In the beginning were the replicators... we know very little about them and we never will. Our windows on the past are limited, and for the ancient past they are reduced to mere speculation. What we do know is that our cells are based upon the intricate relationship between our DNA and our RNA. DNA provides the library of all the protein recipes we have inherited from our ancestral forms. RNA does the labour of building proteins and communicating between cells. We have deduced that RNA preceded DNA, and that there was, therefore, a time in aeons past when there was an "RNA world", although we do not know (and may never know) if there were other replicating molecules that preceded RNA. Even if there was, it remains true that the replicators precede life as we know it.
The replicators were here first. And we owe them our lives.
The first cellular organisms developed out of these primordial replicators. Right from those very first cells it seems that we had both the DNA library and the RNA messengers, astonishing organic technology that may actually deserve the adjective 'miraculous' that we prefer to reserve for our own crude tampering with genetic codes. Replicators begat single celled life forms about a billion years after our planet formed, some 3.5 billion years ago. We did not arrive until 300,000 years ago. That's quite a home field advantage right there.
These unfathomably immense time scales are rather difficult for us humans to grasp, so I sometimes like to index the past using logarithmic time, which is a fancy way of saying "count the zeroes". After writer John McPhee's memorable phrase for geologic time, we can call log time the 'deep time' index of an event, and this number is just a matter of 'counting the zeroes' in a fancy mathematical way. One billion years in the 'short scale' we have come to prefer is written as 1,000,000,000, which is nine zeroes, and the base 10 logarithm of a billion is indeed 9. Last year would be 0 in deep time. Ten years ago was deep time 1. A century ago was deep time 2 (again, count the zeroes!). So each increment in logarithmic deep time is ten times further away than the previous one. The large dinosaurs went extinct at deep time 7.8, whereas the universe is believed to have kicked off about 13.7 billion years ago, at deep time 10.1. The origin of bacteria lies at 3.5 billion years ago, which is deep time 9.5.
Our single cell ancestors at deep time 9.5 are just as amazing as the replicators that preceded them and gave birth to them. They are the archeobacteria, which is to say, the old bacteria, indeed the oldest bacteria. Then as now, patterns in the DNA library were transcribed by the labour of RNA into the complex biochemical building blocks - proteins - that can do all manner of amazing things. These ancient single-celled creatures swam, fed, reproduced through division, and formed protective outer shells to ward off catastrophic conditions such as great heat or high acidity. What's more, they traded. Unlike later life forms, bacteria don't keep a very strict DNA library. On the contrary, through what has been called lateral gene transfer, bacteria (even today) trade genes with each other. That means that rather than their parental heritage determining the entirety of their biology, bacteria can swap genes to make up new patterns all the time - which also means that bacteria develop new forms far faster than the more complex life forms that were eventually to descend from them.
But life was only just getting warmed up. Swapping genes like trading cards seems like child's play next to what the bacteria were to achieve around deep time 9.3. They started co-operating. As Lyn Margulis described in 1966, the differentiated components of plant and animal cells - the energy-making mitochondria of animals, the light-farming chloroplasts of plants and algae, and much more besides - originated through a unique process of symbiotic co-operation. Margulis suggested this was probably the result of a failed attempt at digestion, but no matter how it happened the bacteria discovered they could become more than the sum of their parts. It was yet another miraculous occurrence - and it was directly responsible for the conditions that would eventually lead to our own existence. The separate genetic libraries of these cellular allies would eventually come to be pooled into a single DNA archive (the nucleus of a cell), so that different 'bacteria' were being made by the same gene library.
Now admittedly, for quite a long period of deep time our multicellular ancestors were basically little more than slime moulds. But deep time is full of miracles, and another one occurred at 8.7: the notorious Cambrian 'explosion'. Up to this point, the new superbacteria had no way of maintaining a differentiated form. Yet 'suddenly' (in the deep time perspective, at least), new patterns made it into the library, those encoding shape. We still do not adequately understand all the mechanisms entailed, but what is clear is that the superbacteria continued their billions of years of co-operation with the ancestral replicators that had formed them in entirely novel ways. By expressing certain proteins at specific points in a cycle of cell division, organisms with a profusion of different shapes and forms emerged.
