Tuesday, September 16, 2014

Chemical Faithfulness, Part 3: Natural Laboratories for the Origin of Life


In the past two parts of this series I described how liquid water is living water, its special chemistry shaping geology and biology to give us the world today. Water’s life-giving power extends even deeper than this, as deep as a few billion years back in time. We saw how liquid water’s chemical power created the Puget Sound and sustains deep-sea ecosystems today. Likewise, water could have participated in creation long ago.

The chemical ingredients life needs come together at the deep ocean vents: carbon, sulfur, hydrogen, iron, nickel, and especially energy from within the earth.  Long ago, water’s chemical power may have brought these ingredients together to shape the first life forms.

I once avoided these ideas because I felt that a chemical bridge from non-life to life threatened God’s creative sovereignty. But now I’ve changed my mind. If God came up with the ideas, then they actually convey God’s creative sovereignty. The more I appreciate the dynamic elegance of water’s chemistry, the more I think that God appreciates dynamic elegance, too. All origin of life experiments have an important role for the chemical power of flowing, liquid water.

For example, some deep-sea vents form rocks with holes that look suspiciously like small cells. These cavities naturally stockpile and separate chemicals, like natural laboratories with billions of chambers. They are lined with iron and nickel atoms that react with the sulfur and hydrogen streaming out of the earth like Champagne bubbles.

One of the central molecules in all metabolism, pyruvate, forms spontaneously in these vents, as well as other related molecules that look like the breakdown products of pyruvate found in every cell. It’s as if a biochemical network is budding from the rocks. The holes in the rock can hold different mixtures of chemicals in place, like the 96-well plates scientists use to run 96 experiments at once. In the rock, simple circular chemical cycles could have formed and started to turn, fed by gas bubbles.

Or maybe the heat was more gentle, the toasty temperature of a hot spring at the earth’s surface. This makes a different kind of natural laboratory, where holes in the rock act as gas condensers, collecting steam and letting it drip down in a purifying cycle. Every organic chemistry lab contains complex glass sculptures built to condense and distill. Some hot springs have rocks that do the same chemistry.

Experiments in a similar environment found conditions where simple 4- or 5-atom molecules naturally rearrange into the complex, three-part nucleosides that make up DNA. In an elegant flourish, this fascinating set of reactions is catalyzed, not by a rare element or molecule, but by the very common bio-molecule, phosphate. DNA has phosphate in it, meaning this important molecule may incorporate its own catalyst.

Origin of life chemistry as a field is full of successes like these but also its fair share of failures. One major failure is summed up by Steven Benner as “the asphalt problem”: undirected reactions tend to make tar. What’s interesting to me is where the failures may come from. I think most experiments were too simple, too purified, and too dilute. If the experiments are made dirtier, in many cases with actual “dirt,” they work better. The deep-sea experiment above can’t make pyruvate without the iron and nickel from rocks. In the DNA-making experiment, the DNA nucleosides are not made from a sequence of reactions, but by mixing everything together in one pot and running thousands of reactions at once. The more the experimental conditions mimic the geological complexity of the early earth, the more the resulting chemicals look like biological complexity (that is, pyruvate or DNA nucleosides).

This experiment is run with chemical ingredients provided by the periodic table and the physical forces of mixing and geology, which are mediated by liquid, living water. If God gave the chemical laws, then God gave water this power, and this could be how God created. God works with me patiently and through the world around me – perhaps he did the same at the creation of life.

If we can imagine God giving his power to God’s creation, then origin of life chemistry experiments have no necessary conflict with a strong theology of creation. The first biochemical cycles would have obeyed the rules of chemistry, and we know Who made those rules. Even the deepest part of the sea at the far extent of Earth’s history is part of God’s creation and ordered by God’s Word.

Water is the medium of life-giving grace, and we can see through it to the one who ordered the atoms with the rules of chemical bonding (and the math that sets those rules). In Greek, such rules would be called the logos -- the wisdom and Word by which worlds were created. As a chemist, I am called to seek out the subset of those rules called chemistry, and to understand that God is at work providing and upholding them.

The world looks different if flowing, living water is seen as a chemical gifted with the potential to create life. We know water is powerful enough to carve landscapes, form gemstones and ores, and support fantastic microbes. Now to these powers is added the ability to make life by reacting with rocks, and the story of creation becomes that much more amazing.

The length of this story is incomprehensible to our small experience. Our experiments show that Earth held an ocean of life-sustaining water on its surface for 4 billion years, not boiling it into steam like Venus or losing it to a barrage of asteroid impacts, like Mars. The word for that duration of constancy is faithfulness. Through eons, God has cared for us by upholding a universe with constant chemical laws, rules that convey the simple grace of living water.

