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Steve
Jul 30, 2023
In Bone Cells (Osteocytes)
Osteocytes are a type of specialized bone cell that play a crucial role in maintaining bone health and function. They are the most abundant cells found in mature bone tissue. Osteocytes are derived from osteoblasts, which are responsible for the formation of new bone but, instead of depositing new bone matrix, osteocytes become embedded within the bone matrix that has already been laid down. Osteocytes are located within small spaces called lacunae, surrounded by bone matrix known as the osteoid.   Nanotyranus osteocyte cells - (Images provided by Mark Armitage) Dinosaur osteocyte (bone) cell The lifetime of osteocytes post mortem can vary depending on environmental conditions and preservation methods. After an organism dies, cells start to degrade and undergo various changes. However, osteocytes, being encased within the mineralized bone matrix, can persist for some time after death. The mineralized bone matrix provides protection to the osteocytes, slowing down their degradation and decomposition In some cases, osteocytes remain preserved in bone tissue for several years or even decades.   Under normal conditions however these cells decay and there is no known mechanism to account for their persistence as recognisable bone cells into ‘deep time’ (millions of years). The observation of osteocytes in dinosaur bone samples therefore raises a number of questions, the main one being ‘how is this possible …?’ There are now more than 120 papers in peer-reviewed journal articles reporting soft tissues in dinosaur and other deep-time organic remains. These scientific papers describe biological material, including tissue and DNA, remaining inside fossils. A full list, which is being continually updated, is provided here: *List of Biomaterial Fossil Papers(http://tinyurl.com/4htm54w9) Example papers for this topic: (47) Triceratops blood vessels, osteocytes 2007 (69) Jurassic turtle osteocytes 2012 (73) Dino DNA & proteins actin, tubulin, PHEX, histone 2013 (77) Triceratops osteocytes; soft sheets of fibrillar bone 2013 (114) Hadrosaur eumelanin, blood vessel, osteocytes 2019 (122) Turtle blood vessels and osteocytes 2022 An additional paper not currently in the Biomaterial Fossil List: https://doi.org/10.1101/400176 (https://doi.org/10.1101/400176) Life Inside a Dinosaur Bone: a Thriving Microbiome 2018 *This list of biomaterial papers can provide useful information for research and posting on topics within the Dinosaur Project Community. Thanks to researchgate.net (http://researchgate.net)for making this list freely available.
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Steve
Jul 30, 2023
In Geologic Column
The geological column, also known as the geologic column, is a fundamental concept in geology that represents the organization and relative timing of Earth's rock layers, strata, and the history of Earth's geological events. It is a visual representation of the Earth's history, displaying the sequence of rock formations, fossils, and events that have shaped the planet. The geological column is divided into different units called "geological periods" or "geological epochs," each representing a distinct interval of time in Earth's history. These periods are defined based on the types of fossils found in the rocks and the overall characteristics of the sedimentary layers. The geological periods are arranged in chronological order, from the oldest at the bottom to the youngest at the top. The idea of the geological column was developed in the 19th century by geologists and palaeontologists who studied rocks and fossils from various locations around the world. They noticed consistent patterns of sedimentary layering and fossil succession that allowed them to propose a coherent timeline of Earth's history. The standard geological column is typically divided into four main eras: Precambrian: This is the oldest and longest era in Earth's history, covering about 88% of geological time. It is further divided into several eons, such as the Hadean, Archean, and Proterozoic, which include the earliest known rocks and evidence of life on Earth. Paleozoic: Following the Precambrian, this era covers a significant span of time and is marked by the rise of complex life forms, including fish, amphibians, and early reptiles. It includes periods like the Cambrian, Ordovician, Silurian, Devonian, Carboniferous, and Permian. Mesozoic: This era is often referred to as the "Age of Dinosaurs" and includes the Triassic, Jurassic, and Cretaceous periods. Cenozoic: This is the most recent era, spanning from the end of the Mesozoic to the present day. It includes the Paleogene and Neogene periods, as well as the current ongoing period called the Quaternary. It's important to note that the geological column is a general representation of Earth's history, and local geological variations and unconformities can complicate the complete picture. Nonetheless, it serves as a valuable tool for understanding the relative ages of rocks, their approximate deposition sequence and the timing of events that have shaped the Earth over time. Although it is usually considered to have been laid down over hundreds of millions of years (geological or ‘deep time’) there are a number of observations that call that timescale into question. For example, it is well known and agreed that catastrophic processes of deposition can accelerate the usual ‘slow and gradual’ processes by orders of magnitude [https://creation.com/secular-neocatastrophism ]. Another evidence of rapid formation of the geological column is that soft tissue is found in pre-Cambrian layers [https://doi.org/10.1038/srep03497] as well as Quaternary layers https://doi.org/10.1038/s41586-021-03224-9 ]. In many case the soft tissues have the same form and features irrespective of the age estimates made according to the geological time [Schweitzer et al, Proc. Roy.Soc, B, 2007 (fig 3) doi: 10.1098/rspb.2006.3705). How could soft tissue have remained looking the same over millions of years…? There are now more than 120 papers in peer-reviewed journal articles reporting soft tissues in dinosaur and other deep-time organic remains. These scientific papers describe biological material, including tissue and DNA, remaining inside fossils. A full list, which is being continually updated, is provided here: *List of Biomaterial Fossil Papers Example papers for this topic: (47) Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous 2007 *This list of biomaterial papers can provide useful information for research and posting on topics within the Dinosaur Project Community. Thanks to researchgate.net for making this list freely available.
