How Science Works - And Why Religion Doesn't - Dark Matter - Building Testable Hypotheses

Map of the distribution of dark matter in the Universe.
The bright areas represent its highest concentrations - which is where galaxies form

N Jeffrey/Dark Energy Collaboration

Dark Matter

‘Dark stars’: dark matter may form exploding stars – and observing the damage could help reveal what it’s made of

Dark matter is known to exists, and yet no-one knows what it is.

Creationists, in a desperate attempt to reduce science to the same status as their evidence-free superstition, will claim this shows that science is a religion really. But that childish claim soon disintegrates when we understand how scientists can know that dark matter exists when they don't know what it is.

Unlike religion's god(s), scientists can measure dark matter's effects on stuff they know more about, like the 'normal' matter that you and I are made of - atoms and molecules of which stars, galaxies and super-clusters are made of. They can see the gravitational effects of dark matter, so there must be something with enough mass to produce that gravitational effect.

Theists, on the other hand can never demonstrate any effects of the god(s) they believe in and are reduced to presuppositional claims and assertions, designating their god(s) as the cause of things they don't understand - the god of the gaps false dichotomy fallacy that passes for religious apologetics.

So, what are these effects that dark matter exerts?

The gravity produced by dark matter is what holds spinning galaxies together and prevents the detectable matter in them from flying outwards by the centrifugal force of rotation. It also produces gravitational 'lensing', which is the effect of light being bent by a large mass to act like a giant lens and make distant objects look closer.

So, we know dark matter is out there even though we don't know what it is, so scientists try to work out what it could be composed of and make predictions of what this stuff would do if it existed. This is the testable hypothesis. The trick is to construct experiments to test those hypotheses.

In the following article, Andreea Font, Reader in Theoretical Astrophysics, Liverpool John Moores University, Liverpool, UK, outlines some of the current hypotheses that seek to explain dark matter. Her article is reprinted from The Conversation under a Creative Commons license, reformatted for stylistic consistency.

Malevolent Designer - How Creationism's Putative Designer COULD Have Given Us A Mechanism to Prevent Heart Attacks But Chose Not To

Naked mole-rat, Heterocephalus glaber

Photo: TxanTxunai via Wikimedia Commons

Naked mole rats, Heterocephalus glaber - uniquely able to resist cardiac damage.

FMD - Secrets of the naked mole-rat: new study reveals how their unique metabolism protects them from heart attacks - Queen Mary University of London

Part of creationists mythology is the belief that humans stand at the pinnacle of creation, being the supreme creation of their putative designer. Even those who accept the evidence for evolution, like to imagine that somehow evolution was intended to result in humans being at the apex of it.

As you would expect of creationism, those beliefs are counter-factual and so are not supported by the evidence, and, if they are to be believed, paints their putative creator god in a very poor light, not the least because of the very many examples of where, if it had created humans and all the other species, humans come off at best second best, having inferior versions of organs and processes compared to many other species. I list several of these in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good, for example, the superior eye of the peregrine falcon, the superior immune system of bats and the fact that elephants and sharks rarely get cancer.
Now we have the example of naked mole rats which are able to suffer anoxia without sustaining damage to their cardiac muscles, so they rarely have heart attacks.

The damage during a heart attack, i.e., when a cardiac artery is blocked by a blood clot, is cell death due to being deprived of oxygen. But Naked mole rats have a unique cardiac metabolism and unique genes, that enable their cardiac muscle cells to survive a period of anoxia.

The reason for this, and the mechanism creationism's creative god could have given humans if it were real and is as omnibenevolent as creationists like to pretend, was discovered by researchers from London, Pretoria and Cambridge, led by Dr. Dunja Aksentijevic of the Centre for Biochemical Pharmacology, William Harvey Research Institute, Bart’s and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.

The team have just published their findings, open access, in the journal Nature Communications. It is also explained in a Queen Mary University news release:

Creationism in Crisis - 4,000 Year-Old Human Teeth From Ireland Show No Signs Of The legendary Biblical Flood - But Every Sign of Evolution

The scientists extracted the information from teeth like the one pictured here.

Image credit: Dr Lara Cassidy.

Killuragh Cave, County Limerick, Ireland.

Photo: Sam Moore; Owner: Marion Dowd.

Genetic secrets from 4,000-year-old teeth to illuminate the impact of changing human diets over the centuries - News & Events | Trinity College Dublin

What can you tell from two, 4000-year-old human teeth found in a limestone cave in Ireland?

Firstly, you can tell a great deal about the food their owner ate and what state their oral hygiene was in.

Secondly, you can tell how the microbiome of the human mouth has evolved over the last 4000 years.

Thirdly, you can tell that, wherever creationism's global flood took place, it missed this cave in Ireland, because had the cave been flooded, the remains of bacterial DNA in the plaque on the teeth would have been washed off, even in the unlikely event of the skeletal remains staying in the cave.

And lastly, you can tell the cave is very much older than the 10,000 years creationists believe Earth has existed for because limestone caves form slowly over millions of years due to the action of water on limestone deposits that themselves take millions of years to accumulate and be compressed into limestone.

