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

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:
A new study by Virginia Tech geobiologists traces the cause of the first known mass extinction of animals to decreased global oxygen availability, leading to the loss of a majority of animals present near the end of the Ediacaran Period some 550 million years ago.

The research spearheaded by Scott Evans, a postdoctoral researcher in the Department of Geosciences, part of the Virginia Tech College of Science, shows this earliest mass extinction of about 80 percent of animals across this interval.

This included the loss of many different types of animals, however those whose body plans and behaviors indicate that they relied on significant amounts of oxygen seem to have been hit particularly hard. This suggests that the extinction event was environmentally controlled, as are all other mass extinctions in the geologic record.

Dr Scott D. Evans, lead author
Department of Geosciences
Virginia Tech, Blacksburg, VA, USA
Evans’ work was published today [7 November 2022] in the Proceedings of the National Academy of Sciences, a peer-reviewed journal of the National Academy of Sciences. The study was co-authored by Shuhai Xiao, also a professor in the Department of Geosciences, and several researchers led by Mary Droser from the University of California Riverside’s Department of Earth and Planetary Sciences, where Evans earned his master’s degree and Ph.D.

Environmental changes, such as global warming and deoxygenation events, can lead to massive extinction of animals and profound disruption and reorganization of the ecosystem. This has been demonstrated repeatedly in the study of Earth history, including this work on the first extinction documented in the fossil record. This study thus informs us about the long-term impact of current environmental changes on the biosphere.

Shuhai Xiao, co-author
Department of Geosciences
Virginia Tech, Blacksburg, VA, USA.

[What exactly caused the drop in global oxygen?] The short answer to how this happened is we don't really know. It could be any number and combination of volcanic eruptions, tectonic plate motion, an asteroid impact, etc., but what we see is that the animals that go extinct seem to be responding to decreased global oxygen availability.

Dr Scott D. Evans
The study by Evans and Xiao is timelier than one would think. In an unconnected study, Virginia Tech scientists recently found that anoxia, the loss of oxygen availability, is affecting the world’s fresh waters. The cause? The warming of waters brought on by climate change and excess pollutant runoff from land use. Warming waters diminish fresh water’s capacity to hold oxygen, while the breakdown of nutrients in runoff by freshwater microbes gobbles up oxygen.

Our study shows that, as with all other mass extinctions in Earth's past, this new, first mass extinction of animals was caused by major climate change — another in a long list of cautionary tales demonstrating the dangers of our current climate crisis for animal life/

Dr Scott D. Evans
Some perspective: The Ediacaran Period spanned roughly 96 million years, bookended on either side by the end of Cryogenian Period — 635 million years ago — and the beginning of the Cambrian Period — 539 million years ago. The extinction event comes just before a significant break in the geologic record, from the Proterozoic Eon to the Phanerozoic Eon.

There are five known mass extinctions that stand out in the history of animals, the “Big Five,” according to Xiao, including the Ordovician-Silurian Extinction (440 million years ago), the late Devonian Extinction (370 million years ago), the Permian-Triassic Extinction (250 million years ago), the Triassic-Jurassic Extinction (200 million years ago), and the Cretaceous-Paleogene Extinction (65 million years ago).

Impressions of the Ediacaran fossils Dickinsonia (at left) and related but rare form Andiva (at right) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.
Photo courtesy of Scott Evans.

“Mass extinctions are well recognized as significant steps in the evolutionary trajectory of life on this planet,” Evans and team wrote in the study. Whatever the instigating cause of the mass extinction, the result was multiple major shifts in environmental conditions. “Particularly, we find support for decreased global oxygen availability as the mechanism responsible for this extinction. This suggests that abiotic controls have had significant impacts on diversity patterns throughout the more than 570 million-year history of animals on this planet,” the authors wrote.

Fossil imprints in rock tell researchers how the creatures that perished in this extinction event would have looked. And they looked, in Evans’ words, “weird.”

