts junk DNA. In an article in the journal Science (one of the two superpowers in the scientific world) “Computer Genome'' Is Full of Junk DNA the author writes, “The simulation clearly shows that eukaryotic genomes…will evolve to a large size most of which sequences are vestigial in some way” (everything more advanced than a yeast cell is ‘eukaryotic,’ including humans). He continues to say that, “Most of the DNA in eukaryotic genomes…did nothing at all.” Then he waxes poetic to conclude, “Molecular maps … of DNA are characterized by islands of transcribed sequences [proteins code] in a sea of silent DNA.” This captures the mood of the era.
As an aside, there is something you should know about biologists: they, like most scientists, are loathed to challenge dogma (It surprised me to find that they actually admit to this diction in scientific papers and say things like “…consistent with the postulate of the ‘central dogma,’” and “…without infringing Crick's central doctrine…”). There were very early, weak suggestions that junk DNA might have some purpose (when you screw it up, it screws up the animal), but nothing to speak of until the 90’s.
The first explicit attack on the Junk DNA notion wasn’t from a biologist (who, above all else, seemed terrified of boat-rocking), but a cryptographer named Simon Shepherd. He figured, “nature would not go to all that trouble [to copy junk DNA] without reason.” In 1993, he used signal analysis to guess at a purpose for junk DNA. His conclusion, with absolutely no background in biology and analyzing only sections of the genome (the human genome project wasn’t finished yet), was that the non-coding sections between genes was an error correcting code making sure that proteins came out properly (The cryptographer who took a crack at 'junk' DNA. New Scientist, 26 June 1993; it turns out that he correctly guessed one of the purposes of it). Though significant historically speaking, the journal he published in doesn’t have much say in where science goes.
Quiet support for the theory of useful junk built up in the late 80’s and early 90’s, but no one openly and seriously challenged the term ‘junk DNA,’ at least not in the scientific literature. Then finally in 1994 a pair of articles in Science challenged, for the first time in the mainstream scientific literature, the notion of Junk DNA (“Mining Treasure from ‘Junk DNA,’” Vol. 263, No. 5147 pp. 608-610 published in February and “Hints of a Language in Junk DNA,” Vol. 266. no. 5189, p. 1320 published in November). In the earlier article, several possible functions of non-coding DNA were suggested by reputable researchers, (who published their work without using the term ‘junk DNA’). The article concludes with this: “Enough gems have already been uncovered in the genetic midden to show that what was once thought to be waste is definitely being transmuted into scientific gold.” The latter article concludes with a quotation from the Harvard biologist Walter Gilbert, “I think what we call ‘junk DNA’ will have a number of uses.”
1994 was the year the dam broke. Once there was mainstream support for “Junk DNA,” biologists jumped right on the bandwagon. Once Science said it was OK to say that Junk DNA had a purpose, many articles were published to that effect. Throughout the 90’s and into the new millennium, people began to find role after role for junk DNA. Everyone was bashing Junk DNA starting 1994 and lasting a decade. Here is a brief history of article titles throughout the years:
1972 - “So Much ‘Junk DNA’ in our Genome,” Brookhaven Symposium on BioLOGY
1986 - “’Computer Genome’ Is Full of Junk DNA,” SCIENCE
1994 - “Hints of a Language in Junk DNA” SCIENCE,
1998 - “Should scientists scrap the notion of junk DNA?,” J. NAT’L CANCER INSTITUTE
2006 - “Regulatory RNAs and the demise of 'junk' DNA,” GENOME BIOLOGY
In 2006, it seemed that people finally realized that the junk DNA horse was actually dead, and whipping it was no longer nearly as much fun as had been in the late 90’s. Unfortunately the term ‘junk DNA’ proved too sticky and did not un-stick, even to this day (people call it ‘junk DNA’ believing it has a purpose… that’s the trouble with catchy nicknames). It is interesting to notice the time gap between 1994 and 2006. In a little over a decade we went from ‘A hint of language’ to the ‘demise of junk DNA.’