But then the ignorant goat-herders who invented the mythical global flood knew nothing of limestone cave formation, Ireland, the people who lived there, the state of their oral hygiene, or micro-organisms for that matter, so what did you expect? Miracles?

The two teeth, from the same individual, were part of a large skeletal assemblage excavated from Killuragh Cave, County Limerick, by the late Peter Woodman of University College Cork. They have been used by researchers from Trinity College, Dublin to recover a remarkably well-preserved microbiome which shows major changes in the oral microenvironment from the Bronze Age to today.

The researchers, led by Dr Lara Cassidy, an assistant professor in Trinity’s School of Genetics and Microbiology and including scientists from the Atlantic Technological University and University of Edinburgh, have published their findings, open access in the journal Molecular Biology and Evolution and describe them in a Trinity College News release:

Researchers from Trinity have recovered remarkably preserved microbiomes from two teeth dating back 4,000 years, found in an Irish limestone cave. Genetic analyses of these microbiomes reveal major changes in the oral microenvironment from the Bronze Age to today.

The teeth both belonged to the same male individual and also provided a snapshot of his oral health.

The study, carried out in collaboration with archaeologists from the Atlantic Technological University and University of Edinburgh, was published today in leading journal Molecular Biology and Evolution.

The authors identified several bacteria linked to gum disease and provided the first high-quality ancient genome of Streptococcus mutans, the major culprit behind tooth decay.

While S. mutans is very common in modern mouths, it is exceptionally rare in the ancient genomic record. One reason for this may be the acid-producing nature of the species. This acid decays the tooth, but also destroys DNA and stops plaque from fossilising. While most ancient oral microbiomes are retrieved from fossilised plaque, this study targeted the tooth directly.

Another reason for the scarcity of S. mutans in ancient mouths may be the lack of favorable habitats for this sugar-loving species. An uptick of dental cavities is seen in the archaeological record after the adoption of cereal agriculture thousands of years ago, but a far more dramatic increase has occurred only in the past few hundred years when sugary foods were introduced to the masses.

The sampled teeth were part of a larger skeletal assemblage excavated from Killuragh Cave, County Limerick, by the late Peter Woodman of University College Cork.

While other teeth in the cave showed advanced dental decay, no cavities were visible on the sampled teeth. However, one tooth produced an unprecedented amount of S. mutansDNA, a sign of an extreme imbalance in the oral microbial community.

We were very surprised to see such a large abundance of S. mutans in this 4,000-year-old tooth. It is a remarkably rare find and suggests this man was at a high risk of developing cavities right before his death.

Dr Lara Cassidy, senior author.
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.

The researchers also found that other streptococcal species were virtually absent from the tooth. This indicates the natural balance of the oral biofilm had been upset – mutans had outcompeted the other streptococci leading to the pre-disease state.

The team also found evidence to support the "disappearing microbiome" hypothesis, which proposes modern microbiomes are less diverse than those of our ancestors. This is cause for concern, as biodiversity loss can impact human health. The two Bronze Age teeth produced highly divergent strains of Tannerella forsythia, a bacteria implicated in gum disease.

These strains from a single ancient mouth were more genetically different from one another than any pair of modern strains in our dataset, despite the modern samples deriving from Europe, Japan and the USA. This represents a major loss in diversity and one that we need to understand better.

Iseult Jackson, first author.
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.

Very few full genomes from oral bacteria have been recovered prior to the Medieval era. By characterising prehistoric diversity, the authors were able to reveal dramatic changes in the oral microenvironment that have happened since.

Over the last 750 years, a single lineage of T. forsythia has become dominant worldwide. This is the tell-tale sign of natural selection, where one strain rises rapidly in frequency due to some genetic advantage it holds over the others. T. forsythia strains from the industrial era onwards contain many new genes that help the bacteria colonise the mouth and cause disease.

S. mutans has also undergone recent lineage expansions and changes in gene content related to pathogenicity. These coincide with humanity’s mass consumption of sugar, although we did find that modern S. mutans populations have remained more diverse, with deep splits in the S. mutans evolutionary tree pre-dating the Killuragh genome.

Dr Lara Cassidy.

The scientists believe this is driven by differences in the evolutionary mechanisms that shape genome diversity in these species.

S. mutans is very adept at swapping genetic material between strains. This means an advantageous innovation can be spread across S. mutans lineages like a new piece of tech. This ability to easily share innovations may explain why this species retains many diverse lineages without one becoming dominant and replacing all the others.

Dr Lara Cassidy.

In effect, both these disease-causing bacteria have changed dramatically from the Bronze Age to today, but it appears that very recent cultural transitions in the industrial era have had an inordinate impact.

Technical details and background to the research is given in the team's open access paper in Molecular Biology and Evolution:

Abstract

Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.

