Virus: A Love Story
April 12, 2022
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.
I really liked this essay! I'm sorry I don't have anything to add other than that
Posted by: Ari Cheslow | April 14, 2022 at 04:39 PM
Thanks so much for leaving a comment! It's always nice to know I'm hitting the mark.
All the very best!
Posted by: Chris | April 15, 2022 at 08:05 AM
One lives and learns. Thanks for that.
As an aside I am repeatedly advised by deniers of AGW (including a few scientists) that the high atmospheric CO2 during the Cambrian explosion is proof that life does better with very high CO2, being totally ignorant that the explosion was aquatic!
Posted by: David Boffey | April 16, 2022 at 10:03 AM
Thanks for your comment! Glad you found this piece of interest.
While I'd be the first to admit that some strange claims are made about climate change in all its myriad forms, I would personally never use the term 'denier' in this context. To do so risks pretending that this is not a scientific research topic, which I hope and trust that it is.
If I may play devil's advocate, atmospheric CO2 does dissolve in water, affecting the acidity of the oceans, so even with life entirely in the oceans there could still be significant implications. But I would not be invoking the Cambrian era in any way on the topic of climate change, for fear of making an already blurry topic even more out-of-focus.
Many thanks for commenting!
Posted by: Chris | April 18, 2022 at 09:23 AM
A stimulating exploration.
Here are a few related references
Thermodynamics of self-assembly
in Application of Thermodynamics to Biological and Materials Science
New Scientist 2011 First life: The search for the first replicator
Self replication in dynamic molecular networks
Life’s First Molecule Was Protein, Not RNA, New Model Suggests
Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids
Posted by: Robert | April 18, 2022 at 08:55 PM
Many thanks for the additional references! Appreciated.
Posted by: Chris | April 19, 2022 at 07:44 AM
"climate change in all its myriad forms" I referred specifically to AGW and not climate change. There is a difference you know.
Oceanic CO2 would obviously have been slightly elevated during the Cambrian Explosion, but nowhere near the 6,000 ppm level lovingly quoted by AGW deniers. Also they claim the Cambrian Explosion was of complex terrestrial life and not simple aquatic lifeforms with some semi aquatic plant life.
Regarding the use of deniers, yes, they are deniers. They are not skeptics who are prepared to accept proof, they deny for various reasons, mainly religious ones.
"To do so risks pretending that this is not a scientific research topic". Well, to many of them them science is all lies, even though they use it to spread their denial. The worst kind are those like Roy Spencer with his “Believe it or not, very little research has ever been funded to search for natural mechanisms of warming…it has simply been assumed that global warming is manmade.” Which is a blatant lie, as he well knows. but then he encouraged the use of his own incorrect data set as an icon for global warming skeptics, whilst having committed serial errors in the data analysis and insisted he was right and models and thermometers were wrong. He did nothing to root out possible sources of errors, and left it to others to clean up his mess, as has now been done. The giveaway is that he subscribes to “Earth and its ecosystems — created by God’s intelligent design and infinite power and sustained by His faithful providence — are robust, resilient, self-regulating, and self-correcting”
Also check out Marc Morano, Patrick Moore (not Sir Patrick Moore), Tim Ball, David Legates, Willie Soon, Christopher Monckton, Ian Rutherford Plimer, Will Happer, Richard Lindzen, Joanne Codling aka Joanne Nova, John Christy, Art Robinson, Judith Curry et al for more denials and promulgation of untruths. They pervert science for their religious and/or ideological beliefs.
Posted by: David Boffey | April 23, 2022 at 05:56 AM
Clearly the issue of 'AGW deniers' is an issue that means a great deal to you... I have nothing much to say to your specific examples; the people you name negatively aren't people I've come across, and the people you name positively are just a list of names, which is not much to go on. Feel free to choose some key articles and link them here, if you think it will be helpful, though.
My position is merely this: that on all sides, the discussion of global warming/climate change/whatever the next branding might be has produced partisan political responses that have made it difficult for these topics to be pursued as an open scientific debate and, furthermore, that in terms of scientific process neither side on this issue can claim to have any kind of high ground at this point. I have a read a little on both sides... I find it an ugly political spat that has largely obscured debate of the ambiguities rather than pursuing a robust research programme.
Honestly, I have yet to read anything from the space that has impressed me in terms of scientific rigour. I believe it entered the state of pseudoscience, whereby evidence was no longer persuasive and debate becomes impossible sometime in the last few decades. The moment consensus was claimed by one side, it became difficult to pursue as a scientific matter. This is a shame, as there clearly is an effect here, but the models produced have all proved (unsurprisingly) inaccurate over time, which has only served to accelerate partisanship on the issue.