And what an emergence! The Cambrian explosion is wild and marvellous, full of strange and incredible creatures. Many show body plans that we can still recognise today - the radial symmetry of the starfish; the multi-limbed creepiness of the arthropods that would become insects, spiders, and scorpions; the molluscs that would give rise to squid and cuttlefish; an immense diversity of worms; polyps that would become corals; and of course those plucky little chordates, the little skeletons who could, from which all the fish, reptiles, dinosaurs/birds, and eventually even the humble little mammals would descend.
All in the water, to begin with, where life had begun, but you can't keep a good life-form down. We were onto the land by deep time 8.6 (a clock tick in the logarithmic index, but more than a hundred million years as humans reckon time). We were into the sky soon after. Live birth by around 8.4. Social colonies of the kind we associate with termites and bees by 8.2. Social packs of larger animals by 7.9. The direct ancestors to humans arrive around 6.3. The first humans at 5.4, some 300,000 years ago. Those first five numerals of deep time belong to life in all its diversity. Human history begins at 3.7, our 52 centuries of writing occupying just the shallow end in the immense scope of the time of life.
Now the danger in thinking about these developments in terms of 'progress', as a certain way of thinking invites us to do, is to misunderstand that new life doesn't replace the old. Contrary to the lazy competitive thinking we've been led into believing, bacteria were not invalidated by the arrival of multicellular life. On the contrary, bacteria adapted to live in, on, and around their incomprehensibly larger descendants. Your stomach is a great place for a bacterium that thrives in acidic environments to hang out, and it is quite comfortable there, for all that you might prefer not to think about all your tiny passengers. Likewise, the bacteria did not force the free replicators out of business. Quite the contrary, in fact. Those replicators are still among us. We call them viruses now.
And oh how we have turned upon our ancestors in the last two centuries, after about deep time 2.3. The arrival of scientists in the Victorian era, who supplant and assimilate the natural philosophers around 3.4, brought more of what we like to call 'progress', which is half ignorance and half arrogance. The sciences brought to us an understanding of contagion, of the role of bacteria and replicators in causing disease... but they brought with it a prejudice against germs, our germophobia, if you will. We have all sadly adopted this general inability to distinguish between those scary situations where our ancestral forms are fatal to human life, and the great many circumstances where we depend upon them.
Never forget in the first place that you have some hundred trillion bacteria living in your digestive tract, without whom we would struggle to break down carbohydrates to feed your mitochondria, the bacteria-within-bacteria that power your whole body. For your body is a colony of cells, and each of those cells is analogous to the single-celled bacteria that preceded them. We are not only home to bacteria, we are made of bacteria, our bodies are the most successful and most cosmopolitan bacterial colonies that ever existed.
Ah, but you might say, I'm willing to make peace with the bacteria (or at least to say that my bacteria are good but yours are evil). But not the viruses. They are truly evil... they bring only disease and death. We must exterminate them all. How quickly we turn upon our ancestral forms! We refuse to accept just how essential the replicators were to our even having the chance to come about in the way we have. Just as your body is made of bacteria, those bacteria are made from replicators - we are, at root, beings sustained by the replicators. We are thus the impossibly distant cousins of every virus.
There is a brutal truth to the process of mutation we have not yet accepted. Far from the romantic image of the X-Men, whose freak mutations bring about superpowers, mutations are deadly. Our genetic library encodes all the proteins the many different denizens of our hyperbacterial colony bodies need to live, and when one of them is corrupted - by radiation, by pollutants, by a great many things, the vast majority of which at this point in time have been made in human factories - it causes disease and death. You cannot simply scribble all over our genetic library and expect to shoot force beams, regenerate, or control the weather. When our DNA library is corrupted, we die.
