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

C1) Multiple Nested Hierarchies are generated independently Con mistakes initial assumptions which were later proven for circular reasoning. As I mentioned, if I stopped at a single nested hierarchy, it would be reasonable to Con to argue this point. I don't claim that the mere fact that we can organize into hierarchies to be evidence of common descent. I pointed out why evolutionary processes can generate a unique hierarchy. If the morphological and molecular hierarchies differed - and there is a really big chance of differing - common descent would be disproved. When a different, independent method gives us the same result as our initial assumption with startlingly high statistical significance, the conclusion is that our initial assumption is true. If Con's claim that common descent is false and that the hierarchies were just made up, we should end up with different trees for the different experiments. The chance of ending up with the same tree is 1 in 10^38. Con has continued to attack the independence of the molecular method from the morphological method but has yet to refute my analysis on ubiquitous proteins. Cytochrome c transports electrons and helps cells generate energy. All living organisms do this the same way. It is a fundamental metabolic process. The cytochrome c of humans for example functions in yeast which are as about as far apart as you can get. Yeasts are eukaryotic micro-organisms classified into the kingdom fungi [34]. Con continues to say that molecular similarity is based on morphological similarity yet never refuted my argument about ubiquitous proteins.If common descent isn't true, organisms that are morphologically similar would be molecularly different because of the functional redundancy of cytochrome c. There are 10^93 different sequences of cytochrome c that can perform the same function. Common descent does propose that all species are related. As I've explained in round 1 with the phylogenetic tree, the degree of relation varies. If common descent were false, ubiquitous proteins would be randomly sequenced among life as opposed to being more similar in closely related species. Con looks at it as a dichotomy and says that biologists wouldn't know about unrelated species and that the model for common descent doesn't allow for one. However, nested hierarchies have several branches of separation and it is not an either/or scenario. Humans are more related to chimpanzees than they are to yeast. C2) Scientific agreement and Tomkins study Tomkins study should be discarded for the following reasons: I've shown why it is irrelevant to the debate. My argument was that ubiquitous proteins should be considered. Tomkins doesn't do this. Con didn't refute this point and concedes most of it while asserting that “discontinuities are being ignored.” I've shown exactly why biologists consider ubiquitous proteins. Con was unable to show how Tomkins met this criteria. Tomkins' study doesn't match with studies with the rest of the scientific community. Other studies show human-chimp DNA over 96% alike [35][36][37]. Con claims that scientific agreement is an argument from popularity. Yet, Con was the one who brought it up in the first place. He claimed that scientists disagreed on evolution. I proved that they don't. I showed that his Lynn Margulis evidence actually supports my side. I've also shown why Tomkins study is irrelevant to my argument as it doesn't take into account ubiquitous proteins. It also contradicts the rest of the scientific community. Whether scientists agree was Con's contention to begin with and Con now says that it is a fallacy. C3) Observed speciation combined with fossil record points to common descentCon continues to argue that we cannot observe macro-evolution on a large scale. Yet, it takes tens of millions to years to see vast, large-scale changes. We have fossils to show us that these changes have taken place. Con completely drops the fossils and claims that unless a mechanism is shown, the fossils are void. The mechanism has been shown on a small-scale so we know a mechanism exists that causes speciation and micro-evolution. Con says that adaptation is redundant with evolution. Yet, the only difference is time-scale. The underlying causes are the same. Con's claim of a limiting factor is contradictory and ill-defined. Cows are of the species Bos Primegenius [38]. He says that cows cannot change into anything other than cows which implies that he disagrees with speciation. Yet, he then claims that all cases of speciation result in the same kind of organism implicitly accepting it. Con's definition of kind is also contradictory because on the one hand, he classifies entire kingdoms of microbial life into the same “kind” while also classifying a single species cow into one kind. While he may not agree with the taxonomic classification, it rested on him to define “kind” appropriately which he didn't.With the absence of a coherent limiting mechanism, the logical conclusion is that micro-evolution can be extended to a common ancestor. The fossil record corroborates this conclusion. Con has not responded to my points about the Archeopteryx and whale evolution which gives evidence of the micro-evolutionary process continuing on a large time scale. He has also not refuted that older strata of whale fossils show terrestrial whales and later strata more and more aquatic ones. He has not contested radiometric dating as an independent tool for stratigraphic analysis. Con says that his religious beliefs are irrelevant to the debate and I agree. However, I've shown that his claim of a designer would suggest a highly deceptive designer based on the overwhelming evidence in favor of common descent. CONCLUSION: Common Descent is a scientific explanation for the origin of speciesTo determine science from pseudoscience, we should look at a few key characteristics:Adherence to a scientific method: I've provided a simplified flowchart for this. Con's response makes the same mistake of failing to consider that biologists have looked specifically at ubiquitous proteins which are common to all living organisms.Basis on empirical evidence: The fossil record, molecular evidence from proteins, transitional links between species and the geologic location of those links all point toward common descent.Demonstrability: Evolutionary processes have been observed. Con doesn't deny micro-evolution and speciation. The fossil record shows that this same processes have occurred on a larger time scale.Testability/Falsifiability: Con claims that common descent ought to be assumed. I agree that it was initially assumed as a hypothesis. Science involves gathering evidence to test or falsify hypotheses. This is what science is at its core. My flowchart shows as much. Making assumptions and proposing hypotheses aren't pseudoscience. Since the phylogenic trees generated from the molecular and nested hierarchies are statistically the same, common descent is corroborated.Weighing Mechanism: To show that Universal Common Descent is pseudoscience according to our definition, Con must show that it does not adhere to a valid scientific method which he hasn't. He must show that it lacks supporting evidence or plausibility for which he has ignored the fossil record which shows that observed micro-evolution continues on a large scale. He must show that it cannot be reliably tested or falsified where he fails because independent evidence from morphological, molecular, and fossil evidence all point toward common descent. He must show that it lacks scientific status for which he quickly dropped his attempt to do so by claiming that agreement among scientists is an appeal to popularity.Universal common descent both meets and exceeds the criteria to be considered science. Sources[34] http://en.wikipedia.org...[35] http://tinyurl.com...[36] http://tinyurl.com...[37] http://tinyurl.com...[38] http://en.wikipedia.org...