Religion, Creationism, evolution, science and politics from a centre-left atheist humanist. The blog religious frauds tell lies about.
Friday, 14 February 2025
Refuting Creationism - Where Europeans' Ancestors Came From - Thousands of Years Before 'Creation Week'
New research based on an analysis of the genomes of 435 individuals has revealed the rich history of the ancestors of modern Europeans, especially the mixing of multiple ethnic groups in the Pontic Area - modern Ukraine - between 8,400 and 4,000 year ago which eventually gave rise to the Yamnaya people who get their name from the Russian for 'pit burial' (Yamna in Ukrainian).
Before the Yamnaya spread into Europe, they were preceded by two earlier waves of migration: firstly, hunter-gatherers who arrived about 45,000 years ago having interbred with and replaced the Neanderthals who had lived there for the previous 250,000 years. These were followed by farmers who came from the Middle East, starting about 9,000 years ago.
The Yamnaya, having formed a stable linguistic and cultural group, and either invented or copied ox-drawn carts and skilled horsemanship, which gave them great mobility, began to expand their range, probably under population pressure beginning about 5,300 years ago and lasting for some 1,800 years, eventually reaching all parts of Western Europe including the Iberian Peninsula and the British Isles.
Saturday, 8 February 2025
Unintelligent Design - How Creationism's Heath-Robinson Designer Muddles Through But Still Messes Up.
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Q. How can you tell when something is designed by a supreme intelligence with the inerrant ability of foresight?
A. It works perfectly, without errors and does exactly what it was intended to do, nothing more and nothing less.
Q. How can you tell when something is 'designed' by a natural, utilitarian process like evolution by natural selection?
A. It works most of the time, even if not very efficiently, is over-complex and so prone to errors and doesn't anticipate change. It also frequently requires additional layers of complexity to compensate for its errors and inefficiency.
Sadly for intelligent design advocates, structures and processes found in nature are almost never perfect and free from errors and, when examined closely, are seen to be error-prone, suboptimal and requiring additional complexity to compensate for the errors and inefficiencies. And these error-correction mechanisms are themselves error-prone and prone to failure.
One such mechanism, the details of which have just been worked out by researchers at the Heidelberg University Biochemistry Center (BZH) in collaboration with colleagues from the Australian National University, is the system of spliceosomes found in eukaryote cells, that correct the errors in messenger RNA (mRNA) before they are transcribed into functional proteins.
The reason these large nuclear proteins are required is because the DNA the mRNA is transcribed from is contains 'introns' - small sequences that are not part of the gene being coded for. Imagine a computer database of words, which, when a retrieved, inserts random letters in the middle of the word.
Tuesday, 4 February 2025
Unintelligent Design - Sex Determination in Octopuses - For 480 Million Years
Octopuses have some of the oldest known sex chromosomes | OregonNews
Although few of them will know enough to understand why, the genetic basis for sex determination in different organisms is a problem for intelligent design advocates because it illustrates a few embarrassing things which can't be explained as the design of an intelligent designer.
Firstly, there are several ways in which gender is determines, rather than the single method a single intelligent designer of all living things would have settled for (see the AI information panel). Secondly, the actual basis is consistent within major clades such as mammals, birds and orders of insects such as Hymenoptera (Bees, wasps and ants), and thirdly, because the methods are unstable over evolutionary time, since the sex chromosomes are unpaired in the heterozygous gender, so the unpaired chromosome tends to acquire mutations, which are not corrected by cross over during meiosis, and the non-sex-determining genes tend to be conserved on the chromosome which is paired in the homozygous gender.
In mammals, this means that the Y-chromosome tends to degenerate; in some species of rodents, which have a short generation time and large litters, so evolution can progress faster than in most other mammals, the Y-chromosome has disappeared, to be replaced by an alternative sex-determining system. No intelligent designer worthy of the name would design a process that degenerates and need to be replaced every few million years.
Saturday, 1 February 2025
Refuting Creationism - Humans Have Been Selectively Breeding Sheep Since 1000 Years Before 'Creation Week'
Ancient DNA history of sheep and humans - News & Events | Trinity College Dublin
Domesticated animals are an embarrassment for creationists who believe that their god created all the animals for the convenience of mankind, because just about every domesticated animal (or plant for that matter) has been highly modified by selective breeding to make it suitable for whatever purpose it was domesticated for.
An intelligent god could have made them fit for purpose in the first place, if it had really created them for mankind's convenience. This shows that either the creation myth is wrong, or the creator god lacked the foresight to know what humans would be using the animals for. So, we've had to modify them, in some cases. almost beyond recognition as the descendants of their wild ancestors, to make them fit for purpose.
And it gets worse when we discover that the domestication process began long before the same creation myth says all the animals were created in the same week as humans.
Sheep, for example, according to a study by an international and interdisciplinary team of researchers led by geneticists from Trinity College Dublin, and zooarchaeologists from Ludwig Maximilian University Munich and the Bavarian State Collections of Natural History (SNSB) were first domesticated over 11,000 years ago. An analysis of their genome also reflects patterns of migration in the human population, with whom sheep have been intertwined for over 11,000 years.
Thursday, 30 January 2025
Refuting Creationism - How Horseshoe Crabs Have Evolved And Diversified
Preserving Asian horseshoe crab populations through targeted conservation strategies
In creationist mythology, horseshoe crabs have remained unchanged for 400 million years, so they prove there is no such thing as evolution and Earth is only 6-0,000 years old. Apart from the typical lack of joined-up thinking in that non sequitur, there are a couple of fallacy at work here.
Firstly, evolution does not necessarily involve major changes in the phenotype because it happens at the genetic level, so the genome is where we need to look to find evidence of it (or lack of it); secondly there is no requirement for a species that is already adapted to its environment to change unless its environment changes in a way that requires adaptation. This might include increased predation, depletion of food resource, major changes in temperature or oxygenation, increased competition from another species, etc.
With their child-like understanding of evolution, creationists assume a species must change into something else for evolution to happen.
