Category Archives: Science
Discussions about the nature of science and scientific theories are often confused by the outdated view that such theories are rendered false when anomalies arise.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
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.
I shared the excitement when I read at https://www.nature.com/articles/s41598-021-97778-3 that
in ~ 1650 BCE (~ 3600 years ago), a cosmic airburst destroyed Tall el-Hammam, a Middle-Bronze-Age city in the southern Jordan Valley northeast of the Dead Sea
and that this event could have given rise to the biblical account of the destruction of Sodom and Gomorrah. Then I learned that the work was conducted by a group based on an unaccredited Bible college (Trinity Southwestern University, TSU), that the world’s leading authority on airbursts has denounced the claims as impossible, that eight separate major research groups have questioned the assumptions, reproducibility, and factual accuracy of related earlier work by the corresponding author, that there is an unusually active thread criticisng the work on PubPeer, and that Retraction Watch, which says that criticism has engulfed the paper, is in correspondence with the Chief Editor of the journal, part of the Nature group, where the work appeared.
Problems listed by acknowledged experts in PubPeer include misuse of Mark Boslough‘s account of airbursts (Boslough is a long-standing critic of the claims of the TSU group); and no clear evidence that the destrution of the palace walls was catastrophic, absence of qualified examination of skeletons, anatomically misdescribed bones, claims without evidence that bone damage was associated with traumatic death, rather than later damage, the mixing of kinds of debris is commonplace and not evidence of catastrophe, the connection of the carbon-14 dates to the alleged destruction is not established, and claims of burning of bone lack evidence and consistency (Megan Perry of the Petra North Ridge Project, who knows what this kind of stuff looks like.) There is undeclared image manipulation, eventually admitted, but described as without significance. And the account of diamond vs graphite in the paper
Each diamonoid typically contains carbon atoms that are sp3-bonded (i.e., 3 bonded carbon atoms), as in diamond, rather than with sp2 bonding (i.e., 2 bonded carbon atoms), typical of graphite
does not inspire conidence.
In the paper’s Figure 44c, shadows are cast by a sun shining from the direction labelled North. This obviously cannot happen at Tall el-Hammam, giving rise to further concerns about the quality of the work.
My own browsing in what are for me odd places1 shows that other archaeologists, including Aren Maeir of Bar Ilan University, agree in finding nothing unusual in the report compared to “normal” destruction by fire or warfare) Maeir is quite explicit:
[T]he destruction the report described was not that unusual. “I see some things that remind me of phenomena that we have in the Iron Age IIA (1000–925 BC) destruction at Tell es-Safi/Gath (e.g. vitrified or “melted” bricks, ultra-high temperatures, and other things)—a destruction that is most likely caused by the conquest and destruction of the site by Hazael of Aram,” he said.
Mark Boslough, an expert on cataclysmic events who even has an asteroid named after him, tells me that he is tired of repeated rebuttal of what he considers to be obviously false claims, and of seeing his own theoretical analysis of the effect of airbursts invoked as an explanation of claims completely inconsistent with such a process, or perhaps any credible process. For this reason, rather than publishing yet another counterblast that will be ignored, he has taken to describing the controversy, extending over many years, on Twitter (see here, here, and subsequent threads, and PubPeer).
Phillip Silvia, the author from whom soil samples can be obtained, is an electrical engineer by training, who received his PhD training in archaeology at TSU, and published much of this material through TSU press in 2016 as a paperback, in which his PhD advisor, Steven Collins, strangely absent from the author list of this paper although not from an earlier abstract, states (Foreword, page x) that “the Genesis 19 description of Sodom’s destruction was about good a phenomenological description of a cosmic airburst as one could imagine” and describes Tall el-Hammam as “the site I had identified as Sodom based on geographical details embedded in the boblical text”.
Like I suspect many of the journalists and interested readers who swooped on this story, I failed at first to notice that the paper was not, despite the link, an article in Nature but in Scientific Reports. This is one of the stable of less exclusive journals closely linked to Nature being published by Springer, now controlled by the publishing giant Hotlzbrinck, and profiting from Nature’s reputation for excellence. I was only vaguely aware of the authors’ long history of invoking airbursts, took the many kinds of evidence listed at face value, and did not even blink at the claim that “[a]n airburst-related influx of salt (~ 4 wt.%) [from the Dead Sea, apparently] produced hypersalinity”.
