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Evolution 101, with reference to coronavirus

By T. Ryan Gregory. Reproduced with permission

Mutations occur as chance errors in replication. They’re just mistakes in copying. Most have no effect. Some are detrimental to the organism (or virus), a few may happen to be beneficial — this depends on the environment.

Three main evolutionary processes determine what happens to genetic variation once it arises (and these are independent of the process that generates new variation, namely mutation): genetic drift, natural selection, and gene flow.

We call different versions of a gene “alleles” and we can talk about the proportion of those versions in a population as “allele frequencies”. Genetic drift is a random change in allele frequencies that occurs by chance.

Genetic drift is basically sampling error, in which the genetic variation in a new generation does not accurately reflect what was present in the previous generation. The most obvious mechanisms of genetic drift are founder effects and population bottlenecks. (But see below about genetic drift being common in small populations generally). Founder effects occur when a random, non-representative subset of a population moves to a new location and founds a new population. The allele frequencies in that founder population won’t be the same as in the source population, and there will typically be less variation overall.

Population bottlenecks are sudden, severe declines in population size in which survival happens at random. So, for example, a drought or storm causes a major die-off and the individuals who survive were just lucky (rather than having traits that helped them survive).

Gene flow is movement of genetic variation from one population to another. The overall effect is to introduce new variation into an existing population (if the source population has different alleles) and to make two populations that exchange alleles more similar to each other.

When we think about the early stages of new species evolving, we generally are considering ways that gene flow is being blocked. Lots of gene flow means two populations are less likely to diverge genetically.

The final evolutionary mechanism is natural selection. In this case, the reason some individuals survive and reproduce better than others is *non-random*. It doesn’t occur by chance. It is specifically related to heritable traits that make survival and reproduction more likely.

This is where the concept of “fitness” is relevant. In evolutionary terms, fitness refers to the advantage in survival and/or reproduction due to heritable traits. Fitness depends on the environment. What is fit in one environment may be neutral or unfit in another environment.

There are different forms of natural selection, depending on what part of the distribution of traits is fit/unfit in the population: directional selection, diversifying (or disruptive) selection, and stabilizing selection.

Under directional selection, one extreme of the distribution is fit and the other is unfit. This drives the distribution of traits in a particular direction from one generation to the next.

For example, if the largest individuals leave more offspring on average than smaller individuals in each generation, then the average size will increase over time. Not because individuals start being born larger in response, but because more offspring are born of large parents.

In diversifying selection, it is the two extremes that are fit and the average traits that are unfit. This can cause a population to split into two. For example, if the smallest and largest individuals do well but the medium-sized are at a disadvantage.

Finally, in stabilizing selection the average value is fit and the extremes are both unfit. The result is that this prevents the distribution of traits from changing in the population because deviations from the current average are detrimental in that environment.

I have added an image from Wikipedia to show these three types of natural selection. A is the original distribution of traits, B is the new distribution. 1) Directional, 2) Stabilizing, 3) Diversifying selection.

The different types of genetic selection: on each graph, the x-axis variable is the type of phenotypic trait and the y-axis variable is the amount of organisms. Group A is the original population and Group B is the population after selection. Graph 1 shows directional selection, in which a single extreme phenotype is favored. Graph 2 depicts stabilizing selection, where the intermediate phenotype is favored over the extreme traits. Graph 3 shows disruptive selection, in which the extreme phenotypes are favored over the intermediate. From Wikipedia

There are many factors that affect these evolutionary mechanisms. Mutation rates can be high if there is weak quality control and repair of errors, or if there is some environmental factor (mutagen) that messes up replication.

It also matters how much replication is happening. Every time a genome is replicated, there can be errors. Lots of replication means lots of opportunities for mistakes to occur. (In multicellular organisms, only mutations in the germline are relevant in evolution, of course).

As to what happens to alleles, this depends on the environment as well as population size. Genetic drift, which is sampling error, is stronger when samples (i.e., populations) are smaller. Natural selection, which is non-random, is stronger when populations are large.

Whether an allele is fit or unfit (will be subject to non-random natural selection) or neutral (will evolve by random genetic drift) depends on the environment.

Natural selection and genetic drift can happen at multiple levels. The main one is, of course, among organisms within populations, but these can also happen within organisms. Cancer is an example of cell-level selection that is usually suppressed in multicellular organisms.

When it comes to viruses, there are two levels as well: within hosts and among hosts. Because viruses mutate so quickly (by chance, because their repair mechanisms are weak), there can be new variation arising within a single host.

