F Rosa Rubicondior

Saturday 10 December 2022

Unintelligent Design - How XY Sex Determination Causes Speciation to Avoid Extinction

Did sex drive mammal evolution? How one species can become two
Wild platypus in a Tasmanian stream
Wild platypus, in a Tasmanian stream.
Within a few million years, humans will either be extinct or will have diversified into two or more species. As I explained in my previous post, the gradual degeneration of the Y chromosome, that is carried only by males and which is essential to trigger the development of a male foetus, is degenerating at a rate which will see it disappear altogether within about 5 million years. Since our lineage split from that of the platypus, some, 845 genes have been lost, leaving only 55 active genes and a lot of non-functional junk DNA.

Disappearance of the Y chromosome has already happened in an unknown number of mammals, particularly those with a short generation time such as many rodents, leading to their extinction. With no DNA, there is no way to determine if this was the cause of extinction, and in any case, extinction, at least locally, could occur very quickly if caused by a lost Y chromosome or at least the one remaining essential gene responsible for sex determination.

However, some rodents, especially some Eastern European and Asian mole voles and Japanese spiny rats evolved an alternative method of sex determination, so, unless humans evolve a similar replacement, they too will go extinct.

The replacement in the rodents was a sequence of DNA adjacent to a gene known as the SOX9 gene located on one of the autosomes which controls the development of maleness in the developing foetus. This gene is activated by the SRY gene on the Y chromosome, so, with no Y chromosome and no replacement, no males and no reproduction.

However, there is a problem which will arise during the replacement of Y with some other mechanism, and that mechanism could vary by region. During that period there will be at least two mutually exclusive methods for determining the sex of the offspring, during which any hybrids will be unable to reproduce even if they are viable. This means there will be an evolutionary 'war' between these two methods, during which any mechanism which acts as a barrier to hybridization will give the carriers an advantage because they won't be producing sterile offspring.

These evolving barriers will quickly cause the emerging species to diversify, so, even if humans survive the loss of their Y chromosome, there will inevitably be two or more species of humans.

This has already happened in those families of rodents such as the Eastern European mole voles and the Japanese spiny rats where some species have an alternative sex determination mechanism involving a SOX9 enhancer in males on the same chromosome as the SOX9 gene and the loss of the Y chromosome, so the chromosome with the SOX9 enhancer has picked up the sex-determining baton, while related species have retained the XY method.

The enhancer consists of a simple duplication of a short sequence of DNA that is present in mice but in which it has no known function. Somehow, this activates the SOX9 gene at the right time, taking over the function of the Y Chromosome’s SRY gene.

In the following article reprinted from The Conversation under a Creative Commons licence, professor Jenny Graves Jenny Graves, Distinguished Professor of Genetics, La Trobe University, Australia, explains that it could have been the cause of divergence between the marsupials and the monotremes and between the marsupials and the placental mammals, and so this played a key role in major steps in our own evolution.

The article has been reformatted for stylistic consistency. The original can be read here:

Friday 9 December 2022

Unintelligent Design - Humans On The Path To Extinction, By Design!

Men are slowly losing their Y chromosome, but a new sex gene discovery in spiny rats brings hope for humanity

Northern mole vole
Northern mole vole, Ellobius talpinus.
Males have lost their Y chromosome

Credit: Mikhail Kolesnikov and Marina Korobchenko), Free Software Foundation
Unless the intention was the eventual extinction of the species, no intelligent designer, especially one granted the power of omniscient foresight, would design sex-determinism by a method that guarantees extinction will happen eventually, unless a new method is devised just in time to prevent it.

And yet that appears to be the result of the current XY chromosomes method used by all mammals except the monotremes and a few exceptional rodents of which more later. The problem is that the Y chromosome, which is carried by males, is a degenerate and degenerating chromosome, unlike its sex-determining pair, the X Chromosome, of which females have two copies.
Over time, almost all the genes formerly carried by the Y chromosome have been lost, so, unlike the X Chromosome with about 900 genes, the Y chromosome in humans only has 55 genes and a lot of junk DNA that does nothing at all. The platypus, on the other hand, in which the X and Y chromosomes are perfectly normal paired chromosomes like all the other mammalian chromosomes, both pairs have the full complement of genes. (Sex determination in platypuses is more like that of birds and involves other chromosome pairs). Se we can deduce that in the 166 million years since humans and platypuses diverged from a common ancestor, the Y chromosome has lost 845 genes. If this rate of loss is projected into the future, the human Y chromosome will disappear in 11 million years.

Why does the Y Chromosome tend to degenerate and lose genes if this is disadvantageous? The answer is connected to the way normal chromosomes get rid of deleterious mutations and unwanted intrusions of junk 'jumping genes', and one of the advantages of sexual reproduction - they replace the unwanted stuff for the good stuff on the other one of the pair. However, the Y chromosome has no pair, so is stuck with mutations and junk. Meanwhile, functional genes can migrate to other chromosomes, so the Y chromosome tends to lose quality and quantity over time.

Thursday 8 December 2022

Creationism in Crisis - 275,000 Year-Old Neanderthal Footprints From Spain

Recently found 'Neanderthal footprints' in the South of Spain could be 275,000 years old
Homo heidelbergensis (The Broken Hill skull)
One of the suspect species
The Natural History Museum, London, UK
Some 270,000 years before Creationists believe Earth was magicked into existence, hominins were walking about in what is now Southwestern Spain, leaving footprints in mud that were quickly covered over and preserved by blown sand gto form a protective sand dune. Over time the sand dune solidified into the Asperillo cliff

When first discovered the footprints at Matalascañas, Huelva , Southwest Spain, were dated to around 106,000 ± 19,000 years based on a previous study to determine the age of the Asperillo cliff.

