Viral Origins: They’ve Been With Us Forever

Hydrothermal Vent in Marianas trench
The ‘White Champagne’ hydrothermal vent in the Marianas Trench – where life could have evolved.

While we’re all thinking about viruses, it might be interesting, to some at least, to consider how these things came into being in the first place, which in itself opens up some interesting philosophical questions.

Viruses are beautifully simple.  If you believed in intelligent design, they are the ultimate in design simplicity, if you’re aiming at a ‘thing’ that can replicate itself, albeit a pretty malicious design. Just a bit of genetic material surrounded by a protein coat that protects the genetic material and gets the virus into its host cell.

In the past, it was accepted in evolutionary theory that viruses evolved later than their hosts, from more complex life forms, in common with other parasites.  A tapeworm, for example, cannot live outside its host – it has no sensory organs as such, no motility, no digestive system – it just absorbs food from its host and devotes its entire existence to making tapeworm eggs, to infect more hosts.  It’s not difficult to imagine how such a creature could have evolved from a more complex worm that was eaten by the host, took up residence in its gut, and gradually evolved into a simpler organism because it no longer needed eyes, a mouth, a digestive system, motility, and so on.

But for a virus, it’s difficult to imagine how such simplicity could evolve from a more complex organism.  Also, fossil records (using the word ‘fossil’ broadly to mean all ways of detecting traces of different life forms in very old rocks) show viruses have been around pretty much from the beginning of life on earth.  So how could that be, when there were no more complex animal or plant hosts for them to parasitise?

To ponder this, we have to go back a long way – about two billion years, when life diverged into three groups: Prokaryota, Eukaryota, and Archaea. The difference between Eukaryotes and Prokaryotes is the most fundamental division of life forms on earth.  Prokaryotes are all single cells, but their cells don’t have a defined cell nucleus containing their DNA – it just sits in the centre of the cell.  Prokaryotes are by far the most numerous group, including all bacteria, and the photosynthetic blue-green bacteria (often wrongly called ‘blue-green algae).  Eukaryotes have a defined cell nucleus containing their DNA, enclosed by a nuclear membrane.  This group includes all unicellular and multicellular plants and animals, from amoeba and single-celled plants to higher plants and mammals.  There are other differences between Eukaryotes and Prokaryotes, but it’s the cell nucleus that’s the fundamental difference, and makes it possible for eukaryotic single cells to join together to form multicellular creatures – Prokaryotes are unable to do this.  The Archaea group is a more recent invention (didn’t exist when I studied microbiology) but is a sort of catch-all group for all the weird and exotic lifeforms that don’t easily fit into the other two groups. They mostly live in strange places where other life forms can’t live – for example, boiling water in geysers, salt flats, or concentrated acids.  They also often have exotic metabolisms, for example using the energy in sunlight to fix carbon from inorganic rock such as limestone.

All three of these groups have viral parasites.  Indeed, pretty much all life forms have viral parasites.  So that would imply that viruses evolved well before this fundamental evolutionary crossroads.

There are currently four main theories for how viruses evolved.  These are:

  • Virus-First Hypothesis: this says that viruses are the simplest life forms because they evolved first, they were the first self-replicating life forms.  They later became obligatory parasites by parasitising more complex life forms.  This is rejected by most scientists because if such life forms did exist, they were by definition not viruses, because they must have had some sort of metabolism to replicate themselves.
  • Reduction Hypothesis: this says that viruses evolved from a more complex type of cell that started parasitising other cells, then evolved to be simpler, rather like the tapeworm.  This doesn’t have much support either, as there’s no evidence for any kind of single-celled organism that parasitises cells by getting inside them, nor that such a thing has ever existed.
  • Escape Hypothesis: this proposes that viruses are actually bits of genetic material that ‘dropped off’ the genetic material in a more advanced cell and started to reproduce on their own, but there’s no evidence for that; it seems unlikely and has never been observed.
  • Coevolution Hypothesis, also known as ‘Bubble Theory’. This is an interesting one, and sounds to me the most plausible.  It’s now thought that life on earth evolved in the deep oceans, around hydrothermal vents where the water was warm, and where there were all sorts of food and energy sources (and where some of the most primitive microorganisms are still found). This theory proposes that self-replicating bits of genetic material arose by chance near the vents, driven by energy sources near the vent. These vents also produced primitive fat-like ‘bubbles’ – if a bit of self-replicating material got stuck in one of those, it was protected and had a supply of food, so could drift further from the vent and still reproduce.  This gave rise to two ways to replicate: find your own bubble and replicate in that, or use someone else’s bubble to replicate in, hi-jacking the primitive cellular structures they were beginning to evolve.  So in this theory, viruses were there right from the very start of life – which makes sense because every life form we’ve detected on this planet is parasitised by viruses.