These organisms occur so early in the evolutionary history of animals that in many cases they appear to be experimenting with different ways to build large, sometimes mobile, multicellular bodies. There are lots of ways to recreate how they look, but the take-home is that before this extinction the fossils we find don't often fit nicely into the ways we classify animals today. Essentially, this extinction may have helped pave the way for the evolution of animals as we know them.

Dr Scott D. Evans
The study, like scores of other recent publications, came out of the COVID-19 pandemic. Because Evans, Xiao, and their team couldn't get access to the field, they decided to put together a global database based mostly on published records to test ideas about changing diversity. “Others had suggested that there might be an extinction at this time, but there was a lot of speculation. So we decided to put together everything we could to try and test those ideas.” Evans said. Much of the data used in the study was collected by Droser and several graduate students from the University of California Riverside.
Impressions of the Ediacaran fossil Dickinsonia, one of the first mobile animals, in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.">
Photo courtesy of Scott Evans.
Technical details is in the team's open access paper on PNAS:
Significance
Mass extinctions are well recognized as significant steps in the evolutionary trajectory of life on this planet. Here, we document the oldest known extinction of animals and test for potential causes. Our results indicate that, like younger diversity crises, this event was caused by major shifts in environmental conditions. Particularly, we find support for decreased global oxygen availability as the mechanism responsible for this extinction. This suggests that abiotic controls have had significant impacts on diversity patterns throughout the more than 570-My history of animals on this planet.

Abstract

The Ediacara Biota—the oldest communities of complex, macroscopic fossils—consists of three temporally distinct assemblages: the Avalon (ca. 575–560 Ma), White Sea (ca. 560–550 Ma), and Nama (ca. 550–539 Ma). Generic diversity varies among assemblages, with a notable decline at the transition from White Sea to Nama. Preservation and sampling biases, biotic replacement, and environmental perturbation have been proposed as potential mechanisms for this drop in diversity. Here, we compile a global database of the Ediacara Biota, specifically targeting taphonomic and paleoecological characters, to test these hypotheses. Major ecological shifts in feeding mode, life habit, and tiering level accompany an increase in generic richness between the Avalon and White Sea assemblages. We find that ∼80% of White Sea taxa are absent from the Nama interval, comparable to loss during Phanerozoic mass extinctions. The paleolatitudes, depositional environments, and preservational modes that characterize the White Sea assemblage are well represented in the Nama, indicating that this decline is not the result of sampling bias. Counter to expectations of the biotic replacement model, there are minimal ecological differences between these two assemblages. However, taxa that disappear exhibit a variety of morphological and behavioral characters consistent with an environmentally driven extinction event. The preferential survival of taxa with high surface area relative to volume may suggest that this was related to reduced global oceanic oxygen availability. Thus, our data support a link between Ediacaran biotic turnover and environmental change, similar to other major mass extinctions in the geologic record.

