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

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

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.

Malevolent Design - What Creationism's Divine Malevolence Chose Not To Give Us But Lets Us To Suffer Instead

Tail fin regeneration at 6 hours after injury. Fluorescence microscopy image shows skin cells (magenta), actively dividing cells (cyan), and transiently activated skin cell states (yellow).

African killifish, Nothobranchius furzeri

Stowers scientists uncover a… | Stowers Institute for Medical Research

"God never restore an amputated limb". This fact, better than anything, illustrates either the limit of the power of prayer and 'faith healing' or the limit of power of the god being prayed to. There are no authenticated examples of a restored limb or of the spontaneous healing of a transected spinal cord, despite the steady supply of victims seeking a cure to 'miracle' site such as Lourdes, and the fervent prayers of victims and the families. (We can dismiss the 'Miracle of Calanda' as far too transparent a hoax to be taken seriously.) It just never happens!

An omniscience, omnipotent, omnibenevolent designer would work to minimise the suffering in its creation. To do otherwise tells us that the alleged creator is:

• Unaware of it, in which case it is not omniscient.
• Aware of it but powerless to prevent it, in which case it is not omnipotent.
• Aware of it but indifferent to it, in which case it is not omnibenevolent.

This paradox, known as Epicurus paradox, has never been successfully answered by theists other than by hand-waving dismissals and mumblings about 'inscrutability' and 'divine plans which are not given to mankind to understand'. IOW, their god is omniscient, omnipotent and omnibenevolent even though it doesn't always behave that way and the results of its actions or inaction tell us otherwise.

The facts are not permitted to overrule the sacred dogma - which is creationism in a nutshell.

If you believe in the creationist notion of magic creation, where every species was designed according to some perfect plan, then the fact that some species lack abilities with which other species have, and with which clearly the putative designer knew how to provide, should raise some questions about why the designer made the choice not to provide them.

And if, as most self-centered fundamentalist believe, humans were at the apex of this creator god's design, then it should have the best of everything, and yet there are a myriad of examples of other species being better than humans. (See the AI panel for examples):

Many species have abilities which would be beneficial to humans if we too possessed them* Do you have a list of examples of this? Yes! Many species have evolved unique traits that, if humans possessed them, could greatly enhance our abilities or solve certain challenges. Here's a list of some remarkable examples:

1. Regeneration (Axolotl, Starfish)
   • Benefit: The ability to regrow limbs or even vital organs.
   • Species Example: Axolotls and starfish can regenerate entire body parts. This could help humans recover from amputations, spinal cord injuries, or organ damage.
   
   
2. Echolocation (Bats, Dolphins)
   • Benefit: Enhanced navigation and perception in low-visibility conditions.
   • Species Example: Bats and dolphins use echolocation to navigate in darkness or murky waters. This would allow humans to navigate dangerous environments or see without light.
   
   
3. Photosynthesis (Plants, Algae)
   • Benefit: The ability to convert sunlight directly into energy.
   • Species Example: Plants and algae can photosynthesize, which could eliminate the need for food in some situations, reducing hunger and energy concerns.
   
   
4. Extreme Durability (Tardigrades)
   • Benefit: Surviving extreme environments such as radiation, freezing temperatures, dehydration, and even space.
   • Species Example: Tardigrades (water bears) can endure near-death conditions. This would make humans far more resistant to extreme climates or space travel.
5. Camouflage (Chameleons, Cuttlefish)
   • Benefit: Blending into environments for protection or hunting.
   • Species Example: Chameleons and cuttlefish can change color and texture. Humans with this ability could avoid detection in dangerous situations or during combat.
   
   
6. Electricity Generation (Electric Eel)
   • Benefit: Generating electrical energy for self-defense or powering devices.
   • Species Example: Electric eels produce electric shocks. This could allow humans to power small devices or defend against threats using natural electricity.
   
   
7. Hyper-Speed Healing (Deer Antlers, Certain Lizards)
   • Benefit: Rapid recovery from wounds and injuries.
   • Species Example: Deer regrow antlers each year at an incredibly fast rate. Some lizards regrow tails. Enhanced human healing could lead to faster recovery after surgeries or injuries.
8. UV Vision (Birds, Insects)
   • Benefit: Seeing ultraviolet light to detect environmental changes or patterns invisible to the human eye.
   • Species Example: Many birds and insects can see ultraviolet light, which helps them find food and mates. Humans with this ability could have enhanced perception of their surroundings.
   
