As we are so often reminded by proponents of Intelligent Design creationism, we contain molecular "machines" and "motors". They don't really explain how these motors came to be other than to foist the problem off on some invisible unspecified Designer, which is a poor way to do science—it's more of a way to make excuses to not do science.

Evolution, on the other hand, provides a useful framework for trying to address the problem of the origin of molecular motors. We have a theory—common descent—that makes specific predictions—that there will be a nested hierarchy of differences between motors in different species. Phylogenetic analysis of variations between species allows us to reconstruct the history of a molecule with far more specificity than "Sometime between 6,000 and 4 billion years ago, a god or aliens (or aliens created by a god) conjured this molecule into existence by unknown and unknowable means".

Richards and Cavalier-Smith (2005) have applied tested biological techniques to a specific motor molecule, myosin, and have used that information to assemble a picture of the phylogenetic history of eukaryotes.

Myosin should be a familiar protein to all of us: it's an important component of muscle, and is the motor that drives muscle contractions. Like most biological machines, its function can actually be reduced to something fairly simple, and the complexity arises from the multitude of permutations, the many little tweaks that have been made to it, in a long, long history of random changes filtered by selection.

Myosin is a ratchet. It has a globular head that has enzymatic activity: it hydrolyzes a molecule used for energy storage, ATP. When it burns the energy released from the breakdown of ATP, it undergoes a conformation change, bending the head relative to the tail. It's a small thing, really, a tiny shift in the shape of the molecule.

A small thing repeated many, many times by a large number of molecules can add up to a fair amount of force, however. These small shifts in shape are coupled into a contraction cycle in the muscle. The myosin burns ATP to ADP to change shape, it binds to another molecule, it releases the spent ADP, it flexes back, shifting the other molecule; then it burns more ATP, binds again to the molecule, flexes, and releases. Burn, bind, flex, release…over and over again, shifting sliding strands of protein a tiny fraction of a millimeter at a time. That's the engine that drives every contraction of your muscles.

You have 12 different forms of the myosin gene. Why the diversity? Because they have slightly different properties: what they bind to best, how fast they change shape, when and where they are expressed. There's a special myosin for your heart muscle, a different one for slow muscles for endurance, another for fast twitch muscles that generate lots of power quickly. There's a smooth muscle myosin and a fetal myosin.

Myosin is present in other organisms, too, not just animals with muscles, so don't think of it as simply a muscle component. Amoebae, plants, and mushrooms also have essential myosins. Myosin is a general purpose ratchet that shifts proteins, especially cytoskeletal proteins, relative to one another. Our cells use it to transport organelles and proteins from one part of the cell to another, and we wouldn't be able to sustain long nerves without myosin to move essential components from the cell body to the periphery. Amoebae use it to push out pseudopods; amoeboid movement depends on it. They drive cytokinesis, the process of cell division. If you're a eukaryote, it doesn't matter whether you are capable of pumping iron or not—you've got myosin or a member of the related kinesin gene family to power physical movements within cells.

All of these diverse functions in diverse organisms use the same recognizable core module to do their job, that ATP-binding globular head, but they vary in activity and binding properties to other molecules and in that associated tail you can see in the cartoons above. That means one can fish within genomic data and find the recognizable part of the myosin, and also catalog the differences and assemble a picture of the molecule's evolutionary history. Richards and Cavalier-Smith identified 37 different types of myosin in their investigation, used characters from each to put together a table of similarities and differences.

For instance, plants have a feature in their myosin called the TH1-FYVE-like insert, which is not present in any animals, fungi, or amoebozoa, which suggests that this element evolved after the plant and animal lineages diverged. Likewise, animals and fungi share a MYTH4/FERM duplication that isn't present in any of the other groups, linking them together and almost certainly evolving well after the plant-animal separation. Putting all the information together yields a eukaryotic family tree.

Schematic tree showing myosin-derived synapomorphies (green bars) and three previously published shared characters (grey bars). Yellow bars indicate synapomorphy plus secondary loss. MYSc, myosin head domain.

This tree corresponds well with similar trees generated from other kinds of data; it doesn't place fungi closer to plants than animals, for instance, despite the fact that you might superficially think mushrooms and trees have more in common than mushrooms and monkeys. This is another strength of the scientific approach: we get answers that are consistent with one another and with the idea of relationships by descent.

They were also able to infer some of the properties of the last common ancestor of all eukaryotes. It had three kinds of myosin, that differ mainly in the structure of the tail.

Richards and Cavalier-Smith propose that there were three ancestral myosins in the earliest eukaryotes, each with distinct tail domain structures. Listed are examples of organisms or cells expressing members of each myosin group and their known functions. The TH1 domain would probably bind to charged lipids and target these myosins to membranes. The SMC domain would promote dimer formation and the DIL and MyTH4/FERM domains would target myosins to their cargo or subcellular location.

In addition to three myosin types, it would have also had a single cilium, mitochondria, and pseudopodia, and would probably have been a motile cell. This is one of the powers of modern evolutionary biology: although we weren't there, and although we don't even have fossils of these organisms, the chain of evidence and logical inference can give us a fuzzy glimpse of a creature that lived over 2 billion years ago.

Richards TA, Cavalier-Smith T (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436(7054):1113-1118.

Titus MA (2005) A treasure trove of motors. Nature 436(7054):1097-1099.