Uncommon Descent Serving The Intelligent Design Community

Junk DNA that isn’t

William Dembski
November 21, 2006
Intelligent Design
Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Source: University of Iowa
Date: November 21, 2006
From http://www.sciencedaily.com/releases/2006/11/061113180029.htm

Scientists Explore Function Of ‘Junk DNA’

University of Iowa scientists have made a discovery that broadens understanding of a rapidly developing area of biology known as functional genomics and sheds more light on the mysterious, so-called “junk DNA” that makes up the majority of the human genome.

The team, led by Beverly Davidson, Ph.D., a Roy J. Carver Biomedical Research Chair in Internal Medicine and UI professor of internal medicine, physiology and biophysics, and neurology, have discovered a new mechanism for the expression of microRNAs — short segments of RNA that do not give rise to a protein, but do play a role in regulating protein production. In their study, Davidson and colleagues not only discovered that microRNAs could be expressed in a different way than previously known, they also found that some of the junk DNA is not junk at all, but instead consists of sequences that can generate microRNAs. . . .

Comments
The http://www.junkdna.com site, upon featuring the "death of 'Junk' DNA as a scientific term" crashed under the tsunami set off by the (BTW not unexpected...) announcement of the results of 1% pilot-project of ENCODE. The site (with the same domain name) is now up and running on a better protected and higher capacity server. pellionisz_at_junkdna.comPellionisz
June 19, 2007
June
06
Jun
19
19
2007
06:10 PM
6
06
10
PM
PDT
ENCODE, a $50 M USA (NIH) concerted project has just concluded (see http://www.junkdna.com ) that "Junk" DNA as a scientific term is dead. pellionisz_at_junkdna.comPellionisz
June 15, 2007
June
06
Jun
15
15
2007
10:25 AM
10
10
25
AM
PDT
[...] Also note I’ve blogged in the past about how a design theoretic view predicts things like this. In this comment I described how the NTSC video signal evolved as intelligent designers added additional ways of encoding information to the carrier without effecting the preexisting ways and said we should look for DNA to have multiple encoding schemes one atop the other. These icons link to social bookmarking sites where readers can share and discover new web pages. [...]The Sound of The Neutral Theory Exploding | Uncommon Descent
May 22, 2007
May
05
May
22
22
2007
07:18 PM
7
07
18
PM
PDT
It is dawning on "Scientific PostDarwinism" - see freshly posted lead news on http://www.junkdna.comPellionisz
March 23, 2007
March
03
Mar
23
23
2007
10:24 AM
10
10
24
AM
PDT
There are tons of evidence, accumulating practically every day: http://www.junkdna.comPellionisz
March 14, 2007
March
03
Mar
14
14
2007
02:50 PM
2
02
50
PM
PDT
Just picked this piece of news regarding so called JUNK DNA... We have scientific evidence that shows that what was considered NON-FUNCTIONAL, apparently have important functions after all. http://www.sciencedaily.com/releases/2006/11/061116131608.htm ------------------------------------ Researchers have found that a class of RNA molecules, previously thought to have no function, may in fact protect sex cells from self-destructing. These findings will be published in the November 17 issue of the journal Cell. Central to this discovery is the fundamental process of gene expression. When a gene is ready to produce a protein, the two strands of DNA that comprise the gene unravel. The first strand produces a molecule called messenger RNA, which acts as the protein's template. Biologists call this first strand of DNA the "sense" or "coding" transcript. Even though the other strand doesn't contain a protein recipe, it may also, on occasion, produce an "anti-sense" RNA molecule, one whose sequence is complementary to that of the messenger, or sense, RNA. Antisense RNA has been detected for a number of genes, but is largely considered a genetic oddity. Using common baker's yeast, Cintia Hongay, a postdoctoral researcher in the lab of Whitehead Member and MIT Professor Gerald Fink, discovered that in the case of a gene called IME4, the antisense RNA blocks the sense RNA. In other words, the gene disables its own ability to make protein. "This is the first case where a specific function in a higher cell for antisense RNA has been found," says Fink, senior author on the paper. "This points to an entirely new process of gene regulation that we've never seen before in eukaryotic cells." --------------------------------------- Click on above link for the rest....SeekAndFind
November 24, 2006
November
11
Nov
24
24
2006
11:47 AM
11
11
47
AM
PDT
ID Predicts Agenic Function Intelligent Design theorests predicted that function would be found in agenic or “Junk DNA” in contrast to evolutionary summary expectations of “DNA tombstones”. In 1998, John West, associate director of the Discovery Institute predicted:
“an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.”
