ElShamah - Reason & Science: Defending ID and the Christian Worldview
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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my library, where I collect information and present arguments developed by myself that lead, in my view, to the Christian faith, creationism, and Intelligent Design as the best explanation for the origin of the physical world.

# Chimps, our brothers ?

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#### Otangelo

Estimating the Timescale of Human Genomic Deletions

By Bill Hathawayapril 27, 2023 Deletions’ from the human genome may be what made us human https://news.yale.edu/2023/04/27/deletions-human-genome-may-be-what-made-us-human

The loss of about 10,000 bits of DNA over the course of our evolutionary history helped differentiate us from other mammals, a team of Yale researchers found.

M W Nachman 2000 Sep;  Estimate of the mutation rate per nucleotide in humans.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461236/

With a genome size of approximately 3 billion base pairs, this translates to roughly 60-100 new single nucleotide mutations per diploid genome per generation

With a genome size of approximately 3 billion base pairs, this translates to roughly 60-100 new single nucleotide mutations per diploid genome per generation

Lets  put an average of 35 years per generation

Given information:
- There are 60 mutations per generation.
- Each generation is 35 years.
- The total accumulation is 10,000 mutations.

Step 1: Find the number of generations required to accumulate 10,000 mutations.
Number of generations = Total accumulation of mutations / Mutations per generation
Number of generations = 10,000 mutations / 60 mutations per generation
Number of generations = 166.67 generations

Step 2: Find the total number of years that passed.
Total number of years = Number of generations × Years per generation
Total number of years = 166.67 generations × 35 years per generation

Total number of years = 5,833.00 years

Therefore, it took approximately 5,833  years for the total accumulation of 10,000 mutations to occur, assuming 60 mutations per generation and each generation lasting 35 years.

#### Otangelo

Cardiac Structural Differences: Challenging the Ape-Human Common Ancestry Hypothesis

The following evidence presented poses significant challenges to the hypothesis of ape-human common ancestry, particularly regarding the evolution of cardiac structure. The transition from a highly trabeculated left ventricular wall in apes  ( A trabeculated left ventricular wall refers to a heart structure where the inner surface of the left ventricle is characterized by a network of muscular projections called trabeculae. These finger-like protrusions of cardiac muscle tissue create a spongy or mesh-like appearance within the ventricular cavity, increasing the surface area for blood flow and contributing to cardiac function.) to a smoother one in humans would require numerous, complex, and coordinated changes across multiple biological levels. These changes would need to occur simultaneously or in a precise sequence to maintain cardiac function throughout the evolutionary process.

Key points that challenge the common ancestry hypothesis include:

1. The need for coordinated genetic changes in multiple genes controlling cardiac development.
2. The requirement for simultaneous functional adaptations in heart rate, contractility, and vascular elasticity.
3. The complex molecular basis of trabeculation, involving intricate signaling pathways that are difficult to alter without causing severe defects.
4. The precise developmental timing required for cardiac changes, which would be challenging to modify without affecting other organ systems.
5. The physiological integration of the cardiovascular system with respiratory and metabolic systems, necessitating coordinated changes across multiple systems.
6. The lack of viable intermediate stages between highly trabeculated and smooth ventricular walls.
7. The need for specific adaptations in molecular motors to support increased cardiac twisting.

These factors collectively are evidence that the distinct cardiac structures observed in humans and apes may be better explained by separate designs tailored to each species' physiological needs, rather than a gradual evolutionary transition. The complexity and interdependence of the required changes make it difficult to account for these differences through unguided, incremental evolutionary processes. This evidence challenges the common ancestry hypothesis by highlighting the improbability of such a transition occurring through known evolutionary mechanisms. It suggests that the cardiovascular differences between humans and apes may be too complex and integrated to have evolved from a common ancestor through a series of small, beneficial mutations.

Divergent evolution of the human heart: What we can learn from our evolutionary cousins

Key points and supporting data: Human hearts are different from other great apes: Humans have a smoother left ventricular wall, while other great apes (chimpanzees, bonobos, gorillas, orangutans) have more trabeculated (muscular bundles) left ventricles. This difference was observed across 242 chimpanzees, 7 bonobos, 14 gorillas, 28 orangutans, and 34 humans using ultrasound imaging. Functional differences between human and great ape hearts: Humans show greater rotation of the apex and twisting of the left ventricle during contraction. Non-human great apes with more trabeculation show less rotation and twist. This was measured using speckle-tracking echocardiography. he study has helped establish normative cardiac data for great apes. This information is valuable for diagnosing and managing heart disease, a leading cause of death in captive great apes.

Evidence of Purposeful Cardiac Design in Humans: A Challenge to Evolutionary Theory

The observed differences in heart structure between humans and other apes are evidence of distinct and separate designs, rather than common ancestry. The unique features of the human heart, such as its smoother ventricular wall and greater rotational capacity, align perfectly with our specific physiological needs. This is as an example of purposeful design tailored to human requirements, rather than a gradual evolutionary change. Furthermore, the presence of similar cardiac structures among apes, despite their varied habitats and lifestyles, suggests a common design template for these creatures, separate from humans. The fact that humans stand out so distinctly in this regard is evidence of our fundamental differences.

The transition from a trabeculated left ventricular wall in apes to a smoother one in humans would face significant evolutionary barriers:

Structural changes: Reducing trabeculation would require coordinated changes in myocardial growth patterns during development. This would involve altering the expression of numerous genes controlling cardiac muscle formation and patterning. The transition from a highly trabeculated to a smoother left ventricular wall would indeed require extensive and coordinated changes that are difficult to explain through a stepwise evolutionary process: Multiple genes involved in cardiac development (e.g., NKX2-5, HAND1, HAND2, BMP10, NOTCH1) would need simultaneous mutations. These mutations would have to be beneficial or neutral in intermediate stages, which is unlikely given the heart's critical function. The timing, location, and level of expression for numerous genes would need precise adjustments. This includes not just cardiac-specific genes, but also broader developmental regulators. Altering trabeculation affects blood flow patterns, which in turn influence further cardiac development. Changes in wall structure would require simultaneous adjustments in contractile proteins, ion channels, and metabolic processes. The complex network of transcription factors and signaling molecules controlling cardiac development would need restructuring. This involves intricate feedback loops that are finely tuned and interdependent. Changes would need to occur at specific embryonic stages without disrupting earlier or later developmental events. The precise timing of gene activation and repression would require simultaneous adjustment across multiple pathways. Alterations in structural proteins (e.g., actins, myosins) would need to match changes in gene regulation. This requires coordinated mutations in both coding sequences and regulatory regions. Changes in DNA methylation, histone modifications, and chromatin structure would need to align with genetic changes. These epigenetic alterations would have to be heritable and precisely targeted. The interdependencies between genetic sequence, gene expression, and developmental timing make it implausible that such changes could occur gradually. Each intermediate step would likely result in a non-functional or less efficient heart. The requirement for multiple, coordinated changes occurring simultaneously across various levels of biological organization (genetic, epigenetic, cellular, and organ level) presents a significant challenge to explanations relying on incremental evolutionary processes.

