Category Archives: Evolution
Discussions about the nature of science and scientific theories are often confused by the outdated view that such theories are rendered false when anomalies arise. The notion of a scientific theory as a static object should be replaced with the more current view that it is part of a living research programme, which can broaden its scope into new areas.
For example, take the hypothesis that all swans are white, which seemed pretty good to Europeans until Dutch explorers found black swans in Australia in 1636. So what happens to our hypothesis? There are a number of options.
1) Redefine swan-ness to include whiteness. Then black swans aren’t really swans, and the hypothesis remains true by definition.
2) It’s been disproved. Discard it.
3) Compare different species of swan the world over, and see how well black swans fit in.
(1) is the least useful. Definitions can only tell us about how we are using words. They tell us nothing about the world that those words attempt to describe. (2) is based on the common-sense idea that hypotheses should be discarded when falsified by observation. This was the idea put forward by philosopher Karl Popper in the 1930s, to distinguish between science and pseudoscience.
He saw psychoanalysis, for example, as pseudoscience because disagreement with its findings can always be explained away as a result of repression. Popper’s 1930s view has a great deal to commend it, but throws out a lot of babies with the bathwater. (3) is how science actually works, as Popper and his colleagues, who challenged traditional views of how science works, had realised by the 1970s. https://www.youtube.com/embed/mE590aeTdqE?wmode=transparent&start=0 GoJo Media/YouTube.
In our example, the black swan was an anomaly, but any major scientific theory will have anomalies. Newton’s theory of planetary motion could not explain the orbit of Mercury, an anomaly that was known for decades before Albert Einstein explained it with his general theory of relativity. Despite this anomaly, Newton’s theory was retained because there is so much that it does explain. A theory is not meant to be a final statement of how things are, but just the latest stage of a research programme in continual progress.
Evolution as theory and research
In the 18th century, the existence of family relationships between different species was spelt out in the Swedish naturalist Carl Linnaeus’s grouping of living things into species, genera, orders and so on, but there was no suggestion of how things got that way. By the 1820s, the French biologist Jean-Baptiste Lamarck was talking about inheritance of characteristics acquired as the result of striving (as the giraffe’s ancestors strived to reach higher into the trees).
By 1859, naturalist-biologists Charles Darwin and Alfred Russel Wallace independently came up with the idea of natural selection as the primary driver of evolution. Natural selection, that is, operating on variation, but with no understanding of where the variants came from, or how that variation was inherited.
In the early 20th century came the discovery of mutations as a source of variants and the incorporation of the Austrian botanist Gregor Mendel’s genetics into evolution science, but as yet without knowledge of the material basis of mutation and inheritance. This emerged in the 1940s, when DNA was recognised as the genetic material. Then from the 1950s onwards there was the determination of its structure and the cracking of the genetic code that revealed how it directs the formation of proteins.
Since then, we have recognised that evolution is governed by chance as well as by selection, that inheritance is complicated by things like gene duplication (where a chunk of DNA is copied twice and each copy can then evolve independently), horizontal gene transfer (where DNA is transferred between species), and even the incorporation of genetic material from viruses into our own genetic material. And of course there are plenty of other things that we still don’t understand … Yet.
So at every stage, we have an imperfect theory, full of gaps and inconsistencies, but one that emerges all the stronger from scrutiny of its imperfections. Like atomic theory, it has developed in ways that its originators could not even have imagined, with growing understanding at all levels from individual molecules to the genetics of populations. And like atomic theory it is fundamental to our understanding of the science that has grown up around it. Biology without evolution is like chemistry without atoms.
The possibility of correction
Sometimes we tells students that “the scientific method” consists in gathering data, formulating hypotheses to explain them and then collecting more data to see if the hypotheses stand up. At other times, we tell them that it consists in formulating hypotheses, collecting data and rejecting the hypotheses if the data don’t fit. Such views are much too simple and make scientific research sound like following a rather boring recipe.
The first step in any scientific enquiry is deciding that something is worth looking at. So the possible results must be worth having and the research programme must have some prospect of success. The next thing is continual dialogue between hypotheses and data. The hypotheses must be open to modification in the light of the data and must always remain open in principle to correction in the light of further knowledge. This commitment to the possibility of correction is known as fallibilism, and is one thing that all scientific endeavours have in common.
Beyond that, I see no point in pretending that science has a single method (it doesn’t), or in trying to draw a hard and fast line between scientific knowledge and other kinds of knowledge about the world (there isn’t one).