Pa. Trial Will Ask Whether 'Alternatives' Can Pass as Science, Rick Weiss & David Brown, Washington Post Staff Writers September 26, 2005; pA08 William A. Dembski observed in 1998: predicted in 1998: Science and Design, William A. Dembski, First Things, October 1, 1998
But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.
Robert Hirsch in 2000 observed:
'''2. The complexity of the genome-proteome-phenotype relationship.''' Research in biochemistry and molecular biology is revealing increasing complexity in this relation-ship, beyond the capacity of 'natural selection' and Darwinian theory to deal with. For example, segments of DNA that are not part of any gene nevertheless appear to have critical functional roles in all living organisms; they are not 'junk DNA'."
Analytical Science at the Center of Chemistry and Beyond its Frontier, Robert Hirsch, August 21, 2000; ''Appendix: Some Critical Points about the Theory of Evolution Added Sept 26, 2000''. Jonathan Wells in 2004:Using Intelligent Design Theory to Guide Scientific Research, Jonathan Wells, Discovery Institute, May 10, 2004; PCID 3.1.2, Nov. 2004 p2
'Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or "junk DNA." From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much "junk." It is much more likely that non-coding regions have functions that we simply haven't discovered yet.
DLH
November 23, 2006
November
11
Nov
23
23
2006
08:03 PM
8
08
03
PM
PDT
For some remarkable developments on human diversity, see the top two news items on http://www.junkdna.com/new_citations.html A direct link to the first (to bypass other pertinent material) is: http://www.junkdna.com/new_citations.html#human_diversity There is a lot to evaluate, e.g. why the Chinese science news breakthrough uses the interesting expression of "tale of evolution". pellionisz_for*no*spam*at_junkdna.comPellionisz
November 23, 2006
November
11
Nov
23
23
2006
02:13 PM
2
02
13
PM
PDT
Here we have a wonderful example for an unexpected result in DNA research. The numbers of copys on DNA sequences makes the difference between human individuals: http://www.newscientist.com/article/dn10646-gene-duplications-may-define-who-you-are-.html Unexpected only for evolutionists, not for research on ID basis!klauslange
November 23, 2006
November
11
Nov
23
23
2006
03:09 AM
3
03
09
AM
PDT
Salvador, a.k.a. scordova, I am delighted to be wherever the hardest of hard-core science issues boil. "Junk DNA" is clearly the Zeitgeist of 21st Century, with a confluence of science, philosophy and benefit of mankind. Starting with practicality, those hundreds of millions suffering from "junk DNA diseases" (link above) must be helped if we really care. Second, the exploding number of lethal diseases discovered each day lurking in "non-coding DNA" will inevitably force the question into the fore; why such a colossal (and indeed harmful) "parasitic deadweight" not only hasn't been squeezed out by the pressures of "survival of the fittest" - but as the C-value curve tentatively shows, the relative proportion of "junk DNA" in the genome increased with the emergence of species. (It is more like hyperescalating, reaching the unbelievable ratio of 98.7% in human.) The focus thus will be more and more on science (junk DNA) - not on belief on either side (those believing 98.7% is junk, or those believing otherwise). The challenge in philosophy will become paramount, to what extent nature (specifically, the DNA) is probabilistic, or deterministic. I will focus on science - wherever it leads me... (We have had something similar with an earlier paradigm-shift. The splitting of the atom [an axiom turned into a dogma...] triggered the science of quantum mechanics. "God does not play dice" - said Einstein, on one hand, while pinpointing that the "axiom" of an absolute time-scale was nonsense; nobody can truly understand time without regard of the theory or relativity. At about the same time, Heisenberg, with his theory of uncertainty, did away with yet another dogma [of absolute measures]. Philosophically, they were some distance apart.) Nothing prevented my good old (late) friend and fellow-country-man Ed Teller, to do serious science with both of them. Let there be peace - Happy Thanksgiving, pellionisz_at_junkdna.comPellionisz
November 22, 2006
November
11
Nov
22
22
2006
08:15 PM
8
08
15
PM
PDT
Dr. Pellionisz, Greetings. We're honored you would visit our weblog. I very much enjoyed your writings. Salvadorscordova
November 22, 2006
November
11
Nov
22
22
2006
02:40 PM
2
02
40
PM
PDT
