All Life Starts with Light

All Life Starts with Light

It’s always a little startling when the pastor turns to you in the middle of the sermon and asks a question. When 500 people are attending the service, it gains even more of an edge.

That’s what I get for coming late and sitting in the front row today.

So, when Richard turned to me from the pulpit, in the middle of his discourse on the book of Ephesians, and said, “Ben, isn’t that right?,” at least I was paying attention. I tried to respond with a gesture that conveyed the nuance of the situation, nodding mostly yes, shaking a little no, but overall confirming that it’s the right idea, with a stately and contained mien. My wife says I quivered and grimaced, but I know what I meant.

Everyone else moved on at that point, but since I have a blog, I have unlimited verbal bandwidth to expand my expression with too many words. Here it is.

Before fixing me with his gaze, Richard had said that “All life starts with light.” He’s completely right, then he’s a little wrong, then where it matters most he’s right again. I’ll explain in three parts:

1.)    Yes, every thing started with light: When the universe was created, everything was packed into the space smaller than the size of a city block. And here, “everything” means each and every thing, atoms and energy, from neutrinos to neutron stars. Packed into such a small space, it was so hot that nothing held together and matter itself was melted. Instead, everything was photons and neutrino radiation. Only after space itself expanded could these waves of light cool down and condense into particles. Every bit of matter in you and around you right now was originally light.

That was the first event in the universe, when light was allowed to be light.*

2.)    But at first life got by without light: All this matter took an unimaginably long time to form anything that we could call “life.” Once it was created, life spread through the ancient waters and skies as tiny microbes that Moses never named. The oldest forms of life we can find didn’t live off sunlight, but squeezed energy out of various chemicals lying around the planet. They ate the earth, not the sun. These chemicals only gave energy for a meager existence, but it was all the microbes needed. But without an external source of energy, the earth would slowly run out of juice. Photosynthesis changed all this. Once life started to pull down energy from sunlight, it flourished in new ways and began to change the world (or at least its chemistry).

Even today, whole ecosystems can survive without light. Deep-sea vents give food and energy to weird red and white worms, crabs, and fish far from the reach of the sun. Near these vents, the creatures that are big enough for us to see must have drifted down from above and taken up residence by the dark, bubbling waters, eventually transforming from ordinary creatures into sub-oceanic bottom-dwellers, like Gollum wasting away under the mountains until even the memory of the sun is forgotten. Still, they have their own hidden glory and can eat and make chemicals beyond any human skill. They are so wonderfully weird that they would fit in well to a modern retelling of Job 38-42.

3.)    Complex life starts with light: It took a billion years for the gift of photosynthesis to be fully realized, and another two and a half billion years for it to have its full effect. The net effect of photosynthesis is a trick verging on alchemy: it turns sunlight, water, and exhaust (CO₂) into fresh air (oxygen) and sugar. From our human perspective, oxygen and sugar are definitely part of the good life. Our bodies and brains require huge amounts of each in order to think these thoughts and speak these words. Nothing else on the periodic table can do what oxygen does for us each day. Every breath you take and each bite you eat, something good in it comes from the sunlight pouring over our planet. This torrent of free light energy has persisted day in and day out for an unimaginable length of years. All of this is grace.

So, yes, Richard, the energy of life starts with the energy of light. Now we can even build small devices that, at the far extent of our effort and knowledge, might mimic the light-catching and energy-giving life of the everyday leaf. When we do this we’re still depending on the live-giving gift of light.

 When Paul says to live in the light, and when John says that light was the life of men, those connections are the same as before. Jesus is the light of the world. He made the sunlight and plants to give sugar and life to our bodies. He gave words of life that give sweetness and growth to our souls. There is not a firm line of distinction between the two modes of grace, and each reinforces the other.

Therefore, when the pastor asks you to confirm in front of everyone that all life starts with light, you can nod your head with confidence. Each muscle movement, however awkward, is fueled by the light.

(*By the way, don’t take this too far. This doesn’t mean that if you read the Bible carefully enough that you would come up with the Big Bang model for the creation of the universe. Rather, this means that we can work out each account on its own terms and then juxtapose them. When I set the Big Bang next to the Biblical account, the accounts make sense together and clash in interesting ways. It’s like playing two chords together on a piano to make an unresolved harmony pushing forward through time.)

Poured Out Like Water

A guest post I wrote for the Science and Belief blog put out by the Faraday Institute was just published. Click here to read it.

