This morning I was observing some of the recent comment thread activity on Uncommon Descent, and my attention was drawn to this comment by Nick Matzke on the subject of the “onion test” argument for junk DNA:
I have [The Myth of Junk DNA], and all [Jonathan] Wells does is gloss past T. Ryan Gregory’s onion argument; Wells gives the more important point, the huge variability in genome size as a widespread pattern, much attention at all. Considering Wells’s book is the definitive ID treatment of the junk DNA issue, and us ID critics have been bashing ID for its complete failure on the genome-size variability issue for years, this was a huge omission on Wells’s part.
Here, I offer a few thoughts on this fascinating subject.
What is the “Onion Test”?
Briefly stated, the “onion test” (which originates with T. Ryan Gregory) observes that onion cells have many times more DNA than we do. And since the onion is considered to be relatively simple as compared to the human, this discrepancy can only be accounted for within the context of the view that much of its DNA is, in fact, junk. This phenomenon is also known as the “C-value enigma”, and describes the lack of correlation (among eukaryotes) with respect to genome size and organismal complexity. The human genome comprises about 3 billion base pairs of DNA: Compare this to the genome size of Amoeba dubia (670,000,000,000 bp). Indeed, the human genome is only marginally bigger than that of C. elegans and D. melanogaster. In amphibians, the smallest genomes are just shy of 10 billion base pairs, while the largest are nearly 10^11 base pairs. Interestingly, the C-value paradox does not seem to apply to bacteria.
One Critical Assumption
This whole argument for junk DNA seems to rest on the critical assumption that having seemingly excessive amounts of repetitive DNA has no positive bearing on an organism’s physiology. But this assumption has been invalidated by the scientific evidence.
Transcriptional Delays and Timing Mechanisms During Development
One correlation which has been established is that highly-expressed genes tend to have short introns (Castillo-Davis et al., 2002), a likely reflection of the selective-pressure on transcriptional economy with respect to very highly expressed genes. Other genes are rich in introns: such as the 2400 kb human dystrophin gene, 99% of which is comprised of introns. The time taken to transcribe this gene into mRNA adds up to about 16 hours (Tennyson et al., 1995). To take another example, consider the Y chromosomal loci of Drosophila, which are extremely long — spanning millions of bases and consisting largely of introns. During the G2 phase of the primary spermatocyte (and only in that phase of that cell lineage) the Y chromosome unfolds to form species-specific nuclear architectures. A locus such as DhDhc7(Y) is transcribed over the course of two to three days to give rise to a ~5,100,000 nucleotide pre-mRNA (see Reugels et al., 2000; Piergentili et al., 2007; and Redhouse et al., 2011).
The time taken to transcribe respective stretches of DNA is not inconsequential to physiological fitness. Indeed, Swinburne and Silver (2010) explain,
Transcriptional delays were first invoked in 1970 while discussing biological timing for lambda phage and their use of long, late operons (Watson, 1970). Recognizing correlations between gene size and developmental timing, David Gubb later noted that the Drosophila Antennapedia (Antp) and Ultrabithorax (Ubx) genes owe their extreme lengths to large introns and formally introduced the intron delay hypothesis (Gubb, 1986). With the knowledge that the development of the fly’s body plan is sensitive to the proper expression of these genes in space and time, Gubb proposed that intron length could function as a time delay and aid the orchestration of gene expression patterns.
The paper further observes,
If intron delays have critical roles during developmental programs, then expression networks that depend on intron delays should be sensitive to perturbation of transcription elongation rates. Phenomena supporting this logic emerged in the genetic system of Danio rerio. The foggy and pandora mutants were identified for defects in both heart and neural development with the additional phenotype of shorter tails (Guo et al., 1999; Stainier et al., 1996). The mutants were mapped to the transcription elongation factors Spt5 and Spt6 (Cooper et al., 2005; Guo et al., 2000; Keegan et al., 2002). The nature of these mutants suggests critical roles for transcription elongation rates in the development of particular tissues and cell types. In the pandora (Spt6) background, researchers found that the transcripts of tbx20 (hrT), which encodes a protein required for heart development, are expressed inappropriately late during development and in the incorrect location when compared with wild-type (Griffin et al., 2000). While the molecular mechanism underlying this correlation might entail transcription initiation, elongation, RNA processing, or some combination thereof, the line of evidence suggests that transcriptional kinetics have important roles during vertebrate development.