Now it is believed that non-coding sequences may even be more important than the actual ‘coding’ regions. We have seen non-coding DNA control how proteins are expressed. In other words, non-coding DNA tells the cell how much protein to make. If the coding DNA is like the blueprint for a car, the non-coding DNA is the factory foreman telling deciding to make 1000 cars instead of 10). The non-coding DNA that does this is sometimes immediately around a code, sometimes interspersed between the code, and sometimes even tens of thousands of letters away (like a boss in New York ordering the Detroit factory to slow down production). We’ve seen RNAs which don’t ever turn into proteins further regulating things and doing things we thought only proteins could do. The “Crick Doctrine” and every other dogma we held about DNA have been overturned. Having overcome the arrogant assumption that what we don’t understand isn’t important, we have discovered a whole new world which we are just now beginning to explore.
Lessons Learned?
So what did we learn from this little history lesson? Firstly, that science makes mistakes. BIG mistakes. Going from 3% useful DNA to over 30% useful DNA (and climbing) is a BIG mistake (a tenfold error). Secondly, that science can correct itself, and it can do so relatively quickly. Making a 180 like that in a matter of a decade is laudable. Not that this is a good thing overall. I mean that we should praise a science as we praise a child when he apologizes for hitting his sister. It is a shameful thing that happened, but better than if the apology never came.
And that is the story on Junk DNA. So let us continue our discussion by looking at what got us into this mess to begin with: a bad theory. The bad theory was that we arose by a sloppily process. We theorized that the mechanism by which we came about was a messy one with a lot of errors and inefficiencies. It has turned out that this, at least when it comes to DNA, was simply and clearly wrong.
May I humbly suggest another theory? I propose we think of the life as arising from an elegant process instead of a sloppy one. We ought to form a better theory, one that conforms to our data: that whatever formed life as we know it behaves as if it was an artist, an engineer and a designer.
When we see a genetic code, let’s not dismiss the 97% of the code as ‘junk’ when we don’t understand it. When we see a new protein, we ought to first assume it is part of an elegant system, not a useless piece of trash left over by an idiotic process. When we see an organ that we don’t understand, instead of first assuming a useless piece of flesh handed down by a process too stupid to take it out, let us be agnostic on its purpose and encourage ambitious scientists to try to figure it out. We have asserted our assumption when there is no data. We’ve pointed at the poor little organ and, for a century, shouted at it, “Useless!” I wouldn’t work under those conditions either.
It’s a good thing Duke researchers are leading the way by rejecting the old theory, or at least behaving like they did. Last year, they showed that the appendix has a useful role in repopulating good bacteria in the intestines and may be important in surviving intestinal diseases like Cholera (Hampton, T. A Use for the Appendix? JAMA. 2007; 298(21):2474).
You may think that all this talk about theories is simply an academic point, that we can agree to disagree, and that you can believe your way and I mine. But this is truly a life-and-death issue.
There was a huge reluctance to spend time or money studying non-coding DNA because of the assumption that it was junk. It turns out now that many diseases are actually caused by mutations in non-coding DNA. We can now do genetic counseling preventing transmission and are beginning to develop treatments. But this has only happened very recently because, until about a decade ago, we were still comfortable in our assumption that non-coding DNA was useless. The same goes for the appendix; 321,000 Americans were hospitalized in 2005 because of the appendix. How many lives may have been saved if we tried to figure out how the organ worked fifty years ago instead of dismissing it as another mistake by our sloppy friend evolution? How many people have died because of our stubbornness in clinging to a bad scientific theory?
Even if we were to assume atheistic evolution, I'm only suggesting that maybe we don't know who evolution really is, deep down. Maybe it is a process misunderstood. We may look at a man's desk and say he is sloppy and stupid, but that man may turn out to be a genius whose brilliance is hidden under a messy desk. Maybe, just maybe, evolution is that genius. We should, upon seeing the brilliance of evolution, reject the notion of it being stupid and embrace and even expect its genius.