Molecular basis: Trabeculation is regulated by complex signaling pathways involving Notch, Neuregulin, and BMP10. Altering these pathways without disrupting other critical developmental processes would be challenging. Mutations affecting trabeculation often lead to severe cardiac defects, suggesting a delicate balance. Trabeculation, a critical process in cardiac development, is orchestrated by a complex interplay of signaling pathways, primarily involving Notch, Neuregulin, and BMP10, but also encompassing FGF, Semaphorin/Plexin, and Endothelin-1 signaling. These pathways are intricately regulated by transcription factors like Hand2, Irx3/5, and Nkx2.5, which integrate multiple signals to guide proper trabecular formation. The extracellular matrix, composed of fibronectin, collagen, and proteoglycans, provides not only structural support but also modulates pathway activity. This intricate regulatory network presents significant challenges for manipulation, as it requires precise temporal and spatial control, exhibits dosage sensitivity, and involves extensive pathway crosstalk. Alterations to these pathways often result in severe cardiac defects, including noncompaction cardiomyopathy and hypoplastic left heart syndrome, highlighting the delicate balance required for normal development. The complexity of trabeculation regulation presents a fascinating challenge to evolutionary transitions. The intricate nature of this process, with its multiple interdependent pathways and precise regulatory requirements, raises questions about how such a system could have evolved incrementally. Each component of the trabeculation process appears to be crucial, and alterations often lead to severe defects, suggesting that intermediate evolutionary stages might not have been viable. This "all-or-nothing" characteristic defies the typical gradual nature of evolutionary change. Furthermore, many of the signaling pathways involved in trabeculation also play critical roles in other developmental processes. This pleiotropy complicates evolutionary scenarios, as changes to these pathways to improve cardiac function could potentially have detrimental effects on other organ systems. The evolutionary path to the current trabeculation process would have required a delicate balance between improving cardiac function and maintaining the integrity of other developmental processes. Additionally, the dosage sensitivity of these pathways presents another evolutionary puzzle. Small changes in gene expression or protein activity can lead to significant developmental defects, suggesting that evolutionary innovations in this system would have had to occur within a narrow range of functional parameters. This constraint could have significantly limited the available evolutionary pathways, making the current system even more remarkable in its complexity and efficiency. In essence, the molecular basis of trabeculation exemplifies a biological system that seems to defy simple evolutionary explanations, highlighting the need for more nuanced models of evolutionary change that can account for the development of such intricate, interdependent processes.

Genetic complexity: Multiple genes (e.g., NKX2-5, HAND1, HAND2) are involved in ventricular development. Coordinated changes in numerous genes would be necessary, presenting a significant evolutionary hurdle. The complexity of ventricular development, involving multiple genes like NKX2-5, HAND1, and HAND2, presents a significant challenge to evolutionary explanations for the transition from trabeculated to smooth ventricular walls. These genes operate within a complex regulatory network, where each plays a crucial role in specific aspects of cardiac development. NKX2-5, for instance, is a key transcription factor in early heart formation and chamber specification. HAND1 and HAND2 are essential for ventricular development and trabeculation. Any alteration in one gene would necessitate compensatory changes in others to maintain cardiac function. The coordinated changes required across numerous genes present a formidable hurdle for evolutionary processes. Random mutations would need to simultaneously affect multiple genes in a beneficial way, which is statistically improbable. Even if one gene were to mutate favorably, without corresponding changes in the others, it would likely result in developmental defects rather than improved function. Moreover, these genes are pleiotropic, meaning they affect multiple traits beyond just cardiac development. NKX2-5, for example, also plays a role in thyroid development. Changes to these genes to alter ventricular structure would likely have unintended consequences in other organ systems, further reducing the likelihood of a viable outcome. The interdependence of these genes in developmental pathways means that altering the expression or function of one would disrupt the entire cascade of cardiac development. This interconnectedness makes it difficult to envision a step-wise evolutionary process that could modify ventricular structure without causing lethal developmental errors in intermediate stages. Furthermore, the regulatory elements controlling these genes' expression are highly conserved across species, indicating their critical importance. Modifying these regulatory regions without disrupting essential functions presents another layer of complexity. The need for multiple, specific, and coordinated genetic changes to occur simultaneously, rather than through a gradual accumulation of small modifications, challenges the plausibility of evolutionary explanations. It suggests that the distinct cardiac structures observed in humans and other apes are more likely the result of separate designs tailored to each species' physiological needs, rather than a product of incremental evolutionary changes.

Developmental timing: Changes in cardiac development would need to occur at precise embryonic stages. Altering this timing without affecting other organ systems would be difficult. The precise timing of cardiac development during embryogenesis presents a significant challenge to evolutionary explanations for the transition from trabeculated to smooth ventricular walls. Cardiac development is a highly orchestrated process that occurs in tight coordination with the development of other organ systems. The heart begins forming very early in embryonic development, and its proper formation is crucial for the viability of the embryo. The timing of each developmental stage, including the formation and later remodeling of trabeculations, is precisely regulated. To alter cardiac development to produce a smoother ventricular wall, changes would need to occur at specific embryonic stages without disrupting the timing of other critical developmental events. This presents several problems for evolutionary explanations: Firstly, the genes involved in cardiac development often play roles in other organ systems as well. For example, many cardiac developmental genes are also involved in neuronal development. Altering the expression or function of these genes to change heart development would likely have unintended consequences on brain development or other organ systems, potentially resulting in non-viable embryos. Secondly, the developmental timeline is interconnected across organ systems. The early formation of the heart is necessary to supply blood to other developing organs. Any significant changes to cardiac development could potentially disrupt the blood supply to other organs at critical stages of their development, leading to widespread developmental abnormalities. Thirdly, the signaling molecules and growth factors involved in cardiac development are part of complex signaling networks that operate throughout the embryo. Altering these signals to change heart development would likely affect other developmental processes that rely on the same signaling pathways. Furthermore, the formation of trabeculations and their subsequent remodeling involve complex interactions between the myocardium and endocardium. Changing this process would require simultaneous alterations in multiple cell types and their interactions, which is difficult to achieve through random genetic mutations. The need for multiple, precisely timed changes to occur simultaneously, rather than through a gradual accumulation of modifications, challenges the plausibility of evolutionary explanations. It suggests that the distinct cardiac structures observed in humans and other apes are more likely the result of separate designs tailored to each species' physiological needs, rather than a product of incremental evolutionary changes. This timing issue, combined with the need for coordinated genetic changes and the maintenance of function at each hypothetical intermediate stage, presents a formidable barrier to evolutionary explanations for the observed differences in cardiac structure between humans and other apes.

Intermediate stages: It's unclear how partially trabeculated hearts would function effectively. Each intermediate stage would need to be viable and provide a selective advantage. The transition from a highly trabeculated heart to a smoother one presents significant functional challenges at intermediate stages, making it unlikely that such partially trabeculated hearts would provide any selective advantage. These intermediate forms would likely suffer from compromised blood flow dynamics, potentially leading to areas of stagnant flow and increased risk of clot formation. The partial loss of trabeculations would also likely result in reduced contractile efficiency, as these structures contribute significantly to cardiac contraction. This could lead to decreased cardiac output, a potentially fatal outcome in high-stakes survival scenarios. Structurally, hearts with partial trabeculation might lack the integrity of either fully trabeculated or smooth-walled hearts, increasing the risk of cardiac rupture or aneurysm formation. The reduced surface area would impair nutrient delivery to the myocardium, potentially resulting in areas of weakened or dysfunctional heart muscle. Furthermore, the disruption of the heart's electrical conduction system, which relies in part on trabeculations, could lead to arrhythmias or uncoordinated contractions. Developmental issues could arise as other cardiac structures that depend on trabeculations as scaffolding during embryonic development would not form properly. Metabolically, these intermediate forms would require more energy to maintain proper function, a significant disadvantage in resource-limited environments. The reduced adaptability of such hearts could impair their ability to respond effectively to varying physiological demands. The compromise of cardiac immune function, which partially develops within trabeculations, could leave the heart more vulnerable to infections. Any reduction in cardiac efficiency could also have reproductive consequences, impacting an individual's ability to engage in energy-intensive mating behaviors. Given these potential issues, it's difficult to envision how intermediate forms would be viable, let alone advantageous. Each stage would likely represent a less efficient heart, potentially fatal in challenging environments where optimal cardiovascular performance is crucial for survival. The heart's requirement for continuous, optimal function makes a gradual transition particularly problematic, as even small decreases in efficiency could have severe consequences for an individual's survival and reproductive success.

