Sunday 30 June 2024

Refuting Creationism - The Last Woolly Mammoths Were Dying Out Just As Creationism's God Was Allegedly Comitting Global Genocide.

Wrangle Island landscape
Last surviving woolly mammoths were inbred but not doomed to extinction | ScienceDaily

Just as creationism’s little god was creating a small flat planet with a dome over it in the Middle East and thinking it was the Universe, the last remaining mammoths were becoming isolated on Wrangle Island off the north coast of Siberia.

The cause was a rise in sea-level which isolated a small population of about 8 individuals, which grew to a stable population of about 200-300. They were to survive there for the next 6,000 and so were contemporaneous with early human civilisations such as the Egyptians and Sumerians.

Although there is no mention of them or any other species of elephant in the Bible, creationist dogma says there must have been two (or seven depending on version) and that all elephants have evolved by warp-speed evolution since, including the extinct mammoths and mastodons.

This recent addition to creationist dogma, which used to argue that there was no such thing as evolution, was invented to get round the manifest absurdity of a wooden boat containing two (or seven) of every extant and extinct species. The only problem is that this last remaining group of mammoths went extinct about 4,000 years ago, i.e., at about the time of the legendary genocidal flood, so couldn't have evolved from the survivors, warp-speed evolution or not.

Exactly why they became extinct is still something of a mystery but a recent study by a joint collaboration between the Swedish Museum of Natural History and Stockholm University, led by Love Dalén, an evolutionary geneticist, has shown that, although the population on Wrangler Island was highly inbred, that was probably not the cause.

The researchers have published their findings, open access, in the Cell Press journal Cell. According to information made available by Cell Press ahead of publication:

Saturday 29 June 2024

Refuting Creationism - Why Ammonites Went Extinct - 66 Million Years Before 'Creation Week'

Ammonites basking under the Late Cretaceous sun.>
Artwork by Callum Pursall (@cpursall on X)
June: Ammonites wiped out with dinosaurs | News and features | University of Bristol

Yet more evidence incidentally refuting creationism was published two days ago in the journal Nature Communications. That wasn't the intention of the palaeobiologists who presented them, of course, but the facts they presented simply did that by being entirely inconsistent with creationism and at variance with what the facts would be if creationism had any merit.

The paper, by a research team led by palaeontologists at the University of Bristol, concerns the extinction of the ammonites, apparently very suddenly on a geological time-scale. It had previously been thought that their decline had been a slow, gradual process but the evidence found by the researchers is that it was as sudden as that of the non-avian dinosaurs and caused by the same random astronomical event - a meteor strike, 66 million years ago.

The resulting climate change caused a mass extinction at the end of the Cretaceous and the start of the Palaeogene - the so-called K-Pg boundary. (K for Kreidezeit - German).

The ammonites were cephalopod molluscs related to octopuses, squids and the nautiluses and were a major predator in Cretaceous seas. Judging by the abundance of their fossils which I have picked up in fields in Buckinghamshire, they were common and widespread. On holiday some years ago on the north coast of Somerset, my children and I once spent several hours on the beach at Watchet, breaking open pieces of slate to discover ammonites inside them. My children were excited to think they were the first humans to look at each ammonite as we exposed them for the first time in maybe 100 million years.

However, when it comes to assessing the abundance and diversity of extinct orders such as ammonites, local abundance or rarity can be misleading, because it can lead to sampling bias where a local collection of fossils can be mistaken for a general abundance and a local absence can be wrongly extrapolated to indicate a general scarcity. The authors used techniques to minimise this bias in their reassessment of the rate of extinction of ammonites.

Refuting Creationism - The 40-Million-Year History of Biodiversity in The Indo-Australian Archipelago

Stunning coral formations captured in the waters of the Coral Triangle, Sabah, Malaysia.

Photo credit: David M. Baker.
HKU Ecologists Reconstruct the History of Biodiversity in the Indo-Australian Archipelago and its Rise as a Hotspot - Press Releases - Media - HKU

If you're a creationist fraud trying to fool more scientifically-illiterate simpletons into joining your cult and giving you money so you don't need to earn an honest living, the last thing you need is this constant deluge of evidence refuting your claims that Earth is only a few thousand years old and everything on it was magically created as it is today.

And yet here we have yet another refutation in the form of a research paper detailing the 20-million-year history of one of the most biodiverse places on Earth - the 'Indo-Australian Archipelago', also called 'The Coral Triangle'.

The Indo-Australian Archipelago has been described as a biodiversity hot-spot because it contains so many examples of radiating evolution over the last 20 million years.

Refuting Creationism - Perfectly Preserved Trilobites From The Cambrian - 515 Million Years Before 'Creation Week'.

Microtomographic reconstruction of the head and anterior trunk (“body”) limbs of the trilobite Protolenus (Hupeolenus) in ventral view.
© Arnaud MAZURIER, IC2MP, Univ. Poitiers
June: Prehistoric Pompeii | News and features | University of Bristol

Paleontologists have discovered a site in Morocco where hundreds of trilobites and other Cambrian species have been preserved by a pyroclastic flow of hot volcanic ash that preserved them in exquisite details. They have nicknamed them 'Pompeii' trilobites after the town near Naples in Italy similarly preserved by volcanic ash from Vesuvius, almost as a snapshot of a living Roman town, complete with molds of the bodies of people killed as they slept.

The trilobites were quickly embedded in volcanic ash and even their digestive tracts were preserved as they filled with the ash.

This means, of course, that the fossils can be dated extremely accurately using the uranium/lead (U-Pb) ratios in zircon crystals in the volcanic ash.

Friday 28 June 2024

Creationism in Crisis - A Mass Extinction Of Marine Species 183 Million Years Before Creation Week

Carbon cycle changes during the Toarcian Oceanic Anoxic Event
Ocean’s Loss of Oxygen Caused Massive Jurassic Extinction. Could it Happen Again? | Nicholas School of the Environment

Creationists who claim, against all the evidence, that the Universe is 'fine-tuned' for life, might like to ignore a period in Earth's long pre-'Creation Week' history when Earth quite suddenly, in geological terms, became very hostile to marine life in particular, resulting in a lot of it dying.

This event, one of the mass extinction events, is known as the Toarcian Oceanic Anoxic Event (TOAE) which occurred some 183 million years ago when an increase in volcanic activity associated with the break-up of Pangea, sent atmospheric carbon dioxides (CO2) sky high (literally) precipitating global warming. This, in turn led to a rise in ocean temperatures and, because warm water holds less oxygen (O2) than cold water, marine oxygen levels fell, leaving widespread areas of anoxic marine sediment.

Now a team of archaeologists have discovered evidence in Italian limestone that confirms the cause of the mass extinction was anoxia due to elevated atmospheric CO2. How they discovered it is the subject of a Duke University news release:

Thursday 27 June 2024

Refuting Creationism - Bible Naïvety Brought Into Sharper Focus By 'Pillars Of Creation'

Pillars of Creation Star in New Visualization from NASA's Hubble and Webb Telescopes - NASA Science

In the Hubble version of the model (left), the pillars feature dark brown, opaque dust and bright yellow ionized gas set against a greenish-blue background. The Webb version (right) showcases orange and orange-brown dust that is semi-transparent, with light blue ionized gas against a dark blue background.

Greg Bacon, Ralf Crawford, Joseph DePasquale, Leah Hustak, Christian Nieves, Joseph Olmsted, Alyssa Pagan, and Frank Summers (STScI), NASA's Universe of Learning
The child-like naïvety of those who made up the origin myths in the Bible was brought into sharper focus today with the publication of images of the 'Pillars of Creation' in the heart of the Eagle Nebula.

This fragment of the known universe was discovered by the Hubble Space Telescope in 1995 and opened many people's eyes to the grandeur and size of the Universe compared to the Bible's laughably naïve description of it as a small, flat planet with a dome over it to keep the water about the sky out.

Now this image has been brought into even sharper focus by the James Webb Space Telescope with a new 3D rendering and a movie so viers can experience flying between the birthplace of stars.

Creationism in Crisis - Scientists Have Shown How Fruits of the Solanacea Evolved

Cultivated tomatoes, Solanum lycopersicum
New tomato, potato family tree shows that fruit color and size evolved together | Penn State University

The Solanaceae is a large family of plants which includes potatoes, tomatoes, aubergines and peppers/capsicums, and some highly poisonous plants such as deadly nightshade and thornapple. Some of them are economically and nutritionally important food crops.

A feature of the family is the high level of toxicity of most parts of the plants, even important crops like potatoes, all parts of which, apart from the tubers, are highly poisonous, even the small green tomato-like fruits. Similarly, all parts of the closely related tomato plant, apart from the fruits, are highly toxic.

What can you tell me about the Solanaceae and the time-scale of their evolution? The Solanaceae, commonly known as the nightshade family, is a diverse and economically significant family of flowering plants. This family includes well-known species such as tomatoes, potatoes, eggplants, bell peppers, and tobacco. Understanding the evolution and diversification of the Solanaceae involves looking at their origin, diversification events, and the adaptive radiation that led to the variety of species we see today.

Evolutionary Origin and Timeline
  • Early Origins: The Solanaceae family is believed to have originated during the late Cretaceous period, around 80-90 million years ago (mya). This timing is based on molecular clock estimates and fossil records.
  • Diversification: Significant diversification within the family occurred during the Paleocene and Eocene epochs (about 66-34 mya), likely driven by climatic changes and the availability of new ecological niches.

Key Evolutionary Events
  1. Initial Diversification: The early diversification of Solanaceae likely took place in South America, which is considered the primary center of origin for the family. The varied climates and geographies of this region provided multiple ecological niches.
  2. Dispersal and Adaptation: As members of the Solanaceae spread to different parts of the world, they adapted to a wide range of environments. This includes the arid regions of Australia and the temperate climates of North America and Europe.
  3. Radiation of Major Genera: Key genera within the family, such as Solanum (which includes tomatoes and potatoes), diversified significantly during the Miocene epoch (23-5 mya). This period was marked by further climatic changes that created new habitats.
Morphological and Genetic Diversification
  • Morphological Adaptations: Solanaceae species exhibit a wide range of growth forms, from herbaceous plants to shrubs and small trees. They have also developed various fruit types, including berries, capsules, and drupes.
  • Genetic Studies: Advances in molecular genetics have provided insights into the evolutionary relationships within the family. Phylogenetic studies based on DNA sequencing have helped clarify the lineage and divergence times of different genera and species.
Ecological and Economic Importance
  • Agricultural Significance: Many Solanaceae species are essential crops with significant agricultural value. Tomatoes, potatoes, and peppers are staple foods in many cultures.
  • Medicinal and Toxic Properties: Some members of the Solanaceae family produce alkaloids that have medicinal properties, such as atropine and scopolamine, used in various treatments. However, some species are also toxic and have been used historically as poisons.
Evolutionary Challenges and Research Directions
  • Hybridization and Polyploidy: Hybridization and polyploidy (having multiple sets of chromosomes) have played a role in the evolution of some Solanaceae species, contributing to their genetic diversity.
  • Conservation and Study: Preserving the genetic diversity of wild Solanaceae species is important for both conservation and potential agricultural benefits. Continued research on their genetics and evolutionary history can provide valuable insights into plant evolution and adaptation.

In summary, the Solanaceae family has a rich evolutionary history that spans tens of millions of years. Its members have adapted to a wide range of ecological niches, leading to the diverse array of species we see today. This evolutionary journey has been shaped by climatic changes, geographical dispersal, and genetic diversification.

Which species are the result of hybridization and/or polyploidy?

Hybridization and polyploidy have played significant roles in the evolution of many species within the Solanaceae family. Here are some notable examples:


Hybridization has contributed to the genetic diversity and speciation within the Solanaceae family. Some examples include:
  1. Tomato (Solanum lycopersicum):
    • The cultivated tomato (Solanum lycopersicum) has undergone hybridization with wild relatives, leading to the development of various cultivars with different desirable traits such as disease resistance, fruit size, and flavor.
    • Wild species such as Solanum pimpinellifolium and Solanum cheesmaniae have contributed genetic material to cultivated tomatoes through both natural hybridization and intentional breeding.
  2. Potato (Solanum tuberosum):
    • The cultivated potato (Solanum tuberosum) is a complex hybrid species. It has hybridized with various wild potato species, such as Solanum demissum and Solanum acaule, which have contributed to its genetic makeup and provided resistance to diseases like late blight.
  3. Pepper (Capsicum species):
    • Hybridization among different Capsicum species has been common in the cultivation of peppers. For instance, Capsicum annuum (bell pepper, chili pepper) has hybridized with other species such as Capsicum frutescens and Capsicum chinense to produce new varieties with different heat levels and flavors.


    Polyploidy has been an important mechanism in the evolution of certain Solanaceae species. Polyploid species often exhibit greater genetic diversity and adaptability.
    1. Potato (Solanum tuberosum):
      • The cultivated potato is a tetraploid species (4 sets of chromosomes, 2n = 4x = 48), resulting from the polyploidization of diploid ancestors. This polyploid nature has contributed to its genetic complexity and adaptability.
    2. Tobacco (Nicotiana tabacum):
      • Nicotiana tabacum, the species used for commercial tobacco, is an allotetraploid (4 sets of chromosomes, 2n = 4x = 48). It originated from the hybridization of two diploid species, Nicotiana sylvestris and Nicotiana tomentosiformis, followed by chromosome doubling.
    3. Wild Potatoes:
      • Several wild potato species are polyploids. For example, Solanum demissum is a hexaploid species (6 sets of chromosomes, 2n = 6x = 72), and it has been used in breeding programs to introduce disease resistance genes into cultivated potatoes.
    Importance of Hybridization and Polyploidy
  4. Genetic Diversity: Both hybridization and polyploidy contribute to genetic diversity, providing a broader range of traits that can be selected for in breeding programs.
  5. Adaptability: Polyploid species often have greater genetic variability, which can enhance their adaptability to different environmental conditions and stresses.
  6. Crop Improvement: Understanding the genetic contributions from hybridization and polyploidy is crucial for crop improvement efforts, allowing for the development of new varieties with desirable traits such as increased yield, disease resistance, and improved nutritional content.
Overall, hybridization and polyploidy have been vital in shaping the evolution and diversity of the Solanaceae family, leading to the development of many economically important species and cultivars.
Now researchers at Penn State University, have produced a new evolutionary tree of the family which explains how the fruits of the plants evolved their size and colour together and that fruit-eating animals were probably not the main drivers of their evolution, as was previously thought.

The team have just published their findings, open access, in the journal New Phytologist. It is explained in the press release from Penn State:
Fruits of Solanum plants, a group in the nightshade family, are incredibly diverse, ranging from sizable red tomatoes and purple eggplants to the poisonous green berries on potato plants. A new and improved family tree of this group, produced by an international team led by researchers at Penn State, helps explain the striking diversity of fruit colors and sizes and how they might have evolved.

The team found that the size and color of fruits evolved together and that fruit-eating animals were like not the primary drivers of the fruits’ evolution, as had been previously thought. The study, published in the journal New Phytologist, may also provide insight into breeding agriculturally important plants with more desirable traits, the researchers said.

“There are about 1,300 species in the genus Solanum, making it one of the most diverse plant genera in the world,” said João Vitor Messeder, graduate student in ecology and biology in the Penn State Eberly College of Science and Huck Institutes for the Life Sciences and lead author of the paper. “Since the 1970s and ‘80s, researchers have suggested that birds, bats and other fruit-eating animals have driven the evolution of fruits like those in Solanum. However, the importance of the evolutionary history of the plants has been underestimated or rarely considered when evaluating the diversification of fleshy fruits. To better test this hypothesis, we needed first to produce a more robust phylogeny, or family tree, of this plant group to improve our understanding of the relationships between species.”

Plants in the genus Solanum produce fruits with a wide variety of sizes, colors and nutritional values. They can appear black, purple, red, green, yellow or orange and range in size from less than a quarter of an inch to as much as 8 inches, or 0.5 to 20 centimeters. In addition to agriculturally important plants, some plants in the group are cultivated for their ornamental flowers, and the fruits of many of these plants are eaten by humans and a large diversity of animals, including birds, bats, reptiles, primates and other land mammals.

The researchers collected samples of plants from across the world, including wild plants from Brazil, Peru and Puerto Rico and plants from botanical gardens, and sequenced their genes from RNA. They supplemented with previously collected samples and publicly available data, ultimately comparing the sequences of 1,786 genes from a total of 247 species to reconstruct the Solanum family tree. This included representatives from all 10 of the major clades — the branches of the tree — and 39 of 47 minor clades within the genus.

“By using thousands of genes shared among species that effectively represented the entire genus, we significantly improved the Solanum family tree, making it the most comprehensive to date,” said Messeder, who conducted the research in the lab of Hong Ma, Huck Chair in Plant Reproductive Development and Evolution and professor of biology at Penn State and a co-corresponding author of the paper. “Recent advances in technology allowed us to use more genes than previous studies, which faced many challenges in resolving relationships between species and clades. This improved tree helps us understand when different fruit colors and sizes originated or how they changed as new plant species came about.”

The researchers added considerable resolution of the smaller branches in the group that includes potatoes and tomatoes, as well as their closely and more distantly related wild species. The insights gained, the researchers said, could support crop improvement programs for these species and other crops in the genus.

“If the closest wild relatives of important agricultural crops have desirable traits, it is possible to breed crops with those species or borrow their genes, for example to improve resistance to temperature or pests or to produce larger fruits or fruits of a certain color,” Messeder said.

The researchers found that the color and size of Solanum fruits was fairly conserved over evolutionary history, meaning that closely related species tend to have similar fruits. The evolution of fruit color and size is also correlated, with changes in one trait often corresponding to changes in the other, leading fruits of certain colors to be bigger than fruits of other colors.

“These results suggest that physiological and molecular mechanisms may play a role in keeping the evolution of fruit color and size tied together,” Messeder said. “While frugivores — or animals that primarily eat fruit — and seed dispersers may influence diversification, we need to consider all of the possibilities when studying how fruits became so diverse.”

The researchers also clarified the origin and diversification timeline of this genus, in part by including recent information from the oldest nightshade family fossil — from a different genus in the Nightshade family whose fossil was dated to about 52 million years ago — and from particular genes that improved estimates of the length of evolutionary branches. The researchers dated the origin of Solanum to about 53.1 million years ago — a full 30 million years earlier than prior estimates that were based on genes from other parts of the plant cell. This paints a new picture of the environment that might have shaped how these plants diversified into new groups and species.

“The Earth’s environment changed dramatically during the 30 million years in terms of temperature, carbon dioxide in the atmosphere, geography and animal diversity,” Messeder said. “Now that we know when Solanum and its subgroups originated, we can think about the conditions that might have promoted the diversification of that group, as well as how other organisms might have played a role.”

The team found that the earliest members of Solanum had medium-sized berries that remained green when ripe, and that green and yellow fruits of this group became more diverse around 14 million years ago. The researchers speculated that bats might have played a role in this diversification, given their similar evolutionary timeline and that they are the primary dispersers of modern green and yellow Solanum fruits. As new bat species arose and expanded where they were living during this time, they ate Solanum fruits and carried their seeds to new environments.

Next, the researchers plan to explore how modern interactions between animals and the fruit they eat may shed light on the evolution of both groups as well as explore the evolution of certain genes relevant to fruit color and size.

In addition to Messeder and Ma, the research team includes Tomás Carlo, professor of biology at Penn State; Guojin Zhang, postdoctoral researcher at Penn State at the time of the research; Juan David Tovar at the National Institute of Amazonian Research in Brazil; César Arana at the National University of San Marcos in Peru; and Jie Huang and Chien-Hsun Huang at Fudan University in China.

  • Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships.
  • We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size.
  • Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits.
  • We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.
The fleshy fruits of angiosperms are key innovations that mediate mutualistic seed dispersal by fruit-eating animals (i.e. frugivores) (Eriksson, 2016). This plant–animal interdependence is central to the development and organization of terrestrial communities (Bascompte & Jordano, 2007; Fleming & Kress, 2013). By encapsulating seeds within nutritious pulp, plants take advantage of foraging animals to effectively disseminate their seeds (Schupp et al., 2010). Thus, frugivores can increase plant fitness, and drive the evolution of fruit types (e.g. fleshy fruits) and fleshy-fruit traits (e.g. color) (Lomáscolo et al., 2010.1; Eriksson, 2016; Xiang et al., 2024). Still, it remains unclear how shared evolutionary history influences the evolution of the functional traits of fleshy fruits among related species. Specifically, to examine how frugivores may affect the evolution of fruit traits, it is crucial to assess whether a trait is conserved and has evolved a few or multiple times within a lineage (Ackerly, 2009).

Differences in fruit traits such as size and color when ripe have been interpreted as adaptations to different types of frugivores (Van Der Pijl, 1982; Valenta & Nevo, 2020). For example, birds typically feed on small brightly colored fruits given their highly developed color vision and narrow bill gapes (Janson, 1983; Wheelwright, 1985; Wheelwright & Janson, 1985.1). In comparison with birds, mammals have more limited color vision but highly developed olfaction, teeth, and forelimbs that aid in the manipulation and use of fruits that are large, tough, dull-colored, and odoriferous (Janson, 1983; Nevo et al., 2018). Such trait-matching suggests that frugivores could drive the evolution of fruit traits through natural selection (i.e. dispersal syndrome hypothesis) (Van Der Pijl, 1982; Janson, 1983; Valenta & Nevo, 2020). For instance, fruit traits of figs (Ficus spp., Moraceae) converge to small brightly colored fruits when birds are the main frugivores, or to larger dull-colored fruits when bats and other mammals are the main frugivores (Lomáscolo et al., 2008, 2010.1). Similarly, other phylogenetic comparative studies have also suggested that frugivores are the main drivers shaping fruit characteristics that lead to general ‘syndromes’ that match distinct frugivore groups (Valenta et al., 2018.1; Nevo et al., 2018; do Nascimento et al., 2020.1; Barnett et al., 2023a,2023.1b). It is expected that when selective pressures from frugivores are convergent, the characteristics of fleshy fruits might be less predictable by phylogenetic relationships (Ackerly, 2009; Valenta & Nevo, 2020).

Although the dispersal syndrome hypothesis offers a compelling explanation for fruit trait diversity rooted in selection theory and adaptation, the evidence remains inconclusive (Valenta & Nevo, 2020). This is because many plant species can be effectively dispersed by animals with distinct morphologies and physiologies, leading to diffuse selective pressures that may preclude adaptation to specific frugivores (Herrera, 1985.2). Furthermore, fruit traits may be phylogenetically determined, limiting the selective pressures from frugivores on fruit trait evolution (Fischer & Chapman, 1993; Jordano, 1995; Ackerly, 2009). In such cases, trait matching is more likely the result of ecological fitting (i.e. pre-existing traits fitting new ecological niches without further modification) rather than the evolution of new traits due to selection (Janzen, 1985.3; Agosta & Klemens, 2008.1). Thus, how much fruit traits are the result of adaptations or of phylogenetic constraints and ecological fitting remains unclear. Advance in this field has been constrained by the use of limited phylogenetic frameworks, poorly resolved phylogenies, and additional challenges posed by hybridization and introgression events among species (e.g. Gardner et al., 2023.2).

Recent studies merging phylogenetics and trait evolution have provided important insights into fleshy-fruit evolution. Fleshy fruits have independently evolved multiple times across angiosperms (Xiang et al., 2017, 2024; Frost et al., 2021; Hilgenhof et al., 2023.3). Studies have shown that fruit color can be associated with long-distance dispersal patterns (Lu et al., 2019) and diversification rates (Spriggs et al., 2015; Lu et al., 2019; L. Zhang et al., 2023.4). Fruit developmental processes have been identified as a mechanism underlying the origin of syndromes (Sinnott-Armstrong et al., 2020.2). Still, in-depth studies assessing the role of shared evolutionary histories on fruit trait evolution remain scarce, especially within highly diverse plant groups.

The genus Solanum L. comprises c. 1300 fleshy-fruited species and is the largest genera of Solanaceae and the second largest genus of fleshy-fruited plants (Frodin, 2004). Regarding fruit traits, Solanum shows a remarkably high diversity, producing berries of various sizes, colors, and pulp with different nutritional and chemical profiles (Cipollini et al., 2002; Knapp et al., 2004.1; Hilgenhof et al., 2023.3). For instance, berry size ranges between 0.5 and 20.0 cm, ripening in many colors, including black, purple, red, green, yellow, and orange. Additionally, Solanum fruits with different colors and sizes are eaten and dispersed by distinct animal groups, including reptiles, birds, bats, primates, and terrestrial mammals (Symon, 1979; Cáceres & Moura, 2003; Arruda Bueno & Motta-Junior, 2004.2; Vasconcellos-Neto et al., 2009.1; Jacomassa & Pizo, 2010.2). This unusual fruit diversity within a single genus makes Solanum an excellent group to investigate a wide range of eco-evolutionary questions (Knapp et al., 2004.1; Moyle, 2008.2). Furthermore, humans have cultivated and domesticated many Solanum species, such as the potato (S. tuberosum), tomato (S. lycopersicum), eggplant (S. melongena), and others (S. betaceum, S. muricatum, and S. quitoense), contributing to the global agriculture (Knapp et al., 2004.1). However, uncertainties in the phylogeny of Solanum limit our understanding of the evolution and diversification patterns of fruit traits relevant to plant–frugivore interactions and agriculture. Unclear phylogenetic relationships make it challenging to determine the ancestral form of a trait and track the number of times and the direction of transitions of the fruit trait over time. Furthermore, assessing the lability of a trait may facilitate its manipulation for agriculture.

Previous studies have made significant progress toward reconstructing the evolutionary history of Solanum (Weese & Bohs, 2007.1; Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5), with the identification of three deep lineages (we adopted the informal clade nomenclature proposed in previous molecular phylogenetic studies – Bohs, 2005; Stern et al., 2011; Särkinen et al., 2013.1; Tepe et al., 2016.1; Gagnon et al., 2022). The Thelopodium Clade, comprising three species, diverges first, while the remaining species are divided into Clades I and II. Clade I contains c. 350 species, including tomato and potato, whereas Clade II, with c. 900 species, has many spiny shrubs, including eggplant. Clades I and II were further subdivided into nine major and 47 minor clades (Särkinen et al., 2013.1). However, the placement of many clades is inconsistent among studies using various taxa and genes (Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5) (Supporting Information Fig. S1). Recently, a comprehensive phylogenetic study of 742 Solanum species still found major clades with unresolved relationships (Fig. S1) (Gagnon et al., 2022). For example, the monophyly of Clade I was supported by some analyses using plastid sequences (Fig. S1a–c) but not others using nuclear genes (Fig. S1d,e), and placement of its major clades – especially Regmandra – was uncertain (Fig. S1c–e). These inconsistencies have been described as polytomies near the crown node and reflect difficulties for resolving the deep Solanum relationships (Gagnon et al., 2022). Another recent study (Huang et al., 2023.5) using 1699 genes from 81 Solanum species, along with other members of Solanaceae, presented a well-supported phylogeny, but lacked the Thelopodium Clade and some major clades in Clades I and II, including Regmandra (Fig. S1f–k) and many minor clades. Consequently, a Solanum phylogeny with a more complete lineage representation and well-supported relationships is needed to further understand the ecological factors that shape its evolution, including the drivers behind its remarkable diversity of fruit sizes, shapes, and colors.

Here, we bridge the gap between ecology and phylogenomics using Solanum as study group to examine the tempo and mode of the evolution of fruit traits that are both agriculturally relevant and mediate frugivory and seed dispersal interactions. We used 1786 low-copy nuclear genes across 247 species to reconstruct a highly resolved Solanum phylogeny. We explored the temporal aspects of Solanum's evolutionary history and investigated the phylogenetic effects on the diversification patterns of two important fruit functional traits: size and color when ripe. We evaluated how evolutionarily constrained are fruit size and color in Solanum and discussed implications for the ecology and evolution of seed dispersal mutualisms.
Fig. 2
Divergence time estimation for Solanum indicating its origin in early Eocene and divergence among extant species starting in the middle Eocene. Relevant estimated divergence times of major clade lineages are marked at corresponding nodes. Branch colors match major clade colors of Fig. 1, with their respective names on the right side. Fruit colors and sizes are mapped on terminal tips. At the bottom of the chronogram, geological timescale is shown with periods delimited by vertical lines, the estimated temperature variation for the Cenozoic, and arrows indicating the Mid-Eocene Climatic Optimum and Mid-Miocene Climatic Optimum. Eo, Eocene; LC, late Cretaceous; Mio, Miocene; Ol, Oligocene; Pal, Paleocene; Pli, Pliocene; Q, Quaternary. On the right side, pictures demonstrate some of the variety of colors, sizes, and shapes that can be found in Solanum fruits. Pictures were taken by the authors or downloaded from the internet (Supporting Information Table S6). (Detailed divergence times with species names are shown in Figs S6, S7).

Of special concern for creationists, is not the technical details, which few would understand even if they read it, but the timeline and the fact that the scientists show no hint of giving up on the Theory of Evolution but instead, use it to explain their findings, with no hint that a magic supernatural entity intervened anywhere in the divergence process.

Additionally, the Introduction section contains links to lots of references to papers dealing with the same or related subjects. None of them show any signs of adopting creationism because the TOE isn't up to the task, either.

The entire range of Solanum species, including many important foods, is the result of evolution, with new genetic information being created by the natural processes of gene and whole genome duplication to give polyploidy, and hybridization. The potatoes, tomatoes, peppers, chilis and aubergines we eat contain evidence of evolution in their genomes.

Many of these plants are the product of cultivation and human selective breeding of course, so creationists might like to explain why plants, like domestic animals, which are the descendants of species the Bible says were created for humankind, have had to be improved to make them fit for purpose. Did their designer not know what humans would need, or did the authors of the Bible not understand about domestication, cultivation and selective breeding to improve on the wild type?

Wednesday 26 June 2024

Unintelligent Design - How Painted Lady Butterflies Migrate Thousands of Miles All For Nothing

Painted Lady, Vanessa cardui
div class="credit">Photo credit: Gerard Talavera
Non-stop flight: in a world-first, researchers map a 4,200 km transatlantic flight of the Painted Lady butterfly | About us

Reader with long memories may recall my article from 2011 in which I explained how the annual migration of thousands of painted lady butterflies (Vannesa cardui) from Southern Europe and North Africa into northern Europe made no sense at all from an intelligent design point of view, because not a single one of them or their offspring ever survived even the mildest of European winters.

This, one of the most attractive of butterflies, reaches all parts of the British Isles, in some years migrating as far north as the Orkney and Shetland Island. It is the only butterfly ever recorded in Iceland.

And now a group of scientists have worked out that some painted ladies that turned up on the north coast of South America migrated there across at least 4,200 Km of open Atlantic Ocean in a few days.

Creationism in Crisis - How A 700-Million-Year-Old Chance Mutation Could Explain Why We Have Limbs

A graphic representation of the DNA sequence
How a 700-million-year-old DNA glitch could explain why humans have limbs | National Post

700 million years ago in a remote ancestor of all terrestrial tetrapods - which includes all amphibians, reptiles, birds and mammals, a mutation in a gene happened. To begin with this made no difference because the mutation was neutral - neither deleterious nor advantageous.

But later on, it became the mutation that made the evolution of limbs possible, in an illustration of how redundant or neutral DNA can later be exapted for new functions and structures.

This may seem highly improbable to anyone who doesn't understand how natural selection ensure that beneficial traits accumulate and increase in the species gene pool but in fact, there have been several such chance mutations that opened up the possibility of a new direction in evolution in human genetic history.

Unintelligent Design - An Over-Complex, Heath-Robinson Solution To A Simple Problem

Small Antarctic worms (zoom) rely on microbes to resist the chill of the frigid waters where they live.
Michael Tangherlini, Marco Lo Martire
Bacteria found to produce proteins that act like antifreeze, helping marine worms survive in polar waters

Imagine you're a designer with all the power you need and all the solutions you've designed earlier at your fingertips and your task is to redesign some marine worms that you designer earlier and put into an arctic environment, perhaps not realising they wouldn't survive if they got frozen.

So, what you have to do is give these marine worms some way to prevent this happening and so mitigating your earlier blunder.

At your disposal is the method you gave to some marine bacteria, and even some fish known as icefish, when you made similar blunders years earlier - you gave them some genes for making antifreeze to stop the contents of their cells freezing and the ensuing ice crystals from destroying them.

Do you give these marine worms the same genes you gave the bacteria?

Not if you're creationism's putative intelligent [sic] designer, you don't. That would be far too simple.

Monday 24 June 2024

Creationism in Crisis - Cave Lions In Europe - 590,000 Years Before 'Creation Week'

European cave lion, Panthera spelaea
Unknown artist
Oldest evidence of cave lions in southern Europe | University of Tübingen

The evidence that the authors of Genesis just made up stories to fill the gaps in their knowledge and understanding continues to pile up. The latest is news that there were cave lions in southern Europe at least 600,000 years ago, i.e., 590,000 years before creationists think the Universe was created out of nothing by magic - a daft idea they got from Genesis and which they cling to despite all the contrary evidence.

This latest incidental refutation of creationist mythology comes from an international research team led by Dr. Alessio Iannucci from Terrestrial Paleoclimatology at the University of Tübingen, Germany. The team have just published their findings, open access, in the Journal of Quaternary Science .

Atheism Winning - Church of Scotland To Sell Redundant Churches As Scots Reject Organised Religion

Hundred Scottish churches up for sale as UK turns away from Christianity - Anglican Mainstream

The Church of Scotland - A Presbyterian Protestant church often referred to as simply 'The Kirk' - is facing the same problem as the Church of England - what to do with all the redundant churches as congregations dwindle and buildings fall into disuse and dereliction.

Many of these old churches are also listed building of historical or architectural importance, so the church must maintain them.

An additional problem is that most of them are surrounded by grave which must also be conserved and may not be built on.

So, in an attempt to shore up its finances, the Church of Scotland has placed hundreds of its properties, including apartment blocks, manses and churches on the property market.

Creationism in Crisis - How We Know Earth is 4.5 Billion Years Old.

A groundbreaking discovery: how we found remnants of Earth’s primordial crust near Perth

I frequently write articles that report on events that happened long before creationist mythology says the Universe was magicked up out of noting with some magic words spoken in a language that no-one spoke by a magic man who had self-assembled out of nothing according to a design it made before it existed.

This probably has creationists scratching their heads trying to think of reasons why the science is wrong because it doesn't fit their preferred mythology. The simple explanation which seems too hard for creationists to grasp is that there is nothing wrong with the science; what's wrong is the mythology they're trying to bend the evidence to fit into.

Like trying to force the Pacific Ocean into a teacup and blaming the teacup for being the wrong shape.

The simple reason that so much of the history of the Universe and of Earth and life on it happened before the mythical 'Creation Week', is that is so much more time for it to have happened in, than there is in the 10,000 years since. In fact, 99.99767% of the history of Earth happened before creationism's mythical 'Creation Week' because Earth is 4.5 billion years old, give or take a few million years.

To put that into perspective, imagine the history of the Earth as a year; land plants didn't evolve unto a month ago, dinosaurs made their appearance two weeks ago and all of human history has happened in the last half an hour. A sobering thought is that on that scale a human life lasts about half a second.

So, how do we know how old Earth is?

The secret is hidden inside crystals of zircon which are themselves embedded in grains of titanite that protect them from environmental changes that could give false dates. This technique gives incredibly accurate dates since there a few, if any, ways in which contamination or leakage can distort the ratios of the isotopes involved:

Saturday 22 June 2024

Creationism in Crisis - How Macaques Can Adapt Their Culture When They Need To - Just Like Humans

Hurricane Maria destroyed 63% of vegetation on Cayo Santiago.
Credit: Lauren Brent
Hurricane changed ‘rules of the game’ in monkey society - News

The childish notion of human exceptionalism took another blow recently when a group of researchers showed how macaque monkeys can change their culture to adapt to changes in their environment.

As with humans, macaque cultural ethics is an agreed standard of behaviour that enables the group to remain cohesive and survive in adversity. Unlike creationists, macaques don't require a handbook to know how to behave decently towards others because, like normal humans, they too have empathy and will treat others as they would want to be treated.

This was illustrated recently when macaques were seen to change their behaviour when hurricane Maria destroyed the 63% of the vegetation on their home island of Cayo Santiago, reducing the amount of shelter from the heat of the sun.

Creationism in Crisis - A Newly-Discovered Dinosaur, Lokiceratops - From 78 Million Years Before 'Creation Week'

Newly discovered dinosaur Lokiceratops boasts big, blade-like horns - Warner College of Natural Resources
Reconstruction of Lokiceratops in the 78-million-year-old swamps of northern Montana, as two Probrachylophosaurus move past in the background.

Artwork by Fabrizio Lavezzi © Evolutionsmuseet, Knuthenborg
Colorado State University affiliate faculty member Joseph Sertich and University of Utah Professor Mark Loewen, have identified and named a new species of dinosaur that lived in Northern Montana.

Like almost everything that ever lived, this dinosaur, Lokiceratops, lived in the 99.99975% of history that happened before creationists like to imagine the universe was created. It lived a mere 78 million years before the mythical creation week, to be precise.

An interesting feature of this species - one of a number that appear to have evolved rapidly in the region - is the large 'ornamental' horns that may have been used in courtship, implying female sex-selection played a part. Female sex-selection is a known driver of rapid speciation because it produces genetic isolation and forms an important pre-zygotic barrier to hybridization, just as display and sex-selection does in many birds today.

This could account for the apparent proliferation of these types of dinosaurs.

Unitelligent Design - Using The Theory Of Evolution To Create Better Enzymes

Scientists devise algorithm to engineer improved enzymes - News & Events | Trinity College Dublin

Scientists at Trinity College, Dublin, Ireland have discovered that using the natural algorithm of evolution by natural selection is the best way to improve the efficiency of enzymes in terms of the products of the processes they catalyse.

This begs an embarrassing question for creationists: why can enzymes produced by a perfect designer be improved upon?

The answer of course, is that they weren't designed by a perfect designer; they were designed by a utilitarian evolutionary process in which whatever is better than what went before will be retained and the only reason to improve beyond the sub-optimal that works well enough, is to have some other selectors driving it towards ever greater fitness. There is no 'ideal' nor any process for comparing what is against this idea and trying harder, as there would be if there was an intelligence guiding the process.

Friday 21 June 2024

Creationism in Crisis - How Changing the Environment Affects Evolution - Naturally

The Nile perch is a menace to endemic cichlids
Pictured on the left is the Nile perch, a voracious predator introduced into Lake Victoria by humans to satisfy meat demands in the 1950s. On the right, several species of endemic cichlids that were markedly affected are shown. The populations of some of these species declined so much that their genomic structure remained significantly altered even after their numbers climbed back up.
Nile Perch Invasion Triggered Genetic Bottlenecks in Lake Victoria's Endemic Cichlids The introduction of the Nile perch to Africa’s largest lake impacted the genomic structure of multiple local species | Tokyo Tech News | Tokyo Institute of Technology

The East African cichlids are an embarrassment to creationists because they are one of the best examples of rapid speciation over a known geological age from an initial founder population of one species.

Between 17,000 and 16,000 years ago, towards the end of the last Ice Age, there was a surge of icebergs and glacial meltwater into the North Atlantic which altered ocean currents and changed the weather pattern over the African and Asian monsoon areas, which experienced a resulting mega-drought. Analysis of sediments show that this caused Lake Victoria, Lake Albert and Lake Tana to dry up and disappear.

A similar event 14,000 - 15,000 years ago caused Lake Victoria to dry up again and a subsequent lowering of water levels 5,000 years ago left a small satellite lake, Lake Nabugabo, isolated. From this we know how long ago each lake received its founding population of cichlids from their feeder rivers. In the case of Lake Victoria, this was between 14,000 and 15,000 years ago. We also know that the micro-lake, Lake Nabugabo, has been isolated for just 5,000 years. By contrast, nearby Lake Tanganyika is tens of millions of years old and has remained filled for all that time. See AfricaPaleo - FOCUS 1: Lake levels and evolution.

So, we know exactly the maximum time for which these cichlids have been diversifying.

Creationism in Crisis - How Plants Evolved In Response To Different Environments - Naturally

The experimental plants pollinated by bumblebees displayed significant differences on limestone soil (r) and tuff soil (l).
Image: UZH.
Interaction with Insects Accelerates Plant Evolution | | UZH

A clutch of papers published today serve to refute creationism by showing how evolution occurs in response to environmental selectors with no need to include magic or supernatural deities in the explanation. They also serve to highlight the lie that creationist cult leaders fool their dupes with that mainstream biologists are turning to creationism because the Theory of Evolution is inadequate for explaining the observable evidence.

On the contrary, these papers illustrate the robust nature of the TOE in explaining how plants and fish evolve in response to natural selectors, and the power of the theory to explain the observable evidence.

The first two are from substantially the same team led by biologist Florian Schiestl of the Department of Systematic and Evolutionary Botany at the University of Zurich, Switzerland, and deal with the way flowering plants respond to insects in their environment; both as beneficial pollinators and as harmful herbivores.

Thursday 20 June 2024

Malevolent Designer - A Newly-Discovered Fish Parasite

Red-lipped Blenny.
Credit to Matthew Hoelscher.
Previously uncharacterized parasite uncovered in fish worldwide

Parasites present creationists with an insurmountable problem, especially those who equate the putative designer with the Abrahamic, supposedly omnibenevolent, god of the Bible, Torah and Qur'an.

It is a problem for creationism because there is no way the design of parasites, which appear to have only two functions - Making their hosts sick, so increasing the suffering in the world, and producing more parasites to make more hosts sick - can't possibly be the work of an omnibenevolent designer, and the inevitable resulting arms races between parasite and host are not the act of an intelligent designer.

The traditional explanation offered by creationists, particularly those with only a rudimentary grasp of the subject is to blame 'devolution' [sic] caused by 'genetic entropy' which was made possible by 'Sin' following the mythical 'Fall' as an organism evolves away from some assumed initial perfection at 'creation'. Apart from betraying the religious fundamentalism dressed in a grubby lab coat, that is 'intelligent design' creationism, this is scientifically nonsensical and counter factual, of course.

Wednesday 19 June 2024

Creationism in Crisis - Human Culture Is A Cumulative Process Which Started 590,000 Years Before 'Creation Week'

ASU study points to origin of cumulative culture in human evolution | ASU News
Stone tools that become increasingly more complex over the course of 3 million years. Left: First time period studied — Oldowan core, Koobi Fora, Kenya (below baselines). Center: Second time period studied — Acheulean cleaver, Algeria (around baseline). Right: Characteristic of 600,000 year ago technology — Levallois core, late Pleistocene Algeria.

Image credits: (left) Curry, Michael. 2020. Oldowan Core, Koobi Fora. Museum of Stone Tools. Retrieved June 10. From:;
(middle) Curry, Michael. 2020. Acheulean Cleaver, Morocco, Koobi Fora. Museum of Stone Tools. Retrieved June 10. From:;
(right) Watt, Emma. 2020. Levallois Core, Algeria. Museum of Stone Tools. Retrieved June 10. From:
More evidence was provided yesterday of human history and the beginnings of human culture about 600,000 years ago, i.e., about 590,000 years before creationists claim Earth was magicked up out of nothing as a small flat planet with a dome over it in the Middle East. The evidence comes in the form of a research paper by Arizona State University researcher Charles Perreault and doctoral graduate Jonathan Paige.

Generally speaking, human culture has been like a snowball rolling down a snow-covered hillside. The bigger the snowball gets, the more snow it accumulates, so its growth is exponential. Interestingly, and something for creationists to ignore, is the fact that human cultural evolution began before anatomically modern humans had evolved, so, as Homo sapiens, as with our genes, we inherited the beginnings of our culture from an ancestral species.

Contrast that with the childish creationist origin myth which has humans all descending from two individuals magically created without ancestors.

How the two authors carried out their research is the subject of an Arizona State University (ASU) news release by Julie Russ:

Creationism in Crisis - A Marine Reptile From 246 Million Years Before 'Creation Week'

Reconstruction of the oldest sea-going reptile from the Southern Hemisphere. Nothosaurs swimming along the ancient southern polar coast of what is now New Zealand around 246 million years ago.
Artwork by Stavros Kundromichalis.
Ancient polar sea reptile fossil is oldest ever found in Southern Hemisphere - Uppsala University

Sometimes, it must seem as though everything that happened on Earth happened before creationists believe the Universe was created. The simple reason is that this is precisely so, since about 99.9975% of time has existed between when Earth formed out of an accretion disk around the sun and when creationists believe their magic creator god created a universe as a small flat planet with a dome over it in the Middle East, 10,000 years ago.

For example, by about 246 million years ago, life had evolved to the point where terrestrial reptiles were returning to the sea where they evolved into large, marine predators - the apex predators of their day. This means that there was plenty of other life in the seas for them to predate upon, and the fossilised remains of one of them has recently been found in rocks on the southern coast of New Zealand, making it the oldest marine reptile fossil ever found in the southern hemisphere.

Tuesday 18 June 2024

Creationism in Crisis - A Tiny Bird Refutes Creationism - Again

Titipounamu, Acanthisitta chloris
Photo: Dr. Kristal Cain.
Tiniest bird delivers evolution lesson - The University of Auckland

In case any creationists are still under the delusion that mainstream biologists are abandoning the scientific Theory of Evolution (TOE) in favour of their childish magical story involving a magic man made of nothing who magicked everything into existence out of nothing with some magic words, here is an example of how the TOE is used to understand and make sense of the observable facts.

It addresses the question of how the ability to learn and imitate sounds evolved in birds.

Basically, ornithologists had thought that birds could be divided into two groups - those which can learn sounds (parrots, songbirds, and hummingbirds) and those which can’t - and that this ability in the former group had evolved sometime after modern birds had diversified from their avian dinosaur ancestors, but the fact that a small New Zealand bird, the titipounamu or rifleman, Acanthisitta chloris, has the rudiments of this ability suggests it may have been present in the common ancestor of both groups.

In other words, the ability to learn and imitate sounds may be evidence of common descent.

Web Analytics