Re: Junk DNA. I just got my hands on Ohno's paper. It seems like the link provided by Pellionisz pretty well summarizes what is going on here. Ohno was looking for function, and the paper does seem something like a lament. However, this only appears to negate Bill’s postulate that "the 'junk DNA' hypothesis was originally made on explicitly Darwinian grounds." By using the term "junk DNA", Ohno was offering terminology to summarize one proposal for the role of repetitive DNA. The Ohno paper is one of a number of papers in a collection, and another interesting paper in the anthology, by R.J. Britten, offers an overview of early 70’s perspectives on the origin/purpose of the repetitive DNA. Britten reveals that, "Whether the repeated DNA in its now widely interspersed state is simply spacer between genes or carries out an active role is the subject of intensive current investigation." On the next page, Britten offers 9 possible roles of repetitive DNA, including only one the possibility that it was “2. CARRIED ALONG (Parasitic or garbage).” By using the term "junk DNA", Ohno was offering terminology to summarize the "CARRIED ALONG" proposal for the role of repetitive DNA. Based on this Britten quote above, and a brief review of all of the hits on PubMed for "junk dna," it seems that scientists have been looking for functions in the “junk” all along. As Bill suspected, the default scientific position has been to look for function, as well it should. After the publication of a book in 1976 by Richard Dawkins on the Selfish Gene hypothesis, this book became a common reference for papers seeking to explain repetitive DNA as parasitical, including Crick and Orgel (1980). This would appear to corroborate Bill’s proposal that "the 'junk DNA' hypothesis was originally made on explicitly Darwinian grounds." Though the term was coined by Ohno, who was looking for function, the term has been seen as an apt descriptor for the genetic results of evolutionary processes that were ultimately unguided, unplanned, and unpredictable. It also seems the only ones pushing strongly for a parasitical role were the Darwinists, lead by their standard bearer Richard Dawkins. I have a feeling there is more to this than meets the eye, and when I get time I'm going to look for a prior history of the idea that repetitive DNA is "garbage" or "junk." I fear for Darwinists that their "Junk DNA" icon will turn out to be philosophically motivated junk science.Joey Campana
November 22, 2006
November
11
Nov
22
22
2006
10:50 AM
10
10
50
AM
PDT
The term "Junk DNA" (the mother and father of all misnomers) did not apparently arise in direct support of Darwinism, it is a rather formidable problem for primitive Darwinists. According to their conjecture the very "evolution" that unloads everything but the "fittest" should have long squeezed out the huge (98.7% in human) bulk of the DNA that requires (at the very minimum) huge energy to maintain, and as we know now, harbors an erlier unimaginable array of lethal, potential or actually occurring "glitches" (see "junk DNA diseases" at http://www.junkdna.com/junkdna_diseases.html ) Richard Dawkins has come a long way from completely ignoring "Junk DNA" as "parasites" to a downloadable BBC interview some two years ago (find "Dawkins" on http://www.junkdna.com/new_citations.html), actually admitting the "some" of the "Junk" may not be so. As mentioned above, he referred to the two types of Salamandra, one is with a genome size fitting the so-called C-curve, the other several times bigger - that (in the eyes of the "blind watchmaker") still looks nothing but a big heap of "junk". Wish that Richard Dawkins were a bit more mathematically minded, more befitting the "Charles Simonyi endowed professorship" (Charles Simonyi is world famous computer scientist with a Stanford Ph.D., the "Hungarian notation" named after his work, later a VP at Microsoft). Those who are algorithmically minded know some rather common features of algorithms. According to the "Evolution Revolution" notion of FractoGene, the emergence of species is not unlike the development of a fractal process reaching with various numbers of iteration resulting a small or extremely large points of a set (e.g. Mandelbrot set). It is very common that the very same algorithm results in extremely slow convergence (requiring an enormous number of recursive iteration) - while by simple changes in the parameters the convergence is accelerated, often by orders of magnitude. With the two salamanders fully sequenced, the type of analysis predicted by FractoGene (that in the fugu, with its 1/8 of Genome size compared to the human a fractal template-like