   
9. Extreme Longevity (Greenland Shark, Tortoises)
   • Benefit: Significantly extended lifespan.
   • Species Example: The Greenland shark can live for centuries, and tortoises often live over 100 years. If humans possessed this trait, we could extend lifespans, allowing more time for knowledge acquisition and creativity.
   
   
10. Poison Resistance (Mongoose)
    • Benefit: Immunity to toxins and venoms.
    • Species Example: The mongoose is resistant to snake venom, allowing it to hunt poisonous snakes. This could protect humans from dangerous toxins or make certain medical treatments less risky.
    
    
11. Hibernation (Bears, Ground Squirrels)
    • Benefit: Surviving long periods without food and conserving energy.
    • Species Example: Bears and ground squirrels hibernate during the winter. Humans with this ability could endure long periods without food, which would be useful in survival situations or space travel.
    
    
12. Rapid Adaptation to High Altitudes (Bar-Headed Geese)
    • Benefit: Increased oxygen efficiency in high-altitude or low-oxygen environments.
    • Species Example: Bar-headed geese can fly over the Himalayas at altitudes that would be deadly to most animals. This would allow humans to thrive in high-altitude environments or survive with less oxygen.
    
    
13. Flight (Birds, Bats)
    • Benefit: Self-powered aerial travel.
    • Species Example: Birds and bats have evolved to fly, which could enable humans to travel independently through the air, revolutionizing transportation and exploration.
    
    
14. Magnetic Field Detection (Migratory Birds, Turtles)
    • Benefit: Natural GPS and navigation using Earth’s magnetic fields.
    • Species Example: Some birds and turtles can detect the Earth’s magnetic field for navigation during migration. Humans could use this ability for more accurate navigation without technology.
    
    
15. Temperature Regulation (Camels, Arctic Foxes)
    • Benefit: Surviving extreme heat or cold without external aid.
    • Species Example: Camels can endure extreme desert heat, and arctic foxes thrive in freezing conditions. Humans with this ability could survive in more hostile climates with ease.
    
    

These abilities, if adapted for human use, could offer enormous benefits in fields ranging from medicine and survival to transportation and energy efficiency.

It's in the area of rapid repair and regeneration that research is being concentrated in order to gain a scientific understanding of the processes involved and particularly why they have been lost. One recent example was the discovery that zebra fish can not only repair a transected spinal cord but can regenerate a missing section of their spinal cord and restore it to full functionality.

And now we have another piece of research into how the African killifish can regenerate a missing section of fin, and in particular how the process restores just the missing tissues, no more and no less. This research from the Stowers Institute for Medical Research has just been published, open access, in the Cell Press journal iScience and announced in a Stowers Institute press release:

Stowers scientists uncover a critical component that helps killifish regenerate their fins

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The findings are a step toward closing the gap on how we could one day deploy regenerative medicine in humans

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Spontaneous injuries like the loss of a limb or damage to the spinal cord are impossible for humans to repair. Yet, some animals have an extraordinary capacity to regenerate after injury, a response that requires a precise sequence of cellular events. Now, new research from the Stowers Institute for Medical Research has unveiled a critical timing factor—specifically how long cells actively respond to injury—involved in regulating regeneration.

A recent study published in iScience on September 20, 2024, sought to understand exactly how an organism knows how much tissue has been lost post-injury. Led by former Predoctoral Researcher Augusto Ortega Granillo, Ph.D., in the lab of Stowers President and Chief Scientific Officer Alejandro Sánchez Alvarado, Ph.D., the team investigated how African killifish properly regrow their tail fin following damage. By analyzing tissue dynamics during regrowth, they found that in addition to known factors, including how many cells are participating and where they are located, the length of time cells spend engaged in the repair process is also key.

