Most of the Human Genome is useless junk
Debate Rounds (5)
My burden in this debate is to inject a sufficient threshold of doubt against the claim that most of the human genome is useless junk. Though it is not strictly necessary, I intend to go above and beyond my burden. I intend to provide you with the confidence to believe that the entire genome could well be functional!
the 20th century bore witness to an amazing revolution in our understanding of what drives all life. Just decades after society became largely convinced that Darwin had succeeded in showing what we had always assumed to be designed - life - was nothing more than the appearance of design, we learned that information lies at the heart of life. We learned that DNA is in fact a linear digital code which prescribes the many various proteins necessary for life. This protein coding system lies at the very heart of our debate. Also at the heart of our debate is a clash of two very different views of the origin of this information system and the opposite predictions concerning genetic information.
The seeds of conflict are born of the realization that only a tiny fraction of DNA actually codes for these proteins necessary for life. Various sources place the amount of protein coding DNA between 1.5%-2.5%. What to think of the remaining DNA?
It's time to introduce the players: The view that life can be explained as a chance arrangement of matter; a mere accident of physics and chemistry ( I will refer to this view as the modern synthesis going forward), quickly became the dominant view of the scientific community in advance of the revelation of genetic information. But this revelation challenged the very foundation of the modern synthesis mere decades after it had been established. Functional information never arises out of the mere interplay of matter and energy; it's source is always intelligent agency. Thus, the discovery that digital code drives the processes of life gave birth to the modern Intelligent Design movement. ID acknowledges what we know to be true about the information of life and what we know to be true about the origin of functional information, and concludes that Intelligent Agency is the best explanation for the origin and diversity of life, based on the evidence.
Thus, as we approached the end of the last century, we had two very opposite views of life: the entrenched view which saw life as nothing more than a purposeless accident, and the new kid on the block which saw the deliberate purpose and foresight of intelligent agency. Given that some 98% of the genome does not code for proteins, it might be expected that the former would predict that this portion of the genome served as an evolutionary relic that had mutated itself into uselessness and the latter would predict a purpose that may extend beyond protein coding.
This is exactly what happened, and it is in the context of a study of opposite predictions that I intend to make my case. It is true that a fraction of the non-protein coding regions hinted at function and it is also true that some supporters of the modern synthesis (I will refer to these supporters as Darwinists going forward) urged caution, but the fact is that the view that most of the genome is junk quickly became the dominant view. It is also true that many high profile darwinists were quick to make predictions and that many of these predictions were aimed squarely against ID.
Richard Dawkins, Francis Collins, Douglas Futuymana, Michael Shermer, Kenneth Miller, Jerry Coyne, and John Avise comprise a veritable who's who of leading Darwinist thinkers. All of them have declared that the presence of junk DNA constitutes dramatic evidence in favor of the modern synthesis and damning evidence against ID. For example, Shermer said, "We have to wonder why the Intelligent Designer added to our genome junk DNA", and Coyne said, "the evolutionary prediction that we'll find pseudogenes has been fulfilled - amply." He sets up the clash very well: "Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution; in fact it's precisely what we would expect from evolution"
Indeed, if it is true that the genome is littered with junk, the point these men make is not only reasonable, it is undeniable. But very different predictions were emerging from the ID perspective. As early as the 1990s, several independent design theorists predicted we would learn that much of so-called junk DNA does serve a purpose.
There are several different types of so-called junk DNA. Having laid the groundwork in this round, I will examine many of these different types in the following rounds, revealing the darwininst assumptions and then exploring how things have changed as we have progressed from ignorance into knowledge. In each case, we will find that the more we have learned about these regions of the genome that do not code for proteins ( I will refer to these regions as NCRs - non coding regions - going forward ), the more function we are discovering. The evidence will accumulate, showing an irreversible trend away from junk and toward function.
Within the caveat that what needs to be explained is the origin of genetic information, I agree with Jerry Coyne and the others: if the genome is littered with junk, this constitutes strong evidence in favor of the modern synthesis and against ID. On the other hand, if most of the genome is functional, this is strong evidence in favor of "a skilled and Intelligent Designer," and the closer our knowledge brings us to a completely functional genome, the more problematic (for many reasons), this becomes for the modern synthesis. In the following rounds we will have an opportunity to explore where the evidence of unfolding revelation is taking us. It will be an exciting journey!
I now look forward to my opponent's opening statement.