I don't doubt that you are correct that the people you have singled out have taken up a position and are no longer open to evidence. Openness to new evidence has become surprisingly scarce these days. I would still not deploy the term 'denier' in this context, in part because the term is now extremely politically charged (it became so because it gained currency from its use in 'Holocaust denier'). Provided the evidence for any phenomenon is robust, there is no need to gloss opposition as 'deniers', which is a political appellation.
I will not say you cannot use the term, and I never will. Use your language as you wish, for anything short of inciting violence, which is our agreed limit to free speech. But I would warn you that you will not gain any ground on this topic by using this term... in that respect, it is largely counter-productive. If advocates for any variation on the climate change theme want to be persuasive on the scientific issues, they cannot afford to advertise themselves as politically partisan. Indeed, the important environmental issues (which in my view are in no way restricted to the composition of the atmosphere) are now being wholly obscured by the politicisation of climate change et al.
The especial danger of demonising any given camp as 'deniers' is that once the finger-pointing begins, everyone who lands on the other side of the partisan divide can be conflated with the 'deniers' and thus dismissed. This hinders legitimate scientific debate. It is a sure sign that the state of pseudoscience has broken out that one side claims a consensus and then pushes to discredit opponents, instead of focussing on the evidence and its interpretation, which are the necessary components of scientific processes.
From your description of the people you are flagging as 'deniers', they would seem to pose no threat to robust scientific research whatsoever, given that they are coming down the Intelligent Design path, which gets zero traction in journals or conferences, and as such I see no reason to pour vitriol on them. Evidently, you feel differently... but why? Is it just cognitive dissonance caused by the fact that you find ID offensive (rather than, say, amusing, or fringe etc.)? I don't see a threat to scientific practice here. My arguments against Intelligent Design can be found in my book The Mythology of Evolution, which largely views ID as unnecessary from the position of the religious motivations behind it, a view often obscured by the political ire it stirs up in its opponents.
Clearly this topic matters to you, but the impression I get from reading you (which could be completely wrong) is that you are offended by Intelligent Design far more than you are interested in the scientific issues in climate science. But I could be entirely wrong! It may be that my comment simply riled you up, and if so I apologise. I never set out to aggravate people, although it is rather hard to avoid these days!
I still believe, absurdly perhaps, that the hallmark of good scientific debate is that it hinges on discussion of the evidence. Truly, I would welcome from you a link to a piece by anyone on that list of yours that does this, and does not engage in political partisanship by trying to tar opponents rather than discuss the evidential basis for claims being made. The topic interests me, the political issues of the environment have mattered to me my entire life. But I do not see climate research operating in a scientific mode any more. And that concerns me far more than what the ID crowd are up to.
Many thanks for continuing our discussion!
Posted by: Chris | April 23, 2022 at 08:18 AM
"My position is merely this: that on all sides, the discussion of global warming/climate change/whatever the next branding might be". Thanks for telling is upi don't have a clue.
"The moment consensus was claimed by one side, it became difficult to pursue as a scientific matter." And you claim to be a scientist?
Ever heard of scientific consensus? Wissenschaftlicher Konsens?
“Once science has been established, once a scientific truth emerges from a consensus of experiments and observations, it is the way of the world. What I’m saying is, when different experiments give you the same result, it is no longer subject to your opinion. That’s the good thing about science: It’s true whether or not you believe in it. That’s why it works.”
"During 2013 and 2014, only 4 of 69,406 authors of peer-reviewed articles on global warming, 0.0058% or 1 in 17,352, rejected AGW. Thus, the consensus on AGW among publishing scientists is above 99.99%, verging on unanimity." "The peer-reviewed literature contains no convincing evidence against AGW." This is science, and if you do not agree, then you should stop using modern medicine, transportation, etc
The consensus among research scientists on anthropogenic global warming has grown to 100%, based on a review of 11,602 peer-reviewed articles on “climate change” and “global warming” published in the first 7 months of 2019.
"the models produced have all proved (unsurprisingly) inaccurate over time, Really? Who told you that? A denier of facts and reality, ovious;y.
Posted by: David Boffey | April 24, 2022 at 08:16 PM
"Clearly the issue of 'AGW deniers' is an issue that means a great deal to you..." It does to anyone with any knowledge of science and who cares for the welfare of others and everything on Earth.
"the people you name negatively aren't people I've come across," If you are interested in why the term denier iu used maybe you should actually do some research, it's what scientists do.