African killifish, Nothobranchius furzeri

One of the greatest unsolved mysteries of regeneration is how an organism knows what has been lost after injury. Essentially, the study points to a new variable in the equation of regeneration. If we can modulate the rate and the length of time that a tissue can launch a regenerative response, this could help us devise therapies that may activate and perhaps prolong the regenerative response of tissues that normally would not do so.

Dr. Alejandro Sánchez Alvarado, senior author.
Stowers Institute for Medical Research,
Kansas City, MO, USA.

Shortly after a killifish tail injury, the remaining tissue needs to know how much damage has occurred. Then, this tissue must enlist the right number of repair cells to the site of injury for the right amount of time. Damage sensing, repair cell recruitment, and timing somehow must work together to regrow the tail.

If an animal that can regenerate extremities, like a tail, loses just a tiny portion, how does it know not to regenerate a whole new tail but just the missing piece?

Dr. Alejandro Sánchez Alvarado.

To address this question, the team probed different locations of injury in the killifish tail fin.

Tail fin regeneration at 6 hours after injury. Fluorescence microscopy image shows skin cells (magenta), actively dividing cells (cyan), and transiently activated skin cell states (yellow).

They found that skin cells both near an injury and in distant, uninjured regions launch a genetic program that primes the whole animal to prepare for a repair response. Then, skin cells at the site of injury sustain this response and temporarily change their state to modify the surrounding material called the extracellular matrix. Ortega Granillo likens this matrix to a sponge that absorbs secreted signals from the injured tissue that then guides repair cells to get to work. If the signals are not received or not interpreted correctly, the regeneration process may not restore the tail’s original shape and size.

We very clearly defined when and where—at 24 hours post-injury and in the extracellular matrix—the transient cell state is acting in the fin tissue. Knowing when and where to look allowed us to make genetic disruptions and gain a better understanding of the function of these cell states during regeneration.

Augusto Ortega Granillo, first author
Stowers Institute for Medical Research,
Kansas City, MO, USA.

To investigate whether these distinct cellular states communicate information to the extracellular matrix—the supportive structure surrounding cells—during the repair process, the researchers employed the CRISPR-Cas9 gene editing technique. They specifically targeted a gene known to modify the extracellular matrix, as they had observed its activation at the onset of the regeneration response. By disrupting the function of this gene, the team aimed to determine its role in relaying information from cells to the matrix during regeneration.

These modified animals no longer know how much tissue was lost. They still regenerated, but the speed of tissue growth was deficient. This is telling us that by changing the extracellular space, skin cells inform the tissue how much was lost and how fast it should grow.

Augusto Ortega Granillo.

Tail fin regeneration at 7 days post-injury. Fluorescence microscopy image shows skin cells (magenta), actively dividing cells (cyan), and transiently activated skin cell states (yellow), where these cell states are localized now only in the very tip of the fin.

Indeed, the speed and amount of tissue regenerated in these genetically modified killifish increased regardless of whether the tail injury was mild or severe. This finding opens the possibility that cell states that modify the matrix increase regenerative regrowth. If the cell states could be adjusted, it may be a way to stimulate a more robust regeneration response.

From an evolutionary perspective, understanding why certain organisms excel at regeneration while others, such as humans, have limited regenerative abilities is a driving force in the field of regenerative biology. By identifying general principles in organisms with high regenerative capacity, researchers aim to potentially apply these insights to enhance regeneration in humans. This comparative approach not only sheds light on the evolutionary aspects of regeneration but also holds promise for developing novel therapeutic strategies in regenerative medicine.

Our goal is to understand how to shape and grow tissues. For people who sustain injuries or organ failure, regenerative therapies could restore function that was compromised during illness or following injury.

Augusto Ortega Granillo.

Post-injury fin growth shown over time in the African killifish.

via GIPHY

Additional authors include Daniel Zamora, Robert Schnittker, Allison Scott, Alessia Spluga, Jonathon Russell, Carolyn Brewster, Eric Ross, Daniel Acheampong, Ning Zhang, Ph.D., Kevin Ferro, Ph.D., Jason Morrison, Boris Rubinstein, Ph.D., Anoja Perera, and Wei Wang, Ph.D.