Embarrassing though even that relatively recent dating is for Creationists, the team have now revised the date of the footprints by dating the surface in which they were made, using a technique called Optically Stimulated Luminescence, which basically measures when the surface was last exposed to sunlight before being buried for a prolonged period. This gave a date of 295,800 ± 17,000 years.
The significance of this new date is that rather than being made by Neanderthals from the Upper Pleistocene as was first thought, these tracks were made by ancestor of the Neanderthals, or early Neanderthals from the Middle Pleistocene, during a period known to geologists as the transition from Marine Isotope Stage 9 (MIS-9) to MIS-8 when there was a sudden cooling then warming of the climate in the Iberian Peninsula.
The authors have published their revised findings, open access, in the journal Scientific Reports and written an article in The Conversation. That article is reprinted below under a Creative Commons license, reformatted for stylistic consistency. The original article can be read here:

Tuesday 6 December 2022

Biodiversity News - How Man-Made Climate Change is Damaging German Beech Forests.

Press release: Climate change in the forests of northern Germany - Georg-August-Universität Göttingen
Typical north German beech forest
Typical beech forest in northern Germany: the scientists took samples of wood from dominant trees at 30 locations.

Photo: Banzragch Bat-Enerel
Scientists from Germany have shown the negative effects of man-made climate change on the health of beech trees in German forests. These forests are important wild-life refuges with a rich and complex ecosystem, so any damage to the health of the trees will have a major impact of the biodiversity of Central Europe.

The scientists took samples of wood from major trees in 30 different locations so that comparisons could be made between areas with different average rainfall levels. They then analysed the tree rings to obtain a retrospective measure of tree growth.

The news release from Georg-August-Universität, Göttingen, describes the study and its significant findings:

Human Rights News - Women Fighting Back Against the Chritian Fundies Who Took a Basic Human Right Away

Pro Roe protestors outside the Supreme Court Building
SCOTUS overturned Roe v Wade, despite strong popular support for retaining it.
Pro-choice crowdfunding has surged in the U.S. — but donating that way has risks

America women, who had the basic human right to bodily autonomy taken away from them by Christian extremists who now dominate SCOTUS, are fighting back through crowdfunding.

They need to do this to raise money for travel out of a Repugnican-run state that doesn't respect their basic human rights, to a Democrat-run state where pregnancy termination services are still legal and a woman’s right to choose is recognised and valued over a Christian fundamentalist's assumed right to control others.
However, there are risks, not the least of which are retaliatory measures by extremists seeking to constrain even the right to travel in order to restrict a woman's right to choose, and pressure on social media platforms to deny women the ability to crowdfund their freedom-seeking trips. In an ominous foreshadowing of what a fundamentalist theocracy would be like, not content with forcing their religion on the people in the states they run, extremists also seek to impose it on people who have rejected them at the ballot box.

In the following article reprinted from The Conversation under a Creative Commons license, Professor Jeremy Snyder, Health Sciences, Simon Fraser University, Canada, examines the sharp increase in crowd-sourced funding by women seeking abortion services outside their home states. The article is reformatted for stylistic consistence. The original may be read here:

Monday 5 December 2022

Trumpanzee Cult News - Trump or Desantis? The Nutjobs May Decide It.

Evangelical Christians are crucial voters in Republican primaries. Would they support DeSantis or Trump?
The American Christian far right now has two dogs in the fight for the position of Repugnican candidate in 2024 - the odious, epitome of a sore loser, former president, Donald Trump and the evangelical white supremacist, governor of Florida, Ron DeSantis, who emerged the stronger of the two in the mid-term disaster for Trumpanzee Repugnicans, where candidates who publicly bought into Trump's Big Lie of a stolen election, fared badly.

But is there much to choose between them? To someone like me from outside the USA, there doesn't appear to be a fag-paper's difference between Trump and DeSantis. They both appeal to the hate-filled, neo-fascist, human rights denying, white Christian evangelicals and misogynistic pro-life hypocrites who blame God and the Bible, and thank Trump and his stooges in SCOTUS, for their legalised denial of a woman's right to bodily autonomy.

What will come next? A ban on contraception? Legalised persecution of anyone who isn't heterosexual? Prohibitions on voting for anyone who isn't a white evangelical Christian? The abolition of democracy itself?

Seems a bit exaggerated? All of these have been advocated by the Christian far right at various time very recently and many of them see it as the entire reason for the 'culture war'!

Dominating the judiciary isn't enough for these privileged extremist who will only settle for a Taliban-style self-selecting theocracy which dominates both the Executive and the Legislature, which will be mere rubber stamps for the dictates of the self-appointed evangelical cult leaders. At least one popular televangelist with a huge following has already claimed to a cheering audience that God told him the government should be accountable to him, not the people.

How these extremists, who still form a significant block of American voters, despite the growing rejection of organised religions in the USA, will divide between the two candidates, then unite behind the winner, is still an open question, as is the question of how far their repugnant extremism will push people into the Democrat camp.

One frightening aspect of Christian fundamentalism the USA, is that many of them, the so-called dispensationalists, saw the relocation of the US embassy in Israel from Tel Aviv to Jerusalem by Trump as the first move in setting the precondition for an apocalyptic war, and believe Donald Trump will complete that process. In that war they believe they alone will be saved and 'raptured' to a place of safety until it is safe to return to Earth where they will have everything for themselves and all those who disagreed with them will be dead - the greatest thing they can imagine!

If these self-possessed, entitled nutters gain the political powers they crave, they will have control of the biggest nuclear arsenal on the planet, with enough warheads to destroy all life several time over, all under the command of a narcissistic psychopath with an acute personality disorder, the self-control of a toddler and his own private nuclear bunker.

The stakes in 2024 really are that high!
In the following article reprinted from The Conversation, Professor David Smith, Associate Professor in American Politics and Foreign Policy, US Studies Centre, University of Sydney, gives his assessment of the prospects, and to what extent the unpopular (even amongst Repugnicans) state bans on abortion will affect the outcome of November 2024.

