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

Tuesday 26 March 2024

How Evolution Works - Choas, Catastrophe and Tipping Points


Hyphal mycelium.
credit: Maxim Ohairwe.
Researchers Discover Evolutionary “Tipping Point” in Fungi

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

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

Sadly, the term quickly became entangled with both American nationalism and creationism; the latter because it appears to refute the person whom creationists think is the arch prophet of the 'evil' of evolution - Charles Darwin, the leading figure in creationist demonology - as though the entire body of evolutionary biology hangs on the authority of one 19th century biologist; the former because it appears to have replaced one of the most famous scientific theories with one 'discovered' by Americans, so asserting American pre-eminence in science.
Tell me about 'Punctuated Equilibrium'; who popularized the idea and the arguments for and against it. Punctuated equilibrium is a theory in evolutionary biology that suggests that the tempo of evolution is not constant but rather characterized by periods of relatively rapid change (punctuation) interspersed with prolonged periods of stability (equilibrium). This concept was popularized by paleontologists Niles Eldredge and Stephen Jay Gould in their 1972 paper "Punctuated Equilibria: An Alternative to Phyletic Gradualism."

Arguments for punctuated equilibrium include:
  1. Fossil Record: Eldredge and Gould argued that the fossil record often shows long periods of stasis, where species exhibit little morphological change over millions of years, followed by relatively rapid bursts of evolutionary change when new species appear.
  2. Lack of Transitional Forms: They also pointed out that the fossil record frequently lacks the transitional forms predicted by gradualism, which suggests that evolution may occur in more rapid bursts.
  3. Genetic Mechanisms: Some genetic models also support the idea of punctuated equilibrium, suggesting that small populations undergoing rapid change due to factors like genetic drift and founder effects can lead to rapid speciation.
Arguments against punctuated equilibrium include:
  1. Lack of Evidence: Critics argue that punctuated equilibrium is based more on interpretation of the fossil record rather than direct evidence from genetic or ecological studies.
  2. Sampling Bias: Some scientists suggest that the apparent gaps in the fossil record may be due to incomplete sampling rather than actual periods of stasis.
  3. Mechanistic Explanation: Critics also question the mechanisms underlying punctuated equilibrium, arguing that it may be difficult to explain how rapid evolutionary change occurs in the absence of significant environmental pressures or genetic changes.
Overall, punctuated equilibrium remains a subject of debate within evolutionary biology, with proponents arguing that it provides a more accurate description of patterns of evolution observed in the fossil record, while critics suggest that it may overemphasize the importance of long periods of stasis and rapid bursts of change.

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


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

Photo: Mohammad Javad Shoaee
Persian plateau unveiled as crucial hub for early human migration out of Africa – Griffith News

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

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

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

The team have presented their evidence in an open access paper in Nature Communications and explain it in a Griffith University news item: This study sheds new light on the complex journey of human populations, challenging previous understandings of our species’ expansion into Eurasia.
Pebdeh Cave excavation in the southern Zagros Mountains. Pebdeh was occupied by hunter-gatherers as early as 42,000 years ago.

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

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

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

Photo: Mohammad Javad Shoaee

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

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

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

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

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

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

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

Introduction

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

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

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

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

Monday 25 March 2024

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


Fossil skull of Kermitops gratus
Brittany M. Hance, Smithsonian.
Researchers Name Prehistoric Amphibian Ancestor Discovered in Smithsonian Collection After Kermit the Frog | Smithsonian Institution

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

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

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

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

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

Saturday 23 March 2024

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


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

Image: Aldo Benites-Palomino.
Ancient Giant Dolphin Discovered in the Amazon | | UZH

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

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

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

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

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

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

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

Friday 22 March 2024

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


The female Diadem (bottom left) mimics the African Queen (top left). The male Diadem (right) keeps a distinct pattern to attract mates
Scientists discover how Diadem butterfly mimics African Queen - News

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

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

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

Thursday 21 March 2024

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


Genetic basis for the evolution of hair discovered in the clawed frog
Western Clawed Frog, Xenopus tropicalis
Carries the precursor gene for mammalian hair.


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

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

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

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

Firstly, the evolutionary origin of mammalian hair.