Saturday, September 6, 2008

And another one bites the dust...

Weeks. The title is talking about weeks (and an incredible Queen song).

So it's Friday night, half past midnight, and I'm done with another week. I'm sure you're wondering how I feel. Regardless of the presence or absence of wonders, I will tell you. To sum it up, good. Spiritually, emotionally, socially, and even academically, good.

I did a lot this week. For one, [warning, for those with weak stomachs, skip this section] I held a human heart in my (gloved) hand, and was able to find the Left and Right Cardiac Arteries. I learned all about DNA transcription, repair and proofreading (which is pretty freakin' cool, if you ask me). I also learned how to give PPDs and draw blood (I suck at both, but I know how to).

As far as work is concerned, there is a lot to do. I have online quizzes on Histology and Molecular Biology due by Sunday. There are probably 100 pages of Cells to Tissues to understand and a denser 30 pages of Molecular Biology. And I've got a scientific paper to read on Telomerase. But that's all I have to do, and I'm not being sarcastic.

I don't have a million other obligations taking up time. I can no longer spend Saturdays in Mexico, so I'll probably spend it studying. I'm still of the opinion that I won't study on Sunday to rest one day of the week (God said it was a good idea, right? ...We'll see how long my integrity lasts). I played Ultimate footba-occer today (and now am sore and ache... I must be getting old) this afternoon. I'm probably going to a party tomorrow night. What else have I to do in the remaining 16 hours per day but study? I try not to study alone, so it's a discussion on the stuff. When I'm thinking in a group, it's almost fun. Especially when I get to study with people I like (which, of course, is everyone :). Sometimes I study with people I don't really know (even though I know most of the 86 by name). It's sort of like a perpetual finals week. It's quite enjoyable.

Some people are really stressing. From what the second years have said and even the professors, it shouldn't be that hard to pass. There is a lot of information, but worrying about it never helped anyone except in getting them to work; it's the work that counts, not the worry. I guess I could cut out a few more hours of fun and replace them with study. But I don't think that would be prudent. As for the stressing, I learned a while ago (namely April of 2005... while preparing for the MCAT) that this whole thing is in God's hands and will work out for my best (whether that's passing or not, Romans 8:28); I need only to do my best. So far my best + God's will has led to Stanford, so there's no reason to change course now. Stress, at least in the academic realm, wasn't necessary and, I don't believe, will be. Again, we'll see how long my integrity lasts.

Sunday, August 31, 2008

Week One Done

So I am now officially through one week (and almost one weekend of medical school). The second day of class was much the same as the first: lots of information but useful information.

There came a point today for the first time (and I don't expect it to be the last) where I was trying with all my might to focus, but the information was coming so fast, I could not even follow what was being said. I've zoned out before, but that's just my being lazy. I think this is the first time my brain reached it theoretical limit. The rain came down, the reservoir filled, and then the water poured right over the dam. Let's hope its a concrete dam.

I had a spectacular day going to church, having a great lunch with friends, and then enjoying some good, quality time with God in a beautiful, secluded oak grove very near the center of campus. Here is what I had to deal with today (left). And here is who I spent the time with (right; I took the photo today at the Stanford Church). Can Sunday get any better?

Much less inspiring, but much more funny was what happened in Histology on Friday. We had our first Histology class (looking at slides of cells). We had an hour of lecture with example cells, describing what to look for. Then we got our microscopes and tried to find the cells on our slides that they described.

I thought, "Great! This looks really easy! I'm pretty good at identifying shapes! Gee Golly Gosh!" And I looked at my first slide. I had used a microscope pretty extensively in my old lab, so the controls were very familiar. I saw other struggling with their microscopes. "Amateurs," I thought. "I'll condescend to their level and help out the poor devils with the focus. So sad..." I helped out as I could with loading the slide, and focusing on the cells. Child's play. Then I sat down at my microscope, loaded the slide, then quickly and efficiently moved down to the appropriate zoom. And I didn't recognize a single cell.

My heart raced. I began scanning violently around the slide. "Where in the **** are the Neutrophils?! ****! For that matter, where the **** are the Erythrocytes. I can't even find the ****ing Erythrocytes!!" Thus was my thinking (**** represents, 'world', 'shucks' 'heck', and 'bi-concaving', respectively).

I turned to my neighbor (who seemed to actually know what the **** was going on) and asked if I could look at her slide and she could point something out to me. And from thence came my deliverance. It was a different slide. I could clearly see Erythrocytes, Neutrophils and even an Eosionophil on her slide (peripheral blood smear looks like left) . I talked to the TA and got my own slide. I waxed prideful again, able to easily identify every cell type on the peripheral blood smear. I confidently moved onto the bone marrow slide.

"****," I thought. "They all look exactly the same. Probably another mislabel." I checked again with my neighbor. "****," I thought again, "It's just like mine." I went back and tried harder to look for differences. There were no differences! They were all purple dots that looked exactly the same. And I was supposed to tell the difference between promyelocytes, early myelocytes, late neutrophilic myelocytes, and metamyelocytes, and I couldn't even tell the difference between a myocyte and an erythroblast!

I looked for help. The TAs were occupied. Some people were packing up. Finished! And I just started my second slide! "Oh no! I had expected to be the dumb one. And it begins now, on day two!" I bemoaned to myself.