The article, which can be read here, has been reformatted fos stylistic consistency.

Saturday 3 December 2022

Malevolent Designer News - How Creationism's Favourite Sadist is Spreading Antimicrobial Resistance

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance | Nature Communications
 global map of antimicrobial resistance
During the COVID-19 pandemic, scientists realised the value of analysing the sewerage outflow from major population centres to monitor the prevalence of the virus and its variants in the population. This technique can also be used to monitor microbial prevalence and variants such as antimicrobial resistance.

Now a team of researchers at the Danish Technical University (DTU) has used data from these analyses to produce a map of microbial resistance at the level of resistance genes, rather than of resistant species.

From a Creationist perspective, what this is measuring is how well their pestilential malevolence is doing in its arms race against medical science to ensure its pathogens retain their ability to make us sick.

The results of the meta-analysis were surprising in that it showed the same genes were present in different species and in different places, indicating that exchange of genes between species is more frequent and extensive than was previously thought.

From the DTU News release:

Creationism in Crisis - How Evolution Evolved Intelligently Without a Creator

Intelligent design without a creator? Why evolution may be smarter than we thought

The evolution of evolvability is a fascinating aspect of the Theory of Evolution. For example, the evolution of sexual reproduction seems counter-intuitive because it involves two copies of each allele, with the original often dominating, so any advantage from a beneficial mutation can be lost because it isn't expressed in the phenotype, while a deleterious mutation can be shielded from selection by a dominant allele.

However, because it also involves cross-over between chromosomes it can give rise to new combinations of alleles allowing evolution to 'experiment', with different evolutionary lines coming together to produce synergy where the total is greater than the sum of the parts, so sexual reproduction almost certainly evolved because it gave greater evolvability, i.e. it gave the organisms greater resilience in a changing environment.

Evolution is a process, not an event, and, as such, it can be improved (evolved) to maximise efficiency. Indeed, the mechanism of random change being tested in a selective environment makes that evolution inevitable. In the same way that machine learning is the process which underpins artificial intelligence, so evolution is the process by which species respond to environmental changes. Both processes can be improved by a natural evolutionary process, without the need for supernatural intervention.

In the following article from 2016, reprinted from The Conversation under a Creative Commons license, Professor Richard A. Watson, Associate Professor, Institute for Life Sciences/Electronics and Computer Science, University of Southampton, UK, explains how evolution could be evolving with an evolved natural intelligence which enables it to solve problems without the ability to look ahead the way an intelligent designer would work.

The article has been reformatted for stylistic consistence. The original can be read here:

Friday 2 December 2022

Malevolent Designer News - How The SARS-CoV-2 Omicron Variant Was Made

Where did Omicron come from?: Charité – Universitätsmedizin Berlin
Charts
Fig. 2
Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa

Fischer, C., et al (2022)
Devoted folowers of Creationism's intelligent [sic] designer, whom they credit for creating everything, will normally cite examples of multiple mutations which give rise to a new capability such as resistence to antibiotics or anti-malarial drugs as evidence of design because the probability of so many mutations arising is vanishingly small.

What they ignore is the fact that the multiple advantageous mutations can accumulate over time in the population and don't need to arise as a single event in a single organism, like their phoney maths models.

In fact, one of their gurus, Michale J Behe wrote a book, The Edge of Evolution based on just that mathematical deception, and was roundly exposed as a fraud by Kenneth R. Miller for doing so.
A classic example of this phenomenon in respect of the evolution of the SARS-CoV-2 virus to give rise to the highly infection Omicron variant, which also has the ability to evade the immunity we have either from vaccinations or acquired naturally by pervious infections, was published yesterday in the Journal Science.

The Omicron variant has about 50 mutations which together give it these abilities and a group of researchers from Charité – Universitätsmedizin Berlin and a network of African institutions, led by Professor Jan Felix Drexler, has shown how Omicron almost certainly arose slowly across the viral population in Africa, accumulating a few mutations in local populations, which then eventually came together as the 50 mutations in Omicron which then took off with exponential growth, spreading very rappidly acroos African then the world at large.

Key to this accumulation of mutations was the growign population of humans with immunity which acted as environmental selectors favouring the mutations, just as the neo-Darwinian synthesis of the Theory of Evolution predicts.

This illustrates a feature of evolution that Creationists have to ignore - the ability of populations to accumulate different, parallel lines of mutations with each generation increasing the probability of a chance combination of two or more different lines arising.
As the news release from Charité Universitätsmedizin explains:

Thursday 1 December 2022

Creationism in Crisis - How Asia's Mammals Evolved

The evolution of Asia’s mammals was dictated by ancient climate change and rising mountains | Field Museum
Lead author Anderson Feijó holding a plateau pika in Tibet.
Photograph: Danping Mu.
Carrying traps in the Hengduan Mountains.
Photograph:Anderson Feijó.
No doubt to the consternation of any Creationist fraud trying to sell the idea that the Theory of Evolution (TOE) is about to be overthrown and replaced by their favourite Bronze Age fairy tale, researchers from Chicago's Field Museum of Natural History and the Chinese Academy of Science, used their knowledge of evolution to hypothesise that the main evolutionary changes in Asian mammals was directly related to major geoclimatic changes. To test their hypothesis, they mapped the known evolutionary changes in Asian mammals onto the known geoclimatic changes across the continent, and found there was a very good fit.

This will come as no surprise to anyone who understands how environmental change drives evolutionary change because environmental change inevitably involves a change in the environmental selectors operating on the organisms subject to it.

The Field Museum news release explains the research and its significance:

Wednesday 30 November 2022

Creationism in Crisis - Old World Flycatchers’ Family Tree Mapped

Old World flycatchers’ family tree mapped - Uppsala University, Sweden
European robin in snow
European robin, Erithacus rubecula
Photograph: Tomas Carlberg
In yet another casual refutation of the plaintive Creationist assertion that the Theory of Evolution (TOE) is about to be overthrown by their childish Bronze Age superstition, scientists from Uppsala and Gothenburg Universities, Sweden and Florida University, USA, have produced a family tree of the Old World flycatchers - a family of birds that includes the European Robin.