Soft-bodied fossils of the Ediacara Biota comprise the oldest communities of macroscopic organisms, including animals, and are critical for understanding the advent and diversification of complex life (1, 2). However, equally important are the dynamics that lead to the disappearance of such animals (36). Two major drops in diversity of the Ediacara Biota have been recognized, an initial decrease between the White Sea and Nama assemblages and a second across the Ediacaran–Cambrian boundary (Fig. 1 and ref. (5)). Although these events may be related, they are separated by more than 10 My and vary in magnitude and taxa impacted. The exceptional conditions required to preserve the Ediacara Biota also leave uncertainty around potential taphonomic biases that may contribute to such patterns. Diversity crises shaped the course of evolution in the Phanerozoic. Thus, a comprehensive understanding of each of these Ediacaran events is critical to determine the fate of Earth’s early animals.
Raw generic diversity (black squares), bootstrapped diversity (gray triangles), bootstrapped (42) per taxon extinction rate (solid blue), and origination rate (dashed green). Error bars represent 1 SD. For bootstrapping analysis, database occurrences were randomly subsampled to 50 occurrences.
M
Similar mechanisms have been proposed for losses of diversity during both the White Sea–Nama and Ediacaran–Cambrian transitions. One suggestion is that taxa did not go extinct but instead are not preserved in subsequent intervals (the “Cheshire cat” model of ref. (3)). Biases may include differences in the paleolatitudes and paleoenvironments sampled as well as variable taphonomic windows preserving fossils from each assemblage (7). Alternatively, these events may represent true extinctions triggered by either biotic or abiotic factors or some combination thereof (3, 5). The biotic replacement model, generally attributing the demise of the Ediacara Biota to competition with more advanced “Cambrian-style” metazoans, focuses on the impact of bioturbators as indicated by increases in trace fossil diversity (e.g., ref. (8)). Such ecosystem engineers are proposed to have fundamentally changed carbon packaging and fluid transport in the latest Ediacaran (3, 4, 810). Alternatively, the catastrophic extinction model posits that a major environmental perturbation led to the rapid loss of a variety of Ediacara taxa (3, 5) supported by geochemical data for environmental conditions, such as changes in oxygen availability (e.g., ref. (11)).


Here, we use a holistic approach, combining the distribution, taphonomy, and ecology of constituent taxa, to investigate changes in the Ediacara Biota through compilation of global occurrence data. Specifically, we test for potential sampling biases in the form of major differences in the paleolatitudes, facies associations, or preservational modes that could account for apparent changes in taxonomic composition. Based on the lack of correlation between these factors, we then investigate paleoecological trends through the Ediacaran under the assumption that, as with other diversity crises in the fossil record (12), patterns of selectivity across these intervals should reflect the factors responsible for such change. Analysis was conducted by comparing differences between the three assemblages—necessarily representing time-averaged groups of organisms on the order of millions to tens of millions of years—as in previous studies (e.g., refs. (3, 5, 13)). However, we also examined patterns of change involving taxa that survived and went extinct at the end of the White Sea assemblage to investigate changes on relatively shorter geologic timescales.
Fig. 2. Paleogeographic distribution of fossil localities (A) within the three assemblages of the Ediacara Biota based on continental configurations by Merdith et al. (14) and pie charts with the distribution of paleoenvironments (B) and modes of preservation (C) sampled for each assemblage, with “n” referring to the No. of formations/facies sampled in each time bin. See SI Appendix, Fig. S1 for locality labels.
Mass extinctions alone are enough to refute the childish notion of creation by an omniscient designer, let alone an intelligent one, and of course one reason the Ediacaran biota doesn't get a mention in the Bible is because, like all the other extinct taxons, the primitive Bronze Age authors had not got the slightest idea that they ever existed or that Earth was old enough to have gone through several major geological era lasting hundreds of millions of years, and several mass extinctions which had wiped out most of the earlier species or they wouldn't have assumed everything was magically created as it was then, But then they only had what little knowledge their culture possessed out of which to concoct a believable story.

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:

Friday 8 March 2024

Creationism in Crisis - Like Humans, Bumblebees Learn Through Social Interaction And May Have Cumulative Culture


Buff-tailed Bumblebee, Bombus terrestris
Source: Wikipedia.
Bees master complex tasks through social interaction - Queen Mary University of London

A sacred Tenet of creationism is that we humans are a special creation by the creator of the universe who made everything just for us. They point to the many 'unique' traits and abilities of humans as evidence of this - the ability to teach and learn, to form cultures, even walking upright are frequently cited as examples. It's also a sacred Tenet of creationism that anything which might refute the sacred tenets of creationism must be ignore, hand-waved aside or misrepresented but never, ever acknowledged for what it is - a refutation of creationism.

So, we can expect one or more of those tactics for handling the cognitive dissonance that news that bumble bees can teach and learn and so have at least the basis for forming cumulative cultures. The news itself comes in the form of an open access research paper in Nature by a team Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London.

