Fairy Tale Romance - Neurobiology

Part 3 of 5

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This is your brain on love. From PLoS.

This was supposed to be a four-part post, but I couldn’t resist including material from Monday’s lecture.

As it turns out, there is incredible similarity between opioids (like heroin) and being in love. They act on the same regions of the brain and cause similar physiologic effects. They both reduce the perception of pain in those who took them. The more in love a person is, the greater the effect. They have similar immediate effects: feelings of euphoria, well-being. They have similar withdrawal effects: compulsive thinking, anxiety.

We talked about the four C’s of addiction. Compulsion, Continuation despite harm, lack of Control in using the drug, Cravings. Isn’t this exactly romance? Doesn’t this describe a lover’s desire for his beloved? He must see her. And when he doesn’t see her, he has cravings for her. And it not only matches the addiction profile, but also the features of dependence. What happens if there is sudden removal of the beloved (that is, a breakup)? Lovesickness. GI upset, overwhelming feelings of anxiety. Severe physiological and psychological symptoms. As it turns out, it may be that symptoms are chemically identical to heroin withdrawal.

But, like usual, neurobiology tells us what we already know (it’s Poetry’s job to tell us what we don’t). We know that we feel good when we’re in love. We know it hurts to break up. What we didn’t know (at least what I didn’t know) was that this effect could be mimicked pharmacologically.

Does this mean romantic love isn’t real? Far from it! It means that romantic love is very real, and incredibly powerful, perhaps as powerful as the most addictive substance known to man! Far from ruining the fairy tales, we now (perhaps) know one more detail about them. But an added detail doesn’t ruin the picture. Understanding the physiology of muscle contraction of the knight’s triceps as he swings his sword does nothing to diminish his slaying of the dragon; it is an interesting, if irrelevant, detail. Knowing the names of the chemicals which are giving him an overwhelming urge guarantee permanency with his beloved is yet another interesting, if irrelevant, detail. This medical hypothesis is only another bit of color in the wonderful (and terrible) picture of Romance.  

We also haven’t addressed how these feelings begin. The ancients have as realistic an explanation as we do presently: his heart is pierced with a powerful magic arrow by Cupid/Eros. Perhaps cupid uses dopamanurgic arrows. And we should take heed, lest we rely too much on this powerful magic. A relationship cannot be sustained only on this heroin-like phase. The high will diminish as tolerance builds. But this is exactly what we already knew; there is a honeymoon phase on new love. It lasts for a while, but not forever.

In the previous post, I recounted poetic descriptions from Genesis, Disney and Sex and the City, all describing some deep yearning for romance. This bit of scientific evidence simply confirms their observations. These feelings are real and deep, deeper than we can ignore. Courting customs vary from age to age; neurobiology does not. Scientists have now joined the ranks of poets in describing this same strange phenomenon. Genesis suggests that Romance was not a medieval invention. Neurobiology suggests that Romance was not a ancient invention, either. This feature has been with our race from the beginning; Fairy Tale Romance, it seems, was an invention of God.

Teaching High Schoolers "Real Science"

A few weeks ago, I had the opportunity to teach a group of high schoolers about whatever I wanted. The event was called Splash, and brought thousands of high schoolers and middle schoolers from the bay area in to Stanford to take short classes taught by Stanford students.

I decided to teach: "Real Science - What It Is and How to Spot BS" a lesson on what science was and what it could do. I had about 40 students over 3 classes, and it was a great time. The kids (grades 9-12 in my class) had a good time, and I did too. I am pictured above with Karl Popper.

My main points were:
1. Science works on matter. Matter's not all that matters.
2. Science works by experiments. Experiments have limitations.
3. Scientists are people. People are not objective.

