Most of the Human Genome is useless junk

I hope that Mhykiel will forgive the fact that I was more invested in presenting a context than an argument in my opening statement. Recall that my burden in this debate is to introduce a sufficient threshold of doubt against his defense of the claim that most of the human genome is junk. Therefore I thought it prudent to allow him to establish the direction that this debate will be taking before I could make an effective case. He has certainly accomplished this with his opening statement and for that I thank him. Mhykiel has introduced two issues for us to consider. First, the issue of gene expression (Will junior have mama's blue eyes or papa's green eyes?). The fact is that junior could well end up with eye color somewhere between aqua and turquoise; a mix resulting in a contribution from both mom and dad! Indeed, many of our traits reflect a blend of the chromosomes contributed by each of our parents. This is our first clue that gene expression is not as straightforward as my opponent seems to be suggesting. I'm a little confused about exactly what Mhykiel is saying here and I certainly don't want to argue against a straw man, so I think it best to proceed by examining what a chromosome is. Simply put, a chromosome is DNA, tightly wound around a histone protein. For DNA to be copied (transcribed) into RNA, it must be unwound, unzipped, copied, spliced and edited before the final product is ready to code for a protein. This is a very simple explanation of the protein synthesis process. As we will see, protein synthesis is only one of many functions our DNA codes for. Mhykiel argues: "One could take a mother's contributing 23 chromosomes, duplicate them and have all the information needed for a human. This follows then that 50% of the Human Genome is already extraneous, and useless." Indeed, this seems to be the central claim he is making to support his position. Note that Mhykiel concedes humans need a total of 46 chromosomes (not 23). He is correct. An embryo that does not have exactly 46 chromosomes will more often than not be miscarried.[7] For this reason alone, we cannot conclude that 23 chromosomes are extraneous and useless. If nothing else, their presence is necessary for survival! Mhykiel's concession realizes that 46 chromosomes are needed to supply all of the information a human needs. Here he seems to be helping me make my point. If 23 chromosomes were not necessary, we would not need to copy them. We would not need them at all! Indeed, evidence is mounting that all 46 chromosomes could well play an active role in life's information processing systems. In addition to the digital information of the primary sequence, analog information regulating gene expression exists in the 3-D structuring of chromosomes: "The physicochemical properties of DNA...are determined not by base pairs, but by the interactions of successive base steps."[8] Let us return to the central issue: the DNA/RNA protein synthesis system was the first aspect of life's information system that we have gained a reasonable understanding of. But again, only about 2% of the genome codes for the proteins of life. The rest of the genome (most of it, anyway) has been termed "useless junk." My opponent is correct in pointing out that the conflict between ID and the modern synthesis is not our central issue here, but it does shine a light on why some have concluded that most non protein coding regions of the genome serve no purpose while others insist that it must. We do not understand the other 98% of the genome nearly as well as we understand the protein coding regions. Thus, Jerry Coyne can take advantage of our current state of ignorance and declare that "Our genome - and that of other species - are truly well populated graveyards of dead genes."[5] But this is a "materialism of the gaps" view of what we do not understand. Is this view from ignorance correct? This is what we are here to decide. As noted earlier, the process of gene expression is not as straightforward as we might wish to think. Indeed, the more we peer into the inner workings of the genome, the more complex it becomes. The information for coding a gene may be present in a line of genetic text, but we are learning that when and how it is expressed, and to what extent it is expressed are among many factors that are determined by a hierarchy of genetic instruction. It is in the information contained in this hierarchy of regulation and control that we begin to find the possibility of function for the NCRs Mhykiel's second point concerns the endogenous retroviruses (ERVs) which comprise approximately 20% of our genome. Like the champions of the modern synthesis, Mhykiel dismisses this portion of the genome as junk. The deeper we look into ERVs, the more we begin to see a very different picture emerging. Consider this from "Genome Biology": "TE (transposable elements) promoters, particularly the long terminal repeats of (ERVs), initiate transcription at some protein coding genes...TEs have shaped gene regulation by distributing transcription factor binding sites, spawning enhancers, and possibly by composing highly conserved NCRs...Taken together, these studies demonstrate extensive shaping of gene regulatory networks by TE insertions."[9]. In other words, these ERVs and other transposable elements that were assumed to be useless are turning out to play many different roles in controlling the expression of genes! ERVs are just one of many different genomic features that have been assumed to be mere "junk" by the modern synthesis paradigm. I will consistently show during the course of this debate that the more we replace our ignorance with knowledge, the more we are learning the entire genome is a hierarchy of genetic information, and every new insight brings greater understanding that every piece of the genome has a role to play. the next round represents my final opportunity to introduce new arguments. I will be examining many other genomic features that were assumed (and still are assumed by some despite growing evidence) to be useless junk. [7]http://www.marchofdimes.com... [8]http://link.springer.com... [9]http://genomebiology.com...