UKC

Ever since the pandemic began I have noticed that the language surrounding the virus uses terms that credit it with a psyche. Terms like 'it just loves crowds' or ' all it wants to do is to find new hosts'. I can see that it is there for a reason. It helps to communicate with people who can identify with an adversary that has to be fought by whatever means we prescribe, distance, hygiene, isolation etc.
But what I started to think about is just what is driving the proliferation of this organism. To be precise, what physics, chemistry, thermodynamics, biology, mathematics even, can be used to explain the process.
If we add Hydrochloric acid to Sodium Hydroxide we get Sodium Chloride and water. This inevitable process obeys several chemical & physical principles that we have discovered, it is not because the components 'like' each other and 'want' to exchange ions in some sort of alliance.
So I have two questions firstly this: What are the fundamental forces, principles, mechanisms etc that drive an organism to reproduce exponentially?
The second one is about mutation, is this a random process where some mutations thrive and others die, or is there a driving force behind the process that favours the mutations that thrive and proliferate more extensively?

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Physics. I'd say it's "entropic forces" rather than fundamental forces.  Emergent.

#1 Mutation, selection and adaptation -- for ability to infect the new host (not it's original host, bats), who happen to congregate nicely to permit exponential growth.

#2 mostly random I believe, but selection is the word you are looking for.

You're thinking along the right lines. Evolution* is blind, the virus just happens to have jumped into humans in a form suitable for establishment and successful growth. It doesn't chose or aim to do anything.

Edit: * specifically natural selection. Dogs are a good example of what non-blind (guided) evolution can achieve.

The second one is about mutation, is this a random process where some mutations thrive and others die, or is there a driving force behind the process that favours the mutations that thrive and proliferate more extensively?

Survival of the fittest, otherwise known as evolution. It is just on a very rapid scale, because of the number of replication events, coupled with the relatively poor (compared to humans) proofreading of the replicated genetic material.

Ex virologist here. 

Basically it is total dumb luck,  which is hard to believe when you see the utter precision by which these viruses bind to their receptors.

Somehow mutations have occurred to allow this to happen,  we just made it more likely by increasing our contact with the reservoir animals in the wild.

When you see the 3d images of viral binding proteins and the specificity of their binding targets it is hard to doubt that it happens by chance.

This may explain some of what you're asking about

https://www.breakthroughs.com/advancing-medical-research/how-do-viruses-mut...

Yes, somehow Jon Read and others have not answered Keith Ratcliffe's question. To say it's 'dumb luck' or 'it just happens' is not science. It's precisely for science to explain why things happen ... crux point: in this very integrated, systemic way. We're not there yet.

I think they have answered it really,  inefficient production of the viral genome within infected cells results in mutations which then change different aspects of the viruses then produced.  Could be a means of cellular entry, binding proteins or in the case of hiv it could be the encoded nucleic acid production proteins.

Viruses do not have the same level of nucleic acid quality control that for example humans do,  essentially making sure that the copies produced are the same as the original version.  Where our cells will only tolerate a level of mutation without committing suicide (apoptosis) a virus doesn't have the same issues so much larger changes can happen and it will either be able to infect further cells/organisms or it won't.

Flu is far worse as the 8 genes are separate within the virus so if a creature e.g. a pig is infected with a bird influenza and a human one the range of viral types that could be produced is much higher and easier than the coronavirus with a single genome.

I still find them utterly fascinating even with not being in that world anymore

Science can explain really quite precisely how a lot of it happens.  Emergent processes driven by entropic forces, and an uncanny tendency for matter at every scale to self-organise and in many cases to catalyse or otherwise encourage replication.  

But you asked "why", not "how".  This "why" comes down to asking:

• Why the laws of physics are as they are
• Why the initial conditions for the universe were as they were

Cop-out answers include the anthropic principle and saying "magic man done it".   Beyond that, it's a bit of a mystery.

Yes, exactly. I should have expressed myself more clearly: I was asking how as well as why. Yes, science goes a long way towards explaining the how, except in evolution (without collapsing into circular arguments) And here a large gap still remains. But I suppose the simple answer to the why is that it's mostly not a scientific question. Yet in almost every aspect of science except biology/evolution attempts are made to answer it.

No, I’m with Wintertree, science tries to explain how, not why.

Unless you don’t mind the answer to ‘why C?’ being B, and before that A, and before that quantum uncertainty.

Fundamental Force:  The main fundamental force of much relevance is quantum electrodynamics; the interaction of the charged particles that comprise matter.  Gravity has some say in the matter by shaping the wider environment, and the nuclear forces have a staring role in driving mutation once "life" is achieved.  

Principle:  The main principle is one of catalysis and self-replication, or self organisation.  Some forms of condensed matter (stuff that is liquid, solid or goopy) happen to catalyse the conversion of other forms of matter into one resembling themselves.  Random chance brought a few base elements together to make an amino acid.  Perhaps that amino acid catalysed (encouraged) the formation of more amino acids from the raw elements.  Anything that catalyses the production of things like itself will enter a kind of exponential growth, and this has happened for basic organic molecules and then up through a series of hierarchies until you have people running round shagging each other and making more people.  This exponential growth is only limited when the self organising stuff starts running out of raw materials.   The early stages of this process are lost to the midst of pre-history; it's possible that all of the Earth's crust has been recycled through magma since the self organising materials appeared on Earth.  Mad scientists continue experiments with glass vials, high voltages and liquid goops to try and recreate the process.