The authors have since described this work to a much larger audience in The Conversation, where they repeat their claim, also published in Scientific Reports, of a similar catastrophe at Abu Hureyra in what is now Syria, around 10,800 BCE, assert that “it almost certainly won’t be the last time a human city meets this fate”, claim that such events “pose a severe modern-day hazard”, and advise that “unless orbiting or ground-based telescopes detect these rogue objects, the world may have no warning, just like the people of Tall el-Hammam.” The Abu Hureya paper also repeats a litany of earlier claims that the Younger Dryas, a period of severe cold in the northern hemisphere from around 12,900 to 11,700 years Before Present [Present is fixed at 1950 CE], was caused by a series of impacts with cometary debris, spread over at least four continents. These claims have been severely disputed; see papers listed below.
There are numerous additional reasons for concern about the TSU researh group.
The paper tells us that “The project is under the aegis of the School of Archaeology, Veritas International University, Santa Ana, CA, and the College of Archaeology, Trinity Southwest University, Albuquerque, NM, under the auspices of the Department of Antiquities of the Hashemite Kingdom of Jordan.” Veritas International University believes in “the full historicity and comprehensibility of the biblical record”. It is accredited by the Transnational Association of Christian Colleges and Schools (TRACS), which I have discussed here before. Trinity Southwest University, which now operates from an office in a strip mall in Albuquerque, was formerly in Tulsa, Oklahoma, under the name Southwest Biblical Seminary, and rejects any government accreditation whatsoever as intrusive violation of the separation of Church and State. While the traditional site of Sodom is in Israel (and within the pre-1967 boundaries).
The corresponding author is Allen West, who has been publishing prolifically in this area since 2005 (Evidence for the Extinction of Mammoths by an Extraterrestrial Impact Event) and in 2006 co-authored a book, The Cycle of Cosmic Catastrophes: How a Stone-Age Comet Changed the Course of World Culture, which claims that the debris of a shattered comet was responsible for “a cosmic chain of events [that] began 41,000 years ago and culminated in a major global catastrophe 28,000 years later.” These events include everything from the extinction of the mammoths to the landform of the Carolina Bays to the legend of Atlantis to a purported “mysterious layer of black sediment” found spanning North America to the Younger Dryas discussed in the Abu Hureya paper. West has no academic qualifications or affiliations, and gives his address as Comet Research Group (CRG), Prescott, Arizona (several of the other authors are also members of this group, which is linked to the Rising Light Group, a 501(c)3, tax-exempt charitable organization with a clear Christian and biblical agenda, registered in Allen West’s name.). As detailed by Pacific Standard Magazine, discussing how thing stood regarding CRG’s work in 2017, there have been calls for a for a formal inquiry and
University of Wyoming archaeologist Todd Surovell and his colleagues couldn’t find increased magnetic spherules representing cosmic debris at seven Clovis sites. Nicholas Pinter and his colleagues at Southern Illinois University Carbondale argue the carbon spherules are organic residue of fungus or arthropod excrement. And Tyrone Daulton of Washington University in St. Louis and his colleagues reported that supposed nanodiamonds formed by the impact were misidentified.
On the other hand, in an acrimonious exchange with me in the Comments section of The Conversation, West pointed out that
Our group included, among many others: Dr. James Kennett, emeritus professor at UCSB, specializing in stratigraphy, micropaleontology, paleobiology. He is a member of the National Academy of Sciences, which recognizes the contributions of just 0.1% of all scientists. Dr. Ted Bunch, former NASA section chief and a world-leading meteoriticist. Dr. Robert Hermes, retired from Los Alamos National Labs, world-recognized expert in trinitite or atomic glass. Dr. Wendy Wolbach, chemistry professor who discovered high-temperature soot at the K-Pg boundary.
I replied with a listing of some papers that I have examined criticising West’s own earlier work regarding airbursts, including sampling techniques and claimed evidence for very high temperatures:
Scott AC, Hardiman M, Pinter N, Anderson RS, Daulton TL, Ejarque A, Finch P, Carter-champion A (2017). “Interpreting palaeofire evidence from fluvial sediments: a case study from Santa Rosa Island, California, with implications for the Younger Dryas Impact Hypothesis”. Journal of Quaternary Science. 32 (1): 35–47. doi:10.1002/jqs.2914.
