Tag Archives: oxygen

The People of the Wind

140-133 million years ago

John W. Campbell, the editor of Astounding Science Fiction magazine, used to challenge writers with new premises. One of his challenges was to imagine an alien that is to mammals as mammals are to reptiles. Science fiction writer Poul Anderson took up this challenge by inventing the Ythri, flying intelligent aliens of the planet Avalon, for his novel The People of the Wind. The Ythri were able to support the high metabolisms necessary for flight because they had a special system for supercharging their bloodstreams with extra oxygen.

Since Anderson’s time, we’ve learned that birds – and some dinosaurs – are actually somewhat Ythri-like. To begin with, consider non-dinosaur reptiles, like lizards: their sprawling posture means that their legs compress and expand their lungs as they run, so they can’t run and breathe at the same time. (David Carrier, a biologist at the University of Utah, was a main guy to figure this out.) If you had traveled back in time to the Paleozoic, before the dinosaurs took over, and if you had had good endurance training, you would have found the hunting easy, because the sprawling reptiles of the time would not have been able to run away for more than a short sprints. The predators to worry about would have been ambush hunters, not endurance hunters.

Dinosaurs got around these constraints in the first place by running bipedally (although some later reverted to quadrupedalism). And it now looks like at least some of them also had the sort of respiration we find in birds. Lungs are only part of birds’ respiratory systems. Birds also have an extensive network of air sacs running through their bodies, and even air passages in their bones. Air moves in both directions, in and out, like a bellows, through the air sacs, but only one direction through the lungs. This allows for more efficient circulation than mammalian lungs, where air has to move both in and out of the lungs. Just recently (2008), it’s been shown that Allosaurus, only distantly related to birds, had the same system, so it was probably widespread among dinosaurs. This breathing system may have helped dinosaurs to survive low-oxygen crises at the end of the Triassic, and flourish in the low oxygen Jurassic and Cretaceous. It may also have helped one group of dinosaurs to evolve into birds.

Anderson’s book isn’t just about respiratory physiology. It’s also about perennial issues of loyalty and identity. Avalon also has human settlers, who have so absorbed Ythri values — some of them even yearning, impossibly, to be Ythri — that they fight for an independent Avalon against an expanding Terran Empire. (Compare the movie Avatar.)

We’ll have more to say about bipedalism and breathing — and language — when human evolution comes up.

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.

The People of the Wind

146-139 million years ago

John W. Campbell, the editor of Astounding Science Fiction magazine, used to challenge writers with new premises. One of his challenges was to imagine an alien that is to mammals as mammals are to reptiles. Science fiction writer Poul Anderson took up this challenge by inventing the Ythri, flying intelligent aliens of the planet Avalon, for his novel The People of the Wind. The Ythri were able to support the high metabolisms necessary for flight because they had a special system for supercharging their bloodstreams with extra oxygen.

Since Anderson’s time, we’ve learned that birds – and some dinosaurs – are actually somewhat Ythri-like. To begin with, consider non-dinosaur reptiles, like lizards: their sprawling posture means that their legs compress and expand their lungs as they run, so they can’t run and breathe at the same time. (David Carrier, a biologist at the University of Utah, was a main guy to figure this out.) If you had traveled back in time to the Paleozoic, before the dinosaurs took over, and if you had good endurance training, you would have found the hunting easy, because the sprawling reptiles of the time would not have been able to run away for more than a short sprints. The predators to worry about would have been ambush hunters, not endurance hunters.

Dinosaurs got around these constraints in the first place by running bipedally (although some later reverted to quadrupedalism). And it now looks like at least some of them also had the sort of respiration we find in birds. Lungs are only part of birds’ respiratory systems. Birds also have an extensive network of air sacs running through their bodies, and even air passages in their bones. Air moves in both directions, in and out, like a bellows, through the air sacs, but only one direction through the lungs. This allows for more efficient circulation than mammalian lungs, where air has to move both in and out of the lungs. Just recently (2008), it’s been shown that Allosaurus, only distantly related to birds, had the same system, so it was probably widespread among dinosaurs. This breathing system may have helped dinosaurs to survive low-oxygen crises at the end of the Triassic, and flourish in the low oxygen Jurassic and Cretaceous. It may also have helped one group of dinosaurs to evolve into birds.

Anderson’s book isn’t just about respiratory physiology. It’s also about perennial issues of loyalty and identity. Avalon also has human settlers, who have so absorbed Ythri values — some of them even yearning, impossibly, to be Ythri — that they fight for an independent Avalon against an expanding Terran Empire. (Compare the movie Avatar.)

We’ll have more to say about bipedalism and breathing — and language — when human evolution comes up.

