Showing posts with label Biology. Show all posts
Showing posts with label Biology. Show all posts

Sunday, 10 November 2024

Malevolent Designer News - How The SARS-CoV-2 Virus Steals Proteins From Our Immune System To Protect Itself


AI-Generated depiction of SARS-CoV-2 virus coated in stolen proteins.

ChatGPT4o
SARS-CoV-2 “steals” our proteins to protect itself from the immune system

Although COVD-19 has been mostly brought under control by medical science and the vaccination campaign, it still kills thousands of people a year, but nowhere near the volume of deaths during the initial wave when world-wide health services came close to collapse and economies were on the point of ruin.

But there is still much to learn about why it was so virulent and successful.

To an admirer of creationism’s divine malevolence it must have seemed like a triumph of design, as it filled hospitals, killed millions and wrecked economies, helped by its supporters in the evangelical Christian churches who opposed measures to mitigate the worse effect of the virus, and then opposed the vaccination campaign with lies, scare tactics and the most infantile conspiracy theories imaginable, to help ensure the virus got to as many people as possible.

Now, a team of researcher from the Medical University of Vienna together with colleagues from the Medical University of Innsbruck have discovered how the virus protects itself from the immune system creationists believe their putative intelligent designer designed to protect us from the virus’s and other pathogens it designs to make us sick, would grace the pages of another 'intelligent design' polemic by Michael J. Behe and his Deception Institute. It depends on several components of a system being present in a classic 'irreducibly complex' system that creationists wave around as 'proof' that the locally-popular creator god is real because they can't understand how it could have evolved.

Friday, 8 November 2024

Refuting Creationism - How Bird's and Bat's Wings Evolved


Unlike birds, the evolution of bats’ wings and legs is tightly coupled, which may have prevented them from filling as many ecological niches as birds.

Jason Koski/Cornell University
Bats’ and birds’ evolutionary paths are vastly different | Cornell Chronicle

Unlike an intelligent designer, the process of evolution can't go back to basic and start again. It is normally an additive process that has no control over what it has to work with and simply refines and improves on what is there. That's not to say new structures can't evolve but they do so by enlarging or remodelling something that was already there - the membrane of a bat's wing, for example is the webbing that exists in the tetrapod embryo between the fingers and toes, while the feathers of a bird's wing are highly modified scales. Both those structures evolved out of tissues that were already there. It would have been impossible for a bat to grow wing feathers instead of a membrane, for example, because the earliest mammals had lost their scales and evolved fur.

But of course, that would not have been a problem for an omnipotent intelligent designer who, having designed one wing would not need to set about designing another way to do the same thing.

So, constrained as evolution was by what it could use, it's not really surprising that birds and bats evolved on two different trajectories, with the only thing in common being flight (and of course the basic vertebrate skeletal body plan).

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


A WashU researcher hand pollinates Arabidopsis.

Photo: Joe Angeles/WashU
How plants evolved multiple ways to override genetic instructions - The Source - Washington University in St. Louis

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

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

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

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

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

Refuting Creationism - How Eggs Evolved Hundred of Millions of Years Before Chickens


Chromosphaera perkinsii resembles the early stages of animal embryo development during its multicellular life stage
DudinLab
The egg or the chicken? An ancient unicellular says egg! - Medias - UNIGE

Scientists believe they may have cracked the chicken and egg 'problem' that creationists have been fooled into thinking is a killer problem for the Theory of Evolution. With their child-like understanding of evolution, creationists can't imagine how species emerge over time from earlier species by a process of evolution and think that their mythical magic creation without ancestors is actually what happens, or at least what evolutionary biologists think happens. So, they imagine explaining how the first chicken hatched from the first egg before there was a chicken to lay it, is an insurmountable problem.

In fact, of course there never was a first chicken just as there never was a first human, and eggs are simply a phase in the life cycle of, in this case, chickens, so hens' eggs are chickens just as much so as adult hens are. The ancestral species that the Southeast Asian jungle fowl evolved from had been laying eggs ever since they diverged from the egg-laying avian dinosaurs that had evolved from the egg-laying theropod dinosaurs, etc, etc, back to the egg-laying tunicates and chordates in the Cambrian and their egg-laying ancestors...

Thursday, 7 November 2024

Common Origins - Marmoset and Human Brain Development


As in humans, infants of common marmosets interact with several caregivers from birth and are thus exposed to intensive social interaction.
Image: Judith Burkart/UZH
Brain Development Marmosets | | UZH

Creationists like to pretend there is nothing in common between humans and the rest of the animal kingdom because humans were magically created as the special creation of a god who made all the 'lower' animals for our use, then gave us dominion over everything. This makes creationists feel really important.

The truth however is that we have very much in common with other animals and particularly with the species to which we are most closely relates and with whom we share the most recent common ancestor as we and they evolved and diversified over the same period of time to arrive at our present state.

This is reflected in the nested hierarchies into which the different branches of the evolutionary tree can be arranged in, anatomy, physiology and DNA and in the way our bodies develop through embryology and continued into childhood.


And yet creationists insist we are not only a different species, but a different 'kind' of animal, even a different category of life altogether, even though none of the difference they insist apply to different taxons as evidence of evolution apply to humans in respect of the other great apes.