What about the swans?
Meantime, DNA evidence shows that the different white swan species whooper swan, tundra swan and mute swan are closely related, with the Australian black swan as their first cousin. Surprisingly, the black-necked swan of South America is a more distant relation.
Other questions suggest themselves. Is there any link between geographical distribution and closeness of relationship? When and where did the separate species arise? Do the differences in colour have any survival value, and if so, what?
So by now, our original swan hypothesis, based on appearance, has been greatly modified, and given rise to a whole range of new questions involving molecular similarities, adaptive evolution vs neutral drift, biogeography and the fossil record. That’s science.
An Immense World; How Animal Senses Reveal the Hidden Realms Around Us, Ed Yong, Random House/Bodley Head, June 2022
This book is an enormous achievement. A thrilling read, taking us into the Umwelt, or perceptual world, of numerous mammal, fish, reptile and insect species. A major work of scholarship, with over a thousand references to a 45-page bibliography, as well as accounts of interviews with numerous researchers and visits to their laboratories. An exploration of many ways of sensing the world, some of which we share, while others are beyond our imagining. The evolving interplay of perception and action, communication and deception, environment and response. And an enhanced insight into what it is like to be a bat, a bird, a blue whale, a beetle, or a human.
From the wealth of detail in the book, a consistent grand narrative emerges. Some physical process interacts with living matter. This is the raw material for sensation. Sensory abilities then shape a creature’s Umwelt, being developed according to the demands of its environment. But every perceiver is itself an object of perception to others, and we have colour displays and camouflage, smells as signals and identifiers, sound as communication to others and, by echolocation, back to the creature who generates it, and the same is true of other senses that we do not share, such as the detection of tiny electrical fields. Senses combine and even, we suspect, merge, and what we ourselves perceive is but part of an immense pattern. But the heedlessness with which we amplify our own signals disrupts this pattern, contributing to our destruction of nature, and we ourselves are the poorer for it.
Let me offer a few samples from the book’s wealth of detail.
Yong starts with taste and smell, two ancient senses that operate by direct molecular contact. It is not long before he surprises us. Snakes use their forked tongues to smell in stereo. Humans are poor compared with other mammals at detecting smells at low levels, but are rather good at telling different smells apart. No one knows how smell relates to chemical structure (contrast this with how seeing relates to the wavelength of light, hearing to frequency, or touch to pressure). As every well-trained dog-owner knows, smell is central to the Umwelt of dogs, but I would never have guessed that the same is true of elephants. And the molecules involved in smell include opsins, which are central to vision. As Yong puts it, in a way we see by smelling light.
It is sometimes said that dogs, and most other mammals, are colour blind. This is only half true; they have just two kinds of colour receptors, while we (like other apes, and our cousins the Old World monkeys) have three. The colours that we perceive arise from subtle interactions between these receptors. Thus some neurons are excited by blue cones but inhibited by red or green, while others are stimulated by red but inhibited by green. So the colours are we experience are the result of a kind of neuronal arithmetic, below the level of conscious awareness. I still feel surprise when someone superposes red and green beams of light on a screen, and I see the result as pure yellow. Our colour vision can be represented by a triangle, with red, blue, and green at the corners, and yellow halfway along one edge.
But hummingbirds, like many birds and reptiles, can see four kinds of colour; red, green, blue, and UV. If human colour vision can be represented by a triangle, that of a hummingbird is a pyramid. And while for us the overlap of red, green, and blue are enough to produce white, four kinds of sensor need to be activated to look white to a hummingbird.
Among humans, different individuals have slightly different sensitivities, and some women show a degree of four-colour vision, having inherited different pigments from the sites on their two separate X chromosomes that are responsible for colour vision. Words cannot convey this added perceptual dimension, but the fact that they really do have four-colour vision can be demonstrated by discrimination tests. (This by the way answers a philosophical riddle that intrigues me. How do I know that you are seeing colours the same way that I am? It turns out that there is a real chance that you aren’t.)
Many flowers that appear white to us are coloured in the UV, and appeal to insect pollinators with green, blue, and UV three colour vision. And UV vision evolved in insects long before there were flowers, so the flowers evolved the pigments to attract the pollinators. Thus the ability to see directly influences the evolution of what is there to be seen.