Read the full paper for a list of further examples of this phenomenon.
Could Varying Genome Sizes Reflect Levels of Alternative Splicing?
Perhaps some of the C-value enigma can be accounted for in terms of alternative splicing and alternative polyadenylation. Alternative splicing allows the exons of pre-mRNA transcript to be spliced into a number of different isoforms to produce multiple proteins from the same transcript, as shown in the diagram above. It is known that the level of alternative splicing exhibited in humans (about 90% — perhaps more — with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene). This may, in part, explain why humans have only marginally more genes than C. elegans, which is otherwise seemingly paradoxical given the complexity of humans as compared to the roundworm. Moreover, bacteria do not undergo alternative splicing — which may, in some measure, explain their exemption from the C-value enigma.
Varying Preponderances of Transcription Factors
Approximately 10% of human genes code for transcription factors (a special class of protein which binds to specific sequences of DNA, namely, enhancers or promoters which are adjacent to genes which they regulate the expression of). In contrast, only about 5% of yeast genes code for transcription factors. When coupled with a much larger network of transcriptional enhancers and promoters, such a difference could result in a much larger set of gene expression patterns. This could lead to a non-linear increase in organismal complexity (see Levine and Tjian, 2003).
Are There Limiting Factors on Genome Size?
In 2002, Andrew George published a paper in Trends in Immunology, entitled, “Is the number of genes we possess limited by the presence of an adaptive immune system?” In the paper, he argued that the number of genes is limited in organisms which possess an adaptive immune system by the burden of self-recognition. As the paper explains,
The factors that are important in limiting the number of functional genes contained within the genome of an organism are presently unknown. Here, it is suggested that in organisms that contain an adaptive immune response, the number of genes in the genome might be limited by the need to delete autoreactive T cells, thus preventing autoimmunity. The more genes an organism has, the more autoantigens are generated, necessitating an increase in the proportion of T cells that are deleted.Is human complexity limited by the presence of an immune system? Although immunity is vital for health, the need to be tolerant to all ‘self’ molecules could restrict the number of genes in our genome.
A further correlation, which has been established, is that organisms with rapid development typically have lower C-values, presumably because they don’t have time to replicate lots of DNA between cell divisions.
In The Myth of Junk DNA, Jonathan Wells observes,
There is a strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus — which affects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and teh rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration
In the case of bacteria, which have single replicons per chromosome, they face selective pressure to limit the accumulation of non-genic DNA which might make the replication times longer and thus slow rates of reproduction. This means that their genome size is correlated with gene number, and thus increases in proportion to structural and metabolic complexity.
Larger Cells Require More DNA
Take a look at the following graph, excerpted from Cavalier-Smith (2004):
The graph shows a clear quantitative correlation between cell volume and DNA content. The trap into which the “junk DNA” advocate has fallen — as he so often does — lies with the (erroneous) assumption that all functions associated with DNA are sequence-dependent. But this need not universally be the case (in fact, it has long been shown not to be). This correlation holds not only true of vertebrate animals, but also for plants and unicellular eukaryotes (protozoa). It has been suggested by many that DNA possesses a structural role in controlling nuclear volume, cell size and cell-cycle length. Cavalier-Smith explains that, with increased cell size, “there is positive selection for a corresponding increase in nuclear volume; it is generally easier to achieve this by increasing the amount of DNA rather than by altering its folding parameters.”