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.

The People of the Wind

146-139 million years ago

John W. Campbell, the editor of Astounding Science Fiction magazine, used to challenge writers with new premises. One of his challenges was to imagine an alien that is to mammals as mammals are to reptiles. Science fiction writer Poul Anderson took up this challenge by inventing the Ythri, flying intelligent aliens of the planet Avalon, for his novel The People of the Wind. The Ythri were able to support the high metabolisms necessary for flight because they had a special system for supercharging their bloodstreams with extra oxygen.

Since Anderson’s time, we’ve learned that birds – and some dinosaurs – are actually somewhat Ythri-like. To begin with, consider non-dinosaur reptiles, like lizards: their sprawling posture means that their legs compress and expand their lungs as they run, so they can’t run and breathe at the same time. (David Carrier, a biologist at the University of Utah, was a main guy to figure this out.) If you had traveled back in time to the Paleozoic, before the dinosaurs took over, and if you had good endurance training, you would have found the hunting easy, because the sprawling reptiles of the time would not have been able to run away for more than a short sprints. The predators to worry about would have been ambush hunters, not endurance hunters.

Dinosaurs got around these constraints in the first place by running bipedally (although some later reverted to quadrupedalism). And it now looks like at least some of them also had the sort of respiration we find in birds. Lungs are only part of birds’ respiratory systems. Birds also have an extensive network of air sacs running through their bodies, and even air passages in their bones. Air moves in both directions, in and out, like a bellows, through the air sacs, but only one direction through the lungs. This allows for more efficient circulation than mammalian lungs, where air has to move both in and out of the lungs. Just recently (2008), it’s been shown that Allosaurus, only distantly related to birds, had the same system, so it was probably widespread among dinosaurs. This breathing system may have helped dinosaurs to survive low-oxygen crises at the end of the Triassic, and flourish in the low oxygen Jurassic and Cretaceous. It may also have helped one group of dinosaurs to evolve into birds.

Anderson’s book isn’t just about respiratory physiology. It’s also about perennial issues of loyalty and identity. Avalon also has human settlers, who have so absorbed Ythri values — some of them even yearning, impossibly, to be Ythri — that they fight for an independent Avalon against an expanding Terran Empire. (Compare the movie Avatar.)

We’ll have more to say about bipedalism and breathing — and language — when human evolution comes up.

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.

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.

The People of the Wind

163-154 million years ago

John W. Campbell, the editor of Astounding Science Fiction magazine, used to challenge writers with new premises. One of his challenges was to imagine an alien that is to mammals as mammals are to reptiles. Science fiction writer Poul Anderson took up this challenge by inventing the Ythri, flying intelligent aliens of the planet Avalon, for his novel The People of the Wind. The Ythri were able to support the high metabolisms necessary for flight because they had a special system for supercharging their bloodstreams with extra oxygen.

Since Anderson’s time, we’ve learned that birds – and some dinosaurs – are actually somewhat Ythri-like. To begin with, consider non-dinosaur reptiles, like lizards: their sprawling posture means that their legs compress and expand their lungs as they run, so they can’t run and breathe at the same time. (David Carrier, a biologist at the University of Utah, was a main guy to figure this out.) If you had traveled back in time to the Paleozoic, before the dinosaurs took over, and if you had good endurance training, you would have found the hunting easy, because the sprawling reptiles of the time would not have been able to run away for more than a short sprints. The predators to worry about would have been ambush hunters, not endurance hunters.

Dinosaurs got around these constraints in the first place by running bipedally (although some later reverted to quadrupedalism). And it now looks like at least some of them also had the sort of respiration we find in birds. Lungs are only part of birds’ respiratory systems. Birds also have an extensive network of air sacs running through their bodies, and even air passages in their bones. Air moves in both directions, in and out, like a bellows, through the air sacs, but only one direction through the lungs. This allows for more efficient circulation than mammalian lungs, where air has to move both in and out of the lungs. Just recently (2008), it’s been shown that Allosaurus, only distantly related to birds, had the same system, so it was probably widespread among dinosaurs. This breathing system may have helped dinosaurs to survive low-oxygen crises at the end of the Triassic, and flourish in the low oxygen Jurassic and Cretaceous. It may also have helped one group of dinosaurs to evolve into birds.

Anderson’s book isn’t just about respiratory physiology. It’s also about perennial issues of loyalty and identity. Avalon also has human settlers, who have so absorbed Ythri values — some of them even yearning, impossibly, to be Ythri — that they fight for an independent Avalon against an expanding Terran Empire. (Compare the movie Avatar.)

We’ll have more to say about bipedalism and breathing — and language — when human evolution comes up.