Temperature detection overlaps other senses. There are sensors that can detect hot or cold temperatures, but can also be stimulated in different ways. The sensor for painful heat can be activated, on the skin as well as in the mouth, by habanero peppers, while menthol feels pleasantly cool in the mouth or the smoker’s throat. Menthol also happens to be addictive.
The ability to detect heat at a distance is useful to species that suck blood, from bedbugs and mosquitoes to vampire bats. Ticks can detect body heat from up to 13 feet away, and common insect repellents work with them, not by interfering with smell, but by blocking the heat sensors. These sensors are in spherical pits on their legs, and the pits are covered by a film with a hole in it. So the sensors give directional information as well as detecting the heat source. Rattlesnakes and other pit vipers also have pits with a narrow opening, falling on a sensing membrane that carries around 7000 nerve endings. They can detect the presence and approximate direction of an increase in temperature of 0.001oC, which means that a viper can locate a rodent 1 m away. Information from the temperature sensing pits is combined with information from the eyes, so maybe for them the sense acts as an adjunct to vision, rather than on its own.
Touch organs can be modified for special purposes. The emerald jewel wasp paralyses cockroaches by stinging their brains, and has a touch sensor at the end of her sting to locate the exact location. A wide range of mammals, including the opossum, a marsupial, as well as rats and mice, use touch sensors at the base of whiskers to explore their surroundings several times a second. Since each whisker has its own connection to the somatosensory cortex, this builds up a map of the surroundings. So whisking, as it is called, is perhaps more like seeing than like touch. It would seem to be a very ancient trait indeed, since the last common ancestor of placentals and marsupials was back in the age of dinosaurs. The whiskers of seals are so shaped and angled as to minimise the forces on them as they move through the water, which would otherwise overpower the pressure waves caused by passing fish.
Sound detection is fast, precise, 24 hour, and useful for detecting predators or prey. Sound is also used in communication, as in the finding and assessment of mates. But mating calls come at the cost of giving away one’s location. There is a species of parasitic fly that has developed ears remarkably similar to those of the crickets it preys on, to eavesdrop on their mating calls. On Hawaii, which was once seriously infested by such flies, the crickets have fallen silent. Once again, the overlapping Umwelten of prey and predator drives evolution.
Surprisingly, the first insects were almost certainly deaf, since hearing has evolved separately among them at least 19 different times, on many different parts of the body, having in general been developed from organs that respond to vibration and pressure.
We can only detect parts of how animals use sound to communicate. Birdsong contains more structure than the human ear can resolve, unless it’s played back slowly. In fact, the structure within each note may be more important to the birds than the order that the notes are played in. Whales and elephants both use what we call infrasound, vibrations too low in pitch for our ears to hear, as a way of keeping in touch over long distances. Mice, however, communicate using ultrasound, frequencies too high for us to detect. The terms infra and ultra are arbitrary, relating to our own capacities, but since we are deaf to such sounds they were not even detected, let alone studied, until a few decades ago, and may be much more important in nature than we realise.
Echolocation in particular may be much more extensive than our knowledge of it, when it uses frequencies that our own ears cannot detect. Even bat echolocation, although suspected much earlier, was not clearly demonstrated until 1938. It enables bats to navigate and catch insects in complete darkness. This is an impressive feat; the bats need to generate short pulses of high-frequency sound, and then detect the direction and timing of the faint echo from a small moving target. Some bats can even tune their ears to respond to a frequency slightly different from the one they are emitting, and detect the movement of their prey using the Doppler effect. 
But moths are not merely passive prey. They have ears that can detect bat cries, and dodge and loop to evade capture. Tiger moths produce clicks of their own, which confuse the bats. Some moths even have long flexible tails at the end of their wings, which may also add to the confusion.
Infrasound echolocation by dolphins was detected in the 1950s, and since the 1960s the U.S. Navy has been training them to find sunken equipment and mines, and aiming to reverse engineer their abilities. Humans avoid walking into obstacles using echolocation, and some blind people have developed this to a high skill, building up a model of the world in their visual cortex, in much the same way that most of us do so using sight.
Darwin was puzzled by so-called electric eels, which use electric shocks to stun their prey. After all, evolution regards present organs as the result of a series of incremental improvements, but what use would the electric organ have been in its feeble first stages of development? It took a century to find the answer. Many fish possess a lateral line, sensitive to pressure, and in some cases this has been modified to detect electricity. This confers an obvious advantage, since any living thing moving through water generates tiny electric currents. And electrodetection gains in sensitivity and acuity when combined with the ability to generate one’s own more powerful electric field. So we have passive electroreception and active electroreception, just as we have hearing and the use of echoes. The cells that detect the electrical fluctuations are hair cells, basically similar to the same cells that detect pressure waves on the lateral line, or pressure oscillations in our own ears. Active electroreception operates in every direction, will work as well in cloudy as in clear water, and is so sensitive that some fish can be trained to detect the difference between a clay pot full of river water, and one also containing an insulating glass rod.
