Darwin's theory of evolution.
Debate Rounds (3)
0. Both faith based and scientific arguments are welcome.
1. Burden of proof is on Con.
While the burden of proof is typically on the one making the claim, regardless of whether a position is mainstream, I will accept the burden of proof for this debate. I must demonstrate the invalidity of the standard Neo-Darwinian theory of evolution which is primarily characterized by biological transformation via natural selection acting on genetic mutations. While there exist unorthodox views of evolution such as punctuated equilibrium espoused by Stephen Jay Gould and others. Phylogenetic gradualism is the "mainstream" view of evolution and thus is the theory I will be arguing against.
When considering the validity of a scientific model, we must first determine the viability of its mechanisms. As it were, I actually have no quarrel with most of the mechanisms which incur visible speciation. However, upon reviewing the literature concerning genetic mutations, one will find it futile to search for a single paper demonstrating the type of genetic change which would lend to the phylogenetic gradualism required for the theory. This is not to say there are a lack of papers discussing how observable changes may have allowed amoeba to evolve into humans over millions of years, but that is all one will find, a lot of conjecture.
Given what we now know about genetics, the lack of evidence for genetic mutations as means for the propagation of novel genetic information is not surprising. What was once touted as vestigial "junk" in the genome of living organisms is now known to primarily consist of redundant information which ensures the robustness and continuity of extant genes. This unexpected level of complexity has proved to be quite a conundrum for evolutionary theory and certainly rings the death knell of phylogenetic gradualism via genetic mutations.
The problem of redundant information, which constitutes the vast majority of an organisms genome, can be summarized by the following: to provide evolutionary change which would allow an organism to traverse the bounds of its family for example, genetic mutations would have to affect germ line mutations which would be passed on to an organism's offspring. These genes however are not only actively working against mutations via excision repair mechanisms, in which a battery of enzymes which inherently recognize the genetic mistakes painstakingly work to correct the mutations, but redundant genes insure the continuity of genetic information as even genes which are permanently affected by mutations will be corrected internally within the cell. That organisms are apparently constrained to redundant informational boundaries is evident by the fact that redundant genes cannot be affected by genetic mutations. If redundant information is immune to translation errors, organisms are thus immune to any substantial level of mutational degradation. This is not to say mutations are never passed on to offspring, but harmful mutations are relatively rare due to the multiple levels of information security measures present in genomes.
As for beneficial mutations, these are even rarer, though certainly possible. However, no example of mutations, beneficial or not, have ever constituted as evidence for the addition of novel genetic information since such examples are only ever deletions, duplications, or rearrangings of existing information. Many of the beneficial mutations can also be seen as genetically intentional events triggered by environmental cues such as the example seen in E. coli bacteria digesting citrate.
The issue though is not whether a mutation, however rare, can confer a survival benefit but it concerns their capacity for the induction of novel genetic information. Given that mutations are only ever corruptions of existing information and that redundant genes serve as a bounds for speciation, this would be an expectedly impossible occurrence. Mutations would need to be acting on germ cells at an exceptional rate to allow the rare event of genetic errors, and on top of this, these genetic errors would have to provide novel information in such a gradual way as to lead to a novel trait over many generations. Such mutations which provided piecemeal information would almost certainly be prevented from culminating into any sort of trait as redundant genes would work to correct them.
Thus what we know about genetics demonstrates the infeasibility of phylogenetic gradualism via genetic mutations. Given that there is not even a single published paper providing evidence for the creation of novel genetic information by means of genetic copying errors, even in controlled conditions, the theory of evolution is brought into serious doubt. Without a viable mechanism for genetic change which can be supported by the scientific method, Neo-Darwinian evolution is going upstream without a paddle.
We could discuss fossils and natural selection, but without a mechanism for genetic change which is required by the theory of evolution, any interpretation of fossils and examples of natural selection would both be anecdotal and an unwarranted extrapolation respectively. I will defend any of my claims in the next round. I look forward to an engaging and thoughtful dialogue. On to Pro.
Always interesting to see that people attack evolution on different fronts. This is part of the reason I didn't bother to make much of an argument for round 1. Since the angle of attack by my opponent is unknown at that point. My opponent is attacking on the mutation becoming permanent and passed on front. Citing DNA repair and redundant DNA as safeguards again mutations.
DNA repairs, but its not infallible.
"Of the thousands of random changes created every day in the DNA of a human cell by heat, metabolic accidents, radiation of various sorts, and exposure to substances in the environment, only a few accumulate as mutations in the DNA sequence. We now know that fewer than one in 1000 accidental base changes in DNA results in a permanent mutation; the rest are eliminated with remarkable efficiency by DNA repair." 
