Tag Archives: chemistry

The Boring Billion

1.30-1.24 billion years ago

The Boring Billion* is a billion or so years, from maybe 1.8 to .8 billion years ago, in which Earth’s climate, ecology, and geography were relatively stable. For most of this period, life and Earth seem to have been locked into a very different set of chemical cycles than what we’re used to today.

Today we have a planetary fuel cell that keeps electron-hungry oxygen in the atmosphere and ocean separate from reduced carbon underground. Animals exploit this fuel cell by consuming and oxidizing organic matter. And a few centuries ago, human beings found another way of tapping Earth’s fuel cell: unearthing underground carbon and hydrocarbon stores, and oxidizing (burning) them to fuel the Industrial Revolution.

During the Boring Billion, however, a different, lower-energy, planetary fuel cell operated. There was some oxygen in the atmosphere – a few percent versus 21 percent today, not enough to make it breathable to us. But it’s likely that much of the ocean below a thin surface layer was anoxic, without free oxygen. Atmospheric oxygen still reached the ocean, but indirectly. On land, oxygen combined with sulfur compounds to yield sulfates. When these washed into the ocean, bacteria used them to produce hydrogen sulfide, the chemical that gives rotten eggs their bad smell.

The term of art for this combination of no oxygen and lots of sulfides is euxinia, named after the Euxine, or Black Sea. When the Black Sea flooded 7500 years ago, the decay of organic matter used up all the oxygen below the top 150 meters or so, creating the world’s largest marine Dead Zone. But during the Boring Billion, it looks as if the whole ocean was largely euxinic, a Canfield Ocean.

And it may be that the dominant mode of photosynthesis was different back then too, with purple and green sulfur bacteria exploiting hydrogen sulfide and releasing relatively little oxygen in the process. There are bacteria today that can switch between aerobic and anaerobic photosynthesis depending on the supply of hydrogen sulfide. These photosynthetic bacteria are distinct from true algae, which are not bacteria but eukaryotes with chloroplasts. On the latest evidence true algae evolved around 1.2 billion years ago. They and their multi-cellular descendants – green plants – would eventually make Earth a very different place.

* Middle Proterozoic is the correct, boring name, for the Boring Billion.

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Compost

2,16-2.04 billion years ago

I turned over my compost heap today. It’s looking good now, but it took me years to get the formula right. For a long time, I just let chopped up leaves sit in a pile in a corner of the yard. Nothing much happened. Eventually I wised up and did some research: proper composting requires the right balance of carbon and nitrogen. The nitrogen and some of the carbon go into building organic molecules. Most of the carbon, though, combines with oxygen to make carbon dioxide, releasing energy in the process for the bacteria that make the compost. The amount of energy is appreciable: on a mild winter day, with air temperature just above freezing, the inside of my compost heap was the temperature of a lukewarm bath.  (My secret, if you want to know, is mixing in coffee grounds from the café down the street. The café workers are happy to fill a five gallon bucket I leave there, and to let me carry it off, every week or so. The grounds supply nitrogen that the leaf mulch is short of.)

But composting goes back way longer than my compost heap, and way longer than Homo sapiens has been around. In fact, composting may have gotten its start more than 2 billion years ago. Here’s the story:

Back when I was in college, a guy I knew was taking a course in organic chemistry. He despaired of mastering the material in time for the next exam. Another student who’d already taken the course advised him, “Just remember, electrons go where they ain’t. Everything else is details” This is a pretty good starting point for thinking about how life and Earth have coevolved. Carbon, sitting in the middle of the periodic table, with four electrons to share, and four empty slots available for other atoms’ electrons, is exceptionally versatile. It can form super-oxidized carbon dioxide, CO2, where carbon’s extra electrons fill in oxygen’s empty slots. Or it can form super-reduced methane, CH4, where carbon’s empty slots are filled by hydrogen’s extra electrons. Or it can form carbohydrates, basic formula CH2O, neither super-oxidized nor super-reduced, where the oxygen atom gives the carbon atom some extra empty slots and the hydrogen atoms give the carbon atom some extra electrons.