Passive electroreception is extremely widespread among vertebrates, being used by sharks, catfish, and salamanders, while the platypus has over 50,000 electroreceptors in its bill. Bumblebees can detect the electric fields that surround flowers, and it may well be that electroreception is much more common than we as yet realise among insects, equipped as many are with touch- and current-sensitive hairs.
Yong concludes his list of the senses with the ability to detect magnetic fields. This is a difficult area, if only because magnetic effects are extremely weak, and show subtle variations on a global scale in direction, intensity, and angle of dip relative to the surface. To complicate things further, no one even knows what the magnetoreceptor would look like or how it operates. Some bacteria grow small crystals of magnetite, and can distinguish North from South, but no one has managed to find similar structures in the birds and animals that are known to use magnetic fields as an aid to migration. One current theory invokes what are called radical pairs, molecules raised to high-energy states by the influence of light, but such states are short-lived, and I as a chemist would require a lot of convincing.
Senses interact. Mosquitoes are attracted by body warmth, but only if they can smell carbon dioxide. Electric fish that have learnt to distinguish shapes using their electric sense are then able to do so by sight, and vice versa. I have already mentioned how the mental maps constructed by blind people, who have learnt to navigate using echolocation, reside in the visual cortex. And finally, we need to remember that sensation requires discriminating between the signals that come to an organism from outside, and those that it generates by itself.
So all complex animals, including ourselves, perceive only a small part of the immense world of possible sensations, and construct their own Umwelt from the part accessible to their own senses. But we show brutal insensitivity in how we influence this world. We brighten the night sky and blur the distinction between the seasons, confuse forest insects with the sound from our machines, scatter huge amounts of material that must distract the sense of smell, and make the very oceans reverberate, so that whales navigating by infrasound end up stranding themselves in response to naval sonar.
And when did you last see the Milky Way?
Ed Yong’s earlier book, I contain multitudes: the microbes within us and a grander view of life, was a New York Times bestseller, and in June 2021 he received a Pulitzer Prize for Explanatory Reporting for his writing on the COVID-19 pandemic
1] Red colour perception evolved by accidental duplication of the gene that codes for the green-sensitive receptor, followed by Darwinian selection for a new use – the ability to detect ripe fruit, or tender young leaves, against a green background. A nice example of how evolutionary change generates new information.
2] Yong does not tell us how we know this, and to do so would have required a chapter in itself. But, in brief, the methods involve cross-species comparisons, and, these days, the use of molecular biology to reconstruct family trees for the relevant genes. The simplest assumption is then that a trait prevalent in one particular clade was present in its last common ancestor.
3] This is the familiar increase in the perceived frequency of a sound wave when the distance between source and observer is decreasing. Here the decrease is in the length of the round trip, from bat to target and back again, but with further fine tuning from the motion of the prey, and even the flapping of a moth’s wing has a detectable effect.
This post first appeared in 3 Quarks Daily
The Ark Encounter, an evangelical theme park located near Williamstown, Kentucky, has welcomed between 4 million and 5 million visitors since its opening in July 2016. Hundreds of thousands more are sure to visit this summer.
This theme park boasts a re-creation of the story of Noah’s Ark from the Bible. As described in Genesis 6:14-16, God directed Noah to build this ark to spare eight humans and a male and female pair of every kind of creature from the flood that God was going to unleash on the world as a punishment for sin.
As scholars of fundamentalism and creationism, we have visited the Ark Encounter multiple times. We have also written a book, “Righting America at the Creation Museum,” about the ark’s companion site, the Creation Museum in Petersburg, Kentucky.
What we find particularly striking about Ark Encounter is that it is a tourist site devoted to emphasizing – with great specificity – the wrathful nature of God and the eternal damnation that awaits unrepentant sinners.
What is Ark Encounter’s argument?
According to Answers in Genesis, the fundamentalist organization that launched Ark Encounter, and its CEO, Ken Ham, Ark Encounter is a centerpiece of AiG’s mission to “expose the bankruptcy of evolutionary ideas and bedfellow: a ‘millions of years old’ earth (and even older universe).”