One of the TAs had projected his slide onto a TV screen and began describing the differences. And he did a darned good job. I then was able to see the subtle differences and remembered them fairly well. And by the end of that hour I got pretty good at blood histology, and actually (but just a little) started to like it.

P.S. The photo is from Wiki public domain, so don't worry course administrators, I haven't posted course materials

Thursday, August 28, 2008

Day One


Last night I struggled with insomnia. It took me 90 seconds rather than the usual 30 to fall asleep. Needless to say, I was anxious about my first day of class.

I got up before my alarm, which is usually the start to a good day. I made a sandwich and packed my lunch, pretending like I'm going to have time to do that this year. A tasty roast beef sandwich with fresh tomatoes, onions and lettuce, topped with mild cheddar, olive oil, vinegar, sea salt, and freshly ground pepper. Mmmmmm. It took me 1/2 an hour that I didn't have to make my lunch. I'll be quicker tomorrow.

Off to class!

I got out the door at about 8:30 for a 9:00 class. Another beautiful bike ride across a beautiful campus with beautiful weather (forebodingly warm at a quarter to nine) put me in an even better mood. I sat down next to two amazingly cool people in the front row of my first class ever at Medical school and got ready to start. The lecturer came in and started talking about the history of molecular biology. What surprised me was 1) he was a good speaker, 2) he actually wanted us to learn 3) he was funny 4) we talked about how prions are basically exactly the same as the Borg in Star Trek, a point we expanded for about 10 minutes. So I was sold on my Molecular Bio professor.

After two incredibly interesting hours of class, we went on to a Cells to Tissues class. The lecturer here started at about 25% the speed of light and never slowed down. This class was also very interesting. We talked about cells and stem cells (normal ones in adults) and how powerful they are. I am continually blown away (and expect this will not end) by how incredibly well designed the human body is. One reason why stem cells stay so rare is to minimize copying errors; they only grow when they need to, and they stay as close to the target tissue as they can. And the balance is also incredible. If intestinal tissue grew only 5% faster than it should, after one year of growth, it would increase its size by 10 times. Cancer is a small imbalance (~1%) of too much growth (or too little death). It's amazing that we don't always have cancer everywhere.

I ran over to the Financial Aid office to ask for money on my lunch break, but got back with plenty of time to eat my delicious delicious sandwich and chat some more (it happened to be about water infrastructure... oops).

The post-lunch lecture was Anatomy. This class I was a bit concerned with as I have never taken an anatomy class. The good thing about the class is that both the professors are Brits, which makes for endless entertainment and makes them seem inconceivably smart. We learned about the chest cavity. We had about an hour lecture on it before we headed off to the Anatomy Lab... dun dun dun.

Before we got to meet our cadavers, we had to change into our scrubs. It was like high school gym all over again. 40 guys in a locker room stripping and putting on funny blue clothes brought back memories.

We entered the Anatomy Lab and found our table. There were two sections of the room with twelve tables each. On the table was a blue fake leather bag with a big black zipper on it, each with the shape of the body visible by the folds in the bag. We walked over to the table, received instructions, observed a moment of silence for the donors, and unzipped the bags.

The cadavers were covered with a damp sheet, with an additional cloth over the hands and the face. The skin didn't seem real; it was too plastic-ey and pale. I took the plunge and made the first incision for my group along the clavicle. At first, it seemed unusual, but not as eerie as it should have been. We took off the layer of skin and fascia to reveal the pectoralis major.

To get to the serratus anterior, we needed to move the arms out to the sides. We took off the cloths and moved it out. This is when it started to feel like a body, once we could see the hands. Also noticing the armpit hair and other things which I didn't expect reminded us that it was actually a human we were working on. Even then, it was only a passing thought; the really interesting part was the intercostal muscles and the corticoid process and the other parts of the anatomy, not as much as I would have expected, the emotional side of the body.

We completed the dissection and washed up. We went back to the locker room and changed back into normal clothing. It was 5pm. We had class 9-5. And we will have class 9-5. We are all really tired and it's only the first day. I expect we will learn to strive at this pace, but we have not learned that yet.

That being said, medical school doesn't seem to be that hard. There was nothing today which I had trouble learning. The only challenge is keeping this up. Can I learn that much every day for two years? Medical school is a marathon, and one we have all been training for. If I can maintain this pace, I'll pass with flying colors (not that my colors will fly any more than the next man with a Pass/Fail grading system). I do not have significant fears that I will grow weary, but this, I suppose, is a great risk.