In fact, as a team a research team led by Associate Professor Frank Rheindt from the Department of Biological Sciences at the National University of Singapore (NUS) Faculty of Science have now shown, there are four different species of horseshoe crab which have all diversified from a common ancestor.
Tell me about the evolution and distribution of the horseshoe crabs, please. Horseshoe crabs (order Xiphosura, class Merostomata) are marine arthropods that have existed for over 450 million years, making them one of the oldest living groups of animals. They are often called "living fossils" because their body plan has remained largely unchanged since the Ordovician period.The results of their study are published open access in the journal Conservation Letters and is the subject of a news item from NUS>
Evolutionary History
Horseshoe crabs belong to the subphylum Chelicerata, making them more closely related to arachnids (such as spiders and scorpions) than to true crabs or other crustaceans. Their evolutionary history includes several now-extinct relatives, such as Eurypterids (sea scorpions), which were once dominant marine predators.
Modern Distribution
- Ordovician Period (~450 mya): Early xiphosurans appear in shallow marine environments.
- Paleozoic Era (~300 mya): More advanced forms develop but remain morphologically similar to modern species.
- Mesozoic Era (~150 mya): Horseshoe crabs survive mass extinctions, adapting to various shallow marine environments.
- Cenozoic Era (Present day): Four extant species remain, showing remarkable evolutionary stability.
Today, only four species of horseshoe crabs survive, all found in coastal and estuarine environments:
Ecological Role & Conservation
- Limulus polyphemus (Atlantic Horseshoe Crab) – Found along the eastern coast of North America, from the Gulf of Mexico to the northeastern United States.
- Tachypleus tridentatus (Tri-spine Horseshoe Crab) – Found in coastal waters of China, Japan, and Southeast Asia.
- Tachypleus gigas (Indo-Pacific Horseshoe Crab) – Inhabits the waters of the Bay of Bengal and Southeast Asia.
- Carcinoscorpius rotundicauda (Mangrove Horseshoe Crab) – Found in shallow waters and estuaries from India to Indonesia.
Horseshoe crabs play a crucial ecological role. Their eggs provide an important food source for migratory shorebirds, and they contribute to benthic (seafloor) ecosystems. They are also vital to biomedical research because their blue blood contains limulus amebocyte lysate (LAL), used to detect bacterial contamination in medical applications.
However, populations are declining due to:Conservation efforts focus on protecting nesting beaches, regulating harvesting, and exploring synthetic alternatives to LAL for medical testing.
- Overharvesting (for bait and biomedical use)
- Habitat loss (coastal development)
- Climate change (affecting spawning conditions)
Fossil Record of Horseshoe Crabs (Order Xiphosura)
Horseshoe crabs have an extensive fossil record dating back to the Ordovician period (~450 million years ago). Their morphology has remained remarkably stable, making them classic examples of "living fossils." The fossil record reveals several extinct relatives and a gradual adaptation to different marine environments over geological time.
Key Fossil Discoveries and Evolutionary Timeline
- Ordovician Period (485–443 mya) – Oldest Known Horseshoe Crab Ancestors
- The earliest xiphosurans appeared in shallow marine environments.
- Fossils of Tetraspidella from the Upper Ordovician suggest primitive horseshoe crab-like arthropods already existed.
- Silurian Period (443–419 mya) – Emergence of True Xiphosurans
- More recognizable horseshoe crab relatives evolved.
- Kasibelinurus (Late Silurian) is considered one of the earliest known xiphosurans.
- Devonian Period (419–359 mya) – Diversification and Expansion
- This period saw the emergence of several marine genera with more developed carapaces and feeding structures.
- Bellinurus and Euproops are well-known genera from the Devonian.
- Carboniferous Period (359–299 mya) – Peak Diversity
- This was the golden age of xiphosurans, with numerous species thriving in marine, brackish, and even freshwater environments.
- Genera like Euproops, Bellinurus, and Paleolimulus flourished, some resembling modern horseshoe crabs.
- Some species, such as Euproops danae, had spines and unique adaptations to different ecological niches.
- Permian Period (299–252 mya) – Decline and Extinctions
- The Permian saw a decline in diversity, possibly due to changing environments and competition with other arthropods.
- Many species perished during the Permian-Triassic mass extinction (~252 mya), the most severe extinction event in Earth's history.
- Mesozoic Era (252–66 mya) – Survival and Adaptation
- Xiphosurans survived the mass extinction but were less diverse than in the Carboniferous.
- Fossil genera like Mesolimulus (Jurassic) and Limulitella (Cretaceous) were similar to modern horseshoe crabs.
- Some species adapted to shallow coastal waters, much like their modern counterparts.
- Cenozoic Era (66 mya–Present) – Modern Horseshoe Crabs
- Fossil records show that Limulus polyphemus, the modern Atlantic horseshoe crab, has remained almost unchanged for at least 20 million years.
- Their ability to survive drastic environmental changes has made them one of the longest-surviving arthropod groups.
Key Fossil Finds
- Kasibelinurus (Silurian) – One of the earliest known true xiphosurans.
- Euproops (Carboniferous) – Small, with a reinforced carapace and spines for protection.
- Mesolimulus (Jurassic) – Nearly identical to modern Limulus, showing little evolutionary change.
- Paleolimulus (Permian) – A transitional form between early and modern horseshoe crabs.
Why Have Horseshoe Crabs Changed so Little?
- Stable ecological niche: They have occupied similar coastal and estuarine environments for hundreds of millions of years.
- Efficient body plan: Their tough exoskeleton, simple yet effective feeding structures, and ability to tolerate low-oxygen conditions have helped them persist.
- Survivors of mass extinctions: They have outlived dinosaurs and many other ancient marine species due to their resilience and adaptability.
