Universal Common descent is a scientific explanation for the genetic origins of living organisms

C1) Multiple Nested HierarchiesA nested hierarchy refers to the way taxonomic groups fit completely inside other groups [3]. For example, all humans are mammals, all mammals are animals and so on. A specific method of organizing nested hierarchies is the cladistic method which is based on common descent [10]. If common descent is true, members of a group would have to share unique features which were not present in distant ancestors. These features that are shared between two or more groups and their most recent ancestor are called synapomorphies as shown in Figure 1 [6][11]. Figure 1: The vertical shaded regions show synamorphiesAs we represent these genealogical relationships in a tree, we get a branching tree-like diagram called a phylogeny. A simplified version of the standard phylogenetic tree is shown in Figure 2 [4]. Figure 2: Simplified standard treeAs the phylogeny shows, we can group organisms into various nested sub-groups based on morphological features. The only known processes that specifically generate unique objective nested hierarchical patterns are evolutionary processes [7]. The difference between subjective and objective hierarchies is an important distinction. Any group of things can be organized into a hierarchy. Automobiles can be grouped first by their manufacturer, then by the number of wheels, then by gas mileage etc. Yet, a different classification could be made by grouping by number of wheels first, then by manufacturer and so on. The attribute chosen first is determined by the individual. Many phylogenies that are equally well-supported can be generated which all look different despite having the same initial data. An objective nested hierarchy on the other hand produces a unique, well-supported tree much like the classification of languages which evolved from a common ancestor. The degree to which a phylogeny shows a unique, well supported tree has been quantified with extensive statistical analysis. These tests measure the degree of hierarchical structure within a phylogeny. One such study performed by James Archie of the University of Hawaii randomizes the given data and performs cladistic analysis on the randomized data to obtain a distribution of minimum tree lengths. He then tests whether the minimum tree length generated by the real data is significantly less than that generated by the randomized data as shown in Figure 3 [9]. Figure 3: The minimum lengths are significantly higher after randomizationThis establishes that evolutionary processes generate nested hierarchies that are objective and unique. Species can be easily organized into nested hierarchies based on morphology. As shown in Figure 1, animals can be organized into ones with organs and ones without. Within animals with organs, there are vertebrates and invertebrates. Vertebrates are never found without organs. Similarly, mammals are never found with feathers. This is a very specific consequence of the mechanism described by common descent. Furthermore, species can also be grouped based on independent molecular studies. Certain genes called ubiquitous genes exist in all living organisms because they perform very basic functions. Any given ubiquitous protein has a very large number of protein sequences which can perform the same function. No specific sequence of proteins are functionally necessary for a given organism. Heredity is the only mechanism which causes two organisms to have similar sequences for ubiquitous proteins. Cytochrome c is one such essential and ubiquitous protein found in all organisms. A study by Hubert Yockey shows that there are 2.3 * 10^93 possible sequences for cytochrome c. Humans and chimpanzees however have the exact same cytochrome c protein sequence. [6] Phylogenies made from molecular studies [14] match with phylogenies from pre-molecular morphological analysis [13] with high statistical significance. There are 10^38 different possible trees that could have been developed yet both morphological and molecular studies yield similar trees with greater than 99% confidence [16]. If common descent were false, independent cladistic phylogenies based on common descent generated using different criteria must lead to different phylogenies.C2) Comparative Anatomy Since the standard phylogenic tree is the best approximation of a unique tree, all fossils are expected to conform to it within the error of scientific methods. According to the standard tree, we would expect intermediates between birds and reptiles and between birds and mammals. However, we would not expect to find intermediates between birds and mammals [20]. Archaeopterex is a well-known intermediate species between birds and reptiles. Figure 4: ArchaeopterexThe wrist and finger bones are unfused like in theropod dinosaurs and a long bony tail is present as in reptiles. Like birds, it has wings but those are structurally dissimilar to modern birds. Parahomology is structural similarity with functional differences. When a species branches out, it may acquire new functions. To perform these functions, it works by modifying the existing structures. The same bones in the same relative position of the human hand perform different functions in bat wings, mole forelimbs, and whale and penguin flippers [17]. Independent fossil records confirm that these structures were derived from others with a general chronologic progression of intermediate forms. Theropod dinosaur structures for instance were modified into modern bird structures. Common descent could easily be falsified if the fossil record showed bird wings transforming chronologically into reptilian arms. Fossils records show the origin of whales from terrestrial mammals based on morphological and vestigial evidence. The fossil sequence from terrestrial mammals show more and more whale-like forms appearing until the development of the modern whale. Figure 5: Whale evolution [18]For instance, the anvil of the middle ear in the Pakicetus is morphologically intermediate between modern whales and modern artiodactlys (like cows and hippo). Vestigial structures provide strong and direct evidence of common descent. Vestigial organs are rudimentary body parts smaller and simpler than corresponding structures in ancestral species [21]. Modern whales have rod-like pelvic bones, femora, and tibeae, alll embedded in their musculature while earlier species like Basilosaurus have intermediate sized vestigial pelvis and rear limb bones [19][22]. The chronology also matches as it co-incides with extinction of marine predators which allowed pre-historic whales to move into the sea [22]. To conclude, the morphological and molecular nested heirarchies match closely enough such that it would be nearly impossible for them to be random chance. Furthermore, we can clearly see evidence of common descent from transitional links like the Archeopterex and the fossil evidence of the transition of whales from land mammals to aquatic mammals.Sources[3] http://evolutionwiki.org...[4] http://tinyurl.com...[5] http://tinyurl.com...[6] http://tinyurl.com...[7] http://pandasthumb.org...[8] http://www.math.osu.edu...[9] http://www.botany.wisc.edu...[10] http://www.ucmp.berkeley.edu...[11] http://en.wikipedia.org...[12] http://tinyurl.com...[13] http://archive.org...[14] http://www2.isye.gatech.edu...[15] http://tinyurl.com...[16] http://tinyurl.com...[17] http://tinyurl.com...[18] http://www-personal.umich.edu...[19] http://www.sciencedaily.com...[20] http://tinyurl.com...[21] http://tinyurl.com...[22] http://www.talkorigins.org...[23] http://www.talkorigins.org...