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

Tuesday 19 March 2024

Creationism's Heath-Robinson Designer - Muddling Through With Even More Ramshackle Complexity


Gut Bacteria Make Neurotransmitters to Shape the Newborn Immune System | Newsroom | Weill Cornell Medicine

The story so far, according to the Creationists Gospel:

Once upon a time, just a few thousand years ago, a magic man in the sky magicked a small flat planet with a dome over it in the Middle East, and then made some people to live on it.

It also made lots of harmful bacteria and other parasites to live in them and make them sick, but luckily, it also gave the humans an immune system to stop the parasites it made to make them sick, from doing what it designed them to do.

The only problem was that the ramshackle immune system it designed, which often doesn't do what it was designed to do, is also a little hypersensitive and prone to treating other things like the body it should be protecting as a parasite and mounting an attack on it so we suffer from all sorts of 'autoimmune' diseases that require another layer of complexity to keep in check. The other thing about it is that it needs training and until that's complete, it will treat all manner of things as parasites, including the food babies eat - and that could result in food allergies that would make life miserable!

But rather than do the simple thing and design the immune system to be able to tell the difference between food and harmful parasites, creationism's version of William Heath-Robinson went for one of the most bizarre solutions you can imagine. Rather like William Heath-Robinson's solution to an every-day problem, it co-opted things in the baby's environment to perform functions they were never intended to perform, like an upright piano being used to stand a step-ladder on to give it enough height, or a stick and some string being used to mend a broken spoke in a wheel, creationism's designer co-opted some of the bacteria that live in a baby's gut.

How it did this is explained in a free access paper in Science Immunology by a team of researchers from the Department of Pediatrics at Weill Cornell Medicine, led by Assistant Professor Dr. Melody Zeng of the Gale and Ira Drukier Institute for Children's Research. Their work is described in a Weill Cornel Medicine news item:

Creationism in Crisis - An Ancestral Croccodile from 215 Million Years Before 'Creation Week'


An artist’s interpretation of the newly identified aetosaur Garzapelta muelleri
Márcio L. Castro.
Tanks of the Triassic: New Crocodile Ancestor Identified | Jackson School of Geosciences | The University of Texas at Austin

In that very long period of Earth's history, long before creationism's god decided to create a small flat planet with a dome over it, and before even the dinosaurs rose to pre-eminence, another group of reptiles had evolved into armour-plated tank-like creatures with thick body-plates and fringes of curved spikes to deter predators. Some of these were later to evolve into the modern crocodiles.

Now three researchers from the University of Texas at Austin have identified a new species that lived 215 million years ago in the Triassic. The newly-identified species was found on a museum shelf where it had been since its discovery in Garza County in northwest Texas, some 30 years ago by the palaeontologist, Bill Mueller. The researchers have named the new species in his honor, as Garzapelta muelleri (Pelta = plate).

Friday 15 March 2024

Creationism in Crisis - Bird Watching In The Age Of Dinosaurs - About 70 Million Years Before 'Creation Week'


Archaeopteryx
Credit: Dotted Yeti/Shutterstock
A brief guide to birdwatching in the age of dinosaurs

What would it have been like to go bird-watching in that very long period of pre-'Creation Week' history just before a cataclysmic meteor strike cause the extinction of almost all the dinosaurs, 66 million years before creationists believe their god created a small, flat planet with a dome over it in the Middle-east?

At that time, Earth had a large population of dinosaurs, some of which were later to become modern birds which evolved to fill the vacated niches formerly occupied by the dinosaurs, while another survivor, a small rat-like early mammal, the descendant of mammal-like reptiles radiated into modern mammals.

For a period, these early birds, the avian dinosaurs which had evolved from the bipedal theropod dinosaurs, formed two major groups - the ornithuromorphs and the enantiornithine.

Thursday 14 March 2024

Creationism in Crisis - Rice Paddy Snakes In Thailand Diversified About 2.5 Million Years Before 'Creation Week'


Hypsiscopus murphyi sensu
Photo: Bryan Stuart
Rice paddy snake diversification was driven by geological and environmental factors in Thailand, molecular data suggests | KU News

In one of those far-away places that the simple-minded authors of the story in Genesis about a small flat Earth with a dome over it being magicked up out of nothing in the Middle East, 10,000 years ago, could never have guessed existed, and some 2.5 million years before they though Earth existed, major environmental changes were driving the diversification of a species of snake into several descendant species, just as the Theory of Evolution predicts.