The team showed that a complex, two-step task, which needed to be performed to receive a reward in the form of a sweet liquid could be learned by bees who were allowed to watch a trained 'demonstrator' perform the task. The bees not only learned how to perform the steps involved but that there was a reward to be had for doing so.

The 'demonstrators' had previously been trained by giving intermediate rewards as each stage was completed successfully, which were eventually withdrawn, leaving only the final reward. The experiment and its significance are explained in a Queen Mary University news release:

Unintelligent Design - New Species Of Deep-Ocean Worm - But What Is It For, Exactly?


New Deep-Sea Worm Discovered at Methane Seep off Costa Rica | Scripps Institution of Oceanography

Fig 1. Pectinereis strickrotti gen. nov., sp. nov. in life.

A, B, D. Several epitokous males swimming near methane seeps of Mound 12 (~1,000 m depth) of the Costa Rica margin and videoed via the submersible DSV Alvin. A. A frame grab from a video taken on Alvin dive 4503 on Feb. 4, 2009. B and D. Frame grabs from video taken on Alvin dive 4987 on Nov. 2, 2018. C. A fragment of an atokous infaunal female was collected at the same depth and locality via sediment pushcore on Alvin dive 4984 on Oct. 30, 2018. A white egg ~350 μm in diameter is visible on the exterior. Scalebar 1 mm. E. An epitokous male swimming near methane seeps of Parrita Scar (~1,000 m depth) of the Costa Rica margin. The specimen was initially caught via slurp with the ROV SuBastian (dive S0218, Jan. 11, 2019) but escaped.

Images A, B, D, courtesy of Woods Hole Oceanographic Institute. E, courtesy of Schmidt Ocean Institute.
One of the hallmarks of good intelligent design is that the designed object must be designed for a purpose. No intelligent designer is going to waste time making something that doesn't have any use. Even a decorative use is a function. As the designer William Morris said, "Have nothing in your house that you do not know to be useful, or believe to be beautiful.", but creationism's designer seems to just design things for the sake of it - half a million different beetles, for example. And now we have the example of a deep-ocean worm that appears to have no other purpose than to make more deep-ocean worms.

It's almost exactly like these different organisms are being designed by a mindless, natural process without a plan and no sense of purpose!

According to creationist superstitions in Genesis, every living thing on Earth was created for the benefit of mankind, and, incidentally, named by Adam (as though Adam would have had enough time to name every living species!). So, a challenge to creationists is to tell us what these deep-ocean worms are for in terms of their utility value for humans, and how did Adam dive that deep to name them?

Its discovery if the subject of an open access paper in PLOS ONE and is described in a Scripps Institute for Oceanography news release:

Thursday 7 March 2024

Creationism in Crisis - Evolution of Porcini Fungus


A tale of terroir: Porcinis evolved to the local environment – @theU
Structure of Fungi
This illustration is a little misleading because mycelia are often much larger than any of their mushrooms that appear on the surface of the soil or tree stumps. Fungi can grow up to a half a mile of the thread-like hyphae a day. In fact, the largest known organism on the planet is the Humongous Fungus (Armillaria ostoyae) in The Malheur National Forest, Oregon, measuring 2,385 acres (3.72 square miles) in area. It is estimated to be between 1900 and 8650 years old.
Photo credit: FoodPrint.org
The edible porcine fungus (Boletus edulis) also known as the boletus or penny bun is highly prized culinary delicacy throughout much of Europe. However, there is something strange about it evolution, especially in North America, according to a new report in the journal New Phytologist.

Creationists should note here that the scientists who produced the report see this 'problem' entirely within the Theory of Evolution by Natural Selection (TOE). The strangeness is not a problem for the theory but an example of how a fundamental principle of the theory - environmental selection - operates in North America.

The 'problem' is that while Boletus edulis exists in North America as a number of different varieties and genetically distinct populations, probably caused not so much by geographical isolation as environmental adaptation, albeit with regular ingress from surrounding populations, In Eurasia, a single genetic lineage dominates from Spain to Georgia to Scandinavia, so the interesting question is why does is the species genetically continuous in Eurasia but fragmented in North America; what is the difference between the two landmasses that causes this difference.

