Tag Archives: chemistry

The Boring Billion

1.31-1.25 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 in minerals deep 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 in the anoxic zone 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 at least 1.2 billion years ago, maybe 1.6 billion. They and their multi-cellular descendants – green plants – would eventually (after some extreme Ice Ages) make Earth a very different place.

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

Compost

2.3-2.18 billion years ago

A few days ago, I picked up a five gallon bucket that I had left at the cafe down the street, which they nicely filled up with coffee grounds. These went into my compost heap, where they’ll supply the nitrogen that the leaf mulch in the heap is short of. I’ve developed a kind of pre-capitalist exchange relation with the cafe; summers I bring them some flowers from my garden.

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.

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, a result of major lava flows, are probably the cause of most major mass extinctions.

The development of the planetary fuel cell was erratic. One puzzling episode is the Lomagundi 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 Lomagundi Event marks the invention of composting.

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

Matchmaking life

You can find romance if you want in the periodic table, with elements on the right side of the table, just an electron or two short of a full shell, cruising for partners over on the left side, with an electron or two to share. The folk-singing sisters Anne and Kate Macgarrigle made a song out of this, NaCl, about a love affair between a chlorine atom and a sodium atom. “Think of all the love you eat when you salt your meat.”

And living things are matchmakers, middlemen making a living by arranging liaisons between the two sides of the periodic table, harvesting the energy released by moving electrons around. The basic mechanism is shown below.

protonics

Take a reducing compound willing to give up an electron and an oxidant looking for an electron. Electrons go where they ain’t: starting on the left, electrons (e-) from the first compound pass through a series of protein complexes (grayish circles) embedded in a membrane (horizontal lines). The passage of electrons from one complex to the next in the membrane powers the movement of protons (H+) from one side of the membrane to the other. For each pair of electrons passing down the chain, ten protons are moved across the membrane. Finally the electrons are united with the oxidant (shown as O2 generating H2O). Electrons keep being pulled through the chain as long as reducing and oxidizing agents are available.

This is the first part the job. The result is a lot of extra protons on one side of the membrane and a large difference in electrical potential between the two sides. For the second part, another protein complex (ATP synthase) uses this potential difference to turn ADP (adenosine diphosphate) into ATP (adenosine triphosphate). ATP is the fundamental energy carrier of life, powering the cell’s chemical reactions when it turns back into ADP. (Creatine supplements work for athletes and bodybuilders because creatine helps with ATP synthesis.)

This is the basic mechanism of respiration (and most of photosynthesis), just as DNA replication is the basic mechanism of heredity. Understanding the origin of this mechanism is a major challenge in understanding the origin of life. Nick Lane walks through some of the theories.

At this stage in Earth’s history, living things are tiny and not very interesting structurally. But they are hugely diverse biochemically, making use of a great array of different reducing and oxidizing compounds. For example, methanogens use hydrogen seeping from undersea vents to reduce carbon dioxide, producing methane. This may have been of some importance to the planet as a whole. Methane is a greenhouse gas, trapping infrared radiation even more effectively than carbon dioxide. The Sun three billion years ago was fainter than it is today; it may be methanogens that kept a young Earth from freezing over.

Better living through chemistry

2.72-2.58 billion years ago

Below I discuss some interesting parallels between chemistry on the one hand, and linguistics on the other. Remarkably, a recent article makes a strong case that there is an actual historical connection between the science of linguistics and the science of chemistry. Specifically, Mendeleev’s construction of the Periodic Table of Elements was probably influenced by Pāṇini’s classic generative grammar of Sanskrit, the Aṣṭādhyāyī. This was written somewhere around 500-350 BCE. It has been said to be as central to India’s intellectual tradition as Euclid’s Elements is to the West’s. It probably reached the attention of Mendeleev thanks to the work of his friend and colleague, the Indologist and philologist Otto von Böhtlingk, who translated it.

[F]oundational to the Aṣṭādhyāyī was a two-dimensional, periodic alphabet, which may have intrigued Mendeleev as he struggled to create his own periodic array.

The physicist Eugene Wigner wrote about “the unreasonable effectiveness of mathematics in the natural sciences.” (Here is a cute recent example where repeated rebounding collisions produce successively close approximations of pi.) Perhaps Mendeleev’s debt to Pāṇini via von Böhtlingk is an example of the unreasonable effectiveness of linguistics.

Here’s more on the parallels:

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

10.4-9.9 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 three years back, 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. Here’s a chart showing where the elements in our solar system come from:

stardust

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).

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 at least 1.2 billion years ago, maybe 1.6 billion. 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.

Compost

2,16-2.04 billion years ago

I’m writing this in the café down the street from my house, where I just picked up a five gallon bucket of coffee grounds. These will go into my compost heap, where they’ll supply the nitrogen that the leaf mulch in the heap is short of. I’ve developed some kind of pre-capitalist exchange relation with the cafe; come summer I’ll bring them some flowers from my garden.

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.

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.