These points are not all that controversial. I don't think many scientists who would disagree. But this revelation shook some of the kids pretty profoundly. Comment cards I collected at the end had questions like, "Then how do we know what is true?" and as if defeated, "Do all experiments have limitations?" It seems that many of my students believed in scientism. They believed that the only things that can be known are those that science can find out. And a better understanding of what science really was challenged this. Anyways, this goes along with what JP Moreland says about epistemology (ideas on how we can know things) being the central issue of our age. But that is for another blog post.

For more detail, my Powerpoint (with teaching notes!) can be found here (make sure you download the original to get the animations and teaching notes; click 'file' 'Download original').

Sleep

We 'lose' consciousness for eight hours (hopefully) every day. But our consciousness isn't lost strictly speaking. It's still present. We usually don't have control over it and we often don't remember it. But our conscious goes places and does things. With no sensory input, we (our consciousnesses) have dramatic experiences, do bold (and cowardly) deeds, and live wildly different lives from our waking selves. And we take these nightly vivid hallucinations in stride.

It seems when we don't sleep enough, our waking consciousness is diminished. I felt today, sleep deprived but forced awake chemically by caffeine, much like Bilbo. As he describes, being pulled toward the realm of shadow by the Ring, "I feel all….thin, sort of stretched, if you know what I mean: like butter that’s been scraped over too much bread. I need a change, or something."

Why? There is certainly physical fatigue, but this is not mental. There is also mental drowsiness, but this is countered directly by caffeine; after coffee I have no more difficulty staying awake in class. Though I am not as "present," as I would be well slept and uncaffeinated with an identical level of physiologic 'drowsiness'. What is the difference? There must be some other axis of wakefulness that can only be 'charged' by leaving the physical world.

And not just leaving it. Sleeping 8 hours but preventing stage IV ("REM") sleep, the phase in which we are said to dream, is not restorative of this new sleeping axis. It seems necessary for us that we go somewhere, and the only way we can is through a phase of sleep associated with dreaming. Some postulate that this is simply the random firing of neurons. But if that were true, then using hallucinogens would be as restorative as REM sleep. By all accounts, this is not the case.

More importantly, dreams are not chaotic; they are orderly. It is not a series of flashing lights and sounds. Dreams are a narrative. Certainly the 'rules' of the universe as we understand them are a bit different. Creatures exist there which we do not believe exist here. "Impossible" things like flying and laser vision occur (at least in my dreams). But they are not random in any sense. We recognize our friends, we interact with our families, we fight our enemies.

What happens when we don't sleep? Well, we do sleep. If we try to stay awake, we draw whatever place we go in dreaming to the wakeful world. When you keep someone awake for days at a time, hallucinations and all manner of craziness set in.

All these things seem to point to sleep being a non-chemical thing. But if it is non-chemical, what is it? Here is how a materialst must explain these observations:

Unknown chemicals act by unknown pathways to achieve a state (dreaming) which, though it can be imitated by chemicals (hallucinogens), cannot produce the effects of that same state. When this state is not achieved, fatigue sets in, all the effects of which can be antagonized chemically (sympathetic agonists, caffeine) save for 'wakefulness.' To put it another way, the one conscious effect which cannot be chemically countered (wakefullness) is the result lacking from the element of conscious experience which cannot be chemically induced (dreaming). This lack of any evidence for a chemical connection to this fundamental aspect of the human experience indicates it is a ripe area for research; we ought to search out which chemicals it is exactly that cause wakefullness and dreaming.

A materialist is forced by his faith (or to put it more euphemistically, his worldview) to hold to the baseless claim that all of dreaming and wakefullness is chemical. But, as with all faith, evidence (or lack thereof) does not affect the firmness of one's conviction. Nevertheless, I hope that fairminded people will have the sense to consider, perhaps, that we are not chemical robots, and that there is something higher than chemicals and deeper than Scientism.

Sweet dreams!

The Self and Its Brain

We had a lecture today on “Neuroethics,” and the topic of dualism was briefly touched on, but in a manner which was rather disturbing.

