Author Archives: logarithmichistory

When you were a tadpole and I was a fish

1.17-1.11 billion years ago

The Boring Billion rolls on. The atmosphere is one percent oxygen or so thanks to photosynthetic bacteria and algae. The ocean still largely anoxic and thick with sulfates and sulfate-eating bacteria. Eukaryotes have been around for a while, and are diversified, although still all single celled (as far as we know).

Sexual reproduction begins with eukaryotes, and by now some groups are presumably differentiated into male and female. For those of you who are not bdelloid rotifiers, here’s a poem for Valentine’s Day, by the biologist Langdon Smith. Martin Gardner has a nice account of the poem, in his book “When you were a tadpole and I was a fish,” and here’s a great video of the poem spoken by Jean Shepherd.

By Langdon Smith (1858-1908)

When you were a tadpole and I was a fish
In the Paleozoic time,
And side by side on the ebbing tide
We sprawled through the ooze and slime,
Or skittered with many a caudal flip
Through the depths of the Cambrian fen,
My heart was rife with the joy of life,
For I loved you even then.

Mindless we lived and mindless we loved
And mindless at last we died;
And deep in the rift of the Caradoc drift
We slumbered side by side.
The world turned on in the lathe of time,
The hot lands heaved amain,
Till we caught our breath from the womb of death
And crept into life again.

We were amphibians, scaled and tailed,
And drab as a dead man’s hand;
We coiled at ease ‘neath the dripping trees
Or trailed through the mud and sand.
Croaking and blind, with our three-clawed feet
Writing a language dumb,
With never a spark in the empty dark
To hint at a life to come.

Yet happy we lived and happy we loved,
And happy we died once more;
Our forms were rolled in the clinging mold
Of a Neocomian shore.
The eons came and the eons fled
And the sleep that wrapped us fast
Was riven away in a newer day
And the night of death was passed.

Then light and swift through the jungle trees
We swung in our airy flights,
Or breathed in the balms of the fronded palms
In the hush of the moonless nights;
And oh! what beautiful years were there
When our hearts clung each to each;
When life was filled and our senses thrilled
In the first faint dawn of speech.

Thus life by life and love by love
We passed through the cycles strange,
And breath by breath and death by death
We followed the chain of change.
Till there came a time in the law of life
When over the nursing sod
The shadows broke and the soul awoke
In a strange, dim dream of God.

I was thewed like an Auroch bull
And tusked like the great cave bear;
And you, my sweet, from head to feet
Were gowned in your glorious hair.
Deep in the gloom of a fireless cave,
When the night fell o’er the plain
And the moon hung red o’er the river bed
We mumbled the bones of the slain.

I flaked a flint to a cutting edge
And shaped it with brutish craft;
I broke a shank from the woodland lank
And fitted it, head and haft;
Then I hid me close to the reedy tarn,
Where the mammoth came to drink;
Through the brawn and bone I drove the stone
And slew him upon the brink.

Loud I howled through the moonlit wastes,
Loud answered our kith and kin;
From west to east to the crimson feast
The clan came tramping in.
O’er joint and gristle and padded hoof
We fought and clawed and tore,
And cheek by jowl with many a growl
We talked the marvel o’er.

I carved that fight on a reindeer bone
With rude and hairy hand;
I pictured his fall on the cavern wall
That men might understand.
For we lived by blood and the right of might
Ere human laws were drawn,
And the age of sin did not begin
Til our brutal tush was gone.

And that was a million years ago
In a time that no man knows;
Yet here tonight in the mellow light
We sit at Delmonico’s.
Your eyes are deep as the Devon springs,
Your hair is dark as jet,
Your years are few, your life is new,
Your soul untried, and yet –

Our trail is on the Kimmeridge clay
And the scarp of the Purbeck flags;
We have left our bones in the Bagshot stones
And deep in the Coralline crags;
Our love is old, our lives are old,
And death shall come amain;
Should it come today, what man may say
We shall not live again?

God wrought our souls from the Tremadoc beds
And furnish’d them wings to fly;
He sowed our spawn in the world’s dim dawn,
And I know that it shall not die,
Though cities have sprung above the graves
Where the crook-bone men made war
And the ox-wain creaks o’er the buried caves
Where the mummied mammoths are.

Then as we linger at luncheon here
O’er many a dainty dish,
Let us drink anew to the time when you
Were a tadpole and I was a fish.


Between Darwin and Saint Valentine

Yesterday was Darwin’s birthday (and Lincoln’s). Tomorrow is Valentine’s Day. Here’s a post appropriate for either day.

Imagine sex worked like this:

You’ve been feeling bad lately, getting sick a lot. You’re not at your best. You find someone who seems to be in better shape. One thing leads to another and you wind up acquiring body fluids from the other party – and picking up some new genes from them. The new genes help a lot in fighting off infection. You’re feeling better now.

Reproduction? That’s another matter, nothing directly to do with sex. When you reproduce, your offspring will carry all the genes you happen to have at the moment.

Also, I forgot to mention that you’re neither male or female – the gene exchange could have gone in the other direction if you’d both been in the mood. And your partner in the adventure above might not even have been the same species as you. (Just what counts as a species here isn’t well-defined.)