As Thomas Cavalier-Smith observes,
Nuclear volume is probably functionally important for initiation of DNA replication and the transition from G1 to S: replication appears to initiate and terminate at the nuclear periphery and require a critical nuclear volume for onset (Nicolini et al., 1986); G1 nuclear volume growth must depend on concerted expansion of both chromatin and the nuclear envelope. But the significance of nuclear volume for the evolution of genome size does not depend on this, but on its fundamental significance for transcription, RNA processing and export, the rates of which must universally be adjusted to the rate of cytoplasmic protein synthesis. This unavoidable need for an optimal nuclear/cytoplasmic (karyoplasmic) ratio to allow balanced growth of actively growing and dividing eukaryotic cells means that larger cells must evolve proportionally larger nuclei. They can do that only by having larger genomes or unfolding DNA more; the former is mutationally much easier and quantitatively less limited and therefore predominates during evolution. Selection for economy means that smaller cells must have smaller nuclei. Mutations expanding or contracting the genome are always occurring with high frequency and will be selected long before any changing DNA folding patterns radically occur. Those are the fundamental reasons why genome size increases in larger cells and decreases in smaller ones. Bacteria, chloroplasts or mitochondria have no nuclear envelope attached to their DNA and no segregation of RNA and protein synthesis in two fundamentally different compartments; that is why their genome evolution follows different scaling laws: there is no selection for larger genomes in larger bacterial cells.
Summary & Conclusion
In summary, to point to the C-value paradox — or the so-called “onion test” — as evidence for the preponderance of junk or nonsensical DNA within animal genomes is based on several critical assumptions which are contradicted by recent data. The common naive supposition that having a larger genome size is neither here nor there in terms of organismal physiology has been shown to be untenable. With the ever-increasing expansion of our knowledge of the nature and functional inter-relatedness of the genome, those who choose to continue using the “junk DNA” argument as a club with which to beat intelligent design should find these facts disconcerting.
Very nice overview Jonathan!
Minor edit — my original comment meant to say,
“Wells gives the more important point, the huge variability in genome size as a widespread pattern, NOT much attention at all.”
Typo on my part.
In response to the argument — if most of the genome has merely “sequence independent” function, then Stephen Meyer’s statement that the genome is “chock-full of information” is unsupportable.
Re: C. elegans — (a) C. elegans has about the same number of genes as humans. (b) Your argument is that 3 times the alternative splicing requires 30 times the genome size. Are you also saying that onions have another 3 or 6 times more alternative splicing. And some onions have more than others.
Re: cell-volume. That correlation to genome size is well-known, and I have highlighted it many times. This may be the first time I’ve seen an ID advocate bring up in a vaguely serious way. The problem with the explanation is that there are likely to be all kinds of ways to regulate cell volume, and genome size seems to be the crudest possible one. An alternative explanation is that larger cells = slower growing = fewer generations = weaker selection against the expense and time of replicating larger genomes = larger genomes. Same correlation, reversed causation.
Nick Matzke, not to step in between you and Jonathan’s discussion, but I brought up a ‘minor’ point in the previous ‘Higgs’ post, which inspired this thread, a point which I have brought to you before to, and a few other atheistic neo-Darwinists. A point that you never addressed. In fact the point is usually completely ignored, by other neo-Darwinists, or simply rationalized away as inconsequential with a wave of the hand. Yet ‘the point’ in fact falsifies the entire theory of neo-Darwinism by undermining the materialist foundation upon which it is built. Thus, far from being inconsequential to neo-Darwinism, ‘the point’ is in fact of great scientific importance. Here is ‘the point’:
Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium.
notes:
Falsification of neo-Darwinism;
First, Here is the falsification of local realism (reductive materialism).
Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:
The falsification for local realism (reductive materialism) was recently greatly strengthened:
(of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)
And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality, is now found in molecular biology on a massive scale!
Quantum Information confirmed in DNA by direct observation here;
The necessity of transcendent information, to ‘constrain’ a cell, against thermodynamic effects is noted here:
i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself
not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
,,,To refute this falsification of neo-Darwinism, one must overturn Alain Aspect, and company’s, falsification of local realism (reductive materialism)!
=================
and To dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,
,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, such as what we find encoded in computer programs, and yes as we find encoded in DNA, is found to be a subset of ‘transcendent’ quantum information by the following method:,,,
,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,
Further note:
verse and music:John 1:1-3
Hi Nick:
Actually, C. elegans has about 20,000 genes. We have 30,000. So they’re not quite the same size.
I was not arguing that any one factor is responsible for the lack of correlation. What I am saying is that there is a plethora of factors which make the issue far more complex than it is often portrayed.
I’m not the first ID advocate to bring up cell-volume. Richard Sternberg has also alluded to it in his discussion on the topic. I recommend reading the Cavalier-Smith paper on the subject, as he argues convincingly that a larger cell volume requires more DNA.