The common marmoset, Callithrix jacchus, and their evolutionary relationship to humans. The common marmoset (Callithrix jacchus) is a small primate species native to the forests and scrublands of northeastern Brazil. Known for its expressive face, tufted ears, and squirrel-sized body, it’s a popular species for scientific research, primarily because it shares some interesting genetic and behavioural traits with humans. Here’s an overview of its characteristics, behaviour, and evolutionary relationship with humans.

Physical Characteristics
  • Size: Common marmosets are small, weighing only about 300-400 grams, with a body length of 7-10 inches (18-25 cm) and a long, bushy tail.
  • Appearance: They have a distinctive look with white ear tufts, a small face, and wide eyes. Their fur is mostly brownish-grey with a mix of white and black, allowing them to blend into their arboreal habitat.
  • Hands and Feet: Like other New World monkeys, they have claws on most fingers (rather than flat nails like humans), which helps them cling to trees.

Habitat and Diet
  • Environment: Marmosets thrive in forests, especially in areas with dense foliage where they can find food and avoid predators. They’re highly adaptable and can be found in both natural and urbanized settings in Brazil.
  • Diet: They’re omnivores, feeding on tree sap, insects, fruits, and small animals. They use their specialized incisor teeth to gouge tree bark and access sap, which is a key component of their diet.

Social Structure and Behaviour
  • Social Groups: Marmosets live in family groups typically led by a dominant pair. Groups consist of 5-15 individuals, often including multiple generations, with cooperative care of young by both parents and other group members.
  • Communication: Marmosets are highly social and communicate through vocalizations, scents, and body language. They produce different calls depending on the context, and some sounds are ultrasonic, beyond human hearing range.
  • Reproduction: These primates have a unique reproductive system, where dominant females can suppress the reproduction of other females in the group. They often give birth to twins, and group members assist in raising the young, a rare behaviour in mammals that echoes human familial cooperation.

Relationship to Humans

Marmosets belong to the infraorder Simiiformes, which includes all monkeys and apes, meaning they’re more distantly related to humans than other primates like chimpanzees and gorillas, who are part of the hominoid lineage. However, they still share significant genetic similarities with humans—about 92% of their DNA. They’re one of the smallest primates often studied for insights into human aging, neurological diseases, and genetics because of several interesting parallels:
  • Brain and Behaviour: While their brains are much smaller than humans', they share many structural and functional aspects, including similar regions that govern emotions, memory, and sensory processing.
  • Lifespan and Aging: Marmosets age quickly for a primate, with a lifespan of around 12-16 years. They exhibit aging patterns similar to humans, including changes in the immune system, body mass, and cognitive abilities, which is valuable in studying aging processes.
  • Social and Parenting Behaviours: Cooperative parenting and close social bonds within groups mirror certain aspects of human social structures.

Conservation Status

The common marmoset is currently listed as "Least Concern" by the IUCN, though habitat loss and pet trade are concerns. They adapt well to different environments, which has helped their survival, but their populations are still vulnerable to ecological changes.

In summary, while common marmosets diverged from humans over 40 million years ago, their unique traits and social behaviours make them a valuable species for understanding certain aspects of human biology and psychology, providing insight into genetic, neurological, and social characteristics that bridge the gap between humans and other primates.
Now, as though to drive another nail into the coffin of that primitive superstition, scientists have just shown how the brains of humans and the common marmoset monkey follow parallel development, demonstrating their common origins.

Common marmosets and humans have similar prolonged periods of childhood where child care is shared amongst several adults, so the children experience intense socialisation as they develop juts as human children do, and because their brains are fundamentally the same as human brains, the same areas develop in the same way and at the same stage in their development:
Similarities in Brain Development Between Marmosets and Humans
In common marmosets, the brain regions that process social interactions develop very slowly, extending until early adulthood, like in humans. During this time, all group members are involved in raising the infants, which contributes to the species’ strong socio-cognitive skills.
The development of primate brains is shaped by various inputs. However, these inputs differ between independent breeders, such as great apes, and cooperative breeders, such as the common marmoset (Callithrix jacchus) and humans. In these species, group members other than the parents contribute substantially to raising the infants from birth onwards.

A group of international researchers led by Paola Cerrito from the University of Zurich’s Department of Evolutionary Anthropology studied how such social interactions map onto brain development in common marmosets. The study provides new insights into the relationship between the timing of brain development and the socio-cognitive skills of marmosets, in particular their prosocial and cooperative behaviours.

Prolonged learning from social interactions

The research team analysed brain development using magnetic resonance data and showed that in marmosets, the brain regions involved in the processing of social interactions exhibit protracted development – in a similar way to humans. These brain regions only reach maturity in early adulthood, allowing the animals to learn from social interactions for longer.

Like humans, immature marmosets are surrounded and cared for by multiple caregivers from birth and are therefore exposed to intense social interaction. Feeding is also a cooperative business: the immature animals are fed by group members and as they get older they have to beg for food because their mothers are already busy with the next offspring. According to the study, the need to elicit care from several group members significantly shapes brain development and contributes to the sophisticated socio-cognitive motivation (and observed skills) of these primates.

A model for human evolution

Given their similarities with humans, marmosets are an important model for studying the evolution of social cognition.

Our findings underscore the importance of social experiences to the formation of neural and cognitive networks, not only in primates, but also in humans. This insight could have an impact on various fields, ranging from evolutionary biology to neuroscience and psychology.

Paola Cerrito, first author
Department of Evolutionary Anthropology
University of Zurich, Zürich, Switzerland.

