'Junk DNA' Evolution Intelligent Design

How are lncDNA/RNA and Neutral Theory Compatible?

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There are many “Neutral Theorists” who maintain that there is a lot of “junk-DNA,” among which long, non-coding DNA=lncDNA is some of the “junkiest.”

But now consider this from Wikipedia:

Nevertheless, despite low conservation of long ncRNAs in general, it should be noted that many long ncRNAs still contain strongly conserved elements. For example, 19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions (Siepel 2005). Furthermore, a representative set of human long ncRNAs exhibit small, yet significant, reductions in substitution and insertion/deletion rates indicative of purifying selection that conserve the integrity of the transcript at the levels of sequence, promoter and splicing (Ponjavic 2007).

If lncDNA is ‘junk’, then according to ‘neutral theory’ it shouldn’t be conserved, not even any portion of it. Yet, of the “highly conserved phastCons elements,” 32% appear in unannotated regions. And 19% of the phastCons elements are found in “introns,” yet we’re told that ‘introns’ are just “junk.” How can neutral theorists, then, maintain their position that most mutations come from molecular evolution (neutral drift), work under the assumption that “highly conserved” portions of the genome are under purifying selection, and then tell us that lncDNA is “junk”? If it is “junk,” then why aren’t ‘neutral mutations’ found across their entire length?

Just being curious.

39 Replies to “How are lncDNA/RNA and Neutral Theory Compatible?

  1. 1
    jerry says:

    If it is “junk,” then why aren’t ‘neutral mutations’ popping up all over the place?

    I asked this same question about 3-4 weeks ago and wd400 just said it is not conserved and it takes awhile for mutations to happen. I will see if I can find his exact reply.

  2. 2
    jerry says:

    Actually I was asking about repetitive regions. My question was

    Could someone explain to me how a repetitive region is not a functional region?

    Or if it is not functional, why wouldn’t mutations ruin the repetitiveness over time?

    Most of the DNA is repetitive which implies that most of the genome is functional.

    wd400 answered

    repetitive sequences do ‘rot’ over time, but just at the neutral rate which takes a while so we can still see the repeat motif.

    I have no idea if this is true.

    It is on the thread:

    http://www.uncommondescent.com.....-movement/

    Gpuccio actually asked most of the questions about conservation or conserved sequences. This term however, primarily means closely conserved across different species as opposed to within species. However, I would think that conserved across disparate sub-populations of humans should be applicable also.

    The Nicholas Wade book is all about comparing different populations of humans, some of which split off 50,000 years ago and represent about 1800-2000 generations of separation. In it he refers to the comparison of repetitive sequences.

  3. 3
    wd400 says:

    If lncDNA is ‘junk’, then according to ‘neutral theory’ it shouldn’t be conserved; yet, “32% in uannotated regions” are “highly conserved.” And 19% of “introns” are “highly conserved,” yet we’re told that ‘introns’ are just “junk.”

    You misread the article. Which actually says

    19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions

  4. 4
    PaV says:

    wd400:

    Are you saying that there is very little correlation between actual ‘conservation’ and ‘phastCons’?

  5. 5
    wd400 says:

    No I’m saying you have misunderstood the artice.

    A small percentage of the genome is conserved, among those conserved elements 19% are in introns, 32% are in unannotated regions.

    That’s not the same thing as your sentence:

    “32% in uannotated regions” are “highly conserved.”

  6. 6
    PaV says:

    jerry:

    wd400 answered

    repetitive sequences do ‘rot’ over time, but just at the neutral rate which takes a while so we can still see the repeat motif.

    First, thanks, jerry, for this info and your remarks.

    Second, I don’t see any reason for accepting wd400’s reply. Didn’t Larry Moran calculate that since the split with chimps there have been like 22 million mutations that have been ‘fixed’? I’m not sure, but I suspect that the chimp genome contains lots of lncDNA/RNA, too. So that would mean that “neutral evolution” would go even further back in time, which means that there is even MORE time for the lncDNA to “rot.”

  7. 7
    PaV says:

    So you’re objecting to the “highly”? Is that it?

    Here’s the sentence straight out of Wikipedia:

    For example, 19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions (Siepel 2005)

    Why do you want to ‘split hairs’? Is it because you have no reply to give to the paradox I’m presenting?

  8. 8
    wd400 says:

    No.

    You said “19% of introns are highly conserved”. The article says 19% of conserved elements are in introns.

    These are different things. It’s a bit more than hair splitting to point out that the central thesis of your post is not, in fact, true.

  9. 9
    Dionisio says:

    PaV

    The Wikipedia text you quoted

    19% of highly conserved phastCons elements occur in known introns, and another 32% in unannotated regions (Siepel 2005).