This is more or less how bacteria work out sex. (Joshua Lederberg got the Nobel Prize for figuring this out.) Eukaryotes (you’re one of them) mostly do it differently, combining sex and reproduction. It’s the story you learned in high school about passing on half your genes to a gamete (sex cell), which joins with another gamete to make a new organism.

Most eukaryotes also have two sexes. The best theory we have about why that got started goes like this: Most of the DNA in a eukaryote cell is in the nucleus. But a small fraction is in the mitochondria, little powerhouses outside the nucleus that started out as bacteria, and got domesticated. Imagine that two gametes join together, and combine two sets of mitochondria. There’s a potential conflict here. Suppose your mitochondria have a mutation that lets them clobber your partner’s mitochondria. This is good (evolutionarily speaking) for the winning mitochondria, but very likely to be bad for the cell as a whole. Better for the cell as a whole is if one gamete, acting on instructions from the nucleus, preemptively clobbers all their own mitochondria, so that all the mitochondria come from just the other gamete. This is the beginning of what will eventually lead to a distinction between sperm and eggs, pollen and ovules, male and female. Which means you got all your mitochondrial DNA from your mom, something that will turn out to be important when we look later in the year at geneticists unraveling human prehistory. This is also an example of how selection at one level (within cells) can conflict with selection at another level (between cells). We’ll see such multilevel selection again and again, for example in the evolution of complex human societies.

Sex has to be highly advantageous, although we’re not sure exactly what the advantage is. When eukaryote species give it up, they don’t seem to last long. Dandelions reproduce asexually: based on what we see in other organisms, they probably won’t be around for long, evolutionarily speaking. There’s one mysterious exception, tiny animals called bdelloid rotifers which have been reproducing asexually for tens of millions of years . For readers who are not bdelloid rotifers: Happy Valentine’s Day tomorrow! We’ll have an appropriate evolutionary post up tomorrow

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.

Life goes nuclear

2.05-1.93 Bya

Eukaryotic cells (Domain Eucaryota, which includes multicellular life, like plants, animals, and fungi) are, on average, much larger and more complex than the earlier evolved prokaryote cells (Domains Bacteria and Archaea*). They have organelles, including mitochondria that power them and chloroplasts (at least among plants) that carry out photosynthesis. Their DNA is stored in a nucleus, and consists not just of genes (as in prokaryotes), but of large stretches of non-coding DNA (most of their genome), separating pieces of genes. The ancestor of present-day eukaryotes reproduced sexually, although some eukaryotes have since given up sex.

There are different ways that life increases in complexity. The origin of the Eucarya has something in common with a much later event, the origin of agriculture (coming up September 9 on logarithmichistory!). Starting 10,000 years ago, we Homo sapiens brought other animals and plants under our control, managing their reproduction, and selecting them (first unintentionally, then intentionally) to suit our purposes, until now most domesticated creatures couldn’t survive in the wild. Our own numbers and social scale increased enormously with the rise of agriculture.

At least 2 billion years ago, an archaeon cell gobbled up one or more bacterial cells (or was parasitized by them). The bacteria ended up surviving inside it, and after many generations became a kind of domesticate inside their host. Eukaryotes do domestication one better than humans: they carry their livestock inside their bodies. Eventually this domesticate evolved into mitochondria, the little power packs that pump out ATP for the rest of the cell to use as as an energy source. Over the course of time all but a small fraction of the original bacterial genome was moved into the nucleus. Archaean and bacterial genomes are so intertwined, that the evolution of eucaryotes is better represented as a ring than a tree.


Humans developed agriculture multiple times independently around the world. As far as we know, eukaryotes evolved only once. The evolution of eukaryotes might be a very unlikely chance event. The universe may be full of bacteria, but harbor more complex cells only sparsely.

* Domain Archaea, a billions-of-years-old phylum of single-celled organisms looking like bacteria but biochemically different, should not be confused with the Archaean Eon, a billions-of-years-long stretch of Earth history.


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.


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.

My name is LUCA. I live on the ocean floor.

4.01-3.80 billion years ago

How life began on Earth is still not well understood. The “RNA world” is one popular theory. In modern organisms, nucleic acids, DNA and RNA, store and transfer information, but proteins do the actual work of catalyzing chemical reactions. But RNA can act as a catalyst, so maybe the first replicating systems involved RNA catalyzing its own replication. However, RNA doesn’t spontaneously form very easily, so it’s not clear how the RNA world would have gotten started. Borate minerals might help but it’s not clear they were around that early.

A different approach to the topic is to work backward from living organisms, to reconstruct the biochemistry of LUCA, the Last Universal Common Ancestor (not quite the same as the first living thing). Recent research on these lines implies that LUCA was a heat-loving microbe that relied on hydrogen as its energy source, suggesting an undersea volcano as a habitat.

However the first organisms got established on Earth, it happened very quickly. Here’s a review from just last week of the current state of play on theories of early Earth and early Earth life. Just about as soon as the planet could support life we find chemical evidence for it, from Isua, Greenland (but no fossils yet). This suggests that the origin of life is pretty easy (unless we want to go with panspermia). Mars may have been a more habitable place early in its history, and perhaps Mars exploration will one day solve the mystery of the origin of life in our Solar System.