There’s also a very new theory called the Chimeric Origins Hypothesis, which is a variation of the Coevolution Hypothesis, but I won’t try to explain it as I don’t understand it!  If anyone else does, please add a comment below …

So viruses have probably been around for a very long time, they could well have evolved alongside all other lifeforms 4 billion years ago.

And yet, at the very pinnacle of 4 billion years of evolution, we still don’t have a universal way of dealing with them.  Sudden, spontaneous outbreaks of new viruses, such as we’ve seen with HIV, SARS, MERS and COVID-19, cause havoc, large numbers of deaths, and major disruption of our highly evolved societies.  Of all the ‘disaster scenarios’ that could wipe out our species, from an asteroid impact to nuclear war, the spontaneous evolution of a truly deadly human virus still seems by far the most likely.

If you believe in an interventionist god (which I don’t, nor any other kind of god), it would not be difficult to imagine what viruses were for: to stop any one species becoming dominant, to guard against the hubris and arrogance of a species that could otherwise wreck the planet.  But it doesn’t much matter whether you believe in a god or not, viruses are there and that’s what they have the capacity to do. The simplest, most primitive life form on the planet is still the one that could defeat us absolutely.

CV19: It’s Not a War

Time for some gardening …

I am concerned about the macho, emotive language being used during this viral pandemic.  We’re on a wartime footing. There’s an enemy we have to defeat.  We have to suffer and endure to win.  This is not a ‘war’, and the endless use of wartime metaphors, in the press, BBC, and by the Prime Minister himself is misleading and, I believe, potentially dangerous.  It’s the wrong approach.

A lot of the language being used is unhelpful. To refer to the virus as ‘this cruel bug’, as Mark Easton, the BBC’s home correspondent did, is misleading – it implies that COVID-19 is doing this somehow maliciously, that it’s a conscious enemy that we need to take on and outwit. It isn’t, it isn’t even alive in the normal sense, let alone capable of ‘cruelty’.  We need facts and clear guidance from journalists, not literary hyperbole.

But the real danger with using wartime rhetoric is that it’s not clear who the enemy is.  There is no opponent ‘over there’ who is consciously out to get us, against whom we can direct our hatred.  In that way of thinking, the enemy eventually becomes not the virus, but the people infected, our friends and neighbours.  Any of us with COVID-19 become the threat, a fifth column working for the enemy, handing over our bodies to become factories making billions more virus particles.  This is not a war.  It’s a pandemic.  That’s something very different.  The rhetoric should be about caring, about co-operation, about us all helping each other through this, not whipping up mass hatred against an unseen enemy.  And dare I say it, it should be about pleasure.

The measures that have been taken I believe to be reasonable and measured.  And I think they will need to be enforced if people refuse to stick to them.  I have some quibbles – for example, there would seem to be nothing wrong with going out for a drive in the car, as long as you remain isolated within the car.  When I was young, driving to a flyover over the M1 and watching the traffic, enjoying a cup of tea from the Thermos, then driving home again, counted as a good day out.  And not the remotest chance of any interaction with any other human being beyond the car’s occupants.  I’m not suggesting that we all start doing this of course – it’s important that we stick to the guidelines in their entirety, whether we agree with them or not.

Where I do believe the approach is wrong though is in the official attitude to self-isolation and lockdown.  This seems to be linked to the wartime rhetoric: it’s all about suffering, we have to grin and bear it, keep a British stiff upper lip, keep calm and carry on (or not carry on). But these stringent measures can only hold out if people believe in them, and their lives are tolerable. So rather than Boris Johnson trying to look serious (which he’s never been good at) and Churchillian, he should be stressing how we can actually enjoy ourselves. Generations of advertising executives know that if you want people to change their behaviour, you must make them believe their new behaviour is something they’ll enjoy.  There must be plenty of them with not much to do at the moment, we should be recruiting them to sell us the pleasure of lockdown, what you can do with your time, how you can actually enjoy these restrictions.