*Boslough M, Harris AW, Chapman C, Morrison D (November 2013). “Younger Dryas impact model confuses comet facts, defies airburst physics”. Proceedings of the National Academy of Sciences of the United States of America. 110 (45): E4170. doi:10.1073/pnas.1313495110.
*Boslough M (April 2013). “Faulty protocols yield contaminated samples, unconfirmed results”. Proceedings of the National Academy of Sciences of the United States of America. 110 (18): E1651. doi:10.1073/pnas.1220567110
*Meltzer DJ, Holliday VT, Cannon MD, Miller DS (May 2014). “Chronological evidence fails to support claim of an isochronous widespread layer of cosmic impact indicators dated to 12,800 years ago”. Proceedings of the National Academy of Sciences of the United States of America. 111 (21): E2162-71. doi:10.1073/pnas.1401150111.
*Holliday VT (December 2015). “Problematic dating of claimed Younger Dryas boundary impact proxies”. Proceedings of the National Academy of Sciences of the United States of America. 112 (49): E6721. doi:10.1073/pnas.1518945112.
Thy P, Willcox G, Barfod GH, Fuller DQ (2015). “Anthropogenic origin of siliceous scoria droplets from Pleistocene and Holocene archaeological sites in northern Syria”. Journal of Archaeological Science. 54: 193–209. doi:10.1016/j.jas.2014.11.027.
*Van der Hammen T, Van Geel B (2016). “Charcoal in soils of the Allerød-Younger Dryas transition were the result of natural fires and not necessarily the effect of an extra-terrestrial impact”. Netherlands Journal of Geosciences. 87 (4): 359–361. doi:10.1016/j.jas.2014.11.027
See, however, in defence of the Younger Dryas impact theory, *Sweatman MB (2021). The Younger Dryas Impact hypothesis: Review of the impact evidence. Earth-Science Reviews. 218: 103677. doi:10.1016/j.earscirev.2021.103677. I thank Christopher R. Moore, one of the authors of the paper I am criticising, for drawing my attention to this review.
*Freely accessible via doi; for other papers, doi gives access to abstracts but not full text.
We await further developments with interest.
1] Bit for a rebuttal by a biblical archaeologist involved in the dig, though not an author on this paper, see here
An earlier edition of this post appeared on pandasthumb.org
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.
Every so often you come across a piece of writing so extraordinary that you cannot help but share it. One such piece is a sermon on global warming by American pastor John MacArthur. Full of beautifully constructed rhetorical flourishes, it is forcefully delivered by an experienced and impassioned preacher to a large and appreciative audience.
For me, as a man of science, it is the most complete compilation of unsound arguments, factual errors and misleading analogies as I have seen in discussions of this subject. But it’s important because climate change is a big election issue this November in the US, where there is a growing movement of evangelical Christians who deny its existence, while Joe Biden promises a “clean air revolution”.
The minister of the COVID-denying, law-defying Grace Community Church in Sun Valley, California – which has encouraged worshippers to congregate as normal despite state COVID-19 restrictions – MacArthur is an impressive figure whose Study Bible has sold almost 2 million copies.
He regards the infallibility of the Bible, from Genesis to Revelation, as essential to his faith, and his sermon about global warming can only be understood in that context. MacArthur’s rejection of the science is shared by other major US ministries and organisations such as Answers in Genesis, Creation Ministries International and the Discovery Institute.
Consensus science is the first refuge of scoundrels … invoked only in situations where there is a political, social, financial agenda but no scientific support.
The reverend has the most serious reasons possible for rejecting the scientific consensus concerning the age of the Earth, the origins of humankind, the history and prehistory of the ancient near East and the peopling of continents: it is totally incompatible with the Genesis account of creation, Adam and Eve, the flood and the dispersion of peoples from the Tower of Babel.
Error, denial and misunderstanding
As for global warming itself, the reverend channels standard climate change denial, but all his arguments are unsound and have been convincingly refuted to the satisfaction of an overwhelming consensus of climate scientists (see in-depth discussion at Skeptical Science). He understates the amount of global warming, incorrectly describes the full record as dating back only 30 years, and cites the Little Ice Age as evidence that the changes currently taking place are natural. There’s more:
Here’s the key, friends, this is the real deal. Legitimate science recognises a close correlation between sunspots and climate change … The sun is the source of temperature changes because of its infrared variations. … There is absolutely no evidence that CO₂ contributes to warming. On the contrary the opposite is true. Warming produces CO₂ … It’s the other way round.
