The theory of evolution is well established

Thank you Jellon for a rich opening statement. You quote some quality papers. Whether these actually support your arguments is another matter entirely.In my opening statment, I pointed to the genetic code as the support for random variation in organisms. I proceeded to state that "every living species has a genetic code composed of a series of 4 repeated nucleotide bases", emphasizing the universality of the genetic code. However, con points to a bacterium that was engineered to incorporate new nucleotide bases. [1] The key word here is "engineered". It is perhaps necessary in this case to emphasize that I am referring to naturally occuring living species, although this is what is commonly understood and is evident even in the article cited by con:"All living creatures have a DNA "alphabet" of just four letters, which encode instructions for the proteins that perform most of the key jobs inside cells." [1] Con argues that the genetic code's universality is not evidence for evolution, pointing to a peer-reviewed paper that he claims supports this conclusion. However, he does not develop the point further. I would ask him to clarify which specific claim in the paper negates that proposition. One thing that is asserted in the paper is that the genetic code "is nearly universal" [2] which could be seen as undermining my statement that it is universal. Two points can be raised here. The first is that, in my argument, I judge the universality of the genetic code as a structure rather than through its discrete attributes. That all living species have a genetic code remains true and points to shared ancestry of all species. This is a position that is argued quite explicitely in the paper cited by my debate partner:"in its main features, the structure of the code seems not to have changed through the entire history of life or, more precisely, at least, since the time of the Last Universal Common Ancestor (LUCA) of all modern (cellular) life forms." [2]The above quote is followed by the use of "genetic code" in the sense in which I intended it in my argument:"This universality of the genetic code and the manifest non-randomness of its structure cry for an explanation(s)." [2]The genetic code is thus referred to in two different ways in the paper: by its discrete units; describing it as nearly universal, and as a structure which is universal.The second point that needs to be made is that, even if my argument had centered on the sum of the genetic code's discrete units, a quasi-universal genetic code is still an argument in favor of the theory of evolution. It cannot be stressed enough that what is compelling about the genetic code is that it applies to all living species. Nowadays, this can seem like some form of truism, but before the dawn of genetics, the existence of a shared structure of inheritance for all living beings was not a foregone conclusion. That some species' genetic structures code for additional amino acids or that some viruses use only RNA to encode their genome [3] (another fact con could have used) is irrelevant. Finally, con points to the fact that the quasi-universality of the 4 nucleotide and 20 amino acid remains a puzzle for evolutionary biologists, based on both his opening sources [1][2]. An interesting puzzle, but it does not in any way undermine the fact that the genetic code is universal which in turn consolidates the idea of shared ancestry and, by extension, the theory of evolution.The next argument ventured, that purports to show inconsistency between genetics and predictions that follow from the theory of evolution, is simply baffling. Con makes the following statement:"Evolution predicts that without external causes, we would see an orderly progression of species as determined by molecular homologies [...] There are an overwhelming number of exceptions to this rule."Con then proceeds to quote a source's paragraph whose main point is that the word "homology" is often misused as a placeholder for similarity when talking about sequences, a mistake that con inexplicably makes himself after having read and quoted from this paragraph. [4] The end of the paragraph spells this out clearly:"In all of the above cases, the term “homology” is used basically as a glorified substitute for “sequence (or structural) similarity”." [4] This argument is thus entirely invalid as borne out of misinterpretation. I would encourage con to review the source again in earnest.Con quotes Christian Schwabe extensively, but does not provide specific examples of the quirks that Schwabe takes issue with nor whether his paper or book, written in the 80s and predating the sequencing of the human genome [5], have stood the test of time. I would therefore ask con to expand on some of Schwabe's arguments so that I can properly address them, rather than pointing out what Schwabe had to say, for example, about the scientific establishment. As it stands it is an argument from authority. A fallacy.Con makes the following assertion: "Commonality in DNA in a version of the phylogenetic tree is used as evidence for common ancestry. However, if mutations are indeed random, we would not expect this to be the case."What con has ommited is that, while mutations are random, natural selection is thouroughly non-random. Mutations that are beneficial or simply benign tend to be passed on through the generations and this is obvious in their descendants. Descendants which, given enough time, can belong to different species. This fact alone answers the challenge con set me. Con returns to an earlier source to point out that any explanation would have to account for the fact that "there is more than one genetic code which produces the same function". This undoubtedly refers to the redundancy in codons. It is more accurate to say that more than one codon produces the same amino acid as demonstrated below, but this is hardly an argument against the DNA similarities between two species, it just means that some mutations have a neutral effect as they lead to the same amino acid. http://www.biogem.org...; width="442" height="331" />Convergent evolution shows how powerful a role natural selection plays in evolution, with vital functions such as vision being reinvented many times across the animal kingdom. The piece of research my debate partner presents is certainly groundbreaking. However, the concept, as the paper points out, is not new, only the quantity uncovered by this paper is impressive. [6] In cladistics, we refer to this convergence as homoplasy. [7] As the paper, makes clear, it involves changes in the same genes. It is entirely conceivable that natural selection would favour similar mutations in the same genes in different species, arriving at a similar result, the genes themselves for the most part unchanged between their last common ancestor, except in these crucial ways. A mistake would be to think that the paper advances that genes appear ex-nihilo in one species to resemble the other where there was none. The paper does not defend this, the dolphin and the bat both have modifications in the exact same hearing genes which evolved towards echolocation, the gene framework essentially mostly there already.Punctuated equilibrium is a challenge to gradualism, not an argument against the theory of evolution. Change still happens over long periods of time. Only in geological time are these changes rather sudden. This is one of many internal debates in the field, one documented in a book that chronicles the quarrels between two biologists, Dawkins vs. Gould. Other internal debates include whether group selection occurs. In The Selfish Gene, Dawkins defends the idea that all selection occurs at gene level, another paradigm over which Dawkins and Gould disagreed. What they agree on though is that the theory of evolution is well-established. The following remark by Gould is relevant:"Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists [...] as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abudant between larger groups." [8]It is important to stress continually that nothing in the fossil record blatantly contradicts the theory of evolution and that gaps are not arguments against evolution. It is probably impossible to get the full picture of the tree of life from fossils for the reasons con pointed out but somehow dismisses out of hand. A mere handful of transitional fossils is sufficient to show that evolution works in practice. Any additional transitional fossils found are a bonus. [9]To finish con purports to take my geographical argument apart although does not provide an adequate alternative explanation for the fact that entire groups of species, such as marsupials, are all found in Australia and nowhere else. That marsupials all already existed before the breakup of Australia and all without exception migrated would be extremely random. A randomness that those arguing against evolution themselve abhor. Evolution makes sense of it quite elegantly however, both with fossils and living animals.Again it is important to stress that the evidence put together provides an unecessarily detailed proof of evolution, but that even parts of it could establish evolution alone.[1] http://www.livescience.com... (See above, Jellon [2])[2] http://www.ncbi.nlm.nih.gov... (see above, Jellon [1])[3] http://en.wikipedia.org...[4] http://www.ncbi.nlm.nih.gov... (see above, Jellon [3])[5] http://www.genome.gov...[6] http://www.nature.com...[7] http://en.wikipedia.org...[8] http://www.stephenjaygould.org...[9]