Introduction

The oral cavity is the most well-studied aspect of the ancient human microbiome, mainly due to the excellent preservation of DNA in calculus (fossilized dental plaque). However, three quarters of published ancient oral metagenomes date to within the last 2,500 years, with few full genomes available from prior to the medieval period (Fellows Yates et al. 2022). While a small number of much older preagricultural genomes have yielded important insights (Fellows Yates et al. 2021), prehistoric diversity and the impact of Holocene dietary transitions are not well characterized. Common oral taxa identified in these metagenomes include the “red complex” bacteria Tannerella forsythia, Treponema denticola, and Porphyromonas gingivalis, which are important in the development of periodontitis, a highly polymicrobial disease (Socransky et al. 1998). However, another species with a major impact on public health, Streptococcus mutans, is not preserved in calculus (Velsko et al. 2019), and has no published ancient genomes.

Streptococcus mutans is the primary cause of dental caries (Lemos et al. 2019.1), and is common in modern oral microbiomes (Achtman and Zhou 2020). Its lack of preservation in ancient microbiomes may be largely due to its acidogenic nature; acid degrades DNA and prevents plaque mineralization, which is the main substrate used for sampling (Velsko et al. 2019). Its absence may also reflect less favorable habitats for S. mutans across most of human history. Indeed, metagenomic surveys of ancient and modern microbiomes suggest that the species only became a dominant member of the oral microbiota after the medieval period due to major dietary changes, such as the popularization of sugar (Adler et al. 2013; Achtman and Zhou 2020). However, another study of modern genomes has placed more emphasis on the Neolithic transition as a driver of S. mutans proliferation (Cornejo et al. 2013.1). Caries are observed more frequently in the archaeological record after the adoption of cereal agriculture, but rise in incidence through time with a sharp increase in the Early Modern period (Bertilsson et al. 2022.1).

The relative importance of prehistoric and recent dietary transitions in the evolution of red complex bacteria is also poorly characterized. Tannerella forsythia is one of the better studied species (Warinner et al. 2014; Bravo-Lopez et al. 2020.1; Philips et al. 2020.2; Honap et al. 2023), with 55 genomes currently available (supplementary table S1, Supplementary Material online). Surveys of preagricultural (Fellows Yates et al. 2021) and European medieval diversity (Warinner et al. 2014; Philips et al. 2020.2) have shown no clear temporal trends in T. forsythia phylogenetic structure, although functional differences between ancient and modern genomes have been observed (Warinner et al. 2014; Philips et al. 2020.2). However, these data have not been coanalyzed. Here, we shed light on prehistoric oral pathobiont diversity, as well as recent changes in these species’ demography and functional repertoire, by retrieving the first ancient S. mutans genome and two distinct strains of T. forsythia from a single Early Bronze Age individual.

[…]

Conclusion

Adding a temporal dimension to pathogen genomics allows us to better estimate the timing of key evolutionary changes, as well as to capture extinct diversity. In this study, we have reconstructed ancient genomes for T. forsythia and S. mutans, which demonstrate dramatic changes in oral pathobiont population dynamics and functional composition in the last 750 years. For both species, there is a distinction between postindustrial and earlier genomes in terms of virulence factors. This is clearest in T. forsythia, where there is a temporal transect of ancient genomes: here, preindustrial genomes have a stark difference in functional repertoire compared to industrial and modern genomes. Both the host immune response and interactions with other oral microbes would be impacted by these changes. Although there is only 1 ancient S. mutans genome (KGH2-B) of sufficient quality to compare with the modern dataset, analysis in tandem with phylogenetic information implies that the modern mutacin repertoire is also a relatively recent acquisition.

Concurrent population expansions were inferred in both S. mutans and T. forsythia phylogenies in the postmedieval period, but extant S. mutans populations harbor much deeper diversity compared to T. forsythia. We hypothesize that this is related to the species’ different susceptibilities to genome-wide selective sweeps, which are more likely to occur when within-population recombination is low (Bendall et al. 2016). Streptococcus mutans is a highly recombining species (Cornejo et al. 2013.1), allowing advantageous variation to be exchanged between population members and resulting in gene-specific sweeps. In T. forsythia, genome structure is relatively stable and small-scale mutation appears to be the major driving force of diversification (Endo et al. 2015). This could lead to repeated purges in genetic heterogeneity in the population. These purges may have intensified in the past several centuries, as evidenced by the loss of diversity in modern and industrial populations, relative to prehistoric strains from the same Early Bronze Age individual. In general terms, higher biodiversity in ecosystems makes them more resilient to perturbations from environmental stressors (e.g. dietary changes and colonization by pathogenic bacteria in the case of the oral microbiome). The reduction in T. forsythia diversity over time coincides with a general loss of oral biodiversity discussed in Adler et al. (2013).

Going forward, denser sampling of ancient microbial populations may provide new insights into the evolutionary mechanisms that underlie bacterial taxon formation, adaptation and maintenance of diversity, which can vary depending on species and environment. Some species will be more amenable to dense temporal sampling than others. In particular, low levels of S. mutans preservation in the ancient DNA record may pose a significant challenge. Targeted capture of genes of interest (e.g. mutacins) as well as the core genome may provide a solution, but risks losing pangenomic diversity. In the case of T. forsythia, which is more abundant in the archaeological record, ancient metagenomic assemblies in the future may allow for the identification of hitherto unknown virulence factors in earlier strains; our analysis here is limited to the genomic content of modern T. forsythia samples, as all the ancient genomes are reference-aligned.