True that’s a lot easier for some than others.  Those of us with gardens have plenty to do – my main concern is whether I can get everything done in just three weeks.  But there’s still a good life to be had indoors, and there’s not enough attention being paid to that.  As well as getting everyone to buy into these restrictions for long enough for them to work, we need to think about mental health too, not to mention the risks of domestic violence, and those families who are managing neither to grin nor to bear it.

For those reasons I disagree with Rebecca Long-Bailey.  To make lives tolerable, and indeed enjoyable, we need access to stuff that helps us cope: toys, gardening products, DIY materials, and yes, little luxuries too.  There are few if any risks involved for the recipient in having these things delivered from online orders – fewer risks than with online food deliveries. True, there is a risk with workers having to continue to travel to workplaces to package, despatch and deliver these goods, but that seems like a manageable risk, relative to the huge benefits to the well-being of the wider population, and the absolute necessity to make sure people can and do adhere to these restrictions. This need for pleasure applies especially to our health workers and others under pressure in essential services – when they’re off duty, they need to be able to relax and get some enjoyment, if they’re to cope with this and work to the best of their abilities.

We can get through this, if we modify the rhetoric and we make these difficult times tolerable, or even pleasurable.  The stoic ‘you can’t enjoy yourself, this is a national emergency’ approach is both undesirable and unnecessary, and potentially dangerous if people start to rebel against it.  You can’t take people’s co-operation for granted. We need to make sure the necessary measures taken to stop the spread of the virus are as easy and as acceptable as possible.  If we don’t, it won’t work.

So, stay safe and keep washing your hands! One verse and the chorus of The Red Flag is perfect – sung out loud of course. Now I’m off to do some weeding, and enjoy the sunshine.

West Hill Lift: The Big Wheel Arrives

Today, on a misty morning at about 8am, the new winding wheel for the Hastings West Hill Cliff Railway arrived, and was lifted into place. The wheel failed last year, and had to be re-cast in a foundry in Rotherham. Originally, it had been standard equipment as part of the winding gear for coal mines – now no longer available.

Work on the lift was started in January 1889, at a cost of £16,000. A 363 ft tunnel was constructed through the cliffs, using an existing cave, with a 1 in 3 slope, making it the steepest funicular railway in the country. The lift was powered by a ‘gas engine’ – an internal combustion engine running on coal gas. Steel ropes are attached to both cars which counterbalance each other with the ropes passing around the big wheel, which is turned by the engine to move the lift cars. The lift was completed and opened on March 25th 1891.

Financially, the lift was not a success at the time because of increased construction costs; the company running it failed in 1894. A newly formed lift company operated it until 1947, when Hastings Borough Council bought the lift for £4,500, and has run it ever since. The lift is almost unchanged, still using the original Victorian lift cars, but the gas engine was replaced by an electric motor.

The two cliff railways (East and West Hill) are now very profitable, even after taking into account expensive repairs such as this one. The two railways generate a net income of around £150,000 a year for the council. The installation of the new wheel had been delayed for a couple of months because of bad weather, but it’s still hoped the lift can be re-opened by Easter (virus permitting).

COVID-19: A View from a (former) Microbiologist

Representation of COVID-19 virus, looking like it was made by a community knitting circle.

The COVID-19 Coronavirus outbreak is devastating, and life-changing.  At the moment, we can have no idea whether the advice and restrictions are too little too late, or a huge overreaction … perhaps what’s more disturbing is that governments across the world seem to be so unprepared for a new virus outbreak, which was inevitable, and we’re lucky this one has a mortality rate that’s relatively low.  Hopefully we’ll be better prepared next time – because there will be a next time.

But you really can’t help admiring viruses.  That something so simple can cause such devastation, and has the potential to wipe out our species, is remarkable.  So why do viruses exist, and what are they?

One way of looking at viruses is that they’re the most advanced life forms on the planet.  Assuming the sole purpose of all life is to make more copies of itself, there are two ways you can evolve: to become more and more complex, developing new, innovative ways to dominate your environment and compete with other species, as humans and other mammals have done; or to simplify and evolve into something that’s so reduced that it only includes the most basic means to survive and replicate, as viruses have done.

