Most of the Human Genome is useless junk

Thanks Mhykiel. I think my opponent will agree with me that the most honest thing either of us can say about the genome is that we do not know at this time if or what most of the genome does. Thus, the question at hand is this: Given what we do know, what we are learning, and how our new understandings are shaping our expectations of what lies ahead concerning the genome, is it reasonable to say that most of the genome is junk? I can no more make a certain declaration than Mhykiel can, but in this round I can and will present my best case that the "junk DNA" paradigm is no longer useful or helpful in any way, that indeed it is a paradigm that has been shown to be a science-stopper for a quarter of a century, and that what we have learned this decade demands a radically new and different view. We have examined together one broad type of DNA that has been deemed "junk:" repetitive NCRs, which make up about half of the genome[10]. We have looked primarily at ERVs and have put one particular study under the microscope. As I pointed out, this study identified specific function for a portion of the genome that had been presumed and assumed to be worthless. My opponent has attempted to diminish the fact that this study reported evidence of wide spread function for this part of the genome. He has his hands full. This is by no means an isolated study. Other studies have found that the LTRs (long terminal repeats) of ERVs in human genes help regulate genes involved in fat metabolism and cell signaling in the liver and placenta [11,12]. Another portion of the genome that had long been deemed useless junk are pseudogenes, which appear to be inactive genes. Richard Dawkins has said that psdueogenes, "once did something useful but have now been sidelined and are never transcribed and translated...Most of them lie scattered along the chromosome like useless molecular cadavers." But we now know that at least some pseudogene derived RNAs are translated into proteins, and some psuedogenes are involved in controlling gene expression. English Biologists have speculated that transcribed pseudogenes are a "potential source of a new class of regulatory gene in the nervous system"[13]. There is good reason from an evolutionary standpoint to assume that most of the genome is indeed functional. First, most DNA is transcribed into RNA. This process, briefly described in my round one argument, is a very complicated process involving many different suites of molecular machines, and it expends a good deal of energy. Why would an organism struggling to survive waste so many resources in a useless endeavor? How, indeed, could it possibly afford to? Second, many regions of the genome are highly conserved across species that are not necessarily closely related. By conserved, we mean that the sequences have not been widely mutated. Regions where mutation has a diminished effect suggest function: if there is no function associated with these sequences,they should mutate freely. That they have not done so strongly implies that mutations have been rejected. Mutations are only rejected if the result of the mutation matters! "We now know that "the genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA/RNA protein complex that makes up chromatin; and the three dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence"[14]. We now know that even the anit-sense strand of DNA (the complimentary strand) is even transcribed in at least some cases! All of this indicates that there is reason to believe that every single nucleotide of the genome may well have a role to play in a process that becomes more complex with every single revelation. The more we learn about the genome and NCRs, the more we are seeing the emergence of an interdependent hierarchical system, with various players - long assumed to be junk - coming into focus as crucial components of the system. Biologist John Mattick has said: "I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century. The failure to realize the full implications of this - particularly the possibility that the intervening non-coding sequences may well be transmitting parallel information in the form of RNA molecules - may well go down as one of the biggest mistakes in the history of molecular biology." Mhykiel defends Jerry Coyne's pronouncement as "the best theory presented," based on the "evidence at the time," but Mattick's observation proceeded Coyne's by more than half a decade! We can go to PubMed alone and find literally hundreds of papers by thousands of scientists investigating possible function for so-called "junk DNA." The ENCODE project was a worldwide effort involving 80 organizations and found "biological activity" in over 80% of the genome. biological activity does not indicate "junk." Quite the opposite: the logical implication, whether from the paradigm of Intelligent design or the paradigm of evolution, is that biological activity indicates potential function! The Advance of Science demands that the old paradigm of ignorance; the proven science-stopper known as "junk DNA," must be replaced with a new perspective that more accurately reflects what we are learning and facilitates an era of new discovery. The old paradigm inhibited discovery. It is time to discard the paradigm of junk DNA as junk science! [10] Albers,et. al., "Molecular Biology of the Cell," 4th edition, p. 203 [11] Medstrand, et. al., "Long Terminal Repeats Are Used As alternative Promoters...," Journal of Biological Chemistry 276(2001) [12] Landry and Mager, "Functional Analysis of the ERV Promoter of the Human Endothelin B Receptor Gene," Journal of Virology 77 (2003) [13] Wells, "The Myth of Junk DNA, pp 51,52 [14] Ibid, p.93