I am writing a book that recounts the story of these chemical laws, this logos, that shaped the world around us. Water is so important to that story that I changed the book’s title halfway through to give water a place of honor – now it is called River of Life: How Chemistry Shaped Biology. A river is living water, and water, despite its small size, is the chemical cornerstone of life.

The angle of science and the angle of theology fit together and co-illuminate in the story of “living water.” The creator who emptied himself of power and became so small at Christmas also made the small but powerful molecule H2O, then gave us oceans of it. The more things we discover about that molecule, the more we can delight in the hand that gave it yesterday and continues to give it today.

Monday, September 15, 2014

Chemical Faithfulness, Part 2: How Water Shapes Geology and Biology


In Part 1 of this series I wrote about the chemical power hidden in a glass of water, and how, chemically speaking, water is truly the “living water” of Scriptural metaphor. Living water is creative -- its flow shapes both your feet and the ground beneath them.

Every place on Earth, even the driest desert, has been shaped and washed by the power of water. Twenty years ago when I moved from Florida to Seattle, I moved from one place shaped indelibly by water to another.

In Seattle, our rainfall is famous. Our familiarity with water also runs deep in time. Long ago frozen water carved the landscape of the Pacific Northwest with flowing, “living” glaciers. Long ago, an advancing ice sheet from Canada traveled southwest and ran into the Olympic mountains around where Vancouver is today. The mountains stood firm, cracking the ice in two. One sheet turned west and joined the Pacific, carving the Strait of Juan de Fuca. The other turned south and scooped out the Puget Sound.

In Florida, the water is different, both temperamental and constant. Routine 4pm summer thunderstorms suddenly pour down rain that pools in your sandals, then just as suddenly stop. There are no glacial valleys in Florida, but there are miles of beaches, rock atomized by surf. The water has also carved deep aquifers underneath Florida, which would stay hidden if not for the occasional sinkhole.

All this power is wrapped up in a tiny package. Water is the mustard seed of molecules. It is composed of two hydrogens and one oxygen, bonded with electrons, as H2O.

You can make a molecular model of water with two grapes (for the hydrogens), two toothpicks (for the shared electrons), and a plum (for the oxygen). If you can make the grapes stick out from the plum with an angle of 104.5°, then you have just made a scale model of the molecule that carved Seattle’s valleys and fills Florida’s aquifer. In a sense, you’d be making the model of water from water -- the fruit that you’d be using to make this model is mostly water itself, sweetened with some natural sugar.
 
Water may be small but this makes it more exceptional, because it is small yet liquid. It’s always easier for a bunch of molecules to go to extremes than to sit in the middle.  It’s easy for big molecules to stick together tightly and freeze (to become solid) or for small molecules to fly apart in a thousand directions (to become gas). It’s not easy for a molecule to find an inbetween state, neither too hot nor too cold, close enough to touch and yet energetic enough to slide around, flowing as a liquid, condensing into an ocean. Life needs to be in this inbetween state, its atoms coherent yet always in motion. Therefore, life as we know it needs water, and you are alive because of the liquid water in you.

If liquids are living, then the universe is mostly dead, because liquids are rare. Looking at the periodic table, only two elements out of more than 100 are liquid at room temperature: mercury and gallium. Likewise, most molecules as small as water are gases. Big, complex molecules are harder to make. Here on earth, only water is the only molecule that combines liquidity with simplicity, and we literally have oceans of it.

Oceans are Earth’s defining characteristic in the solar system, a gift to our planet that changes its distant color to that of a “pale blue dot,” perceptibly different from yellow Venus and red Mars. Oceans made our rocks different as well. The geologist Robert Hazen estimates that the action of water on the Earth brought about more than 3000 new minerals when there were only about 500 before, a multiplication of diversity in the rocks from this one chemical.

Jade, sapphire, emerald, all were made when water mixed and reacted with the Earth. Mother lodes of ores are found by following the ancient paths of water to where precious metals were deposited. Panning for gold requires a stream of running, living water.

Look at a drop of water in a microscope and you’ll see another way it is “living” water. Even the most crystal-clear pond water is home to thousands of undulating, spinning, pulsing amoebae and protozoa, a microscopic menagerie. Remove all of these, looking even closer at the atoms in water, and you would see that water is constantly moving around itself, forming, unforming, and reforming bonds, in what Bill Bryson described as a “quadrille.” This movement is unbridled, even joyful.

Liquid water hosts life even in extreme conditions. In the deepest parts of the oceans, ecosystems hidden from the sun cluster around bubbling clefts where hot, energy-laden gases escape from the earth. These vents are rich with crabs, lobsters, octopi, pale white dappled with red. Six-foot-long tube worms waving like ghostly grass. These animals bask and feed on the sulfurous energy of the earth itself, mediated by the water, which is only kept liquid at such intense temperatures by the massive pressure of the fathoms above.