The early-life social inputs that characterize infants’ life in cooperatively breeding species may be a driving force in the development of humans marked social motivation.

Publication:
Abstract
Primate brain development is shaped by inputs received during critical periods. These inputs differ between independent and cooperative breeders: In cooperative breeders, infants interact with multiple caregivers. We study how the neurodevelopmental timing of the cooperatively breeding common marmoset maps onto behavioral milestones. To obtain structure-function co-constructions, we combine behavioral, neuroimaging (anatomical and functional), and neural tracing experiments. We find that brain areas critically involved in observing conspecifics interacting (i) develop in clusters, (ii) have prolonged developmental trajectories, (iii) differentiate during the period of negotiations between immatures and multiple caregivers, and (iv) do not share stronger connectivity than with other regions. Overall, developmental timing of social brain areas correlates with social and behavioral milestones in marmosets and, as in humans, extends into adulthood. This rich social input is likely critical for the emergence of their strong socio-cognitive skills. Because humans are cooperative breeders too, these findings have strong implications for the evolution of human social cognition.


INTRODUCTION
Strong social cognition and prosociality are, from a very young age, hallmarks of the human mind compared to the closest living relatives, the nonhuman great apes (1). Because of our peculiar life history, characterized by early weaning and extensive allomaternal care starting from very early in infancy, human development is embedded in a world filled with other individuals, including parents, siblings, and other family members. Thus, this is the context in which human toddlers’ strong social cognition and prosociality develops (2). It is this same period that is also the most important for the formation of the neural bases of higher-order social, emotional, and communicative functions (3). Not unexpectedly then, several independent lines of evidence, spanning neuroscience, pediatrics, primatology, and psychiatry, point to the fundamental role that the relative timing of brain development and social interactions have for the acquisition of social cognition and prosocial behaviors (4).

During ontogeny, total brain volume increases until reaching its adult levels. This volumetric increase is the product of gray matter (GM) volume (GMV) increase until a peak value is reached in childhood, after which it decreases concurrently with synaptic pruning and white matter volumetric increase (5). In addition, the ontogenetic trajectories of cerebral GM are heterochronous, such that both maximum GMV and GM reduction rate vary across brain regions. The importance of the temporal patterns of brain development in shaping the adult phenotype becomes apparent, for example, in the case of autism spectrum disorder (ASD). Deviations from the normal range of developmental timing of the cortex can profoundly affect socio-cognitive skills and are one of the main factors linked to the occurrence of ASD (3). Specifically, several studies have found that early brain overgrowth during the first years of life strongly correlates with ASD [e.g. (6)] and a meta-analysis of all published magnetic resonance imaging (MRI) data by 2005 revealed that the period of greatest brain enlargement in autism is during early childhood (7), with about a 10% volume increase compared to controls during the first year of life. Hence, individuals affected by ASD present an accelerated early-life brain growth and achieve a final brain volume that is not different from that of controls, but they achieve it earlier than controls. Recent works with human brain organoids has confirmed the accelerated maturation of the cortex in the ASD phenotype, especially interneurons (8, 9). Consequently, given this accelerated early-life brain development, fewer social inputs are available during the period when the GMV reduces to adult size and differentiates via experience-dependent pruning. Accelerated development of functional connectivity between certain brain areas [e.g., amygdala–prefrontal cortex (PFC)] can also be a consequence of early-life stress, which, in turn, can cause adverse physiological conditions such as increased anxiety and cortisol levels (10). Unfortunately, so far, nothing is known regarding the impact of changes in brain developmental timing within nonhuman species. That is, we do not know if, within a given nonhuman species, alterations in ontogenetic trajectories of the brain have an impact on the adult behavioral phenotype. However, comparative studies across species with different ontogenetic trajectories and social behaviors can help us shed light on the relationship between the two.

The importance of social inputs occurring during prolonged brain maturation and slow developmental pace has also been highlighted in the context of human evolutionary studies. The remarkable brain growth and development occurring postnatally in humans arguably allows the brain to be influenced by the social environment outside of the uterus to a greater extent than that seen in other great apes (11), who are not cooperative breeders (12). Hawkes and Finlay (13) show that, in addition to weaning our infants earlier than expected (based on allometric scaling with other life-history variables), human neonates have an especially delayed neural development, which is likely correlated with the energetic trade-offs stemming from the large size and high caloric demand of our brain (14). In addition, we observe that, in humans, compared to other great apes, myelination is much prolonged and continues well into adulthood (15).

Common marmosets (Callithrix jacchus) are cooperatively breeding platyrrhine monkeys. Like humans, but unlike other great apes (12), they rely on extensive allomaternal care and share many life-history traits (e.g., short interbirth intervals and a hiatus between menarche and first reproduction) with humans (16). They also show remarkable prosociality (4, 15) [much more than great apes (16)] and strong socio-cognitive abilities, which have been argued to correlate with cooperative breeding (1720). However, the neurobiological features underlying the socio-cognitive abilities promoting the prosocial behavior are poorly understood. Moreover, experimental research has shown that, in common marmosets (hereafter marmosets), there is a critical period for the development of social behaviors (21), although the relationship between developmental timing of the brain and these early-life social interactions is poorly understood.