Preserving Asian horseshoe crab populations through targeted conservation strategies
NUS biologists conduct the first comprehensive population study of all three Asian horseshoe crab species, mapping their population distribution, evolutionary histories and vulnerabilities to climate change to propose customised conservation strategies
Horseshoe crabs are often referred to as the “living fossils” of our planet — the four known species, including three in Asia and one in North America, remain nearly identical to their ancient relatives from hundreds of millions of years ago. These arthropods are a fundamental building block of coastal marine ecosystems. Their eggs, for example, serve as a major food source for shorebirds, some of which have evolved to time their migrations to coincide with peak horseshoe crab spawning activity. In addition to their ecological role, horseshoe crabs are also used in biomedicine to test for harmful toxins in vaccines.
The photo shows the moult of a young tri-spine horseshoe crab, Tachypleus tridentatus – an endangered species – found on the beach at Beihai, China. The genomic data gathered by NUS researchers on this species provides a launchpad for conservation strategies.Photo: Dr Tang Qian.
Among the four species, only the Atlantic horseshoe crab (Limulus polyphemus), found along the Atlantic coast of the United States and the Gulf of Mexico, has been extensively studied. In contrast, scientific information about the three Asian species is so scant and scattered that the IUCN Red List, which tracks the extinction risk of species around the world, listed two of them (the mangrove horseshoe crab and the coastal horseshoe crab) as “data deficient”. This designation indicates insufficient data to assess their extinction risk. On the other hand, the tri-spine horseshoe crab is considered endangered.
Understanding our planet’s living fossils
to help fill in these knowledge gaps, a research team led by Associate Professor Frank Rheindt from the Department of Biological Sciences at the NUS Faculty of Science conducted the first comprehensive population genomic study of all three Asian horseshoe crab species: the mangrove horseshoe crab (Carcinoscorpius rotundicauda), coastal horseshoe crab (Tachypleus gigas), and tri-spine horseshoe crab (Tachypleus tridentatus).
The study underscores the importance of Southeast Asia’s Sunda Shelf, a shallow-marine region, as a critical coastal marine habitat. Importantly, this region has sustained the survival of these ancient arthropods for millennia and could continue to act as a refuge for Asian horseshoe crabs amid accelerating anthropogenic climate change.
The researchers have also established the first-ever genomic baseline dataset for these species, which lay the groundwork for targeted conservation planning. Their findings, which propose different conservation strategies for each species, were published in Conservation Letters on 16 December 2024.
Back to the basics: Filling data gaps to advance conservation efforts
To protect and conserve these species, it is crucial that we first cover the basics — understanding their population structure, evolutionary histories and climate-change-driven vulnerabilities. This foundational knowledge will enable us to develop targeted conservation strategies and prioritise habitats critical for their survival.
Associate Professor Frank E. Rheindt, co-corresponding author
Department of Biological Sciences
National University of Singapore, Singapore.
Tracking and monitoring Asian horseshoe crabs is in and of itself a challenging feat. They spend most of their lives on the seabed, making them difficult to observe, and they take 14 years to mature — too long to assess population changes effectively through traditional surveys. To overcome these challenges, the researchers turned to population genomic approaches, where they analysed DNA from 251 horseshoe crabs collected across 52 sites in 11 countries.
Using this data, NUS researchers created the first genomic baseline dataset for Asian horseshoe crabs. This dataset enabled the team to map population structures and delineate genetic boundaries among the three species.
Such distinctions are important, as they highlight populations that harbour unique genetic traits essential for adapting to specific local environments. Genomic data also helps us pinpoint coastal hotspots that should be prioritised for conservation.
Dr Tang Qian, first author.
Department of Biological Sciences
National University of Singapore, Singapore.
The study also revealed how horseshoe crabs have responded to environmental fluctuations over time. The Sunda Shelf emerged as a vital refuge for horseshoe crabs during periods of past climate change. By reconstructing the species’ evolutionary histories, the researchers found that the region has not only preserved genetic diversity but also served as a migratory corridor, which allowed populations to remain connected despite environmental changes.
Tailored conservation strategies needed
The study highlighted that future climate change poses varying levels of risk to the three species of Asian horseshoe crabs. While all are vulnerable, their ability to adapt differs. For instance, the mangrove horseshoe crab, with its limited dispersal capacity, faces higher threats of local extinction compared to the more mobile coastal and tri-spine horseshoe crabs.
Based on these findings, the researchers have proposed tailored conservation strategies to support each species in adapting to climate change:
Mangrove horseshoe crabsCoastal horseshoe crabs
- Protect and restore mangrove habitats, which are essential for the species’ survival and ability to migrate southward in response to rising temperatures.
- Prioritise the conservation of populations in the Gulf of Tonkin and South China as they face the highest evolutionary pressures from climate change.
Tri-spine horseshoe crabs
- Protect the Sunda Shelf region, which serves as a critical refugial habitat, particularly around the Bay of Bengal, the Malacca Strait and Southern Vietnam.
- Maintain connectivity between populations by safeguarding coastal corridors to mitigate the species’ vulnerability to habitat fragmentation.
- Implement sustainable fishery regulations and restore coastal habitats, especially in areas with a history of intensive development, such as Japan, Taiwan and China.
- Focus conservation efforts on reducing human-driven threats like harvesting and habitat loss as these currently pose greater risks than climate change.
Next steps
Our study provides an important impetus and the necessary baseline data for the preservation of key habitats for horseshoe crabs’ future survival. As an important caveat, however, our work is only based on environmental factors and does not take into account future human activities that may directly alter habitats, such as coastal development. The survival of horseshoe crabs will therefore critically depend on interventions based on local contexts.
Dr Tang Qian.
Looking ahead, the researchers plan to further explore the evolutionary potential of Asian horseshoe crabs. This includes studying how specific functional genes contribute to their ability to adapt to local environments and changing climates.
We have established the Horseshoe Crab Global Biorepository, with its physical collection located at the Lee Kong Chian Natural History Museum at NUS, to support ongoing and future research. Through this resource, we hope to foster collaborations and secure funding to advance genomic research on horseshoe crabs. We are currently working with the Chinese University of Hong Kong on genomic research specifically focused on the tri-spine horseshoe crab.
Associate Professor Frank E. Rheindt.