If those simple-minded Bronze Age pastoralists had known about it and understood its significance in terms of the history of life on Earth and the dynamic geology of the planet, just imagine how different their imaginative tale would have been! As it was, they had to do their best with what little knowledge and understanding they had.

The snake in question was the Rice Paddy snake, otherwise known as a mud snake, and the far-away place was Thailand where the rise of the Khorat Plateau caused environmental changes that resulted in the evolutionary diversification of the Hypsiscopus genus.

The team of researchers from various American and Southeast Asian Universities, who have shown this link between environmental change and evolutionary radiation in a genus was led by Dr. Justin Bernstein, of the University of Kansas Center for Genomics. Their findings are published open access in Scientific Reports and are explained in a Kansas University news release:

Creationism in Crisis - Dinosaur Footprints In Alaska from 100 Million Years Before 'Creation Week'!


A theropod track lies in rock near the west bank of the Kukpowruk River.

Photo: Anthony Fiorillo
Alaska dinosaur tracks reveal a lush, wet environment | Geophysical Institute

About 100 million yearsd before creationism's god decided to create a small flat planet with a dome over it to keep the water about its sky out, there were dinosaurs living in what is now northern Alaska. The problem for creationists is that the people who wrote their favourite creation myths were ignorant both of dinosaurs and Alaska so had no idea their tales needed to include something about them, which is why everything they wrote about either happened within a day or two's walk if the Canaanite Hills or were plagiarized from nearby cultures.

Now a team of paleontologists and archaeologists have discovered fossilised dinosaur footprints and the remains of plants in the Nanushuk Formation that show the climate there was warmer and wetter than today, at a time when species were migrating over the landbridge between Siberia in Asia and North America.

Unlike the Paluxy hoax, which had creationists fooled for the best part of a decade, there were no human footprints (hand-carved or otherwise) associated with these dinosaur tracks.

Because creationists will try to falsify the aging of the Nanshuk Formation, claiming the method must have been flawed to such an extent that if made 10,000 years or less look like 100 million years, here is actually how the dating was done - it’s; those dreaded zircons in volcanic deposits again, plus stratigraphy based on index fossils found in rocks of known age:
Do you have any information on the Nanushuk Formation in northern Alaska and how its age was estimated? The Nanushuk Formation is a geological formation located in northern Alaska, particularly in the North Slope region. It is primarily composed of sandstone, siltstone, and shale, and it contains significant oil and gas reserves. The formation is of great interest to geologists and petroleum geologists due to its hydrocarbon potential.

The age of the Nanushuk Formation has been estimated through various methods, including biostratigraphy and radiometric dating of volcanic ash layers within the formation. Biostratigraphy involves the study of fossil assemblages found within the rocks to determine their relative ages. By comparing the fossils present in the Nanushuk Formation to those found in other formations with well-established ages, geologists can infer the approximate age of the Nanushuk Formation.

Additionally, radiometric dating techniques, such as radiocarbon dating or uranium-lead dating, can be used to determine the absolute ages of specific minerals or volcanic ash layers within the formation. These methods rely on the decay of radioactive isotopes within the rocks to estimate the time since their formation.

Through a combination of these techniques, geologists have estimated that the Nanushuk Formation was deposited during the Late Cretaceous period, approximately 70 to 80 million years ago. However, the precise age estimates may vary depending on the specific location within the formation and the methods used for dating.
The team, led by Dr. Anthony R. Fiorillo of the New Mexico Museum of Natural History & Science, Albuquerque, USA and including Professor Paul McCarthy of University of Alaska Fairbanks (UAF) College of Natural Science and Mathematics, have published their findings open access in the journal Geosciences. It is explained in a UAF news item:

Wednesday 13 March 2024

How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?


Reticulated giraffe, Buffalo Springs, Kenya. Photo: Mogens Trolle

Photo: Mogens Trolle
Gene flow in giraffes and what it means for their conservation – Department of Biology - University of Copenhagen

In an evolutionary picture that resembles that of humans, giraffes appear to have speciated, or partially speciates at different times and in different parts of their range, then hybridized, before splitting again with regular gene-flow between the groups.