Chemically, life is pretty much about reducing and oxidizing carbon compounds. Nowadays, this means, on the one hand, photosynthesis – using the sun’s energy to go from carbon dioxide to carbohydrates – and, on the other hand, aerobic respiration – running the same reaction in reverse to release energy. But this modern arrangement took eons to develop. It depended on geochemistry, specifically on the evolution* of what has been called a planetary fuel cell, with an oxidizing atmosphere and ocean physically separated from buried reduced minerals. Given a breach in this separation, the oxygen and the reduced minerals will react and release energy. In future posts we’ll see how such short-circuits in the planetary fuel cell are (probably) the cause of most major mass extinctions.

The development of the planetary fuel cell was erratic. One puzzling episode is the Logamundi Event, where oxygen levels went up 2.2 billion years ago and then back down 2.08 billion years ago. One theory is that the Event began with photosynthetic cyanobacteria pumping oxygen into the atmosphere. When these bacteria died, they just piled up, leaving a growing accumulation of organic matter in the world’s oceans. According to this theory, the end of the Event happened when other bacteria discovered they could oxidize the accumulated organic matter, and used up a good part of the atmosphere’s oxygen. In other words, the end of the Logamundi Event marks the invention of composting.

The return to higher oxygen levels in the atmosphere would take some time, and deposition of reduced sediments.

*Are we allowed to call this “evolution”? Maybe.

Better living through chemistry

3.20-3.04 billion years ago

Chemistry plays a big role once Earth forms. Different mineral species appear, with different chemical compositions. Magnesium-heavy olivine sinks to the lower mantle of the Earth. Aluminum-rich feldspars float to the top.

Chemistry is an example of what William Abler calls “the particulate principle of self-diversifying systems,” what you get when a collection of discrete units (atoms) can combine according to definite rules to create larger units (molecules) whose properties aren’t just intermediate between the constituents. Paint is not an example. Red paint plus white paint is just pink paint. But atoms and molecules are: two moles of hydrogen gas plus one mole of oxygen gas, compounded, make something very different, one mole of liquid water.

A lot of important chemical principles are summed up in the periodic table.

periodictable copy

On the far right are atoms that have their electron shells filled, and don’t feel like combining with anyone. Most, but not all the way, to the right are atoms with almost all their shells filled, just looking for an extra electron or two. (Think oxygen, O, with slots for two extra electrons). On the left are atoms with a few extra electrons they can share. (Think hydrogen, H, each atom with an extra electron it’s willing to share with, say, oxygen.) In the middle are atoms that could go either way: polymorphously perverse carbon, C, with four slots to fill and four electrons to share, and metals, that like to pool their electrons in a big cloud, and conduct electricity and heat easily. (Think of Earth’s core of molten iron, Fe, a big electric dynamo.)

Another example of “the particulate principle of self-diversifying systems” is human language. Consider speech sounds, for example. You’ve got small discrete units (phonemes, the sounds we write bpskchsh, and so on) that can combine according to rules to give syllables. Some syllables are possible, according to the rules of English, others not. Star and spikythole and plast, are possible English words, tsar and psyche are not (at least if you pronounce all the consonants, the way Russians or Greeks do), nor tlaps nor bratz (if you actually try to pronounce the z). Thirty years ago appblog, and twerk were not words in the English language, but they were possible words, according to English sound laws.

You can make a periodic table of consonants.

phonemes

Across the top are the different places in the vocal tract where you block the flow of air. Along the left side are different ways of blocking the flow (stopping it completely –t-, letting it leak out –s-, etc.) The table can explain why, for example, we use in for intangible and indelicate, but switch to im for impossible and imbalance. (The table contains sounds we don’t use in English, and uses a special set of signs, the International Phonetic Alphabet, which assigns one letter per phoneme.) This is why a book title like The Atoms of Language makes sense (a good book by the way).

So sometimes the universe gets more complex because already existing stuff organizes itself into complex new patterns  – clumps and swirls and stripes. But sometimes the universe gets more complex because brand new kinds of stuff appear, because a new particulate system comes online: elementary particles combine to make atoms, atoms combine to make molecules, or one set of systems (nucleotides to make genes, amino acids to make proteins) combines to make life, or another set of systems (phonemes to make words, words to make phrases and sentences) combines to make language.