Given these similarities with humans, marmosets are becoming an ever-more important model in neuroscience (2225) and particularly in research investigating the neurobiological and neurodevelopmental bases of social cognition. As in humans, immature marmosets are surrounded and cared for by multiple caregivers from the first day on. The entire family is typically present during birth, and oxytocin levels increase not only in mothers but also in all group members (26). Group members contribute appreciably to carrying the infants and, once infants start eating solid food, frequently share food with them. After a peak provisioning period, adults are increasingly less willing to share food with them (2729). During this period, intense and noisy negotiations over food are frequent, with immatures babbling and begging and adults eventually giving in—or not. Intriguingly, when doing so, immatures appear to take into account how willing individual adults are to share and will insist in more and longer attempts with adults who are generally less likely to refuse them. Soon after, immatures have to compete for attention and food not only with their twin sibling but also with the next offspring that are born far before they themselves are independent because, like in humans, marmosets are weaned early and mothers have their next offspring soon after (30). By now, the immatures still have not reached puberty; this only happens shortly before yet another set of younger siblings is born. Typically, with these new arrivals, the immatures start to act as helpers themselves and thus face the developmental task of switching from being a recipient of help to becoming a provider of help and prosocial acts (31). This is thus the developmental context in which marmosets’ socio-cognitive skills develop.

The goal of this study is to map these behavioral milestones specific to a cooperatively breeding primate to its region-specific brain development to better understand the social interactions in which infants engage during the differentiation period of brain regions selectively implicated in processing social stimuli. Our working hypothesis is that, like in humans, social interactions with several caregivers during this critical period profoundly contribute to the co-construction of the marmoset brain, the maturation of socially related associative areas, and therefore the emergence of prosocial behaviors. For that purpose, we sought to determine if there is a relationship between the temporal profile of the developing marmoset brain and the early-life social interactions that may help explain their sophisticated socio-cognitive skills at adulthood.

To compare the timing of brain development to that of these behavioral milestones and developmental tasks of attaining nutritional independence, we focused on brain regions that, in adult marmosets, are selectively activated by the observation of social interactions between conspecifics but not by multiple but independently behaving marmosets, as identified by Cléry et al. (32). We tested if these brain regions share similar developmental trajectories based on the developmental patterns of regional GMV. To potentially reveal a coordinated ontogenetic profile underlying the “tuning” of the social brain in marmosets, we then compared these neurodevelopmental patterns to longitudinal data of infant negotiations with caregivers in relation to food (as measured by the frequency of food begging). Last, because it is known that brain regions whose activations correlate with performance on a given task strengthen and get fine-tuned with age (33, 34), we assessed if there is stronger connectedness between areas that develop according to similar developmental trajectories and share similar response to social interaction stimuli.

We thus combined several types of previously published data from marmosets to provide a unified picture of structural brain development alongside the development of social interactions between infants and multiple caregivers necessary to ensure survival (infant provisioning). These included structural MRI (sMRI) data of GM of 53 cortical areas and 16 subcortical nuclei acquired from a developmental cohort (aged 13 to 104 weeks) of 41 male and female marmosets (35), functional MRI (fMRI) data mapping the brain areas activated by the observation of social interactions in marmosets (32), food sharing interactions in five family groups of marmosets including a total of 26 adults and 14 immatures [from 1 to 60 weeks of age (27)], and cellular-resolution data of corticocortical connectivity in marmosets obtained via 143 retrograde tracer injections in 52 young adult marmosets of both sexes (36).

Overall, we make the following predictions:
  1. P1: Cortical regions that show significantly stronger activation during the observation of social interactions (32) share similar structural neurodevelopmental profiles, which are distinct from those regions showing significantly stronger activation during the observation of nonsocial activities.
  2. P2: That those same brain regions showing a significantly stronger activation during the observation of social interactions exhibit a protracted development, reaching their adult volume later than the other regions.
  3. P3: The developmental trajectory of infant negotiations with caregivers in relation to food (as measured by the frequency of food begging) is more similar to that of brain regions responding more strongly to the observation of social interactions than to the other regions.
  4. P4: Functional connectivity is stronger between regions with similar developmental timing and response strength to the observation of either social or nonsocial behaviors and weaker between regions with different developmental timing and response strength.
If the brains of humans an marmosets are fundamentally similar and develop the same way, perhaps a creationist could explain in what way, apart from their tail and their claws in place of human flat finger nails, marmosets are a different 'kind' to humans, and then explain why the same reasoning doesn't place the great apes in the same 'kind' as humans.

Refuting Creationism - Domestication of Sheep Long Before 'Creation Week'


Eastern Anatolian sheep (Konya sheep), Ovis orientalis anatolica
Population History of Domestic Sheep Revealed by Paleogenomes | Molecular Biology and Evolution | Oxford Academic

I've previously noted how almost all our domestic animals have been selectively bred to improve upon their wild ancestors, sometimes to the extent that the wild ancestor is hardly recognisable as the same species. Indeed, in some instances, the genetic isolation of the wild and domestic varieties is so wide that they are regarded as different species.

And Bible-literalist creationists believe all animals were magically create out of dirt without ancestors, specifically for the use of man - which begs the question, why have we had to improve on them to make them fit for purpose? Did an omnipotent creator god not know what we would use them for?

In a recent post I describes the domestication of modern cattle from their wild auroch ancestors, which, because of their size and aggressive nature, were too dangerous for herding and milking, and the domestic breeds have evolved from a very small founder population, probably because of that difficulty so animals placid enough were only rarely found.