Similarly, though over a greater range, humans seems to have partially speciated into isolated populations in Africa before coming together again and spreading to Eurasia as Homo erectus which then split into Neanderthals, Denisovans and possibly others before meeting up with H. sapiens coming out of Africa in a second wave, to interbreed with the Eurasian species. The result is genetically distinct populations with evidence of ancient hybridization and gene flow.

Because conservation efforts tend to be directed at the species level, it is important for giraffe conservation to determine whether there is a single pan-African species with local sub-species or whether there are four or more species, each with a smaller population and therefore more vulnerable to habitat destruction and extinction.

To try to resolve this issue, as part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen, scientist carried out an extensive genome analysis to establish whether the different populations have been genetically isolated for long enough to be regarded as distinct species, even though, in captivity, they freely interbreed.

The results were a little surprising but highlight the difficulty in determining whether speciation has occurred within a population where differentiation is still in progress and few barriers to hybridisation have arisen. The problem is compounded by the fact that there is not a fixed definition of species, although biologists understand what the term means in a given context.

I've previously written blog posts about this problem, using the Eurasian crows as an example - an article incidentally which was recommended reading for Scottish biology students doing their 'Highers'.

The researchers have published their findings open access in the online Cell Press journal, Current Biology and explain it in a news item from the University of Copenhagen Biology Department:

Tuesday 12 March 2024

Malevolent Design - How The Malaria Parasite is 'Designed' To Evolve And Outwit Medical Science


The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic | EMBL

Devotees of creationism’s divine malevolence would be conflicted by this news if they understood it, because it shows the creative genius of any intelligent designer who could come up with this system, but, it looks like it did so (if you believe it couldn't happen naturally) by setting up an evolutionary process that creationists are obliged by dogma to believe doesn't work.

The news is that the organisms that causes malaria, Plasmodium falciparum, is 'designed' to quickly find a way to overcome the anti-malarial drugs medical science has developed to cure people suffering from it and to prevent others from getting malaria, by evolving very quickly.

The discovery was by researchers at European Molecular Biology Laboratory's (EMBL’s) European Bioinformatics Institute who have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. Copy-paste' is a way of doing something creationists insist is impossible without the aid of god-magic of increasing the genetic information in a genome and making it available for evolution by mutation and selection without any loss of function in the original copied genes.

The team have recently published their finding in the open access journal PLOS Biology and describe it in an EMBL news item:

Unintelligent Malevolence - Pathogens 'Designed' to Beat Medical Science In Two Different Ways


Acinetobacter baumannii seen under a scanning electron-microscope

Escherichia coli
What makes a pathogen antibiotic-resistant? | Sanford Burnham Prebys

One of todays examples of the stupidity of creationism is something of a novelty. Usually, by applying the central tenets of creationism, any putative designer of living things like parasites either appears malevolent (and sometime it has to be said, malevolent at a near genius level in the ways it finds to make us and other animals sick) or it looks incompetent in that its 'solutions' are often to problems of its own making and more often than not to solutions it designed for one side of an arms race which it now trets as problems for the other side.

But today's example can only be described as an example of incompetent malevolennce, as creationism's putative designer, faced with the same 'problem' of medical science developing antibiotics effective against two different species of pathogen, set about designign two completely different 'solutions' to this problem. - Talk about re-inventing the wheel!

The pathogens are: Escherichia coli and Acinetobacter baumannii.

Creationists will probably be familiar with Escherichia coli (E. coli) because they believe their guru, Michael J Behe, 'proved' their god exists by claiming (falsely) that E. coli's flagellum must have been intelligently designed because he didn't know it evolved out of a pre-exiting structure and couldn't think how else it could have evolved. But then such is the standard of creationist apologetics!

What Behe had unwitting done was destroy the traditional excuse creationists use to explain pathogens like E. coli by blaming them on another 'designer' called 'Sin' which somehow creates living organisms although the creationit designer god is the only entitiy capable of designing livign things, so any example of 'intelligent design, real or imaginary, if 'proof' of this designer god's existance.

So, what creationists are now left with is an E.coli with a flegellum designed by their god to make it better at making us sick, and now resitant to antibiotics to help it win against medical science trying to prevent it makign us sick!