So, according to AiG, when Genesis 1 says God created the Earth in six days, it literally means six 24-hour days. Similarly, when the Bible says Adam and Eve were created on the sixth day and gives details about their descendants and how long they lived, this is interpreted as recounting real history. And all of this means that, according to AiG, the Earth is “about 6,000 years old.”
While scientists have estimated the Earth to be about 4.5 billion years old, AiG counters by claiming that radiometric dating is not reliable. Instead, they assert that the catastrophic biblical flood created all the geological formations that make the Earth look ancient.
Over the past few decades, this argument has become a doctrinal touchstone for many American evangelicals.
An enormous structure
We most recently visited the Ark Encounter on March 15, 2022. Measuring 510 feet (155 metres) long, 85 feet (25 metres) wide, and 51 feet (15 metres) high, the Ark Encounter is, to quote one visitor we overheard, “so huge!”
After purchasing tickets that cost US$54.95 per adult, we and other visitors boarded buses and made the ascent up a long hill. Getting off the bus, we walked to the Ark, keenly aware of how small we were in relation to this ginormous structure.
Inside the Ark, visitors walk through three enormous decks, encountering rows of clay food storage containers, burlap sacks and animal cages. They observe over 100 bays featuring placards and digital animations that, among other things, go far beyond the Bible to explain Noah’s training in shipbuilding, carpentry and blacksmithing. The same creativity applies to the various displays explaining how eight human beings on the Ark fed, watered and managed the waste of 7,000 or so creatures.
Visitors also walk through a life-size diorama of the plush living quarters of Noah’s family, where they learn about the skills, gifts and interests of Noah’s sons – details not included in Genesis. They also learn about Noah’s wife and his sons’ wives. The Bible never identifies these women by name, much less describes them. Nevertheless, the Ark gives them names, different ethnic complexions, biographies and even hobbies.
Notwithstanding the occasional placard acknowledging that designers have taken “artistic license” with these dioramas, we couldn’t help but notice how much of what is in the Ark is not actually found in the Bible.
But visitors to the Ark seem to embrace these dramatic additions to the biblical text. As religion scholar Paul Thomas observes in his new book, “Storytelling the Bible at the Creation Museum, Ark Encounter, and the Museum of the Bible,” the world created by the designers of the Creation Museum and Ark Encounter satisfies the evangelical longing “for a time and place governed by biblical principles, even if that idealized time and place … never really existed.”
A very angry God
AiG requires all Ark Encounter employees to affirm a 46-point faith statement. They must agree, for example, that “gender and biological sex are equivalent and cannot be separated,” modern understandings of “social justice” are “anti-biblical,” and all humans “are sinners” and “are therefore subject to God’s wrath and condemnation.”
This emphasis on the overwhelming wrath of God is perhaps the most noteworthy feature of Ark Encounter as a tourist site.
Genesis 7:16 states that, as the flood waters rose, God slammed shut the door into the Ark. Once shut, all the humans and animals on the other side of the door were doomed to drown.
According to a placard displayed at Ark Encounter, there may have been upwards of 20 billion people on Earth at the time of the Genesis flood, a number that would have included children and infants, not to mention the unborn.
Another placard asks, “Was it just for God to judge the whole world?” The answer: “Since He is the one who gave life, He has the right to take life. Secondly, God is perfectly just and must judge sin. Third, all have sinned and deserve death and judgment.”
Remarkably, Ark Encounter has placed a “keepsake photo” placard near the door that, in the Ark’s depiction, sealed the fate of all those on the other side. As we have witnessed every time we have toured Ark Encounter, happy visitors line up to have their photos taken in front of this door.
According to AiG, this ancient divine slaughter prefigures a future divine slaughter. As the Ark Encounter website puts it, “God will judge this wicked world once again, but this time it will be by fire … God always keeps His promises – judgment will come.” According to AiG, we can escape this fate by believing in Christ, but for the billions (past and present) who have not or do not, the result is “everlasting, conscious punishment in the lake of fire (hell).”
As historian Doug Frank makes clear in his 2010 book, “A Gentler God,” this understanding of a wrathful God is alive and well in American evangelicalism. Frank’s argument is supported by a 2014 Pew Research report that revealed that 82% of American evangelicals believe in a literal hell.