J
There’s a lot of seemingly “extra” DNA in onions. Who’s to say that extra DNA even has anything to do with onions? Maybe it contains the extra data needed to get a giraffe from a tapir or a bat from a rodent.
I have no idea. I’m not suggesting that any of this is the case. But we clearly do not understand what all DNA is for, just as we don’t understand half of what we see in biology, such as that bats resemble rodents but have wings and echolocation.
I’m not saying that we should chase down wild, crazy ideas. But darwinism has a limiting, narrowing effect. It forces us to think inside a very small box. Maybe the extra DNA is junk. Maybe it’s informational, not functional. Perhaps it has some very specific purpose unrelated to onions.
I’m not saying any of this is so. I don’t believe it myself. But darwinism is a science-stopper. It’s the small-minded teacher who tells the next Einstein to quit asking stupid questions and just read the book. Perhaps only someone who ignores it can figure out what the extra onion DNA is for.
“Briefly stated, the “onion test” (which originates with T. Ryan Gregory) observes that onion cells have many times more DNA than we do. And since the onion is considered to be relatively simple as compared to the human, this discrepancy can only be accounted for within the context of the view that much of its DNA is, in fact, junk.”
Boy, I hope that’s not the argument. It would be about as stupid as most of the other “junk DNA” statements over the years. The funny part is that you have an increasing number of researchers (yes, even those who believe evolution through and through) recognizing that the whole idea of “junk DNA” is not helpful and that there are many functions for non-coding DNA. Then at the same time you have these almost militant orthodox Darwinists who keep repeating “junk DNA” “junk DNA” with their fingers stuck in their ears. Kind of sad, actually.
The junk DNA argument is just a variant on the failed and invalid family of “bad design” arguments that are based, not on science in most cases, but on the philosophical/religious preferences of those who espouse them.
Humans have something like 22,000 genes. 30,000 is an old estimate. Wikipedia says 23,000: http://en.wikipedia.org/wiki/Human_genome
[On this, you are correct. I stand corrected. I have amended the article above. JM]
Re: Cavalier-Smith. I’ve read basically all of his work, including his 1985 book, IIRC with the title Evolution of Genome Size. He advocates skeletal DNA there also. I found it an appealing theory for quite awhile, until I saw others point out that it seems like the relationship between number of protein products and cell volume could be regulated in a much simpler way by just tuning up and down gene expression. T. Ryan Gregory is the leader in the generation after Cavalier-Smith, and he points out other issues.
But, even if Cavalier-Smith’s idea is true, the genome isn’t “chock-full of information”, it’s “chock-full of spacer”. Even if it’s functional, “sequence-independent” DNA is “functional” in the same way that the junk in a landfill that then becomes an island park or hill park is functional.
I am familiar with Sternberg’s and a few others extremely minimal discussions of the issue.
When hundreds of ID fans are going around for years decrying the death of junk DNA and the bias and ignorance of the “Darwinists”, and when *the most important data* in the junk DNA debate — data which deals with most of the DNA (90%+) in large genomes, pseudogenes and regulatory DNA are a tiny fraction compared to the variable, repetitive fraction — a very few brief mentions don’t cut it. They either represent a simple not understanding of the relevant scale of the issues, or they represent an attempt to hide the most relevant data from their innocent antievolutionist readership.
That’s not really the argument. The argument also involves the fact that different onions have different amounts of DNA — one onion can have several human genome’s worth of DNA more DNA than another onion.
It’s not exactly an argument FOR junk, either. Gregory himself has taken the opinion that use of the word creates more heat than light because of the strong emotions that are raised by calling something “junk”. BUT — the onion test is a challenge to the large group of people — lots of creationists/IDists, lots of journalists, some scientists, some cranks — who make bold declarations about how most/all DNA is functional and how stupid scientists were to ever think that a lot of it was junk. Your proposed function(s) had better be able to pass the Onion Test, or else you really haven’t got any evidence that most DNA is functional.