Some mutants will do better within the host — that is, they will be better at invading host cells or will be replicated more quickly than other versions of the virus within a host.

So, there is natural selection within the host.Some mutants will do better at getting into new hosts. For example, maybe they form smaller aerosol particles and spread father when sneezed out. Or maybe they are in high concentration in the nose rather than deeper in the lungs, so they get shed more easily.

The mutant viruses that do best within a host are not necessarily the same ones that do better at infecting new hosts. In fact, a highly virulent version might be very effective at invading host cells but do so much damage that the host never spreads it to another host.

There can be a trade-off between virulence (replication within a host that causes damage to the host) and transmissibility (spread to new hosts). Which versions of a virus evolve depends on the mutations that happen to occur by chance replication errors and the outcome of genetic drift and natural selection both within hosts and among hosts.

Whether viral evolution involves increased or decreased virulence and/or higher or lower transmissibility depends on many factors. Number of replication events happening. Rates of replication errors. Selective pressures within and among hosts. Viral and host population sizes.

Virulence and transmissibility are not the same thing, and there may be trade-offs between them, but it’s also a concern that a virulent (damages or kills the host) virus can still be successful at the host population level if it is able to spread to many new hosts.

Viruses that are both highly virulent and transmissible will eventually run out of hosts to infect, but they can do great damage before that happens.

One of the many positive effects of reducing transmission (e.g., with vaccines, masks, etc.) is that this imposes a selection pressure for less virulence. If only versions of the virus that don’t incapacitate or kill the host manage to reach new hosts, then those are fitter. Reduced transmission also means fewer replication events happening and this means fewer new mutations.

A mild but highly transmissible version of a virus can spread quickly through a population and then fizzle out as hosts become immune, and many people seem to be assuming this will happen with Omicron, but that also means a lot of replication and new mutations.

The Omicron variant in particular has many, many mutations specifically in the spike protein, which is one reason it is so much more transmissible and escapes previous immunity. And this may now be the starting point for new variants.

It is possible that Omicron is milder (than Delta, at least) and that it will infect pretty much everyone and that this will be a step toward SARS-CoV-2 becoming endemic (like flu, requiring seasonal vaccinations).

But it is also possible that Omicron may undergo more chance mutations that make it more virulent as well as highly transmissible. Then it spreading rapidly will mean many hospitalizations and deaths before it runs out of hosts. We do know it is still evolving.

Viruses don’t want anything. They just spread to new hosts or they don’t, and replicate effectively in hosts or they don’t. Mutation, genetic drift, gene flow, natural selection. There are many factors we can’t control, but there are some that we can. We really ought to try.

No photo description available.
Molecular phylogeny of Covid-19 variants. From via T.Ryan Gregory’s posting

Evolution, the Horrible Science – antidote to creationism

EvolveOrDie1For some time I have been looking for a good way to immunise children (and others) against the absurdities of creationism, as the virus spreads  across the Atlantic. I may have found what I’m looking for in the children’s section of my local public library.

Horrible Science – Evolve or Die. Horrible Science is a sister series to Horrible Histories, popular on both sides of the Atlantic, but especially in the UK. This book promises, and delivers, “science with the squishy bits left in”. We learn, for example, what “coprophagous” means, and that rabbits are coprophagous, and why. And what coprolites are. And how this relates to the personal habits of leaf-eating dinosaurs and why we think they must have produced thunderous farts.

All part of a calculated strategy of demystification, which is one of the most delightful things about this book. Scientists are shown disagreeing, admitting ignorance, being proven wrong, being mean to each other, and you could be a scientist too. Children (and adults) who read this book will end up less frightened of science, more impatient with the pomposity, complexity, and jargon that goes with bad science teaching, sceptical about authority, and aware that any scientific claim must be based on evidence and could be overturned by further evidence.

EvolveOrDie2The book does this by example, rather than by exhortation. For example, we have Alfred Wegener being laughed at by his contemporaries, although we now know he was right about how continents drift and even about how molten rock beneath them makes this possible (I never knew he got that bit right too, although as I said in an earlier post it was Arthur Holmes who explained what drives the process). We are given four separate theories about what wiped out the dinosaurs, and when we are told which one is correct (or rather, as the book says, “the one most scientists favour”) we are given a quick rundown of the evidence; cratering on planets and asteroids, other collisions between Earth and smaller asteroids, the monster crater off the coast of Mexico, and the iridium-rich layer laid down some 65 million years ago all over the world. When we are told that the adder’s tongue fern has 630 pairs of chromosomes, we are also told that no one knows why.