Overall, our findings demonstrate the utility of ancient genomes in characterizing different modes of pathobiont evolution. Temporal resolution of virulence genes can provide further insight into the shifting selection regimes of pathobionts in the human oral microbiome. In addition, these results highlight that recent cultural transitions, such as the popularization of sugar, are most relevant to understanding the shaping of present-day oral pathobiont diversity.

Iseult Jackson, Peter Woodman, Marion Dowd, Linda Fibiger, Lara M Cassidy
Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts Molecular Biology and Evolution, Volume 41, Issue 3, March 2024, msae017, https://doi.org/10.1093/molbev/msae017

Copyright: © 2024 The authors/Society for Molecular Biology and Evolution.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

There is a lot there for creationists to try to ignore or lie about, either to themselves or to the fools they are trying to recruit into their money-making scam.

1. There is the geological evidence of a limestone cave which takes millions of years to form.
2. There is the evidence for evolution in the differences between the genomes of the micro-organisms found on the plaque on the surface of the teeth.
3. There is the absence of any evidence for a global flood in the fact that the contents of the cave have not been submerged in water and have none of the inevitable deposits on them that would have resulted from such a flood.
4. There is the evidence that there were people living in Ireland 4,000 years ago when creationists legend says they should all have been drowned in a global flood (which apparently never reached County Limerick).
5. There is the evidence for evolution in both the micro-organisms themselves and also in the biodiversity of the human oral microbiome which have changed significantly as the main sources of food have changed, showing how the environment drives evolutionary change.

All in all, a great deal of cognitive dissonance for which creationists will need to employ their usual coping mechanisms.

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Old Dead Gods - What Does The Cerne Abbas Giant Depict And When Was It Created?

Aerial view showing the field below the giant and the “herepath” curving up onto Giant Hill from the bottom right,
Cerne Abbas, Dorset, England.

Photo: Pete Harlow, CC BY-SA 3.0, via Wikimedia Commons.

The Cerne Abbas Giant, Cerne Abbas, Dorset, England.

Photo: Ray Gaffney. © National Trust.

Uncovering the mystery of Dorset’s Cerne Giant

The thing about most of the ancient monuments and hill markings like the Uffington White Horse after whom the district of Oxfordshire I live in was named, is that no-one knows what religion the people who made them believed in or how, if indeed it did, their religion inspired (or required) them to create these monuments. I have written extensively about monuments such as Stonehenge, Durrington Walls, Silbury Hill, Avebury Stone Circle and West Kennet Long Barrow as example of how little we know about these ancient people and their religion(s) because these ancient monuments stand as testament to the transient and ephemeral nature of gods and religions on the scale of human history.

Unlike science, which, if some disaster befell humankind and all memory of a major science were expunged from memory, could be reconstructed from basic principles because it describes reality, religions, once lost and forgotten are lost forever because there is nothing substantial upon which to found a rediscovery. The entire edifice of religion is unsupported and insubstantial, being nothing more than collective imaginings and handed-down stories and myths, dependent entirely on faith to sustain them in the absence of evidence.

How Evolution Works - Choas, Catastrophe and Tipping Points

The fitness landscape of hyphae showing that natural shapes are constrained by a tipping point.

Credit: Maxim Ohairwe

Hyphal mycelium.

credit: Maxim Ohairwe.

Researchers Discover Evolutionary “Tipping Point” in Fungi

An interesting paper has just been published which illustrates how chaos theory and catastrophe theory are related and explain the appearance of 'punctuated equilibrium' in the fossil record. It concerns the small environmental change that can trigger a large phenotypic change in the growth and shape of fungal hyphae.

One of the more annoying things to emerge in evolutionary biology during the last 30 years or so is the idea that 'Punctuated Evolution' (PE) somehow either falsifies or replaces Darwinian evolution as the explanation for biodiversity. Of course, it does neither. The term was invented by Stephen J Gould and Niles Eldredge, to explain the appearance of sudden change in the geological column, where species appear to remain unchanged for prolonged periods of time, then change, in what, with the compression of time in the geological column, looks like instantaneously.

Sadly, the term quickly became entangled with both American nationalism and creationism; the latter because it appears to refute the person whom creationists think is the arch prophet of the 'evil' of evolution - Charles Darwin, the leading figure in creationist demonology - as though the entire body of evolutionary biology hangs on the authority of one 19th century biologist; the former because it appears to have replaced one of the most famous scientific theories with one 'discovered' by Americans, so asserting American pre-eminence in science.

Tell me about 'Punctuated Equilibrium'; who popularized the idea and the arguments for and against it. Punctuated equilibrium is a theory in evolutionary biology that suggests that the tempo of evolution is not constant but rather characterized by periods of relatively rapid change (punctuation) interspersed with prolonged periods of stability (equilibrium). This concept was popularized by paleontologists Niles Eldredge and Stephen Jay Gould in their 1972 paper "Punctuated Equilibria: An Alternative to Phyletic Gradualism."