Millions of evangelicals visit Ark Encounter for all sorts of reasons, including, perhaps, its sheer immensity. That said, the message they get from Ark Encounter is clear and simple.
The wrathful God has determined that those who do not accept Jesus as savior, those who are resolutely on the wrong side of culture war issues like abortion and LGBTQ+ rights, will pay for their sin eternally.
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.
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.
A friend asked me why I bother about creationism. This article spells out my reasons. It has had some 150,000 reads since first published in The Conversation in February, and has been featured in Snopes and Yahoo! News, and attacked by Ken Ham and Bodie Hodge of Answers in Genesis, Jake Hebert Ph.D [sic] at the Institute for Creation Research, and others.
Many people around the world looked on aghast as they witnessed the harm done by conspiracy theories such as QAnon and the myth of the stolen US election that led to the attack on the US Capitol Building on January 6. Yet while these ideas will no doubt fade in time, there is arguably a much more enduring conspiracy theory that also pervades America in the form of young Earth creationism. And it’s one that we cannot ignore because it is dangerously opposed to science.
In the US today, up to 40% of adults agree with the young Earth creationist claim that all humans are descended from Adam and Eve within the past 10,000 years. They also believe that living creatures are the result of “special creation” rather than evolution and shared ancestry. And that Noah’s flood was worldwide and responsible for the sediments in the geologic column (layers of rock built up over millions of years), such as those exposed in the Grand Canyon.
Such beliefs derive from the doctrine of biblical infallibility, long accepted as integral to the faith of numerous evangelical and Baptist churches throughout the world, including the Free Church of Scotland. But I would argue that the present-day creationist movement is a fully fledged conspiracy theory. It meets all the criteria, offering a complete parallel universe with its own organisations and rules of evidence, and claims that the scientific establishment promoting evolution is an arrogant and morally corrupt elite.
This so-called elite supposedly conspires to monopolise academic employment and research grants. Its alleged objective is to deny divine authority, and the ultimate beneficiary and prime mover is Satan.
Creationism re-emerged in this form in reaction to the mid-20th century emphasis on science education. Its key text is the long-time best seller, The Genesis Flood, by John C Whitcomb and Henry M Morris. This provided the inspiration for Morris’s own Institute for Creation Research, and for its offshoots, Answers in Genesis and Creation Ministries International. [Note added: Ken Ham points out in his rebuttal that Answers in Genesis arose independently of the Institute for Creation Research, and that his article concerning denial of divine authority, cited in the previous paragraph and below, does not mention Satan by name.]
Ken Ham, the founder and chief executive of Answers in Genesis, is also responsible for the highly lucrative Ark Encounter theme park and Creation Museum in Kentucky. As a visit to any of these websites will show, their creationism is completely hostile to science, while paradoxically claiming to be scientific.
Demonising and discrediting
These are common conspiracy theory tactics at play. Creationists go to great lengths to demonise the proponents of evolution, and to undermine the overwhelming evidence in its favour.
There are numerous organisations, among them Biologos, the American Scientific Affiliation, the Faraday Institute, and the Clergy Letter Project, which describes themselves as “an endeavour designed to demonstrate that religion and science can be compatible”, that is, promoting evolution science within the context of religious belief. Even so, creationists insist on linking together the separate topics of evolution, materialist philosophy, and the promotion of atheism.
According to Answers in Genesis, evolution science is a work of Satan, while former US Congressman Paul Broun has described it as “a lie straight from the pit of hell”. When he said that, by the way, he was a member of the House of Representatives Committee on Science, Space, and Technology.
Like other conspiracy theorists, creationists immunise themselves from fact-based criticism. They label the study of the past as based on unprovable assumptions, thus disqualifying in advance the plain evidence of geology.
They then attack other evidence by focusing on specific frauds, such as Piltdown man – a hoax skeleton purportedly of a missing link between humans and other apes that was debunked more than 60 years ago – or the dinosaur-bird amalgam “Archaeoraptor”, discredited by sharp-eyed scientists before ever making it into the peer-reviewed literature (although not before making it into National Geographic).
One favourite target is Ernst Haeckel, whose pictures of embryos, published in 1874, are now considered to be seriously inaccurate. However, they do correctly draw attention to what most matters here: the features shared during development by different organisms – including humans – such as gill arches, a long tail, and eyes on the side rather than the front of the head, confirming they have a common ancestry.