Dualism, as described by the Stanford Encyclopedia of Philosophy (SEP) is, “…the theory that the mental and the physical — or mind and body or mind and brain — are, in some sense, radically different kinds of thing.” This is the view that has been traditionally held by the majority of people, and the view that most easily allows one to believe in an immortal soul (so obviously favored by religious folks through the ages). At least it’s a valid theory, right?

Well, not according to what we learned today in lecture.

"The whole universe of your perceptions, your thoughts, your actions, your intentions, your motives your purposes, it's neurons giving off and taking up packets of neurotransmitters, and that's pretty much all there is...The “I” that they experience is really just dopamine and serotonin and other stuff being given off and picked up, and ions going in and ions coming out.... There's certainly no scientific evidence for dualism, for the idea that there's a little homunculus someplace, incorporeal, not physical, that somehow through some magical method connects to your brain, but that it is you and your brain isn't. Your mind, as far as we can tell, is what your brain does."

The strength of the rejection was jarring. I thought it was a legitimate theory. Nope. It’s “some magical method.” But because of the strength of rejection, I was forced to second-guess myself. So I did a bit of research. Who supported it?

I did not expect what I found. Beyond the usual suspects who are way too smart to count for anything (people like Aristotle, Augustine, Plato, Aquinas, Descartes), dualism found support among a very impressive list of scientists and philosophers in the twentieth century. There are strong supporters even in Neuroscience itself.

And I’m not talking about fringe characters. I’m talking about people who laid the foundations of neuroscience. A dualist (Sherrington) won the Nobel Prize for "discoveries regarding the functions of neurons” in 1932. I’d say neurons are pretty important to neuroscience. A decade later, Sherrington wrote a book called “Man on his Nature” expressing dualism. Another dualist named Eccles got the Nobel Prize in 1963 for figuring out how synapses worked and then went on to defend dualism the rest of his life. Later in his life, he worked with a famous philosopher of science, Karl Popper. Popper was hugely influential in our modern understanding of science (he introduced the idea of science having to be ‘falsifiable’). Popper and Eccles published, “The Self and its Brain” in 1977 defending dualism.

It’s hard for me to imagine a better list of advocates for my position: the most important philosopher of science last century, the guy who discovered neurons, and the guy who figured out synapses. Of course there are others. Jeffry Schwartz, a Psychiatrist at UCLA is treating people with OCD according to the philosophy that the mind is not just the brain. Roger Penrose, a giant in mathematical physics, argues for the inadequacy of physics to explain consciousness. Daniel Robinson, a brilliant scholar trained both in philosophy and neuroscience (and who co-authored a book with Eccles), speaks and writes extensively on this topic.

If such brilliant people support it, why is there such opposition? Robinson offers one possible reason, “It would be naive to ignore one fundamental difference between that world [of Sherrington] and the present: the gargantuan monetary stakes and associated perquisites on offer to those who can make and keep the brain sciences big science. There is so much of all this to go round that even philosophers of the right sort stand to gain.” In other words, you can get huge grants to investigate ‘the neurological cause of crime,’ only so long as crime is a brain state. If human responsibility exists beyond the brain, you can’t study it with expensive fMRI machines.

Are all modern philosophers against dualism? According to SEP, the answer is ‘No’: “Amongst mainstream philosophers, discontent with physicalism led to a modest revival of property dualism in the last decade of the twentieth century.” So I am satisfied. If I looked around on my side and saw nobody (as was suggested was the case by our lecturer today), I would be concerned. But indeed the case is reversed. On this philosophical question, I have all on my side but most modern scientists and some philosophers, whose views are severely biased by preexisting commitments to Materialism and money. Even the agnostic founders of neuroscience agree with me. Indeed, as the SEP entry on dualism describes, “although dualism has been out of fashion … the argument is by no means over.”

http://plato.stanford.edu/entries/dualism/ - Most of my references come from here.

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!

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’.

Conclusion
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”.

Objections
"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).

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.]

Introduction

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.