Thursday, January 31, 2008

On the Fifth Day, Part 2: Creation and Un-Creation

Then God said / “Let the waters abound with an abundance of living creatures / and let birds fly above the earth / across the face of the firmament of the heavens” / So God created great sea creatures / and every living thing that moves / with which the waters abounded / according to their kind / and every winged bird according to its kind / And God saw that it was good / And God blessed them / saying “Be fruitful and multiply / and fill the waters in the seas / and let birds multiply on the earth” / So the evening and the morning were the fifth day.

In Latin: "Pleni sunt coeli et terra gloria tua" = "Heaven and earth are full of Thy glory." The seas were first, and then the land, then the heavens. Day 5 tells about the seas and heavens filling with creatures great and small.

The earth doesn't always look full with life, but life always finds ways to surprise us. In the 1830s, a respected biologist, Edward Forbes, announced that from his studies of the ocean, nothing could live below 2000 feet, so it would obviously be foolish to try to explore for deep-ocean life. No one had any ability to go down there and check, so his conclusions became the de facto conclusion of the scientific world. After all, the transatlantic telegraph cable had been laid and no deep-sea mermaids had come crawling up it. So the voice of experience had spoken.

Until that experience changed. In the 1860s, the transatlantic cable had to be dragged to the surface for maintenance. When they pulled it up, it came up with all sorts of life on it: the cable was crusted with shells and strange sea creatures from the bottom of the ocean. Immediately the paradigm shifted. Even the deep ocean, where no man could go, teemed with abundant life.

Fast forward to the 21st millenium. Craig Venter, genome plumber extraordinare, wanted to sail his yacht around the world, like the H.M.S. Challenger did in the 1870s. What's better than sailing around the globe? Sailing around the globe and doing science on the way. Venter and his team stopped every 200 miles and collected seawater microbes, then sequenced the DNA to find out how diverse and different they would be. According to a recent Time article, they found 6 million new genes and 400 new species. "Most people thought the ocean was a homogenous soup," Venter says. "But 85% of the species we found were unique."

That's just skimming the surface. Deep-sea submersibles travel to the bottom of the ocean, near deep-sea vents, at pressures that would crush your lungs to about the size of a thimble, and take pictures like this:

Ten-foot tube worms live off the water boiling up from heat inside the earth there. Clams are crusted on rocks, even strange shrimp (I wonder how they taste?). No one had even imagined that. The Little Mermaid doesn't hold a candle to bizarre sulfide biochemistry -- but I may be biased in that.

In Romania, a deep cave was explored in the 1980s, containing 33 blind, albino species. Other caves have revealed blind white salamanders, blind white scorpions, all sealed off from sunlight so long that they lost both color and eyes. In terms of sheer elegance, a mechanism that can populate these caves with species, filling them with life, seems more amazing and creative to me than individual acts of special creation for each cave and each species.

There's even life miles down in the earth's crust, where buried microbes live off water and rock, slowly transforming the energy from radioactive decay into life. Take my biochem class (or listen to the podcast next September) if you want to know more.
Because life is based on solution chemistry, it exploded in the water first, producing jellyfish, fish with backbones, tribolites, sea dragons, and corals. Some of these were able to venture above the water and move into a new kind of living, breathing in reactive oxygen from the air and growing to huge, almost unthinkable sizes. From time to time, when you look at fossils, new forms just explode across the scene with joy. Fish first, then dinosaurs, then birds filled the sea, earth, and sky. Species we would only know by their unthinkably huge bones ruled the earth before us.
But of course, there's a flip side to the joy of exploding life. Where did it all go? Why can you only find dinosaurs as audio-animatronics at Disneyland? Why did they all die? This abundant life is always paired with abundant death. That's not just a biological statement. Consider the abundant life Jesus had -- with the Garden of Gethsemane and the "place of the skull" taking up chapters upon chapters in his four biographies. There is constant creation, shadowed by constant un-creation. This tree of life we celebrate is burnt, cauterized at each limb.
Wave after wave of extinctions have rolled over the earth and beneath the seas. 95% of all species may have been lost in one event in the Permian. However you cut it, more than 99% of all species that ever existed are now extinct, and only can be seen as bones, shells, or genetic fossils. For instance, consider the trilobite. You can find them all through the fossil eras, but at one point along the way they just didn't make it. I'm guessing I'll never lay eyes on a trilobite. (The closest I'll get is a horseshoe crab, and I find them kind of creepy, actually.)
If there's anything to Darwin's descent with modification, then life by its nature overproduces and get ruthlessly cut back in waves by a cold, hard world. All nature suffers, as intense as birth pangs, but also as meaningful -- we trust.
You can't talk about how beautiful life is without talking about how fragile it is. You also can't talk about the goodness of God without at some point talking about what God is not, at which point you're talking about the judgment of God. Look at Isaiah 6 and 9, always quoted at Christmas, but very carefully cut and pasted so that Isaiah's pronouncements of judgment are not heard. The Messiah figure in Isaiah is sometimes a child, sometimes a warrior, sometimes looking like David, sometimes like Goliath.
It reminds me of Scott Becker, once again. The first sermon I heard from Scott was on the Magnificat. He read that famous text of upheaval, and told us, you know the rich who are being uprooted? That's you! The last message I heard from Scott was on his blog, Aufbehung, and it quoted Job contending with God, just as Scott was as his body broke down. Being a Christian won't save your body from dying. Being a Christian doesn't directly increase your odds of bodily survival or passing your genes on to your offspring. Whole Christian societies in the East have gone extinct. I don't know why God let that happen. Or, what I can't even write about, The Holocaust. Read Elie Wiesel's Night. We live in a world where death is written into the very letters of the language we use. Death is the lynchpin of the mechanism of creation.