Haeckel’s name appears on the Answers in Genesis website 92 times. He is also the subject of a lengthy chapter in Jonathan Wells’ Icons of Evolution; Science or Myth?. This book, which even has its own high school study guide, was what first convinced me, back in 2013, that creationism was a conspiracy theory.
It is a splendid example of creationist tactics, using long-rectified shortcomings (such as those in early studies on Darwinian evolution in peppered moths, in response to changing colours following reduced pollution) to imply that the entire science is fraudulent. Wells has a real PhD in biology, a PhD acquired with the specific goal of “destroying Darwinism” – meaning evolution science – from the inside.
Wells is a senior fellow at the Discovery Institute, a conservative thinktank which promotes creationism under the banner of “Intelligent Design”, and is also linked to other conspiracy theories, such as claims that the consensus on climate change is bogus, and that last November’s US presidential election was stolen. An article by a senior fellow at the Discovery Institute on the subject has now being removed from its website, but can be found here.
Conspiracy theories are always driven by some underlying concern or agenda. The theory that Obama’s birth certificate was a forgery, or that the 2020 US election was stolen, are about political legitimacy and will fade as the politicians promoting them fade from memory. The idea that COVID-19 does not exist is proving a little harder to dislodge, but scientists, such as those behind Respectful Insolence, are organising to fight back on science denial and misinformation.
I fear that the creationist conspiracy theory will not be so short-lived. It is driven by a deep-seated power struggle within religious communities, between modernists and literalists; between those who regard scripture as coming to us through human authors, however inspired, and those who regard it as a perfect supernatural revelation. And that is a struggle that will be with us for a long time to come.
Western Washington University, a well-respected publicly funded university in Bellingham, WA, is conducting a review of the naming of its buildings, in the course of which demands were expressed for the renaming of the [TH] Huxley College of the Environment, and as a result the University’s Legacy Review Task Force has invited comment. Background information including links to solicited academic comment is available at https://president.wwu.edu/research-and-resources.
My own initial reaction was outrage, but closer examination convinced me that serious engagement is a more appropriate response, given aspects of Huxley’s legacy of which I was not aware. There is no doubt, however, that the movement to rename is seriously misguided, and can be traced back to the long-standing creationist tradition of pretending that evolution science is responsible for racism. The attack on Huxley, as spelt out in a submission by one member of the Task Force (Why is TH Huxley Problematic?) has therefore evoked a detailed rebuttal by Glenn Branch of the [US] National Center for Science Education.
With the encouragement of a WWU faculty member, I have drafted the following letter, for which I invite signatures. If you wish to add your name, and especially if you have some academic, educational, or related standing, and please let me know, either by comment here or by email to me at psbratermanATyahooDOTcom, giving me your name, and position(s) held. I will then include you among the signatories when I forward the letter to Paul Dunn email@example.com – President’s Chief of Staff and Chair of the Task Force, with copy to Sabah Randhawa firstname.lastname@example.org – President of the University. Alternatively, you may wish to write to them directly as an individual.
We welcome the opportunity to comment on the proposed renaming of Huxley College of the Environment.
We are used to making allowances for people of the past, on the grounds that their behavior was conditioned by their time and place. For example, your own University, and the State that it serves, are named after a slave-owner. But Huxley, his detractors may be surprised to hear, requires no such forgiveness. Like most Englishmen, and most scientists, of his time, he believed in the racial superiority of Europeans, and this misguided perspective affected his anthropological studies. It did not, however, affect his progressive social outlook, and as the evidence submitted to the Task Force shows, he was deeply opposed to slavery and to all forms of unequal treatment and discrimination, argued in favor of equal treatment for women and against Spenserian “Social Darwinism”, and campaigned vigorously on behalf of Abolition during the American Civil War.
The attack on Huxley has deep roots, and is part of a wider creationist strategy to discredit evolution science. For this reason, the case has attracted attention from as far away as Scotland and New Zealand. The creationist connection accounts for the presence, among critics of Huxley cited in support of renaming, of the creationist Discovery Institute, and of Jerry Bergman, associated with Creation Ministries International, among other suspect sources. Ironically in this context, Bergman once wrote for support to the National Association for the Advancement of White People.
However, despite these tainted connections, current discussion of renaming at Western Washington is part of a praiseworthy worldwide process of re-evaluation, and student involvement in this is to be commended. It may therefore be helpful to display prominently in the Huxley Building a brief summary of his achievements, including his campaigning against slavery, and on behalf of equal treatment for women, in which he was far ahead of his time.
