Category Archives: Evolution
Black swans and other deviations: like evolution, all scientific theories are a work in progress
Discussions about the nature of science and scientific theories are often confused by the outdated view that such theories are rendered false when anomalies arise.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.Read the rest of this entry
Sensory Worlds Beyond Our Imagining
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.Read the rest of this entry
At a popular evangelical tourist site, the image of a ‘wrathful God’ appeals to millions
Susan L Trollinger, University of Dayton and William Trollinger, University of Dayton
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.Read the rest of this entry
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.
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.
Why creationism bears all the hallmarks of a conspiracy theory
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.
More from The Conversation’s Expert guide to conspiracy theories here.
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.
TH Huxley’s legacy, a campus college renaming controversy, and appeal for signatures
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.
More musings on Kitzmiller
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 (review; long)
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