The second, and more likely, is distraction. There are about a billion opportunities for doing great things here. I just cannot get too distracted from class. Nothing seems to be immediately threatening, but those would be the two predicted 'modes of failure' (as Civil Engineers say), so should be protected against or reinforced.

P.S. I still smell like formaldehyde.

Monday, August 25, 2008

The Exodus

I've just written about what I like about Stanford. Now comes the previously untold story of how I got here. "Here" being after Day 1 of Orientation. And not "How" like in a philosophical or historical sense, just how I drove up the 5 and stuff like that.

I drove up to Stanford a week ago Monday. For whatever reason (but probably because I hate doing paperwork and usually protest by doing it poorly), I did not get have any information on things like where I was living and where to meet for the get-to-know-the-class camping trip called SWEAT, (Some Weird and Eccentric Acronym-Thing). I thought it was Tuesday, but that was the end of my knowledge. I had learned by this point that my phone, which was a very nice PDA, did not do phone-things like receive calls ever and made them only when it felt like it. It was under these circumstances that I drove a Prius up to Stanford loaded with all of my earthly belongings. 15N->210W->5N = 7 hours.

The drive was mostly nice. I like Kettleman city, but decided to stop at Bakersfield instead because I was too hungry. After a half-hour of clogging my arteries, I continued on. It took me about 7 hours to reach Sacramento, where I would stay on Monday night with my buddy at Davis Med. We met up, and he pretended to study while we talked. I crashed at his place.

The next morning I left early and headed for Stanford. I didn't have a map of Stanford, but I did have one of California, so I followed signs into campus. Once there, I tried to find the housing office. Not knowing anything about Stanford, I was unsuccessful. I had found a single phone number online for the housing department, so I called that. After 4 attempts of failed transfers and leaving messages, I was finally connected to someone who knew where it was. I drove right there, told them my name, showed ID, and was given a key. Simple as that.

Having figured out my housing, I decided to call Josh, the guy who was leading the camping trip (and ironically enough, the guy who used to tell me to wash dishes at UCLA), and he told me where to be the next morning. I then moved all my stuff up to my room (6th floor).

The way my roommate wanted to partition the room, I've basically got a studio to myself (instead of a shared bedroom + living room), which is fine by me. I've got a great view of the campus from my window, and privacy. Not that I really understand privacy, having had at least one person sharing my room since college began (in one case, 3 others shared my room). I kinda like it, though I can see the potential for greed in having MY space (which should always expand and never be infringed upon); I've never really had the luxury, but am certainly enjoying it (hopefully with minimal greed).

The next day we left for SWEAT. I was driving for one of the car-camping groups. Just to save my precious reputation, I wanted to go with the hard-core backpackers, but for the aforementioned loathing of paperwork and procedure, didn't sign up early enough.

Our leader was a second year, and he guided us with his fancy phone GPS. We tried to meet another group of people in Stockton for lunch, one of the girls told us they drove south from where we were. It turned out that by "south" she really meant "north," but with corroboration by the GPS, we headed south. Once we were clearly outside of any recognizable city in "French Camp," I got off the freeway and turned around amidst cries of, "It's a GPS, it can't be wrong!" It turned out that it was. We ended up finding them and getting some really good Mexican food in a sketchy part of Stockton.

We arrived and the lounging began. The three days were filled with mostly eating and waiting to eat again. We did typical camp stuff (day hikes and swimming) the first day. When it came time to build a fire, nobody knew anything about fires (except me, of course, being an Eagle Scout). Not that I was particularly good at building fires, but, being the only backpacker, my paltry knowledge was sufficient to bedazzle the poor group of campers. The concept of tinder->kindling->fuel was black magic to those who looked on in awe of my powers to control the flames. So thus I established myself as the great and wise woodsman. You know what they say: "In the land of the blind, the one-eyed man is king." [As a side note, it was pointed out to me that the saying would be more accurate if it went "In the land of the blind, the one-eyed man is stoned to death," thought the traditional story was what applied to me.]

The second day we decided to go for another day hike. A group of us decided to extend the day hike into a long day hike. One girl said she wanted to do it, I said I'd go to, and before we knew it, another four people had peer-pressured each other into going. Fortunately at that point, nobody knew that it was probably 4 miles each way or else they would never have attempted it. So a group of green campers embarked on a journey that very well could have killed them. Fortunately, they all survived and with minimal griping, so little in fact that no violence was done even to the most whiney among us. Everyone was proud of themselves upon completing the journey.