brain cell should show - and it DID; see the peer-reviewed science article experimentally supporting quantitative prediction of an algorithmic theory on "junk DNA"; http://www.junkdna.com/fractogene/05_simons_pellionisz.pdf), those who are truly interested in the hard-core science issue of the "junk DNA" (causing much problem to Darwinism - while not a problem for those suspecting a "design") would be expected to plunge into direct experimentation. Of course, Dr. Dawkins is not an experimentalist, he is Prof. of "Public understanding of Science". The "Public", apparently, is mostly interested in publicity; "don't bother me with the facts". Both Dr. Collins and Dr. Dawkins agree that SOME "junk DNA" may be very important. Dr. Collins went on record that "it took some hubris to call any part of the DNA 'junk'" - yet his book leaves a backdoor open for "some" of the "junk" may indeed be without useful contribution to the functioning of DNA. Dr. Dawkins, on the contrary, considers most of the "junk" useless (parasites) but leaves a backdoor open for a little amount potentially being useful. The two scientists, one might expect, could perhaps be engaged in some heated debate about the very explorable hard-core science issue of "junk DNA". Instead, not a single word in their publicity-stunt of recent Time-"debate" (with lots of name-calling and character assasination-attempts) NOT A SINGLE WORD WAS MENTIONED ABOUT "JUNK DNA". Regrettably. pellionisz_at_junkdna.comPellionisz
November 22, 2006
November
11
Nov
22
22
2006
09:24 AM
9
09
24
AM
PDT
Sladjo makes a big point. In addition to that a software code not only has funtionality or active sequences but commentary lines, too. A speculative but interessting question now is: Could we find some "comment line" in DNA or other structures in nature...?klauslange
November 22, 2006
November
11
Nov
22
22
2006
02:02 AM
2
02
02
AM
PDT
Absolutely right! If you can think "out of the (evolutionary) box", and try to imagine that DNA structure is more than just coding for proteins, you will end up with some very interesting (and logical) hypothesis. A software programmer or an engineer will predict immediately for this complex molecular machines within cells stuff like backup, adaptive, and (environment) change detection systems. An organism - to be capable to adapt himself to new environments - must be robust and must DETECT the external change, must apply an ALGORITHM to ADAPT to the new change, and must have a BACKUP system in order to try to survive if some key elements are destroyed by this new environment... This processes simply cannot came only by blind, unguided mutations, because the organism will die quickly waiting for that "hopeful" mutation to appear... I would suggest to ID scientist some experiments in which to check for the existence of such backup, adaptive & detection systems in the "noncoding" DNA sequences. I'm 100% sure they will find some interesting stuff...Sladjo
November 22, 2006
November
11
Nov
22
22
2006
12:33 AM
12
12
33
AM
PDT
"Programmers try to imagine unexpected situations, not sure of how they might actually arise in use, but nonetheless shove in code that will gracefully handle the contingency should it somehow happen. If there’s any of that going on in the genome it’s almost a sure sign of intelligent design." Excellent point and an intriguing possibility . . .Eric Anderson
November 21, 2006
November
11
Nov
21
21
2006
10:07 PM
10
10
07
PM
PDT
bdelloid Wow. It took me a moment's consideration of miRNA (which I'd never heard of before) to accurately describe how they might make synonymous substitutions not so neutral. See how actual designers of codes in real life can drill right through to these things based upon intuition and experience? Additionally, synonymous substitutions could be used as an additional information carrying channel where the information in one channel doesn't effect the information in the other. In RF (radio frequency) electronics we use the same carrier (analogous to DNA sequences as a carrier) and encode information on it in different ways. Perhaps the best example is an NTSC television carrier. There are three information carrying channels on one carrier wave. We use what's called amplitude modulation to encode the black & white information, phase modulation to carry the color information, and frequency modulation to carry the sound. Altering the information content of one modulation channel has no effect on the others. Similarly a synonymous substutition on a coding gene has no direct effect on the protein product but the substitution can carry