All that took place thousands of years before creationists believe there was an Earth with life on it, as is usual with almost all of Earth's and human history.

Now, as an added embarrassment to creationists, palaeogeneticists have managed to trace the ancestors (wild mouflons) of modern domestic sheep to discover where they were domesticated and how long ago. It goes without saying that it happened long before creationists believe the god magicked sheep out of dirt, in common with almost all of Earth's history.

Wednesday, 6 November 2024

Common Origins - Stem Species of Horseshoe Crab's Scorpions & Spiders From 450 Million Years Before 'Creation Week'


The Megacheiran candidate: Fossil hunters strike gold with new species | YaleNews

It's another of those 'non-existent' transitional fossils days that come round several times a month, as scientists find yet another fossil which is clearly of an intermediate species between two different taxons.

Today's example is of an intermediate or stem species from which horseshoe crabs, spiders and scorpions evolved. It lived about 450 million years before there was an Earth for it to live on, according to creationists superstition, which believe Earth was created by magic as a small flat planet with a dome over it between 6 and 10,000 years ago.

New Book - Refuting Creationism: Why Creationism Fails In Both Its Science and Its Theology


My latest book is now available in Kindle, paperback and hardcover versions.

It is a comprehensive rebuttal of the main planks in the creationist anti-science campaign, showign why creationism is not only based on bad science and deliberate misinformation and misrepresentation of science and scientists, from the Big Bang, through abiogenesis to evolution of species.

I present evidence not only for speciation, including creationists' favourite fallacies - 'no transitional fossils' and 'no evidence of "macro-evolution"'. I also expose the lies and disinformation with which the creationist website misinform their cult mebers.

And lastly I show how fundemental Bible-literalism is based on bad theology by regarding stories that can't possibly be true as literal science and real history, rather than the simple tales parochial Bronze Age pastoralists invented to brige the yawning chasms in their knowledge and understanding, setin the small part of the Middle East that was all they knew anythign about.

Sunday, 3 November 2024

Malevolent Design - How Sleeping Sickness Parasites Are 'Designed' to Evade Our Immune System


Sleeping sickness
Discovery Illuminates How Sleeping Sickness Parasite Outsmarts Immune Response | Johns Hopkins | Bloomberg School of Public Health

Trypanosoma brucei is a blood-borne eukaryote parasite that should leave believers in an intelligent designer, open-mouthed in admiration for its inventive genius. Christian fundamentalist creationists of the white supremacist persuasion should also admire the racist that, through T. brucei, has managed to keep large parts of Africa technologically under-developed due to the difficult in maintaining herds of domestic animals where the vector of these parasites - the tsetse fly - is common.

As a vector, the tsetse fly is a triumph of malevolent design which I mentioned in my popular book, The Unintelligent Designer: Refuting the Intelligent Design Hoax, but it would have been all for nothing without the nasty little T. brucei to cause sleeping sickness in humans and the debilitating disease "nagana" in cattle.

What creationist admires of the divine malevolence they believe designs these things should now be marveling at is the sheer brilliance of the design by which it manages to evade the immune system, which they believe was created by the same designer god which now regards his design as a problem to be overcome oh parasites like T. brucei can continue making Africans and their cattle sick.

Refuting Creationism - First Steps to Abiogenesis


Diagram of the atmospheric evolution of Earth's ancient atmosphere estimated by this study
© Yoshida et al.
Research News - How Life Began on Earth: Modeling Earth's Ancient Atmosphere | Tohoku University Global Site

The fact that living organisms arose on Earth from inorganic sources rather than being made of nothing by magic, is an indisputable fact because there are living organisms on Earth and the chemicals they are composed of all exist on the planet in inorganic minerals and gases. 'Life' contains nothing that 'non-life' doesn't contain.

This much we know, but what we don't yet know and can probably never know with certainty, is precisely how and where that happen. In fact, we don't even know whether it did all start in the same place at the same time because the reason there are two different prokaryote cells - bacteria and archaea - could be because life arose on Earth not once but twice, by two different processes in two different places at two different times.

What we have though is lots of working hypotheses in the process of being validated.

What role would Earth's atmosphere have played in abiogenesis? Earth's early atmosphere was crucial in creating the right conditions for abiogenesis—the process by which life originated from non-living matter. While the exact composition of Earth’s primordial atmosphere is still debated, its unique conditions likely contributed in several essential ways:
  1. Provision of Basic Building Blocks
    • Earth’s early atmosphere likely contained simple molecules like methane (CH₄), ammonia (NH₃), hydrogen (H₂), carbon dioxide (CO₂), nitrogen (N₂), and water vapor (H₂O). These molecules are rich in carbon, nitrogen, oxygen, and hydrogen—elements that are vital for organic compounds and, ultimately, for life.
    • When exposed to energy sources like ultraviolet (UV) radiation from the Sun or electrical discharges from lightning, these molecules could recombine into more complex organic molecules, such as amino acids and nucleotides, which are the building blocks of proteins and nucleic acids, respectively.

  2. Facilitation of Prebiotic Chemistry
    • Experiments like the famous Miller-Urey experiment in 1953 showed that simple gases (methane, ammonia, hydrogen, and water vapor) in an atmosphere subjected to electrical sparks could produce amino acids. This suggests that Earth’s early atmosphere could have been instrumental in initiating chemical reactions that synthesized complex organic molecules.
    • Without a protective ozone layer, the early atmosphere allowed substantial UV radiation to penetrate the Earth’s surface, providing the energy necessary to drive these prebiotic reactions.