Arguments for punctuated equilibrium include:

1. Fossil Record: Eldredge and Gould argued that the fossil record often shows long periods of stasis, where species exhibit little morphological change over millions of years, followed by relatively rapid bursts of evolutionary change when new species appear.
2. Lack of Transitional Forms: They also pointed out that the fossil record frequently lacks the transitional forms predicted by gradualism, which suggests that evolution may occur in more rapid bursts.
3. Genetic Mechanisms: Some genetic models also support the idea of punctuated equilibrium, suggesting that small populations undergoing rapid change due to factors like genetic drift and founder effects can lead to rapid speciation.

Arguments against punctuated equilibrium include:

1. Lack of Evidence: Critics argue that punctuated equilibrium is based more on interpretation of the fossil record rather than direct evidence from genetic or ecological studies.
2. Sampling Bias: Some scientists suggest that the apparent gaps in the fossil record may be due to incomplete sampling rather than actual periods of stasis.
3. Mechanistic Explanation: Critics also question the mechanisms underlying punctuated equilibrium, arguing that it may be difficult to explain how rapid evolutionary change occurs in the absence of significant environmental pressures or genetic changes.

Overall, punctuated equilibrium remains a subject of debate within evolutionary biology, with proponents arguing that it provides a more accurate description of patterns of evolution observed in the fossil record, while critics suggest that it may overemphasize the importance of long periods of stasis and rapid bursts of change.

Creationism in Crisis - New Evidence Shows What Homo Sapiens Were Doing In Persia, Long Before 'Creation Week'

Pebdeh Cave in the southern Zagros Mountains.
Occupied by hunter-gatherers up to 42,000 years ago.

Photo: Mohammad Javad Shoaee

The Persian Plateau, where early human migrants may have lived for several thousand years before dispersing to other parts of Eurasia.

Photo: Mohammad Javad Shoaee

Persian plateau unveiled as crucial hub for early human migration out of Africa – Griffith News

In that period of the history of Homo sapiens, long before creationism's little god got the idea of creating a small universe resembling a small, flat planet with a dome over it, according to their legends, early migrants out of Africa settled for a prolonged period in the Persian, or Iranian, Plateau where they lived from about 28,000 years, before dispersing to other parts of the Eurasian landmass.

They had earlier migrated out of Africa where they had been evolving from the common ancestor they shared with the other African Great Apes, leaving others behind to evolve into the modern African peoples, while the migrants dispersed across the rest of the globe to become modern Eurasian, Melanesian and American people, interbreeding with the descendants of an earlier migration out of Africa as they did so.

The evidence for a prolonged occupation of the Persin Plateau and the Zagros Mountains comes from a combination of genetic, palaeoecological, and archaeological evidence by a team from multiple Italian Universities and including Professor Michael D. Petraglia, of the Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia.

The team have presented their evidence in an open access paper in Nature Communications and explain it in a Griffith University news item: This study sheds new light on the complex journey of human populations, challenging previous understandings of our species’ expansion into Eurasia.

Creationism in Crisis - Now It's An Ancestral Amphibian from 270 Million Years Before 'Creation Week' - And Another Gap Closes

Fossil skull of Kermitops gratus

Brittany M. Hance, Smithsonian.

Fossil skull of Kermitops gratus

Brittany M. Hance, Smithsonian.

Researchers Name Prehistoric Amphibian Ancestor Discovered in Smithsonian Collection After Kermit the Frog | Smithsonian Institution

Once upon a time, about 10,000 years ago, a magic man made of nothing appeared from nowhere and decided to create a universe that looked like a small flat planet with a dome over it, or so some ignorant Bronze Age pastoralists told their children.

Of course, they were doing their best with what little knowledge they had of the world they lived in and its history, so they filled the gaps in their knowledge and understanding with stories, and of course got it almost entirely and spectacularly wrong.

We know this because, unlike the story-tellers from the fearful infancy of our species, we now have the knowledge and understanding that centuries of careful science has revealed to us - at least those of us with the capacity to learn and understand the science know it. This is why those still unable to believe their mummy and daddy could be wrong about the superstitions they were taught as children but have since learned some science, are increasingly calling the creation stories in the Bible allegorical or metaphorical, while those who have a more objective view dismiss then as the work of ignorant people who knew no better.

Of course, despite herculean mental efforts, none of the creation myth can be forced into an allegory or metaphor for the existence of early proto-amphibians 270 million years before the little domed universe was magicked up out of nothing, and the existence of just such an animal was shown to be a fact of history when it was examined by palaeontologists from George Washington University who examines a fossil in the collection of the Smithsonian’s National Museum of Natural History and found to be 270-million-year-old fossil of a previously unknown proto-amphibian, which they have named Kermitops gratus after Kermit the Frog.

The three scientists who made this discovery, led by Calvin So, a doctoral student at the Department of Biological Sciences, George Washington University, Washington, DC, USA, have pubished their finding open access in the Zoological Journal of the Linnean Society and explained it in a Smithsonian Museum news release:

Religious Child Abuse News - Those Believing Absurdities Commit Atrocities - Chidren Starved and Tortured For Being 'Possessed By Satan'

Religious fanatics Ruby Franke and Jodi Hildebrandt. 30 Years in Jail for aggravated child abuse.

Photo: Washington County (Utah) Sheriff's Department

Religious fanatics Jodi Hildebrandt, left, and Ruby Franke, center, being arrested on child abuse charges on Aug. 30, 2023, in Ivins, Utah.