In doing so, they found not the slightest hint that the TOE is inadequate to explain the observations. In fact, as expected, it is entirely consistent with what they found.

As the article in Uppsala University news by Elin Bäckström explains:

Monday 28 November 2022

Creationism in Crisis - Scientists Debate How Evolution Works, Not Whether it Happens

Charles Darwin by George Richmond (1809-1895)

The study of evolution is fracturing – and that may be a good thing

Creationists who have been fooled into believing that the Theory of Evolution (TOE) is being increasingly rejected by mainstream scientists will undoubtedly take some comfort from the fact that there is an ongoing, and increasing debate amongst serious biologists about the theory.

Sadly for Creationists, however, the debate isn't about whether species evolved and are evolving or whether they were made by magic; it's about how exactly evolution happens.

Debate, is of course, healthy and essential within science. It is the Darwinian environment in which scientific ideas evolve and improve, because, science, unlike religion, is based on the idea that when the facts change, opinions should change to accommodate the new information.

In other words, the debate is about the detail, not the fact. No serious biologist is in any doubt about the fact of evolutionary change being the cause of speciation, and why species changes over time and vary between populations under the influence of environmental selectors, just as Darwin and Wallace outlined in 1859.

In the following article, reprinted from The Conversation under a Creative Commons license, Professor Erik Svensson of Lund University, Sweden, explains the background to the debate, why debate is healthy and how it poses no threat to the basic idea of evolutions. The article has been reformatted for stylistic consistency. The original can be read here.

Sunday 27 November 2022

Unintelligent Designer News - Podcast Now Available

Well, the live show went okay, despite a slight technical hitch with getting the presentation video to run, which gave more time for debate but, sadly, less time for the video. So here it is for anyone who wants to see the entire thing.


Also, the entire show can be viewed again here:
As I said, my book, "The Malevolent Designer: Exposing the Intelligent Design Hoax", contains many more examples of the things in nature that show there was no intelligence or design in what we can observe.

An illustrated companion book, "The Malevolent Designer: Why Nature's God is not Good", is also available in hardcover, paperback or ebook for Kindle, as are my other books on science and religion.

Thank you for sharing!









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Creationism in Crisis - How the Arthropod Brain Evolved 525 million Years Ago

525-million-year-old fossil defies textbook explanation for brain evolution | University of Arizona News
Artist's impression if Cardiodictyon catenulum
Credit: Nicholas Strausfeld
A paper published a couple of days ago in Science closes yet another of those gaps so beloved of Creationists who fool their dupes with the false dichotomy fallacy that, if science hasn't explained something, the only alternative on offer is that their version of a creator god did it. This save them the bother of producing any evidence for their pet superstition and keeps their dupes believing that they have better answers than science does and so are much more clever than those elitist scientists with their big words. If there is one thing Creationists can't stand it's uncertainty, with the dreadful prospect that they might have to change their minds if the evidence changes.

The paper was written by a group of scientists led by Nicholas Strausfeld, a Regents Professor in the University of Arizona Department of Neuroscience, and Frank Hirth, a reader of evolutionary neuroscience at King's College London. It describes a fossil of Cardiodictyon catenulum, a 1.5 cm long, worm-like arthropod, found in China's southern Yunnan province. Close detailed analysis has revealed delicately preserved nervous system, including a brain. This is believed to be the oldest fossilised brain so far discovered.

The University of Arizona News describes the research and its significance:

Saturday 26 November 2022

Creationism in Crisis - Fossils from Gondwana Show Evolution and Ecosystems 266 Million Years Ago

Exquisite new fossils from South Africa offer a glimpse into a thriving ecosystem 266 million years ago
plant fossils
Creationist frauds who want to convince their cult members that the Theory of Evolution is about to be replaced in mainstream science by their childish superstition, and so become the first scientific theory ever to be replaced with an evidence-free superstition involving imaginary supernatural entities, have to keep them ignorant of papers such as this one which has just been published in Communications Biology.

The paper, by a team of scientists led by Rosemary Prevec, a palaeontologist with Rhodes University Department of Botany, and the Department of Earth Science, Albany Museum, Makhanda, South Africa, reports on an exceptionally well preserved collection of fossils of novel freshwater and terrestrial insects, arachnids and plants - what is known to science as a 'Lagerstätte'. What's more, the formation has 'robust regional geochronological, geological and biostratigraphic context', in other words, the fossils can be accurately placed in time and the changing geography of the time - some 266–268 million years ago in a river delta, when Earth had just two major landmass known as Gondwana and Laurasia, the northern and southern parts of Pangea respectively, before they were broken up and in some cases forced together by tectonic forces to form today’s major continents.

Breakup of Pangea
Break-up of Pangea into major landmasses
These fossils enabled the team to reconstruct the ecosystem of the time. An ecosystem is the result of interactions between species of animals and plants in a given area - the fundamental conditions for evolution to occur, as the ecosystem changes in response to internal and external pressures.

The team leader, Rosemary Prevec, has written the following article in The Conversation to explain the background to the discovery and its significance in terms of understanding the evolution of some species and the extinction of others. The Theory of Evolution is, of course, fundamental to research such as this in order to make sense of the observations. Note that nowhere does the author show the slightest doubt about the TOE's value in that understanding.

Her article is reproduced under a Creative Commons license, reformatted for stylistic consistency. The original can be read here.

Find out more about The Conversation, here.

Exquisite new fossils from South Africa offer a glimpse into a thriving ecosystem 266 million years ago


A fossilised insect wing with some of its colouration preserved is just one tiny treasure emerging from the site.