Oh, no ScottAndrews. We don’t know what the “extra” onion DNA is, and, therefore, it has no function. And it must be junk. Just like the human junk DNA we’ve told you about for all these years, (which unfortunately turned out to have a function and even though we said it wouldn’t have function we were just kidding), but we’ve found unknown DNA in another organism (so there!), and it has just got to be junk, because we don’t know its function. And no creator worth his salt would do that (I’m referring to the creator that doesn’t exist, but if one did exist, then I know what the creator would be like because I have a special capacity to know what any non-existent creator would be like, if there were to be such a creator, which there isn’t), so it must not have been created, but must have come about from some bumbling, mistake-prone natural process. Oh, and by the way, that’s what our theory predicted — lots of junk. Except for the times when nature stumbled upon exquisite design. In those cases our theory predicted that nature would produce exquisite design. Either way our theory is true. And don’t bother looking for function in that extra DNA, because we don’t know of a function and, therefore, it must be junk. There is nothing of value to learn here with this extra DNA. Please stop trying to learn something more about it. Just accept that it is useless junk and that it proves our theory is right. Oh, and by the way, by making a philosophical/religious argument from our ignorance, we are not stopping “science,” because “science” can only deal with things that come about naturally by chemistry and physics, so we are definitely supporting true science.
/Darwinist Thought Process
Nick,
Only a person as wise and learned as yourself could express contempt for someone mystified by nature, even a simple onion. If only I could share your thoughts for a moment and see the mysteries of the universe unraveled and exposed before my eyes. (Except perhaps for that onion DNA.)
I don’t know why there’s extra DNA. Neither do you. Some people are smart enough to ask. Some are even smarter – they already know everything so they slap a label on it.
I won’t speak to scientists in general. But if wanted to impress you I would stop reasoning, stop asking questions, and just make crap up. I already know it works.
further notes on the falsification of neo-Darwinism:
The following describes how quantum entanglement is related to functional information:
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
A bit more detail on how teleportation is actually achieved is here:
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which all functional information ‘emerges’ in life, in the atheistic neo-Darwinian framework, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of!
Thus the burning question, that is usually completely ignored by the neo-Darwinists I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply completely IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ’emerge’ from, any basis of material particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a small matter in the least as far as developments in science have gone!!
music and verse:
Nick,
The delicious irony is that the only DNA you even attempt to explain is the supposed junk. (And maybe some or all is junk.) You have a nice story on where that comes from.
Explain the functional DNA, and – forget your ‘real scientists’ – then I’ll be impressed.
I’m not sure why “junk” DNA is even an issue.
Is DNA all being not-junk very important to the ID argument?
As to:
Well since neo-Darwinists have tried to establish some fairly contentious points of common ancestry, and even tried to establish ‘theological points’ of ‘God would not have done it that way, using ‘junk DNA’ as their starting presumption, then the validity of whether or not we are actually dealing with junk DNA has become important.,,, And remember atheistic neo-Darwinists are using this line of ‘junk DNA’ argumentation despite the fact that we now know the coding in DNA is vastly superior to anything man has ever accomplished in his most advanced computer programs, and despite the fact that this is almost exactly the same line of argumentation that was used for decades by atheistic neo-Darwinists for ‘vestigial’ organs;
notes:
further notes:
Among the most blatant failed predictions of materialists is this one. For many years materialists predicted much of human anatomy was vestigial (useless and leftover evolutionary baggage). Yet once again, they were proven completely wrong in this prediction.
For a prime example of evolution’s failed predictions of vestigial organs, recently in October 2007, the appendix has been found to have essential purpose in the human body:
Further notes:
It is simply ‘criminally blind’, for a supposedly ‘non-partial’ scientist, to look at this evidence and argue as forcefully for junk DNA as Nick has. The impartial scientist, who was geniuinely concerned with finding the truth, would surely be humbled by such staggering levels of poly-functional complexity!!! But alas, we are not dealing with impartial scientist are we Nick???
Nick Matzke et al.:
It is my position that introns do or did have a function. This does not mean that every single “chunk” of introns are functional. This means that the original introns did have functions; but if whole-genome duplication occurred then the duplicated introns might become functionless, since there would be no selective pressure to keep them functional. This would be the answer to the onion test, effectively.
Non-functional DNA isn’t an issue for either position. What is and has been an issue ad nauseam has been the argument that purported ‘junk DNA’ is reason to discredit ID [Miller, Shermer, Coyne et al], similar to the ‘bad design’ variant pointed out by Kurt.