 The Sequence Hypothesis, Francis Crick
 note that genetic information manifests the hallmarks of human language and computer information; i.e., code, syntax, and semantics. This is in contrast to what is know as "shannon" information, which concerns itself only with probability, not with function or meaning.
4] Shermer, "Why Darwin Matters: The Case Against Intelligent Design," 2006, pp74-75
 Coyne, "Why Evolution is True, 2009, pp 66-67, 81.
 William Dembski, Perry Marshall, and Mike Gene, for example
Thank you con for debating this with me. I apologize for the confusion it was my mistake. To clarify I will be arguing Pro that "Most of the Human Genome is useless junk".
First I want to begin with an illustration. Imagine in the creation of a human cell the father's donation of genes are all recessive and the mother's genes are all dominant. During the protein coding of the combined genome The father's contribution would be ignored (no blue eyes). The mother's genes would be coded for. And the produced baby would have brown eyes.
From the start we know that Humans have 46 chromosomes. 23 of which are from the mother. Therefore 50% of the Genome is a set of base pairs that are corresponding copies, or the mirror of an allele. The copy is a contender vying for coding preference (dominant genes having veto power). The illustration still maintains in pairings that are not completely recessive or completely dominant, because even if some of the genes of the father were dominant, and the mothers recessive you would have 50% non coding genes. 
If both genes contributed were dominant, half the combined genes would be copies.
Synonyms of "useless" are ineffectual, fruitless, unproductive etc..
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.
Because I'm arguing for "Most" I now wish to turn our attention to the remaining 50% of the Genome. We know some of that is from endogenous retroviruses. Even taking the BEST CASE scenario as reported by ENCODE  we would still be left with 20% of the entire genome being from virus or mutation.
For the sake of argument we cut this in half for 10%, being the contribution only from the mother. and this follows that 40% of the genome is the required amount of unique information from parental contribution to produce a human being.
Therefore 60% (Most of the human genome) is useless in that it is redundant, noncoding, endogenous virus, or mutations.
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. 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."
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." 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.". 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.
The following amendment to the debate has been agreed upon: I will be allowed to present new arguments in round 5 as part of my agreement to forego this round.
I want to take a bit of time to point out what the position of con can really do to defeat this resolution. My opponent has presented many rebuttals and all of them attack the resolution in a different way. He can make his case to prove one of the following:
1. Some of the Human Genome is useless junk
2. Most of the Genome is useful junk
3. Most of the Genome is useful stuff
I will now proceed with the rebuttals.
My gracious opponent says, " Indeed, many of our traits reflect a blend of the chromosomes contributed by each of our parents." This is correct the expression of brown eyes or blue eyes is not one gene. It is actually at best guess to be 6 genes near a gene known near the OCA2 gene site. OCA2 controls coloring for hair, skin and eyes as well. More than likely these genes do not even code for eye color in the traditional sense. They control for how long OCA2 is to be producing pigment. The system is in reality even more complicated. Here is a good link that covers the basics: http://genetics.thetech.org... You can see that genes still have a recessive quality and a dominance quality. We get different colors because instead of one straight forward Brown eye dominant, blue eye recessive, We have more like A, C, E, genes are dominant and B, D, F are recessive.
My original premise still holds. My example was a simple expression from one gene. There are no one gene yes or no expressions. Many require other genes to be of a certain SNP to cause their desired effect. My example was simple but can be applied to all the 6 genes in eye color. You can still have a mom with the genes A,C,E and the Dad with the recessive genes. My goal was simple illustration not an education in the particulars of eye, hair, and skin color.
My opponent attempt to establish number 2 from the list above. He identifies useless as completely ineffectual. But other words for useless can be garbage. He attempts to assert that the contribution of all recessive genes still has use because it takes 46 chromosomes to produce a human. But I say those recessive genes are just place holders. The human cell needs 46 chromosomes. But in real life you won't have one line of all recessive genes. For the sake of diversity the cell will accept both contributions in calculating a result. But in the illustration the recessive father's genes are useless. In real life the cell wants 46 chromosomes so it has the information of 23 chromosome lengths for genes expression. 23 chromosomes worth, ie amount of, information will be used to express the human being's properties.