That's not under debate. But Christians have a choice. When grace allows, we can look back at Jesus and forward to Jesus, and we can see that one day, death will be no more. Death is and should be a foreigner to us, and we don't accept its grinding inhuman say in things, but we trust that God will work through us and despite us to do something about it. This universal, ingrained death in the universe is an enemy and will be defeated. I wonder, as a chemist, does this mean that one day the degrading force of entropy be no more, and the laws of Thermodynamics will be rewritten? Or will entropy itself be transformed, redeemed, or reversed?

I just know that some things will be thrown away, but many things will be remain, changed in an instant of recreation. In the meantime, we create and nurture life. The Christian response is creative hope in the face of uncreation. And so I try my best to fix my proteins and make them work better, yes, evolving them by my (students') own hands into something different, hopefully better. I teach undergrads in the process so they can go on and do greater things. That is my calling to follow Jesus by, yes, fixing proteins. And, more importantly, by teaching.

In the face of all this, the last word is Jesus, the king on the cross at the center of creation, summing up and bringing together all things to himself, a man dying and God giving life, the root of the tree of life with water and blood flowing out, like on that church mosaic in Rome. I'll finish with a quote from Denis Alexander at the 2007 Edinburgh ASA/CIS conference, himself quoting Diogenes Allen from Princeton Theological Seminary:

‘Through Christ it is possible to understand how the Father’s love is present in all things, even in suffering. Suffering can be regarded as a mark of our distance from God because we are subject to the cosmos simply by being creatures. Yet, depending on a person’s response to suffering, a person can be in contact with God through their suffering and in suffering. To be in touch with the reality God has made, even when it is a painful touch, is to have indirect contact with him who is above it and who is above all else, love. Insofar as it is contact, it is good; insofar as it is painful, it is not. But what a difference when the same pain results from the grip of a friend, and not the mindless grip of nature’.
It was evening, and it was morning. The fifth day was done.

Sunday, January 27, 2008

Don't Call Me Bartman

This post's title has a double meaning for those with ears to hear, joining two otherwise disparate topics:

1.) Today during our pastor's sermon he mentioned a quote from a few seasons ago on the Simpsons, the episode "The Father, Son, and Holy Guest Star" (the third is Liam Neeson, who voiced an Irish priest). The episode is about Bart and Homer's attempts to convert to Catholicism and is one of my favorites. The operative line from the clip is "Our God can kick your God's butt!" Note for skeptics: the passage was used with irony.

Anyway, during the afternoon I found the clip, burned it to DVD, and Laurie got it to church where it was used for evening services. I'm sure Scott Becker is watching over all this with a laugh.

2.) I took my unlucky Mariners glasses out of the back of the cabinet and took a drink. I'm full aware this is risky behavior: something bad happens to the Mariners every time I use these glasses. The last time I used them Chris Snelling was injured (OK, he was no longer a Mariner, and he's always getting injured, but STILL!). I think I was using them the night Soriano got a concussion from a line drive to the right ear, and then traded for The Worst Pitcher in Baseball ... I think I was using them that day too. SO, I use the glass today, and the Adam-Jones-for-Eric Bedard trade went through, reported today, WHILE I WAS SIPPING MY DRINK.

I'm still hopeful that Bedard can actually turn out to be a very nifty addition to our team, but I really doubt that the price of Adam Jones' potential (and probably two others who may be very good as well) is worth it in the long run.