Rose Prevec

Rosemary Prevec, Rhodes University

South Africa is famous for its amazingly rich and diverse fossil record. The country’s rocks document more than 3.5 billion years of life on Earth: ancient forms of bacterial life, the emergence of life onto land, the evolution of seed-producing plants, reptiles, dinosaurs and mammals – and humanity.

Many will be familiar with hominid fossils such as the Australopithecus africanus skull Mrs (or is it Mr?) Ples and the paradigm-shifting Taung child. Less well known and equally important fossils such as the oldest terrestrial vertebrates in the ancient supercontinent Gondwana, which document the first steps from the ocean and onto land, have also emerged from South Africa. The country’s wealth of fossils is due in part to the region’s unique geology, which documents 100 million years of nearly continuous deposition in its Karoo Basin.

Fossils also hold clues to climatic shifts, from the great Carboniferous ice age over 300 million years ago, to the huge dunes of blazing Jurassic deserts where dinosaurs roamed 200 million years ago. Scientists can read the devastation of the mass extinction events that destroyed global ecosystems and changed the course of Earth’s history.

But in the race to understand the “big picture” of the evolution of life and to distil its dramatic ups and downs into punchy headlines, it is easy to forget the small and quiet things. Pause, and consider what life looked like on an average day, in a world without humans, mammals, birds, butterflies, flowers, or even dinosaurs. What was it like on the shores of a rippling lake, on a drowsy summer afternoon, 266 million years ago in what’s now the Northern Cape province of South Africa?

The search, and what we found

In a new paper, my colleagues and I provide the first glimpse of such an ecosystem. We have found a profusion of fossils of tiny insects that have never been found before, as well as important plant specimens that are changing our understanding of how they evolved.

Our findings give fresh insights into the effects of extinction events on ecosystems. The subject has taken on great urgency in the face of what scientists are calling the sixth great extinction event, which is being driven by the current trend of global warming.

For the past few years we have been excavating a small, nondescript rock outcrop near Sutherland in the Northern Cape.

This outcrop is yielding untold fossil treasures of plants, insects and other invertebrates that are new to science. These unique fossils, some only a few millimetres long, are telling us about what lived in and around a calm pool on a delta plain during the middle Permian period between 266 million and 268 million years ago. Rocks of this age contain fossils of the oldest therapsids, a group of reptiles that eventually gave rise to the mammals.

Other life of this time included the lizard-like ancestors of tortoises, large amphibians that lurked like crocodiles just below the water surface, and forests dominated by a tree called Glossopteris with an understorey of spore-producing plants such as mosses, ferns and horsetails.
Teams of palaeontologists have discovered and excavated many hundreds of vertebrate fossils in the western and southern Karoo of South Africa that date back to the Permian, including the Sutherland District and surrounding areas. But the kinds of rocks that are rich in vertebrate fossil bones tend not to preserve plants and invertebrates. These seem to require the more anoxic, acidic conditions present in calm lakes and pools for high fidelity preservation, whereas bones preserve well in more oxygen-rich settings.

This makes it difficult to understand the ecosystems of this time – and means our discoveries are especially astonishing. These include the oldest freshwater leech, a record that pushes back the known range of this group by 40 million years, and the oldest water mites by 166 million years.

Other exciting finds include the oldest damsel-fly and oldest stoneflies from Gondwana, as well as a profusion of the tiny, aquatic, immature stages (nymphs) of an extinct group called the Palaeodictyoptera. Many of the insect wings we have found have yet to be identified.

A fossil of an insect nymph - so tiny that it is dwarfed by a human hand - and, on the right, seen under a microscope.

Credit: Rose Prevec
There are also mosses and liverworts, tiny soft plants that were among the first to colonise land. They too, have a very poor fossil record, and we have found both at our site. The liverwort is the oldest in Africa and one of only a few records for the Permian period globally.

One of the most exciting finds is the dense accumulations of the male and female cones of the Glossopteris plant, an unbelievably rare occurrence that is shedding light on the evolution and classification of this important coal-forming plant.

Male and female cones of the Glossopteris plant.
Credit: Rose Prevec
Great potential

Our work has been slow. Excavations have involved a lot of sitting on spiky rocks in the sun for weeks on end, extracting tiny pieces of mudrock and then examining them with a magnifying hand lens.

The fossil site is still producing new weird and wonderful plants and invertebrates, and will keep us busy for a while. There is also great potential for finding other sites in the region. The thousands of plants and insects we have collected so far are being carefully curated and studied at the Albany Museum in Makhanda. We are keenly aware of the need to conserve this precious part of South Africa’s protected natural heritage.

Our work to better understand the organisms we’re finding provides knowledge about how and when they evolved and interacted as well as about local climate, how their distributions changed through time, how the positions of the continents changed, and the effects of deserts, mountain ranges and seas on the movement and evolution of life.

This is very important when trying to understand extinction events such as the Great Dying, which marked the end of the Permian 252 million years ago. It destroyed most life in the oceans and on land and – in a chilling echo of the current global climate crisis – was driven by hundreds of thousands of years of volcanic activity that produced huge amounts of greenhouse gases, leading to an increase in global temperatures. The Conversation
Rosemary Prevec, Palaeontologist, Rhodes University

Published by The Conversation.
Open access. (CC BY 4.0)
plant fodsils
Fig. 4: Key plant fossil discoveries from the Onder Karoo locality.
a Glossopteris leaf with abundant platyspermic seeds to the left. Arrow indicates adjacent Lidgettonia sp. 1 fructification, the likely source of the seeds. b Lidgettonia sp. 1: large scale leaf with at least five pairs of cupules attached. c Slab showing mixed mat of male and female cones of the Glossopteris plant. d New dictyopteridean, seed-bearing glossopterid fructification Ottokaria. e Female cone of Glossopteris plant: multiple Lidgettonia sp. 2 fertiligers attached to a shoot. f Male cone of Glossopteris plant: multiple Eretmonia sp. polleniferous scales attached to a shoot. g Glossopteris leaves, arrows indicate sites of margin-feeding by insects. h Glossopteris leaf with arrows indicating large excisions caused by insect feeding, note pronounced staining of plant reaction tissue. i Probable moss sporophytes, arrows indicate moss capsules. j Thallose liverwort with dichotomous branching, notched termini, hydroids, typical epidermal patterning (ep, arrow) and possible gemma cups (gc, arrows).


