Refuting Creationism - Another Gap Closed - No God Found

A mating pair of wild-type (left) and mir-193 mutant (right) Bicyclus anynana butterflies.

Photo credit: Shen TIAN

A mating pair of peppered moths, Biston betularia, showing the melanistic and pale forms.

A microRNA solves an evolutionary mystery of butterfly and moth wing colouration - NUS Faculty of Science | NUS Faculty of Science

A regularly-cited example of observed Darwinian evolution is that of the peppered moth which occurs in two forms, the white, speckled form and a melanistic, almost black form. During the industrial revolution, as English northern towns grew and became polluted by smoke from coal-burning factories, so the melanistic form became more common.

Experiments showed that the lighter form became easier for predators to see when the moths were roosting on tree trunks that had become coated in soot, while the melanistic form became harder for predators to see.

Following the decline of the northern towns, the light form again increased back to the former ratio, showing the importance of environmental change in evolution.

This tendency to have melanistic forms is common in the lepidoptera (moths and butterflies) and this tendency was believed to be under th control of as single genomic region surrounding the protein-coding gene “cortex“, common across many species, showing their descent from a common ancestor.

However, new research by international researchers from Singapore, Japan, and the United States of America, led by Professor Antónia MONTEIRO and Dr Shen TIAN from the Department of Biological Sciences at the National University of Singapore (NUS), has shown that 'cortex' is not directly involved in producing melanism, instead, this is controlled by a microRNA from within the 'cortex' genomic region, as another example of how microRNA's control many functions within cells, particular gene expression.

Unintelligent Design - How Evolution Rescued an Unintelligent Heath-Robinson Design Blunder

A WashU researcher hand pollinates Arabidopsis.

Photo: Joe Angeles/WashU

How plants evolved multiple ways to override genetic instructions - The Source - Washington University in St. Louis

The thing about evolution that distinguishes it from intelligent design is that evolution is utilitarian. It settles for something that works better than what preceded it, which is different from designing a perfect solution to a problem. Near enough is good enough because anything which is an improvement gets pushed up the frequency listing in the gene pool. So, organisms over time have accumulated sub-optimal systems that sometimes fail and cause other problems.

One of those systems is the way DNA is replicated - which is so error prone that error correction mechanisms have evolved over time, but they don't always work either, so we have the phenomenon of the 'jumping genes' that get inserted in the wrong place in the genome, sometime in the middle of a functional gene or in a control section adjacent to a functional gene, causing genetic defects.

So, in the best Heath-Robinson approach to design, rather than abandoning that design and starting again, the way any intelligent designer would do, another layer of complexity is needed to try to mitigate the occasion when the system fails.

So, what organisms have evolved over the years is a process for neutralising these 'jumping genes' by attaching methyl groups to one of the bases which prevents it being transcribed. This is a part of the epigenetic system by which the specialised cells of multicellular organisms turn of unwanted genes and only allow the genes for their speciality to be active - a layer of complexity needed because the way cells replicate was inherited from their single-celled ancestors where the whole genome needs to be included in every daughter cell.

Animals, such as mammals have two enzymes which attach this methyl group depending on the DNA 'context', but plants have multiple enzymes for doing the same thing. The question is why do plants need these multiple enzymes?

Refuting Creationism - Ancient Aurochs From Long Before 'Creation Week'

A cave painting from Chauvet's cave, showing horses and aurochs.

Wikipedia (CC2.0)

An aurochs skull, St Petersburg.

Image: Prof. Dan Bradley.

Ancient DNA brings to life history of the iconic aurochs - News & Events | Trinity College Dublin

On problem with believing a myth that Earth was made out of nothing by magic 6-10,000 years ago is that there are paintings in caves in France that are older than that, showing animals that were around before then.

And a problem with believing that the same magician created all living things just as they are today without any ancestors, is that those same cave paintings show species that were ancestral to some of the animals that are around today, such as domestic cattle.

And a problem with believing that the same magician created all the animals for the benefit of humans is the evidence that all our domestic animals, with almost no exceptions, have been improved by selective breeding from wild ancestors. Did their putative creator not know what humans would need or how they would use the animals it created for them?

Aurochs, their evolution and relationship to domestic cattle. Aurochs (Bos primigenius) were large wild cattle that roamed parts of Europe, Asia, and North Africa. They are considered the ancestors of modern domestic cattle, playing a significant role in human history and agriculture. Here's an overview of the aurochs, their characteristics, history, and their relationship to modern cattle.

Physical Characteristics

• Size: Aurochs were significantly larger than modern cattle, with bulls standing up to 6 feet (1.8 meters) at the shoulder and weighing up to 1,500 pounds (700 kg) or more. Cows were generally smaller than bulls.
• Appearance: They had a muscular build with long legs and a slender body, which allowed them to move quickly. They possessed a distinctive hump over their shoulders.
• Color: Bulls were typically dark with a lighter "eel stripe" down the back, while cows were generally reddish-brown.
• Horns: Aurochs had large, forward-curving horns, which could reach up to 31 inches (80 cm) long. These horns were crucial for defense against predators and in fights between males.

Evolution and Extinction

• Evolution: The aurochs evolved around 2 million years ago in India and spread across Europe, Asia, and North Africa. Over time, isolated populations adapted to their environments.
• Extinction: The last recorded aurochs died in 1627 in Poland due to hunting, habitat loss, and diseases spread by domesticated cattle. Their extinction marked the end of the species, but they live on genetically through domestic cattle, which were bred from aurochs around 8,000 to 10,000 years ago.

Relationship to Domestic Cattle

• Domestication: Modern domestic cattle (Bos taurus and Bos indicus) were domesticated from different auroch populations. Early humans domesticated aurochs in two main areas:
  • Bos taurus was domesticated in the Fertile Crescent (modern-day Middle East).
  • Bos indicus (zebu cattle) was domesticated in the Indian subcontinent.
• Genetic Influence: Domestic cattle have inherited many traits from their auroch ancestors. Selective breeding by humans introduced variations in size, color, horn shape, and other physical traits to better suit agricultural needs.
• Behavior: Domestic cattle have been bred for docility and other traits that make them manageable for farming. Aurochs, on the other hand, were more aggressive and less tolerant of human presence.