The glasses have spoken. I am now even more skeptical of the trade ... let's go M's ... ?

Thursday, January 24, 2008

What is Cloverfield?

Well, it's a monster movie that I had to close my eyes in, not because I was scared (why would you think that??), but because the constant point-of-view camera-held-while-running jostling made me very sick. But when they weren't running, and I could open my eyes, it was an interesting variant on some old themes.

Many reviewers have said Cloverfield = Blair Witch Project + Godzilla. I don't think that gets to how the movie feels. My equation is different:

Cloverfield = Alien + Run Lola Run

I think that its pacing is more like Lola and its intense personal character and unseen monster are more like Alien.

So, yeah, it's a big ol' monster movie, and it's got some cleverness in it, but mostly it just comes at you fast and has an inventive "found this on tape" editing scheme. It was cool, but deep in my heart I think JJ Abrams can do better. (Maybe that's just my Lost-watching part hoping that the mysteries add up to be more, not less, than the sum of their parts!)

Tuesday, January 22, 2008

Now it's Noteworthy

So, at least for the last five minutes, my new podcast has been featured on the front page of iTunesU, under the headline "Noteworthy in Science and Health."

Let's see ... that means I'm down to 7 minutes and 35 seconds of fame left in my life. I'll take it.

What? No papparazzi? It's OK, I'm having a bad hair day anyway.

Here's the link to the main page if you have iTunes installed and want to see for yourself if it's still up:

Friday, January 11, 2008

So I Really Say "Um" THAT MUCH?

I've started podcasting my biochemistry lectures publicly on iTunesU. They're broken up into chunks for easy downloading and listening, so my last two lectures show up as 7 files. Also, one is missing because I forgot to press record twice, but I'm learning as I go.

I'm also learning that I say "um" a surprising amount. Yipes! Um, I'm hoping, um, it's because I'm a little jittery knowing that I'm being recorded. And I need to enunciate more clearly. Um. But I'll keep working on my delivery and the rest of my lectures will be posted. It may be hard to follow because we don't have the slides I show posted, but feel free to try a little listening in.

If you want to hear about biochemistry (with a little bit of the rustling of my shirt), and hey, who doesn't?, go to the following link:

Note for family members: At about 16-17 minutes into the first lecture I describe our visit to the National Academy of Sciences a few weeks ago -- thought you might want to listen in!

Note to biologists: What a say near the end of podcast #7 is a joke. Really!

Wednesday, January 9, 2008

On the Fifth Day, Part 1: Tree of Life and Grace

In Rome, one of the most astonishing mosaics is found in the Basilica of San Clemente. There, the cross in the center dominates the scene, but out of its foot an acanthus bush grows with many curly vines. In the circles formed by the vines are many scenes, some sacred, but most what we would call secular. There's a woman feeding chickens (right now, that would be Aidan up there, he loves chickens) and other humble professions of the time found on that church wall with the saints. Animals drink from the waters flowing out of the foot of the cross, streams of living water that evoke the Psalms, Ezekiel, even the end of Revelation.
This mosaic shows that even the most "non-sacred" things can be centered on the cross and done as worship, say, feeding the chickens, paying taxes or making dinner. By extension, the most mundane little experiments in the lab are acts of worship. A "scientific" version of the same mosaic could be made today, with the biologist, the ecologist, the chemist, the teacher, the computer programmer, each in their circle, enfolded by the tree of life springing from the foot of the cross.

The animals, too, each have their place on that mosaic, overshadowed and encircled by the cross at the center of creation. I imagine a "biological" version of the tree where each animal is encircled by the acanthus and joined to the same root. The deep connection that comes from being formed by the same creator is shown by the acanthus embracing them all.

Little did they know at the time just how deep that connection runs, and shows throughout biochemistry. If you sample jellyfish DNA and rabbit DNA, you'll find that the same four chemicals make up all of it. The DNA carries the blueprints for making proteins, and the proteins are made of the same twenty amino acid chemicals in jellyfish as are in rabbits. Because these are the same chemicals, we have been given the extraordinary power to take tiny molecular scalpels and sculpt the DNA, moving it around as a chemical using other chemicals. Here's a vivid example. Some jellyfish have a protein that glows green under a black light. Using biochemical tools, you can take this gene out of the jellyfish, put into an albino rabbit, and behold, you get a green glowing bunny:

This is only possible because the same 4 pieces make up DNA in both species. It's a little funny and of course a little scary too. It brings up the question of what we do with this power, questions that deserve to be talked about more, in other blog posts. But my point here is that, like it or not, this power has been given to us because bunny biochemistry and jellyfish biochemistry rely on the same 4 chemicals.