Washington County Attorney’s Office via AP

YouTuber Ruby Franke's child abuse case rooted in religious extremism | AP News

Only a few days ago I wrote an article explaining why people who believe absurdities can be persuaded to commit atrocities and now we have a spectacular example of the truth of that claim.

It comes in the form of an Associated Press story of how a fanatical Mormon and mother of six, Ruby Franke, who held the absurd belief that magic demons can take over and 'possess' people because her religion teaches that these demons exist, became convince that her twelve-year-old son and nine-year-old daughter were the Devil incarnate and inflicted physical punishment, including deliberate starvation, on them, "to teach them how to properly repent for imagined ‘sins’ and to cast the evil spirits out of their bodies".

Belief in a magical 'evil' Devil figure is of course fundamental to the Abrahamic superstitions, of which Mormonism is a recent manifestation, and is found in all forms of Judaism, Christianity and Islam and their derivative superstitions. It was particularly strong during the Middle Ages when thousands of (mostly) women were burned alive in the belief that they were so possessed.

Ruby Franke and a business associate, Jodi Hildebrandt, have each been sentenced to 30 years in jail after pleading guilty to four counts of aggravated child abuse after the 12-year-old boy managed to escape through a window from the room he was locked in and alerted a neighbour who called the police.

Franke is a well-known YouTuber who made her name lecturing gullible people who assumed her religious fanaticism gave her special insight into how to be a good parent. She and Hildebrandt, a fellow Mormon and mental health counsellor, were arrested after neighbours, the Clarksons, answered their door to find an emaciated boy with bruising and other injuries on their doorstep.

Creationism in Crisis - How The Milky Way Was Formed - 12-13 Billion Years Before 'Creation Week'

A visualisation of the Milky Way galaxy, with the stars that Khyati Malhan and Hans-Walter Rix identified in the Gaia DR3 data set as belonging to Shiva and Shakti shown as colored dots. Shiva stars are shown in green and Shakti stars in pink.

© S. Payne-Wardenaar / K. Malhan / MPIA

Researchers identify two of the Milky Way's earliest building blocks | Max Planck Institute for Astronomy

Between 12 and 13 billion years before creationism's little god decided to create a small flat planet with a dome over it in the Middle east, where the only people to notice were simple goat-herders from the Bronze Age, natural forces were creating the Milky Way galaxy out of two smaller galaxies that astronomers have named Shiva and Shaki.

The discovery was made by two scientists working at the Max Planck Institute for Astronomy, Heidelberg, Germany who have identified the components of two proto-galaxies that merged to form the Milky Way, by combining data from ESA’s astrometry satellite Gaia with data from the SDSS survey. The astronomers have published their findings in a highly technical paper in The Astrophysical Journal and explain it in a Max Planck Institute for Astronomy news release:

Who are Shiva and Shaki? Shiva and Shakti are two fundamental concepts in Hinduism, representing aspects of the divine.

1. Shiva: Shiva is one of the principal deities of Hinduism. He is often referred to as the destroyer within the Trimurti, the Hindu trinity that includes Brahma (the creator) and Vishnu (the preserver). Shiva is also known as the god of meditation, yoga, and arts. He is usually depicted as a yogi, adorned with snakes and a crescent moon on his head, with a third eye on his forehead representing wisdom and insight. Shiva is often associated with asceticism, but he's also a family man, as he's married to the goddess Parvati and has two sons, Ganesha and Kartikeya.
2. Shakti: Shakti is the divine feminine energy and the primordial cosmic power in Hinduism. She is the personification of the creative energy of the universe. Shakti is often depicted as a goddess, sometimes alongside Shiva, and sometimes as an independent deity. She represents the dynamic forces that move through the entire cosmos. Shakti is considered the mother goddess, the source of all, and is revered in various forms such as Durga, Kali, Parvati, and others.

In some philosophical interpretations, Shiva represents the male principle (Purusha) while Shakti represents the female principle (Prakriti), and their union is seen as the basis of creation and existence. This union is often symbolized as Ardhanarishvara, a composite androgynous form of Shiva and Shakti, depicting the inseparable nature of masculine and feminine energies.

Astronomers have identified what could be two of the Milky Way’s earliest building blocks: Named “Shakti” and “Shiva”, these appear to be the remnants of two galaxies that merged between 12 and 13 billion years ago with an early version of the Milky Way, contributing to our home galaxy’s initial growth. The new find is the astronomical equivalent of archeologists identifying traces of an initial settlement that grew into a large present-day city. It required combining data for nearly 6 million stars from ESA’s Gaia mission with measurements from the SDSS survey. The results have been published in the Astrophysical Journal.

The early history of our home galaxy, the Milky Way, is one of joining smaller galaxies, which makes for fairly large building blocks. Now, Khyati Malhan and Hans-Walter Rix of the Max Planck Institute for Astronomy have succeeded in identifying what could be two of the earliest building blocks that can still be recognized as such today: proto-galactic fragments that merged with an early version of our Milky Way between 12 and 13 billion years ago, at the very beginning of the era of galaxy formation in the Universe. The components, which the astronomers have named Shakti and Shiva, were identified by combining data from ESA’s astrometry satellite Gaia with data from the SDSS survey. For astronomers, the result is the equivalent of finding traces of an initial settlement that grew into a large present-day city.