  3. Supporting a Reducing Environment
    • The presence of reducing gases (such as methane and ammonia) would favor the formation of organic molecules because such conditions prevent the oxidation (and hence destruction) of organic compounds. Oxygen is highly reactive and can break down organic molecules, so the absence of free oxygen in the early atmosphere was likely a key factor that allowed these molecules to accumulate and react.
    • This reducing environment might have helped organic compounds to survive long enough to form stable, self-replicating systems.

  4. Encouraging Geochemical Interactions
    • The interaction between the early atmosphere and the oceans, along with geothermal activity like volcanic eruptions and hydrothermal vents, provided a diverse range of chemical environments. In particular, hydrothermal vents may have supplied essential minerals and additional energy sources, further driving complex chemical reactions that are believed to be important in the formation of life.
    • The cycling of materials between the atmosphere and oceans would have contributed to creating localized "hotspots" for prebiotic reactions.

  5. Protection and Concentration Mechanisms
    • The atmosphere also played a protective role by preventing the immediate dissipation of important compounds into space. It allowed the concentration of molecules and gases at Earth’s surface, increasing the chances of interactions among the essential precursors to life.
    • Early atmospheres may have helped regulate surface temperatures, preventing extreme fluctuations that would have been hostile to complex chemistry.

  6. Encouraging Self-Organization and Membrane Formation
    • Interactions in the early atmosphere could have contributed to the formation of lipid molecules that could aggregate to form primitive cell-like structures or vesicles. These structures would eventually help in containing and protecting reactions necessary for early metabolic pathways.
    • These early "proto-cells" or vesicles would have been necessary to create a boundary for molecular interactions, which is a critical step toward the organization needed for cellular life.

In summary, Earth’s early atmosphere provided a chemically conducive, energetically rich environment that fostered the synthesis and concentration of organic molecules necessary for abiogenesis. This atmosphere also shielded these nascent molecules, allowing them to organize and evolve toward increasingly complex systems, eventually leading to the first living organisms.
One of which is the precise details of the atmosphere on the Early Earth, which is important because it would have had a major impact on the rest of the environment in which life arose. To gain a better understanding of that, a team from Tohoku University, Tokyo University and Hokkaido University, Japan, led by Tatsuya Yoshida have succeeded in modelling that atmosphere, as explained in a Tohoku University press release and published in the journal Astrobiology:
How Life Began on Earth: Modeling Earth's Ancient Atmosphere
The key to unlocking the secrets of distant planets starts right here on Earth. Researchers at Tohoku University, the University of Tokyo, and Hokkaido University have developed a model considering various atmospheric chemical reactions to estimate how the atmosphere - and the first signs of life - evolved on Earth.

Ancient Earth was nothing like our current home. It was a much more hostile place; rich in metallic iron with an atmosphere containing hydrogen and methane.

Shungo Koyama, co-author
Graduate School of Science
Tohoku University, Sendai, Japan.
These molecules contain an important clue to how life was initially formed. When exposed to solar ultraviolet (UV) radiation, they undergo a chemical reaction that produces organics (also known as the "building blocks of life"). Part of these organics were precursors to essential biomolecules, such as amino acids and nucleic acids. However, understanding the role of UV radiation is difficult. Firstly, this type of atmosphere is unstable and likely underwent rapid changes due to atmospheric chemical reactions. Secondly, when UV radiation efficiently breaks down water vapour in the atmosphere and forms oxidative molecules, the precise branching ratio and timescale has not been determined. In order to address these issues, a 1D photochemical model was created to make accurate predictions about what the atmosphere was like on Earth long ago.

The calculation reveals that most hydrogen was lost to space and that hydrocarbons like acetylene (produced from methane) shielded UV radiation. This inhibition of UV radiation significantly reduced the breakdown of water vapour and subsequent oxidation of methane, thus enhancing the production of organics. If the initial amount of methane was equivalent to that of the amount of carbon found on the present-day Earth's surface, organic layers several hundred metres thick could have formed.

There may have been an accumulation of organics that created what was like an enriched soup of important building blocks. That could have been the source from which living things first emerged on Earth.

Tatsuya Yoshida, lead author
Graduate School of Science
Tohoku University, Sendai, Japan.

The model suggests that the atmosphere on ancient Earth was strikingly similar to what we see on current day neighbouring planets: Venus and Mars. However, despite their proximity, Earth evolved into a completely different environment. Researchers are trying to understand what makes Earth so special. As such, this model allows us to deepen our understanding of whether atmospheric evolution and the origin of life on Earth are unique or share common patterns with other planetary systems.

These findings were published in the journal Astrobiology on October 22, 2024.