We hear about mosquitos, malaria, and mutations, and the evolution of drug resistance by malaria parasites. We are given numerous other examples of evolution, with discussion of how complex organs originated. The wings of pterosaurs could have started out as temperature control membranes, and the lungs of land animals are directly related to those of lungfish. The eye, of course, elaborated in stages from a simple pinhole like the one still found in snails. I would have liked a page or two here on dinosaur feathers, still a rare novelty when the book was first published (1999), but well established by the time of the current (2008) edition.

We are also repeatedly reminded that science is a human activity, and that humans often make fools of themselves. So we have a Hall of Fame, with Lamarck, Darwin of course (not Wallace, though he does get a fair mention), Hippocrates who got inheritance wrong but at least had a go, Mendel, Wegener, Watson and Crick (I’d have liked to see Rosalind Franklin too, of course),[1] and Louis and Walter Alvarez, each of them fleshed out with details of their times, accomplishments (more varied than I’d realized), and at times shortcomings and absurdities.

You are invited to make your own observations; “Could you be a palaeontologist? You need a hammer, goggles, tons of patience!” There follows a very clear explanation of the difference between igneous, sedimentary, and metamorphic rocks, and reasoned advice that sedimentary rocks are what you should be looking at when fossil hunting. The section on Mendel is followed by a suggested experiment on pollen transfer using nasturtiums and a paint brush, and there is a very squishy suggested experiment (see below) to illustrate the principle of continental drift.

EvolveOrDie3An amazing amount of information is clearly and accurately presented in the book’s 142 pages. This includes an excellent account of the species concept, and “the way that one species separates into two” (the book successfully avoids jargon terms such as “speciation”), illustrated by the way that English has diverged between the two sides of the Atlantic. This is used later in a very clear explanation of how hominids and chimps have both diverged over the same length of time from a common ancestor. Not a trivial point. One of the most common and most irritating questions that creationists coach children to ask is “If evolution is true, why are there still monkeys?” A child (or teacher) who has read this book will immediately realise that this makes as much sense as asking “If I descended from my grandparents, why do I still have cousins?”

I particularly liked the way the book treats continental drift. You’re invited to test your teacher by asking for an explanation of the fact that identical mosasaur fossils are found in both South America and Africa (long distance swimming, or riding logs, or vanished land bridges – an explanation that was actually taken seriously for many decades – or identical evolution in both continents, or the two continents having once been joined together). This leads on to the idea of continental drift, and hence to what we grown-ups call biogeography; you find mosasaurs on both sides of the Atlantic, because they evolved before it opened, but the difference between Old World and New World monkeys is the result of evolution since that time.

I do have some criticisms. Much too much is made of “living fossils”, ignoring how far they actually differ from their ancestors. For example, it was already known when the current version of this book appeared that coelacanths are a diverse clade. Of the dozen pages in the section on hominid evolution, one is wasted on Piltdown Man, a forgery exposed 60 years ago. And while it is inevitable that the human evolution section has a rather old-fashioned appearance about it (in 2008, Ardipithecus was only represented by fragments, it was not yet known that humans and neanderthals had interbred, and Australopithecus sediba was still undiscovered), it is nonetheless too apologetic about the deficiencies of the (then) fossil record. After all, The Last Human, which lists 22 separate species, had appeared in 2007. I have already mentioned dino feathers as another development that should have been included in the 2008 update. However, all of these criticisms are at a high level, and reflect my sensitivity towards what the creationists call “weaknesses” in the science of evolution.

I particularly value this book because it builds on what every child knows; the poo-laden squishiness of reality, fascinating, beautiful, and cruel. Children who have read this book will have no difficulty in recognising the creationists’ prelapsarian perfection, with its vegetarian velociraptors and lamb-cuddling lions,  for what it is – so much dino dung. And they will know how best to respond – with a dino-size fart or if, like me, they are pretending to be grown-ups, with a philosophical and factual analysis, which will come to much the same thing.

[1] The central role of experimental crystallography in unravelling the structure of DNA was acknowledged by giving a share of the resulting Nobel Prize to Maurice Wilkins, Franklin’s nominal boss. Franklin herself was by then ineligible because she was dead. She is remarkable for having been involved with two separate Nobel prize winning enterprises, the other one being the structure of the tobacco mosaic virus.

Why I do NOT “believe in Darwin’s theory of evolution”

File:Origin of Species title page.jpgFact not theory; 150 years on from Darwin’s watershed publication; evidence not belief. Words matter.