"and the people you name positively" I did no such thing, did I?
are just a list of names, which is not much to go on. Feel free to choose some key articles and link them here, if you think it will be helpful, though."
"From your description of the people you are flagging as 'deniers', they would seem to pose no threat to robust scientific research whatsoever, " What? Roy Spencer is a principal research scientist at the University of Alabama in Huntsville, and the U.S. Science Team leader for the Advanced Microwave Scanning Radiometer (AMSR-E) on NASA's Aqua satellite. He has served as senior scientist for climate studies at NASA's Marshall Space Flight Center.
"you are offended by Intelligent Design far more than you are interested in the scientific issues " What? I simply quoted Spencer, so maybe you have things the wrong way round, don't you.
" I never set out to aggravate people" Really? I get the opposite impression.
"I still believe, absurdly perhaps, that the hallmark of good scientific debate is that it hinges on discussion of the evidence. Truly, I would welcome from you a link to a piece by anyone on that list of yours that does this," Given they are all deniers that would be difficult.
The hallmark of good scientific debate is that people actually know what they are talking about. You obviously don't, so why not do some research. That is what scientists do rather than parrot political memes as you have done.
"The especial danger of demonising any given camp as 'deniers' is that once the finger-pointing begins," You need to look into the subject, Chris, rather than point your finger in ignorance.
"everyone who lands on the other side of the partisan divide can be conflated with the 'deniers' and thus dismissed." Seems that is your problem for not knowing anything.
"This hinders legitimate scientific debate." That started some time ago by the deniers, as anyone with any knowledge knows.
"It is a sure sign that the state of pseudoscience has broken out that one side claims a consensus and then pushes to discredit opponents, instead of focussing on the evidence and its interpretation, which are the necessary components of scientific processes." Sorry Cht=ris, but you are either very, very naive and poorly informed or being willfully contrarian.
Posted by: David Boffey | April 24, 2022 at 08:51 PM
Thanks for returning to continue our discussion. I seem solely to be aggravating your further, so I'm not sure there is much point in our continuing, but I'll make some short remarks.
I've briefly reviewed your links... The two peer-reviewed papers are both metareviews of publications that do not compare data (only the general positions taken up), and all your other links are journalism. I was hoping for some key papers from within climate science around which the scientific case hinges. There must be some; a field does not usually take up agreement over an issue without common references.
I must apologise, however, as I misread your original list: I thought you were singling out 'deniers', and then providing a second list of credible researchers. You meant the entire list as 'deniers'. I apologise for the misunderstanding.
I also want to clarify that my claim about the accuracy of models was not meant to undermine the general claim of a warming effect, which is an implication from the physics known since at least the 1970s. My comment was rather a general claim about the limits of computer modelling in empirical topics. Freely do I confess that I have spent less time reading papers in climate science than in other scientific fields... I have however been interested in discovering which are the key papers that the issues hinge upon. I am still in the dark about this.
As a result of our exchange, I am now reviewing Hausfather, Drake, Abbott, and Schmidt (2020) "Evaluating the Performance of Past Climate Model Projections", Geophysical Research Letters, vol. 47... Hausfather et al seems to acknowledge the issue I was referring to when they talk about "comparing the relationship between forcing and temperatures in both model projections and observations" i.e. in validating the underlying physics in the models, irrespective of the actual predictions, allowing them to admit that the models they are reviewing have been superseded by new techniques which "have rendered virtually all of the models described here operationally obsolete". Again, the topic is still hinging around the modelling, and how one assesses the modelling. This is definitely not a field in the form of, say, optics, where there are no remaining research questions to investigate. It looks very much like a live research topic to me.
Given the intensity of your response to my comments, I would suggest there is little to be gained by our continuing our discussion, such as it is. I don't think you'll ever be satisfied with my comparatively neutral position on this topic, and whatever views I have on climate science aren't going to be positively swayed by a 'flame war'. I am genuinely sorry that you find my views so offensive, and in that regard I can only suggest that you just stop reading me to avoid future aggravation, or else perhaps take a break from this discussion and return to it later.
Either way, many thanks for engaging at all,
Posted by: Chris | April 25, 2022 at 08:19 AM
Oh dear, poor Chris with your faux outrage when others treat you in the same way you treat them, and your pubescent schoolgirl accusation of emotions when you were mocked and put in your place with facts. Flat Earth cultists and evolution deniers do that all the time.
And as for continuing of course it is pointless as you are being an adolescent playing a game rather than embracing facts and reality.
Posted by: David Boffey | May 03, 2022 at 04:36 AM