From the paper: A comparative ultrasound study, assessing cardiac form and function across all great apes, suggests humans evolved away from a trabeculated myocardium common to all other apes, towards a comparatively smoother left ventricular wall, which may help to facilitate a greater cardiac output in humans.
Published in Ecology & Evolution and Anatomy & Physiology

Left ventricular trabeculation in Hominidae: divergence of the human cardiac phenotype - Communications Biology An echocardiographic study examining the left ventricle across all extant members of Hominidae suggests divergent evolution of the human heart from a trabeculated to a more compact phenotype with comparatively greater deformational characteristics.

Mammals are an extraordinary group of animals demonstrating vast biological diversity, ranging from the mighty blue whale (Balaenoptera musculus) that rules our oceans, to the diminutive fennec fox (Vulpes zerda) native to the harsh Sahara Desert. The ability of mammals to thrive across the world happened over many millennia by evolutionary adaptation, a process that selects physiological traits that favor survival and reproductive success. Whilst adaptation has influenced many aspects of physiology, such as the respiratory and immune systems, it was previously suggested to have bypassed the heart, leaving it highly conserved among mammals1. Previous research from our group, however, suggested that the structure of the human heart may be different from that of our closest evolutionary relative, the chimpanzee (Pan troglodytes)2. In adult male chimpanzees, the left ventricle - which receives oxygenated blood from the lungs and pumps it around the body - contains bundles of muscles that extend into the chamber cavity, called trabeculations. Whereas, the left ventricle of the human heart has a comparatively smoother ventricular wall. We became particularly excited by this finding, and wanted to examine whether left ventricular trabeculations were also common among the other great apes. And if so, why might humans be the odd one out? Trabeculation: A normal phenotype among non-human great apes Over six years, in collaboration with a remarkable team of dedicated veterinary and care professionals from four sanctuaries and five zoos across Africa, Asia and Europe, we created a large cardiac dataset covering all extant great apes. Using ultrasound, we examined and compared the structure and function of the left ventricle across 242 chimpanzees, 7 bonobos (Pan paniscus), 14 gorillas (Gorilla gorilla), 28 orangutans (Pongo) and 34 humans. In contrast to the comparatively smoother ventricular wall typically observed in humans, we identified a more trabeculated ventricular myocardium across all non-human great apes, regardless of age or sex. This difference was particularly noticeable at the apex, the bottom of the left ventricle, where the difference between humans and great apes was approximately four-fold (Fig 1).

Figure 1. Comparison of left ventricular trabeculation in great apes. The bullseye plots represent the trabecular:compact (T:C) ratio for each segment of the left ventricle. A greater T:C ratio reflects a higher degree of trabeculation. The outer layer of the bullseye plots represents the basal segments, the middle and innermost layers represent the midpapillary and apical segments of the left ventricle, respectively. Echocardiographic images of the parasternal short-axis at the apex are shown at end-diastole. *No data were available for the basal or midpapillary segments in the orangutans due to artefact from laryngeal air sacs.

Functional implications of trabeculation? As form and function are often closely linked, we were interested as to whether the differences in structure between the human and non-human great ape heart coincided with differences in function. We used a technique called speckle-tracking echocardiography, which traces the pattern of the cardiac tissue throughout the cardiac cycle, to examine the deformation, rotation and twisting of the left ventricle. Our findings indicated a negative curvilinear relationship between the degree of trabeculation and the amount of twist and rotation at the apex during contraction. In other words, humans, which have the least trabeculation, have much greater rotation of the apex and twisting of the left ventricle, whereas non-human great apes, which have much greater trabeculation, have less rotation and twist (Fig 2).

Figure 2. Relationship between markers of left ventricular (LV) function and apical trabeculation in great apes. (a) Peak apical rotation, shown in red, and (b) peak LV twist during contraction, shown in green. Analyses of LV twist was not possible in any of the orangutans due to artefact from laryngeal air sacs. The exponential plateau curve is shown, with the 95% confidence bands represented by the dotted line. The mean and standard error are shown in black for each species.

Divergent evolution of the human heart Since human’s divergence from our last common ancestor with chimpanzees ~8 – 6 million years ago, our brain underwent a considerable increase in size and we became bipedal, engaging in greater amounts of daily activity. These are associated with a much larger metabolic cost and greater thermoregulatory stress, which may have placed selective pressure on the heart to adapt. The evolutionary divergence of the human left ventricle away from a trabeculated myocardium, towards a comparatively smoother ventricular wall may have facilitated greater cardiac deformation, rotation and twisting. In turn, this could result in a larger volume of blood to be ejected from the heart to meet the augmented metabolic and thermoregulatory demands of the human environment. Overall, these data suggest that rather than being bypassed by evolutionary adaptation as previously suggested1, there are a number of subtle differences between the hearts of closely related mammalian species; and that these may reflect the selective pressures of distinct environments. Working with our evolutionary cousins While all data collection has its challenges, working with great apes in remote locations can be particularly tricky! It required an enormous amount of preparation beforehand to ensure we had all the necessary equipment and medical consumables for every animal. Once we arrived, we were often in remote geographical locations (think long car journeys on unpaved roads with minimal suspension, and rocky boat rides along the river with expensive equipment; Fig 3), facing extreme environmental conditions (we can confidently say we have never seen torrential downpours quite as bad as those during the rainy season in Congo!). However, the logistics of coordinating the research and care teams (often across three continents), the establishment of productive relationships with all stakeholders, and the transportation of the equipment and supplies were only made possible through the combined efforts of a large (and fantastic) interdisciplinary team. Through this combined approach, we have had the honor of working with our closest evolutionary cousins, many of which are recognized as critically endangered. Importantly, whilst our research is focused on the evolution of the human heart, we are also heavily invested in the healthcare of these incredible species. In captive great apes, cardiac disease is a leading cause of death. However, before our work with these species, little was known about their normal cardiovascular physiology. Together with veterinary practitioners, our work through practical workshops and the establishment of normative data 3–7 have also improved the understanding, diagnosis and management of heart disease in great apes.

#### Otangelo

The Genetic Unity of Humanity: Australian Aborigines and the 99.9% DNA Similarity

https://osf.io/vcemj

Introduction

This article explores the genetic evidence supporting the fundamental unity of the human species, with a particular focus on Australian Aborigines. The main points discussed include:

The Human Genome Project's finding that all humans share 99.9% of their DNA sequence.
The use of mitochondrial DNA (mtDNA) haplogroups to trace human prehistory and migration patterns.
The relatively low mtDNA variation among Australian Aborigines and its implications for understanding their history.
Challenges to the conventional 50,000-year timeline for Aboriginal presence in Australia based on genetic evidence.
Discussion of the unreliability of molecular clock calculations for dating human origins.
An alternative interpretation of the genetic evidence supporting a more recent and rapid diversification of human populations.

The Genetic Homogeneity of Humans: A Closer Look

In the realm of modern genetics, groundbreaking discoveries have shed light on the unity that exists within the human species. One of the most striking revelations to emerge from the Human Genome Project, spearheaded by the National Human Genome Research Institute (NHGRI), is the fact that all human beings share 99.9% of their DNA sequence. This remarkable genetic similarity serves as a powerful testament to the shared heritage and interconnectedness of all human populations across the globe, including the Australian Aborigines. In this exploration, we will unravel the genetic evidence supporting this claim, with a particular focus on the fascinating world of mitochondrial DNA (mtDNA) haplogroups and their implications for understanding the rich history of Australian Aborigines.