I think that the step from a dead planet to the first living cell was far more immense than the step from that cell to the or me.  It's also the one we know the least about.

Mechanism: The details depends on the scale of the organism, but it's invariably thermodynamics - creating local structure (decreasing local entropy) by destroying wider structure (increasing global entropy).

The amazing thing is that the universe happened to have the right laws and conditions to support atoms organising in to molecules, molecules in to amino acids, the production of the nucleic bases, the creation of RNA and DNA, the independent production of lipid vesicles, the happenstance of RNA and RNA enzymes meeting lipid vesicles and the myriad steps from that to a functional cell and then from a cell to a human.  I'm not sure anyone should think about the odds of that too much.

I don't think you read what I said: 'I suppose the simple answer to the why is that it's mostly not a scientific question.'

His post was six minutes after your clarification. So he probably hadn't read it, and was commenting on your earlier post; the one he quoted.

That's true, but it's OK, it would take more than that for Gordon to upset me!

Dawkins wrote some good books that cover this in a very accessible way. Well worth reading, as it is a fascinating subject.

That's a bit anthropic isn't it?  There must be countless universes where the physical constants are a bit different and chemistry just works differently and presumably life does too.  Things work the way they do here because of the prevailing conditions and couldn't do otherwise. 

Admittedly, there must be countless universes where it's all a bit difficult with darkness on the face of the deep etc.

I'm always wary of appealing to the anthropic principle, but it does feel a bit unavoidable.  I've long been fascinated by the way that you can't muck around with several of the fundamental constants of the universe without it becoming untenable for life - and yet them seem to be arbitrary.  Change the electronic charge by not very much and atoms stop working; vary G by a little and stars and galaxies either fail to form or collapse very quickly; change the fine structure constant by only a very little and nuclear fusion stops working.  All of these values seem to be 'tuned' to provide a universe within which life is possible.

I quite like the idea that there have been infinite universes - possibly big crunch followed by big bang followed by big crunch, forever and ever - and these constants get changed every time, so almost every universe cannot support life.  Obviously the only universe in which some monkeys might sit around pondering the unlikelihood of it would be the one universe in which the constants happened to be the right ones... and at least this explanation gets rid of the need for someone to have done the tuning!

Thanks - that was really useful and what my original request was about.

those other universes, while interesting in concept, are purely hypothetical - we only have this one at the moment.

Though I'd love to see evidence of others, and the "hidden extra dimensions"  - perhaps there already is but we haven't yet recognised it.

Read the Selfish Gene and the Blind Watchmaker.  Both accessible and clear...and I think addressing what you're asking.

Well, that's the question, isn't it...  

Only some of them multiverse theories support the idea of different physical laws or constants in different universes, and there's really nothing but conjecture about their existence right now.   If it turns out we're heading for a Big Crunch and there's a cyclical cosmology you might just convince me that symmetry breaking could happen to go differently on different cycles...

It's hard to avoid considering the atrophic arguments, although as I always caution people when thinking about alien life, we mustn't assume that the only forms of matter, life and consciousness are those were are used to - there could be other options possible within the laws of our universe but beyond the bounds of our current knowledge and understanding.  

Perhaps we just can't conceive of how consciousness may arise in a different set of physical laws - not surprising as we don't yet have any testable theories on how it arrises now under our physical laws...

Of course.  That raises the slightly unsettling question of how those constants turned out to be so finely tuned...

Bilberry: having re-read the thread I was just about to suggest The Selfish Gene.  It's quite dated now, of course, but it's a wonderfully clear description of the apparent 'drive' that biological mechanisms display.

I think it's pretty clear that we're not heading for a big crunch, but according to Roger Penrose at least that isn't necessarily a prerequisite for a 'cyclical cosmology'.  I went to a talk he gave a couple of years ago, but I'm not going to even try to give you the gist of what he had to say beyond that.

It certainly doesn't look that way, but I'm not sure we understand enough to predict the distant future yet.

He's certainly gone in an interesting direction of late.  

Yes, Iain Banks (isn't it always?) has sentient interstellar gas clouds and draws a distinction between Fast organisms (the sort we'd immediately recognise as alien creatures) and the Slow, which includes many life forms we don't recognise because they operate in timescales vastly beyond the lifetimes of Fast intelligences. 

The talk was both interesting and interesting.  Maybe it seemed less outrageous than it was because I didn't fully understand it, but I think there are theories now accepted as fact that I find almost as boggling.

Quite.  I wouldn't pretend to have a cutting edge understanding of cosmology - I had some specialism in it 20-odd years ago - but the complexity of dark matter and dark energy seems rather too much to make any real sort of prediction yet.

Indeed.