Far from being the 'living fossils' that 'prove evolution never happened', these four species of horseshoe crab turn out to be evidence that it has happened, driven by environmental changes that produced the present distribution and diversity, and then stabilised, resulting in a prolonged period of evolutionary equilibrium because the species were optimally adapted to their environments in warm, shallow seas with sandy beaches on which to spawn.ABSTRACT
Horseshoe crabs are unique living fossils that have remained almost unaltered through 400 million years of global change. They face rapid worldwide declines under increasing anthropogenic pressure. Using comprehensive geographic and genomic sampling combined with approaches that integrate DNA with environmental and climatic datasets, we assessed the population genetic structure, demographic histories, and vulnerability to future climate change in three out of four extant horseshoe crab species, all centered in Asia. Our study highlights that the Sunda Shelf, a complex and dynamic shallow-marine landscape, has been the sole repository of most genetic diversity among all three Asian species, and therefore crucial to the long-term survival of horseshoe crabs. Our study not only provides the first genomic baseline data for the evaluation of Asian horseshoe crabs’ conservation status but also identifies core habitats that potentially act as refugia and corridors for Asian horseshoe crab populations with impending anthropogenic global warming.
1 Introduction
Horseshoe crabs are one of the planet's foremost “living fossils”. They are known for their high morphological conservatism and a consistently slow evolutionary rate over hundreds of millions of years (Bicknell and Pates 2020). Although they are a fundamental building block of coastal marine ecosystems where they occur (Botton 2009), only four geographically restricted species remain today (Sekiguchi and Shuster 2009.1): the Atlantic horseshoe crab (Limulus polyphemus) along the Atlantic coast of the United States and the Gulf of Mexico, and three Asian horseshoe crabs, the mangrove horseshoe crab (Carcinoscorpius rotundicauda), coastal horseshoe crab (Tachypleus gigas), and tri-spine horseshoe crab (Tachypleus tridentatus), in coastal East, Southeast, and South Asia (Figure 1). Although anecdotal reports suggest declines of horseshoe crabs worldwide (John et al. 2018; Wang et al. 2020.1), important baseline population data remain scant and are mostly only available in economically advanced regions. Hence, the Atlantic horseshoe crab is more intensively studied compared with its Asian cousins (Luo et al. 2020.2), two of which (C. rotundicauda and T. gigas) are currently classified as data deficient in the IUCN Red List, whereas T. tridentatus is considered endangered.
FIGURE 1
Distribution and genetic divergence of Asian horseshoe crabs. Top left: map of the sampling localities; colored coastal lines (see legend) highlight the natural range of the three Asian horseshoe crab species; dotted lines delimit seven geographical regions (A–G) identified in genetic analysis; sampling localities are color coded according to each of the seven geographical regions. Top right: Principal component analysis (PCA) plots of horseshoe crab individuals (based on SNP dataset with 10% missing data and linked loci filtered). Colors in PCA plots correspond to colors of sampling localities on the map. Bottom: consensus population assignments (thick lines above the bar plots) and individual population assignments using ADMIXTURE (bar plots based on SNP dataset with 10% missing data and linked loci filtered) and discriminant analysis of principal components (membership assignments across SNP datasets displayed as lines under the bar plots). The consensus populations’ pairwise Fst and Dxy values (calculated based on the SNP dataset with 10% missing data and linked loci filtered) are depicted on the right of the corresponding population assignments.
The biology of all four extant horseshoe crab species has been tightly adapted to ephemeral coastline habitat and shallow-marine conditions since the late Paleozoic (Blażejowski et al. 2017; Bicknell and Pates 2020). The three Asian species’ ranges broadly overlap across the Southeast Asian Sunda Shelf, which is known as one of world's biodiversity hotspots for terrestrial (Myers et al. 2000), freshwater (He et al. 2018.1), and coastal marine (Hoeksema 2007; Schumm et al. 2019) flora and fauna. Owing to accelerated diversification rates fueled by habitat dynamics across glacial cycles, the Sunda Shelf has become a cradle of terrestrial and freshwater endemism following its first submergence at ∼400 ka (Cros et al. 2020.3; Husson et al. 2020.4; Salles et al. 2021; Sholihah et al. 2021.1; Garg et al. 2022). The region also exhibits high marine biodiversity but relatively low endemism (Costello et al. 2017.1), suggesting niche filling by dispersion (Ludt and Rocha 2015; Pinheiro et al. 2017.2), which may have turned the Sunda Shelf into a sanctuary for coastal marine biodiversity during interglacial periods.
To understand population structure, evolutionary histories, and climate change-driven vulnerability, we comprehensively sampled the three Asian horseshoe crab species across their natural range. Our results provide baseline data for conservation action geared toward the continued existence of a species group that has survived global change almost unaltered since before the age of the dinosaurs.
To anyone with the courage to lean about evolution and what causes it, which of course excludes creationists, the horseshoe crabs are not a problem for the Theory of Evolution but a vindication of it.
Wednesday, 29 January 2025
Unitelligent Design - How The Giant Clam Has a Needlessly Complex Way To Get Nutrients
How tiny algae shaped the evolution of giant clams | CU Boulder Today | University of Colorado Boulder
You can depend on creationism's idiot designer to never do something the obvious uncomplicated way when there is an obscure and much more complicated way to achieve the same result. It's almost exactly like it's a mindless fool, blundering about without a plan who sometimes happens across something that works and sticks with it, trying to make the best of it with more blundering.
Quite the opposite of what anyone other than a creationist would call intelligent, in fact.
For example, having designed a giant clam to live in nutrient poor coral reefs, it then designed them to have algae living symbiotically inside them, supplementing their megre diet got by filtering the seawater, with sugars manufactured by photosynthesis. This enables the giant clam to grow up to 4.5 feet (1.4 metres) in length and weigh over 700 pound (317 Kg).
Any intelligent designer could have either designed them to live in a less nutrient-poor environment or given them the chloroplasts the algae have to achieve the same result far more simply.