Here we have a collection of half-truths and misunderstandings, typical of denialists claiming to represent “legitimate science”. As the graph below shows, the 11-year sunspot cycle is a minor deviation, and the temperature increase since 1980 has occurred despite the fact that over that period the amount of solar energy falling on Earth has gone down slightly. Incidentally, this solar energy input is concentrated mainly in the visible, not the infrared, region of the spectrum, and it is the roughly balancing heat outflow from the Earth that is in the infrared.
MacArthur offers a false dichotomy between saying that CO₂ warms the oceans, and warmer oceans release more CO₂. Unfortunately, both these statements are true. There is a positive feedback loop: human-released CO₂ is the primary driver, but its effect is amplified by the fact that yet more CO₂ is then released from non-human sources. Regarding CO₂ itself, MacArthur seems to be even more confused:
By the way, plants produce CO₂. What man produces is marginal … Industry doesn’t affect CO₂ in the environment or atmosphere.
Plants do produce CO₂ but they absorb more than they emit. However, when it comes to humans, their activity may cause only a small imbalance each year between CO₂ emission and natural uptake, but this imbalance is cumulative. CO₂ levels are now 50% above pre-industrial, and subtle atomic differences clearly show that fossil fuel is the source. But according to MacArthur, “There is no scientific reason to believe that ice caps are melting”.
Despite the Arctic Monitoring and Assement Programme’s video on this subject, the reverend does not think that the evidence for ice-cap melting is scientific, and that other factors are at play:
This is all political [and] financial agendas, class warfare, class envy … By the way, US$100 billion has been spent to make a case for global warming … driven by the socialist mentality … even some of the feminist mentality that resents male success.
All is now clear. Talk of global warming is part of a politically motivated conspiracy. But US$100 billion? That’s 600 years’ worth of all federal climate research spending. Clearly, those pesky socialists and feminists are formidable fundraisers. However, none of this matters because environmentalism is fundamentally misplaced. As MacArthur puts it, citing Revelation and the integrity of scripture:
God intended us to use this planet, to fill this planet for the benefit of man. Never was it intended to be a permanent planet. It is a disposable planet. Christians ought to know that.
And that is a statement that would leave anybody who cares about this world speechless.
This piece first appeared in The Conversation, where it has had over 300,000 reads. I thank my editor there, Jane Wright, for many helpful suggestions.
Young Earth Creationists (YECs) argue from the rapid and dramatic events observed at the Mt St Helens 1980 eruption to the conclusion that the Earth’s geological record, as displayed for example at the Grand Canyon, could be the results of the even more dramatic events associated with a biblical worldwide flood. Geochristian, in the post I link to below, dismantles specific examples of this claim, and goes on to challenge the view that the Bible describes Noah’s Flood as a worldwide catastrophe anyway. Illustration: Step Canyon, Mt St Helens; Google Earth via Geochristian
Regarding geology, the YEC arguments derive their rhetorical power from the all-or-nothing thinking that runs through all their positions. They claim that Mt St Helens demonstrates the correctness of catastrophism over geological gradualism. If all this much can happen so quickly, why assume that the Earth’s deep geology really required deep time? If the flowing ash and mud from Mt St Helen’s shows lamination and cross bedding, does that not destroy the geologist’s argument that the lamination and cross bedding of shales and sandstones are the result of slow deposition? If in a matter of days snowmelt carved a canyon in the Mt St Helens deposits, would not the waters of a year-long flood have sufficed to carve out the Grand Canyon? If the Mt St Helens eruption rapidly uprooted and re-deposited large number of trees, could not the Earth’s fossil fuel deposits have been formed in the same manner?