    Your own statement says

    “32% in uannotated regions” are “highly conserved.” And 19% of “introns” are “highly conserved,”

    The two statements seem to say different things.

    Let’s assume there are 100 highly conserved phastCons elements.

    19 of them would occur in known introns.

    32 of them would occur in unannotated regions.

    Now, let’s assume there are 1000 known introns.

    According to your statement, in this hypothetical example, 190 highly conserved phastCons elements occur in introns. That’s a contradiction, because there are only 100 highly conserved phastCons elements in this hypothetical example.

    The part about the unannotated regions does not seem clear either.

    You may want to review your text and rewrite any part that could be confusing. Also, note that the word ‘unannotated’ appears misspelled (the n after the initial u is missing).

    I hope this helps clarify the discussion.

    Perhaps the confusion does not affect the bottom line problem you’re trying to present, but it definitely dilutes the strength of your argument.

  10. 10
    gpuccio says:

    PaV:

    The part of the human genome which is conserved can vary according to the type of conservation and the threshold of conservation we consider.

    The recent ENCODE paper here:

    http://www.pnas.org/content/ea.....ith-ds=yes

    in Fig. 1, referring to conservation in mammals, shows about 10% of conserved elements (the number is not really specified, it’s the area of the red circle). Of these, little more than 1% is made of protein coding genes (as you can see from the figure, most (but not all) protein coding genes, the purple circle, are conserved. That means that about 9% of the non coding genome is conserved in mammals.

    This other source:

    http://www.garlandscience.com/.....9_ch09.pdf

    referring to “highly conserved regions”, says:

    As detailed in Chapter 10, sequence comparisons with other mammalian genomes and vertebrate genomes indicate that about 5% of the human genome has been strongly conserved during evolution and is presumably functionally important. Protein-coding DNA sequences account for just 1.1% of the genome. The other 4% or so of strongly conserved genome sequences consists of nonprotein-coding DNA sequences, including genes whose final products are functionally important RNA molecules, and a variety of cis-acting sequences that regulate gene expression at DNA or RNA levels. Although sequences that make non-protein-coding RNA have not generally been so well conserved during evolution, some of the regulatory sequences are much more strongly conserved than protein-coding sequences.

    Interesting details can be found in Table 9.4.

    So, we could say that about 4-9% of non coding DNA is conserved. That is not a lot, but it is much. Anyway, in absolute (not percentage) terms it is 4-9 times more than conserved protein coding DNA. And it includes ultraconserved elements which are more conserved than protein coding DNA.

    Moreover, as I have argued many times, non conservation in regulatory functions can be the mark of function even more than conservation. That’s because regulatory functions (mainly non coding genes) must change, from species to species, much more than effecor functions (most proteins). HARs are a good model of that. The recent FANTOM5 promoterome data suggest that, too, as I hope I can discuss more in detail as soon as I have time.

  11. 11
    gpuccio says:

    Dionisio:

    As always, you are very precise and careful and impartial.

  12. 12
    bornagain77 says:

    Semi related:

    98.5% Identical to Chimps? Chrome Fusion? No and No! – Ian Juby with Jeffrey Tomkins – 5:53 minute mark – video
    https://www.youtube.com/watch?feature=player_detailpage&v=Ph3FCNT0dKk#t=353

  13. 13
    Evolve says:

    Haha, good job wd400

  14. 14
    PaV says:

    I’ve re-worded the post.

    If we can now move on to an intelligent discussion. The point still remains that what is supposed to be “junk,” rendered “junk” via neutral drift, has portions that are conserved. This requires some kind of explanation by those who rely on the DNA being “junk” to support their notion that neutral drift is a legitimate driver of evolution, people like Larry Moran, and, I suppose, wd400–although I think his position isn’t, at this time, sufficiently clear.

  15. 15
    wd400 says:

    I’m afraid the point does not remain.

    No one says all introns are all junk. Just mostly junk. The fact 19% of the elements the phastCons team found are in the ~30% of the genome that is intronic is hardly evidence against that proposition.

    I find it kind of bizarre that, after all these mistakes, you would still think evolutionary biologists haven’t thought about these kind of questions.

  16. 16
    PaV says:

    wd400:

    I find it kind of bizarre that, after all these mistakes, you would still think evolutionary biologists haven’t thought about these kind of questions.

    The trend we’ve been seeing for some time, especially via
    ENCODE, is that more and more kinds of function (or, the more modest, ‘molecular activity’) is being ascribed to the putative “junk DNA,” even lncDNA. What thoughts, then, do you have if this trend continues? What would be your position then?