But of course, the giant clam wasn't intelligently designed; it evolved by the utilitarian evolutionary process that is constrained by its evolutionary history and so finds suboptimal but functional processes that a needlessly complex. This complexity impresses creationists because, not understanding how evolution works, they imagine it reflects intelligent design, instead of refuting it.
Monday, 27 January 2025
Refuting Creationism - How Leaf Beetles Got New Genes
Max Planck Institute for Chemical Ecology
Reading the genome and understanding evolution: Symbioses and gene transfer in leaf beetles
Creationists who have been fooled by the disinformation pumped out by the Discovery Institute, especially by William Dembski, believe that the only way an organism can gain new genetic information is by being given it, pre-prepared, by a magic intelligent designer, who has the magical power to assemble new DNA in just the right order and insert it into a species' genome, by a mysterious process that neither Dembski, nor one of his co-misinformers, are willing to explain.
This, of course, ignores the scientific evidence that new genetic information can be acquired by a species in several different ways, not the least of which is by horizontal gene transfer from another species, as researchers from the Max Planck Institute for Chemical Ecology in Jena, the Max Planck Institute of Biology in Tübingen, Germany, and a consortium of international scientists have just shown in respect of the leaf beetles, one of the most successful group of beetles with more than 50,000 different species worldwide.
Saturday, 11 January 2025
New Book - Twenty Reasons To Reject Creationism: Understanding Evolution
This book looks at the ID/Creationism vs evolution debate from multiple angles and analyses why the science of evolutionary biology refutes the childish notion of intelligent design.
I wrote it because, creationism is dangerous. It replaces evidence-based knowledge with superstition and creates the impression that cultural prejudice and ignorant incredulity are better measures of reality than observation, analysis and reason.
Now more than ever we need our politicians, law-makers and captains of industry to be able to make sense of complex data and use it to make wise decisions, not dismiss it as based on ‘flawed’ concepts and the result of conspiracies designed to turn people away from the ‘truth’ as revealed in ancient texts declared to be holy. As is clearly shown in the Discovery Institute’s Wedge Document and in the wilful misrepresentations of science its fellows dutifully feed to the largely scientifically-illiterate public, there is a hidden political agenda that depends on people believing falsehoods and thinking anti-science is some sort of moral crusade to restore Western civilisation to a notional ideal golden age in pre-renaissance Europe when the slave trade was booming and witch-burning was a regular spectacle in the local town square.
This was a time when people like Copernicus and Galileo would be persecuted and deprived of their livelihood and even their life, for revealing the empirical evidence that Earth orbits the sun – not because they had falsified the data but because the data falsified the Bible. The sacred superstitions, even though empirically proved wrong, had to be defended against the truth as revealed by the physical data.
Friday, 10 January 2025
Common Origins - How The Mammalian Outer Ear Evolved - From Our Ancestral Fish Gills
An earful of gill: USC Stem Cell study points to the evolutionary origin of the mammalian outer ear | USC Stem Cell
I'm sorry if this spoils a creationists new year, but a bunch of scientists from the Stem Cell Lab of the University of Southern California have just published a paper showing an ancient ancestor of mammals, including of course us humans, was a fish.
It comes in the form of evidence that our outer ear develops from the same tissues in the embryo as the gills of fish. These tissues have been exapted by evolution for many new structures, one of which is the outer ear of mammals.
Monday, 9 December 2024
Refuting Creationism - Another Gap Closed - No God Found
A microRNA solves an evolutionary mystery of butterfly and moth wing colouration - NUS Faculty of Science | NUS Faculty of Science
A regularly-cited example of observed Darwinian evolution is that of the peppered moth which occurs in two forms, the white, speckled form and a melanistic, almost black form. During the industrial revolution, as English northern towns grew and became polluted by smoke from coal-burning factories, so the melanistic form became more common.
Experiments showed that the lighter form became easier for predators to see when the moths were roosting on tree trunks that had become coated in soot, while the melanistic form became harder for predators to see.
Following the decline of the northern towns, the light form again increased back to the former ratio, showing the importance of environmental change in evolution.
This tendency to have melanistic forms is common in the lepidoptera (moths and butterflies) and this tendency was believed to be under th control of as single genomic region surrounding the protein-coding gene “cortex“, common across many species, showing their descent from a common ancestor.
However, new research by international researchers from Singapore, Japan, and the United States of America, led by Professor Antónia MONTEIRO and Dr Shen TIAN from the Department of Biological Sciences at the National University of Singapore (NUS), has shown that 'cortex' is not directly involved in producing melanism, instead, this is controlled by a microRNA from within the 'cortex' genomic region, as another example of how microRNA's control many functions within cells, particular gene expression.
Friday, 8 November 2024
Unintelligent Design - How Evolution Rescued an Unintelligent Heath-Robinson Design Blunder
How plants evolved multiple ways to override genetic instructions - The Source - Washington University in St. Louis
The thing about evolution that distinguishes it from intelligent design is that evolution is utilitarian. It settles for something that works better than what preceded it, which is different from designing a perfect solution to a problem. Near enough is good enough because anything which is an improvement gets pushed up the frequency listing in the gene pool. So, organisms over time have accumulated sub-optimal systems that sometimes fail and cause other problems.
One of those systems is the way DNA is replicated - which is so error prone that error correction mechanisms have evolved over time, but they don't always work either, so we have the phenomenon of the 'jumping genes' that get inserted in the wrong place in the genome, sometime in the middle of a functional gene or in a control section adjacent to a functional gene, causing genetic defects.
So, in the best Heath-Robinson approach to design, rather than abandoning that design and starting again, the way any intelligent designer would do, another layer of complexity is needed to try to mitigate the occasion when the system fails.
So, what organisms have evolved over the years is a process for neutralising these 'jumping genes' by attaching methyl groups to one of the bases which prevents it being transcribed. This is a part of the epigenetic system by which the specialised cells of multicellular organisms turn of unwanted genes and only allow the genes for their speciality to be active - a layer of complexity needed because the way cells replicate was inherited from their single-celled ancestors where the whole genome needs to be included in every daughter cell.