We have heard it before with religious institutions distorting science to propagate their religious text. Here my opponent reverses this process. Where it would normally be "God of the gaps", my opponent uses "materialism of the gaps". The problem is materialism has to be the religion of science. Every experiment completed has to be repeatable and peer reviewed. If there was a chance that the results were played with by some devil, then why not all the results? Why not all the experiments trying to discern the same value? With that none of us could trust any result from any scientific method and the whole discussion of what was out there or in our bodies or in outer pace would be mute. Luckily we do not have supernatural forces interfering with verifiable tests. If the tests done by different groups return the same result we call this evidence.
My opponent is stating that because we don't know what the rest of the DNA does it is useful. Given a more logical answer would have been "We don't know" but the evidence at the time Jerry Coyne said that, it was the best theory presented. Science changes all the time. It is completely capable of doing so. But it assumes the safest bet and works from there. It assumes the safest bet and changes when evidence approaches. Currently the evidence is incomplete.
Now my opponent moves to the meat of things that have been truly deemed the graveyard of genetic code. This are area of the genetic code filled with the remnants of different genome evasions. They are known as Long Intergenic Non Coding RNA's or lincRNAs. It is better to describe these areas as battle fields. The fragments of were virus tried to iplant genetic information and these areas were like safety nets to catch the other trash.
I think my opponent may have skipped a few points in his quote. I urge the readers to read the article it makes a few things clearer. lincRNAs and they're smaller cousins ncRNAs used to have an important job. In the simplest of creatures, the earliest bacteria the lincRNA were a kind of genetic defense system. They responded to chemical and outside transfers of genetic material. In the early anaerobic waters of early earth cells did not have good defenses. They were attacked by marauding virus and other bacteria. The cells own coding DNA was a precious gold, it was the next generation of cells. It had to be protected. Mechanisms arose to check and recheck the core protein coding DNA segments for intrusions and errors. This is why in the coding parts of the DNA fewer ERV's are found. Viruses try to inject their own DNA and take over the cells machinery. By surround the coding DNA in fake bits of DNA the viral DNA would be snared. In addition to this the network of fake DNA also became a kind of genetic antenna that picked up signals from the outside and released chemical signals that reacted the core DNA. These signals were how the bacteria knew "Danger, go left" or "Food, go right". It's not surprising they still attempt to send signals and contain a high amount of TEs and ERV's.
Some of the signals of the ERV's in lincRNAs do get interpreted. Sometimes with really bad results to the human host. There can be one mutation at one loci of a particular lincRNA that causes brain stem atrophy. Because this is a strong site for genetic disease scientist are naturally curious about it's formation and functioning. What has been found is that these chains get turned on differently depending on the tissue the cell turns into. That is what this article really talks about. It talks about how the Transposable Elements hi jack and spread through more and more of the ncRNA. From that same article we read "Conversely, lincRNAs devoid of TEs are expressed at greater levels than lincRNAs with TEs in all tissues and cell lines, particularly in the testis" That's correct. lincRNA that are healthy unravaged by the intruding TE's are expressed more often.
((side note to my opponent who I think intends to make a case for ID. In that article you should research this "Collectively, these studies suggest that while many species have numerous lncRNAs, they rapidly evolved in a species-specific manner or exhibit other mechanisms of evolutionary constraints"))
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. 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".
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". 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!
 Albers,et. al., "Molecular Biology of the Cell," 4th edition, p. 203
 Medstrand, et. al., "Long Terminal Repeats Are Used As alternative Promoters...," Journal of Biological Chemistry 276(2001)
 Landry and Mager, "Functional Analysis of the ERV Promoter of the Human Endothelin B Receptor Gene," Journal of Virology 77 (2003)
 Wells, "The Myth of Junk DNA, pp 51,52
 Ibid, p.93
My opponent is not making this easy.
I want to draw the readers attention to where my opponent talks about the ENCODE project. They place biological activity in quotes as well as they should. The ENCODE project has been critized of what they consider functioning. http://www.genomicron.evolverzone.com...
Similar to the case of pseudo genes, some DNA is transcribed or reactive to other biological chemicals. But just becuase it is reactive or displays some "Biological Activity" does not mean this starts a chain ending in protein synthesis or anything of functioning use.
It makes evolutionary sense to conserve portions of the DNA code from mutations. Even if that code is no longer being transcribed into functioning proteins. Better the devil you know the the one you don't. Any of these mutations could be the injection of harmful DNA code.
I want to thank my opponent for the skiped round and for that I present no new arguments just defend the ones I have made and rebuttal his last round. Thank you.
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