Here's the first few paragraphs:

My calling as a scientist is to produce and analyse protein structures, which are complex arrangements of atoms. These structures are beautiful, messy things. Because atoms have no colour, we protein scientists can paint our structures any colour we want. Most of us, myself included, choose bright, bold, primary colours, the colours of children’s toys. In our computer-generated models, the atoms are polished and shiny, reflecting virtual spotlights as if placed in a tiny photography studio.

When I think of life, I think first of proteins and their atoms, stacked up and shiny like baubles in a store window. This image of life is accurate in its details, but incomplete. Just like an old yearbook photo is an accurate but incomplete representation of you, a protein structure is a single, static image of a much more dynamic whole.

Those shiny atoms don’t belong exclusively to that protein structure. Before the carbon atoms were in the protein, they were brought into the animal as food. Before that, they may have been carbon dioxide gas that were tied together into a sugar molecule by sunlight and photosynthesis. Long, long before that, the twelve protons and neutrons that made the carbon atom were fused together inside a star.

... click to read more ...

Invisible Power and the Role of the Artist

Fascinating interview with a filmmaker in Artspace that I found inspiring for my own writing. Here's the key quote, which focuses on invisible political power:

"The current system of power is fundamentally pretty invisible to us. It resides in finance, in all sorts of new kinds of management, and within computers and the media, which involves invisible algorithms that shape and manage what information we get. I think one of the most beautiful things artists and journalists can do at this moment in time is to be sympathetic and understanding to the people who voted for Brexit and Trump, and then bring to the fore the invisible power structures that those people feel completely distanced from so that they know where power is. And do it in such a way that isn’t obscure so people like me don’t have to read it three times just to understand it. Do it in a way that really grabs ordinary people’s imaginations."

This is what science writing does, in a way -- it brings to the fore the invisible power structures that shaped our world, although because those power structures are natural and bigger than humans, there's a lot different to the implications than the ones described in this quote or this interview.

As the subtitle to A World from Dust puts it, it tells "how the periodic table shaped life." The periodic table is an invisible power structure! And chemistry is the science of finding it out.

Blog Post on Replaying the Tape of Life at BioLogos

I just wrote another blog post for BioLogos titled "Replaying the Tape of Life and Finding a Chemical Sequence." (Warning: mild spoilers if you haven't seen Forrest Gump yet. And if you haven't, what's stopping you? It's a great movie!)

A World from Dust (Plus): Neanderthal Chemists

In Chapter 11 of A World from Dust, I mention the evidence of chemistry at Pinnacle Point, where early humans used fire to cook food and make paint. Now there's evidence that Neanderthals were chemists, too. This recent study analyzes the black manganese oxide rocks found in France where Neanderthals once lived. Earlier scientists assumed these were used for their color as something like body paint. Heyes et al. point out that it's a lot easier to find other black rocks for this purpose, so the Neanderthals must have had another reason for collecting this special mineral.

Heyes et al. show that manganese oxide can spark flames (as mentioned in Chapter 7), and find evidence of combusted manganese in the Neanderthal fire pits. The Neanderthals collected this for its chemistry as a firestarter, not as a mere pigment. Personally, I didn't know that manganese had this use before researching A World from Dust, which means that I didn't know as much about this element as my Neanderthal ancestors. Guess there's always something to learn.

12 Colorful Rules that Shaped Our World now online

Here's the 12 lectures I put together a few months ago. Each one has a rule and corresponds to a chapter in A World from Dust, and has a DIY chemistry experiment:

DIY: Simulate Mono Lake in a bucket

DIY: Dye fabrics using sticky metals

DIY: Make colored birthday candles – and predict a plugged-in pickle’s color.

DIY: Making white lead pigment.

DIY: Making a glowing green flowing pattern from fluorescein (from highlighters).

DIY: Making a striped Winogradsky column (and finding explosive methane at the lower levels).

DIY: Purifying different pigments from different red plants in your kitchen.

DIY: Making indigo dye (with the help of oxygen) and removing stains.

DIY: Making edible spheres from calcium chemistry through “spherification.”

DIY: Two Rothkos for the price of one.

DIY: Make your own colored nanoparticles like found in stained glass.

DIY: Look at life from a new angle.

A World from Dust (Plus): How Calcium May Turn DNA Into an Antimicrobial Net

One of the ways immune cells catch germs is with a net made of DNA. The immune cells are called neutrophils, and the nets are called Neutrophil Extracellular Traps, or NETs for short. The nets work because of a clever use of calcium that underlines one of the central balances of life as shown in the figure above.