Courtroom Sketch of Ken Miller testifying at the Dover trial, via betterrightthanhappy
The lesson of Kitzmiller: Science bridges divides, by Nathan H. Lents and S. Joshua Swamidass, Dec 28, 2020 , shows how the Kitzmiller trial itself, and, more generally, the defence of science against obscurantism, bridges the gulf between believers and nonbelievers. My own view is that the deeper gulf is one found within all three Abrahamic religions, between those who are willing to accommodate their reading of the sacred texts to scientific (and I would add historical) reality, and those who insist that these texts, literally interpreted, are the infallible word of God.
Ken Miller, Genie Scott & Barbara Forrest: 15 Years After Dover, by Faizal Ali, Dec 26, 2020, with links to interviews of three major participants; Ken Miller, Eugenie Scott, and Barbara Forrest. As many readers will know, Ken Miller, biology professor and major textbook author, has been defending evolution against creationist attacks for 40 years, Eugenie Scott was at the time director of the (US) National Center for Science Education, which acted as consultant to the plaintiffs and was instrumental in forming the legal strategy, and Barbara Forrest, philosopher, testified that the trial that Intelligent Design should not be considered science because of its reliance on the supernatural.
As this blog piece points out, that last argument (technically: intrinsic methodological naturalism) should give us pause, and is now rejected by many philosophers and scientists, including me, in favour of a provisional methodological naturalism that would be willing to examine supernaturalist explanations on their merits, if they had any. Indeed, the piece argues that judge Jones’ blistering verdict in this case was only made possible by the incompetence of the School Board, who made their religious motivation obvious.
The Discovery Institute continues to claim that Kitzmiller was wrongly decided, and even that “recent scientific discoveries have confirmed and extended the concept of irreducible complexity.” https://www.discovery.org/2019/01/revolutionary-michael-behes-intelligent-design-documentary-is-now-free-online/ Most recently, to mark the 15th anniversary of the trial, the DI featured a debate on the issues https://www.discovery.org/v/the-kitzmiller-v-dover-trial-and-intelligent-design-fifteen-years-on/ between Michael Behe and Joshua Swamidass. While I have a poor opinion of Behe’s ideas, I admire his willingness to discuss them. I would also praise him for not abandoning his post at the trial when things got difficult, unlike several of his Discovery Institute colleagues.
I was curious to see what are the major creationist organisations had to say about the trial, even though they were not directly involved. Answers in Genesis mentions Kitzmiller as part of a recent (December 2020) long discussion of US court cases, claiming that “The Kitzmiller ruling has stifled debate in classrooms and prevented full discussion of topics related to biological origins. The result is that indoctrination has replaced education, at least in this one area.” No need to spell out my own reaction to that claim. Also in December 2020, Creation Ministries International offers us a review, by Jerry Bergman, of Ron Milliner’s Fake Evidence: A look at evolutionary evidence for over 90 years in the court cases from Scopes to Kitzmiller, Elm Hill (Elm Hill Books appears to be a self-publishing service under the umbrella of HarperCollins Christian Publishing). This review is not yet available to non-subscribers, but it seems clear from elsewhere that the book’s title is a fair summary of its thesis, that it is yet another example of the evolution-is-a-conspiracy genre, and that Jerry Bergman can be expected to approve.
Timefulness: How thinking like a geologist can help save the world, Marcia Bjornerud, Princeton University Press, 2018/2020
There are many excellent overviews for the general reader of how life on Earth has changed over time (see, for a recent example, Neil Shubin’s Some Assembly Required, which I reviewed here recently. The history of the Earth itself has not been so well served, and Timefulness; How Thinking Like a Geologist Can Help Save the World, by Marcia Bjornerud, Professor of Geology and environmental Sciences at Lawrence University, is a welcome and timely addition to this badly under-represented genre.  The book is beautifully written, in plain language, with complex ideas explained with great simplicity and the use of strikingly appropriate verbal imagery. Behind this transparency of language lies a deep love and knowledge of her subject. The book should appeal to anyone looking for an overview of the Earth as the abode of life, or a perspective on our place in time, and how recklessly we are compressing the tempo of natural change.
The author presents her book as an argument for what she calls timefulness, the perception of ourselves as living in and constrained by time, of time itself as having both extension and texture, of the acceptance of our own mortality, and of our own responsibilities. This she sees as severely lacking in our society. We expect people to know something about distances on the map, but Read the rest of this entry