  17. 17
    wd400 says:

    My thoughts are

    The best arguments for junk aren’t simply that most of the genome cannot be assigned to a function,

    The proportion of a genome assigned can only really go up, so it’s not great surprise new functional peices are gound

    In the grand scheme, the proportion of the genome known to be functional is still small

    lncDNA isn’t a thing, so you should stopping using that word.

    If there were good evidence that most of the genome was truly functional I would, of course, have to change my mind. Now, what’s your position on this post now that you’ve found out it’s based on a misreading of the article?

  18. 18
    Dr JDD says:

    I do not think it is just about functionality, I think that is a rather linear view of the matter. It is context – i.e. if neutral evolution is as it is presented, and natural selection too, there are certain observations that do not quite make sense.

    Regardless of your view wd400, the facts of the matter are before we knew about functionality of many parts of the genome we now know as functional, these were being touted by most (perhaps not all but certainly most) evolutionists as junk DNA and leftover from evolution. As soon as function starts to be attributed, there is resistance to that as junk is necessary for neutral theory for one. Evolutionists use the terminology “neutral theory makes sense because most of the human genome is junk.” So if we show that most of the genome is NOT in fact junk, where does this theory stand?

    All of the evidence from a purely scientific point of view, points to us not having the full picture. I.e. more and more evidence points to more function than we thought. There comes a tipping point when the evolutionary theories that dominate, no longer make sense with more and more discoveries as such.

    For example as here:
    http://news.indiana.edu/releas.....ered.shtml
    Note:

    “As usual in science, we’ve answered a number of questions and raised even more. For example, we identified 1,468 new genes, of which 536 were found to reside in previously uncharacterized gene-free zones.”

    The drosophila genome is probably the most well characterised there is (maybe second to C elegans??) and is hugely useful as a model organism (although having shared a lab with such researchers, not good for pesky flies getting loose and the smell of ether). Yet so recently we have discovered a huge number of new genes, 1/3 residing in apparent gene-free areas! Most of these were triggered either tissue type specific and/or environmental cues and stresses. Things perhaps not easy to do with the human genome. That certainly implies that there is much undiscovered about our own genome.

    I think that the argument is fair that if this is the case, neutral theory becomes harder as a theory to accommodate that. Maybe it doesn’t though, but that would seem logical to me and others. In fact as you probably know, we are more and more identifying function for introns:

    http://www.ncbi.nlm.nih.gov/pubmed/22518112

    Perhaps we simply do not understand function for introns that seem, “functionless.”

    Finally, I think it is always useful to bring up the point about the genome having multiple novel roles that have only recently been discovered. You say to give up the lncDNA but it is an important point – they are real, previously thought to be functionless but we now see them as having function. So why should it not be used as an example? Why do so many people live in the “if we don’t know what it does now then we can be confident it doesn’t do anything” mindset? It baffles me.

    Also, why is 50% of the human genome made up of repetitive sequences? Why has the neutral theory not got rid of that or disrupted the genome so that that number is not so high (which, by the way makes next generation sequencing quite difficult).

  19. 19
    wd400 says:

    I’m afraid none of this adds up to much, JDD.

    Regardless of your view wd400, the facts of the matter are before we knew about functionality of many parts of the genome we now know as functional, these were being touted by most (perhaps not all but certainly most)

    I don’t think anyone was saying the bases 122323:124122 on chromosome 21 are junk so there. So I guess you mean classes of sequences like SINES, unannotated regions and introns. I don’t thin anyone said these would all be junk, just most. I dont’ see any reason to change that view.

    Evolutionists use the terminology “neutral theory makes sense because most of the human genome is junk.”

    You have this backwards. Neutral theory explains a lot of genomic data, so most of the genome is probably junk. If it’s not, then why does so much of the genome evolve right around the neutral expectation?

    You say to give up the lncDNA but it is an important point – they are real, previously thought to be functionless but we now see them as having function

    I say stop using the term lncDNA because it’s not used by anyone else. lncRNAs are real, but pav is using the term to mean any non-coding DNA which is likely to add to even more muddled thinking.

    Also, why is 50% of the human genome made up of repetitive sequences? Why has the neutral theory not got rid of that or disrupted the genome so that that number is not so high (which, by the way makes next generation sequencing quite difficult).

    Why would it? The neutral expectation is that sequences will change slowly as they accrue mutations. That slow process, and the continued addition of new copies of the repeats, means we’ll have diagnosable repeat sequences for a very long time.

  20. 20
    Dr JDD says:

    As per usual, I will have to agree to disagree with a naturalist/materialist. Something I am quite used to!!

    I don’t think anyone was saying the bases 122323:124122 on chromosome 21 are junk so there. So I guess you mean classes of sequences like SINES, unannotated regions and introns. I don’t thin anyone said these would all be junk, just most. I dont’ see any reason to change that view.