Note how calcium is ejected from the cell in the lower southwest portion of the figure. This is why Chapter 10 of A World from Dust talks about calcium signals that are instigated by opening up calcium doors in the membrane and letting the calcium flow in. A NET begins with such a calcium influx, like many other signals. Calcium floods the cell and uses its unusual charge to aggregate and reshape proteins, reconfiguring the cell in myriad ways, resulting in the formation of the NET.

But then something remarkable happens: calcium's chemistry builds a NET. The cell just turns itself inside out, and a NET forms. The reason why this works is because the NET is made from DNA, and when DNA is ejected into the high calcium concentrations outside the cell, the sticky calcium binds phosphate in DNA, crosslinking it into a dense net that engulfs and immobilizes the germs. I'm reminded of Spiderman on the Electric Company (see 2:21):

So because of the imbalance of calcium outside the cell, all it takes to catch a germ is for one cell to play Spiderman, turn itself inside out, and spill its DNA. Calcium automatically solidifies DNA and the immune system uses a fundamental aspect of biochemistry to make an automatic net. Long ago, calcium was ejected to avoid cross-linking DNA. Now, DNA ejected into the calcium-rich exterior of a cell automatically makes a net.

I'd expect a system like this to evolve wherever water-based life uses a periodic table like ours.

The Natural Chain of Command

One of the take-home messages of A World from Dust is that concepts like causation and function can look different at different "levels" of the world. I was listening to Walter Isaacson's The Innovators: How a Group of Inventors, Hackers, Geniuses and Geeks Created the Digital Revolution this morning when a historical analogy occurred to me.

You may have heard that the Internet was created as a radically decentralized system so that it could withstand a nuclear attack. You have also have heard the scientists who invented the Internet loudly proclaiming that it had no such purpose. Which purpose was it? Both are true, and Isaacson does a good job of showing how.

The engineers and academics working on the nascent Internet technology were building a new way to pass around information. They had no reason to anticipate its military use or purpose. Yet the higher up the chain of command you go, the more you find the military purpose layered on top of the basic communications purpose. The people getting the money from Congress justified its expense with the military purpose that it could withstand a major, disruptive attack. The scientists didn't need that purpose at their "layer" of knowledge; the politicians required it at theirs.

In the same way, a process that is for one purpose locally may serve an additional purpose globally. A chemical process may serve and shape a biological function. Random gene flow and change may interact with a chemically ordered environment to produce a predictable change and even increase in complexity. In fact, a random process can gain a function at a higher level. The genes and elements may not "know" that the network they're building has a biological purpose, but that in no way negates the biological purpose.  (For more on how this might happen, read Terrence Deacon's Incomplete Nature.)

In A World from Dust I focus on the "politicians" of the process, the legislative branch of chemical law-makers that we call the periodic table. These chemical rules result in predictable patterns emerging from random flow. You can stand close to the waterfall to see the random flow, or step back to see that it inexorably flows down and looks similar from moment to moment. It's all a matter of the width of your scope and your point of focus on the chain of command.

"Streams in the Martian Desert" Posted at the BioLogos Blog

I wrote a response to NASA's recent press conference about water on the surface of Mars, and the resulting public shrug from most commentators. It also has a paragraph about a recent scientific finding that highlights the unique nature of Earth's geology. Here is the article, enjoy!

Book Review: Incomplete Nature by Terrence Deacon

It's been half a decade since I read a science book that inspired me this much. (The previous one was The Chemistry of Evolution by Williams and da Silva, and I've just written a full book inspired by that one.)* Deacon has built a dynamical theory of how things happen. By itself, that sounds kind of abstract, but he applies it to two mysteries that preoccupy my time: the origin of life and the workings of consciousness, or in short, evolution and mind.

The theory does appear to offer a possible ways forward on the first front, although I'm not as sure about the second, but that's not my primary area and I'm fascinated by the chemical possibilities. Deacon's take on physical chemistry and the nature of energy is solid enough and unique enough that I'm considering how to teach it in my physical chemistry course. Much better than I could do on neuroscience (Deacon's primary area), that's for sure.