In the absence of actual discovery of DM particles, it's never really proven, it's just a model that fits the data nicely.  Likewise with DE - and we haven't experimentally verified gravity in a weak field limit.  With the new generation of giant rockets and the Breakthrough Startshot program, that no longer feels like an insurmountable problem. 

The Lambda-CDM model contains explicit free parameters as well as implicit ones (embodied in the choice of model).  Fitting a model to experimental evidence does not give it predictive power - and this applies all the way from a pandemic through to cosmology.

Many years ago I studied genetic algorithms as part of a computer course which is based on Darwinian selection of the fittest. You started with a set of random solutions to a problem, find the best solutions (of the set), evolve those using biologically inspired operators such as mutation, crossover and selection and repeat. Typically after about 11 generations you get to an optimal solution. In covid’s case the optimal solutions are the ones that make it spread best.  No magic or intent, just science and chance.

If you look at time as having no beginning then the constants would have been random and maybe ever changing until the values aligned enough to become stable. Or maybe they automatically gravitate to stable values. 
 

There wouldn’t be alternative universes where they’re different because those universes would be unstable and be shimmering in and out of existence all the time. 
 

Maybe our constants don’t produce a completely stable universe but it’s stable enough to exist for a few billion years...

As I understand it, a version of the universe with different values of e, G or alpha wouldn't necessarily be unstable; they'd just not produce the conditions we think are necessary for evolution of complex life.  Making G a bit bigger, for example, would give you a universe quite like this one but all stars would burn out in a matter of a few million years.  There wouldn't be enough time for life to evolve before the parent star went giant.

But yes, we don't really know enough even to say our universe is stable.  One of my pet nightmares is that the matter/antimatter asymmetry is only locally true, and that other parts of the universe are wholly antimatter...

He certainly made a distinction on timescales and the difficulty of crossing them; I don't recall the dust clouds but my interest tailed off towards his last few books.  

I'm far from convinced we'd recognise all possible forms of life - if they're too far removed from ours on spatial or temporal scales.  Space-time itself is governed by a set of non-linear field equations.   The derivation of these laws from thermodynamic treatment of information and the properties of entropy on black holes and closed time like curves...  Breadcrumbs; perhaps classical or quantum space-time can be twisted up enough to do computation and therefore achieve consciousness.  Perhaps it exists in a wavefront propagating outwards from some cataclysmic event; after all the 1-d cellular automata "Rule 110" is turning complete...

I’ve had to think about that, but it’s more true now than ever.  All this eating and drinking and not getting enough exercise is good evidence of the Strong Atrophic Principle!

The virus mutates all the time, but it's only the ones which become more virulent or deadly that we get to know about, the others which give milder, less contagious disease, aren't news worthy because they either make people less sick or die out.

Ha! You would have regarded me as one your mad scientists when I was doing my PhD 45 years ago on deep processes in the Archaean crust. At one point , I was doing experiments in my bed-sitter into magma convection using a fish tank filled with Tate & Lyle's Golden Syrup (many canteen cans of the stuff!), heated from below with plate warmers. I had a way of projecting light through this to make kind of Schlieren images of the flow movements, and I was throwing in rice grains or pieces of chopped up aluminium foil to mimic the movement of xenoliths in the magma! I was interested in how they distributed themselves.

BTW, I have found many instances of self-organisation in geology during my career.

Fantastic.  Triangulating every grain of rice with a couple of cameras should be possible these days, and using a scanning laser diode you could illuminate a horizontal or vertical plane so that people could look at the convective patterns directly.  Sounds like a great thing to build for a museum or other interactive science place!   I love the idea of a giant Schlieren image on a screen from a tank of syrup.  It's not often you can combine optics, catering supplies and geology I'd imagine...

I've looked at the odd rock with a beady eye about how it came to be.  The universe seems to approve of self organisation at every level.  I was nothing this the other night when simmering some long grain rice until it was out of water; this ends up with a quasi-regular grid of holes between the grains of rice on a characteristic scale of a few cm; I imagine some physicists somewhere have a model that explains it...

I’m wondering what happened to the Golden Syrup after the experiment ended. A giant treacle tart perhaps?

Discovery of the Total Perspective Vortex if Fairy Cake was present ...

I've completely forgotten how I disposed of the sticky mess. It probably wasn't very enviromentally friendly, so I think I did it quickly and didn't give it another thought!

I am fascinated by how nature favours different mechanisms at different time and length scales. Geology straddles an enormous range of time scales, from about one ten trillionth of a second (thermal vibrations) to many billions of years. Yet, in spite of millions or billions of year, many rocks and fluids in geology are not in equilibrium with the surroundings, except locally. Equilibrium reversible thermodynamics is very useful at some scales, but completely useless and inappropriate at others. I am working on a colloidal mechanism for fluid flow in the subsurface that looks as though it could be completely self-organising and self-adjusting to input flux rates.

Brilliant

One of the best things I've seen on TV ever was the geology series Earth Story fronted by the zoologist Aubrey Manning.

https://www.amazon.co.uk/Earth-Story-DVD-Danielle-Peck/dp/B000FS9SGE

I'm sure T&LGS came up while they were explaining mantle plumes, and now I'm going to have to watch it again!

ff