additional information in a different modulation scheme. An intelligent watchmaker would almost certainly utilize the additional information capacity. Maybe even a blind watchmaker might stumble onto it by accident as it's just begging to be used and it isn't very complicated how to use it. Another thing about junk DNA is that releasing a DNA sequence from immediate selection pressure so that mutation can run wild on it seems to be an underlying principle of genetic drift where unused sequences in the present can be beneficially employed in the future. Maybe a lot of junk DNA is a vast assortment of trial balloons to be launched at a future time. Ack... genetic drift was the wrong term. Gene duplication is more the term I was struggling to find. Trial balloons are contained in an area often termed a sandbox in human invented applications. Another lesson from computer programming is that most programs contain many sequences that are seldom if ever traversed. Programmers try to imagine unexpected situations, not sure of how they might actually arise in use, but nonetheless shove in code that will gracefully handle the contingency should it somehow happen. If there's any of that going on in the genome it's almost a sure sign of intelligent design. Intelligent watchmakers anticipate things that haven't yet happened. Blind watchmakers do not. Planning ahead of time is a hallmark of intelligence.DaveScot
November 21, 2006
November
11
Nov
21
21
2006
09:04 PM
9
09
04
PM
PDT
Stephen Meyer notes:
For example, neo-Darwinism affirms that new functional sections of the genome arise by trial and error process of mutation and subsequent selection. For this reason, historically many neo-Darwinists expected or predicted that the large non-coding regions of the genome--so-called “junk DNA”--would lack function altogether (Orgel & Crick 1980). On this line of thinking, the nonfunctional sections of the genome represent nature's failed experiments that remain in the genome as a kind of artifact of the past activity of the mutation and selection process.
Stephen C. Meyer, Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington November 30, 2005 Orgel, L. E., & F. H. Crick. 1980. Selfish DNA: the ultimate parasite.--Nature 284:604-607.DLH
November 21, 2006
November
11
Nov
21
21
2006
08:24 PM
8
08
24
PM
PDT
DS- In fact, miRNAs in plants often target for regulation RNA sequences that code for proteins. The target sequences within the mRNA are very conserved and there was a time that people thought these sequences were conserved for their protein function - ie, some motif within the protein that had some very important function. In fact, within these motifs, the third positions of the codons were also often conserved. This turned out to be because the miRNA regulatory interaction was being conserved, not the protein function per se. Additionally, it is also widely known that synonymous substitutions are not necessarily neutral because of something known as codon bias. Specifically, there seems to be constraint on silent sites due to selection for translational efficiency as constrained the the relative abundances of tRNAs within the cell (though there are many other theories regarding codon bias).bdelloid
November 21, 2006
November
11
Nov
21
21
2006
08:16 PM
8
08
16
PM
PDT
MicroRNAs are an example of why synonymous substitutions in coding genes might not be so neutral after all. Suppose a microRNA (uRNA?) is generated from a junk (non-coding) sequence and its function is to interact with tRNA from a coding gene before a protein is generated. In that case it would be essential that the tRNA and uRNA sequence precisely match. Since the protein has yet to be produced a synonymous substitution would render the sequences non-matching. This is something that computer scientists recognize immediately. A good example is how computer virus scanners work. They search through files looking for a virus "signature". The signature is a snippet of the virus code that is short enough to make the search practical but long enough to make it quite unlikely that any code that isn't the virus is identified as the virus. Computer viruses can mutate (usually by design AFAIK) by the mere synonymous substitution of one instruction for another in the signature sequence. The virus keeps on doing what the virus was designed to do but it becomes unrecognizable by virus scanners. The source code for the virus isn't even required as it's a no-brainer for someone to make a synonymous substitution with a hex editor - it's literally child's play. It's things like this that have made the calibration of so-called "molecular clocks" a cottage industry rather than the simple, reliable way of dating genomic divergence that the neutral theory of molecular evolution predicted it would be.DaveScot