As Deacon admits, this book is only a sketch, albeit a 545-page sketch. I could have used more. Since dynamical processes have particular structures, I could have used more figures to clarify some of Deacon's terms and "levels" of dynamics. Although the evolution and mind subjects are interrelated, I think we could have gotten one book on evolution and a second book on mind, and that would have left room to explore more side roads and give more examples. But I'm intrigued enough to come up with examples on my own.

The biggest ally left unenlisted may be theology. Apophatic theology involves double negatives and absential qualities like Deacon's work. Again, this is an open door for others to walk through. I think there's fruitful progress to be made in taking Deacon's ideas seriously and then using those as a basis for natural theology (a la McGrath, not a la Paley, of course!).

In sum, this is a book that I've only begun to soak in. It already makes the short list of "10 most influential books" in my life.


* Deacon and RJP Williams do both emphasize constraints, so much so that I'm already seeing new things by juxtaposing the two. My first public reflection on Williams was a lecture titled "The Chemical Constraints on Creation" no less!

A World From Dust (Plus): Why Pepto-Bismol Kills Bacteria but not Humans

Chapter 2 of A World From Dust explains how Pepto-Bismol works. That pink stuff kills ulcer bacteria because of its chemistry -- the bismuth in it is so sticky that it sticks to and jams up proteins in bacteria.

The sharp-eyed reader will notice that a key part of this story is left out. Human and bacteria proteins have the same basic chemistry, being made of the same CHON atoms. If bismuth is sticky to bacterial proteins, it must be just about as sticky to human proteins. So if bismuth kills bacteria, it should kill human cells as well. So why is it that we can drink the stuff? Why is there a novel titled Arsenic and Old Lace but Bismuth and Old Lace doesn't scare anyone?

Human cells can survive a dose of Pepto because they have an extra layer of chemical protection. Our internal chemical shield is built from sulfur, in the form of the molecule glutathione, mentioned in another part of Chapter 2. How this shield works is shown in a 2015 PNAS paper titled "Glutathione and multidrug resistance protein transporter mediate a self-propelled disposal of bismuth in human cells" (which, incidentally, is so well done that other scientists would do well to pattern their metal-life investigations on it).

As shown in the diagram above, purple bismuth (Bi) approaches from the left. It crosses the cell membrane and sticks to yellow glutathione's (GSH's) sulfur atoms. Bismuth is so sticky it collects multiple glutathiones, then the cell takes the assembly and tucks the dangerous metal away into a small sulfurous bubble (or vacuole) shown in gray on the right. This is what glutathione is for -- to preemptively stick to the sticky things before they can stick to something else.

The really nifty part of this is that as this process depletes glutathione, the cell senses that and turns on the machinery for making more glutathione. The more bismuth abounds, the more glutathione super-abounds to fix it. Excess glutathione is then available for sticking to other toxic metals as well, so that Pepto may incite a more general protection.

The bacteria killed by Pepto-Bismol don't have a complex glutathione system like this, so its stickiness turns their insides to solids, and they die. Human cells can resist internal petrification because of the chemistry of sulfur as corralled by glutathione's structure. Our cells sweep the sticky bismuth into a side chamber and our proteins remain nice and fluid.

This has implications for cancer therapy. Some forms of chemotherapy kill cancer cells with sticky, toxic metals like platinum. Cancer cells resist the chemo by turning up their glutathione production. Understanding how that system works should allow us to find a way to turn it off, which would make metal-based chemo much more effective. More details can be found in this summary article related to the research article above.

This is also why understanding the chemistry is so helpful. Bismuth-sulfur chemistry may lead to more effective chemo. So support your neighborhood chemist -- you never know what she'll find next.

Chemistry: The Motion Picture (Animated Version)

Todd Martinez and colleagues at Stanford have become directors on the smallest movie set of all time. The paper they published describes how they animate chemical reactions using computer models. The unique angle they take is to watch a simple chemical reaction zoomed in to a medium point. At this point they are focused neither on just one molecule nor on an incomprehensible flaskful of molecules. At this Goldlocks level of complexity, they can see atoms reacting and can catch fleeting side reactions that wouldn't be seen by other techniques -- yet are certainly important. Most of all, the motion of the atoms is as mesmerizing as a lava lamp. I spent decades learning how molecules move so I can have movies like this in my head when I read about a chemical reaction. You can skip to the back of the book and see what's in my head by watching the movie at this link. Try it and let me know what you see.

A Site with Beautiful Chemistry

How is chemistry like a snowfall?

To find out, see the "precipitation" videos at this wonderful website: BeautifulChemistry.net.