What this means is despite the DNA repair system being incredible efficient, the repair system is overwhelmed by constant environmental factors. Therefore, DNA damage happens despite the repair system.
Claim 1: Redundant DNA helps organisms survive despite mutations.
Warrant 1: "New findings from a Princeton-led team of researchers suggest that repeated instructional regions in the flies' DNA may contribute to normal development under less-than-ideal growth conditions by making sure that genes are turned on and off at the appropriate times. If similar regions are found in humans, they may hold important clues to understanding developmental disorders." 
Impact 1: Oddly, the redundant DNA provides supporting evidence for Darwin's theory of evolution. What redundant DNA means is the the organism can survive despite detrimental mutations. Therefore, the chances of the mutation being passed onto the next generation is increased. Think about it, without the redundant DNA the organism with the detrimental mutation would be more likely to die and not reproduce.
DNA repair mechanisms provide supporting evidence for Darwin's theory of evolution. Otherwise, we would have the opposite problem, rampant permanent mutations everywhere. DNA repair mechanisms explain why permanent mutations are so rare.
Redundant DNA helps protect the organism with mutations. Allowing the organism to function normally despite permanent mutations and pass their permanent mutations onto their offspring.
Unfortunately it seems that my opponent has failed to understand my argument. He states, "My opponent is attacking on the mutation becoming permanent and passed on front. Citing DNA repair and redundant DNA as safeguards again mutations." I myself stated that mutations can be passed on and be either harmful or beneficial. Allow me to quote myself, "Mutations would need to be acting on germ cells at an exceptional rate to allow the rare event of genetic errors, and on top of this, these genetic errors would have to provide novel information in such a gradual way as to lead to a novel trait over many generations. Such mutations which provided piecemeal information would almost certainly be prevented from culminating into any sort of trait as redundant genes would work to correct them."
Thus, while mutations can certainly be carried on to offspring, the types of gradual, information-adding mutations which would lead to specified code are highly improbable. Consider the purported evolution of birds from dinosaurs; the genotypic changes required would mean that literally millions of germ line mutations would have to act on thousands of generations of dinosaurs and transitional creatures to randomly culminate into specified genes which code for entirely novel traits such as feathers, chambered lungs, and avian nervous systems. While such a scenario is overtly improbable as stated, given what we now know about redundant genes and how they preserve genetic continuity, the claim of phylogenetic gradualism via the induction of novel genes through mutations becomes scientifically, extremely improbable. Given that a model for such a mechanism has never even been published, let alone evidence for it, phylogenetic gradualism in light of modern genetics is wishful thinking at best. With all that said, allow me to address my opponent's primary claim.
Pro states, "Oddly, the redundant DNA provides supporting evidence for Darwin's theory of evolution. What redundant DNA means is the the organism can survive despite detrimental mutations. Therefore, the chances of the mutation being passed onto the next generation is increased. Think about it, without the redundant DNA the organism with the detrimental mutation would be more likely to die and not reproduce." Firstly, your cited quotation does not support your statement at all. Findings of genes which are "switched" on or off by environmental cues triggering redundant genes only supports my statement concerning the potential for many beneficial mutations to be programmed responses rather than mutations randomly conferring a beneficial trait. Regardless, your statement that redundant genes support evolution because it enables an organism to survive in spite of mutational degradation reflects your failure to understand my argument. Yes, redundant genes help an organism survive, but they do so by preserving genetic continuity and ensuring genotype robustness. This, in turn, means that slight, successive modifications are highly improbable since redundant genes will act to fix errors over many generations. Since mutations are not acting on redundant genetic information, these genes will preserve genotypes from any significant change (which in genetic terms is a very small number).
Allow me to reiterate my argument: redundant genes, which constitute the vast majority of an organisms genome, and which are not the product of genes duplication, but are purely inherited genes, serve as a virtually incorruptible back up file to every actively coding gene as well as genes which are not "switched on." While this allows for variation within the bounds of the redundant genetic information, these genes prevent the induction of significant genotypic changes. While mutations are occasionally passed on to offspring, the types of mutations required by evolution are not able to occur, even if such a hypothetical mechanism was able to be modeled. Here's why====>the standard theory of evolution which describes phylogentic gradualism via natural selection acting on random genetic copying errors requires millions of mutations which add bytes of digital code over many generations that will culminate into a novel trait. While this is an improbable event in and of itself, the discovery of redundant genes astronomically increases the improbability. As corrupted genes are passed on through germ line cells, redundant genes within the organisms of each generation will work to prevent any culmination of mutations which would significantly alter a genotype.
Figure 2. A very simple scheme of a small robust network comprised of A–E, where several nodes are redundant.