November 21, 2006
November
11
Nov
21
21
2006
07:58 PM
7
07
58
PM
PDT
"But from the point of view of the selfish genes themselves, there is no paradox. The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA." Oh, rats! Dawkins has once again led us down the garden path. And managed at the same time to demonstrate by live example that his ridiculous selfish gene nonsense not only is incapable of leading us to a proper understanding of DNA, but in fact leads away from the kinds of questions that need to be asked and answered. Blind faith in blind processes. Great science stopper. Ah well, when you lack any real comprehension of the biology you can always bluster away with silly concepts like selfish genes . . . or perhaps spend your time writing books about religious delusions.Eric Anderson
November 21, 2006
November
11
Nov
21
21
2006
07:55 PM
7
07
55
PM
PDT
"I suspect that the 'junk DNA' hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse?" The best I can do is:
It appears that the amount of DNA in organisms is more than is strictly necessary for building them: a large fraction of the DNA is never translated into protein. From the point of view of the individual organism this appears paradoxical. If the 'purpose' of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. (Richard Dawkins, The Selfish Gene (1976), pp. 43-44)
j
November 21, 2006
November
11
Nov
21
21
2006
07:26 PM
7
07
26
PM
PDT
Dr. Susumu Ohno did not introduce the notion of "Junk DNA" in 1972 from either Darwinian or other viewpoint, see http://www.junkdna.com/new_citations.html#junk_dna_origin He merely expressed frustration over a huge number of genes that turned out to be pseudogenes. Just like a rich lady walking into a marvelleous butique, still not finding anything she'd pick might say "there is so much junk here". It is very true, though, that most simple-minded Darwinists picked up the term that made their life simpler - it was a convenience to dismiss most of the genome just because they did not understand it. Sadly, as disappointing as that... pellionisz_at_junkdna.comPellionisz
November 21, 2006
November
11
Nov
21
21
2006
06:59 PM
6
06
59
PM
PDT
The first reference in the literature, as far as I know, is in 1972 by Susumu Ohno. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=5065367&dopt=Abstract I can't find an abstract, but here is a discussion of this article: http://jncicancerspectrum.oxfordjournals.org/cgi/content/full/jnci;90/14/1032bdelloid
November 21, 2006
November
11
Nov
21
21
2006
05:34 PM
5
05
34
PM
PDT
Bill asked: I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse?
There is not a chapter and verse to my knowledge, however, it was partly an indirect result of Haldane's dilemma. Haldane's dilemma and the problem of protein polymorphisms forced Kimura and friends to argue the majority (say 90+%) of molecular evolution could not be Darwinian, thus 90% of the genome must be subject to neutrality not selection. Since neutral sites would not be presumed to be functional (since only natural selection can supposedly design functional systems), 90% of the neutral genome could not possibly be functional. If the neutral genome is functional but not visible to natural selection we have prima facie evidence of designs that arose that could not have possibly been the result of selection. It is not a matter of incredulity, but proof by contradiction. Tada!!!! If we accept close to 100% of the genome is functional or better yet, multi-functional, this lead to a major problem in population genetics, how could Darwinism (in the case of humans) possibly have the population resources to manage and evolove 4 Billion nucleotides??? There were not enough creatures to hardly manage a 2000 nucleotides, much less 4 Billion. Salscordova
November 21, 2006
November
11
Nov
21
21
2006
05:00 PM
5
05
00
PM
PDT