But if this is so, if mutation is death, then how did our ancestors acquire new traits, new proteins, new biological capabilities? The answer is that the replicators role in the story of life did not end at deep time 9.5 with the arrival of bacteria. They kept doing what they had always done... copying themselves. Even as the younger forms of life built the genetic libraries and deployed them to unfold the story of life as we know it, the replicators kept copying, making changes, hacking life by accident, and even becoming domesticated by the replicators in our cells to serve new purposes. Beneficial mutations (by far the least common kind) happen either because our own replicators 'slip' and make transcription mistakes, or because the other replicators - the viruses - give them a nudge in a new direction.
In 1982, Stephen Jay Gould and Elizabeth Vrba proposed exaptation (ex-ap-tation) as a description for the taking on of new functions for which a certain aspect of an organism was not originally adapted. This was an important turning point in our thinking about the development of biological capabilities, since the tendency to treat every feature as having developed for its apparent purpose severely limited the range of explanations available, sometimes to the point of absurdity. Back-projecting the role that feathers now serve in flight effectively limited the explanations considered for how they might actually have developed. Gould and Vrba proposed seeing feathers instead as an exaptation: a feature which originated with a role in temperature regulation that only later opened up possibilities for flight.
Since then, researchers have repeatedly discovered new kinds of exaptations, perhaps most amazingly in the context of viruses. Far from the image of the virus as 'them' to the human 'us', ancestral viruses inserted themselves into our genetic library, and in so doing opened up remarkable new capabilities for humanity. Consider as just one example the syncytins (sin-sigh-tins), genes originating in retroviruses that were captured and domesticated by a variety of mammal species in parallel. These genes opened up all the amazing possibilities of placental mammals from ancestors that were egg-layers - and they did so not once, but apparently multiple times. Primates, mice, cats, and dogs all have different genes domesticated from varying ancestral viruses that are essential to the placenta that sustains life in the womb. Lateral gene transfer - the trading of genes - isn't just something that bacteria do... viruses have brought this genetic marketplace to the multicellular life forms too.
What's more, even our immune system - the means by which we fight off unwelcome viral intrusion - owes its effectiveness to viral co-operation. Around deep time 7.7, we seem to have acquired a viral stowaway in our genetic library (an endogenous retrovirus) that now plays a pivotal role in our immune system. A gene that has been named AIM2 can become activated in response to viral infection, triggering immune responses that include instructing infected cells to effectively 'self-destruct' to prevent further viral spread. As Kat Arney put the matter, these ancestral viruses which are now part of our own DNA act as 'double agents', protecting us from hostile viral intrusion. A reminder that not all viruses are 'the enemy'.
The replicators were here first, and they are still here now. They enabled the bacteria to exist. They empowered multi-cellular life to specialise and diversify. They maintained genetic libraries through untold millennia, such that even now we owe our very lives to the tireless and unfathomably ancient workings of these chemically-inscribed forms of proto-life. Even the viruses, those rogue replicators that nomadically pass between our gigantic colonies of intricately co-relating cells are not merely our enemies. We have incorporated them into our library, and they have opened up new biological possibilities for our species and so many others.
There are times when we fight with our viral neighbours. This is nothing new... our genetic library demonstrates that this has been going on throughout deep time. There are times when we need to take steps to defend ourselves. But still, we should not fool ourselves. The viruses are never solely our enemies... we are dependent upon them, upon the replicators in our cells and the domesticated viruses that have joined them, for everything we are as living beings. That we must sometimes take steps to defend against that minority of viruses that disrupt the elegant workings of cellular life is inevitable. Yet this is merely the biological analogue to the rule of law, and in medicine - just as with law - we do not always make wise choices.
The replicators were here first, and they will likely be here long after we are gone. If we want to continue accompanying them for some tiny fraction of the great journey they have been on - a voyage that is nothing less than the tale of life itself - we might consider paying them the respect they are due.