Highlights

• Amputation position changes tissue-wide proliferation response
• Regeneration deploys transient regeneration-activated cell states.
• Sqstm1 slows down regenerative outgrowth in distal injuries.
• Prediction: positional information is transduced by ECM changes during regeneration.

Summary
Injury is common in the life of organisms. Because the extent of damage cannot be predicted, injured organisms must determine how much tissue needs to be restored. Although it is known that amputation position affects the regeneration speed of appendages, mechanisms conveying positional information remain unclear. We investigated tissue dynamics in regenerating caudal fins of the African killifish (Nothobranchius furzeri) and found position-specific, differential spatial distribution modulation, persistence, and magnitude of proliferation. Single-cell RNA sequencing revealed a transient regeneration-activated cell state (TRACS) in the basal epidermis that is amplified to match a given amputation position and expresses components and modifiers of the extracellular matrix (ECM). Notably, CRISPR-Cas9-mediated deletion of the ECM modifier sequestosome 1 (sqstm1) increased the regenerative capacity of distal injuries, suggesting that regeneration growth rate can be uncoupled from amputation position. We propose that basal epidermis TRACS transduce positional information to the regenerating blastema by remodeling the ECM.

Graphical abstract

Introduction
For many organisms, including humans, the preservation of anatomical form and function depends in great part on the periodic elimination and restoration of cells. This process is referred to as tissue homeostasis. In mammals, the rate of tissue homeostasis varies widely across organs; i.e., self-renewal of the intestinal and lung epithelia has been estimated to take 5 days and up to 6 months, respectively.^1,2 As such, specific mechanisms exist in adult tissues responsible for sustaining specific rates of tissue homeostasis to mitigate normal, physiological wear and tear. The intricate balance of tissue homeostasis can be severely disrupted by injury. During their lifespans, all multicellular organisms are likely to experience some kind of injury. Unlike physiologically regulated tissue homeostasis, injuries and the extent of the damage incurred are unpredictable. This creates a challenge for organisms to monitor and deploy an anatomically specific regeneration response proportional to the magnitude of the injury.

During regeneration, a specialized structure known as blastema forms through the rapid proliferation and subsequent differentiation of multiple cell types to restore the missing tissue.³ For instance, it has been shown that osteoblast differentiation is accelerated in regenerating fins. Newly differentiated osteoblasts appear 4 days earlier in regenerated tissue compared to the pre-existing tissue, also referred to as the stump.⁴ It is not known whether there is a regeneration-specific osteoblast differentiation program or if differentiation trajectories used during tissue homeostasis can be accelerated during regeneration. Regeneration has also been shown to alter rates of tissue growth. In vertebrates, the speed of regeneration differs when different amounts of tissue are lost.⁵ For example, fish caudal fin amputations close to the base of the appendage, a proximal amputation, display higher growth rates than amputations performed further away from the base of the fin, a distal amputation.^6,7

To date, it is not known how injured tissues detect amputation position and what processes may encode positional information during regeneration. Efforts to identify deposited positional information prior to injury led to the identification of transcripts and proteins that are differentially expressed along the proximo/distal (P/D) axis in the intact zebrafish fin.⁸ However, these differences are lost during regeneration, leading to the hypothesis that positional information must be redefined during regeneration.⁸ Alternatively, it has been proposed that migratory progenitor cells retain positional identity from their locations prior to injury. This opens up the possibility that progenitors communicate positional information to the new tissue to determine regeneration growth rate.^9,10 But the mechanism of positional information retention and potential relay to other cells has not yet been identified.

Furthermore, it has been suggested that positional information is encoded in the tissue within the thickness of the bone at the plane of amputation^11,12 and that mechanical distension of the epidermis during wound closure constitutes a direct measurement of the amputation position by the wound epidermis. A wave of mechanical distension in the basal epidermis was shown to propagate to different lengths according to the amputation position.¹³ To add to the complexity of this process, it was shown that there is a 2-day time window at the beginning of regeneration when positional information is possibly reestablished de novo. If blastemas are impaired in their proliferative ability during this time window, the wrong positional information is encoded in the regenerated appendage, so multiple rounds of regeneration consistently grow abnormal tissue sizes in the absence of any further impairment of proliferation.¹⁴ It is conceivable that independent mechanisms of positional information coordinating the regenerative response exist. There may be redundant and complementary means to adequately relay and deposit positional information into the new tissue. This would ensure that form and function are restored following diverse and unpredictable injury.