invertebrate fossils
Fig. 5: A selection of newly discovered invertebrate fossils from the Onder Karoo locality.
a AM14859: exuviae of a nymph (Palaeodictyopterida). b AM13265: stonefly nymph (Plecoptera). c AM11348: cluster of plecopteran nymph exuviae associated with glossopterid seeds. d AM11296: distal fragment of a wing of Afrozygopteron inexpectatus45, a Protozygoptera (an early damselfly-like Odonatoptera), with sclerotized costo-apical pterostigma (arrow). e AM11389: forewing of an ‘ice crawler’, Colubrosopterum karooensis (a new genus of ‘Grylloblattodea’, Liomopteridae46). f AM14864d: two forewings of Protelytoptera. g AM14864e: two forewings of Anthracoptilidae (Paoliida). h AM14858ab: composite image of part and counterpart of a hemipteran forewing (Prosbolidae). i AM11298a: hemipteran forewing with pattern of wing colouration preserved (Scytinopteridae). j AM11157a: large forewing of a cicadamorph with pattern of colouration preserved (Hemiptera, Pereboriidae). k terrestrial nymph/nymph exuviae (Hemiptera, Sternorrhyncha). l annelid worm, probable Clitellata (leech) with circular sucker (arrow). m AM11282b: elytron of a beetle with punctate ornamentation (Coleoptera, Permocupedidae). n AM14856: water mite (Acari, Hydrachnidia).
Copyright: © 2022 The authors.
Published by Springer Nature Ltd. Open access. (CC BY 4.0)
More detail is given in the abstract to the team's open access paper in Communications Biology:
Abstract

Continental ecosystems of the middle Permian Period (273–259 million years ago) are poorly understood. In South Africa, the vertebrate fossil record is well documented for this time interval, but the plants and insects are virtually unknown, and are rare globally. This scarcity of data has hampered studies of the evolution and diversification of life, and has precluded detailed reconstructions and analyses of ecosystems of this critical period in Earth’s history. Here we introduce a new locality in the southern Karoo Basin that is producing exceptionally well-preserved and abundant fossils of novel freshwater and terrestrial insects, arachnids, and plants. Within a robust regional geochronological, geological and biostratigraphic context, this Konservat- and Konzentrat-Lagerstätte offers a unique opportunity for the study and reconstruction of a southern Gondwanan deltaic ecosystem that thrived 266–268 million years ago, and will serve as a high-resolution ecological baseline towards a better understanding of Permian extinction events.

And another research paper casually refutes the Creationist lie that the TOE is being increasingly rejected by serious scientists.

Friday 25 November 2022

Creationism in Crisis - How a Small Cluster of Genes Made us Human

Human Evolution Wasn’t Just the Sheet Music, But How it Was Played | Duke Today
The fluorescent glow of mouse brain cells on the right indicates the effectiveness of a human-derived gene enhancer, HAQER0059, versus a 6 million year old version of the enhancer at left.
Riley Mangan, Duke University
A group of researchers from Duke University, Durham, NC, USA, has identified a group of human DNA sequences that drive changes in brain development, digestive tract length and immunity that evolved quickly following our split from the common ancestor we share with the chimpanzees, but before we diverged from Neanderthals. In other words, these probably arose sometime in the last 7.5 million years which means they were probably present in Home erectus and maybe the Australopithecines.

The DNA sequences in question act as regulatory switches, turning other genes on and off to regulate development in the embryo.

As the news item in Duke Today explains:
Our brains are bigger, and are guts are shorter than our ape peers.

“A lot of the traits that we think of as uniquely human, and human-specific, probably appear during that time period,” in the 7.5 million years since the split with the common ancestor we share with the chimpanzee, said Craig Lowe, Ph.D., an assistant professor of molecular genetics and microbiology in the Duke School of Medicine.

Specifically, the DNA sequences in question, which the researchers have dubbed Human Ancestor Quickly Evolved Regions (HAQERS), pronounced like hackers, regulate genes. They are the switches that tell nearby genes when to turn on and off. The findings appear Nov.23 in the journal CELL.

The rapid evolution of these regions of the genome seems to have served as a fine-tuning of regulatory control, Lowe said. More switches were added to the human operating system as sequences developed into regulatory regions, and they were more finely tuned to adapt to environmental or developmental cues. By and large, those changes were advantageous to our species.

“They seem especially specific in causing genes to turn on, we think just in certain cell types at certain times of development, or even genes that turn on when the environment changes in some way,” Lowe said.

A lot of this genomic innovation was found in brain development and the GI tract. “We see lots of regulatory elements that are turning on in these tissues,” Lowe said. “These are the tissues where humans are refining which genes are expressed and at what level.”

Today, our brains are larger than other apes, and our guts are shorter. “People have hypothesized that those two are even linked, because they are two really expensive metabolic tissues to have around,” Lowe said. “I think what we’re seeing is that there wasn’t really one mutation that gave you a large brain and one mutation that really struck the gut, it was probably many of these small changes over time.”

To produce the new findings, Lowe’s lab collaborated with Duke colleagues Tim Reddy, an associate professor of biostatistics and bioinformatics, and Debra Silver, an associate professor of molecular genetics and microbiology to tap their expertise. Reddy’s lab is capable of looking at millions of genetic switches at once and Silver is watching switches in action in developing mouse brains.

