F Rosa Rubicondior: Archaeology
Showing posts with label Archaeology. Show all posts
Showing posts with label Archaeology. Show all posts

Thursday 28 March 2024

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.

Advertisement



Thank you for sharing!







submit to reddit

Tuesday 26 March 2024

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.

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.

Saturday 9 March 2024

Creationism in Crisis - Geobiologists Discover The Cause of Earth's First Mass Extinctions Event - 550 Million Years Before 'Creation Week'


Impressions of the Ediacaran fossils Dickinsonia (at center) with the smaller anchor shaped Parvancorina (left) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.
Photo: Scott Evans.
Geobiologists shine new light on Earth’s first known mass extinction event 550 million years ago | VTx | Virginia Tech

A big problem for Creationists, especially those who believe the Bible was written by an infallible creator god, so think Earth is just a few thousand years old, is that science keeps finding evidence that Earth is billions of years old, and finding fossils of the life-forms that were around then.

As though that wasn't refutation enough, a team of scientists from Virginia Tech have now explained the mass extinction that wiped out most of these early life forms several billion years ago - giving the lie that they were intelligently designed by a god with the ability of foresight. Such a god would have known about the future mass extinctions and either prevented it, designed his creations to survive it or at least waited till it was safe to create things. Creating things to go extinct is not the act of an intelligent or sane creator.

This mass extinction appears not to have been a sudden event, such as that that resulted in the extinction of the non-avian dinosaurs and large marine reptile predators, but to have occurred in two phases that resulted in a loss of about 80% of species and separated by about 10 million years.

But before creationists get over-excited, this does not mean all the Ediacarans were extinct at the Cambrian 'explosion' so the Cambrian biota had no ancestors. It means that there were still about 20% of the Ediacaran biota to evolve over the 6 million years of the Cambrian 'explosion' into the Cambrian biota.

The Ediacaran mass extinction was probably caused by falling Oxygen levels as Ediacarans that had evolved large mass to surface-area ratios suffered from a loss of oxygen more so than those which had retained a smaller mass to surface area ratio.

How this mass extinction was identified and related to changes in global oxygen levels was the subject of an open access paper in PNAS and a Virginal Tech News item:

Creationism in Crisis - Earth's Oldest Forest Was In Present-Day Dorset, UK - 390 Million Years Before Creationism's 'Creation Week'


Cliffs of the Hangman Sandstone Formation, where many of the fossils were found.
Credit: Neil Davies
Earth’s earliest forest revealed in Somerset fossils

Archaeologists have found what are believed to be the remains of the earliest forest so far discovered in Devonian sandstone rocks dated to 390 million years ago, which makes them 4 million years older than the previous record found in New York State, and means they were living almost 390 million years before creationism's 'Creation Week' when their god decided to create a small flat planet with a dome over it, centered on the Middle East.

The fossils were discovered in coastal cliffs near Minehead, Dorset, England in what is known as the Eifelian Hangman Sandstone Formation and consist of primitive trees which were ancestral to today's trees but looked more like palm trees. The discovery is the subject of a paper in the Journal of the Geological Society and a news release from the University of Cambridge, UK.

First a little about this rock formation:

Wednesday 6 March 2024

Creationism in Crisis - Giant Sea Lizards From 66 Million Years Before 'Creation Week'


Fossil skull of Khinjaria acuta
Reconstruction of the skull of Khinjaria acuta
Dr. Nicholas R. Longrich
Fossils of giant sea lizard show how our oceans have fundamentally changed since the dinosaur era

Creationists only have themselves to blame. By insisting that Earth is only 6-10 thousand years old, they are consigning the vast majority of Earth’s 3.8-billion-year history to the pre-'Creation Week' period, before they believe Earth Existed.

So, they then need to perform the most ludicrous of intellectual gymnastics to avoid dealing with all the evidence that they are wrong about the age of Earth and wrong about their denial of what else that evidence shows. For example, there is no way a 66-million-year-old fossil of a marine lizard could be assimilated into creationist superstition, so their only recourse is to devise a way to dismiss it. Favorite tactics are straight denial; bear false witness against the scientists by impugning their honesty and professional integrity; claim, without any evidence to support it, that the dating methods were so flawed they somehow made 10,000 or less look like 66 million.