I exploit this similarity in my research. We study human immune system proteins, but we need a lot of pure protein for our studies. So to make it, we take DNA for the human protein and put it in bacteria and tell them to make it. For our proteins, the bacterial make a protein that is functionally and structurally the same as the human-made proteins. There are some peripheral differences, but the primary protein is the same, and we can use it to study how the system works and, if grace allows, to improve on it.

This biochemical snap-in/snap-out interchangability is indeed universal. If each species were a separate creation, there would be no need for it. But it would have to be universal if every species grew from a single root. Geology gives us the time, and DNA gives us the similarity between creatures and also the fluidity to change one to another. Remember that DNA is a chemical in solution. That means it floats around, degrades, breaks apart, in short, that it's fluid. This fluidity can happen in small changes (point mutations) or large changes (big chunks of DNA flying around like mentioned before for viruses). But when coupled with the old age of the universe, it provides an elegant mechanism for animals spouting up from a single root. These species, or as Darwin called them "records of Creation," contain the same language deep down in their DNA, and once you read the language from those records, it tells a story of relatedness and change.

Humans and mice have 90% of the same genes in their DNA. Even humans and flies have 60% of the same genes. You can take a mouse eye gene and put it in a fly and it will grow an eye like that gene tells it to (thank goodness this doesn't work all the time). We even have the same tail genes as a mouse does, but they are permanently switched off (again, whew!). You can see this yourself with free databases online: you can look up a gene in one species and find its equivalent in another. Invariably, the genes from species that look more alike also look more alike on the chemical level. But across the biosphere, there's so much similarity that we can look at stromatolites (from Day 4) and look at us and find the same protein with the same function, using about the same order of amino acids. To quote Bill Bryson: "About half the chemical functions that take place in a banana also take place in you." When you scratch the surface of anything alive, you find the same chemicals underneath doing almost the same things.

See for yourself. Below is a simplified picture of two "thioredoxin" proteins, lined up. The red protein is the human version and the yellow protein is the fly version. At this level, you can see that they are pretty much the same in structure, and they serve the same function.

This deep biochemical similarity gives us a mechanism for how creation could have happened, that there is enough biochemical fluidity for one animal to change into another over time, and that they can look very different and yet use the same chemicals underneath. It has other amazing benefits as well. It means at the Fred Hutchinson Cancer Research Center that there's a whole floor of scientists who work with yeast. Yeast don't get cancer, but they do grow using the same genes as human cells, so if you're interested in how human cancer grows you can study how yeast grows and get ideas for how to fight cancer. This even resulted in a Nobel Prize in 2001 for an FHCRC scientist. The fact that you can get a handle on how cancer works from studying the microorganism used to make beer and bread is a clear gift of grace.

Some scientists like Michael Behe object that the differences between species are just too great to be accounted for by chemical kinds of change. Behe says that small changes might happen, but big changes couldn't. As a metaphor he says you can't jump over a 100-foot wide canyon, the distance is too great, and changing from one species to another requires a "jump" too far. He says that biologists claim that species changed incrementally, requiring 9 buttes 10 feet apart to jump across the canyon, and then that the buttes disappeared. He points out that this sequence of events is unlikely. (Darwin's Black Box)

I agree that it's unlikely, but I disagree with Behe's metaphor. Animals deep down are not like rocks. They are fluid collections of chemicals. So I would expand his metaphor just a bit. Remember that at the bottom of every canyon there's a river, and stuff floats down that river. If the river's fluid enough, you can cross a 100-foot canyon by jumping from log to log across the stream. In a fluid system, you could have that kind of change adding up. It's like a game of Frogger when you get down to it. Remember that species have all the same chemicals deep down, and to get from species to species you require a rearrangement of chemicals: the deep fluidity of the tree of life allows it all to connect. (My friend Scott Becker actually used a similar metaphor involving a river for revelation to the church, but that's neither here nor there -- I just like to cite Scott when I can.)

If proteins are essentially flexible and fluid, then they should be able to do a lot of different things, and they should be able to change what they're doing. In the lab, they can. A good example is the recent work of Michael Hecht and Shona Patel. They made 1 million simple proteins in a test tube, and made them randomly, with only the constraint that they should fold up into a coherent protein structure, or in other words, that they shouldn't stick together into globs like scrambled eggs or fall apart without warning. They didn't encode for or select for any chemical function whatsoever. As far as they knew starting out, the proteins should have just been oily blobs floating in the water. But they were actually highly chemically active, just by chance. From this random pool they found the following:

1.) a subgroup of proteins that could bind heme (like red blood cell proteins can)

2.) a subgroup of proteins that could make oxygen radicals (like immune cells can)

3.) a subgroup of proteins that could break ester linkages (like digestion proteins can) and

4.) a subgroup of proteins that could break lipids (like cobra venom can).