“Our contribution was, if we could bring both of those technologies together, then we could look at hundreds of switches in this sort of complex developing tissue, which you can't really get from a cell line,” Lowe said.

“We wanted to identify switches that were totally new in humans,” Lowe said. Computationally, they were able to infer what the human-chimp ancestor’s DNA would have been like, as well as the extinct Neanderthal and Denisovan lineages. The researchers were able to compare the genome sequences of these other post-chimpanzee relatives thanks to databases created from the pioneering work of 2022 Nobel laureate Svante Pääbo.

“So, we know the Neanderthal sequence, but let's test that Neanderthal sequence and see if it can really turn on genes or not,” which they did dozens of times.

“And we showed that, whoa, this really is a switch that turns on and off genes,” Lowe said. “It was really fun to see that new gene regulation came from totally new switches, rather than just sort of rewiring switches that already existed.”

Along with the positive traits that HAQERs gave humans, they can also be implicated in some diseases.

Most of us have remarkably similar HAQER sequences, but there are some variances, “and we were able to show that those variants tend to correlate with certain diseases,” Lowe said, namely hypertension, neuroblastoma, unipolar depression, bipolar depression and schizophrenia. The mechanisms of action aren’t known yet, and more research will have to be done in these areas, Lowe said.

“Maybe human-specific diseases or human-specific susceptibilities to these diseases are going to be preferentially mapped back to these new genetic switches that only exist in humans,” Lowe said.
Copyright: © 2022 The authors.
Published by Elsevier Inc. Open access. (CC BY 4.0)
The authors give more technical detail in the Highlights and Summary sections of their open access paper in Cell:
Highlights
  • HAQERs are human genomic regions highly divergent from the human-chimpanzee ancestor
  • HAQERs evolved under elevated mutation rates and positive selection
  • HAQERs are enriched for bivalent chromatin and disease-linked variation
  • HAQER divergence forged hominin-unique enhancers in the developing cerebral cortex

Summary

Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term “human ancestor quickly evolved regions” (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.

And once again, with monotonous regularity, a group of researchers refutes creationism, and especially the childish claim that the Theory of Evolution is a theory in crisis, about to be overthrown by the superstition of intelligent [sic] design Creationism.

Creationism in Crisis - Genetics Confirms Common Ancestry of 'Oddball' Fungi

Genome studies uncover a new branch in fungal evolution | Folio
Earth tongue fungi
The earth tongue is one of 600 “oddball” fungi that were found to share a common ancestor dating back 300 million years, according to University of Alberta researchers.
Photo: Alan Rockefeller, (CC-BY-SA-4.0)

In a stunning example of the power of the Theory of Evolution (TOE) to explain otherwise puzzling observations, a team of scientists led by principal investigator, Toby Spribille an associate professor in Alberta University's Department of Biological Sciences, has shown how some 600 'oddball' fungi share a common ancestor that lived about 300 million years ago.

The problem was that the usual Linnaean method of classification, using the appearance of organisms, some 600 strange fungi were difficult to fit into any single taxon.

In addition to this obvious confirmation that the TOE is the basis of biology, confirmed by genetics, there is the additional embarrassment for Creationists in the finding that the diversity of this group is due to a loss of genetic information, made possible by a symbiotic existence, where the co-symbiont has taken on some of the basic functions. That a loss of information is always detrimental and evolution requires an increase in information is now a central dogma of Creationism that flies in the face of evidence such as this.

The Alberta University news release explain the research:

Thursday 24 November 2022

Wednesday 23 November 2022

Creationism in Crisis - Modern Humans Are Not The First To Appreciate Art

How we discovered that Neanderthals could make art
Neanderthal woman
Reconstruction of a Neanderthal woman

Morten Jacobsen (CC BY 2.5)
Creationist superstition says that human beings were made somehow differently to all the other animals, although they can never say how, exactly. Some believe only humans have an unproven and undefined magic entity living inside their body, called a 'soul', but other animals don't have this magic ingredient; others argue that animals also have this magic ingredient. They disagree endlessly on this point simply because they have no facts by which to determine the truth. If the 'soul' was detectable, the issue could be resolved easily and quickly. As it is, all they have is dogma.

But whatever their view of who has a magic soul and who doesn't, high on their list of abilities that humans have that other animals allegedly don't have will be aesthetic appreciation of art, music, love, etc. Some attribute this to the magic soul thing, others are happy to regard it as part of some unique aspect of human psychology, neuro-physiology, and/or genetics, so, of course, any evidence that another species has aesthetic appreciation is a major embarrassment for them.

However, with regard to artistic appreciation, there is now strong evidence that our cousin species, Neanderthals, could make artistic or symbolic designs, so, since we are related through a common ancestor - probably Homo heidelbergensis or Homo erectus, if indeed they were different species, it is highly likely that at least the potential for making symbolic drawings was present in that ancestor.

How do we know Neanderthals could make art?

In this article reprinted from The Conversation under a Creative Commons license, Dr Chris Standish, Postdoctoral Fellow of Archaeology, and Professor Alistair Pike, Professor of Archaeological Sciences, both of Southampton University, Hampshire, UK, present the evidence.

The article is reformatted for stylistic consistence. The original can be read here:

How we discovered that Neanderthals could make art

Neanderthal art.
Credit: P. Saura

Chris Standish, University of Southampton and Alistair Pike, University of Southampton

What makes us human? A lot of people would argue it is the ability of our species to engage in complex behaviour such as using language, creating art and being moral. But when and how did we first become “human” in this sense? While skeletal remains can reveal when our ancestors first became “anatomically modern”, it is much harder for scientists to decipher when the human lineage became “behaviourally modern”.

One of the key traits of behavioural modernity is the capacity to use, interpret and respond to symbols. We know that Homo sapiens have been doing this for at least 80,000 years. But its predecessor in parts of Eurasia, the Neanderthal, a human ancestor that became extinct around 40,000 years ago, has traditionally been regarded as uncultured and behaviourally inferior. Now our new study, published in Science, has challenged this view by showing that Neanderthals were able to create cave art.