The NHGRI's findings highlight a paradox: while humans appear incredibly diverse on the surface, our genetic makeup tells a story of remarkable similarity. The vast majority of genetic variation among individuals is confined to a mere 0.1% of the genome. This tiny fraction of genetic diversity is responsible for all the myriad differences we observe in human populations, encompassing physical traits, susceptibility to various diseases, and a wide array of other characteristics that make each person unique. Australian Aborigines, despite their distinct cultural heritage and unique historical background stretching back millennia, are no exception to this fundamental rule of human genetics. Their DNA, like that of any other human population on Earth, is 99.9% identical to that of individuals from completely different ethnic backgrounds, whether they be from Europe, Asia, Africa, or the Americas. This genetic commonality underscores the fundamental unity of the human species, transcending superficial differences and highlighting our shared biological essence.

Mitochondrial DNA and Haplogroups: Unraveling Human Prehistory

To gain a deeper understanding of human genetic diversity and ancient migration patterns, scientists often turn to the study of mitochondrial DNA (mtDNA). Unlike nuclear DNA, which is inherited from both parents, mtDNA is passed down exclusively through the maternal line. This unique inheritance pattern makes mtDNA an invaluable tool for tracing ancestral lineages and unraveling human prehistory. Human mtDNA can be categorized into several major haplogroups, each of which is further subdivided into numerous sub-haplogroups. These haplogroups, identified by specific genetic markers, serve as genetic signposts that can be traced back to common maternal ancestors. By studying the distribution and diversity of these haplogroups across different populations, researchers can piece together significant information about ancient human migrations, population bottlenecks, and the spread of early human groups across the globe. In the case of Australian Aborigines, genetic studies have revealed that they primarily belong to the mtDNA haplogroup N. This haplogroup is one of the three major mtDNA lineages found in human populations worldwide, alongside haplogroups M and R.

The establishment of haplogroups M, N, and R as the three major mtDNA lineages in human populations worldwide has been a gradual process, unfolding over several decades of genetic research and analysis. This journey of discovery began with the concept of a "Mitochondrial Eve," a hypothetical common female ancestor of all living humans. This idea, which emerged in the 1980s based on early mtDNA studies, provided the foundation for tracing human mtDNA lineages back through time. As genetic research advanced, scientists employed increasingly sophisticated phylogenetic analysis techniques to construct detailed family trees of mtDNA sequences from diverse populations around the globe. This work allowed researchers to identify major branching points in human mtDNA evolution, revealing the deep ancestral relationships between different lineages. A key breakthrough in establishing these haplogroups came from the identification of specific mutations that define each major lineage. For example, haplogroup L3, which is considered the ancestor of M, N, and R, is characterized by mutations at certain positions in the mtDNA sequence. These genetic markers serve as signposts, allowing researchers to categorize mtDNA samples and trace their evolutionary history. The process of defining these haplogroups relied heavily on extensive global sampling efforts. Scientists collected and analyzed mtDNA samples from populations across all continents, building a comprehensive picture of human genetic diversity. This worldwide sampling revealed distinct distribution patterns of haplogroups in different regions, helping to confirm their status as major lineages. For instance, haplogroup M is predominantly found in South Asia, while N and R are more common in West Eurasia. To estimate the age of these haplogroups, researchers employed molecular clock techniques. As human populations migrated across the globe, they carried these mtDNA lineages with them, leaving genetic footprints that can be traced today. The distinct regional prevalence of M, N, and R haplogroups offers insights into ancient migration routes and population dynamics. Technological advancements have played a role in refining our understanding of these haplogroups. The development of more powerful DNA sequencing technologies has allowed for increasingly accurate and comprehensive analysis of mtDNA. These improvements have enabled researchers to detect subtle variations and sublineages within the major haplogroups, providing a more nuanced view of human genetic diversity. The establishment of M, N, and R as the three major mtDNA lineages has also been supported by studies of other genetic markers. Research on Y-chromosome DNA and autosomal DNA has provided complementary evidence, corroborating the patterns observed in mtDNA and offering a more complete picture of human genetic history.

Recent discoveries like Graecopithecus in the Balkans,  Dmanisi Fossils in Georgia, Denisovans in Siberia, Homo luzonensis in the Philippines, and Homo floresiensis in Indonesia have complicated our understanding of human origins and migration patterns, challenging not only the traditional "Out of Africa" model. Ancient settlements near Mount Ararat are the oldest known settlements that have been discovered in this region, leading to the proposal of an "Out of Ararat" model. Archaeological findings in the vicinity of Mount Ararat, including sites like Göbekli Tepe in Turkey (dated less than 10,000 BCE), have led researchers to propose an alternative model for human dispersal. This model suggests that the area around Mount Ararat may have been a crucial center for early human civilization and migration. The region may have served as a refuge during the Last Glacial Maximum. It could have been a starting point for post-glacial repopulation of Eurasia. The area's diverse ecology might have facilitated the development of agriculture. These findings indicate a more complex picture of human migration patterns and early cultural development. The emerging view suggests a multi-regional, interconnected process of human dispersal. Over time, as evidence accumulated from multiple studies and research groups, a scientific consensus emerged recognizing M, N, and R as the three major mtDNA lineages. This model has become widely accepted in the scientific community, forming a cornerstone of our understanding of human genetic diversity and ancient migrations. These haplogroups represent the initial diversity present in the human population following the biblical flood. The study of these major mtDNA haplogroups continues to progress as new research techniques emerge and more populations are sampled. Scientists are now exploring the fine-scale structure within these haplogroups, uncovering new sublineages and regional variations. This ongoing research promises to reveal even more about our shared genetic heritage and the complex history of human migrations and interactions across the globe. The story of how haplogroups M, N, and R were established as the major mtDNA lineages demonstrates the power of genetic research in unraveling human history. It shows how the accumulation of data, the development of new technologies, and the collaborative efforts of scientists worldwide can come together to build a comprehensive understanding of our genetic past.  These three major haplogroups can be interpreted as corresponding to the descendants of Noah's three sons: Japheth, Shem, and Ham. This framework suggests that in the aftermath of the Great Flood, as described in the Book of Genesis, the descendants of these three patriarchal families spread out across the earth, giving rise to the diverse array of mtDNA haplogroups we observe in modern human populations today.

Low mtDNA Variation Among Australian Aborigines: Implications and Interpretations

One of the most remarkable aspects of genetic research on Australian Aborigines is the discovery of relatively low mtDNA variation within their population compared to other human groups. This reduced genetic diversity is evidence of a long period of genetic stability and relative isolation from other populations. For instance, a comprehensive study conducted by van Holst Pellekaan et al. in 2006 found that the mtDNA diversity among Australian Aborigines is significantly lower than that observed in other populations around the world. This finding lends support to the idea of a long-standing, stable population that experienced limited gene flow from outside groups over an extended period. The low mtDNA variation among Australian Aborigines has several important implications for our understanding of their history and origins. On one hand, it aligns with the traditional view of Australian Aborigines as one of the oldest continuous cultures on Earth, suggesting a long period of isolation on the Australian continent. On the other hand, it raises questions about the nature and timing of their initial settlement in Australia, as well as their subsequent population dynamics.

Questioning the 50,000-Year Timeline: A Critical Examination

The prevailing scientific claim posits that Australian Aborigines have been present on the Australian continent for over 50,000 years. This timeline is based on a combination of archaeological discoveries, including ancient human remains and artifacts, as well as genetic estimates derived from molecular clock calculations. However, the relatively low genetic variation observed in mtDNA among Australian Aborigines presents a thought-provoking challenge to this established timeline.  If Australian Aborigines had indeed been isolated on the continent for such an extended period, spanning tens of thousands of years, one might expect to observe more substantial genetic drift and variation within their mtDNA. Genetic drift, the random changes in gene frequencies within a population over time, typically leads to increased genetic diversity in isolated populations over long periods. The fact that Australian Aborigines show less mtDNA variation than expected based on the conventional timeline raises important questions about the accuracy of these long-standing estimates.