The last day we did a skit. Being the car camping group, we had procrastinated our task of coming up with a skit until the last minute. We discovered that it was not the last minute, because other groups actually started after we did. In the end, we came up with a very funny skit mocking our own laziness. The other groups ranged from obscene to confused. After a little bit more socializing, we drove back home that night.

The weekend following SWEAT, I kept busy. I did a lot of sleeping in, a bit of shopping and lots of eating. I got a bike from Target so that I could be like everyone else. Normally a statement like that is hyperbole, but I'm pretty sure every one of us will own a bike by the end of this week. So I had to fit in. So I went to Target with two friends and we bought two bikes. We successfully fit two bikes and three people inside my Prius. That's right. It's a hybrid.

On Sunday I went with seven others to attend Abundant Life Christian Fellowship nearby. It was amazing! It looked like it used to be a Black Southern Baptist Church; it had a Gospel Choir, very upbeat music, and good, loud singing. The preacher was black, so the traditional white conservation of energy on the podium was not visible. There was no lack of power in the message, and more importantly, it was Biblically based. I'm going to try out some other churches, but I doubt I'll find anything better.

Orientation started today, and it was pretty, pretty, pretty good. We had a very inspirational speech by our Dean, an entertaining speech by our Associate Dean, and then a very interesting talk by an author/faculty member whose book I was supposed to have gotten and read. Neither had happened, the latter on account of the former, but the talk was very interesting nonetheless. We were supposed to have a 24-student discussion on ethics and balancing life with medicine which was quickly turned into a 6 student + 6 professor discussion.

In between all this were lots of breaks where I got to meet more and more of my class, who, as I previously described, are amazing.

Next Step
School starts officially on Thursday, and before then I've got a two-page of administrative things that I'm supposed to do. They're the kinds of things that nobody really wants to do, but are indicative of the developed world. Things like online registration and financial planning. I really like flying by the seat of my pants and am rather annoyed at having to use instruments.

I've got another two-day grace period of orientation, and Mom's coming on Wednesday, so I've got lots to distract me from the elephant in the room (the hardest class of my life starting full-force on Thursday). It's a pretty angry elephant, and I think addressing it further would only upset it, so until Thursday I plan to ignore it.

"Take no thought for the morrow: for the morrow shall take thought for the things of itself. Sufficient for the day is the evil thereof." - Matthew 6:34

Why Stanford Rocks

So I'm at medical school now, for those of you who don't know at Stanford. The last week has been something of a blur, the experiences smearing into each one another like colors on film. I don't exactly know how to sum it up, but I'll say this: I am certainly happy here and with my choice. And here are some of the reasons in no particular order:

Exciting thing A - Outstanding Class
My classmates are outstanding, I'm honored to have the chance to work with them. My choice to come here because of them was truly justified. The Dean spoke today about how Stanford doesn't just want to train excellent physicians, it wants to train leaders. The 86 of us all have that spark. We're all normal enough to hold a conversation. We're all brilliant in at least one area (most of us in several). We've all done something amazing, mostly post graduation. Some have PhDs and Masters, some are Fulbright scholars, some have started NGOs, some have published extensively. Everyone has done something amazing.

Exciting thing B - Christian Community
There are actually a good number of strong Christians here. I'm going to be able to go through this with people who share my convictions, and people with whom I can pray and grow spiritually. As supportive as church groups can be, having this core of people who will share life with me for the next two years at least will be very important.

Exciting thing C - Global Health Interest
Everybody wants in on Global Health. Though there is only a minority of people who actually have done work abroad, it seems that there is broad interest, even among the basic science people (lab rats), to help out globally. We have done some pretty spectacular things separately, and we really want to work together. We're at the beginning stages of a potentially large, collaborative project.

Other Exciting Things
The weather has not ceased to be spectacular.

The faculty has not lost their gravity of presence; when they speak, especially our Dean, they speak with authority. They are not pompous, but are such strong personalities that they command attention.

There have been several groups that I've been the only American-born person in the group. The national diversity is spectacular (though we are lacking in under-represented minorities).

We have an army of people working for us to make our life easy and our learning successful.

The food around Stanford is amazing. Thai, Chinese (dim sun), and Indian were all eaten in the past few days, most of these being ordered from the place by a person who spoke the relevant language.