But the fact remains, no matter that creationists stamp their feet and cover their eyes and ears and demand the Universe changes to conform to their requirements, there were orca-sized marine lizards in the seas 66 million years ago.

This is explained in a recent paper by researchers from the University of Bath in the UK, the Marrakech Museum of Natural History, Morocco, the Museum National d’ Histoire Naturelle (NMNH) in Paris, France, Southern Methodist University in Texas, USA, and the University of the Basque Country, Bilbao, Spain. Their paper is published in Cretaceous Research and explained in a Bath University news release.

First, a little background on the dating of the phosphate deposits in Morocco where the fossils were found:

Saturday 24 February 2024

Creationism in Crisis - Evolution Of The Carnivores 315-251 Million Years Before 'Creation Week'


Dimetrodon, an early predatory synapsid from the early Permian (~298-272 Million years ago). (Display at the Royal Tyrell Museum, Canada).

Credit: Suresh A. Singh
February : Killer instinct drove evolution of mammals’ predatory ancestors | News and features | University of Bristol

The ancestors of all modern mammals, the synapsids, first appeared in the fossil record long before the dinosaurs. Some were vegetarian while others were the top land predators for 60 million years before being replaced by the dinosaurs. Their evolution followed the same pattern of an arms race with their prey species in which the carnivores had to get better at killing to survive.

This gives the lie to the claim of any involvement of a single intelligent designer in their evolution since no intelligent designer worthy of the name would compete with itself in an arms race in which there are no winners or losers while all the time additional complexity is needed to keep up.
Tell me all about the synapsids, please. Synapsids are a group of vertebrates that includes mammals and their extinct relatives. They are characterized by several key features, including a single temporal opening behind the eye socket, teeth set in sockets, and a more erect posture compared to earlier reptiles. Synapsids first appeared during the late Carboniferous period, about 315 million years ago, and they were a dominant group throughout much of the Permian and Triassic periods. Here are some key points about synapsids:
  1. Evolutionary History: Synapsids evolved from reptilian ancestors, specifically from a group called the pelycosaurs. One of the most famous pelycosaurs is Dimetrodon, which lived during the early Permian period and is often mistakenly identified as a dinosaur. Synapsids evolved further into two main groups: the therapsids and the cynodonts.
  2. Therapsids: This group includes the most mammal-like synapsids. They had more advanced jaw structures, with larger temporal fenestrae (openings behind the eye socket) and specialized teeth. Therapsids diversified during the Permian period, with some species evolving into large herbivores like the iconic sail-backed Dimetrodon, while others were carnivorous predators. Towards the end of the Permian, some therapsids gave rise to the first true mammals.
  3. Cynodonts: Cynodonts were a subgroup of therapsids that emerged during the late Permian and diversified extensively during the Triassic period. They exhibited several mammalian characteristics, including a more upright posture, specialized teeth, and possibly hair-like structures. Some cynodonts were quite small and likely had a lifestyle similar to modern mammals, while others were larger predators.
  4. Mammalian Evolution: The transition from cynodonts to true mammals occurred during the Triassic period. Early mammals retained many reptilian features but also displayed characteristics that are distinctly mammalian, such as lactation and specialized jaw joints. By the end of the Triassic period, mammals had become more diverse and widespread.
  5. Impact on Evolutionary History: Synapsids, particularly therapsids and cynodonts, played a crucial role in evolutionary history. They were among the dominant land vertebrates during the Permian and Triassic periods, occupying various ecological niches as herbivores, carnivores, and omnivores. The extinction of many synapsid groups at the end of the Permian, possibly due to environmental changes and the effects of the Permian-Triassic mass extinction event, paved the way for the rise of dinosaurs as the dominant land vertebrates during the Mesozoic Era.
  6. Modern Descendants: The only surviving descendants of synapsids are mammals, which have diversified into a vast array of species occupying nearly every terrestrial and aquatic habitat on Earth. From tiny shrews to massive whales, modern mammals exhibit remarkable diversity in terms of size, shape, behavior, and ecological adaptations.
Overall, synapsids are a fascinating group of vertebrates that played a significant role in the evolutionary history of life on Earth, ultimately giving rise to the diverse and successful lineage of mammals that we see today.
Now a team of researchers from Bristol University, together with a colleague from the Open University, Milton Keynes, have traced the evolution of the carnivorous synapsid jaw and body size and discovered a major change in the jaw about 270 million years ago which would have been associated with a shift in the behaviour of these carnivores as they became better at killing their prey more quickly, so reducing the risk of injury.
Their findings are the subject of an open access paper in Communications Biology and is the subject of a Bristol University news release:

Monday 19 February 2024

Old Dead Gods - With Long Forgotten Religions - And No Way To Recover Them


Joint interment of a dog and a human perinate.

Photo by S.R.Thompson, courtesy of SABAP-VR Soprintendenza archeologia, belle arti e paesaggio per le province di Verona, Rovigo e Vicenza.

Laffranchi Z, Zingale S, Tecchiati U, Amato A, Coia V, Paladin A, et al. (2024)
Some Pre-Roman humans were buried with dogs, horses and other animals | ScienceDaily

I've made the point several time before, but another paper published recently, reinforces it again, that when old gods are forgotten and old religions die, there is nothing on which they can be reconstructed because religions are never founded in verifiable evidence.

Unlike religion, science, which is a description of reality, could be rediscovered if it, or a major branch of it, was somehow wiped from our collective memories and all text books on the subject were wiped clean. And the rediscovered science would be the same as it is today. Atoms would have the same structure and properties, chemistry would do what we know it does today; physics would have the same explanations for the different colours of light, for the way energy is conserved; entropy and the laws of thermodynamics would be the same; and the description of the universe, together with the Big Bang, how suns form and how planets form around them, would be the same.

In fact, we can be as sure as eggs is eggs, that if ever we contact intelligent life from another planet, their science will be the same as ours, although they'll use different words to describe it and their numbering system may well have a different base.

But, expunge every trace of Christianity, Islam, Judaism, Hindi, Shintoism, etc., and erase everyone’s memory of them, and we would never again know what the followers believed or what they believe their god(s) did or didn't do. We would know no more about the major religions of today than we know about the ancient religions before writing was invented. We have not the slightest idea what inspired the builders of Stonehenge and Silbury Hill in Wiltshire; we don't have a clue what the people who built the oldest existing roofed building in Europe, in Menorca in the Balearic Islands believed or what the Minoans of Crete believed, or even the names of their gods, and, unless someone decodes the language the Minoans wrote, we never will. We only know anything about the Egyptian and Sumerian pantheons because someone learned to read their writing.

And we know nothing about the gods and religion of the people who buried horses and dogs with their dead in Late Iron Age, Northern Italy - the subject of a recent paper in PLOS ONE.

In information from PLoS, cited in Science Daily, the authors explain their findings:

Saturday 17 February 2024

Creationism in Crisis - Now It's Evidence In Spain From 6,200 Years Ago That Survived Creationism's Favourite Genocide


Stratigraphic units (SU) from which P. lineatus shells analysed in this investigation were recovered: SU 1406 (C), SU 1704 (D), SU 705 (E) and SU 1516 (F)

Neolithic groups from the south of the Iberian Peninsula first settled in San Fernando (Cadiz) 6,200 years ago - Universitat Autònoma de Barcelona - UAB Barcelona

Another terrible week for creationism is coming to an end with news that archaeologist from the Universitat Autonòma de Barcelona (UAB) and the University of Càdiz, together with colleagues from the Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany, have uncovered evidence that Neolithic groups from the south of the Iberian Peninsula first settled in San Fernando (Càdiz) 6,200 years ago and supplemented their diet with shellfish.

This news comes on top of the news that the remnants of a stone plaza in Peru and the body of the victim of a sacrificial bog burial in Denmark, that could not have survived creationism's mythical global genocidal flood if it had really happened as described in the Bible, had also been revealed by archaeologists.