"Genes never operate alone but in redundant scale-free networks with an incredible level of buffering capacity. In a simple non-linear biological system—presented in figure 2—with nodes A through E, A may cause B, but A also causes D independent of B and C. This very simple network of only five nodes demonstrates robustness due to redundancy of B and C. If A fails to make the link with D, there are still B and C to make the connection. Extended networks composed of hundreds of interconnected proteins ensure that if one network becomes inactivated by a mutation, essential pathways will then not be shut down immediately. A network of cooperating proteins that can substitute for or bypass each other’s functions makes a biological system robust. . .In a cascade of activation and deactivation of signalling proteins, external messages are transported to the nucleus with information about what is going on outside so it can respond adequately. If one of the interactions disappears, this will not immediately disturb the balance of life. The buffering capacity present in redundant genetic networks also provides the robustness that allows living systems to propagate in time. In a linear system, one detrimental mutation would immediately disable the system as a whole: the strength of a chain is determined by its weakest link. Interacting biological networks, where parallel and converging links independently convey the same or similar information, almost never fail. The Golden Orb’s web only crumbles when an entire spoke is obliterated in a crash with a Dragonfly, an event that will hardly ever happen. Biological systems operate as a spider’s web: many interacting and interwoven nodes produce robust genetic networks and are responsible for genetic redundancy" (http://creation.com...).
It is possible for harmful mutations, even ones which may confer a survival benefit, to be unchanged by redundant genes, but these are often point mutations or corruptions of relatively tiny segments of DNA. The culmination of mutations which would lead to novel traits would constitute millions of sequences of specified digital coding segments of DNA. These large segments would certainly be prohibited by redundant genes since we know from today's observations that they are actively maintaining and preserving the genome of organisms and correcting even small segments of corrupted DNA. The tombstone on the grave, as it were, of phylogentic gradualism is the fact that evolution does not require a single event of millions of random mutations culminating into a single novel traits but tens of thousands of these events all converging into a single, well-adapted organism. Whatever the scientific improbability of a single culmination event, must logically be multiplied (not statistically, but logically) by tens of thousands of times. A statistical argument can certainly be made using the information of redundant genes and complex genetic networks, but this is not such an argument. Again, I am arguing from scientific improbability based on what we know about the function of redundant genes and their preservation of the continuity of genotypes. I will gladly clear up any confusion and address any additional rebuttals in the next round.
Thank you for your time and consideration of my argument. On to Pro.
Con has the burden of proof and has failed to falsify Darwin's theory of evolution. How could evolution be proved false? Here's the answer
" If it could be shown that organisms with identical DNA have different genetic traits.
If it could be shown that mutations do not occur.
If it could be shown that when mutations do occur, they are not passed down through the generations.
If it could be shown that although mutations are passed down, no mutation could produce the sort of phenotypic changes that drive natural selection.
If it could be shown that selection or environmental pressures do not favor the reproductive success of better adapted individuals.
If it could be shown that even though selection or environmental pressures favor the reproductive success of better adapted individuals, "better adapted individuals" (at any one time) are not shown to change into other species. " 
Impact, my opponent has only used words and conjecture. I don't understand how this works, so therefore it must be false. "There is no evidence for p.
Therefore, not-p." 
My opponent uses this form of the fallacy. There is no evidence for how mutations get past the DNA repair mechanism and redundant DNA in reproductive cells. Therefore, not Darwin's theory of evolution. Yet, this isn't the way science works. You must prove the hypothesis false. Thanks for your time and energy reading.
Pro states, "My opponent uses this form of the fallacy. There is no evidence for how mutations get past the DNA repair mechanism and redundant DNA in reproductive cells. Therefore, not Darwin's theory of evolution. Yet, this isn't the way science works. You must prove the hypothesis false. Thanks for your time and energy reading." Firstly I would point out that this was not my argument. For the third time I must clarify that I am not arguing that mutations cannot be passed on to offspring, this would obviously be a silly argument. Secondly, I do not have to prove a hypothesis false for it to not be true. I can argue the hypothesis that God exists, but you don't have to prove it false for it to not be true. Science works to establish the veracity of an hypothesis through experimentation and observation; science does not determine truth by seeing if a hypothesis can be disproved but by seeing if it can be substantiated.
I find it unnecessary to restate my argument and, although Pro has claimed he did not fully comprehend it, he also did not point out any particular areas of confusion. My argument was based on the known function of redundant genes and their inhibition of the cumulation of any sort of information-adding mutations which would give rise to phylogenetic gradualism. My arguments have gone unrefuted while I have conclusively refuted my opponents claims.
I hope readers are able to understand my argument and that it might interest them enough to do some further research of their own. If someone thinks they can rebut my argument then I will gladly accept their challenge. Thank you for your time and consideration of my case gains evolution. :)
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