Creationism in Crisis - How Early Modern Humans Survived a Massive Super-Volcano Which Spurred Their Migration Out Of Africa

Northern Africa.
Inset: Part of South West Ethiopia around Shinfa-Meta 1 site

Excavations at a Middle Stone Age archaeological site, Shinfa-Metema 1, in the lowlands of northwest Ethiopia, revealed a population of humans at 74,000 years ago that survived the eruption of the Toba super-volcano.

Photo courtesy https://topographic-map.com, Open Database License (ODbL) v1.0

Toba super-eruption unveils new insights into early human migration | ASU News

This, the fourth in a clutch of very recent papers that casually and unintentionally refute creationism simply by revealing the facts that run counter to the claims of creationists. It concerns the effects of a devastating volcanic eruption of Mount Toba in Indonesia 64 thousand years before creationists think there was life on Earth, or even an Earth to have life on it.

They believe this because a bunch of Middle Eastern pastoralists made up a tale to fill the gaps in their knowledge and understanding and describe a magic man in the sky creating a small flat planet with a dome over it, just a few thousand years earlier.

The facts are those revealed by a research team which included Curtis Marean, Christopher Campisano and Jayde Hirniak from Arizona State University who have shown that not only did African populations of humans survived the effects of this volcano, the most devastating in human history, but that its effects may have facilitated human dispersal out of Africa into Eurasia. They have presented their evidence in the form of a paper in Nature and explained the research in a University of Arizona news release:

Creationism in Crisis - Now It's a Giant Amazon Dolphin from 16 Million Years Before 'Creation Week'!

Type specimen (holotype) of Pebanista yacuruna, including a photo of the specimen and a surface 3D model in dorsal view.

Image: Aldo Benites-Palomino.

Ancient Giant Dolphin Discovered in the Amazon | | UZH

The third in a clutch of very recent papers casually refuting the childish beliefs of the creation cult.

This one concerns a giant freshwater dolphin that inhabited the Amazon 16 million years before creationists think there was a Universe, let alone an Earth with life on it.

Tell me about the Peruvian Amazon 16 million years ago. Around 16 million years ago, during the Middle Miocene epoch, the Peruvian Amazon region would have been significantly different from its present-day appearance. This period falls within the broader geological timeframe known as the Neogene Period, characterized by significant changes in climate and biodiversity.

During this time, the Amazon basin was undergoing a transformation from a relatively dry environment to a more humid and tropical one. The climate was warmer and wetter compared to today, with vast stretches of lush tropical rainforest covering much of the region.

The landscape would have been dominated by dense forests, rich in diverse flora and fauna. Ancient ancestors of many of today's Amazonian species would have been present, including various types of plants, mammals, birds, reptiles, and insects. Megafauna such as giant ground sloths, glyptodonts, and various types of large herbivores and predators may have roamed the area.

The river systems of the Amazon basin would have been different as well, as the Andes Mountains continued to uplift and shape the landscape. However, the basic hydrological structure of the Amazon River and its tributaries would have already been established, providing the necessary water sources for the flourishing ecosystems.

Overall, the Peruvian Amazon 16 million years ago would have been a vibrant and biodiverse ecosystem, albeit with species compositions and environmental conditions differing from those of today due to ongoing geological and climatic changes over millions of years.

Creationism in Crisis - How Batesian Mimicry In The Female Diadem Butterfly Evolved - Convergently

Female Diadem Butterfly, Hypolimnas misippus

Photograph: A Coetzer

The female Diadem (bottom left) mimics the African Queen (top left). The male Diadem (right) keeps a distinct pattern to attract mates

Scientists discover how Diadem butterfly mimics African Queen - News

This is the second in a sudden spate of research papers that casually and unintentionally refute creationism without even trying, simply by revealing the facts. It deals with the evolution of Batesian mimicry in a species of butterfly.

Scientists working at the universities of Exeter, Edinburgh and Cambridge, and Mpala Research Centre in Kenya have discovered the genetic basis for the clear example of Batesian mimicry to be found in the female of the pantropical species of butterfly, the Diadem butterfly, Hypolimnas misippus, which closely resembles the toxic African queen butterfly, Danaus chrysippus.

Batesian mimicry is the natural phenomenon where an otherwise harmless species evolves to resemble a harmful or distasteful species as a defence mechanism. The prerequisite for Batesian mimicry to evolve is that a prey species is predated upon by the predator of a harmful species which coexists in the same locality. The predator learns to avoid the dangerous or distasteful species so any other species that comes to resemble the harmful or distasteful species might be mistaken for it and avoided. The more closely it comes to resemble the avoided species, the more likely it is to survive and reproduce.

Creationism in Crisis - How Hair Evolved From A Keratin Gene In A Frog-Human Common Ancestor

Western clawed toad, Xenopus tropicalis

Genetic basis for the evolution of hair discovered in the clawed frog

Western Clawed Frog, Xenopus tropicalis
Carries the precursor gene for mammalian hair.

