Monthly Archives: January 2020

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.


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.


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.

4.03-3.81 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 recent review 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). And there’s some more tentative evidence for fossils formed around hydrothermal vents all the way back at 4.28 billion years ago. 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

Sun, Earth, Moon, Earthrise, “Terra”

4.56 billion years ago

The Hadean eon begins with the origin of the Earth 4.56 Gya.

Take a look at the Moon tonight. It’s a waning crescent, a few days from the new moon; you can cover it with your thumb. 4.56 billion years ago the new moon was ruddy with volcanic activity even on its far side. The Moon seen from Earth was 16 times wider, covering 250 times more sky, and 250 times brighter when full. That is what you would have seen just after Earth acquired a surface you could stand on, although you would have needed an oxygen mask. And watch out for massive meteorites, still falling frequently, and volcanism.

Chance events late in the history of planet formation played a huge role in shaping the solar system, including the collision with the planet Theia (named after the Greek goddess of the Moon) that gave Earth her outsized satellite. We’ve known about Theia for a while; the latest theory is that the collision resulted in the formation of a synestia, a donut of vaporized rock, which condensed to form Moon and Earth. Life might have developed very differently – there might be no intelligent life — without the Moon’s influence on tides and on Earth’s axis.

Here’s a movie from NASA showing the whole moon, including her far side, as seen by the Lunar Reconnaisance Orbiter. And here’s the famous picture of Earthrise, taken December 24, 1968, by William Anders abroad Apollo 8.earthrise copy

In 1969, the Brazilian singer Caetano Veloso was imprisoned by Brazil’s military dictatorship. He was expelled from the country and lived in exile until 1972. In prison he saw a picture of the Earth from space and wrote this song, “Terra” (Earth).

TerraQuando eu me encontrava preso, na cela de uma cadeia 
Foi que eu vi pela primeira vez, as tais fotografias 
Em que apareces inteira, porém lá não estava nua 
E sim coberta de nuvens
Terra, terra, Por mais distante o errante navegante Quem jamais te esqueceria?

Ninguém supõe a morena, dentro da estrela azulada
. Na vertigem do cinema, mando um abraço pra ti 
Pequenina como se eu fosse o saudoso poeta 
E fosses a Paraíba
Terra, terra, 
Por mais distânte o errante navegante Quem jamais te esqueceria

Eu estou apaixonado, por uma menina terra,
 Signo de elemento terra. Do mar se diz terra à vista 
Terra para o pé firmeza, terra para a mão carícia
 Outros astros lhe são guia
Terra, terra,
 Por mais distânte o errante navegante Quem jamais te esqueceria

Eu sou um leão de fogo, sem ti me consumiria
 A mim mesmo eternamente, e de nada valeria 
Acontecer de eu ser gente. e gente é outra alegria 
Diferente das estrelas
Terra, terra,
 Por mais distânte o errante navegante Quem jamais te esqueceria

De onde nem tempo e nem espaço, que a força te de coragem
 Pra gente te dar carinho, durante toda a viagem 
Que realizas do nada, através do qual carregas 
O nome da tua carne
Terra, terra, 
Por mais distânte o errante navegante Quem jamais te esqueceria
Terra, terra, 
Por mais distânte o errante navegante Quem jamais te esqueceria
Terra, terra,
 Por mais distânte o errante navegante Quem jamais te esqueceria?

Na sacadas do sobrado, Da eterna São Salvador 
Há lembranças de donzelas, do tempo do Imperador
 Tudo, tudo na Bahia faz a gente querer bem
A Bahia tem um jeito
Terra, terra,
 Por mais distante o errante navegante 
Quem jamais te esqueceria. Terra

EarthWhen I found myself arrested
 In a prison cell
, That’s when I first saw
 Those famous pictures
 In which you appear entire, 
However you were not naked 
But covered by clouds.
Earth! Earth!
 However distant 
The wandering navigator 
Who could ever forget you?

Nobody thinks of the brunette
 Inside the bluish star. 
In the vertigo of the movie
 I send you an embrace, 
Little one – as if I were
 the homesick poet 
And you were the Paraíba
Earth! Earth!
 However distant 
The wandering navigator 
Who could ever forget you?

I’m just in love 
With an earth girl, 
Sign of the element “Earth.” 
From the sea is said “Land in sight.” 
Earth to the foot: solidity. 
Earth to the hand: a caress.
 Other stars are guides for you
Earth! Earth! 
However distant 
The wandering navigator 
Who could ever forget you?