 I’m defining ‘life form’ here as something capable of self-replication.  Viruses aren’t ‘living’ in the normal sense, in that they have no metabolism of their own.  Because they are entirely dependent on more complex life forms to replicate themselves, they must have evolved from something more complex, which simplified and adapted to an entirely parasitic lifestyle.  Pretty much all other life forms are parasitized by viruses, including bacteria, which are attacked by relatively large and complex viruses called phages.  But most viruses are tiny – imagine a queue of 10,000 of them lined up end-to-end; it would be about a millimetre long.  That’s only about a thousand times the size of a single atom of iron.

The viruses that parasitise all eukaryotic organisms (life forms that aren’t bacteria, mostly) really are very simple.  They are a short strand of DNA or RNA carrying the viral genetic code enclosed in a protein capsule.  Coronaviruses use RNA to carry their genetic code. The capsule has receptors on it that make it stick to particular cells in the species it parasitises, and gets itself absorbed into the cell.  Inside the cell, there is all the equipment to make proteins, and to duplicate the virus’s genetic material.  Once in the host cell, the virus protein capsule dissolves, and the bit of genetic material inside hijacks this equipment to make more copies of the virus. 

There are disadvantages to being so simple.  Our DNA, inside the nucleus of our cells, is what normally instructs this cellular equipment to make the proteins we need to build ourselves and keep our bodies running.  It’s well protected, with enzymes that check the DNA replication process to ensure mistakes don’t happen when new strands of DNA are made for new cells. Viruses do have these ‘proofreading’ systems, but they’re less sophisticated – so when their genetic material is copied, there are a lot more mistakes.  Most of these mistakes result in errors in the genetic code that mean it simply doesn’t work anymore.  But very occasionally, a random mistake will occur that changes the virus in a way that’s beneficial to the virus – which is what happened with COVID-19, allowing it to ‘species jump’ to humans. 

In eukaryotic and bacterial cells, DNA is used exclusively as the repository of genetic information, with identical coded strands of DNA in almost every cell in the organism. RNA is copied from the DNA and is similar in that it has the same ‘base pair’ structure as DNA that defines the genetic code.  But it has shorter strands, made in the nucleus to copy the code carried by the DNA, and then transmit that code to cellular structures called ribosomes. There, the code is used to determine the structure of the proteins made at the ribosomes.  That kind of RNA is called ‘Messenger RNA’ or ‘m-RNA’ – there are other types of RNA, but explaining all those gets complicated! 

Rather than using DNA to make RNA as happens in cells normally, some RNA viruses use the RNA to make DNA, which then works in the ‘normal’ way to code more copies of the virus – hence they’re sometimes known as ‘retroviruses’, because the coding works in reverse. Such retroviruses can even incorporate the DNA they make into the host cell DNA, so the infection becomes permanent, it’s part of the host’s own genetic material (which is how HIV works). However, Coronaviruses don’t do that, they replicate their RNA genetic code directly by getting the host cell to simply make more identical RNA.

There are disadvantages to using RNA for genetic coding.  RNA is less stable than DNA, so it’s more susceptible to physical damage than DNA, especially from UV light. 

The cells infected by the virus need to serve the virus two purposes: firstly, to make copies of the virus, and secondly, to get those viruses to a new host.  So infecting cells in the respiratory tract is ideal, as by provoking coughs and sneezes, the virus gets easily spread to a new host.

That’s it about viruses. Nifty, simple, adaptable, beautifully efficient.  So what does all that mean for COVID19?  Probably nothing much, beyond the hand-washing, self-isolation and all the other  advice, but it’s useful to know your enemy and know how they function.   COVID-19 does seem to have some unusual features that it’s managed to evolve, in particular the ability to survive three days on surfaces (although not outdoors, because of the UV light damage).  But it’s new, so we don’t understand its epidemiology.  Knowing how it works is one thing.  Knowing how its characteristics play out in an epidemic, or pandemic, is something quite different.

