When my children were young and I asked them to name their favourite species they would say lion, dolphin or dog. I failed to persuade them of the merits of species like Candidatus Prometheoarchaeum syntrophicum strain MK-D1, a species of single-celled organism found in the depths of the ocean. Each new MK-D1 cell starts life as a blob and develops by growing tentacle-like projections. These thin structures search out bacteria that acquire their energy from hydrogen molecules, and having found them, MK-D1 then gets the energy to power its metabolism from their waste products. MK-D1 lives off the poo of species of bacteria that do not use oxygen, a gas we often think of as essential for life.
Strain MK-D1 is a form of life you might be unfamiliar with. Biologists divide all life on Earth into three domains called the Bacteria, the Archaea and the Eukarya. Bacteria and archaea are always single-celled organisms, and these cells are relatively simple. In contrast, eukaryotes have more complicated cells, subdivided by internal membranes. Some species, like yeast, are single-celled organisms, but eukaryotes can also be multicellular species such as seaweed, fungi, trees and animals. Each of these three domains of life can be subdivided again and again, into hierarchical levels of organization called kingdoms, phyla, classes, orders, families, genera and species, until each species is eventually classified. I remember this with the pneumonic ‘Do Keep Pigs Clean Or Farm Gets Smelly’ with the D in Do representing domain. Our full classification from the species up is Homo sapiens, in the genus Homo, which sits in the Hominidae family, which in turn is classified as being in the Primate order, in the Mammalia class, in the Chordata phylum, in the Animalia kingdom and, finally, in the Eukarya domain. In contrast, the microbe species Escherichia coli that can sometimes make you sick is classified as: genus Escherichia, family Enterobacteriaceae, order Enterobacterales, class Gammaproteobacteria, phylum Pseudomonadota, and domain bacteria. I’ll spare you the full classification of strain MK-D1, simply stating that it is a member of the Archaea domain, a group of single-celled organisms that biologists once thought were bacteria but have more recently realized are not, and are instead more closely related to animals, plants and fungi.
Species in the same genus are closely related to one another, typically having shared a common ancestor within the last few million years. Humans and chimpanzees are not in the same genus but they really should be, and our common ancestor lived between about 6 and 10 million years ago. As we move up through the classification system to family, order, class, phyla, kingdom and domain the species we encounter become progressively less closely related to us. MKD1 and humans are in different domains, and we shared a common ancestor over 3 billion years ago.
The reason I like strain MK-D1 is not only because it lives an unusual life but because it does so very slowly. It takes almost a month for a single cell to grow and divide into two cells. You might think that a month isn’t very long, but in the world of single-celled species it is an eternity. E. coli, for example, divides every twenty minutes. In the time it takes for one MK-D1 cell to become two individuals, if E. coli had access to unlimited food, one cell could grow to produce a colony of two raised to the power of 2,190 bacteria, a number so astronomically large that my computer returns infinity when I ask it to calculate it. Another example of the power of exponential growth.
Strain MK-D1 is also much more biologically interesting than a lion, dolphin or dog. It has genes that, until its discovery, were thought to be found only in eukaryotes, leading scientists to hypothesize that MK-D1 can shed light on how the complicated cells that eukaryotes such as you and I are built from evolved from the much simpler cells of archaea. As an example, single-celled eukaryotes are able to do something called endocytosis, a feat beyond bacteria. Endocytosis is the process these species use to envelop small objects such as particles, viruses and sometimes even smaller cells in order to bring them across their cell membrane. It is a process that helps bring nutrients inside a cell for it to use. Cells do this by bending their membrane to form a bubble around the object to be brought into the cell, before pinching the bubble off to create a small membranous sphere in the cell’s interior that contains the object. It is the cellular equivalent of you swallowing a morsel of food. MK-D1 produces a protein called actin that is necessary for endocytosis, and which is found in all eukaryotes but in no bacteria. Strain MK-D1 provides insight into the common ancestor of archaea and eukaryotes by providing clues into how life made a major jump in complexity, and biologists think it may also help us understand how endocytosis evolved. However, gaining this knowledge was difficult because it is very hard to keep MK-D1 cultures alive outside of its ocean habitat. It is only in the last few years that a group of biologists in Japan succeeded in keeping a population of MK-D1 alive in their laboratory. Lions, dogs and dolphins are not only much easier to keep in captivity but could never have existed if species similar to MK-D1 had not evolved genes that produce actin, a gene central to all complex life.
Strain MK-D1, E. coli and you all use the same genetic code. We all use twenty amino acids to build proteins, and these amino acids are coded by the same set of nucleobase triplets. Thymine–thymine–thymine codes for the amino acid phenylalanine not only in these three species, but in all species of life on Earth. The genetic code is universal to life on our planet. Although every species uses the same genetic code, different species have different genetic sequences, allowing them to make different proteins. By comparing how similar genetic sequences are between species, biologists can work out how closely related different species are. Because humans and chimpanzees shared a common ancestor only a few million years ago, the genetic sequences of the two species are much more similar than the genetic sequences of humans and MK-D1.
Despite the ubiquity of the genetic code, the very earliest life would not have used it, but it didn’t take long for life to adopt it. Inferring exactly what happened and when 4 billion years ago is not easy, but the genetic code we use today was probably in operation only a few million, or perhaps tens of millions, of years after life appeared on Earth. Although we do not know exactly how long ago the genetic code evolved, we do have a name for the organism that first used it: LUCA, or the Last Universal Common Ancestor, a term that scientists have used since the 1990s. You, me, the trees outside, the birds that sit in them, along with the bacteria in their guts, the invertebrates that parasitize them and the microscopic fungi that can cause them disease, are all descended from LUCA. There is a direct line of descent from LUCA to you, from LUCA to MK-D1, and from LUCA to E. coli. You might feel fortunate you have a direct line of descent from LUCA, but so too does every organism alive on Earth today, from each cockroach, to Woofler, to you. LUCA has very many and very diverse descendants. In this chapter, I explore how and why complex animals such as humans evolved. Why are we so different from dogs, E. coli and strain MK-D1? What had to happen in the 4 billion or so years since the genetic code evolved for our genetic self-assembly manuals to arise? Evolution is the process that has moulded life on Earth, and to understand it it is necessary to turn to the workings of DNA, phenotypic traits, and natural and sexual selection, terms I define in the coming pages.