Animals, such as mammals have two enzymes which attach this methyl group depending on the DNA 'context', but plants have multiple enzymes for doing the same thing. The question is why do plants need these multiple enzymes?
Wednesday, 6 November 2024
Refuting Creationism - Ancient Aurochs From Long Before 'Creation Week'
Ancient DNA brings to life history of the iconic aurochs - News & Events | Trinity College Dublin
On problem with believing a myth that Earth was made out of nothing by magic 6-10,000 years ago is that there are paintings in caves in France that are older than that, showing animals that were around before then.
And a problem with believing that the same magician created all living things just as they are today without any ancestors, is that those same cave paintings show species that were ancestral to some of the animals that are around today, such as domestic cattle.
And a problem with believing that the same magician created all the animals for the benefit of humans is the evidence that all our domestic animals, with almost no exceptions, have been improved by selective breeding from wild ancestors. Did their putative creator not know what humans would need or how they would use the animals it created for them?
Aurochs, their evolution and relationship to domestic cattle. Aurochs (Bos primigenius) were large wild cattle that roamed parts of Europe, Asia, and North Africa. They are considered the ancestors of modern domestic cattle, playing a significant role in human history and agriculture. Here's an overview of the aurochs, their characteristics, history, and their relationship to modern cattle.And all these questions come from a paper published recently in Nature which reports on the analysis of the genome of 38 Aurochs from bones stretching back over some 50,000 years from sites across Eurasia from the UK to Siberia. The team of geneticists from Trinity College and other universities have explained their findings in a Trinity College press release:
Physical Characteristics
- Size: Aurochs were significantly larger than modern cattle, with bulls standing up to 6 feet (1.8 meters) at the shoulder and weighing up to 1,500 pounds (700 kg) or more. Cows were generally smaller than bulls.
- Appearance: They had a muscular build with long legs and a slender body, which allowed them to move quickly. They possessed a distinctive hump over their shoulders.
- Color: Bulls were typically dark with a lighter "eel stripe" down the back, while cows were generally reddish-brown.
- Horns: Aurochs had large, forward-curving horns, which could reach up to 31 inches (80 cm) long. These horns were crucial for defense against predators and in fights between males.
Evolution and Extinction
- Evolution: The aurochs evolved around 2 million years ago in India and spread across Europe, Asia, and North Africa. Over time, isolated populations adapted to their environments.
- Extinction: The last recorded aurochs died in 1627 in Poland due to hunting, habitat loss, and diseases spread by domesticated cattle. Their extinction marked the end of the species, but they live on genetically through domestic cattle, which were bred from aurochs around 8,000 to 10,000 years ago.
Relationship to Domestic Cattle
- Domestication: Modern domestic cattle (Bos taurus and Bos indicus) were domesticated from different auroch populations. Early humans domesticated aurochs in two main areas:
- Bos taurus was domesticated in the Fertile Crescent (modern-day Middle East).
- Bos indicus (zebu cattle) was domesticated in the Indian subcontinent.
Genetic Influence: Domestic cattle have inherited many traits from their auroch ancestors. Selective breeding by humans introduced variations in size, color, horn shape, and other physical traits to better suit agricultural needs. Behavior: Domestic cattle have been bred for docility and other traits that make them manageable for farming. Aurochs, on the other hand, were more aggressive and less tolerant of human presence.
Breeding Back Efforts
In recent years, there have been efforts to "breed back" cattle that resemble the aurochs. Breeding back does not resurrect the aurochs genetically but seeks to produce cattle that resemble aurochs in appearance and behavior.
- Heck Cattle: In the early 20th century, German zoologists Heinz and Lutz Heck attempted to recreate aurochs by selectively breeding European cattle breeds with certain aurochs-like features.
- TaurOs Project: Launched in 2008, this project uses selective breeding of various cattle breeds to produce animals that physically and behaviorally resemble aurochs, focusing on rewilding European landscapes.
Role in Ecosystems and Rewilding
Aurochs once played a critical role in their ecosystems by grazing on grasses, which helped maintain the balance of plant species and created habitats for other animals. In rewilding efforts, cattle resembling aurochs are introduced to landscapes where their grazing patterns help to maintain open grasslands and support biodiversity.
Cultural Significance
Aurochs appear in ancient art, mythology, and folklore across many cultures. They were revered as symbols of strength and vitality and often featured in prehistoric cave paintings, such as those in Lascaux, France, which date back over 17,000 years.
Summary
- Ancestors of Domestic Cattle: Aurochs are the wild progenitors of domestic cattle, with genetic links to both Bos taurus and Bos indicus.
- Distinctive Features: Large, muscular, and possessing large horns, aurochs were much larger than modern cattle.
- Rewilding and Conservation: Through efforts like the Heck Cattle and TaurOs Project, conservationists attempt to restore the ecological impact that aurochs once had on European landscapes.
- Legacy: Although extinct, the aurochs' genetic legacy continues in domestic cattle, and they remain an iconic symbol in history and conservation.
The story of the aurochs highlights the powerful connection between humans and wild animals, showcasing how our ancestors' choices shaped the landscapes and species we see today.
Ancient DNA brings to life history of the iconic aurochs
Geneticists from Trinity, together with an international team of researchers, have deciphered the prehistory of aurochs – the animals that were the focus of some of the most iconic early human art, and whose tale is intertwined with climate change and human culture.
The team analysed 38 genomes harvested from bones dating across 50 millennia and stretching from Siberia to Britain in this work.
The aurochs roamed in Europe, Asia and Africa for hundreds of thousands of years. Adorned as paintings on many a cave wall, their domestication to create cattle gave us a harnessed source of muscle, meat and milk. Such was the influence of this domestication that today their descendants make up a third of the world’s mammalian biomass.
We normally think of the European aurochs as one common form or type, but our analyses suggest there were three distinct auroch populations alone in Europe – a Western European, an Italian, and a Balkan. There was thus a greater diversity in the wild forms than we had ever imagined.