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Steve
Jul 27, 2023
In Biochemicals (Other)
In the last 60 years, the advent of powerful mass spectrometers has led to advances in the field of proteomics (analysis and identification of amino acids, lipids, polypeptides and proteins). The discovery, by many researchers of proteins in the geological column, has led to the new and emerging field of paleoproteomics. Large proteomic databases such as Swiss-Prot are able to identify individual proteins such as collagen and keratin with a high degree of certainty. In 2019 a review of all the papers published in the scientific literature since 1966, documenting soft tissue (including proteins) in the geological column, was undertaken. The results were startling; at that point (2019) there were over 70 papers documenting such finds found all over the world. Since then to date (2023), a further 50 papers have been published, making the total over 120. Once thought to be impossible, the use of these advanced materials analysis techniques has revealed fragile proteins in a range of fossils extending throughout the geological column. Since so many biochemicals can now be identified to a high degree of certainty in these deep-time soft tissues (a few listed above), what can they contribute to our ‘knowledge’ of the true ages of the fossils? There are now more than 120 papers in peer-reviewed journal articles reporting soft tissues in dinosaur and other deep-time organic remains. These scientific papers describe biological material, including tissue and DNA, remaining inside fossils. A full list, which is being continually updated, is provided here: *List of Biomaterial Fossil Papers Example papers for this topic: (106) Anchiornis feather keratin 2019 (96) Melanin in nodosaurus dino (and other biologicals) 2017  (58) Hadrosaur biomolecules, collagen & other proteins 2010 (10) Dinosaur proteins and polysaccharides 1974 *This list of biomaterial papers can provide useful information for research and posting on topics within the Dinosaur Project Community. Thanks to researchgate.net for making this list freely available.
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Steve
Jul 27, 2023
In DNA, Proteins & Amino Acids
It could be argued that the ‘ultimate’ soft tissue is DNA. The sequence of nucleotide bases in DNA encodes the genetic information in an organism and this information is used to synthesize proteins and other molecules essential for the proper functioning and development of the organism. Although DNA is stable, it is fragile; certain chemicals, such as strong acids or alkalis, can break the sugar-phosphate backbone of DNA or modify the bases, resulting in DNA damage. DNA can be physically damaged by mechanical forces such as shearing forces that break the strands or by physical disruption during cell division or other cellular processes. Enzymes known as nucleases can degrade DNA by cleaving its phosphodiester bonds, and these enzymes are crucial for various cellular processes including DNA repair and DNA degradation during programmed cell death (apoptosis). Over time, DNA naturally degrades and this begins immediately post-mortem. The presence of water can accelerate this process. Researchers and scientists handling DNA in laboratories take special precautions to preserve its integrity. For example, DNA samples are often stored at low temperatures and protective measures are taken to avoid exposure to UV light and contaminants. Additionally, special techniques, such as DNA extraction and purification protocols, are used to minimize damage during experimentation. Based on experimentation some researchers have calculate DNA half-life of less than 1000 years: “By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 x 10-6 per year” (Allentoft et al, Proc. R. Soc. B (2012) 279, 4724–4733). But DNA has been reported in mammoths and more recently in dinosaurs…So, the question is, how does any DNA survive into deep time (> 1M years)? Could it be that the concept of deep time itself has a half life and at we are approaching the end of its time as a useful concept? There are now more than 120 papers in peer-reviewed journal articles reporting soft tissues in dinosaur and other deep-time organic remains. These scientific papers describe biological material, including tissue and DNA, remaining inside fossils. A full list, which is being continually updated, is provided here: *List of Biomaterial Fossil Paper Example papers for this topic: (58) Dino DNA & proteins actin, tubulin, PHEX, histone 2012 (109) Cretaceous DNA for mitochondrial cytochrome b 2012 (121) Caudipteryx chromatin/DNA 2021 *This list of biomaterial papers can provide useful information for research and posting on topics within the Dinosaur Project Community. Thanks to researchgate.net for making this list freely available.
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