Reasons to be cheerful?  The sensitivity of the RNA in the virus to UV light could help kill it off as UV levels start to rise through spring.  The huge majority of cases have been recorded in the northern hemisphere, where it’s winter and there’s less UV light around.  And maybe governments will learn some lessons, to make us better prepared for the next time this happens.  If the mortality rate of this virus had been significantly higher (Ebola has a mortality rate of 90%) the consequences could have been catastrophic, and potentially a near-extinction event.  We have to learn from this – we must make sure that after this is over, we don’t all just forget about it and get on with everything as normal.  We need to find ways to develop vaccines faster, and create international facilities to make new vaccines in bulk, as soon as they’re developed. We need to make sure the structures are in place to support vulnerable groups, prevent panic buying, and protect the economy, rather than making it up as we go along.  We need to do some sophisticated modelling of different potential scenarios, and prepare for them.

We will get through this, and it probably won’t be as bad as the worst-case scenario we’ve been hearing about – that’s the thing about ‘worst case scenarios’, they’re not likely to be realised.  The worst-case scenario for driving to the shops is that you get killed in a car crash on the way.  That doesn’t mean you expect it to happen, but you prepare for it, or the car manufacturers do, because just occasionally, it will happen to someone.

So enjoy your self-isolation, and try to limit your anxiety – being anxious depresses your immune system.  We have to see this through, help others in whatever ways we can, and learn from it.

Peter Chowney, head and shoulders, outdoors. out

This blog is by Peter Chowney, former Labour leader of Hastings Council, resident of Maze Hill, St Leonards on Sea, UK, and councillor for Tressell ward on Hastings Council. It serves no particular purpose, beyond entertainment, debate and constructive comment. You need to be registered and logged in to comment, but if you do, please make sure it is constructive! Click on the post title to comment.

A New Blog

This Wednesday, I cease to be leader of Hastings Council. That’s because I decided to resign, after almost five years of doing the job. The new leader will be Kim Forward, in whom I have every confidence, and who I know will be an excellent council leader. The timing of my resignation was intended to be a few weeks before the May council elections. It seemed a bit disingenuous to resign immediately after the election, the local electorate needed to know who they were going to end up with as their leader if Labour were again successful and retained control of the council. In the event, the elections have now been cancelled, but I’m still resigning anyway, and Kim will formally take over on Wednesday.

I became leader unexpectedly in 2015, following the sudden and tragic death of Jeremy Birch, who was taken ill in the town centre while handing out leaflets for the 2015 general election (I was with him at the time), and died a few days later. I still miss him – he was a good comrade and a good leader. Being council leader wasn’t something I ever expected to do – we all thought Jeremy would be there for years to come.

I have been involved in local government for a long time – first working for Hackney Council in 1982, then becoming a councillor in Hackney and chair of the Housing Committee, then working in and around local government, for the Audit Commission, as a freelance consultant., and as an interim manager for several different councils, of varying political colour. I was first elected to Hastings Council in 2000. I had vowed never to be a councillor again after my experiences in Hackney, but was persuaded back into the fray.

Back in the 1980s under the Thatcher government, we thought the cuts to local government were severe, and put our lives on the line by setting ‘illegal’ budgets and risking surcharge. But none of that came close to the cuts to local government we’ve seen over the last ten years, and in the last five in particular. Illegal budgets and surcharge are no longer possible (Thatcher changed the law to prevent that), but these five years as leader have been especially dispiriting. So much of my time has been taken up by meetings where we’re constantly trying to find more services we can cut, whom we can make redundant. True, there have been some inspiring innovations in income generation that have helped, and new technology has enabled online applications for council services and payments, saving more money, although that’s led to yet more redundancies.

There have been some good times, and some things the council has done that I’m particularly proud of: the Grotbuster programme to improve eyesore properties, the Coastal Space project to create social housing from derelict properties in St Leonards, the world-first natural filtration system in Alexandra Park to improve bathing water quality, being one of only two councils in the country to retain 100% Council Tax reduction for people on out-of-work benefits, restoring the abandoned White Rock Baths as the world’s largest underground BMX arena … and lots more. But all this has been achieved against a backdrop of continuous, deepening, cruel cuts … it’s time to let someone else have a go. Besides, five years isn’t a bad length of time for anyone to be a council leader – it was never supposed to be a job for life, or anywhere near that.

Will I miss it? Yes, some of it. What will I miss most? The view out to sea from the leader’s room in Muriel Matters House.

So I’ll have a bit of time on my hands, and will be able to do a blog, for which this is the first post. It will include politics of course (local and national), but also a bit of gardening, chicken-keeping, classic cars, microbiology (that’s what I did, originally), and general reflections on life. I hope you enjoy it.