The DNA of these animals can be read like a book, and it matches the DNA of more familiar species. The pale creatures near the vents came to that place without sun long ago, and were kept alive by the water and the earth’s energy. Eventually they lost what they didn’t need -- pigments, eyes, and in the case of the tube worms, even mouths (they let the bacteria that live inside them eat for them, which is just as strange as it sounds). Life can live without sunlight, but it cannot live without water’s liquid flow.

Life needed water and energy to survive, and it changed its form to survive, morphing in ways unthinkable and amazing. Through liquid water, life was able to fill what had previously been empty, to thrive and to surprise. That sounds like grace to me.

Deep-ocean vents may shed light on another dimension to water’s power. At that extraordinary place, living, liquid water may have shaped the first living things on this planet, bringing a good creation to life 4 billion years ago. I will describe experiments that point in this direction in part 3 of this series.

Saturday, September 13, 2014

Book Review: Slaughterhouse-Five by Kurt Vonnegut

My brain wants to give this five stars. My heart wants to give it less, but my brain's going to win this one. That's because this book manages to walk an impossible line: it jumps around in time yet somehow keeps a driving, disjointed narrative; it is harsh as war yet gentle as an epitath (and so it goes); it is an absurd circus to the tune of a classical dirge. Every word is true, but I don't believe the sum of the words, and I believe I'm right to do so. Still, no one writes of devastation better than Vonnegut. This voice needs to be heard and this book needs to be read. In the audiobook I listened to, Ethan Hawke gave a masterful, hushed reading, so I recommend listening to that even if you've already read it.

But what about my heart? Well, near the end of listening to this I started reading In Sunlight and In Shadow by Mark Helprin, which describes a WWII veteran upon his return, much like Billy Pilgrim. But the voice is a bit different. Light-years, in fact.  It was like reading through 3-D glasses: Vonnegut was the blue lens and Helprin the red (the color of roses, iron, and blood). I want to set Helprin's words next to Vonnegut's:

" He straightened in his seat, lifting himself until he seemed taller, unconsciously positioning his upper body as if for a fight -- not with Catherine, but with an idea. His eyes narrowed a bit as they seemed to flood with energy. " ... People like that always want to show you that they're wise and worldly, having been disillusioned, and they mock things that humanity has come to love, things that people like me -- who have spent years watching soldiers blown apart and incinerated, cities razed, and women and children wailing -- have learned to love like nothing else: tenderness, ceremony, courtesy, sacrifice, love, form, regard ... The deeper I fell, the more I suffered, and the more I saw ... the more I knew that women are the embodiment of love and the hope of all time. ... Love of God, love of a woman, love of a child -- what else is there? ... those are the things that lacerate and wound, and make you suffer incomparably, because in the end, you lose them." "

Helprin and Vonnegut are not diametrically opposed. Vonnegut's words can be tender, he has his ceremony (and so it goes), he is courteous to his characters, at least to Billy. But love is as hard to find in this novel as free will -- it is nowhere. It is not in Billy's marriage, or in his friends, or his children. I don't think this is just because Vonnegut was in Dresden when Helprin was a child. It's because of a choice each of them made and one everyone has to make. That choice has rarely been put so clearly as in these two books side by side. That's why you should read Vonnegut. Just make sure you read something like Helprin too.

Wednesday, September 10, 2014

Chemical Faithfulness, Part 1: The Power of Water

The most ordinary things are also the most incredible. Every day I have to relearn this. This truth is so big, it can only fit into my neurons when it’s cut down and reduced to a particular angle. Science can give one angle. So can history, or visual arts, or music, or theology. What’s really fun is to take two of those angles and put them together again. As a biochemistry professor and a Christian, I can “see” how atoms and proteins work from the science angle, and I can “see” how this relates to how I love God and neighbor from the theology angle. Both angles come together to bring light to even the most seemingly mundane of subjects: a cool drink of water.

Consider the power in a drop of water. If given to a dehydrated infant with cholera, it extends life. If it pushes a turbine around inside the Hoover dam, that pushes electrons and creates electric power. The electrons in water even carry power that is evoked through chemical rearrangement. If the sun’s power can be focused by the right catalyst into that drop of water, then the H2O molecule can be split into H2 hydrogen and O2 oxygen – which are later recombined to release energy. Right now water is split inefficiently. If water could be split efficiently, then a bottle of water could make enough hydrogen to ignite in a generator and power a house. Who would have anticipated that water could burn?

You are thirsty when you need this power. More than anything, it’s the liquid state of water that provides the power. Liquids flow and change, giving biochemistry the ability to detect outside information through sense receptors, and then to respond to that information through flowing change. Flowing water has always been a fitting metaphor for life -- physically, and by extension, spiritually.

