Stupendous contrivances

Nature does not only work mechanically, but by such excellent and most compendious as well as stupendous contrivances, that it were impossible for all the reason in the world to find out any contrivance to the same that should have more convenient properties. 

from Micrographia by Robert Hooke (1665)

Take a ride down into one of your cells, let’s say a heart muscle cell. Its rhythmic contractions are powered by ATP, which is flooding out from the any large mitochondria…Shrink yourself down to the size of an ATP molecule, and zoom in through a large protein pore in the external membrane of a mitochondrion. We find ourselves in a confined space, like the engine room of a boat, packed with overheating protein machinery, stretching as far as the eye can see. The ground is bubbling with what look like little balls, which shoot out from the machines, appearing and disappearing in milliseconds. Protons! The whole space is dancing with the fleeting apparition of protons , the positively charged nuclei of hydrogen atoms. No wonder you can barely see them! Sneak through one of those monstrous protein machines into the inner bastion, the matrix, and an extraordinary sight greets you. You are in a cavernous space, a dizzying vortex where fluid walls sweep past you in all directions, all jammed with gigantic clanking and spinning machines. What your head! These vast protein complexes are sunk deepening into the walls, and move around sluggishly as if submerged in the sea. But their parts move at amazing speed. Some sweep back and forth, too fast for the eye to see, like the pistons of a steam engine. Others spin on their axis threatening to detach and fly off at any moment, driven by pirouetting crankshafts. Tens of thousands of these crazy perpetual motion machines stretch off in all directions, whirring away, all sound and fury, signifying…what? 

You are at the thermodynamic epicentre of the cell, the site of cellular respiration...

from The Vital Question by Nick Lane (2015)


Image: complex 1 of the respiratory chain in a bacteria by David Goodsell via RCSB.  For image of complex 1 from mammalian cell see here (from Baradaran et al)

Through which we see

The light from this image is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.

PDB

Image by David S. Goodsell, the Scripps Research Institute

An invisible sun within us

We use about 2 milliwatts of energy per gram - some 130 watts for an average person weighing 65kg, a bit more than a standard 100 watt light bulb. That may not sound like a lot, but per gram it is a factor of 10,000 more than the Sun (only a tiny fraction of which, at any one moment, is undergoing nuclear fusion). Life is not much like a candle; more of a rocket launcher.

from The Vital Question by Nick Lane (2015)

Image of ATP synthase by David S. Goodsell, the Scripps Research Institute via PDSB

Not unimaginably small

Typical human cells are about 10µm in length. This is roughly 1,000 times smaller than the last joint in your finger.  A 1,000-fold difference in size is not difficult to visualise: a grain of rice is about 1,000 times smaller in length than the room you are sitting in. Imagine your room filled with grains of rice. That will give you an idea of the billion or so cells that make up your finger tip. 

Another 1,000 times reduction takes us to the world of molecules...An average protein, taken from any cell, contains about 5,000 atoms and is about one-thousandth the length of a typical cell, or about one-millionth the width of your fingertip. Again, to get of the idea of these sizes, think of a room filled with rice grains. This will give an idea of the size of the proteins that are packed into each of your cells.

— from The Machinery of Life by David Goodsell (2009)

Image: macrophage and bacterium by David S. Goodsell, the Scripps Research Institute

An infinite storm

The force that drives life at the smallest scale is not a mysterious, supernatural force, but it is a surprising one nevertheless. The force that drives life is chaos. 

At room temperature, air molecules reach speeds in excess of the fastest jet aeroplane. If we were reduced to the size of molecule, we would be bombarded by a molecular storm so fierce it would make a hurricane look like a breeze. 

To make the molecular storm a useful force for life...it is tamed by molecular machines.

— from Life's Ratchet by Peter M. Hoffman (2012)

Image: The Giantess by Leonora Carrington (1947) via Apollo Magazine.

The phrase 'an infinite storm' is from Travels in Alaska by John Muir (1910).

All possible paths simultaneously

Below you lies just one of the trillions of photosynthetic machines that manufacture the world's biomass [some 16,000 tonnes every second]. From your vantage point you can see that...although there are plenty of billiard-ball like turbulent molecular collisions going on, there is also an impressive degree of order. The membranous surfaces of the thylakoid is studded with craggy green islands forested with tree-like structures terminating in antennae-like pentagonal plates. These...are light harvesting molecules call chromophores, of which chlorophyl is the most famous example.

from Life on the Edge: the Coming Age of Quantum Biology by Jim Al-Khalili and Johnjoe McFadden (2014)

The very best photovoltaic cells...convert sunlight to electrical energy with an efficiency of around 35%; for more affordable cells the figure is closer to 20%. Plants accomplish the same process with about 90% efficiency during the first stage of photosynthesis. 

Efficiently converting light into electricity requires preserving the energy of an exciton [an electron-ion pair] as it travels deep within reaction centre of the leaf [and] the key to [this] lies in way it travels to the reaction centre. Researchers discovered to their great surprise in 2007 that plants use a [trick] from the realm of quantum physics to help excitons find their way. Rather than bumping randomly through a forest of chlorophyll molecules until they happen to reach their destination...each exciton spreads out over all possible paths simultaneously, and then funnels down through the most efficient route.

from How plants exploit sunlight so efficiently, The Economist.

Image from synechocystis.asu.edu

The rotary mechanism of mitochondrial ATP synthase

It ever was, and is, and shall be, ever-living fire, in measures being kindled and in measures going out.

— Heraclitus

Click here for animation.

Image credit: MRC MBU

Ribosome

The ribosome is a tiny organelle present in all living cells in thousands of copies that manufactures the protein molecules on which all life is based. It effectively operates as a highly organized and intricate miniature factory, churning out those proteins – long chain-like molecules – by stitching together a hundred or more amino acid molecules in just the right order, and all within a few seconds. And this exquisitely efficient entity is contained within a complex chemical structure that is some 20-30 nanometres in diameter – just 2-3 millionths of a centimetre.

-- from What is Life? by Addy Pross

Added 27 October 2014: Listen to this section of Radiolab's translation show.

Added 26 Jan 2015: "We are all just different kinds of homes to the ribosomes!"


Image: David S. Goodsell, the Scripps Research Institute via RSBC Protein Data Bank