Here, we deploy spatial and temporal analysis of proliferation and single-cell transcriptomic profiling to measure molecular and cellular changes along the caudal fin P/D axis. We chose the African killifish Nothobranchius furzeri for our studies because of the reduced complexity of differential gene expression and gene regulation compared to the more broadly utilized zebrafish.¹⁵ We show that amputation position influences the length of time (persistence) it takes for tissues to progress through regeneration. We report on the discovery of a basal epidermal subpopulation that shows a transient regeneration-activated cell state (TRACS) likely to participate in mediating positional information in the regenerating blastema. Altogether, our study demonstrates that amputations along the P/D axis result in defined spatial and temporal rates of proliferation. We propose that such dynamics likely initiate the proportional changes in tissue architecture that may ultimately define the scale and rate of regeneration of amputated tissues.

It's worth repeating what the Sowers Institute news release said at this point:

From an evolutionary perspective, understanding why certain organisms excel at regeneration while others, such as humans, have limited regenerative abilities is a driving force in the field of regenerative biology.

No doubts there then on the part of the authors that the facts can't be explained by evolution and are better explained by creationism's childish superstition, and of course the Theory of Evolution explains it fully without the need to explain why something which evolved for one species or from a common ancestor is retained by one line but not another in terms of the intention, malevolent, benign or indifferent, of the mindless, directionless natural process that drives it.

Creationism, on the other hand, has to try to reconcile the reality with what they believe about their putative designer, which includes explaining why, if it isn't malevolent, it designs organisms to look as though a malevolent designer designed them.

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Malevolent Design - A Newly-Discovered Gut Bacterium That Suppresses Immunity!

Drs. Thaddeus Stappenbeck, M.D., Ph.D., (left) and Qiuhe Lu, Ph.D., in the lab.

Cleveland Clinic Discovers Bacterium Causing Gut Immunodeficiency

The human gut, like that of other mammals, birds and vertebrates in particular and the gut of many insects and worms, in fact any organism with a moth and an anus, is an ideal environment for a whole host of other organisms, most of which will have co-evolved with humans and have been with us since our ancestors were small insectivores, skulking in the dark of the night to avoid dinosaurs and predatory proto-birds.

They for a complex and dynamic ecosystem of competing and cooperating bacteria, viruses, fungi and protozoa which exists in a more or less stable balance of arms races, predation and symbiosis.

Malevolent Design - How Bacteria Are 'Designed' With a Protective Coat

Bacterial cell wall structure

AI generated (ChatGPT40)
With apologies for the spelling!

Study unveals a novel protective mechanism in bacterial cell wall

Structure of gram-negative cell envelope

By Jeff Dahl - Own work, CC BY-SA 4.0, Link

Here's a conundrum for creationists who have fallen for the Deception Institute's biologically nonsensical excuse for parasites - that they weren't designed by the only entity capable of designing living organisms, but by a process of 'devolution' [sic] from an initial created perfection caused by 'genetic entropy'. This excuse was hastily cobbled together by Michael J Behe when he realised his 'intelligent [sic] design' notion was making creationism's putative creator look like a pestilential malevolence, especially after Behe had gone to such lengths and scuppered his academic credentials with how 'irreducibly-complex-therefore-magically-created' E. coli flagellum, then his claim that resistance to antimalarial drugs in Plasmodium falciparum must have been designed.

The problem was that having produced an excuse for parasites that was designed to appeal to religious fundamentalists, Behe inadvertently abandoned any pretense that creationism is science not religion, by incorporating Christian fundamentalism in his excuse - initial created perfection followed by 'genetic entropy' caused by 'Sin', which depends on a belief in 'The Fall' and original sin.

Although Behe insists he's not a Christian fundamentalist YEC, his books invariably appeal to, and reinforce the prejudices of, those who are, and feed their insatiable demand for validation from the science they despise and continually attack as biased/Satanic/lies/flawed, etc.