The earliest examples of symbolic behaviour in African Homo sapiens populations include the use of mineral pigments and shell beads – presumably for body adornment and expressions of identity.

However, evidence for such behaviour by other human species is far more contentious. There are some tantalising clues that Neanderthals in Europe also used body ornamentation around 40,000 to 45,000 years ago. But scientists have so far argued that this must have been inspired by the modern humans who had just arrived there – we know that humans and Neanderthals interacted and even interbred.

Wall in Maltravieso Cave showing three hand stencils (centre right, centre top and top left).

Credit: H. Collado
Cave art is seen as a more sophisticated example of symbolic behaviour than body ornamentation, and has traditionally been thought of as a defining characteristic of Homo sapiens. In fact, most researchers believe that the cave art found in Europe and dating back over 40,000 years must have been painted by modern humans, even though Neanderthals were around at this time.

Dating cave art

Unfortunately, we have a poor understanding of the origins of cave art, primarily due to difficulties in accurately dating it. Archaeologists typically rely on radiocarbon dating when trying to date events from our past, but this requires the sample to contain organic material.

Calcium carbonate crust overlying pigment in La Pasiega.

Credit: J. Zilhão
Cave art, however, is often produced from mineral-based pigments which contain no organics, meaning radiocarbon dating isn’t possible. Even when when it is – such as when a charcoal-based pigment has been used – it suffers from issues of contamination which can lead to inaccurate dates. It is also a destructive technique, as the sample of pigment has to be taken from the art itself.

Uranium-thorium dating of carbonate minerals is often a better option. This well-established geochronological technique measures the natural decay of trace amounts of uranium to date the mineralisation of recent geological formations such as stalagmites and stalactites – collectively known as “speleothems”. Tiny speleothem formations are often found on top of cave paintings, making it possible to use this technique to constrain the age of cave art without impacting on the art itself.

A new era

We used uranium-thorium dating to investigate cave art from three previously discovered sites in Spain. In La Pasiega, northern Spain, we showed that a red linear motif is older than 64,800 years. In Ardales, southern Spain, various red painted stalagmite formations date to different episodes of painting, including one between 45,300 and 48,700 years ago, and another before 65,500 years ago. In Maltravieso in western central Spain, we showed a red hand stencil is older than 66,700 years.

Ladder shape in red painted in the La Pasiega cave.

Credit: C.D Standish, A.W.G. Pike and D.L. Hoffmann
These results demonstrate that cave art was being created in all three sites at least 20,000 years prior to the arrival of Homo sapiens in western Europe. They show for the first time that Neanderthals did produce cave art, and that is was not a one off event. It was created in caves across the full breadth of Spain, and at Ardales it occurred at multiple times over at least an 18,000-year period. Excitingly, the types of paintings produced (red lines, dots and hand stencils) are also found in caves elsewhere in Europe so it would not be surprising if some of these were made by Neanderthals, too.

Drawing of the ladder symbol painted on the walls.

Credit: Breuil et al. (1913)
We don’t know the exact meaning of the paintings, such as the ladder shape, but we do know they must have been important to Neanderthals. Some of them were painted in pitch black areas deep in the caves – requiring the preparation of a light source as well as the pigment. The locations appear deliberately selected, the ceilings of low overhangs or impressive stalagmite formations. These must have been meaningful symbols in meaningful places.

Our results are tremendously significant, both for our understanding of Neanderthals and for the emergence of behavioural complexity in the human lineage. Neanderthals undoubtedly had the capacity for symbolic behaviour, much like contemporaneous modern human populations residing in Africa.

To understand how behavioural modernity arose, we now need to shift our focus back to periods when Homo sapiens and Neanderthals interacted and to the period of their last common ancestor. The most likely candidate for this ancestor is Homo heidelbergensis, which lived over half a million years ago.

It is perhaps also now time that we move beyond a focus on what makes Homo sapiens and Neanderthals different. Modern humans may have “replaced” Neanderthals, but it is becoming increasingly clear that Neanderthals had similar cognitive and behavioural abilities – they were, in fact, equally “human”. The Conversation
Chris Standish, Postdoctoral Fellow of Archaeology, University of Southampton and Alistair Pike, Professor of Archaeological Sciences, University of Southampton

Published by The Conversation.
Open access. (CC BY 4.0)

Religious Superstition News - Continuing Widespread Belief in Witchcraft

Witchcraft beliefs around the world: An exploratory analysis | PLOS ONE
A map showing country-level prevalence of witchcraft beliefs around the world.

Boris Gershman, 2022, PLOS ONE, (CC-BY 4.0)
The belief that certain individuals, often as the result of possession by demons, have the power to suspend the laws of nature at will and make unnatural events occur, sometimes with the casting of magic spells but often with a look, still persists even in some technologically advanced economies.

This is revealed in a database, newly-compiled by Boris Gershman, associate professor of economics, American University in Washington DC, USA, and published today in the journal PLOS ONE.

Belief in witchcraft, demons and the power of magic words and/or thoughts to control natural objects and forces is just another manifestation of the teleological thinking of childhood which causes Creationism, and to some extent, religion when retained in an adult. It is based on the assumption that everything, including atoms, molecules and forces such as gravity have a personality and are sentient, so can be controlled by words and telepathically by thoughts ,and that there is a magical entity 'somewhere out there' who is controlling everything telepathically, or making laws which force them to comply.
There is, of course, no evidence to support that notion which has been part of human culture since the fearful infancy of our species, when a belief in evil magic seems a rational explanation for diseases that are now known to be caused by poisons, parasitic organisms, genetics, physiological disorders, dietary deficiencies or surfeits, etc - explanations which don't require magic and supernatural forces.

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