So yes, it is an issue, but a contrived one.
Oh really? It wasn’t the evolutionists who made the IDists write books like Wells’s The Myth of Junk DNA or Stephen Meyer’s Signature in the Cell — the latter of which asserts that the genome is “chock full” of information.
Random example:
http://www.google.com/search?h.....8;ie=UTF-8
More examples from Meyer:
http://pandasthumb.org/archive.....in-th.html
Furthermore, says Meyer, not only is this established truth, but it is a prediction of ID theory, and furthermore it was predicted by ID advocates a decade or more ago:
However, at numerous places in the book, Meyer notes (correctly) that repetitive sequences have little information:
Unfortunately for Meyer, he seems to not realize that 40-50% of the human genome (and most animal genomes of similar size) consists of LINEs, SINEs, segmental duplications, and other repeating elements.
This from a biology layman:
It appears that DNA is but the list of ingredients, stumbled upon and arrogantly and very prematurely counted as grasped or even understood. The recipe is somewhere else, deeper and more complex and wonderful.
notes as to how detached from reality Matzke is with his junk DNA assertions::
further excerpt from preceding paper:
other notes:
As to the underlying assumption of ‘random change’, that is a primary pillar of neo-Darwinian thought, there simply isn’t any ‘randomness to speak of in the genome:
etc.. etc.. etc..
verse and music:
I’m predicting, and I don’t know, that giant disparity in genome size not correlated with the organisms was not predicted, wasn’t searched for and the first discoverers were quite surprised. If so it can’t be trumpeted as a confirmation. Correct if wrong someone.
However well you think ‘junk dna theory’ comports with the observation of the huge variability in amounts of DNA in different genomes, such variability is the question at hand. Can you agree that the strength of declaring some part of a system non functional is at least related to exactly how well you know the systems workings? Thorough understanding has yet to be shown.
DNA from the ‘assumed junk’ column has moved to the functional column. Why would one not think that will continue?
Should actual junk be found, the ID position that it resulted from degradation, contamination etc, due to [real]evolutionary and biological-physical-chemical processes acting on a junk-free designed genome would be a far stronger hypothesis, certainly just as consistent with observation. Real evolution as in observations that IDists/creationists and everyone else all believe in – natural selection, mutation rates , allele frequency change etc etc.
Oh wow so what are the implications of the onion test for ogre DNA?
Most of that transcription on the sequence level appears to be low-level transcriptional noise (on the bulk level, what gets transcribed is mostly genic and regulatory, with the rest of the genome making up only a small percentage of the transcripts). The relevant enzymes just aren’t that precise, and will transcribe any DNA at some low-but-detectable level. In other words, junk RNA.
Well Nick contrary to your atheistic gut reaction to label everything that you don’t understand in life as ‘junk’, there are ‘cooler heads’, who are not so predisposed to twist science for atheistic propaganda purposes, as you clearly are, people who do ACTUAL research, who would whole heartily disagree with your ‘junk RNA’ assessment!
moreover there is a very solid scientific reason for presupposing functionality for the entire genome:
Thus Nick, it certainly seems that the only junk around here, that we can be absolutely 100% certain is junk, is in fact your very own junk science, in that you are forcing your very own philosophical bias onto the evidence prior to investigation, and without any regard for any trends in science that preceded your forced declaration of junk!!!
Just ain’t so. The energetic cost of replicating the genome is quite small compared to the costs of metabolism, protein synthesis etc., at least in large cells.
Well as usual you are completely wrong again Nick:
This recent paper also found the gene duplication scenario to be highly implausible:
Geez if genes code for proteins, and there are more than 100,000 proteins, that should tell people (especially scientists) that there are more than 30,000 genes.
And thanks to alternative gene splicing, there are. Ya see alternative gene splicing can take what appears to be one gene and make several genes out of it- that is several different proteins can come from one gene by rearranging the exons of any one particular gene.
But to do that takes knowledge- knowledge of editing, splicing- what to edit, what to splice, the order of the splicing- knowledge and only intelligence has the capabilities to pull that off.
As for Nick’s “anyievolution” tripe- well Nick just how are YOU defining “evolution”? Or are you going to run away from that question AGAIN?