Publication Details:
Tatsuya Yoshida, Shungo Koyama, Yuki Nakamura, Naoki Terada and Kiyoshi Kuramoto
Self-Shielding Enhanced Organics Synthesis in an Early Reduced Earth's Atmosphere Astrobiology DOI: 10.1089/ast.2024.0048
Abstract
Earth is expected to have acquired a reduced proto-atmosphere enriched in H2 and CH4 through the accretion of building blocks that contain metallic Fe and/or the gravitational trapping of surrounding nebula gas. Such an early, wet, reduced atmosphere that covers a proto-ocean would then ultimately evolve toward oxidized chemical compositions through photochemical processes that involve reactions with H2O-derived oxidant radicals and the selective escape of hydrogen to space. During this time, atmospheric CH4 could be photochemically reprocessed to generate not only C-bearing oxides but also organics. However, the branching ratio between organic matter formation and oxidation remains unknown despite its significance on the abiotic chemical evolution of early Earth. Here, we show via numerical analyses that UV absorptions by gaseous hydrocarbons such as C2H2 and C3H4 significantly suppress H2O photolysis and subsequent CH4 oxidation during the photochemical evolution of a wet proto-atmosphere enriched in H2 and CH4. As a result, nearly half of the initial CH4 converted to heavier organics along with the deposition of prebiotically essential molecules such as HCN and H2CO on the surface of a primordial ocean for a geological timescale order of 10–100 Myr. Our results suggest that the accumulation of organics and prebiotically important molecules in the proto-ocean could produce a soup enriched in various organics, which might have eventually led to the emergence of living organisms.

So, by the action if UV radiation from the sun on the inorganic molecules in Earth's early atmosphere for a period of some 10-100 million years, the oceans could have accumulated the basic building blocks for organic organisms to get started, and all th result of chemistry and physics with no magic gods involved at any point.

And, as usual with scientific discoveries, the truth is shown to have little resemblance to the origin myths the parochial Bronze Age pastoralists made up to fill the yawning chasm in their knowledge and understanding of the world around them, with their belief that Earth had only existed for a few thousand years, so were blissfully ignorant of the 99.9975% of its history that occurred before then.

Wednesday, 30 October 2024

Refuting Creationism - Walking With Dinosaurs 70-75 Million Years Before 'Creation Week'


Paleontologists discover Colorado ‘swamp dweller’ that lived alongside dinosaurs | CU Boulder Today | University of Colorado Boulder

Paleontologists dig for fossils in northwestern Colorado.
Credit: John and ReBecca Foster.
AI-Generated illustration of life in a Cretaceous swamp near the Western Inland Seaway

ChatGPT4o
For some reason creationists have a fixation with dinosaurs, probably because, deep down, they know their existence refutes the biblical nonsense of an Earth that's only 6-10,000 years old. After all, there is nothing quite like a 75 million-year-old fossil of a living creature for falsifying the idea that the Universe, Earth and life on it were all created in a single week, just a few thousand years ago.

So, their cult leaders are forever scraping around trying to find evidence that human beings and dinosaurs lived together and even that Jesus would have been familiar with T. rex or Diplodocus and was probably used to pterosaurs flying overhead. But of course, there is none - which was never a reason for a creationist to abandon a delusion.

What there is, however, is evidence that dinosaurs were around until about 66 million years ago then promptly went extinct to be replaced by birds and mammals as the dominant terrestrial life forms.

And now we have evidence of an early mammal living amongst dinosaurs in what if now Colorado, USA. Sadly, there is no evidence that the early mammal resembled Jesus or any other humans for that matter; it was more like a muskrat.

Sunday, 27 October 2024

Refuting Creationism - Producing 'Life' in The Laboratory


Biological systems serve as examples for the simplified artificial systems used to create synthetic cells.
Beeld Willy Arisky via Pexels
Creating a simplified form of life | News articles | University of Groningen

One of the more amusing questions creationists keep asking is how did 'life' come from non-life? Or more dogmatically, they claim 'life' from 'non-life' is impossible.

They then scuttle off to hide when asked to define, 'life' and state how it can be measured to assess whether something like a rock, a bacterium or a bowl of chicken soup has any life in it. It causes the same tactic of avoidance when asked to explain how dead food becomes living tissues during the process of digestion and metabolism, if that's impossible?

The problem is creationists have been brainwashed into thinking that 'life' is something magical; some special force that turns inorganic chemicals into 'living' structures. In fact, 'life' is a process involving atoms and molecules doing their chemistry according to the fundamental laws of chemistry and physics. And the function of the process is to manage entropy - the tendency of a system to become disordered - using the energy in nutrients.

And rather than 'life' being something magical which is magically inserted into a developing embryo at some unspecified day of its development from a zygote to a free-living organism, it's actually a continuation of the life processes of the egg and sperm that united to form the zygote. There never is a 'new life', just a continuation of the parent's entropy management process.

Refuting Creationism - Humans Were Butchering Elephants In India 300-400,000 Years Before 'Creation Week'


Rare fossils of extinct elephant document the earliest known instance of butchery in India – Research News
Having taken a short break from writing blog posts to work on a new book, I'm now taking a short break from writing a book to catch up on an accumulation of papers that refute creationism, not intentionally (few serious working scientists bother to do that nowadays) but quite incidentally by simply revealing facts that are entirely inconsistent with creationist dogmas.

This news release, for example, exposes the fact that there were humans butchering elephants in India between 300,000 and 400,000 years ago in that 99.9975% of Earth's history that happened before creationists believe there was even an Earth for people and elephants to live on.

The evidence is the cut marks on the remains of a three extinct giant elephants, Palaeoloxodon turkmenicus, which died near a river at what is now Pampore in the Kashmir Valley. Soon after they died, they were covered in sediment and buried along with 87 stone tools that had been used to butcher them along with the bone flakes that show the bones were struck in exactly the right way to extract the marrow. The butchers clearly knew what they were doing.