This limited variation, characterized primarily by haplogroups M and N and their derivatives, presents a puzzling scenario when interpreted through the lens of traditional molecular clock rates. Using these conventional methods, the observed mtDNA diversity suggests a population age of approximately 15,000 to 30,000 years for Australian Aboriginals. This estimate stands in stark contrast to the widely accepted timeline of 50,000 to 65,000 years. The discrepancy is substantial, with the mtDNA-based estimate suggesting a population age that is roughly 20,000 to 50,000 years younger than the conventional timeline. This significant gap between the mtDNA evidence and the established chronology raises important questions about the accuracy of molecular clock rates, the potential impact of population bottlenecks, and the overall complexity of human migration patterns. The mtDNA data, taken at face value, implies a much more recent arrival or expansion of the Aboriginal population in Australia than commonly thought, challenging long-held beliefs about the continent's settlement history. This divergence between genetic and archaeological evidence underscores the complexities involved in reconstructing ancient population histories and highlights the need for careful interpretation of genetic data in the context of human migration studies.

The unreliability of Calculations of mitochondrial Eve based on molecular clocks, which are set arbitrarily

Inconsistent mutation rates: Mitochondrial DNA appears to mutate much faster than previously thought, with some studies suggesting up to 20-fold faster rates. This challenges the fundamental assumption of a constant mutation rate used in molecular clock calculations. When researchers studied mtDNA mutations in family pedigrees, they found much higher mutation rates than previously assumed. For example, Howell's team studied an Australian family and found a mutation rate that, if applied broadly, would yield much younger dates for evolutionary events. Studies looking at mtDNA changes over a few generations in living populations have consistently found higher mutation rates than those inferred from long-term evolutionary comparisons. These studies challenge our understanding of mitochondrial DNA (mtDNA) mutation rates and their implications for evolutionary timelines.

Parsons et al. (1997): Published in Nature Genetics Observed 10 mutations in 327 base pair segments from 357 individuals across 134 independent mtDNA lineages. Calculated mutation rate: 1 in 33 generations, or about 2.5 mutations per million base pairs per year. This rate was about 20 times higher than previous estimates 1

Howell et al. (1996): Studied an Australian family with a known mtDNA mutation. Found a much higher mutation rate than expected. Their findings suggested that if applied broadly, human mtDNA could trace back to a common ancestor just thousands of years ago, rather than hundreds of thousands 2

Denver et al. (2000): Studied mutation accumulation in Caenorhabditis elegans (a model organism) Found mutation rates 100 times higher than previous phylogenetic estimates 3

Sigurðardóttir et al. (2000): Analyzed Icelandic pedigrees. Estimated the mutation rate to be 0.32 mutations per site per million years. This was about 10 times higher than phylogenetic estimates 4

Santos et al. (2005): Studied deep-rooting Portuguese pedigrees . Found evidence for a higher mutation rate in the control region of mtDNA 5

These studies consistently show mutation rates that are significantly higher than those inferred from phylogenetic comparisons. The discovery that individuals often carry multiple mtDNA types (heteroplasmy) suggests more frequent mutations than previously thought. The observed rates in these short-term studies often range from 10 to 100 times faster than the rates used in traditional evolutionary calculations. If these faster rates were applied to evolutionary timelines, they would suggest a much more recent common ancestor for all humans, potentially just a few thousand years ago. Some researchers argue that many of these mutations might be eliminated over longer time periods due to natural selection, explaining the discrepancy between short-term and long-term rates. The higher observed rates might be partly due to better detection of heteroplasmy (multiple mtDNA types in an individual), which could be transient over generations. Different regions of mtDNA might mutate at different rates, complicating the use of a single mutation rate for the entire molecule. These findings highlight potential problems with how molecular clocks are calibrated, often using assumed divergence times between species.  These studies and their implications have sparked significant debate in the field of molecular evolution. They challenge the traditional view of a constant, slow mutation rate in mtDNA and raise questions about the accuracy of long-standing evolutionary timelines.

If we apply these faster mutation rates to existing evolutionary models, the implications are indeed dramatic:

If the mutation rate is 20 times faster than previously thought, it reduces the estimated time to the most recent common ancestor (often called "Mitochondrial Eve") from 100,000-200,000 years to just 5,000-10,000 years. This revised timeline provides evidence for a much more recent common ancestor for all living humans, potentially aligning more closely with some archaeological and historical records of human civilization. It would imply that human genetic diversity arose much more recently and rapidly than currently believed.

Arbitrary calibration

The molecular clock is typically calibrated using an assumed divergence time between humans and chimpanzees, often set at 5 million years ago. This calibration point itself is an estimate, not a firmly established fact.  The commonly used 5 million year divergence time between humans and chimpanzees is an estimate based on limited fossil evidence. Using this uncertain date as a calibration point introduces a fundamental weakness into the method. Calibrating the molecular clock with this estimate and then using it to date other events in human evolution creates a circular logic that undermines the scientific validity of the results. The assumption that mutation rates remain constant over millions of years in human evolution lacks empirical evidence. Evolutionary rates can vary due to factors like generation time, population size, and environmental pressures. Molecular clock dating often fails to account for the complex processes of human evolution, including potential variations in mutation rates between different lineages or time periods. Any inaccuracy in the initial calibration point is carried through all subsequent calculations, potentially leading to compounded errors in estimating dates of human evolutionary events. The use of assumed calibration points makes it difficult to test or falsify the underlying assumptions of the molecular clock hypothesis in human evolution. The assumption that most mutations are neutral may not hold true for all genetic regions in human evolution. Some parts of the genome may be under strong selective pressure, altering their rate of change. The scarcity of fossils for many stages of human evolution complicates the validation of molecular clock estimates and the establishment of reliable calibration points. The effects of population structure and incomplete lineage sorting in human evolution can confound molecular clock analyses, leading to discrepancies between gene trees and the actual pattern of human speciation. Instances of interbreeding between closely related human species, such as Homo sapiens and Neanderthals, can complicate molecular clock analyses by introducing genetic material from one lineage into another. Applying molecular clock methods to very ancient events in human evolution is particularly problematic due to the accumulation of multiple substitutions at the same genetic sites over time. In Bayesian analyses, the choice of prior distributions can significantly impact the resulting time estimates for human evolution, introducing a subjective element to the process. These issues collectively undermine the reliability of molecular clock dating in providing precise timelines for human evolution. While the method can offer rough estimates and comparative insights, presenting its results as definitive evidence for specific dates in human evolutionary history is problematic. A more robust approach to understanding human evolution requires the integration of multiple lines of evidence, including fossil records, archaeological findings, and careful interpretation of genetic data, rather than relying heavily on molecular clock dating alone.

Widely varying results: Different calibration methods yield vastly different results. For example, one calculation suggests humans arose only about 6,500 years ago, while others point to 100,000 to 200,000 years ago. The image mentions that using faster mutation rates could place "mitochondrial Eve" at just 6,000 years ago.
Heteroplasmy complications: The presence of heteroplasmy (multiple mitochondrial DNA types in an individual) further complicates the accurate dating and tracing of lineages.
Limited studies on living populations: There have been few studies on mutation rates in living people, making it difficult to establish accurate baselines for evolutionary calculations.
Conflict with archaeological evidence: The molecular clock estimates often conflict with archaeological dates, raising questions about their reliability.
Skepticism among experts: Researchers express concern about the accuracy of these methods, with some calling it an "illusion" or "false precision."