Other great videos include the Chemical Garden and Hydrogen Bonds in Water (which I used in class today).

Here's a video that combines science and art:

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.

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.

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.

The Chemistry of "Old Book Smell"

One day I'm going to be able to teach a course entirely built around wonderful infographics like this:

Here's where I got it. Enjoy.

The Chemistry of Ashes

In me thou see’st the glowing of such fire
That on the ashes of his youth doth lie,
As the death-bed whereon it must expire
Consumed with that which it was nourish’d by.
-- Sonnet 73, Shakespeare

Today is Ash Wednesday, in Latin, "dies cinerum," the Day of Cinders.

How long can you sit and watch a fire? The constant motion of the flickering flames fascinates and nearly hypnotizes. The live flames tell a story, whispering kinship. That's true at levels that run as deep as chemistry.

You warm yourself with the same reaction that makes fire burn. Carbon chains + oxygen = steam and carbon dioxide gas. You exhale the exhaust of fire. The structures so carefully built and pieced together in the growing limb are fuel for the flame, vaporized into a gas that slips away like so much vanity. Gas comes from the same root as "chaos." The old order melts away.

Yet there is something left when the fire is complete. Some elemental carbons sit solid in the fireplace, a residue only suitable for marking a line that soils a forehead.

Along with the carbon, if there was anything metal, especially one of the larger metals like iron, nickel, copper, silver, gold, these are too heavy to become gas and would be left behind as well, indistinguishable from the black carbon but assuredly there, broken in tiny bits. The constructed chains, the facade, it all burns away but the heavy metals stay. The elements may melt with the fervent heat but they persist. What is scattered can be gathered and used again.

What can take ashes and put them together into new life? You would need to reverse the reaction, to pull down the heaven above, catching carbon dioxide and water vapor, then shaping it like a potter shapes clay. The second law of thermodynamics says, rightfully, that this is very hard to do.

What you would need to reverse the reaction is an exhaled breath from another life. You would need to take in what another fire breathed out. "Breath" in Hebrew is "nephesh" which also means "soul." You would take in this exhaled soul and you would inhale, and if it was reorganized and reborn in the right configuration, you would live. Exhaust would become new life.

The second law of thermodynamics says that this is very hard to do. It is extremely improbable in a closed system. But it is not impossible. And we do not live in a closed system.

Today we watch the fire burn and draw stick figures with the ashes, crosses, plus signs, made from the elements of lost life. Any life, no matter how well lived, ends in ashes. All intentions, whether selfless or selfish, all the piecing together of the puzzle, all of it burns, igniting from the pressure of its own useless weight. Your mitochondria, where you burn all your carbon chains and run the combustion reaction that warms your skin, are also the direct cause of the poison molecules, the reactive oxygen species and the runaway electrons, that careen out of control and break apart your cells, aging your body and shattering your DNA. All fire has its exhaust. This can be papered over for a day, but it can never be avoided. Thanks be to God.

The next forty days are the age of carbon, of soot and charcoal, of smouldering vapors, a time to wait in the ashes, continuing the slow burn, sitting in the broken pieces, waiting for a breath from above.

Draw Your Own Graphene Circuits

The distinct electronic properties of carbon when layered in graphene sheets have always intriguied me. What kind of electronic properties lurk in what is mistakenly called pencil "lead"? And now it turns out that you can unleash some of these properties ... by drawing with a pencil on paper.

In this story the implications of this are explored. Bending even a simple circuit changes how it conducts electricity, and vapors affect the resistance of the pencil circuit lines. Because of this, you can actually draw your own circuit and make a vapor sensor from pencil lines.

So can this be used in the teaching lab? Or could the answer to a test question be drawn on a piece of paper -- and then checked by attaching electrodes to each end?

Heirloom Chemistry Set

If there's a word that's overused right now, it's "artisan." Its definition is so squishy it can be applied to any material, and if the material is shoddily made it may be considered more realistic and therefore more worthy of the label! But this item on Kickstarter is worthy of the word: an artisan's chemistry set.

Not only is the box sturdy and wooden, not only are the instruments and glassware simple, elegant, and thick, but each of the chemicals is homemade (ok, home-purified but you get the idea). The campaign was funded above and beyond the necessary, so now I'm caught outside the shop window wondering how I can get one of these for myself. What a great idea!

(The shop that the set-maker owns looks pretty incredible as well. I'll have to drop by if I'm in the area ... )