These functions are just waiting to happen from a random group of proteins. Something about proteins, they just can't wait to do biochemistry. From each of these subclasses, just a few minor changes could make an efficient protein that would do each of these four different reactions, from the same randomized starting point.

This causes a problem for some people. These chemical reactions are random. When DNA gets a mutation, that's a chemical event, and it's caused by the jostling of various waters and carbons around. If this is the basis of life, doesn't that mean life is built on a foundation of randomness? Doesn't that mean life is meaningless?

Some scientists, the "anti-Behes," would say just that. But they are just as wrong as Behe, because meaning can and does emerge from randomness. In chemistry, we have an entire field of statistical mechanics, which is all about what predictable (and I would say meaningful) results come from random collisions among a large collection of molecules. Life is based on solution chemistry, and the random behavior of solutions is what allows life to proceed predictably. I would go one step beyond "predictably" and add the implication of "therefore it's meaningful," but when I do that, I step outside what science can do and must shed my lab coat. The opposite's true too. When anyone draws the opposite inference, by focusing on the randomness at the bottom levels of life and saying that what springs from randomness must be meaningless, they, too, are stepping outside of the science of randomness into the philosophy of meaningfulness, and I don't think they're right.

You know, the best proof to me that proteins changed and were modified over time is that if I want to make a protein do something new, I can evolve it myself in the lab. I can use the tool of "descent with modification" in a test tube to create a new protein and new functions. I think the tool of being able to modify and grow new protein functions is a gift of grace. This convinces me that God could have used it too. He didn't have to, but this is the way I'm convinced he did it, and I am trying to figure out what it means. Once the framework for multicellular life was set, DNA recombined, new life forms grew, died, grew again, creation itself accelerated and the earth began to celebrate with fruitfulness and abundance. The result is beautiful and terrible.

Then God said / “Let the waters abound with an abundance of living creatures / and let birds fly above the earth / across the face of the firmament of the heavens” / So God created great sea creatures / and every living thing that moves / with which the waters abounded / according to their kind / and every winged bird according to its kind / And God saw that it was good / And God blessed them / saying “Be fruitful and multiply / and fill the waters in the seas / and let birds multiply on the earth” / So the evening and the morning were the fifth day.

In part 2, we'll take a closer look at the "abundant life" that exploded across the scene at this stage of history, which was abundant in every way imaginable.

Thursday, January 3, 2008

POINT: God is Big.

Here's a quote from Richard Dawkins that I agree with. Well, for the first sentence only, the second two sentences are wrong. But it's a start. I'll quote him and then give 2500-year-old evidence that his second two sentences are wrong:

First, Dawkins:
“The universe is genuinely mysterious, grand, beautiful, awe-inspiring. The kinds of views of the universe which religious people have traditionally embraced have been puny, pathetic, and measly in comparison to the way the universe actually is. The universe presented by organized religions is a poky little medieval universe, and extremely limited.”

Counterpoint, from Isaiah:
Who has measured the waters in the hollow of his hand, and meted out the sky with the span, and comprehended the dust of the earth in a measure, and weighed the mountains in scales, and the hills in a balance? Who has directed the Spirit of Yahweh, or being his counselor has taught him? With whom took he counsel, and who instructed him, and taught him in the path of justice, and taught him knowledge, and shown to him the way of understanding? Behold, the nations are as a drop of a bucket, and are accounted as the small dust of the balance: Behold, he takes up the isles as a very little thing. ... Have you not known? have yet not heard? has it not been told you from the beginning? have you not understood from the foundations of the earth? It is he who sits above the circle of the earth, and the inhabitants of it are as grasshoppers; who stretches out the heavens as a curtain, and spreads them out as a tent to dwell in; who brings princes to nothing; who makes the judges of the earth as vanity. ... To whom then will you liken me, that I should be equal to him? says the Holy One. Lift up your eyes on high, and see who has created these, who brings out their host by number; he calls them all by name; by the greatness of his might, and because he is strong in power, not one is lacking.

A bigger universe makes the God who created it more impressive, not less, and makes Isaiah 40 more poignant, not less. Don't get so hung up on cosmological details like the poetic "sits above the circle of the earth" phrase that you miss the fundamental implication here: God's universe is big, and he is even bigger.

(For further discussion of the immensity of the universe, see Days 1 and 2 in the series on the left sidebar.)