I am a lion of fire
 Without you 
I would burn myself up eternally 
And it would be worth nothing, 
The fact of my being human. 
And human is another joy 
Different than the stars’
Earth! Earth! 
However distant 
The wandering navigator 
Who could ever forget you?

From where there’s neither time nor space 
May the force send courage 
For us to treat you tenderly
 During all the journey 
That you carry out through nothing
 Through which you bear
 The name of your flesh
Earth! Earth!
 However distant 
The wandering navigator 
Who could ever forget you?
Earth! Earth! 
However distant
 The wandering navigator
 Who could ever forget you?
Earth! Earth! 
However distant
 The wandering navigator
Who could ever forget you?

In the townhouses’ terraces 
Of eternal Salvador 
There are reminders of maidens 
From the time of the Emperor 
Everything, everything in Bahia
 Makes us fond 
Bahia has such a way.
Earth! Earth! 
However distant
 The wandering navigator
 Who could ever forget you? 

Rare Earth

4.76-4.51 billion years ago

A big day on Logarithmic History, the biggest since the beginning of the year: the origin of our Solar System including planet Earth. First a note on what’s odd about our planetary system.

Two preceding posts wrestled with the Fermi Paradox: If the universe is full of advanced civilizations, why haven’t we seen any sign of them so far? One answer to the paradox might be that our solar system is wildly unusual, so that abodes for the evolution of complex life are rare. We can finally start to address this matter with some real evidence. According to the NASA exoplanet archive, we’ve now discovered 4,108 exoplanets (planets outside our solar system; up from 3885 last year at this date), with many more unconfirmed candidates. This is enough to do some statistics, and indications are that our solar system might indeed be out of the ordinary.


Exoplanets smaller than Jupiter are overwhelmingly closer, mostly a lot closer, to their primary stars than Earth is to the Sun. And the same models of planet formation that have done a pretty good job predicting some of the wild variation we see in other systems – “Hot Jupiters” orbiting closer to their primaries than Mercury, “Super Earths” in between Earth and gas giants in size – don’t readily generate systems that look much like ours. One model that does seem to do a good job with our solar system, the Nice Model, involves something special, a Grand Tack, where Jupiter and Saturn are caught in an orbital resonance that carries them into the inner solar system and back out, shaking up inner-system planet formation in the process. Wild stuff, but another variation on the Nice model is even wilder: at the beginning of planet formation, there may have been a generation of Super Earths in the inner solar system. The Grand Tack of Jupiter and Saturn would have sent these planets colliding into one another. The Super-Earths and most of the debris of these collisions would have fallen into the sun, but what the debris left would then have condensed into the unusual inner planets we know, Mercury, Venus, Earth, Mars. And Theia. (Theia? you ask. See the next post). Remarkably, we may have recently found evidence here on Earth of minerals that formed deep inside a lost planet or protoplanet from the earliest days of the solar system.

If this model holds up, the formation of our solar system, like other major events in our history, takes on some of the flavor of mythology. This isn’t quite the old story about Chronos slaying Ouranos, and Zeus slaying Chronos. Instead, in the new story, two giants, Jupiter and Saturn, travel closer to the sun and set a generation of Titans – their like will not be there again – to fighting and destroying one another. Jupiter and Saturn depart, and a new generation is spawned from the wreckage. An unlikely sequence of events, but then our planet could be a very unlikely place. And all the more special for that.

Where is everybody? Maybe we’re (some of) the first

A followup to the previous post on the Fermi Paradox, some reasons the Universe could have been less suitable for the evolution of complex life until recently, making us one of the first intelligent species to evolve.

1) Metallicity. Chemical elements heavier than helium are formed inside stars, after the Big Bang. Elements heavier than iron are formed in exploding supernovas. These elements have been building up over time. Maybe they had to reach a threshold abundance to make complex life possible. Consider that in the “family tree” for the Sun, based on the concentrations of different elements, the Sun is the oldest member of its subfamily. Maybe it is only planetary systems associated with this subfamily that are well-suited for the evolution of intelligent life. And recent work suggests that phosphorus in particular may be a limiting and cosmically limited resource for the evolution of life.