A recent Harris poll asked Americans “Do you believe in Darwin’s theory of evolution?” Others more eminent have commented on the answers; I would like to comment on the question.

Darwin, of course, never used the word “evolution,” but let that pass. As for the rest, it would be difficult to cram a larger number of serious errors into so small a space. Errors of presentation, of logic, and of scientific and historical fact, all of which play into the hands of our Creationist opponents.

Start with the obvious, the word “theory.” In common language a theory always involves speculation. In academic discourse, it means a coherent set of ideas that explain the facts. Calling something a theory in this sense tells you nothing at all about how certain it is. A theory can be wrong (phlogiston theory), known to be approximate from the outset (ideal gas theory), very close to the truth but since improved on (Newton’s theory of planetary motions), or as certain as human knowledge ever can be (number theory in mathematics). Of course you can explain all this, but you should not put yourself in such a vulnerable position in the first place. It wastes time in debate, or in the classroom. It puts you on the defensive, and thus, paradoxically, confers legitimacy on the attack. It allows the focus to shift from what we know about the world to the words we use to talk about it. This takes us away from science to the domain of the philosophers, lawyers, and expositors of Scripture who are fighting on behalf of Creationism.

And so it distracts from what you should be talking about, namely the facts. Evolution, whether we mean changes in the genetic make-up of populations over time, or the common descent of living things on earth, is a fact. It is supported by, and explains, innumerable more specific facts concerning the fossil record, molecular phylogeny (the same kind of evidence that is used every day in DNA paternity tests), the frozen-in historical accidents of organs that have lost or changed their function, the distribution of species throughout space and time, and much more besides. Creationism cannot explain these facts, except by appeal to the whims of the Creator.

Next “Darwin’s.” Darwin did indeed have a theory, as independently had Wallace, which was that different species had arisen gradually by natural selection operating on variation. This he supported by meticulous observation, but the range of evidence available to him was far more limited than what we have today. He lamented the poverty of the then known fossil record, laments that Creationists echo to this day as if nothing had changed. He knew nothing about mutations or even about the existence of specific genes, and so he had no idea how new variants could arise and spread. His assumption of gradualism is in contrast to later ideas such as punctuated equilibrium, and we now know that much if not indeed most variation arises through neutral drift. Thus not only do we know far more facts about evolution than Darwin could have dreamt of, but our theories, too, incorporate numerous additional concepts.

Finally, worst of all, “believe in.” Believing always carries with it the feeling that disbelief is an option. Some members of the jury believe the witness, others don’t. Some people believe that Hillary Clinton will be the next President of the United States, but no one would say they “believe” that Barak Obama is the current incumbent, because no sane person doubts it. I don’t “believe in” atoms, or gravity, or quantum mechanics, because I regard them as established beyond dispute, although our notions about them will no doubt continue to change as we learn more. And exactly the same is true of evolution.

Does it matter? Yes, it matters enormously. Creationists often maintain that evolution and Creation are both beliefs, whose respective advocates differ, not about observable facts, but about how those facts are to be interpreted. They obsess about Darwin, referring to evolution as “Darwinism,” and to those who accept this reality as “Darwinists.” The aim here is to bypass 150 years of experimental and intellectual discoveries, to bog us down in the day disputes of the late 19th century, or even (“Darwin’s doubt,” see here and here) to enlist Darwin himself as an unwitting ally.  And they contrast evolution, as “only” a theory, with facts or even with scientific laws, in order to claim that it is far from certain and that different views deserve a hearing.

Most people have not thought long and hard about evolution. And in the US at least, much of what they have heard about it will have come from its theologically motivated opponents. These opponents, whether through “statements of faith” that make obscurantism a virtue, or through “academic freedom bills” that disguise telling lies to children as open intellectual debate, use carefully crafted words to stake spurious claims to the moral high ground.

We should not, ourselves, be using words that help them do this.

No evidence for evolution, says the Reverend

The Rev David Blunt is Minister at North Uist and Grimsay Free Church of Scotland (Continuing), Bayhead, North Uist, not to be confused (Heaven forbid!) with the benighted folks at North Uist, Grimsay, and Berneray Free Church of Scotland, Carinish.

He subscribes to a catechism that states that unless God arbitrarily decides otherwise, I (he, too, come to think of it) am “foreordained to dishonour and wrath, … to the praise of the glory of his (God’s,not the Reverend’s) justice” because of the guilt of Adam’s first sin, rendering us liable to “everlasting separation from the comfortable presence of God, and most grievous torments in soul and body, without intermission, in hell-fire for ever.”