These factors demonstrate that the molecular clocks used to calculate the age of mitochondrial Eve and other evolutionary events are based on assumptions and estimates rather than definitive empirical evidence. This makes them inherently arbitrary and potentially unreliable for precise dating of human evolutionary events, calling into question many widely accepted timelines in human evolution.

Reinterpreting the Genetic Evidence

The genetic evidence surrounding Australian Aborigines can be interpreted in a way that supports a more recent and rapid diversification of human populations. The observed genetic similarities among all human groups, including Australian Aborigines, align closely with the idea of a recent, common origin for all of humanity. This interpretation is consistent with the biblical account of human history, which posits a young age for the human species as a whole.
The genetic data, rather than supporting a 50,000-year history for Australian Aborigines, actually indicates a more recent settlement of the Australian continent and subsequent rapid adaptation to its unique environmental conditions. This perspective challenges the deep-time evolutionary model and offers an alternative framework for understanding human prehistory. The low mtDNA variation among Australian Aborigines can be explained by a founder effect – a loss of genetic variation that occurs when a new population is established by a small number of individuals from a larger population. In this scenario, a small group of early humans, possibly descendants of one of Noah's sons, could have migrated to Australia relatively recently (within the past few thousand years), bringing with them a limited subset of the original genetic diversity present in the post-Flood human population. This interpretation suggests that after the global Flood described in the Book of Genesis, Noah's descendants rapidly spread out across the earth, diversifying into various genetic lineages and populating different regions of the world, including Australia. The unique genetic profile of Australian Aborigines, characterized by low mtDNA variation, could thus be seen as evidence of this recent dispersal and rapid adaptation to new environments.

The genetic evidence, including the remarkable 99.9% DNA similarity shared among all humans and the specific mtDNA haplogroups found in Australian Aborigines, serves as a powerful reminder of the fundamental unity of the human species. While celebrating the rich cultural diversity and unique heritage of Australian Aborigines, we must also recognize the profound genetic connections that bind all of humanity together. The low mtDNA variation observed among Australian Aborigines continues to spark important discussions and debates about the conventional timelines of human history. It challenges researchers to reevaluate long-held assumptions and consider alternative interpretations of the genetic data. As genetic research continues to advance at a rapid pace, it promises to provide even deeper insights into the fascinating history and unity of humankind. Whether viewed through the lens of evolutionary theory or creationist interpretation, the genetic evidence consistently points to the shared heritage and close relationship among all human populations. This scientific understanding of our genetic unity has the potential to foster greater empathy, respect, and cooperation among diverse human groups, reminding us that despite our surface-level differences, we are all part of one human family.

If the evolutionary narrative were true, we might indeed expect to see a more gradual continuum between ape and human genomes, rather than the distinct separation observed. The lack of intermediate genomes between humans and other primates is a point of discussion in evolutionary biology. Regarding human adaptations, there are indeed examples of populations with specific traits that could be considered adaptations to their environments, though these are generally less extreme than what should be predicted and expected:

Lactase persistence

The evolution of lactase persistence in human populations, particularly those with a history of dairy farming, is often cited as an example of recent human adaptation. However, when examined closely, this phenomenon also raises questions about the conventional evolutionary timeline. Lactase persistence, the ability to digest lactose (milk sugar) into adulthood, is indeed a significant adaptation. In populations with a long history of dairy farming, such as many European, Middle Eastern, and some African groups, a high percentage of adults retain the ability to produce lactase, the enzyme that breaks down lactose. This trait is less common in populations without a dairying tradition.
This perspective on lactase persistence challenges us to reconsider assumptions about human evolutionary timelines. It suggests that significant genetic adaptations can occur relatively quickly in human populations in response to cultural and environmental factors. This rapid adaptability, combined with the overall genetic similarity among human populations worldwide, supports a model of recent human origins and diversification, rather than a process of gradual evolution over vast periods of time.

The absence of more extreme adaptations, are challenging the conventional evolutionary timeline. The relative genetic homogeneity of humans worldwide, despite diverse environments, is indeed a topic of ongoing research and debate in the scientific community.

Concluding Remarks

The genetic evidence presented challenges to long-held assumptions about human history and the timeline of Aboriginal presence in Australia. While celebrating the unique cultural heritage of Australian Aborigines, the profound genetic connections suggest that current genetic data could be interpreted to support a more recent common origin for all humans. Regardless of one's perspective on human origins, genetic evidence consistently points to the fundamental unity of the human species, encouraging greater empathy and cooperation among diverse populations and ethnicities.

References

1. Parsons, T.J., Muniec, D.S., Sullivan, K., Woodyatt, N., Alliston-Greiner, R., Wilson, M.R., ... & Holland, M.M. (1997). A high observed substitution rate in the human mitochondrial DNA control region. Nature Genetics, 15(4), 363-368. Link. (This study reported a mutation rate in the mtDNA control region about 20 times higher than previous phylogenetic estimates.)

2. Howell, N., Kubacka, I., & Mackey, D.A. (1996). How rapidly does the human mitochondrial genome evolve?. American Journal of Human Genetics, 59(3), 501-509. Link. (This paper studied an Australian family with a known mtDNA mutation and found a much higher mutation rate than expected.)

3. Denver, D.R., Morris, K., Lynch, M., Vassilieva, L.L., & Thomas, W.K. (2000). High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science, 289(5488), 2342-2344. Link. (This study found mutation rates in C. elegans 100 times higher than previous phylogenetic estimates.)

4. Sigurðardóttir, S., Helgason, A., Gulcher, J.R., Stefansson, K., & Donnelly, P. (2000). The mutation rate in the human mtDNA control region. American Journal of Human Genetics, 66(5), 1599-1609. Link. (This analysis of Icelandic pedigrees estimated a mutation rate about 10 times higher than phylogenetic estimates.)

5. Santos, C., Montiel, R., Sierra, B., Bettencourt, C., Fernandez, E., Alvarez, L., ... & Lima, M. (2005). Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal). Molecular Biology and Evolution, 22(6), 1490-1505. Link. (This study of Portuguese pedigrees found evidence for a higher mutation rate in the control region of mtDNA.)

#### Otangelo

How similar are human and chimpanzee genomes?

https://richardbuggs.com/2018/07/14/how-similar-are-human-and-chimpanzee-genomes/?fbclid=IwY2xjawEVsytleHRuA2FlbQIxMAABHTYKaaviQWXIRN1xOPm2-ZsN-S6lwKIrC9vASd_hhMeAICd8XxgB-Tq-Dw_aem_oOgPs3WDxLbRAYe_eA7m3g

Richard Buggs 2018

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%

In order to assess how improvements in genome assemblies can change these figures, I did the same analyses on the alignment of the older PanTro4 assembly against Hg38 (see discussion post #40). The Pantro4 assembly was based on a much smaller amount of sequencing than the Pantro6 assembly (see discussion post #39). In this Pantro4 alignment:

6.29% had no alignment to the chimp assembly
5.01% was in CNVs relative to chimp
1.11% differed due to SNPs in the one-to-one best-aligned regions
0.28% differed due to indels within the one-to-one best-aligned regions

The percentage of nucleotides in the human genome with one-to-one exact matches in the chimpanzee genome was 82.34%.

In 2008 I wrote “I predict that when we have a reliable, complete chimpanzee genome, the overall similarity of the human genome will prove to be close to 70% (and very far from 99%).” This prediction is not borne out by the more recent data above. I made a mistake in my 2008 calculations in the way in which I dealt with CNVs, which put me out by 2.7%, but this was only a minor component of why my estimate was so low.

Richard Buggs: Here is a final summary of my position.

https://discourse.biologos.org/t/human-chimp-genome-similarity/38409/119

The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%.

Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70%

Jeffrey P. Tomkins February 20, 2013

The key information about percentage similarities between chimpanzee and human chromosomes is as follows:

1. For chimpanzee autosomes (non-sex chromosomes), the DNA sequence similarity to human chromosomes ranged between 66% and 76%, depending on the specific chromosome.
2. Only 69% of the chimpanzee X chromosome was similar to the human X chromosome.
3. Only 43% of the chimpanzee Y chromosome was similar to the human Y chromosome.
4. Overall, genome-wide, only 70% of the chimpanzee DNA was similar to human DNA under the most optimal sequence-slice conditions.

These percentages were derived from the study described in this article, which was conducted by Jeffrey P. Tomkins and published in the Answers Research Journal on February 20, 2013. The authors did not cite another scientific paper for these specific numbers; rather, they performed their own analysis using the latest available chimpanzee genome assembly at the time (a 6X coverage assembly) and compared it to the human genome using the BLASTN algorithm with optimized parameters.

#### Otangelo

Gene Expression and Regulatory Elements that Differ Between Humans and Primates

Brain Expression Differences:
- Human-specific transcriptional networks not found in other primates have been identified, particularly in the context of transposable elements (TEs) and transcription factor (TF) interactions. Studies have revealed that primate-restricted TEs contain binding sites for lineage-specific transcription factors, influencing gene expression during human gastrulation and fetal development  1, 2
- Marnetto et al. identified human genome regions with regulatory chromatin marks that cannot be aligned to other mammalian genomes. These human-specific regulatory regions (HSRRs) are enriched for genes involved in neural processes, CNS development, and neuropsychiatric diseases. Link
- Barbosa-Morais et al. found that splicing profiles of organs are more similar within species than between species, suggesting rapid evolution of splicing regulation.

Human-Specific Genetic Elements:
- Over 35,000 fixed human-specific neuro-regulatory single nucleotide changes (hsSNCs) have been identified.
- Bitar's study found 856 genes with high-confidence human-specific genomic variants, primarily associated with protein-coding regions. Many of these genes are essential for survival and development. Link
- Hundreds of human-specific long non-coding RNAs (lncRNAs) have been identified, many expressed in the brain. ARHGAP11B-AS1 is involved in human-specific aspects of cortical development.
- Reilly et al. identified thousands of human-specific enhancers, particularly those active in fetal brain development.
- Many human-specific regulatory elements are derived from transposable elements, such as MER130 elements contributing to the rewiring of progesterone receptor binding sites specifically in humans.

Facial Expression Differences

Unique Human Proteins:
- Endo's study identified FAM75, a protein containing the WRWSH sequence that is unique to humans. This supports the "constituent hypothesis" that humans have unique genes and proteins not present in chimpanzees. Link

Functional Implications and Human-Specific Traits:
- Bitar's analysis shows that human-specific genes are primarily involved in brain, immune, and metabolic pathways.
- Many of these genes are functionally associated with neural activity and the expanded human cortex.
- Significant morphological differences between humans and primates include:
- Skeletal features (e.g., jaws and hands)
- Hair thickness
- Muscle tissue
- Speech and language capabilities

These findings collectively suggest that even small genetic differences can lead to significant functional divergences between species, particularly in areas like brain development, immunity, and metabolism. The regulatory landscape of the human genome contains many elements without direct analogs in other primates, especially in regions associated with brain development and function.

The human brain is triple the size of chimpanzees
The human brain has about 86 billion neurons, compared to an estimated 33 billion in our ancestors 3.5 million years ago. This represents an increase of about 151,400 neurons per generation over 350,000 generations. Each neuron can have up to 10,000 synaptic connections, meaning an increase of about 1.514 trillion new synaptic connections per generation. Creating these new neurons and connections precisely would require an extremely complex coordinated process, specifying cell types, functions, positions, interconnections, etc. For comparison, simulating just 1 second of human brain activity took a supercomputer 40 minutes using 82,944 processors. Furthermore, the human body contains about 37.2 trillion cells, each with an estimated average of 2 billion proteins, totaling around 7.44 x 10^22 proteins. The probability of random sequences forming functional protein domains is estimated to be extremely low, around 1 in 10^77.Link

Long non-coding RNAs (lncRNAs) play crucial epigenetic roles in various cellular processes, such as stem cell differentiation, tissue type regulation, organ function, and body plan development. The following points highlight how the differences in lncRNAs between humans and chimps challenge the theory of common ancestry:

Stem Cell Differentiation: LncRNAs are essential in regulating the self-renewal and multi-lineage differentiation of stem cells. The significant differences in lncRNAs between humans and chimps suggest distinct regulatory mechanisms that could not have arisen from a common ancestor.

Tissue Type Regulation: Studies have shown that lncRNAs define tissue type identities. The vast number of novel lncRNAs identified in humans, which are not present in chimps, indicates species-specific regulatory roles that are not conserved.

Organ Function: LncRNAs are involved in organ development and function. The differences in lncRNA profiles between humans and chimps imply unique regulatory pathways that govern organogenesis and physiological processes.

Body Plan Development: LncRNAs are involved in the resculpting of body plans during development. The diversity and number of lncRNAs expressed during critical developmental stages in humans are significantly higher than in chimps, suggesting distinct developmental programs.

Non-Conservation of lncRNAs: The number of different lncRNAs in humans (172,216) is almost nine times higher than in chimps (18,604). This non-conservation of lncRNAs challenges the idea of a common ancestor, as such a vast difference could not have evolved through mutations, especially given that lncRNAs do not tolerate mutations well.

Mutational Intolerance: LncRNAs are highly sensitive to mutations, with malfunctioning lncRNAs linked to severe diseases. The absence of positive mutations in these regulatory lncRNAs further refutes the idea that they could evolve through random mutations.

Chromosome Fusion Argument: The claim that the difference in the number of lncRNAs could have arisen after a chromosome fusion is implausible. Chromosome fusions typically reduce biological information, not increase it.

Chromosomal differences:
Humans have 46 chromosomes while chimps have 48. The fusion of two chromosomes (as seen in human chromosome 2) is a rare event, and the functional differences resulting from such a fusion are significant.

Genomic alterations:
Both species have undergone numerous changes in their genomes, including rearrangements, additions, and deletions of DNA segments. Many of these changes are unique to each species, suggesting distinct genetic origins.

Mobile elements:
While humans and chimps share some insertion sites for mobile genetic elements (like Alu sequences), these could be the result of intentional design rather than common ancestry. It suggests that shared insertion sites might serve specific functional purposes in both species.

Rarity of chromosomal changes:
The significant chromosomal difference between humans and chimps is presented as unusual for closely related species, suggesting a more fundamental genetic divergence.

Mobile Elements and Genomic Differences
While humans and chimpanzees share some insertion sites for mobile elements like Alu sequences, LINEs, and SVA elements, there are significant differences in their overall genomic landscape. Humans possess approximately 1.8 million Alu sequences, whereas chimpanzees have about 1.1 million. Similarly, the human genome contains around 516,000 L1 elements, compared to 480,000 in chimps. SVA elements also show a disparity, with humans having about 2,700 and chimps approximately 2,400. These mobile elements are not mere genomic clutter but can have profound functional implications. They can act as regulatory sequences influencing gene expression, create new splice sites leading to alternative protein products, and in some cases, cause genomic instability resulting in mutations or chromosomal rearrangements.