Dr Mikkel-Holger S. Sinding, co-author
Department of Biology
University of Copenhagen, Copenhagen, Denmark.
Intriguingly, climate change also wrote its signature in aurochs genomes in two ways:
First, European and north Asian genomes separated and diverged at the beginning of the last ice age, around 100,000 years ago, and did not seem to mix until the world warmed up again at its end.
And second, genome-estimated population sizes dropped in the glacial period, with a more pronounced hard time endured by European herds. These lost the most diversity when they retreated to separated refugia in southern parts of the continent before repopulating it again afterwards.
The most pronounced drop in genetic diversity occurs between the period when the aurochs of southwest Asia were domesticated in the north of the Fertile Crescent, just over 10,000 years ago, to give the first cattle.
Remarkably only a handful of maternal lineages (as seen via mitochondrial DNA which is handed down via mothers to their offspring) come through this process into the cattle gene pool.
A Pleistocene aurochs from the Upper Rhine Valley, around 50,000 years old.Image credit Staatliche Schlosser and Garten Hessen.
Although Caesar exaggerated when he said it was like an elephant, the wild ox must have been a highly dangerous beast and this hints that its first capture and taming must have happened with only a very few animals. However, the narrow genetic base of the first cattle was augmented as they first travelled with their herders west, east and south. It is clear that there was early and pervasive mating with wild aurochs bulls, leaving a legacy of the four separate preglacial aurochs ancestries that persists among the domestic cattle of today.
Professor Dan Bradley, senior author
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.
Publication:
AbstractOne interesting finding is that the aurochs split and diversified during a glacial period when different populations were in different refugia, where they diversified genetically. This is reflected in the DNA inherited by domestic cattle and shows allopatric speciation in progress.
Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwest Asian, North Asian and South Asian—each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.
Rossi, C., Sinding, MH.S., Mullin, V.E. et al.
The genomic natural history of the aurochs. Nature (2024). https://doi.org/10.1038/s41586-024-08112-6
© 2024 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.
Another interesting finding is how the domesticated cattle and the wild aurochs continued to interbreed with domestic cattle, with auroch bulls mating with domestic cows, showing how diverging species can interbreed for a period until barriers to hybridization evolve.
All this paints a much more interesting picture of the origins of domestic cattle from wild ancestors than the childish one involving magic that creationists find easier to understand. It also poses the question for creationists - why didn't their putative designer design domestic cattle fit for purpose - docile and a high milk yield - that had to be bred into them through an extended period of selective breeding because their wild ancestors were too big and dangerous?
Tuesday, 15 October 2024
Refuting Creationism - The Japanese People Didn't Notice Noah's Genocidal Flood!
Traces of ancient immigration patterns to Japan found in 2000-year-old genome | SCHOOL OF SCIENCE THE UNIVERSITY OF TOKYO
Being parochial Bronze Age pastoralists who knew about nothing and nowhere that was more than a day or two's walk from their hill pastures in Canaan, those who made up the Hebrew creation myths could not possibly have been aware that there were other cultures in far-away places like China, Korea and Japan, which had ancient histories going way back before the myth-makers thought Earth was created, and which were unscathed by an global flood at the time in which they set that tale.
Had they been aware of them, they could have made up slightly more plausible myths with a more realistic timeline, instead of requiring their believers to try to compress everything that's happened in the entire 14-billion-year-old Universe into 10,000 years.
But how could they have done so when they had no-one to teach them the real history of the planet and the people living on it? All they had was their own limited imagination and a handful if inherited myths from neighbouring culture, like Egypt and Sumeria, for theirs was a backward, illiterate culture from the fearful infancy of our species, dependent on oral traditions and superstitions.
How could they possibly have known, for example, that a population of humans had been more or less isolated for about 6,500 years, ending at about the time the myth-makers believed Earth was made out of nothing by magic, complete with a dome over it to cover the small, flat place they called home? They would have known nothing about immigration from China or from the Korean Peninsula into the Japanese archipelago that brought this period of isolation to an end and probably resulted in the present-day population of Japan.
So, of course, they saw nothing wrong with inventing a tale about a genocidal flood killing everyone apart from 8 related survivors, or of building a tower to reach above the dome or about a panicking god making them all speak different languages so they couldn't work in cooperative groups any more, and yet, if their tale is to be believed, the descendants of those few survivors, all speaking different languages, migrated to places like China, Korea and Japan where they all adopted the local language and writing that had been used for several thousand years, forgot all about Noah and his flood and invented new gods and religions, whereas the myth-makers of Canaan remembered it all word-perfect in every detail...
So, how do we know the record they left was wrong?
Unintelligent Design - The Blunder That Causes Cancers
Ludwig Cancer Research
It has often been a theme of my blog posts how, if we regard cells as the result of conscious (I won't use the term 'intelligent' as that's singularly inappropriate, as we shall see) design then the picture quickly emerges of a bungling incompetent, cobbling together Heath-Robinson solutions to problems of its own incompetent making and lack of foresight.
The entire system of epigenetics, for example, is only necessary in a multicellular organism with its cell specialisation because specialised cells only need a small subset of the entire genome, yet, because cells replicate using exactly the same process that single-celled organisms use, where the entire genome needs to be replicated in every daughter cell, the cells of multicellular organisms such as humans each receive the entire species genome. So, most of it needs to be turned off.
This is where the epigenetic system comes in where methyl groups are attached to key bases in the DNA which prevents that section being transcribed into RNA, effectively switching the gene off. There are other components to the epigenetic system, but that is the pertinent component as far as this particular blunder is concerned.
The problem starts when a methyl group is attached to a cytosine base (C in the CGTA genetic code) which is next to a guanine(G) base.
Monday, 14 October 2024
Refuting Creationism - How A Beetle Evolved To Eat Toxic Plants
Red milkweed beetle genome sequence offers plant-insect co-evolutionary insights
We are continually being assurd by gullible cretionists that the Theory of Evolution (TOE) is 'a theory in crisis' becase a growing body of biologisdts have abandonned it in favour of the creationists superstition of intelligent [sic] design.