If he really believes that  that is what he believes and preaches, that is no one’s business but his own and his congregations (although I would have grave misgivings should he be preaching such sadistic doctrine to children.)

The Reverend also believes that the devil seeks to confuse us through the teaching of evolution, and  that everything was created over a period of six days, and in order to justify this belief he takes from time to time to the pages of the Hebridean News, where he tells us that

The notion that evolution is responsible for a process of development in living things, beginning with microbes and leading ultimately to men, must be rejected as there is not a single proven fact to support it.

I initially responded,

The Rev David Blunt says that “there is not a single proven fact” to support evolution. If he goes to the website he will find, spelt out in detail, 29 separate arguments and hundreds of supporting facts that show that evolution is true. If he goes to the Biologs website, and looks up Dennis Venema, he will find a brilliant explanation of all this by a  devout evangelical.

If the Rev does not choose to inform himself about the facts,that is his business. But he denies their existence, he is bearing false witness.

The Reverend is clearly a fast reader, since within two days he had digested the 60 or so sections in talkorigins, and Dennis Venema’s excellent 28-part series. And so he was able to reply:

The sort of ‘facts’ which are essential for the theory of evolution to be true include the following: the existence of mutations representing the increase in genetic information necessary to arrive at more advanced life forms; the existence of life forms (extant or extinct) which are obviously transitional in character; the existence of billions of years of time.

Mutations … overwhelmingly detrimental… We still look in vain for specimens which are intermediate between one life form and another. The fossil record, which Darwin expected to provide examples of missing links, has yet to yield them.

Aeons of time are crucial to the theory of evolution yet it cannot be proved that the earth is billions of years old: indeed many scientific facts point to a much younger earth… [Evolution] must be able to account not simply for microbes to men but molecules to men – or even more precisely – particles to people. In other words it must be able to explain how life can arise from non-life. That is a real leap of faith!

There is no observable evidence for the theory of evolution. It is not testable over time and cannot be verified.

My response:

To pretend that biological evolution has to include an explanation of the origins of life is at best mistaken, at worst dishonest. Consider that before the 1950s, we did not know the origin of atoms. Nonetheless, atomic theory had been the central concept of chemistry since before the 1820s. Similarly, we do not know the origins of life, but evolution has been the central concept of biology since before the 1870s.

No one doubts that most mutations are harmful. A few of them do increase fitness. Harmful mutations are bred out, while fitness-enhancing mutations spread. It’s really that simple. Indeed, the whole of plant and animal breeding is one vast demonstration of evolution, albeit evolution directed by us rather than by the pressures of the natural environment. The Rev Blunt admits the occurrence of evolution under the pressure of artificial selection. How then can he claim that it is in principle impossible under natural selection, or that evolution has never been verified?

Australopithecus afarensis skull, through
Museums are full of intermediate forms, if not the great-great-grandparents of living species, then at any rate their great-uncles. If the Rev cares to visit  (free article) he will find a whole series of intermediates between land mammals and present-day whales. If he visits the Smithsonian museum‘s site at, he will find out about over a dozen extinct species intermediate between apes and modern humans. If evolution is not true, why were these intermediates ever created?The age of the Earth is dated at over 4 billion years using some half-dozen different radiometric techniques. These the Rev Blunt will find explained, by an evangelical Christian, at “Radiometric Dating – A Christian Perspective“. We have known since 1928 that radioactive decay rates depend on the general laws of physics. If these had been different 4 billion years ago, the rocks wouldn’t have formed in the first place. If they had been almost 1000 fold faster in the past, as Young Earth creationists must claim, the rocks would have been melted by the heat produced.

I conclude by pointing out that the fossil record clearly shows that whales are descended from land mammals. Yet Genesis states that whales were created on Day 5, and land mammals on Day 6. One of two things follows. Either Genesis is not, and was never meant to be, a science textbook. Or God has deliberately deceived us by creating a highly detailed but totally misleading fossil record.
This is a choice that each of us has to make in our own way. There are no alternatives.
I predict that the Reverend will reply, challenging me to turn a bacterium into a biochemist within the timescale of a research grant.
Update: Actually, rereading his material, I see that he did better than that, accusing me of clutching at whiskers (that’s a good line, I think I’ll use it) in my discussion of whale phylogeny, repeating the claim, long since refuted,  that data from Mt St Helen’s shows radiometric dating to be unreliable, and finally asserting that the only valid evidence is eye-witness evidence.
There is no eye-witness evidence of the Ice Ages, which helped shape the mountains of North Uist. Does the reverend therefore think they never happened?
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