Protein and Gene Expression Differences
The differences between humans and chimpanzees extend beyond mobile elements to proteins and gene expression patterns. Despite high DNA sequence similarity, studies have shown that about 80% of proteins differ between humans and chimps. Chimpanzee proteins tend to have more amino acid differences from human proteins than expected based on DNA sequence similarities. Some proteins, particularly those involved in immunity, reproduction, and olfaction, show accelerated evolution in humans compared to chimps. Gene expression patterns also exhibit significant differences. Approximately 10% of genes show expression differences between humans and chimps in the brain, with these differences being particularly pronounced in the prefrontal cortex, a region associated with higher cognitive functions. Genes involved in neuronal function, synaptic plasticity, and energy metabolism display notably different expression patterns between the two species. From a design perspective, the shared insertion sites of mobile elements can be viewed as intentional placements for functional purposes, while the differences in numbers and types of mobile elements between humans and chimps can represent species-specific optimizations or adaptations. The significant differences in protein structure, function, and gene expression patterns further support the idea of distinct genomic histories for each species. These differences are consistent with the concept of separate origins for humans and chimpanzees. The shared elements could be interpreted as evidence of a common design template, with species-specific modifications tailoring each genome for its unique biological role. This perspective challenges the notion of common ancestry and suggests that the similarities between human and chimpanzee genomes might be better explained by common design rather than common descent. While humans and chimps share many genomic similarities, the substantial differences in their genomes, proteins, and gene expression patterns provide compelling evidence for separate origins and distinct genomic histories. These differences encompass not just the presence or absence of genetic elements, but also their arrangement, function, and expression. Such distinctions point towards intentional, species-specific design rather than gradual divergence from a common ancestor.

The gene in question is typically referred to as the TBXT gene (T-box transcription factor T), also known as the T gene or brachyury gene.

Argument from Proponents of Evolution and Common Ancestry:

Evolutionary biologists argue that the TBXT gene provides strong evidence for common ancestry between humans and other primates. In most mammals, including many primates, this gene plays a crucial role in tail development. In humans, the gene is present but has undergone mutations that render it non-functional for tail growth.

The argument goes as follows:
1. The TBXT gene is highly conserved across vertebrates, indicating its importance in development.
2. In tailed mammals, including most primates, this gene is active and contributes to tail formation.
3. Humans possess this gene, but it contains specific mutations that prevent tail development.
4. Occasionally, due to rare genetic variations, some humans are born with vestigial tails.
5. This pattern fits perfectly with the evolutionary narrative: humans evolved from tailed ancestors, and the TBXT gene was gradually silenced through mutations as tails became unnecessary.

Proponents argue that this is exactly what we would expect to see if humans evolved from tailed ancestors - the retention of a now-defunct gene that once served a specific purpose.

Refutation:

While the evolutionary argument seems compelling at first glance, there are several critical points that challenge this interpretation:

1. Multifunctionality: The TBXT gene is not solely responsible for tail development. It plays crucial roles in early embryonic development, including the formation of the notochord and the regulation of mesoderm differentiation. Its presence in humans can be explained by these essential functions, rather than as a vestige of tail development.

2. Regulatory Complexity: Gene expression is controlled by intricate regulatory networks. The fact that TBXT doesn't lead to tail growth in humans could be due to designed regulatory mechanisms rather than random mutations. The gene's expression pattern in humans may be precisely calibrated for its non-tail-related functions.

3. Embryonic Tail: Human embryos do develop a tail-like structure early in development, which is then reabsorbed. This process, controlled in part by TBXT, is crucial for proper spinal and nervous system development. The gene's role in humans may be to guide this important developmental stage rather than being a non-functional remnant.

4. Misinterpretation of "Vestigial" Structures: The rare occurrences of humans born with tail-like structures are often not true tails but rather developmental abnormalities involving the coccyx or other spinal structures. These are not evidence of atavism but rather of developmental disorders.

5. Genetic Plasticity: The variations in TBXT across species could be evidence of designed adaptability within created kinds, allowing for diversification without implying common ancestry.

6. Common Design: The presence of similar genes across species with varying functions can be interpreted as evidence of a common designer using a similar genetic toolkit, adapting it for specific needs in each created kind.

7. Lack of Transitional Forms: If the loss of tails in human evolution was a gradual process, we would expect to find fossil evidence of hominids with progressively shorter tails. Such evidence is notably absent from the fossil record.

8. Functional Constraints: The high conservation of TBXT across species could be due to functional constraints related to its crucial developmental roles, rather than common ancestry.

In conclusion, while the TBXT gene's presence in humans is consistent with the evolutionary narrative, it is not conclusive proof of common ancestry with tailed primates. The gene's complex roles in development, the lack of true vestigial tails in humans, and the absence of clear transitional forms in the fossil record all challenge the simplistic interpretation of TBXT as a remnant of our tailed ancestors. A design-based interpretation, accounting for the gene's multiple functions and regulatory complexities, provides an equally, if not more, coherent explanation for the observed data.

Prescott, S. L., Srinivasan, R., Marchetto, M. C., et al. (2015). Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell, 163(1), 68-83. Link

Wilderman, A., VanOudenhove, J., Kron, J., et al. (2018). High-resolution epigenomic atlas of human embryonic craniofacial development. Cell Reports, 23(5), 1581-1597. Link

8. Gokhman, D., Agranat-Tamir, L., Housman, G., et al. (2019). Extensive regulatory changes in genes affecting vocal and facial anatomy separate modern from archaic humans. bioRxiv, 106955. Link

Body Expression Differences:

9. Cotney, J., Leng, J., Yin, J., et al. (2013). The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell, 154(1), 185-196.

10. Glinsky, G. V. (2016). Mechanistically distinct pathways of divergent regulatory DNA creation contribute to evolution of human-specific genomic regulatory networks driving phenotypic divergence of Homo sapiens. Genome Biology and Evolution, 8(6), 2774-2788.

11. Perdomo-Sabogal, A., Nowick, K., Piccini, I., et al. (2016). Human lineage-specific transcriptional regulation through GA-binding protein transcription factor alpha (GABPa). Molecular Biology and Evolution, 33(5), 1231-1244.

12. Ryu, H., Inoue, F., Whalen, S., et al. (2018). Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors. bioRxiv, 256313.

13. Franchini, L. F., & Pollard, K. S. (2015). Human evolution: The non-coding revolution. BMC Biology, 13(1), 1-4.

These papers provide insights into gene regulatory expression patterns exclusive to humans across brain, facial, and body differences. They highlight the importance of regulatory changes in human evolution and the development of human-specific traits.

Citations

1. Julien, Pontis.... Didier, Trono. (2022). Primate-specific transposable elements shape transcriptional networks during human development. Nature Communications, 13(1) doi: 10.1038/s41467-022-34800-w Link

2. Julien, Pontis..... Matthias, P., Lutolf. (2021). Primate-specific cis- and trans-regulators shape transcriptional networks during human development. bioRxiv,  doi: 10.1101/2021.08.18.456764  Link

#### Otangelo

May 6, 2021 Most human origins stories are not compatible with known fossils

"When you look at the narrative for hominin origins, it's just a big mess -- there's no consensus whatsoever," said Sergio Almécija, a senior research scientist in the American Museum of Natural History's Division of Anthropology and the lead author of the review. Overall, the researchers found that most stories of human origins are not compatible with the fossils that we have today. "People are working under completely different paradigms, and that's something that I don't see happening in other fields of science. "There are two major approaches to resolving the human origins problem: "Top-down," which relies on analysis of living apes, especially chimpanzees; and "bottom-up," which puts importance on the larger tree of mostly extinct apes. For example, some scientists assume that hominins originated from a chimp-like knuckle-walking ancestor. Others argue that the human lineage originated from an ancestor more closely resembling, in some features, some of the strange Miocene apes.
https://www.sciencedaily.com/releases/2021/05/210506142133.htm

7 May 2021 Fossil apes and human evolution
https://www.science.org/doi/10.1126/science.abb4363