The discovery, and details of how the date was calculated is the subject of an open access paper in the journal Archaeological and Anthropological Sciences and the subject of a UAB new release:

Creationism in Crisis - A 4750-Year-Old Stone Plaza in Peru That Survived Creationists' Favourite Genocide


Callacpuma archaeological site, Peru
UW Anthropologists’ Research Unveils Early Stone Plaza in the Andes

Imagine for a moment that you're dating someone who told you they were 30 years old, then you discover a photograph of them as a teenager, in a newspaper dated 1984. Would you conclude that someone had been lying to you and your date was really about 55 years old, or would you assume the photograph had been faked or the newspaper had the wrong date?

Imagine now being a creationist who believed Earth was devastated by a global flood that covered the highest mountains, about 4000 years ago, which would have scoured the Earth and destroyed everything on it, then someone shows you the remains of a building in Peru that had been there for 4750 years, and showed no signs of ever being submerged in even a few feet of water, let along several thousand feet of it!

If you're a creationist, you dismiss the evidence or assume the dates are wrong or that somehow the inevitable layer of silt had been cleaned up, even if the building had managed to escape the destruction going on around it, because, if you're a creationist, the last thing you can admit to is that your beliefs could be wrong because that would make you feel less important that you think you should be, so you're prepared to perform any mental contortions necessary to avoid that thought.

And this is why belief in a literal interpretation of the Bible has been in headlong decline ever since science began providing evidence of an old Earth and evidence that there never was a global genocidal flood just a few thousand years ago, because people with intellectual integrity who value truth and have the humility to let the evidence lead their opinions, even if it leaves them feeling less important than they think they should be, have realised that the evidence tells them that the Bible is wrong, despite their mummy and daddy believing otherwise.

And of course, just such remains of a building have been found in Peru by two University of Wyoming anthropology professors, and dated to about 4750 BP. It is the remains of a stone plaza and is the oldest stone structure so far found in the Americas, being older even than the Egyptian pyramids and about the same age as Stone Henge (both of which, incidentally, also survived the alleged genocidal flood).
How they did it is explained in a University of Wyoming news release:

Friday 16 February 2024

Creationism in Crisis - How The Fossil Record Provides Evidence For Evolution - No Magic Needed


Desert sand dune landscape of the Upper Cretaceous Djadokhta/Baruungoyot Formations. Foreground: the large-bodied monstersaurian lizard Estesia mongoliensis predating on the enantiornithine bird Gobipteryx minuta.

Illustration by Nathan Dehaut
A Lighthouse in the Gobi Desert | Natural History Museums of Los Angeles County

We are regularly told by creationists who have either been fooled by a lie, or are trying to fool us with one, that biomedical scientists are increasingly rejecting the Theory of Evolution and replacing it with the notion of intelligent design.

This was, of course, the aim of the Discovery Institute's 26-year-old, 5-year[sic] strategy detailed in The Wedge to insert Bible literalism into mainstream science, apparently believing that for the first time in the history of science, a well-established scientific theory is going to be replaced by a an evidence-free superstition based on misrepresentation of the data and including unproven supernatural entities doing magic.

Intelligent design creationism, of course, doesn't meet the basic criteria to be called a science, which is why any scrutiny of the relevant scientific literature will find no hint that the TOE is inadequate for explaining the data or that magic explains it in a more scientifically satisfying way. Indeed, as I repeatedly show in these blog-posts, virtually every piece of scientific research casually refutes creationism by revealing the evidence and not a single peer-reviewed biomedical science paper ever concludes that intelligent design is the only way to explain the observations.

As Michael J Behe was forced to admit in the Kitzmiller case, "There are no peer-reviewed article by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred". And that situation has not changed since Behe effectively sank the Wedge Strategy with that grudging admission under oath in an American court. Instead, we find papers like this technical one in which a team of researchers led by Dr. Hank Woolley, a Postdoctoral Research Fellow at the Dinosaur Institute, Natural History Museum of Los Angeles County, and the Department of Earth Sciences, University of Southern California, Los Angeles, California, discuss and evaluate the degree to which exceptional collections of fossils, such as those found in the Gobi Desert of Central Asia can influence our understanding of evolutionary relationships between fossil groups - what they term the lagerstätten effect .

The team have explained their research in a news release from the Natural History Museums of Los Angeles County:
Web Analytics