But what creationists are less likely to be familiar with is the pathogen, Acinetobacter baumannii, so here is a little background:

Monday 11 March 2024

Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It


The world’s most prolific CO2-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO2) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.
Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

Malevolent Design - How a Bacterium Carries a Virus That Selectively Kills Male Insects And Only Allows Infected Females To Breed


How does a virus hijack insect sperm to control disease vectors and pests? | Penn State University

Wolbachia are a genus of bacteria that form a symbiotic relationship with about 50% of arthropod species, including insects and spiders but they can also manipulate the species for their own ends (in terms of breeding success). They are aided in this by a virus which is incorporated in their genome which has been shown to join forces with Wolbachia to ensure their own reproductive success in the form of females infected with the virus-bearing Wolbachia.

So completely have Wolbachia integrated with insects that one species of fruit fly has the entire Wolbachia genome incorporated into its own genome, making it, biologically, both bacterium and fruit fly.

One way Wolbachia ensure their own survival at the expense of the species of insect they infect is by making the sperm and egg incompatible if the female is not also a carrier of the right species of Wolbachia. And, to be on the safe side, two proteins produced by the virus break the sperm's DNA so any resulting embryo will be defective and will fail to develop. This ensures that only the females carrying the infection can breed, so increasing the Wolbachia and its virus in the gene pool.

The team who discovered this nasty little virus and how it acts selfishly, was co-led by Professor Seth R. Bordenstein, of the One Health Microbiome Center at Pennsylvania State University. They have published their findings in Science and described it in a Penn State News item.

But first, a little background on Wolbachia:

Sunday 10 March 2024

Covidiot News - Just Because You Haven't Had COVID-19 Yet, Doesn't Mean You Won't!


Haven't had COVID yet? It could be more than just luck

There are some scary questions for creationists at the end of this article. They follow on naturally from what's being discussed, so creationists should probably avoid reading too far, unless they have a responsible adult with them.

This article from The Conversation is from May 2022, when we were into the second year of the COVID-19 pandemic and most vulnerable people had had the two-step vaccinations and many would have had the spring booster. At that point neither me nor my partner had had COVID-19, which we put down to rigorously following the recommendations regarding mask-wearing, social distancing, hand washing, etc. and had tried to reduce our vulnerability to the sever forms of it by losing about 3 stone in weight and, in my case, getting my blood pressure under control with medication. We also tried to ensure our immune systems were healthy by taking vitamin D3, vitamin C, zinc and iron supplements.

In the early days of the pandemic, even before the official restrictions on social contact, we had observed the basic rules of hygiene and everyone who came into the house used hand-cleanser at the front door. I had even managed to obtain a supply of face-masks and plastic gloves online, which we wore at all times outside the house. Every package that was delivered to the house was left for several hours before we touched it, and all our weekly shopping was delivered or bought with click and collect. Delivered bags were left for four hours before unpacking. And we took weekly tests just in case we had it asymptomatically. All that might seem a little over the top now, but we were vindicated as events were to prove.

We put the fact that we hadn't caught it by mid-2022 down to our preventative measures, not to luck or genetics - a view that was vindicated last year when we both came back from a two-week vacation in France with a mild form of COVID-19, despite having had all the boosters on offer. We probably picked it up in a crowded airport or on the plane, where all the social distancing measures had been forgotten and even face masks were no longer worn. We both felt like we had a mild case of flu for a couple of days and after a week we were testing negative. Had we contracted it in Spring 2020, the outcome would probably have been very different as we had no immunity, and both had three of the risk-factors - overweight, high BP and over 70. In addition, my partner had had a mastectomy and was receiving treatment for breast cancer.

One reason you can't ever be sure that you won't catch COVID-19 is because the virus keeps mutating to produce new variants so, even if you were fortunate enough to have natural or acquired immunity to the variants so far, it is quite possible that the next or subsequent variants will have evolved a way round it. The following chart from the UK NHS, shows the rise and fall of the main variants over the course of the pandemic:
But still, a few people managed to stay free from the virus. In the following article, reprinted from The Conversation under a Creative Commons license, Lindsay Broadbent, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, explains why. Her article has been reformatted for stylistic consistency:

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:

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently


Revealing the evolutionary origin of genomic imprinting 
Caenorhabditis elegans

Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.

This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.

Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:
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