Breeding Back Efforts
In recent years, there have been efforts to "breed back" cattle that resemble the aurochs. Breeding back does not resurrect the aurochs genetically but seeks to produce cattle that resemble aurochs in appearance and behavior.

• Heck Cattle: In the early 20th century, German zoologists Heinz and Lutz Heck attempted to recreate aurochs by selectively breeding European cattle breeds with certain aurochs-like features.
• TaurOs Project: Launched in 2008, this project uses selective breeding of various cattle breeds to produce animals that physically and behaviorally resemble aurochs, focusing on rewilding European landscapes.

Role in Ecosystems and Rewilding
Aurochs once played a critical role in their ecosystems by grazing on grasses, which helped maintain the balance of plant species and created habitats for other animals. In rewilding efforts, cattle resembling aurochs are introduced to landscapes where their grazing patterns help to maintain open grasslands and support biodiversity.

Cultural Significance
Aurochs appear in ancient art, mythology, and folklore across many cultures. They were revered as symbols of strength and vitality and often featured in prehistoric cave paintings, such as those in Lascaux, France, which date back over 17,000 years.

Summary

• Ancestors of Domestic Cattle: Aurochs are the wild progenitors of domestic cattle, with genetic links to both Bos taurus and Bos indicus.
• Distinctive Features: Large, muscular, and possessing large horns, aurochs were much larger than modern cattle.
• Rewilding and Conservation: Through efforts like the Heck Cattle and TaurOs Project, conservationists attempt to restore the ecological impact that aurochs once had on European landscapes.
• Legacy: Although extinct, the aurochs' genetic legacy continues in domestic cattle, and they remain an iconic symbol in history and conservation.

The story of the aurochs highlights the powerful connection between humans and wild animals, showcasing how our ancestors' choices shaped the landscapes and species we see today.

And all these questions come from a paper published recently in Nature which reports on the analysis of the genome of 38 Aurochs from bones stretching back over some 50,000 years from sites across Eurasia from the UK to Siberia. The team of geneticists from Trinity College and other universities have explained their findings in a Trinity College press release:

Ancient DNA brings to life history of the iconic aurochs

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Geneticists from Trinity, together with an international team of researchers, have deciphered the prehistory of aurochs – the animals that were the focus of some of the most iconic early human art, and whose tale is intertwined with climate change and human culture.

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The team analysed 38 genomes harvested from bones dating across 50 millennia and stretching from Siberia to Britain in this work.

The aurochs roamed in Europe, Asia and Africa for hundreds of thousands of years. Adorned as paintings on many a cave wall, their domestication to create cattle gave us a harnessed source of muscle, meat and milk. Such was the influence of this domestication that today their descendants make up a third of the world’s mammalian biomass.

We normally think of the European aurochs as one common form or type, but our analyses suggest there were three distinct auroch populations alone in Europe – a Western European, an Italian, and a Balkan. There was thus a greater diversity in the wild forms than we had ever imagined.

Dr Mikkel-Holger S. Sinding, co-author
Department of Biology
University of Copenhagen, Copenhagen, Denmark.

Intriguingly, climate change also wrote its signature in aurochs genomes in two ways:

First, European and north Asian genomes separated and diverged at the beginning of the last ice age, around 100,000 years ago, and did not seem to mix until the world warmed up again at its end.

And second, genome-estimated population sizes dropped in the glacial period, with a more pronounced hard time endured by European herds. These lost the most diversity when they retreated to separated refugia in southern parts of the continent before repopulating it again afterwards.

The most pronounced drop in genetic diversity occurs between the period when the aurochs of southwest Asia were domesticated in the north of the Fertile Crescent, just over 10,000 years ago, to give the first cattle.

Remarkably only a handful of maternal lineages (as seen via mitochondrial DNA which is handed down via mothers to their offspring) come through this process into the cattle gene pool.

A Pleistocene aurochs from the Upper Rhine Valley, around 50,000 years old.

Image credit Staatliche Schlosser and Garten Hessen.

Although Caesar exaggerated when he said it was like an elephant, the wild ox must have been a highly dangerous beast and this hints that its first capture and taming must have happened with only a very few animals. However, the narrow genetic base of the first cattle was augmented as they first travelled with their herders west, east and south. It is clear that there was early and pervasive mating with wild aurochs bulls, leaving a legacy of the four separate preglacial aurochs ancestries that persists among the domestic cattle of today.

Professor Dan Bradley, senior author
Smurfit Institute of Genetics
Trinity College Dublin, Dublin, Ireland.

Publication:

Rossi, C., Sinding, MH.S., Mullin, V.E. et al.
The genomic natural history of the aurochs.
Nature (2024). https://doi.org/10.1038/s41586-024-08112-6

Abstract
Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia¹. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs—European, Southwest Asian, North Asian and South Asian—each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago², but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

Rossi, C., Sinding, MH.S., Mullin, V.E. et al.
The genomic natural history of the aurochs. Nature (2024). https://doi.org/10.1038/s41586-024-08112-6

© 2024 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

One interesting finding is that the aurochs split and diversified during a glacial period when different populations were in different refugia, where they diversified genetically. This is reflected in the DNA inherited by domestic cattle and shows allopatric speciation in progress.

Another interesting finding is how the domesticated cattle and the wild aurochs continued to interbreed with domestic cattle, with auroch bulls mating with domestic cows, showing how diverging species can interbreed for a period until barriers to hybridization evolve.

All this paints a much more interesting picture of the origins of domestic cattle from wild ancestors than the childish one involving magic that creationists find easier to understand. It also poses the question for creationists - why didn't their putative designer design domestic cattle fit for purpose - docile and a high milk yield - that had to be bred into them through an extended period of selective breeding because their wild ancestors were too big and dangerous?

Refuting Creationism - The Japanese People Didn't Notice Noah's Genocidal Flood!

Representation of Jomo-period life in Japan in the shadow of Mount Fuji

AI-generated (ChatGPT4o)

Human remains from the Yayoi period, approximately 2,300 years ago, from which DNA was extracted.

Map of Japan showing Sakhalin (far north) and the Kuril and Ryukyu Islands

Google Map

Traces of ancient immigration patterns to Japan found in 2000-year-old genome | SCHOOL OF SCIENCE THE UNIVERSITY OF TOKYO

Being parochial Bronze Age pastoralists who knew about nothing and nowhere that was more than a day or two's walk from their hill pastures in Canaan, those who made up the Hebrew creation myths could not possibly have been aware that there were other cultures in far-away places like China, Korea and Japan, which had ancient histories going way back before the myth-makers thought Earth was created, and which were unscathed by an global flood at the time in which they set that tale.

Had they been aware of them, they could have made up slightly more plausible myths with a more realistic timeline, instead of requiring their believers to try to compress everything that's happened in the entire 14-billion-year-old Universe into 10,000 years.

But how could they have done so when they had no-one to teach them the real history of the planet and the people living on it? All they had was their own limited imagination and a handful if inherited myths from neighbouring culture, like Egypt and Sumeria, for theirs was a backward, illiterate culture from the fearful infancy of our species, dependent on oral traditions and superstitions.

How could they possibly have known, for example, that a population of humans had been more or less isolated for about 6,500 years, ending at about the time the myth-makers believed Earth was made out of nothing by magic, complete with a dome over it to cover the small, flat place they called home? They would have known nothing about immigration from China or from the Korean Peninsula into the Japanese archipelago that brought this period of isolation to an end and probably resulted in the present-day population of Japan.

So, of course, they saw nothing wrong with inventing a tale about a genocidal flood killing everyone apart from 8 related survivors, or of building a tower to reach above the dome or about a panicking god making them all speak different languages so they couldn't work in cooperative groups any more, and yet, if their tale is to be believed, the descendants of those few survivors, all speaking different languages, migrated to places like China, Korea and Japan where they all adopted the local language and writing that had been used for several thousand years, forgot all about Noah and his flood and invented new gods and religions, whereas the myth-makers of Canaan remembered it all word-perfect in every detail...

So, how do we know the record they left was wrong?

Unintelligent Design - The Blunder That Causes Cancers

Ludwig Cancer Research

It has often been a theme of my blog posts how, if we regard cells as the result of conscious (I won't use the term 'intelligent' as that's singularly inappropriate, as we shall see) design then the picture quickly emerges of a bungling incompetent, cobbling together Heath-Robinson solutions to problems of its own incompetent making and lack of foresight.

The entire system of epigenetics, for example, is only necessary in a multicellular organism with its cell specialisation because specialised cells only need a small subset of the entire genome, yet, because cells replicate using exactly the same process that single-celled organisms use, where the entire genome needs to be replicated in every daughter cell, the cells of multicellular organisms such as humans each receive the entire species genome. So, most of it needs to be turned off.

This is where the epigenetic system comes in where methyl groups are attached to key bases in the DNA which prevents that section being transcribed into RNA, effectively switching the gene off. There are other components to the epigenetic system, but that is the pertinent component as far as this particular blunder is concerned.

The problem starts when a methyl group is attached to a cytosine base (C in the CGTA genetic code) which is next to a guanine(G) base.

Refuting Creationism - How A Beetle Evolved To Eat Toxic Plants

Red milkweed beetle, Tetraopes tetrophthalmus

CC BY 2.5, Link

Red milkweed beetle, Tetraopes tetrophthalmus

Red milkweed beetle genome sequence offers plant-insect co-evolutionary insights

We are continually being assurd by gullible cretionists that the Theory of Evolution (TOE) is 'a theory in crisis' becase a growing body of biologisdts have abandonned it in favour of the creationists superstition of intelligent [sic] design.

This has been a creationist fantasy for at least the last 50 years since when it is supposedly about to happen, any day now, real soon (a bit like The Second Coming of Christ - something which, despite regular announcements that it will happen next Wednesday at noon, never happens - but its gunna, you see!)

However, when we read the scientific publications of these biologists who are allegedly abandoning the TOE, we see no signs whatever of any abandonment; quite the opposite. We see the TOE as firmly embedded in biological science as the Laws of Thermodynamics and the Theory of Gravity are embedded in physics, Atomic Theory is embedded in chemistry and Germ Theory is embedded in epidemiology. It forms the bedrock of the science, without which very little makes any sense.

For example, when a bunch of entomologists wanted to understand how a species of herbivorous beetle can eat a toxic plant, they compared it genomically with a related species that doesn't eat the toxic plant to see how the ability to proccess the toxins evolved.

Of course, being scientists, they reject the idea that the beetle was magically created that way by an unproven supernatural entity because none of that can be falsified and the existence of such an entity can't be established, so there is no logical reason to include one in any answer. The fact that their mummies and daddies might have believed in it is irrelevent to their science, because belief doesn't create facts.

Unintelligent Design - How Creationism's 'Designer' Needs Plan B For When Plan A Fails To Mend Its Previous Design Blunder

Plants like Arabidopsis, seen here, have two options to ensure accurate chromosome division—a molecule called DDM1 and a process known as RNAi. If Arabidopsis loses one of these, it’s fine. But if it loses both, it’s in trouble.

Developmental defects of double, triple and quadruple mutants in RNA-dependent RNA polymerase (rdr1, rdr2, rdr6) and DNA methylation (ddm1) in floral organ identity, leaf shape and fertility (silique length).

Shimada, A., et al (2024)

Plants have a backup plan | Cold Spring Harbor Laboratory

The secret to being a good designer or planner is to always have a Plan B. I say that as a former emergency operations centre manager where the future is unpredictable, so I needed to keep as many options open as possible because, as I used to joke, my Plan B was to tear up Plan A and start again.

Now, you can play the percentages game, for example, I could be fairly sure town centres would be fairly busy around 11 pm, especially on a Friday and Saturday night, when in the UK the pubs close, or as we call it, 'chucking out time', and a lot of inebriated people would be out on the streets, fighting over available taxis, over girl/boyfriends or who had got served at the bar out of turn (queue-jumping is a big no-no in the UK).

I also knew from 17 years operational experience that most of the calls would require little more than smoothing ruffled feathers, running checks to exclude underlying medical problems and sending them on their way, so turnover time would be relatively short, and I would get a crew back fairly quickly.

Another peak would be around 1 am when the nightclubs closed, but with a few exceptions such as those the rest of the week would resemble a system in chaos where medical emergencies, traffic accidents and every other imaginable emergency occurred more or less randomly, with statistical patterns only being noticeable over time with a sufficiently large database.

Later on, I became the data analyst who looked for those patterns and used them to devise deployment plans to minimise average emergency response times, but that's another story.

Juggling acts were the daily routine for an emergency operations centre like mine, as we tried to maintain as much emergency cover as possible while getting help to people who needed it as quickly as possible. And you never knew you had made the right decision until it turned out not to have been the wrong one.

Our major handicap was of course being unable to accurately forecast the future, not just weeks or days ahead but hours and minutes. What we singularly lacked was omniscience for which educated guesses were a poor substitute.

So, to a creationist it might come as something of a shock to learn that their putative designer behaves like a designer/planner who can't foretell the future because, if nothing else, it is allegedly omniscient, and its designs are perfect. As such it shouldn't need a Plan B because Plan A will be perfectly designed for the precise future needs of the species. There should never be an occasion where it needs to tear up Plan A and starts again; it shouldn’t need to consult a large database to look for patterns then work out the probability of that pattern repeating itself and planning its responses accordingly, never knowing if it was the right plan until it turned out not to be.

And yet a team of researchers from Cold Spring Harbor Laboratory, New York, USA has found that the plant, Arabidopsis has a Plan B for when Plan A fails. Plan A is all about making the ramshackle, Heath Robinson process for ensuring mistakes in DNA replication get attended to. In a design which seems to be a characteristic of creationism putative intelligent [sic] designer, a shoddy process needs another layer of complexity to try to make it works, but even that fix breaks and the result of growth defects, sterility and, in many cases in animals, cancers or developmental disorders.

Unintelligent Designe - Creationism's Blundering Heath-Robinson 'Designer' Strikes Again - And Causes Cancer

Broken DNA and lncRNA repair mechanism

AI generated image (CHATGPT4o)

Intelligently designed apparatus for teaching mountaineers.

William Heath-Robinson

How Cells Recognize and Repair DNA Damage -

One thing you can depend on with creationism's putative designer is that there will never be a simple solution when there is a more complicated way to solve the problem it just created, and just like William Heath-Robinson, it will try to use pre-existing structures that were designed for an entirely different function, like a pile of books under the legs of a ladder to make it tall enough, and every piece of string holding things together will have knots in it.

And when we look beneath the superficial resemblance of design in, for example, a living cell, we find all manner of if-it-works-it'll-do solutions to problems, like the solution to the problem of breaking DNA that a team of scientists, led by Kaspar Burger, from Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany, have discovered.

The problem arises of course because the method for replicating DNA as cells divide is poorly designed and unnecessarily complicated in the first place. If the putative designer had devised a more sensible method for replicating cells in multicellular organisms than that used for replicating single cells where the whole genome needs to be replicated, many of the problems of erroneous copying wouldn't arise because only a small subset of the genome is needed for specialised cells.

Refuting Creationism - How Ants Were Cultivating Crops 66 Million Years Before 'Creation Week'.

A lower-fungus-farming worker of the rare fungus-farming ant species Mycetophylax asper, collected in Santa Catarina, Brazil, in 2014, on its fungus garden.

Credit: Don Parsons.

Atta colombica queen

By Christian R. Linder - own photo, Barro Colorado Island, Panama (1999), CC BY-SA 3.0, Link

Ant Agriculture Began 66 Million Years Ago in the Aftermath of the Asteroid That Doomed the Dinosaurs | Smithsonian Institution

One of the 'uniquely human' abilities that creationists traditionally cite in support of their childish superstition that humans were magically created out of dirt as a species separate from other animals, is the fact that humans for the most part, indulge in agriculture - i.e., we grow plants as food - or at least other people do. Most of us in the developed economies buy their produce in shops.

a Like all their other claims of human exceptionalism, it's a nonsense fairy tale, of course. Humans have some unique characteristics that make them a distinct species, but then so does every other species, by definition. There is nothing materially different about humans that makes them subject to different laws of chemistry and physics than other species, of course.
And in respect of agriculture, we are far from unique - ants have been at it for about 66 million years - well before creationists imagine the entire Universe was magically created from nothing by a magic god made of nothing. But this is hardly surprising, since some 99.9975% of the history of life on Earth happened before creationism's legendary 'Creation Week'.

Unintelligent Design - Doing The Same Thing In Two Different Ways

Brassica fruticulosa

Photo: Sílvia Busoms, UAB.

Brassica fruticulosa

Photo: Sílvia Busoms, UAB.

Different adaptation strategies to saline soils identified in neighbouring populations of the same plant species - Universitat Autònoma de Barcelona - UAB Barcelona

Imagine you're a design engineer tasked to design part of a manufacturing process to be used in two different factories. You produce a solution which works in one factory, so what do you do for the second factory?

If you're creationism putative designer, you forget all about the solution that works, and you design a completely different method for the second factory. It would be far too simple to use the first method you designed for the second factory, obviously. It would be as though there is no communication between the two factories and no sharing of ideas or testing to see which method was the most efficient in terms of time, materials and labor. Each factory would work to its own methods, oblivious of anywhere else or any better solutions.

And that just what creationism's alleged creator appears to have done with two populations of a common coastal plant in Catalonia - a wild member of the cabbage family, Brassica fruticulosa - where different populations have adapted to soil salinity in two different ways.

What can you tell me about the plant Brassica fruticulosa, its distribution and adaptation to different soil conditions? Brassica fruticulosa, commonly known as Mediterranean cabbage, is a wild species within the Brassicaceae family. It is native to the Mediterranean region, where it thrives in a variety of habitats, including rocky, disturbed, and coastal areas. The species is highly adapted to different environmental conditions, including poor, dry, and calcareous soils, which is a key feature of its resilience.

Distribution:
Brassica fruticulosa is primarily found in Southern Europe, North Africa, and parts of the Middle East. Its distribution spans countries like Spain, Italy, Greece, Turkey, and Algeria, extending into coastal regions with Mediterranean climates.

Adaptation to Soil Conditions:

1. Drought Resistance: The plant is well-suited to dry and nutrient-poor soils, a characteristic of Mediterranean ecosystems. Its deep root system allows it to access water in arid environments, contributing to its drought tolerance.
2. Calcareous Soils: The species is adapted to alkaline soils, often thriving in limestone-rich areas. It can tolerate high pH levels, which would limit the growth of less adapted species.
3. Disturbed and Rocky Soils: Brassica fruticulosa also thrives in disturbed habitats, such as roadsides and rocky outcrops. Its ability to grow in these challenging environments shows its resilience to various soil types and disturbances.

This adaptation to different soil conditions is likely linked to its ecological strategy of thriving in marginal habitats, where competition from other plants is less intense.

This was discovered by three researchers from the Universitat Autònoma de Barcelona (UAB) Plant Physiology Lab, in collaboration with researchers from the University of Nottingham (UK), the Max Planck Institute for Biology (Germany), and Charles University in Prague (Czech Republic).

Their findings are the subject of a recent open access research paper in Proceedings of the National Academy of Science (PNAS) and a UAB news release.

Different adaptation strategies to saline soils identified in neighbouring populations of the same plant species

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Researchers from the Faculty of Biosciences have identified two divergent adaptive responses to soil salinity in populations of the same wild species found in the Catalonia’s coastal area, the Brassica fruticulosa, and have pinpointed the genes involved. The study will help to investigate the ways to improve resilience in agricultural species of the same plant family, such as rapeseed and mustard, in the face of a globally relevant stressor as is soil salinization.

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The study was recently published in Proceedings of the National Academy of Sciences (PNAS) and is signed by researchers Sílvia Busoms, Glòria Escolà and Charlotte Poschenrieder from the UAB Plant Physiology Lab, in collaboration with researchers from the University of Nottingham (UK), the Max Planck Institute for Biology (Germany), and Charles University in Prague (Czech Republic).

Over the past few years, UAB researchers have worked in close collaboration with members of the University of Nottingham to develop a study model along the Catalan coast to understand the interaction between environmental factors such as salinity and the adaptation of wild populations of the Brassicaceae family. They developed several studies focused on populations of Arabidopsis thaliana, a model organism for biological research, but in this case, they focused on Brassica fruticulosa, a species genetically and morphologically closer to cultivated brassicas such as rapeseed (Brassica napus) and mustard (Sinapis alba).

This research has allowed them to demonstrate that in Catalonia coastal populations of B. fruticulosa use two different strategies to tolerate soil salinity: those from the north (Cap de Creus region) are able to restrict root-to-shoot sodium transport, preventing the damage of the aerial parts. In contrast, those from the centre accumulate sodium in the leaves, but they use efficient mechanisms of osmotic adjustment and compartmentalisation that allow them to tolerate high concentrations of this compound.

The fact that two populations of the same plant species located so close geographically have evolved differently under the same environmental conditions surprised the researchers.

“In general, in all organisms it is expected that species adapting to similar stressors also evolve in a similar way. In our case, however, although in the coastal habitats of the Catalan coast soil salinity can be considered the main selective agent, there must be other factors that have altered the recent evolutionary process of this Brassicaceae species.

Sílvia Busoms, lead author
Department of Plant Physiology
Universitat Autònoma de Barcelona, Barcelona, Spain

This divergence in plant populations so close to each other has rarely been described, not so much because it is an exception, but because in many cases the studies are carried out at the macro-scale.

The Tramontane wind may explain this divergence

In their study, researchers examined in detail the characteristics of the soils and the climatology of all the populations’ location. The only parameter that showed significant differences was evapotranspiration, which was higher in the north due to the Tramontane wind that regularly blows there.

When there is high evapotranspiration, plants absorb more water and at the same time more sodium if they do not have mechanisms to exclude it. Therefore, the strategies used by the plants of the central coastal areas may be insufficient in the conditions of the northern coast. In the study we hypothesise that although they are neighbouring populations, the northern B. fruticulosa evolved differently in order to tolerate both high salinity levels and high evapotranspiration.

Charlotte Poschenrieder, co-author Department of Plant Physiology
Universitat Autònoma de Barcelona, Barcelona, Spain

To characterise the genetic basis of the two adaptive strategies identified, researchers first created the reference genome of B. fruticulosa, which will contribute to the expansion of the catalogue of reference genomes of eukaryotic species from the Catalan-speaking territories (within the Earth Biogenome Project) and will allow further research with this species. Subsequently, the sequencing of 18 populations and the subsequent genetic and transcriptomic analyses validated the two strategies observed and allowed researchers to propose candidate genes involved in the mechanisms of salinity tolerance.

Salinity is a threat to the planet's agricultural soils and its consequences are greater when it affects impoverished soils such as those found in the Mediterranean basin. A better understanding of the mechanisms of salt tolerance used by plants living there and which have adapted to these conditions is essential to improve the resilience of cultivars that must adapt to the new environmental conditions. “This study, therefore, establishes B. fruticulosa as a promising source of desirable alleles, and the population diversity present in Catalonia as a powerful model for the study of adaptations to saline soils,” researchers conclude.

Original article:

Silvia Busoms, Ana C. da Silva, Glòria Escolà and Levi Yant.
Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa.
September 24, 2024. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.2407821121

Significance
One might expect that closely related populations of a given species should adapt to the same environmental stressor in the same way due to genetic or physiological constraints. However, this is not commonly tested due to practical limitations. Here, we show that, even at the level of neighboring populations, contrasting adaptive strategies control adaptive responses to high coastal salinity in Brassica fruticulosa, a close wild relative of many crops of worldwide importance. This indicates multiple options for engineering an agriculturally crucial adaptation: soil salinization. These results will be of interest to not only those studying fundamental mechanisms of adaptation, but also resilience improvement in Brassica species.

Abstract
It is normally supposed that populations of the same species should evolve shared mechanisms of adaptation to common stressors due to evolutionary constraint. Here, we describe a system of within-species local adaptation to coastal habitats, Brassica fruticulosa, and detail surprising strategic variability in adaptive responses to high salinity. These different adaptive responses in neighboring populations are evidenced by transcriptomes, diverse physiological outputs, and distinct genomic selective landscapes. In response to high salinity Northern Catalonian populations restrict root-to-shoot Na⁺ transport, favoring K⁺ uptake. Contrastingly, Central Catalonian populations accumulate Na⁺ in leaves and compensate for the osmotic imbalance with compatible solutes such as proline. Despite contrasting responses, both metapopulations were salinity tolerant relative to all inland accessions. To characterize the genomic basis of these divergent adaptive strategies in an otherwise non-saline-tolerant species, we generate a long-read-based genome and population sequencing of 18 populations (nine inland, nine coastal) across the B. fruticulosa species range. Results of genomic and transcriptomic approaches support the physiological observations of distinct underlying mechanisms of adaptation to high salinity and reveal potential genetic targets of these two very recently evolved salinity adaptations. We therefore provide a model of within-species salinity adaptation and reveal cryptic variation in neighboring plant populations in the mechanisms of adaptation to an important natural stressor highly relevant to agriculture.

Today’s accumulation of high-profile cases detailing repeated evolution capture the fascination of biologists. Independently evolved adaptive coloring shifts in mammals and insects, defensive armor in fish, and serpentine and altitude adaptation in plants: these all present not only additional evidence for candidate mechanisms underlying adaptations, but also an optimistic outlook toward “predicting” the course of evolution and inspiring expositions for the public (1–6). Given these iconic cases, an expectation may arise that even at the functional level, neighboring populations of the same species should, due to genetic or developmental constraints and mutation limitation, share evolved strategies of adaptation to the same stressors (7). The logical extension is that natural selection might be expected to predictably drive the origin and maintenance of adaptations at strategic or mechanistic levels. However, this idea has not been sufficiently tested due to restraints on study systems, sampling, resolution, and scale (8). We thus lack a clear understanding of how often an expectation of uniform or repeatable species-wide adaptation strategies is violated in favor of diversity even within single species.

Here, we test this expectation by taking a “hyperlocal” approach in the study of plant adaptation to coastal stressors, focusing on adaptation to high coastal salinity in a strip of coastline in Catalunya, Northern Spain. Previous work on local adaptation of Arabidopsis thaliana in this region detailed geographically and temporally fine-scale adaptive variation in fitness-related traits across environmental salinity gradients, even at the scale of a few kilometers (9, 10). This region is characterized by a positive gradient of soil salinity from inland to the coast, shaping plant species communities and driving the evolution of salinity tolerance mechanisms at the local population- (deme-) level (11). Plant evolutionary responses to these conditions have been observed even in the selfer A. thaliana at fine (3 to 5 km) scale, resulting in functionally adaptive variation (12). Functional confirmation of this is evidenced by selective sweep of a hypomorphic ion transporter HKT1;1, which modulates Na+ leaf concentrations in response to rapid (monthly) temporal and spatial variation in rainfall and soil salinity (9).

Unfortunately, work in A. thaliana has two major limitations: first, due to its overwhelmingly selfing reproductive mode, relative to its outcrossing relatives A. thaliana has 10-fold lower genetic diversity and high rates of spontaneous, population-specific mutations (13). This low diversity also has important consequences in respect to increased homozygosity and effective population size, resulting in genetic drift, reduced effective recombination rates, genomic background effects, and the fixation of maladaptive alleles (reviewed in ref. 14). Second, Arabidopsis is substantially divergent from important Brassica crops, limiting the translational potential of discoveries in this otherwise convenient lab model. Wild outcrossing Brassicas, on the other hand, harbor higher levels of genetic diversity, directly facilitating studies of adaptation (15). Motivated by these considerations, we searched for wild Brassicaceae species with contrasting, recently evolved (within-species) phenotypes in complex coastal adaptations, focusing specifically on salinity tolerance. This resulted here in the identification of a model for local adaptation to coastal salinity, Brassica fruticulosa, and allows us to test hypotheses regarding the scale of local adaptation to high coastal salinity.

The genus Brassica belongs to the Brassicaceae (mustard) family and contains nearly 100 species, many of which are grown globally as vegetables like cabbage, broccoli, kale, and radish, as mustards, as oil crops (placing 3rd after palm and soy), and as fodder for animal feed (16). Brassicas are widely proficient at adapting to new habitats due to recent and recurrent polyploidy events, hybridization, and plastic genomes. These characteristics also make them great targets for genetic manipulation to further enhance resilience (17).

Here, we first perform a large-scale, genus-wide natural variation survey of diverse, wild outcrossing Brassicas in coastal Northeast Spain, eventually testing six candidate species for within-species adaptation to high salinity. From these, we identify and develop one particularly promising model of within-species variation in adaptation to extreme salinity and complex coastal stressors, B. fruticulosa. First described in 1792 by Cirillo (18), B. fruticulosa has not yet been recognized as harboring population-specific salinity adaptation. This has been a missed opportunity, as B. fruticulosa is closely related to Brassica rapa (19, 20) and shares many affinities with this global crop. We then assemble the B. fruticulosa genome using Oxford Nanopore long read sequencing polished with Illumina short reads, and sequence 90 individuals from 18 populations (nine coastal, nine inland) contrasting in salinity and soil parameters defined by ionome levels in leaves and soil in the root space of every individually sequenced wild plant. Using transcriptome data of leaves and roots, we reveal divergent adaptive strategies in response to high salinity in neighboring plant populations. We then perform common garden, physiological, and ion homeostasis experiments to detail these different strategies that evolved in closely neighboring adapted plant populations. Finally, we perform environmental association analysis (EAA) (with soil ionome as phenotype) and genome scans by ecotype to seek a genomic basis of divergent adaptative strategies to high salinity in neighboring B. fruticulosa populations. Taken together, these experiments reveal contrasting adaptive responses to extreme salinity, at the local scale, differing mechanistically at the scale of kilometers.

Fig 6.

Overview of the contrasting salinity tolerance strategies of the North and Central B. fruticulosa coastal metapopulations. Hypothetical model of genes, ion transport, and signaling pathways involved in salinity tolerance mechanisms. Gene symbols are shown in bold letters. Ion fluxes are indicated with black arrows. Gene activation/repression and molecule increase/decrease are indicated with red arrows. Star-framed symbols denote signaling pathways and hormone molecules are circled in green. “ST” = Salt tolerant.

Silvia Busoms, Ana C. da Silva, Glòria Escolà and Levi Yant.
Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossing Brassica fruticulosa.
September 24, 2024. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.2407821121

Copyright: © 2024 The authors.
Published by National Academy of Science. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

This example is interesting in that it shows the process of allopatric speciation in progress even though the two populations are still regarded as the same species. It's not clear from this paper whether the two population can or do interbreed, but if they do, what would be the consequences for the hybrids? Depending on the mode of inheritance, the offspring's genes could express in three different ways:

1. Adapted like the northern population.
2. Adapted like the southern population.
3. Adapted like both populations.

In the case pf 1 and 2, 50% of the offspring would be maladapted for the local conditions and in the case of 3, it would be adapted for neither and could be non-viable. We can exclude any advantage from being adapted for both locations otherwise there would not be two different populations since they would both carry the same dual adaptation.

So, hybridization would be wasteful with reduced survival of the hybrids. This is environmental pressure to establish barriers to hybridization because plants that don't hybridize will tend to produce more successful offspring than those which do.

From an intelligent [sic] design perspective, this example of doing the same thing in two different ways makes no sense as the work of the same designer. However, given that there is no mechanism for isolated populations to share information and make informed decisions about the best way to adapt to local conditions, then ensure they evolved that way, this makes perfect sense from an evolutionary perspective.

Again, the detail behind a superficial appearance of designs reveals that there was no intelligence involved in the process; instead, the process was a mindless utilitarian process that produced two different solutions to the same problem.

Refuting Creationism - Oldest Modern Human DNA Ever Recovered From South Africa - From About The Time Of 'Creation Week'!

Life at the Oakhurst Rock Shelter, 10,000 years ago

AI Generated (ChatGPT4o)

Oldest DNA from South Africa decoded to date | Max-Planck-Gesellschaft

Cape Point promontory, Cape Point Nature reserve, South Africa

© R. Gibbon

A San family group.

Just as creationism's legendary creator god was creating a small flat planet with a dome over it in the Middle East, there were modern humans living (or rather dying) in South Africa.

A team of scientists led by the Max Planck Institute for Evolutionary Anthropology and including palaeoanthropologists from University of Cape Town, Cape Town, South Africa, have now succeeded in reconstructing the genomes from the remains of 13 individuals who died between 1,300 and 10,000 years ago, including the oldest human genome from South Africa to date.

If the creation myth had any element of truth in it, humans would have radiated from the legendary founder couple to form a thriving community living in a rock shelter in South Africa's Cape Province. Moreover, the evidence now shows that these people were isolated from the rest of humanity for many thousands of years.

Refuting Creationism - How Daisies Speciated On Isolated Islands

Top: Pleurophyllum speciosum
Bottom: Pulicaria canariensis

Top: Bidens mooreensis
Bottom: Argyroxiphium sandwicense

Pleurophyllum speciosum - Campbell Island.

Credit Phil Garnock-Jones.

Isolated daisies have the greatest diversity | Naturalis

Creationists try to get round the absurdity of the Bible myth which has two (or seven) of every species being packed into a wooden boat small enough to survive turbulent seas for a year, by introducing a new element to the myth that their god forgot to include - that there were just two (or seven) of each 'kind' and all of them underwent a period of warp-speed evolution (that non-one seemed to have noted) with several new species popping into existence each generation to give the many millions of known terrestrial species we have today.

Understandably, creationists are reticent to put any numbers on their claim. They won't say how many different 'kinds' there were on the boat, how many new species arose at each generation and for how long this period of fantastical speciation lasted. Nor will they define 'kind' in any meaningful way that matches any recognisable taxon. I have even been told it can mean 'animal kind' and 'plant kind'. It seems to vary according to the needs of the argument.

And they won't say why some 'kinds' have just one or two species while others have hundreds, or in the case of the Asteraceae family of plants, some 34,000 distinct species, so some must have been speciating much faster then other while some hardly bothered if at all.

In the later case, we now have a substantial database compiled by a team at the Naturalis Biodiversity Center, Leiden, The Netherlands which catalogues all 34,000 different species with their geographical distribution, showing how they radiated and diversified into new species, colonising isolated islands and, like Darwin's finches, radiating into different species on each island in an archipelago.

Refuting Creationism - How New Genes Arise - No Magic Required

Researchers Publish Breakthrough Study on How New Genes Evolve | University of Arkansas

Four researchers working at the University of Arkansas have found a natural mechanism by which new genes can arise, which gives the lie to creationist claims that this is impossible.

Before moving on to the details of their discovery which has just been published, open access, in the Oxford University Press journal Molecular Biology And Evolution, I'll first discuss the current state of understanding of how new genetic information arises naturally, without the need for magic.

Refuting Creationism - Arctic Sled Dogs Had Already Diversified Into Two Types At Least 1,700 Years Before 'Creation Week'

A predicted phenotypic reconstruction of the ancient Zhokhov sled dog

Smith, T.A; Srikanth, K; Huson, H.J. (2024)

A team of Siberian huskies races in the Anchorage Fur Rendezvous in 2013 in Alaska.

Britt Coon

Genomics reveals sled dogs’ Siberian lineage | Cornell Chronicle

The History of dogs and their co-evolution with humans as they diverged from their wolf ancestors is a fascinating and complex story, most of which, like 99.9975% of all of the history of life on Earth occurred before creationist's legendary 'Creation Week'.

'Creation Week' is when creationists believe a magic god made of nothing magicked a small universe consisting of a single flat planet with a dome over it, centred on the Middle East, all out of nothing, in just 6 days about 10,000 years ago, (although why an omnipotent god couldn't have done it all in an instant and needed 6 full days, with a day to recover from the effort, is never explained).

Refuting Creationism - Migration Into Iberia When Creationists Think Earth Was Under A Genocidal Flood

AI generated depiction of Yamnaya life in Central Asia

ChatGPT4o

AI-gerated depiction of a Yamnaya migration caravan.
(Spot the errors!)

Theory of a violent invasion of the Iberian Peninsula in Late Prehistory now questioned - Universitat Autònoma de Barcelona - UAB Barcelona

Had the ancient inhabitants of the Iberian Peninsula contrived to get their oral history and origin myths written down in the same way that the Bronze Age Canaanite pastoralists did, we might have had a slightly more accurate and less implausible history. It certainly wouldn't have had daft tales about a global genocidal flood just at the time newcomers with new ideas, a new language and new techniques of animal husbandry were migrating into the area having traversed Western Europe from the Steppes of Central Asia.

Unlike the parochial Canaanite nonsense, it might well have had people, places and animals from more than a day or two's walk from the Canaanite Hills.

Archaeological evidence shows that, at the time when creationist superstition says everyone had been drowned in a genocidal, global flood several thousand feet deep, by a vindictive god, people originating on the Steppes of Central Asia were migrating across western Europe and into the Iberian Peninsula, as though nothing unusual was happening.

Refuting Creationism - How Butterflies Evolved Dark Wing Patterns Millions of Years Before 'Creation Week'

Heliconius erato showing mosaic mutations for the ivory incRNA

Genomic dark matter solves butterfly evolutionary riddle | Media Relations | The George Washington University

Heliconius erato with one wing (right) altered by CRISPR gene. Dorsal view

Luca Livraghi.

Heliconius erato with one wing (right) altered by CRISPR gene. Ventral view

Luca Livraghi.

This is one of those research papers that creationists traditionally misrepresent as 'proving' that something biologists have long known about is wrong, and so it somehow discredits the entire body of science, and, in this specific case, that the existence of RNA that is non-coding but functional, somehow proves there is no such thing as 'junk' DNA.

In reality, of course, it simply shows us that sometimes, evolution happens in unexpected ways.

The assumption, which is almost always valid and based on sound scientific evidence, is that DNA is transcribed into messenger RNA (mRNA) that mRNA is transcribed by ribosomes into proteins. Proteins then serve functions such as structural proteins or as enzymes catalysing chemical processes in the cell. In the special case of so-called homeobox genes (hox genes) these have a regulatory function in a developing embryo, stimulating groups of cells to organise into specific tissues such as limbs, eyes and other specialised tissues, by switching other genes off and on at certain times.

Refuting Creationism - How an Ancient Gene Shaped Spider Evolution

Texas brown tarantula, Aphonopelma hentzi,
showing cephalothorax and abdomen

By Mothore - Own work, CC BY-SA 3.0, Link

Texas brown tarantula, Aphonopelma hentzi.

Ancient gene gives spiders their narrow waist | ScienceDaily

Although both have evolved from a segmented ancestor, as can still be seen in the larvae of insects, spiders and mites differ from insects in the number of major body-parts. While insects have well-defines head, thorax (to which wings and legs are attached) and an abdomen, where the reproductive organs or normally located, spiders, scorpions, tics and mites (arachnids or chelicerates) have just two - a cephalothorax, combining the head and thorax, and an abdomen.

Now scientists have discovered a gene in the chelicerates that controls the development of the 'waist' between the cephalothorax and the abdomen, which is missing in insects. The loss of this gene could be the reason the two groups of arthropods evolved in different directions.

The team of scientists, led by Emily V. W. Shetton, of the Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA, have just published their findings, open access, in PLOS Biology and explained it in a press release reprinted in Science Daily:

The research team also included: Jesús A. Ballesteros of the Department of Biology, Kean University, Union, New Jersey, USA and Pola O. Blaszczyk, Benjamin C. Klementz, and Prashant P. Sharma all of Department of Integrative Biology, University of Wisconsin-Madison.

Refuting Creationism - The World's Largest Animal Genome - 30 Times Larger Than The Human Genome!

South American lungfish, Lepidosiren paradoxa

© Katherine Seghers, Louisiana State University

South American lungfish, Lepidosiren paradoxa

© Katherine Seghers, Louisiana State University

Decoding the world’s largest animal genome

A favourite creationists straw man parody of science says that evolutionary biologists believe evolution is a process of increasing complexity, leading eventually to humans - the most complex of all species.

This is utter nonsense, of course, being intelligently designed to easily attack and make evolutionary biology look like something no rational person would believe, so creationists dupes can feel smugly superior to scientists without bothering to learn any real science.

Creationists dogma also says that a genome was intelligently designed, so does not contain any redundant or non-coding DNA, since an intelligent designer would not have designed needless complexity and prolific waste (both characteristics of a mindless evolutionary process).

So, it leaves creationists floundering when science discovers genomes many times larger (for larger read 'more complex', in creationist terminology) than the human genome. In fact, the human genome is about average for the number of genes and size of the genome compared to other animals and very much smaller than that of many animals and plants.