"When sorrows come, they come not single spies but in battalions" - Claudius in Hamlet.

That was never more true of creationism than it is today with the publication of not just the usual casual refutation of creationism we've come to expect most days, but of four disparate papers each of which casually and unintentionally refutes creationism to anyone who understands biology and is familiar with the basic dogmas of the creation cult, simply by revealing real-world facts.

The papers range from this one, which shows how mammalian hair has its genetic origins in a common human-amphibian ancestor, through how a female butterfly evolved Batesian mimicry, through the discovery of a giant Amazonian dolphin from 16 million years before creationists think Earth existed, to how early modern humans survived a super-volcano eruption in South-West Ethiopia a mere 64,000 years before 'Creation Week'.

With so many papers I'll do my best to cover all of them in the next few days, so keep checking back!

Firstly, the evolutionary origin of mammalian hair.

The gene for this originated in a common ancestor of humans (and the other mammals) and a modern clawed frog. The gene controls the growth of keratin, of which the claws of a clawed frog are composed, as is mammalian hair. The evidence for this common origin was found by researchers from the Medical University of Vienna, Austria, led by led by Leopold Eckhart. The team have published their findings open access in Nature Communications and described their work in a Medical University of Vienna new release:

Creationism in Crisis - Order From Chaos in The Namibian Desert

Fairy circles from Iona National Park in Angola

Image: © Michael Fay,
National Geographic Creative.

A typical fairy circle on the Kamberg on the edge of the Namibian Desert

Photo: Stephan Getzin.

Information for the Media - Georg-August-Universität Göttingen

Scientists are hotly debating how the 'fairy circles' which arise in the vegetation on the edge of the Namib desert actually form. Whatever the process, they are examples of order emerging from chaos by the operation of natural forces. The debate is over what exactly those forces are.

Typical of the mindless parroting that constitutes creationism in the social media, is the claim that 'you can't get order from chaos', which of course is nonsense, since any chaotic system will tend to order if a directional force is applied to it.

Suns and galaxies condense out of the chaos of dust and gas clouds under the directional force of gravity; raindrops form in clouds under the directional forces of gravity and electrostatic attraction; and 'fairy rings' form in grassland under the influence of fungal hyphae and nutrient depletion, and rings form in ell grass because of a build-up of toxic sulphides in the marine sediment, just to cite a few examples

Here's a little bit of fun which you can use to show any creationist acquaintance what nonsense they've been fed. Next time you're playing Scrabble, place all the tiles in the upturned box lid and make sure no tile is on top of another. Ask them to swirl it round to show you're not cheating. Observe that the tiles are in a chaotic arrangement. Now apply a directional force in the form of gravity by tipping the box lid about 15 degrees to produce a slope and tapping it or shaking the lid gently to provide a little energy to the system. Observe now that the tiles have formed themselves into neat rows and columns at one end of the lid. If not, give it a little more shaking or tapping.

Order has emerged out of chaos under nothing more magical than the directional force of gravity.

More examples of emergence of order out of chaos are:

Creationism in Crisis - Closing The Last God-Shaped Gap - How The Simplest Cells Could Have Evolved, Naturally

Last Chance Lake in British Columbia

Credit: Zachary R. Cohen

Last Chance Lake in September 2022. At the end of the summer, the water has almost all evaporated, leaving a salty crust on the surface.

Credit: Zachary R. Cohen/Washington University

Did the first cells evolve in soda lakes?

According to a new study by Zachary R Cohen of the Chemistry Department of Washington University, Seatle, WA, USA and colleagues, soda lakes which are rich in sodium and carbonates could have provided the right conditions for the simplest, RNA-based cells to have arisen.

It is widely assumed that the earliest simple cells were based on RNA enclosed in a lipid membrane but there is a problem in that RNA requires divalent ions such as Magnesium (Mg²⁺ to function, but Mg²⁺ damages lipid membranes, so it isn't easy to explain how they could have co-existed within the same cell structure.

So the question is whether the low levels of (Mg²⁺ found in soda lakes, such as the Last Chance Lake in British Columbia, Canada, could have provided the right conditions of enough (Mg²⁺ for RNA to function but not so much as to prevent the formation of an enclosing membrane.

To explore this possibility, Zachary Cohen and his colleagues collected water from Last Chance Lake and the similar but subtly different Goodenough Lake after seasonal evaporation. According to information from Washington University published in phys.org:

These soda lakes each contained ~1 M Na⁺ and ~1 mM Mg²⁺ at pH 10. The authors found that spontaneous extension of short RNA primers occurred in lake water at a rate comparable to the rates in standard laboratory conditions.

The authors added fatty acids, which could have been available on the early Earth, to the lake water to see if the molecules would assemble into membranes. The membranes formed in dilute water that simulates a rainfall event, and the membranes persisted even when surrounded by concentrated lake water from the dry season.

According to the authors, soda lakes on the early Earth could have supported key features of protocell development, with RNA copying and ribozyme activity taking place in the dry season and vesicle formation occurring during the wet season.

The scientists give more technical details in their open access paper in PNAS Nexus: