Malevolent Design - How The Black Widow Spider's Toxins Harm Us Mammals

Latrodectus hesperus

By Ken-ichi Ueda - https://www.inaturalist.org/photos/121,
CC BY 4.0,Link

Latrodectus hesperus female with egg sac.

Scientists decode black widow spider venom

Black widow spiders have a cocktail of toxins, most of which are effective against their arthropod prey such as insects, but one of them, α-latrotoxin, is very effective against vertebrates, including humans, although even the smallest vertebrates don't normally feature in the black widow's diet.

So why did this toxin evolve?

Normally, a species which is capable of delivering a nasty, even lethal, bite to a threat, rather than to prey, evolves strategies for avoiding doing so, while warning that it could if it wanted to - rather like a creationists avoiding answering a question while pretending they could if they wanted to, only without the pretense. Most species do this with warning colours or, in the case of the rattlesnake, a warning rattle. This is because using venom against a threat might mean there isn't enough left if the next potential meal wanders by, so it's better to warn and threaten than to actually bite.

But not so the black widow, except for the strikingly marked European species, Latrodectus tredecimguttatus, and the South American, Latrodectus curacaviensis. If anything, the black widow is cryptocamoflaged to not be noticed in the dark places they inhabit.

Refuting Creationism - How Biologists Are Refining The Theory of Evolution, Not Abadonning It In Favour Of Creationist Superstition

This article is best read on a laptop, desktop or tablet

New Findings Supply Corrective to Evolutionary Hypothesis | University of Arkansas

In a highly mathematical, technical paper in PLOS Computational Biology, some of which is above my paygrade, two evolutionary biologists have shown that the mysterious apparent accelerations in the rate of evolution are actually due to statistical 'noise' and not a true change in the rate of evolution.

I've written this post about it not because it contains some interesting information about biological organisms or that long history of life on Earth that occurred before creationists believe their little god created a small, flat planet with a dome over it, but so creationists can see how badly they've been deceived by their cult leaders who have been telling them for the best part of half a century that mainstream biologists are about to abandon the Theory of Evolution any day now in favour of their childish superstition with its magical creation of species without ancestors.

Of course, to a simplistic, black vs white thinking creationist, any discovery that scientists might have been wrong about some precise detail or others can be presented as 'proof' that the entire body of science is wrong, but that's not how grown-up science works. To think otherwise is the equivalent of thinking having to detour round a parked car in a road means the satnav is broken.

Two computational biologists have recently published evidence that the appearance of accelerated rates of evolutionary change is due to statistical 'noise' in the data* What impact would this finding have on the basic principles of evolution? If the recent findings by computational biologists suggesting that accelerated rates of evolutionary change are largely due to statistical noise are accurate, this would have several important implications for the study of evolutionary biology. However, it is essential to clarify that these findings would likely not overturn the basic principles of evolution (such as natural selection, genetic drift, mutation, and gene flow), but they could impact how we interpret the tempo and mode of evolutionary change. Here are a few possible impacts:

1. Reevaluation of Evolutionary Rates
   
   • One key implication would be that observed patterns of rapid evolutionary change (in specific lineages or over short time periods) might need to be reinterpreted. If statistical noise has exaggerated the perception of these rates, what may have seemed like "punctuated bursts" of rapid evolution could, in fact, represent more gradual processes.
   • Some models of evolution, such as punctuated equilibrium (which argues that species experience long periods of stasis interrupted by short, rapid bursts of change), might need reconsideration. While this does not disprove punctuated equilibrium, it could require revisiting the evidence used to support it.
   
   
2. Statistical Models in Evolutionary Biology
   
   • The study would emphasize the importance of statistical rigor in evolutionary studies. Researchers would need to account for and reduce noise in their data more carefully to avoid overestimating rates of evolution.
   • This might lead to more robust methods for analyzing phylogenies, genomic sequences, and fossil data to ensure that we distinguish genuine signals of evolutionary change from artifacts produced by incomplete data or noisy statistical models.
   
   
3. Impact on Molecular Evolution Studies
   
   • Much of the evidence for accelerated evolution, especially at the molecular level, comes from comparative genomics, which measures changes in DNA sequences over time. If noise in the data has been overestimating these rates, it would affect interpretations of molecular clocks, the timing of divergence events, and the rates of adaptive evolution.
   • This could also alter our understanding of when certain key evolutionary transitions took place, such as the divergence between major groups (e.g., between humans and chimpanzees) or the timing of the origin of new traits.
   
   
4. Evolutionary Innovation and Adaptation
   
   • If rapid changes are less common than previously thought, this could affect theories about the mechanisms underlying evolutionary innovation. For example, the appearance of new traits or adaptations may occur more slowly than we assumed, and might more often involve cumulative changes rather than rapid shifts.
   • This might challenge the idea that certain environmental pressures (e.g., mass extinctions or rapid climate change) consistently trigger bursts of rapid adaptation.
   
   
5. Reevaluation of Case Studies
   
   • Many well-known examples of rapid evolution (e.g., the finches of the Galápagos, the peppered moth) might need closer scrutiny to ensure that the rates of change observed in these cases are genuine and not artifacts of noisy data.
   • Fossil and genomic data used to reconstruct evolutionary timelines might also need reevaluation in light of these findings, with the possibility that some inferred rates of change may need adjustment.
   
   
6. Broader Implications for Evolutionary Theory
   
   • The fundamental concepts of evolution—such as descent with modification, natural selection, and common ancestry—would remain intact, as these are supported by a vast range of evidence beyond the statistical models of evolutionary rates. However, the findings could influence the details of how we model evolutionary dynamics, especially over short timescales or within particular lineages.
   • The study could lead to a greater emphasis on distinguishing between "real" evolutionary signals and those that result from data imperfections, potentially improving the accuracy of evolutionary research going forward.

In summary, the basic principles of evolution are robust and unlikely to be overturned by this finding. However, it could lead to more refined methods in evolutionary biology, impacting how we interpret rates of change and the timing of evolutionary events, potentially leading to more accurate evolutionary histories.

The truth is that biologists have no doubt about the basic principle of evolutionary diversification from a common ancestor, driven by environmental selectors; their debate is only over the details of the processes and how they relate to environmental changes.

The scientists' work is explained in a University of Arkansas news release:

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.

Refuting Creationism - Ancient Deluges - In Australia, 90,000 years Before 'Creation Week'

Pinnacles at Nambung National Park

Picture: Matej Lipar

Pinnacles at Nambung National Park

Iron nuggets in the Pinnacles unlock secrets of ancient and future climates - News at Curtin | Curtin University, Perth, Australia

For another o todays casual and incidental refutations of creationism, we have news about the climate in Western Australia, 90,000 years before creationists little god magicked up a small flat planet with a dome over it, according to the book of Bronze Age creation myths that creationists have mistaken for a science textbook.

Of course, when everything else about Earth's history occurred in the 99.9975% of its history that occurred before the mythical 'Creation Week', this will come as no surprise to anyone who is not functionally illiterate with the thinking ability of a slow 9year-old.

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 Pterosaurs Became Flying Giants - 252-66 Million Years Before 'Creation Week'

Representation of pterosaurs

AI generated image (ChatGPT4o)

Life restoration of a group of giant azhdarchids, Quetzalcoatlus northropi, foraging on a Cretaceous fern prairie.
A juvenile titanosaur has been procured by one pterosaur, while the others stalk through the scrub in search of small vertebrates and other foodstuffs.

Witton MP, Naish D (2008)

Pterosaurs needed feet on the ground to become giants | News | University of Leicester

New research by scientists led by the University of Leicester has filled in another of those gaps much sought after by creationists as somewhere to fit their ever-shrinking little god. The gap was in our understanding of how and when the pterosaurs evolved to their gigantic size from their small beginnings.

Because this took place over the almost 190 million years that pterosaurs were around before going extinct, along with the dinosaurs, 66 million years ago, most creationists will probably have ignored it because it all happened so long before 'Creation Week'. Any reference to gaps in the fossil record that long ago will mean simultaneously holding two mutually exclusive views about the age of Earth, with all the painful cognitive dissonance that entails, so creationists frauds will most likely have kept quiet about it if they were even aware of it.

Refuting Creationism - Living Bacteria Sealed Inside 2 Billion-Year-Old Rock

Microbial cells stained green

© Y. Suzuki, S. J. Webb, M. Kouduka et al. 2024/ Microbial Ecology

2-billion-year-old rock home to living microbes | The University of Tokyo

The Bushveld Igneous Complex (BIC), South Africa.
This picture shows a very famous outcrop where nearly horizontal black and white layers are observed. The BIC made of layers of igneous rock in a basin shape, formed over a period of about 1 million years, after which it seems to have barely changed.

© Y. Suzuki.

In today's incidental rebuttal of creationist dogma, archaeologists have discovered living colonies of microbes sealed within cracks in 2-billion-year-old rocks from South Africa.

The microbes became sealed in the cracks by tightly-packed layers of clay so effectively creating sealed chambers from which nothing could escape and, more importantly, nothing could enter. They have survived over geological time by firstly having an extremely low metabolic rate, with a generation time measured in thousands, even millions of years, compared to surface-dwelling microbes with generation times in hours or minutes, and by utilising sulphates as their energy source.

What they demonstrate, apart from the fallacy of Earth only being made by magic 10,000 years ago, is that in a highly stable environment, a plentiful source of energy and the ability to recycle their dead with almost no loss of energy, there is no environmental pressure to evolve, so the microbes have remained virtually unchanged for hundreds of millions, even billions of years.

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'.

Refuting Creationism - How Endosymbiosis Evolved

Bacteria are injected into a fungus with an extremely fine tip. The bacteria migrate into the spore-forming tissue (yellow) and are passed on to the next generation.

Image: Sean Kilian

How a bacterium becomes a permanent resident in a fungus | ETH Zurich

Endosymbiosis is fundamental to multicellular life since all multicellular organisms are collections of eukaryote cells, which are themselves alliances of prokaryote cells i an endosymbiotic relationship.

It illustrates as well and any other evolved cooperative alliances how natural selection, which make genes look like they are relentlessly selfish and the deadly rivals of other alleles of the same gene, often results not in rivalry and competition but alliances and cooperation.

However, for one cell to enter another cell, take up residence in it and be transmitted vertically from one generation to the next, as must have happened with the earliest eukaryote cells, a number of barriers must be overcome, not the least of which is that a cell with a potentially parasitic organism inside it is either going to try to reject it or be less efficient, therefore less competitive, then uninfected cells and would tend to be eliminated in the struggle to succeed.

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 - If We Discovered The Bible Today We Could Date It's Authorship By The Scientific Illiteracy In It

An artist’s rendering of what’s called an active galactic nucleus at the center of NGC 4151. The galaxy’s black hole sits at the center, immediately surrounded by an accretion disk shown in blue.

Image credit: JAXA

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XRISM has shown that the accretion disk surrounding a black hole in an active galactic nucleus is warped, confirming earlier hypotheses reflected in this artist’s conception from 2015.

Image credit: International Center for Radio Astronomy Research

First data from XRISM space mission provides new perspective on supermassive black holes | University of Michigan News

I've often remarked on how the stark difference between their laughably childish description of the Universe in the Bible and the reality science is revealing, illustrates the scientific illiteracy of its parochial authors, and so gives the lie to claims that it was written or inspired by a creator god.

They were writing with the knowledge and understanding of Bronze Age pastoralists - which is hardly surprising, since that's exactly what they were. They only knew of the small area around the Canaanite Hills, so nothing that was more than a day or two's walk for them was included, which is why it seemed to them like a small flat planet with a dome over it, and fixed to the dome were the sun, moon and stars; stars being mere small points of light and only those that were visible to the naked eye.

So, just imagine what they would have made of the information if some time traveler from today went back and told them about black holes and the centre of a galaxy 120,000 light years across and containing a billion suns with planets orbiting them! How could they have comprehended the idea of mass bending space-time or something smaller than a grain of sand weighing the same as a million suns?

What would they have made of distances so great that it takes light 120,000 years to travel its length? To them, light was instantaneous; it mattered not whether it came from the sun or the campfire, and the sun was merely a lamp hanging from the dome over the earth. What on Earth was this nonsense about the sun being really big and Earth going round it, things weighing millions of times more than the sun or light taking more time than they thought there had been to travel from one place to another?

They knew nothing of laws of motion and how forces make things move, so they had no concept of gravity. They walked on Earth because they didn't float above it, and they couldn't fly. Only gods and supernatural beings could travel up and down at will. So, what on Earth would mass causing gravity and gravity being an attractive force mean?

Black holes would have been simply beyond their comprehension and outside their experience of the world.

So, of course, they could have included nothing of any of this stuff in the stories they invented to explain things they didn't understand. Had they done so, we might have had some cause to think something must have told them. As it was, they wrote tales that illustrated their scientific illiteracy because they had no option but to do so. They were scientifically illiterate by today's standards.

Refuting Creationism - "The Universe is Much Bigger Than Our Prophets Said, Grander, More Subtle, More Elegant..."

ESO telescope captures the most detailed infrared map ever of our Milky Way | ESO

PR Image eso2413a

This Picture of the Week shows a new view of NGC 3603 (left) and NGC 3576 (right), two stunning nebulas imaged with ESO’s Visible and Infrared Survey Telescope for Astronomy (VISTA). This infrared image peers through the dust in these nebulas, revealing details hidden in optical images. NGC 3603 and NGC 3576 are 22,000 and 9,000 lightyears away from us, respectively. Inside these extended clouds of dust and gas, new stars are born, gradually changing the shapes of the nebulas via intense radiation and powerful winds of charged particles. Given their proximity, astronomers have the opportunity to study the intense star formation process that is as common in other galaxies but harder to observe due to the vast distances.

The contrast between reality and the Bible's description of it can scarcely be more stark than that between the description of the Universe as a small flat planet with a dome over it as described in Genesis 1: 3-18, and the reality of the universe as it's being revealed in ever greater detail by science.

It's stretching credulity to breaking point to pretend the Bronze Age pastoralists knew full well how large and magnificent the Universe really is, with its countless trillions of galaxies each with half a trillion stars or more, but chose to describe it in some metaphorical way instead, complete with stars that shake loose from the dome and fall to earth during earthquakes. That's not allegorical; it's a mistake from assuming that meteorites burning up in the atmosphere were falling stars - an easy mistake to make if you know neither what stars are nor what meteorites are.

And like the description of meteorites, their description of the rest of it is based on guesses made from a position of ignorance, and an underlying assumption that somewhere up there above it all were magical, superhuman figures creating it all and making it work.

Covidiot News - Research Shows a Correlation Between Unmedicated Mental Illness and Low COVID-19 Vaccination Takeup

Researchers show a correlation between low COVID-19 Vaccine uptake and unmedicated mental health.

Unmedicated mental illness linked to lower COVID-19 vaccination levels | Karolinska Institutet

I've often thought, with such a high risk of catching COVID-19 and such a high risk of serious illness, both short and long term from 'long COVID', that people must be mad not to take up the offer of the initial vaccine and the regular boosters.

Now a Swedish team at the Karolinska Institutet have analysed data from seven studies in Sweden, Norway, Iceland, Estonia and Scotland and found a significant correlation between unmedicated mental illness and low vaccine take-up.

Refuting Creationism - Octopuses Show Leadership and Strategic Thinking Skills On Multi-Species Group Hunting Trips

© Eduardo Sampaio

Unlocking the secrets of multispecies hunting | Max Planck Institute of Animal Behavior

Strategic thinking, group leadership and planning is normally associated with a high level of intelligence and cognitive awareness of others in the group so the group can work efficiently to achieve a given objective.

So it will come as a surprise to those who cite these human abilities as evidence of human exceptionalism pointing to special creation as a species materially different o other species, that octopuses have been shown to exhibit the same skills when leading inter-species hunting groups consisting of themselves and one or more species of fish who collectively find hidden prey species which the octopus can flush out.

Unlike humans, however, leadership power in octopuses does not lead to despotism, as it often does with humans and octopuses show flexibility of roles, sometime letting one of the fish lead the group. However, there is evidence that octopuses control the dynamics within the group and enforce social hierarchies.

Unlike with human-led multi-species hunting groups which may include dogs and horses, where it is invariably a human who leads the group and who determines how the prey is shared if at all, with octopus-led groups, the octopus needs the cognitive skills and social awareness to understand the group dynamics and social structure across several species, but the prey is consumed by whoever catches it with no attempt to impose a precedence by the leader.

The objective is to capture the prey, not massage the ego of the leader.

These group hunting strategies allow goatfish to forage more effectively, taking advantage of teamwork to find hidden prey and exploit food resources in their habitats.