Friday, 18 October 2024

Refuting Creationism - Seven New Frogs In Madagascar And How They Evolved


Boophis marojezensis. Now know to be 8 different species.

Seven New Frog Species Discovered in Madagascar: Sounds Like Something from Star Trek – University of Copenhagen

An international research team have discovered seven new species of tree frog in Madagascar, all members of the Boophis genus, previously thought to be a single species. They are characterized by their distinctive sounds. Their high-pitched whistles are unlike the sounds normally associated with frogs and sounding more like something from science fiction prompted their discoverers to give them all names based on Star Trek captains: Boophis archeri (Archer), Boophis burnhamae (Burnham), Boophis janewayae (Janeway), Boophis kirki (Kirk), Boophis picardi (Picard), Boophis pikei (Pike), Boophis siskoi (Sisko).

The basis for the revised taxonomy is two-fold - genetic and bioacoustic. Although there are all morphologically similar, differing mainly in size, the genetic evidence shows they have diverged into genetically isolated populations and the acoustic evidence shows how genetic separation is maintained by a prezygotic barrier to hybridization. The high pitch of their calls is believed to make them audible above the sound of running water in their normal environment.

Speciation in Progress - A Genetically Isolated Population of Harbor Seals


Alaska’s Iliamna Lake harbor seals commonly move more than 200 kilometers. Researchers hypothesized that they move regularly between freshwater and marine habitats.
Photo credit: David Withrow, NOAA Fisheries.
FAU | Iliamna Lake Harbor Seals Genetically Isolated from Pacific Ocean

The Iliamna Lake harbor seals are one of only a handful of seals that live wholly in fresh water, the best-known example of which is the Lake Baikal seal in Russian Central Asian.

The Alaskan seals have probably been isolated for thousands of years having entered the lake when it was connected to the Pacific before it became isolated from the ocean. The seals have lived there in isolation ever since. These are the classic conditions for allopatric speciation to occur as the founder effect, genetic drift and local environmental selectors cause them to diverge genetically from their parent population in the Pacific.

Tuesday, 15 October 2024

Unintelligent Design - The Blunder That Causes Cancers


Ludwig Cancer Research

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

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

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

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

Monday, 14 October 2024

Unintelligent Design Or Sheer Malevolence? - Defective Sperm Puts Mother And Baby At Risk


AI-generated graphic illustrating preeclampsia
(with AI spelling)
ChatGPT4o
Defective sperm doubles the risk of preeclampsia | Lund University

Christian superstition insists that every person conceived is a creation of their omniscient, omnipotent god who knows and has always known, exactly who is going to be born and has an oven-ready plan for their entire existence. Each baby conceived was exactly as the Christian god intended, down to the last detail of the DNA Exactly which sperm fertilizes which egg when, is part of the god's omniscient, perfect plan.

Leaving aside the absurdity of throwing millions of sperms at a single egg to produce that conception, when only a predetermined one was going to be the winner in order to produce the predetermined genome, when a single sperm would have been just as effective, we are left with the disturbing idea that any and all genetic defects were the intended outcome of that conception; the intention of a supposedly omnibenevolent god.

Now, it might, in fact it definitely is possible for a Christian to imagine some ultimate good will come from a child with a genetic defect, but what if a defect in the sperm causes harm not just to the baby, but to the mother? Are we to conclude that a mother whose life is put at risk by a defective sperm from her partner was the intended victim of an 'all-loving' god? What possible good can come from a mother's (and almost invariably her baby's) life being in danger from something beyond her control? What possible good can come from preeclampsia?

Refuting Creationism - How A Beetle Evolved To Eat Toxic Plants


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

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

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

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

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

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

Saturday, 12 October 2024

Malevolent Design - How Chlamydia Is 'Designed' to Cause Maximum Sufferring.


Schematic representation of how a C. pneumoniae cell infects a human cell. The bacterium injects the protein SemD (green) into the cell, which activates the cell protein N-WASP, which in turn initiates vesicle formation.
Credit: HHU/Fabienne Kocher.
Universität Düsseldorf: Original or copy: How Chlamydia manipulate the host cell

The problem of parasites for creationists is one that, despite the best efforts of apologists like Michael J Behe of the Deception Institute, just won't go away.

Sadly, Behe shot himself in the foot with his original claim to have proven 'intelligent [sic] design in living organisms with his choice of the bacterial flagellum in E. coli, where he persuaded his willing audience that these nasty little pathogens had been intelligently designed - and by unspoken assumption, designed by the locally-popular god.

Now creationists wave his 'proof' of design as evidence for their creator god because only their god is capable of creating living organisms.

But, with characteristic double-think, creationists also argue that their god is omnibenevolent, so something else must have created parasites like E. coli, and, courtesy again of Michael J. Behe, they cite 'Sin' causing 'genetic entropy' and the absurd idea of 'devolution' this supposedly causes, as the cause of parasites and pathogens (but not the bacterial flagellum, obviously!).

The problem with that notion is that they need to do their double-think trick one more time and believe that a trait with improves a pathogens ability to live and reproduce in its host makes it somehow less perfect that one without that trait. So, in the creationist's world, an improvement is a move away from perfection!

But, with a cult that appears to believe learning is a move away from the 'perfection' of pristine ignorance (from whence comes expertise in all aspects of science), that's probably not too difficult a feat of mental gymnastics for a creationist to perform.

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