Geochristian discusses each of these claims in detail (spoiler; none of them will stand up to examination). What I want to point out here is how much they all have in common. They all depend on imposing absolute either/or divisions on reality, cherry picking similarities and ignoring differences, and imposing the simplest of models on complex reality. The dispute between catastrophism and gradualism, although repeatedly revived by creationists (see e.g. here https://www.allaboutcreation.org/catastrophism-versus-uniformitarianism-faq.htm ) was pronounced dead by TH Huxley, “Darwin’s bulldog”,in his Presidential Address to the Geological Society in 1869 https://mathcs.clarku.edu/huxley/SM3/GeoAd69.html. It’s simply a matter of perspective. Catastrophic events do happen from time to time, but not very often, giving the impression of gradualism over long periods of time. Cross bedding can occur catastrophically, in well-understood special circumstances, but geologists have never had any difficulty in distinguishing between what is found in sudden volcanic outpourings and the completely different wind-blown cross bedding observed in desert sandstones, including ironically the Coconino Sandstone within the Grand Canyon itself. Canyons such as Mt St Helens Step Canyon can indeed form very rapidly in uncompacted sediments, but the Step Canyon is straight, and carved on a steep slope through soft debris, while Grand Canyon has bends and is carved through extremely hard rock by a river flowing over a plateau with, overall, a gentle gradient. And the tree debris from Mt St Helens bears no resemblance, either in texture or in amount, to the world’s coal fields.
Next, Geochristian attacks the YEC interpretation of Genesis. In particular, the word “eretz”, describing the territory immersed in the flood, can mean either the Earth, or a more limited region. Here his motivation is to preserve faith in the text, while rebutting the interpretation that requires the flood to be worldwide. My own approach would be rather different. In the biblical narrative, God sets out to destroy mankind, apart from the virtuous relic represented by Noah and his family. This could hardly have been accomplished by a merely local flood, though one could well argue that the author(s) of Genesis did not make a clear mental distinction between local and worldwide. However, the entire problem disappears if you regard the Genesis narrative (or, rather, fused narratives) in context within a much more ancient Mesopotamian literature, and I argue https://paulbraterman.wordpress.com/2018/11/12/noahs-flood-and-how-to-talk-to-creationists-about-it/ that this is actually more respectful of the text than supernaturalist literalism. However, in my experience discussions between those who do, and those who do not accept a supernatural origin for Scripture are rarely productive.
So why I am I, an unbeliever, re-blogging Geochristian’s material at all? Because as I see it, the crucial gulf is not between religious believers and unbelievers, but between those who are willing to accept reality in all its complexity, and those who prefer to impose their own dogma. And this does not affect only such matters as evolution and the age of the Earth, but such intensely practical matters as conservation, global warming, the regulation of market-based economies, and, right now, our reaction to one particular virus that happens to have mutated and evolved.
h/t Michael Roberts https://michaelroberts4004.wordpress.com/2020/05/19/what-does-mt-st-helens-teach-us-about-noahs-flood-almost-nothing/
All I got from Mt St Helens (MSH) in the days following its May 18, 1980 eruption was a few pretty sunsets. I was an undergraduate student in my first year at the University of Utah, and most of the ash cloud passed far north of Salt Lake City. MSH became more significant for me a few years later as a geology graduate student at Washington State University, where my research project involved analysis and correlation of Cascade Range tephra (volcanic ash) layers buried at various levels in the Quaternary Palouse Loess of eastern Washington. Some of these tephra layers correlated to ancient eruptions of MSH, dated around 13,000 and 36,000 years ago.
Credit: USGS, Robert Krimmel, public domain
Due in part to easy accessibility, the 1980 eruptions of MSH have been studied more closely than just about any other explosive volcanic eruption in history. Geologists have learned…
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Another delightful posting from my friend Marli Miller.Thanks, Marli. I’ve blogged here earlier myself about the famous unconformity at Siccar Point, and the depositional contact at the Giants Causeway between a later lava flow, and the paleosol formed by weathering of the one before it.
Geologic contacts are the surfaces where two different rocks touch each other –where they make contact. And there are only three types: depositional, intrusive, or fault. Contacts are one of the basic concerns in field geology and in creating geologic maps –and geologic maps are critical to comprehending the geology of a given area. For those of you out there who already know this stuff, I’ll do my best to spice it up with some nice photos. For those of you who don’t? This post is for you!
Depositional contacts are those where a sedimentary or volcanic rock was deposited on an older rock (of any type). Intrusive contacts are those where igneous rocks intrude older rock (of any type). Fault contacts are… faults! –surfaces where two rocks of any type have moved into their current positions next to each other along a fault.
In a cross-sectional sketch they may…
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