F Rosa Rubicondior

Thursday 28 March 2024

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


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 human 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


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.

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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Wednesday 27 March 2024

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


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.

Tuesday 26 March 2024

How Evolution Works - Choas, Catastrophe and Tipping Points


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'


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.
Pebdeh Cave excavation in the southern Zagros Mountains. Pebdeh was occupied by hunter-gatherers as early as 42,000 years ago.

Photo: Mohammad Javad Shoaee
The study, published in Nature Communications, highlights a period between 70,000 to 45,000 years ago when human populations did not uniformly spread across Eurasia, leaving a gap in our understanding of their whereabouts during this time frame.

Key findings from the research include:
  • The Persian plateau as a hub for early human settlement: Using a novel genetic approach combined with palaeoecological modelling, the study revealed the Persian plateau as the region where from population waves that settled all of Eurasia originated.
  • This region emerged as a suitable habitat capable of supporting a larger population compared with other areas in West Asia.
  • Genetic resemblance in ancient and modern populations: The genetic component identified in populations from the Persian plateau underlines its long-lasting differentiation in the area, compatible with the hub nature of the region, and is ancestral to the genetic components already known to have inhabited the plateau.
  • Such a genetic signature was detected thanks to a new approach that disentangles 40,000 years of admixture and other confounding events. This genetic connection underscores the plateau’s significance as a pivotal location for early human settlement and subsequent migrations.
Study co-author Professor Michael Petraglia, Director of Griffith University’s Australian Research Centre for Human Evolution, said the findings painted a much clearer picture of these early human movements.

Riverine landscape in the southern Zagros region providing fresh water resources for Homo sapiens populations.

Photo: Mohammad Javad Shoaee

Our multidisciplinary study provides a more coherent view of the ancient past, offering insights into the critical period between the Out of Africa expansion and the differentiation of Eurasian populations. The Persian plateau emerges as a key region, underlining the need for further archaeological explorations.

Professor Michael D. Petraglia, co-author
Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia

The discovery elucidates a 20,000-year-long portion of the history of Homo sapiens outside of Africa, a timeframe during which we interacted with Neanderthal populations, and sheds light on the relationships between various Eurasian populations, providing crucial clues for understanding the demographic history of our species across Europe, East Asia, and Oceania.

Leonardo Vallini, fist author
Department of Biology
University of Padova, Padova, Italy.

The revelation of the Persian plateau as a hub for early human migration opens new doors for archaeological exploration, enriching our understanding of our species’ journey across continents and highlighting this region’s pivotal role in shaping human history.

Professor Luca Pagani, senior author
Department of Biology
University of Padova, Padova, Italy.
The study ‘The Persian Plateau served as Hub for Homo sapiens after the main Out of Africa dispersal’ has been published in Nature Communications.
Abstract

A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.

Introduction

A growing body of evidence indicates that the colonisation of Eurasia by Homo sapiens was not a simple process, as fossil and archaeological findings support a model of multiple migrations Out of Africa from the late Middle Pleistocene and across the Late Pleistocene1,2,3,4,5,6. Traces of these early dispersals are also evidenced in the genome of our Neanderthal relatives, which illustrate interbreeding events as humans moved into Eurasia7,8,9,10. Early dispersals of our species were likely accompanied by population contractions and extinctions, though succeeded by a subsequent, large-scale wave at ~70–60 kya11,12,13,14,15, from which all modern-day non-Africans descend16,17.

The geographically widespread and stable colonisation of Eurasia appears to have occurred at ~45 kya through multiple population expansions associated with a variety of stone tool technologies18,19. Earlier incursions into Europe have been recorded20,21,22,23, however, they failed to leave a significant contribution to later populations. A chronological gap of ~20 ky between the Out of Africa migration (~70–60 kya) and the stable colonisation (~45 kya) of West and East Eurasia can be identified, for which the geographic location and genetic features of this population are poorly known. On the basis of genetic and archaeological evidence, it has been suggested that the Eurasian population that formed the first stable deme outside Africa after ~70–60 kya can be characterised as a Hub population18, from which multiple population waves emanated to colonise Eurasia, which would have had distinct chronological, genetic and cultural characteristics. It has also been surmised that the Hub population cannot be seen as simply the stem from which East and West Eurasians diverged. Instead, this was a more complex scenario, encompassing multiple expansions and local extinctions18. Previous studies, however, have failed to delve into the potential geographic location of this Hub population24, the overall scarcity of fossil evidence of Homo sapiens between 60 and 45 kya anywhere across Eurasia.