2) Gamma Ray Bursts (GRBs). GRBs are bursts of gamma rays (high frequency radiation) lasting from milliseconds to minutes, like GRB 080319B. (Check out this tweet from January 11.) GRBs are probably supernovas or even larger explosions where one pole of the exploding star is pointed at the Earth. A major GRB could irradiate one side of the planet, and also affect the other side by destroying the ozone layer, causing mass extinctions. GRBs may have swept the Milky Way frequently in the past. The good news is they’re probably getting less frequent. This could be the first time in the history of the Milky Way that enough time has passed without a major GRB for intelligent life to evolve. If true, we should think about how to protect ourselves from the next one – lots of sunblock recommended.

If GRBs are such a threat, we might expect to find evidence that they have caused mass extinctions in the past (not wiping out all life obviously). For more on this, check out upcoming blog posts and tweets for the end-Ordovician, March 3.

3) Panspermia (life from elsewhere). Pretty much as soon as Earth could support life, we see evidence of single-celled organisms. Then life evolves slowly for a long time. The usual story about this is that the origin of life is easy, and it happens as soon as possible. But there is another possibility (illustrated below). It may be that the transition from simple replicating chemical systems to bacteria with genomes of tens of thousands of DNA base pairs is a slow process that happened over many billions of years somewhere other than Earth. Then newly forming planets in the nebula that gave rise to Earth were “infected” by this source, by meteorites carrying early cells. (It would have been easier for meteorites to carry life from star system to star system when the Earth was first formed than it would be today.) Back when our hypothetical “Urth” was forming, a billion years before Earth, there might not have been any planets with cellular life on them as potential sources of life-bearing meteorites.


Where is everybody?

5.04 – 4.77 billion years ago

Tomorrow is a big day on Logarithmic History, the origin of our solar system, of the Sun and planet Earth. But is this really such a big deal in a cosmic perspective? After all, stars and planetary systems have been forming a fast clip in the Milky Way and other spiral galaxies since long before this date. So let’s suppose … Suppose there was a star like the Sun, but older by a billion years. And suppose this star had a planet like Earth orbiting around it – call it Urth. And suppose life originated on Urth more or less as on Earth and followed more or less the same evolutionary path. With this head start, intelligent life could have evolved a billion years ago, and today there could be intelligent Urthians (or their self-replicating robot descendants) a billion years ahead of us.

There’s an urban legend that says that Einstein called compound interest the strongest force in the universe. Einstein didn’t actually quite say this, but it’s not a crazy thing to say. For example, consider how compound interest works, backward, on our Logarithmic History calendar. December 30 covers a period 5.46% longer than December 31, December 29 is 11.2% longer (because 1.0546 * 1.0546 = 1.112), and so on. At this rate of compounding (and allowing for 2020 being a leap year) we wind up with January 1 covering 751 million years. The same math implies that if we invested 1 dollar at 5.46% interest, compounded annually, then after 365 years we’d have 751 million dollars.

With even the slightest compound rate of increase, a billion year old Elder Race would have plenty of time to fill up a galaxy, and undertake huge projects like dismantling planets to capture more of their suns’ energy. Indeed, they could arguably colonize the whole reachable universe.

Traveling between galaxies – indeed launching a colonization project for the entire reachable universe – is a relatively simple task for a star-spanning civilization, requiring modest amounts of energy and resources. … There are millions of galaxies that could have reached us by now.

Which raises the question, posed by Enrico Fermi in 1950: “Where is everybody?” There are more than 100 billion stars in our galaxies, more than 100 billion galaxies in the visible universe (actually, according to recent estimates, the number is more than  1 trillion). If there are huge numbers of billion year old Elder Races around, why hasn’t at least one of them taken the exponential road and made themselves conspicuous? Yet a recent survey of more than 100,000 galaxies found no evidence of any really advanced civilizations harnessing the power of stars on a large scale.

A possible resolution of the paradox has been suggested recently. The argument goes like this: the easiest route to estimating the number of advanced civilizations in the universe is to multiply point estimates of the probabilities of events like the formation of an Earthlike planet around an appropriate star, the origin of life on such a planet, the origin of human-level intelligence, and so on. But there are enormous uncertainties in these estimates. Properly speaking, instead of just multiplying mean estimates, we should be doing a convolution of the range of estimates. The general point is that if you’re multiplying a whole lot of probabilities, and you’re not certain what those probabilities are, there a strong likelihood that at least one of those probabilities is close to 0, so their product is also close to 0. The authors therefore suggest that there is a strong possibility that there are few or no advanced civilizations, or even other human-level civilizations in the Milky Way or even the observable universe.

In short, if this is true, tomorrow on Logarithmic History may mark a truly momentous occasion, not just in the history of the Earth, but in the history of the universe.