The curve of binding energy

More stardust

Looking at the abundance of different elements in the universe, we get the following:

element abundances

Note that the vertical scale is logarithmic, so there is vastly more hydrogen and helium in the universe than any other element. As noted in the last post, all the elements except hydrogen and helium were formed after the Big Bang, spewed out by supernovas and the collisions of neutron stars. In general, heavy elements are less abundant because it takes more steps to produce heavy elements than light ones. But the curve is not smooth. The lightest elements after hydrogen and helium (lithium, beryllium, boron) are relatively rare, because they get used up in the nucleosynthesis of heavier elements. And there is a saw tooth pattern in the chart, because nucleosynthesis favors atoms with even numbers of protons. So we get lots of oxygen, magnesium, silicon, and iron, the main constituents of our planet. Lots of carbon too. Finally, iron (Fe) is more than 1000 times more abundant than might be expected based on a smooth curve. Iron nuclei are especially stable because binding energy, the energy that would be required to take the nucleus apart into its constituent protons and neutrons, reaches a maximum with iron. Here’s the famous curve of curve of binding energy (nucleons are protons and neutrons):

curve of binding energy

An implication of this curve is that if you can split a really heavy nucleus, of Uranium-235 say, into smaller nuclei (but still heavier than iron), you will release energy equal to the vertical difference between U-235 and its lighter fission products (not shown) on the vertical scale. This is lots of energy, way more than you get from breaking or forming molecular bonds in ordinary chemical reactions. And if you can fuse two light nuclei, of hydrogen say, into a larger nucleus, you can get even more energy. When we split uranium, we are recovering some of the energy that a star put into synthesizing elements heavier than iron, before or as it went supernova. When we fuse hydrogen, we are extracting energy from the Big Bang that no star got around to releasing.

Starting to figure this all out was part of a scientific revolution that made physics in 1950 look very different from physics in 1900. The new physics resolved a paradox in the study of prehistory. Geologists were pretty confident, based on rates of sedimentation, that the Earth had supported complex life for hundreds of millions of years. But physicists couldn’t see how the sun could have kept shining for so long. The geologists were right about deep time; it took new physics to understand that the sun got its energy from fusing hydrogen to helium (via some intermediate steps).

As the scientific revolution in atomic physics was picking up steam, it was natural to assume that it would be followed by a revolution in technology. After all, earlier scientific revolutions in the understanding of masses and gases, atoms and molecules, and electrons and electromagnetism, had been followed by momentous innovations in technology: the steam engine, artificial fertilizers, electrification, radio, to name just a few. But in some ways, the Atomic Age hasn’t lived up to early expectations. The atom bomb brought an earlier end to the Second World War, but didn’t change winners and losers. The bomb was never used again in war, and it’s a matter for debate how much the atom bomb and the hydrogen bomb changed the course of the Cold War. Nuclear energy now generates a modest 11% of the world’s electricity (although this number had better go up in the future if we’re serious about curbing carbon dioxide emissions). And a lot of ambitious early proposals for harnessing the atom never got anywhere. Project Plowshare envisioned using nuclear explosions for enormous civil engineering projects, digging new caves, canals, and harbors. Even more audacious was Project Orion, which developed plans for a rocket propelled by nuclear explosions. Some versions of Orion could have carried scores of people and enormous payloads throughout the solar system. Freeman Dyson, a physicist who worked on the project, said “Our motto was ‘Mars by 1965, Saturn by 1970.’”

On the purely technical side these plans were feasible. There were concerns about fallout, but the problems were not insurmountable. Nevertheless both Plowshare and Orion were cancelled. Dyson said “… this is the first time in modern history that a major expansion of human technology has been suppressed for political reasons.” The history of the Atomic Age  and its missed opportunities is a refutation of pure technological determinism. How or even whether a new technology is exploited depends on social institutions, politics, and cultural values.

We are stardust

10.4-9.86 billion years ago

The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.

Carl Sagan (h/t to commenter remanandhra)

There’s a long gap between the origin of the universe, the first stars, and early galaxies, and the origin of our Solar System and our planet Earth. If we were using a linear scale for our calendar, the Solar System would get started in September. Even on our logarithmic scale, Sun and Earth wait until late January. A spiral galaxy like the Milky Way is an efficient machine for turning dust into stars over many billions of years. But the earliest stars it produces are poor in “metals” (to an astronomer, anything heavier than helium is a metal). It takes generations of exploding stars producing heavier elements and ejecting them into space before a star like the Sun — 2% metal – can form.

And just last year, a spectacular discovery provided support for another mechanism of heavy element formation. Astronomers for the first time detected gravitational waves from the collision of two neutron stars, 300 million light-years away. Such collisions may be responsible for the formation of some of the heaviest atoms around, gold and silver in particular. So your gold ring may be not just garden-variety supernova stardust, but the relic of colliding neutron stars.

Alchemists thought they could change one element into another – lead into gold, say. But it takes more extreme conditions than in any chemistry lab to transmute elements. The heart of a star makes heavy elements out of hydrogen and helium; it takes a supernova to make elements heavier than iron. So it’s literally true, not just hippy poetry, that “we are stardust” (at least the part of us that isn’t hydrogen).

Better living through chemistry

3.20-3.04 billion years ago

Chemistry plays a big role once Earth forms. Different mineral species appear, with different chemical compositions. Magnesium-heavy olivine sinks to the lower mantle of the Earth. Aluminum-rich feldspars float to the top.

Chemistry is an example of what William Abler calls “the particulate principle of self-diversifying systems,” what you get when a collection of discrete units (atoms) can combine according to definite rules to create larger units (molecules) whose properties aren’t just intermediate between the constituents. Paint is not an example. Red paint plus white paint is just pink paint. But atoms and molecules are: two moles of hydrogen gas plus one mole of oxygen gas, compounded, make something very different, one mole of liquid water.

A lot of important chemical principles are summed up in the periodic table.

periodictable copy

On the far right are atoms that have their electron shells filled, and don’t feel like combining with anyone. Most, but not all the way, to the right are atoms with almost all their shells filled, just looking for an extra electron or two. (Think oxygen, O, with slots for two extra electrons). On the left are atoms with a few extra electrons they can share. (Think hydrogen, H, each atom with an extra electron it’s willing to share with, say, oxygen.) In the middle are atoms that could go either way: polymorphously perverse carbon, C, with four slots to fill and four electrons to share, and metals, that like to pool their electrons in a big cloud, and conduct electricity and heat easily. (Think of Earth’s core of molten iron, Fe, a big electric dynamo.)

Another example of “the particulate principle of self-diversifying systems” is human language. Consider speech sounds, for example. You’ve got small discrete units (phonemes, the sounds we write bpskchsh, and so on) that can combine according to rules to give syllables. Some syllables are possible, according to the rules of English, others not. Star and spikythole and plast, are possible English words, tsar and psyche are not (at least if you pronounce all the consonants, the way Russians or Greeks do), nor tlaps nor bratz (if you actually try to pronounce the z). Thirty years ago appblog, and twerk were not words in the English language, but they were possible words, according to English sound laws.

You can make a periodic table of consonants.

phonemes

Across the top are the different places in the vocal tract where you block the flow of air. Along the left side are different ways of blocking the flow (stopping it completely –t-, letting it leak out –s-, etc.) The table can explain why, for example, we use in for intangible and indelicate, but switch to im for impossible and imbalance. (The table contains sounds we don’t use in English, and uses a special set of signs, the International Phonetic Alphabet, which assigns one letter per phoneme.) This is why a book title like The Atoms of Language makes sense (a good book by the way).

So sometimes the universe gets more complex because already existing stuff organizes itself into complex new patterns  – clumps and swirls and stripes. But sometimes the universe gets more complex because brand new kinds of stuff appear, because a new particulate system comes online: elementary particles combine to make atoms, atoms combine to make molecules, or one set of systems (nucleotides to make genes, amino acids to make proteins) combines to make life, or another set of systems (phonemes to make words, words to make phrases and sentences) combines to make language.

We are stardust

The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.

Carl Sagan (h/t to commenter remanandhra)

There’s a long gap between the origin of the universe, the first stars, and early galaxies, and the origin of our Solar System and our planet Earth. If we were using a linear scale for our calendar, the Solar System would get started in September. Even on our logarithmic scale, Sun and Earth wait until late January. A spiral galaxy like the Milky Way is an efficient machine for turning dust into stars over many billions of years. But the earliest stars it produces are poor in “metals” (to an astronomer, anything heavier than helium is a metal). It takes generations of exploding stars producing heavier elements and ejecting them into space before a star like the Sun — 2% metal – can form.

Alchemists thought they could change one element into another – lead into gold, say. But it takes more extreme conditions than in any chemistry lab to transmute elements. The heart of a star makes heavy elements out of hydrogen and helium; it takes a supernova to make elements heavier than iron. So it’s literally true, not just hippy poetry, that “we are stardust” (at least the part of us that isn’t hydrogen).