The aforementioned scenario was grounded in evidence stemming from ancient genomes from West and Central Eurasia25,26 and China27, indicating that the ancestors of present-day East Eurasians emerged from the Hub at ~45 kya (Fig. 1A, red branch). These emergent groups subsequently colonised most of Eurasia and Oceania, though these populations became largely extinct and were assimilated in West Eurasia28 by a more recent expansion that took place by ~38 kya (Fig. 1A, blue branch). The first of these two expansions, whose associated ancestry we name here the East Eurasian Core (EEC), left descendants in Bacho Kiro, Tianyuan, and most present-day East Asians and Oceanians. The second expansion, which we name the West Eurasian Core (WEC), left descendants in Kostenki14, Sunghir, and subsequent West Eurasians, and in the genome of palaeolithic Siberians29. Crucially, the Hub population accumulated some drift together with the WEC in the millennia that elapsed between the EEC and the WEC expansions (Fig. 1A, grey area). Despite its key role during the peopling of Eurasia, the geographic location and the genetic characteristics of the Hub population, remain obscure24. The outlined scenario is complicated by the need to account for the Basal Eurasian population (Fig. 1A, green), a group30 that split from other Eurasians soon after the main Out of Africa expansion, hence also before the split between East and West Eurasians. This population was isolated from other Eurasians and later on, starting from at least ~25 kya31,32, admixed with populations from the Middle East. Their ancestry was subsequently carried by the population expansions associated with the Neolithic revolution to all of West Eurasia.
Fig. 1: Relationship and legacy of the West and East Eurasian Core populations.
Summary of the major population events (A) and schematic representation of our reference space and expected position of admixed and unadmixed populations (B – note that this panel is a rotation of the blue and red portion of A); derived allele sharing of each ancient or modern individual/population with Kostenki14 and Tianyuan (C); East Asians in red, Oceanians in orange, Native Americans in pink, South Asians in yellow, Northern South Asians in green, West Eurasians in blue, Levantines in cornflowerblue, ancient samples in black (N stands for Neolithic, WHG for Western Hunter Gatherers). A graph with all populations analysed, and individual population names are in Supplementary Fig. 1, Source Data in Supplementary Data 3.
Given the current impossibility of directly inferring the homeland of the Hub population from fossil remains, here we combine available genetic evidence (including both ancient and present-day genomes) and palaeoecological models to infer the geographic region that acted as a Hub for the ancestors of all present-day non-Africans during the initial colonisation of Eurasia. With our work, we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa, therefore pointing to the Persian Plateau as suitable for human occupation throughout 60–40 kya, indirectly shedding light on the early interactions and admixture of our species with Neanderthals33 and the relationships between the main Eurasian and the elusive Basal Eurasian human population30 as well as informing on where future archaeological investigations should be focused.
The Persian Plateau, immediately to the east of Mesopotamia, from whence the authors of Genesis plagiarized a lot of their origin myths, would have been known to the Mesopotamians, but it seems no knowledge of it was transmitted to the Canaanite Hills where the Bronze Age authors of Genesis were making up their origin myths, or they might have incorporated the knowledge into their tales. But even the Mesopotamian written records don't go back to between 45,000 and 70,000 years ago so probably that knowledge had passed out of human memory by the time the Babylonians were writing about Gilgamesh and their pantheon of gods.

So the authors of Genesis had to make do with virtually no information about world or human history, and nothing at all about evolution in Africa and migration out into Eurasia via the Persian Plateau. Had they done so, they might have produced stories with at least a modicum of truth, but alas, all they could manage were the childish fairy tales that got incorporated into the Bible and declared to be the inerrant word of a god - making that god look more and more like either a massive liar or an ignoramus as science discovers more and more of the truth about human origins and the history of the planet.

Monday 25 March 2024

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.
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 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.

Sunday 24 March 2024

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


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:
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.
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:
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.

Saturday 23 March 2024

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


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.

Friday 22 March 2024

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


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.

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