This has been a creationist fantasy for at least the last 50 years since when it is supposedly about to happen, any day now, real soon (a bit like The Second Coming of Christ - something which, despite regular announcements that it will happen next Wednesday at noon, never happens - but its gunna, you see!)
However, when we read the scientific publications of these biologists who are allegedly abandoning the TOE, we see no signs whatever of any abandonment; quite the opposite. We see the TOE as firmly embedded in biological science as the Laws of Thermodynamics and the Theory of Gravity are embedded in physics, Atomic Theory is embedded in chemistry and Germ Theory is embedded in epidemiology. It forms the bedrock of the science, without which very little makes any sense.
For example, when a bunch of entomologists wanted to understand how a species of herbivorous beetle can eat a toxic plant, they compared it genomically with a related species that doesn't eat the toxic plant to see how the ability to proccess the toxins evolved.
Of course, being scientists, they reject the idea that the beetle was magically created that way by an unproven supernatural entity because none of that can be falsified and the existence of such an entity can't be established, so there is no logical reason to include one in any answer. The fact that their mummies and daddies might have believed in it is irrelevent to their science, because belief doesn't create facts.
Monday, 7 October 2024
Unintelligent Design - How Creationism's 'Designer' Needs Plan B For When Plan A Fails To Mend Its Previous Design Blunder
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The secret to being a good designer or planner is to always have a Plan B. I say that as a former emergency operations centre manager where the future is unpredictable, so I needed to keep as many options open as possible because, as I used to joke, my Plan B was to tear up Plan A and start again.
Now, you can play the percentages game, for example, I could be fairly sure town centres would be fairly busy around 11 pm, especially on a Friday and Saturday night, when in the UK the pubs close, or as we call it, 'chucking out time', and a lot of inebriated people would be out on the streets, fighting over available taxis, over girl/boyfriends or who had got served at the bar out of turn (queue-jumping is a big no-no in the UK).
I also knew from 17 years operational experience that most of the calls would require little more than smoothing ruffled feathers, running checks to exclude underlying medical problems and sending them on their way, so turnover time would be relatively short, and I would get a crew back fairly quickly.
Another peak would be around 1 am when the nightclubs closed, but with a few exceptions such as those the rest of the week would resemble a system in chaos where medical emergencies, traffic accidents and every other imaginable emergency occurred more or less randomly, with statistical patterns only being noticeable over time with a sufficiently large database.
Later on, I became the data analyst who looked for those patterns and used them to devise deployment plans to minimise average emergency response times, but that's another story.
Juggling acts were the daily routine for an emergency operations centre like mine, as we tried to maintain as much emergency cover as possible while getting help to people who needed it as quickly as possible. And you never knew you had made the right decision until it turned out not to have been the wrong one.
Our major handicap was of course being unable to accurately forecast the future, not just weeks or days ahead but hours and minutes. What we singularly lacked was omniscience for which educated guesses were a poor substitute.
So, to a creationist it might come as something of a shock to learn that their putative designer behaves like a designer/planner who can't foretell the future because, if nothing else, it is allegedly omniscient, and its designs are perfect. As such it shouldn't need a Plan B because Plan A will be perfectly designed for the precise future needs of the species. There should never be an occasion where it needs to tear up Plan A and starts again; it shouldn’t need to consult a large database to look for patterns then work out the probability of that pattern repeating itself and planning its responses accordingly, never knowing if it was the right plan until it turned out not to be.
And yet a team of researchers from Cold Spring Harbor Laboratory, New York, USA has found that the plant, Arabidopsis has a Plan B for when Plan A fails. Plan A is all about making the ramshackle, Heath Robinson process for ensuring mistakes in DNA replication get attended to. In a design which seems to be a characteristic of creationism putative intelligent [sic] designer, a shoddy process needs another layer of complexity to try to make it works, but even that fix breaks and the result of growth defects, sterility and, in many cases in animals, cancers or developmental disorders.
Saturday, 5 October 2024
Unintelligent Designe - Creationism's Blundering Heath-Robinson 'Designer' Strikes Again - And Causes Cancer
How Cells Recognize and Repair DNA Damage -
One thing you can depend on with creationism's putative designer is that there will never be a simple solution when there is a more complicated way to solve the problem it just created, and just like William Heath-Robinson, it will try to use pre-existing structures that were designed for an entirely different function, like a pile of books under the legs of a ladder to make it tall enough, and every piece of string holding things together will have knots in it.
And when we look beneath the superficial resemblance of design in, for example, a living cell, we find all manner of if-it-works-it'll-do solutions to problems, like the solution to the problem of breaking DNA that a team of scientists, led by Kaspar Burger, from Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany, have discovered.
The problem arises of course because the method for replicating DNA as cells divide is poorly designed and unnecessarily complicated in the first place. If the putative designer had devised a more sensible method for replicating cells in multicellular organisms than that used for replicating single cells where the whole genome needs to be replicated, many of the problems of erroneous copying wouldn't arise because only a small subset of the genome is needed for specialised cells.
Friday, 4 October 2024
Refuting Creationism - How Ants Were Cultivating Crops 66 Million Years Before 'Creation Week'.
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One of the 'uniquely human' abilities that creationists traditionally cite in support of their childish superstition that humans were magically created out of dirt as a species separate from other animals, is the fact that humans for the most part, indulge in agriculture - i.e., we grow plants as food - or at least other people do. Most of us in the developed economies buy their produce in shops.
a Like all their other claims of human exceptionalism, it's a nonsense fairy tale, of course. Humans have some unique characteristics that make them a distinct species, but then so does every other species, by definition. There is nothing materially different about humans that makes them subject to different laws of chemistry and physics than other species, of course.
And in respect of agriculture, we are far from unique - ants have been at it for about 66 million years - well before creationists imagine the entire Universe was magically created from nothing by a magic god made of nothing. But this is hardly surprising, since some 99.9975% of the history of life on Earth happened before creationism's legendary 'Creation Week'.