But now we have research that shows how bacteria are 'designed' with a protective cell wall which helps them resist enzymes which would otherwise destroy them. Defensive structures and processes cannot logically be described as 'devolutionary', they therefore either evolved naturally, or, if you reject evolution in favour of intelligent [sic] design, were intelligently designed to make the bacteria better at making us sick, i.e., with malevolent intent.

Refuting Creationism - Tiny Shells Hold a Record of Sea Temperature Changes 10,000 Years Before 'Creation Week'

Earth's last ice age may provide crucial insights into the future behavior of El Niño events,

Foraminifera fossils

Ice age clues point to more extreme weather patterns in our future | University of Arizona News

With so much of Earth history occurring before creationism's little god allegedly created a small flat planet with a dome over it in the Middle East, it's useful to be able to recover data on global events such as climate change and sea temperature changes that can be projected into the future to predict what changes we can expect.

The 'El Niño' is a climate phenomenon that has a profound effect on world climate. It occurs every 2-7 years and is characterized by a warming of the sea surface in the central and eastern Pacific Ocean. It changes ocean currents, atmospheric humidity and rainfall, and jet streams that drive weather patterns, so understanding when these events occurred in the past and mapping them onto known climate patterns can help us predict future weather patterns.

Now scientist at the University of Arizona have developed a model for predicting how El Niño affects global weather patterns which needs to be validated against actual data, so they have analyzed the record of sea temperature change recorded in deposits of tiny foraminifera shells in ocean sediment, going back to the last Ice Age, 10,000 years before creationists think Earth existed.

Of course, the reason was not to refute creationism - it does that incidentally - but to provide a longer history on which to base future predictions than are currently available.

Malevolent Design News - Researchers Show Another Of The Devine Malevolence's Nasties - HIV's Little Brother HTLV-1

HTLV-1 virus-like particle

© Nature Structural & Molecular Biology/Obr et al.

A viral close-up. HTLV-1 virus-like particles with a close-up view of the building blocks forming the viral lattice.

© Nature Structural & Molecular Biology/Obr et al.

ISTA | A Viral Close-Up

Not content with increasing the suffering and misery in the world with its brilliantly designed Human Immunosuppressive Virus (HIV), creationism's favourite pestilential malevolence also produced a related virus, Human T-lymphotropic virus type 1 (HTLV-1).

HIV is a deadly, (normally) sexually-transmitted retrovirus which medical scientists has managed to bring under control, but not cure or eradicate or even produce a vaccine against. What they have produced are anti-retroviral drugs which prevent the virus replicating so it doesn't kill its victims and, more importantly it isn't passed on to sexual partners.

Sadly for creationists, they have been denied the excuse of 'genetic entropy' and 'devolution' to absolve their favourite sadist of responsibility for HIV because they have also jubilantly declared it to be a 'gay plague' sent by their 'loving' god to punish homosexuals for behaving how it designed them to behave.

HTLV-1 is not nearly so deadly as HIV when left untreated, but, being closely related to it, it uses the same modus operandi as HIV and in some cases causes cancer and neurodegenerative disease that can be more deadly and debilitating than HIV treated by anti-retroviral drugs.

Refuting Creationism - Evolutionary History of the Grape is Enough to Make Creationists Wine

Nekemias mucronata sp. nov. Complete leaflet
Scale bar: 1 cm.

Tosal, A. Vicente, A. & Denk, T. (2024)

Nekemias mucronata fossil lateral leaflets from the collection of the Natural Science Museum of Barcelona.

Reconstructing the evolutionary history of the grape family

For today's refutation of creationism, we have the history of the grape, stretching back to between 40 and 23 million years before creationists think Earth was created.

Like almost everything else about the history of life in Earth, the evolution of the modern grape took place in the 99.9975% of time that preceded 'Creation Week' when creationism's little god made a small, flat planet with a dome over it in the Middle East.

This history has now been reconstructed by a team of three palaeontologists led by Aixa Tosal, from the Faculty of Earth Sciences and the Biodiversity Research Institute (IRBio) of the University of Barcelona, with Alba Vicente, also from the University of Barcelona, and Thomas Denk from the Swedish Museum of Natural History (Stockholm).