The term Junk DNA arose out of a problem in early evolutionary genetics, the problem known as the C value paradox. It was apparent that organisms (such as salamanders) have HUGE genomes whereas others don't. In facts, some salamanders have genomes much bigger than the human genome. At the time, this seemed to be a paradox, because salamanders weren't that much more "complex" than humans. The hypothesis then arose that much of the differences in genome size between salamanders and humans were due to "junk dna", ie, DNA that had no function. With regard to how this fit into the Darwinian arguments, it could fit under the umbrella of "neutrality" (or slightly deleterious). This idea - an important role for neutral evolution being important rather than Darwinian evolution - only really got going in the Modern era with Kimura and the synthesis of molecular biology (ie, DNA sequencing) with evolutionary theory. However, this hypothesis never argued that ALL the differences between genome size of humans and salamanders had absolutely ZERO function, just that a lot of it probably did. To clarify - microR NAs are not Junk DNA. We just used to think that most regions of the genome that didn't code protein sequence were junk. However, it turns out, a lot of it is probably functional. However, the fact that this is the case doesn't say there is still NO junk DNA. We can be pretty confident that there is junk DNA because we know that there are chunks of sequence that can be completely deleted with no phenotypic effect. Furthermore, the distribution of many of these deletions are in accordance with predictions of neutral theory. Specifically, deletions within old transposable element insertions that have begun to decay.bdelloid
November 21, 2006
November
11
Nov
21
21
2006
04:55 PM
4
04
55
PM
PDT
Are non-coding genes like micro-RNAs the same as 'junk DNA?' It seems like transposons and such are possibly non-functional genome parasites. Joseph explains why their existance might not refute evolution. But micro-RNAs seem distinct from these, and are conserved between organisms (in fact, their conservation is one way they are identified). So I'm a bit confused-if on one hand, there is some tolerated, non-functional genomic junk, and the other hand, a array of 'conserved' non-protein coding genes, how does this harm/help darwinism or ID?RobertC
November 21, 2006
November
11
Nov
21
21
2006
01:21 PM
1
01
21
PM
PDT
“Discussion over evolution and Intelligent Design really has centered on whether pseudogenes, sometimes called ‘junk DNA,’ have a function or not. The suggestion is that an Intelligent Designer would not make junk DNA, so if a pseudogene does have a function, this is claimed to support the idea of an Intelligent Designer,” Dr. Nicholls said. “But there is no evidence that any of the 20,000 pseudogenes are functional. Our research proves this Makorin pseudogene does not have a function. It has continued to mutate over its short life of a few million years, a fact that supports evolution, and eventually will be discarded from the mouse genome.” http://www.sciencedaily.com/releases/2006/08/060801230141.htm Hang on there Dr Nichols, you said that if junk DNA has a purpose "this is claimed to support the idea of an Intelligent Designer" Well now we have found that at least some "Junk DNA" has a purpose, and that is what ID predicts, then will you now say that ID is supported by evidence? I doubt it. I have contended for 10 years that junk DNA has the structural information for phenotypes. I think it is being verified by recent discoveries. I would like one of these biologists to snip out all the junk DNA from a lizzard and see what grows in the egg. That would test their silly and primative idea that protein coding DNA constructs complex organisms.idnet.com.au
November 21, 2006
November
11
Nov
21
21
2006
01:15 PM
1
01
15
PM
PDT
I have the following respponse on my blog Junk DNA and ID:
There is of course a major difference between Prokaryotes and Eukaryotes. Prokaryotes have little or no 'junk DNA' except in recently evolved plasmids etc. But Eukaryotes have lots. This has been adressed in a couple of papers by Michael Lynch. He argues that Mildly deleterious DNA such as viruses, selfish elements etc. can persist is eukaryotes because genetic drift can allow mildly deleterious 'junk' to accumulate because of a decreased population size compared to prokaryotes. The large population size of prokaryotes allows for increased selection against junk and reduced genetic drift making their genomes compact and almost completely free of junk. Junk DNA is not only entirely consistant with evolution and can be explained by the action of natural selection and it is a prediction of the equations of evolutionary genetics. Evolution explains again! see: The Origins of Eukaryotic Gene Structure Michael Lynch Molecular Biology and Evolution 2006 23(2):450-468. abstract The Origins of Genome Complexity Michael Lynch and John S. Conery Science 21 November 2003: Vol. 302. no. 5649, pp. 1401 - 1404 abstract
Hope that helps...Joseph
November 21, 2006
November
11
Nov
21
21
2006
12:05 PM
12
12
05
PM
PDT

Leave a Reply