The Eurasian and North American populations are believed to have become separated during a period of climatic change and the onset of glaciation, 1.62–2.66 years ago. Attempts to segregate populations of Boletus edulis into distinct species based on phenotype have foundered on the genetic evidence, illustrating how small genetic differences can give large phenotypic differences and how a species in the process of speciating passes through a stage at which the diverging populations have not diverged sufficiently to qualify as new taxons because the practice of taxonomy tries to fit a continuous process into a series of distinct events.

The 'problem' is the subject of a free access paper in the journal New Phytologist by Keaton Tremble and Bryn T. M. Dentinger from Utah University, Utah, USA. together with J. I. Hoffman from Bielefeld University, Germany, and was described in a University of Utah press release:

Creationism in Crisis - 500 Million Year-Old Fossils Reveal the Answer to an Evolutionary Riddle


500 million year-old fossils reveal answer to evolutionary riddle | EurekAlert!

It must be galling to the leaders of the Creationist cults when science closes yet another gap and casually refutes the misleading claims they have fooled their cult followers with. It's much easier for the frauds to play to the parochial ignorance and childish thinking of their followers who will always assume that if science can't explain something, the locally popular god must have done it, ignoring the false dichotomy fallacy underpinning that deception.

Some of the gaps are artificial, obviously, being created by Creationists from misrepresentations of the actual science, such as claiming there are no transitional fossils showing, for example, a half chimpanzee - half human, but some of them are genuine gaps in the fossil record, although these tend to be ignored by creationist frauds because it would require a detailed knowledge of the evidence to appreciate where the real gaps are, and a detailed knowledge of the evidence is something no Creationist can afford to have.

One such gap, until now, was the early evolution of skeletal animals. The first fossils of skeletal animals appeared in the fossil record 550-520 million years ago during the so-called the Cambrian Explosion, which must be one of the slowest explosions on record, occurring over several tens of millions of years, but nevertheless a period of rapid evolution and diversification into different body-plans in the early history of multicellular organisms.

Many of these early fossils are simple hollow tubes ranging from a few millimetres to many centimetres in length. However, what sort of animals made these skeletons was almost completely unknown, because they lack preservation of the soft parts needed to identify them as belonging to major groups of animals that are still alive today.

Now though, a team of palaeontologist led by Dr Luke A. Parry of the Department of Earth Sciences, University of Oxford, Oxford, UK, Dr Xiaoya Ma and PhD student Guangxu Zhang, of the Institute of Palaeontology, Yunnan University, Kunming, People's Republic of China, and Dr Jakob Vinther from the Schools of Earth Sciences and Biological Sciences, University of Bristol, UK have analysed a collection of exceptionally well preserved fossils from 514 million years ago that include four specimens of Gangtoucunia aspera with soft tissues still intact.

Just to clarify that , soft-tissue term, before Creationist quote miners misrepresent it: fossilised soft tissue is not soft. It simply means the soft tissue was preserved long enough for it to become mineralised, just as bones, shells and teeth become mineralised in fossils of hard tissue. It is not evidence that these fossils are just a few thousand years old, like Creationist fraud claim dinosaur soft tissue fossils are (they are not soft either, by the way).

Before long, we can expect Creationists to either be claiming these 'soft tissues' have been carbon-dated and found to be recent, or that they haven't been carbon-dated because the scientists were afraid they would be found to be recent!

As the Oxford University News release explains:

Wednesday 6 March 2024

Creationism in Crisis - Earliest Toothless Bird From 120 Million Years Ago


Imparavis attenboroughi, a 'strange bird' named after Sir David Attenborough, British broadcaster and naturalist
Fossil named “Attenborough’s strange bird” was the first of its kind without teeth - Field Museum

It seems every week is a bad week for creationists, yet the wackadoodle cult staggers on, albeit with dwindling numbers, managing as always to ignore anything that shows their childish superstition to be wrong.