“Everyone who thirsts, come to the waters,” cries Isaiah. Jesus answers Isaiah, “If anyone thirsts, let him come to Me and drink.” To the woman at the well, Jesus gave living water, but not like she expected. From John the Baptist to the water basins in the Tabernacle to the Temple’s brazen circular sea, for thousands of years the flow of water has washed bodies, souls, and minds.

Speaking as a chemist familiar with molecules of all sorts and sizes, there is no molecule more deserving of the scriptural adjective “living” than the water molecule. No other single molecule is as intimately associated with life.

The rain that falls on the just and the unjust is truly living water, and is truly good. Liquid water is “living” on all scales, whether large as a solar system, small as a protein, or old as the Earth. Geology, chemistry, and biology show connections between water and life both obvious and hidden.

Water gave life when this planet was created. Water is a unique and life-giving gift, and very often we see right through it, until taking the time to look closer. Looking closer with science always surprises me. My original beliefs about how the world works are challenged and corrected. Old hypotheses are traded for new. But my core beliefs, the beliefs that are truly deserving of that name, they are not destroyed by this challenge. They are washed and grown, even baptized. The more I learn about water, the more I see it “live” around and in me, and the more I can see in Scripture’s metaphor of “living water.”


I see chemical evidence for “living water” today, yesterday, and even a billion yesterdays ago. This consistency in the universe is one sign of God’s chemical faithfulness across ages. In the next two posts, I will describe the chemical signs of this faithfulness at two times: today in places and creatures, and in the distant past, at the origin of life itself.

Sunday, September 7, 2014

Book Review: Paul and the Faithfulness of God, Parts 3 and 4 (Book 2) by NT Wright

Looking back on it, I had to train for this book like a climber has to train for Mt. Rainier. I've read and listened to Wright's other books and lectures (including the first three in this series), but I'm happy to announce I didn't fall into a crevasse or anything. There's no way that a few sentences here can really express what I got out of these 1519 pages (or 50 hours of reading), but I have a few scattered thoughts upon completion:

-- Wright's intention to describe theology as a narrative rather than propositions is parallel to what I try to do in science. I learned a lot from him in how to disagree and argue with a broad range of other academics. Whatever you think of his conclusions, theology is stronger for Wright's arguments, and I think science can be stronger if similar narrative arguments are made in it (it also helps that I think those arguments are essentially right). Therefore I wrote a book.

-- The decision to lop off a lot of the arguments and put them into a separate book (Interpreters) is much appreciated. That said, there were several places where I drifted along because I just don't have a dog in that fight, or I already know where my "dog" sits. These amount to maybe 100 pages at most. In other books that would bog the book down. In this one it's 5% of the book so the point may be insignificant.

-- What I appreciate most is how Wright integrates history into the narrative and insists that we need to use the historical categories, not modern ones, to understand Paul's train of thought. And things that before I thought were intrusions or leaps of intuition turn out to be much more solid and make perfect sense in the light of the history. He did this for Jesus in Book 2, and now he does it for Paul in Book 4. Paul makes sense in new ways for me.

-- Wright writes well. Allusions to Pride and Prejudice and Midsummer Night's Dream play major roles in particular chapters, and he is a master of the biblical allusion (big surprise there). At the end he brings in Walter Benjamin, a philosopher friend of Hannah Arendt's I have never heard of but intend to find out more.

-- Wright's pastoral care is also integrated into the book. This is not just about the mind, but it is about practice and the entire life. So, if you care to train, this mountain is worth climbing. Excuse me while I decompress.

Tuesday, August 26, 2014

Book Review: Mr. Mercedes by Stephen King

Mr. Mercedes reads more like a novella than a novel, or a good two-part TV show, perhaps. It's a typical crime story but Stephen King shows his masterful writing in the pacing and suspense throughout (as well as the plot convolutions needed to involve a retired detective rather than an active one). The most amazing character, as usual, is the (all too human) monster, very much evil and very much human at the same time. King completely explains his character's evil without excusing it, and you can easily see how this guy got to be so messed up that you're almost sad for him. Almost. This is too "normal" of story to reach the heights of Joyland or 11-22-63, but it's very well done and a master class in writing.

Thursday, August 21, 2014

Book Review: The Graveyard Book by Neil Gaiman

Second time through on this (and second time reviewed on this blog). This time the story was read aloud to a 10 and 11-year-old. The second half was read in the car on a long drive and it pulled in the 43-year-old mother of those two as well, especially with its themes of growing up and finding, then leaving, home. To anyone turned off by the book's dark beginning, I'd say, read it through to the end, see where it's going. The pacing and storytelling of the long climactic chapter seven is a writer's workshop of skill, and then chapter eight is a melancholy coda that brings it all home. This is simply a good book, as good in its way as its inspiration (Kipling's Jungle Book). For a book about ghosts it has more humanity in it than many books about the living. It deserves the Newbery it won.