On top of the recently-reported predatory marine lizard, from 66 million years ago, we now have the earliest bird without the teeth of its enantiornithine ancestors. The enantiornithines were a diverse class of avian dinosaurs that went extinct 66 million years ago following the meteor impact that killed most of the dinosaurs. Only the ornithuromorphs survived, for reasons not completely understood, and they gave rise to all modern birds.

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


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

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

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

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

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

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

Tuesday 5 March 2024

Abiogenesis News - New Evidence For The 'RNA World' Hypothesis


Stylized rendering of the full-length hammerhead ribozyme RNA molecule
Source: Wikipedia
Modeling the origins of life: New evidence for an “RNA World” - Salk Institute for Biological Studies

On way of looking at cellular life is that it is based on RNA, not DNA. In that model, DNA is RNA's data store. All the functional processes that DNA codes for are first transcribed into RNA and short lengths of RNA still regulate some of the cell processes. RNA can even act as a catalyst playing the role normally performed by protein enzymes - proteins that are themselves transcriptions of RNA triplet codes for amino acid sequences.

On that model, early self-replicating systems were based on RNA, and DNA was late to the game.

Now three researchers at the Salk Institute for Biological Studies, La Jolla, California, USA, have shown how such a system could have bootstrapped from simple, self-catalysing lengths of RNA which not only self-replicate but can continue to do so even when there are variations stemming from faulty replications. This system would have created the variation needed for Darwinian evolution by natural selection as some variant performed better in terms of competing for resources and ultimately making more copies, so coming to predominate in the pool of RNA-based organisms.

How the scientists discovered this is the subject of a research paper in PNAS which sadly is behind a paywall with only the abstract and statement of significance freely available. It is also the subject of a news release from the Salk Institute.

Since the team refer to an RNA structure known as the 'hammerhead ribozyme', it might help to understand a little about it first:

Creationism in Crisis - A Mystery In Plant Evolution - 125 Million Years In The Making In That Long Pre-'Creation Week' History Of Life On Earth



A 'Ginormous' tomato produced by an unregulated CLV3 gene.

An evolutionary mystery 125 million years in the making | Cold Spring Harbor Laboratory

In an example of one of those lovely gaps in the record of the evolution of a species into which creationists try to shoehorn their ever-shrinking and increasingly homeless little god, there is something about the evolution of tomatoes and Arabidopsis thaliana that scientists can't yet explain.

But the problem for creationists is that this gap is somewhere in the evolutionary history of these plants that occurred almost 125 million years before creationism’s god decided to create a small flat planet with a dome over it to keep the water above the sky out, centred on the Middle East, in what creationists like to call 'Creation Week'.

The problem comes from the fact that what creationists think is a science and history text book was written by ignorant people who knew nothing of the world outside their small part of it and who had no idea about the history of the planet or of life on it, so they wrote an imaginative story to fill the gap in their knowledge and understanding, and, quite understandably, got almost every aspect of it complete wrong.

And of course, they would never have imagined that one day someone almost as ignorant as they were, would gather their tales into a book and declare it to be the inerrant word of a god - an idea that would be hilarious if it wasn't taken seriously by adults who can become dangerously violent when their superstition is questions.

The mystery that Cold Spring Harbor Laboratory (CSHL) biologists have uncovered is that sometime during the last 125 million years, tomatoes and Arabidopsis thaliana plants experienced an extreme genetic makeover. Just what happened remains unclear. But the mystery surrounds CLV3, a gene key to healthy plant growth and development.

CLV3 controls the growth of fruit in these plants and, if uncontrolled will result in large, even gigantic, fruits, so there is an evolutionary trade-off between a few large fruits and lots of smaller fruits. The mystery is just how and why this balance was achieved differently in two distantly-related plants.

As the CSHL press release explains:
Web Analytics