    Sorry, that is avoiding my point. My point is at timepoint x, people said 98% of the genome was junk. Then we learnt more about other parts of the genome and that became 90%. Then more and if you believe ENCODE’s more conservative estimates 80% could be attributed. Given there is so much repetitive DNA which cannot be true junk (as it is repetitive therefore not random), the figure is smaller still. My point is that as time increases from point x, less and less becomes junk i.e. more and more function is asssigned. My point revolves around the most logical explanation based on all the observed evidence of gDNA function is that what we think is functionless probably has function. Probably more often than no function. I think that if this is the case, neutral theory does not make as much sense as is currently claimed. You can disagree with that, but it is an observation I feel is one valid interpretation.

    You have this backwards. Neutral theory explains a lot of genomic data, so most of the genome is probably junk. If it’s not, then why does so much of the genome evolve right around the neutral expectation?

    Direct quote from N Matzke:
    “The fact that most molecular evolution is neutral makes sense because most of the genome of humans (and other large-genomed organisms) is junk.”

    Does Nick have it backwards too then? It seems pretty clear to me he is saying it the same way around I was quoting. He certainly did not phrase it like you are.

    I say stop using the term lncDNA because it’s not used by anyone else. lncRNAs are real, but pav is using the term to mean any non-coding DNA which is likely to add to even more muddled thinking.

    Fair point, perhaps it would be more helpful to explain that originally. After all, every time people in ID world try to say something has function outside of DNA our good friends the materialists selfish gene lovers will always take it back to DNA as being the cause 😉 , so technically lncRNA must come from DNA but I agree the lnc is confusing as it implies the DNA is non-coding (which it is for protein ultimately) when it does encode RNA. Perhaps I am being naive there as whenever I see lncDNA I automatically understand it to refer to lncRNA’s and not all non-coding DNA.

    Why would it? The neutral expectation is that sequences will change slowly as they accrue mutations. That slow process, and the continued addition of new copies of the repeats, means we’ll have diagnosable repeat sequences for a very long time.

    Because very simply (and perhaps too simplistic) if 50% of the genome is repetitive, it is therefore not been subjected to the same selective forces and mutational events which in itself is a bit odd if it serves no function, but also when you start adding up all of the various bits of DNA that we now know DO have function (i.e. not just the ~2% that are classical genes), we are getting a smaller and smaller value that we can attribute to being real junk. Again, my interpretation of what other quite prominent evolutionists have stated, is that going to a much smaller percentage of the genome as being able to attribute as junk poses more problems to the evolutionary model than having “most” of the genome as junk.

    And the fact that apparently most of the genome is junk (as per N Matzke et al) does not square up with 50% of the genome being repetitive (untouched by neutral evolution). Therefore most (which by definition would be >50%) is quite simply not true.

  21. 21
    wd400 says:

    My point is at timepoint x, people said 98%

    I reapeat myself: no one that knew what they were talking abut said all non-coding DNA was junk. Just most of it.

    Direct quote from N Matzke:
    “The fact that most molecular evolution is neutral makes sense because most of the genome of humans (and other large-genomed organisms) is junk.”

    What is it with you guys and basic reading comprehension? Nick’s comment is exactly the same as mine. It is known that most molecualr evolution is nuetral, this makes sense if most of the genome is junk and is very hard to explain otherwise.

    Perhaps I am being naive there as whenever I see lncDNA I automatically understand it to refer to lncRNA’s and not all non-coding DNA.

    Which illustrates exactly why PaV describing all noncoding DNA as lncDNA is a bad idea?

    Because very simply (and perhaps too simplistic) if 50% of the genome is repetitive, it is therefore not been subjected to the same selective forces and mutational events which in itself is a bit odd

    Why do you think repetitive DNA can’t persist under neutrality?

  22. 22
    Dr JDD says:

    What is it with you guys and basic reading comprehension? Nick’s comment is exactly the same as mine. It is known that most molecualr evolution is nuetral, this makes sense if most of the genome is junk and is very hard to explain otherwise.

    You said:

    Neutral theory explains a lot of genomic data, so most of the genome is probably junk.

    Nick said:

    The fact that most molecular evolution is neutral makes sense because most of the genome of humans (and other large-genomed organisms) is junk.

    Simplified, you said:
    A is true therefore B.

    Nick said:
    A is true because of B.

    To me, those are different.

    I originally said:

    neutral theory makes sense because most of the human genome is junk.

    Which is the same as:
    A is true because of B.

    Which is what Nick said.

    So why did you pull me up on what I said and say I have it backwards?

    Anyone else apart from wd400 – is what I said any different to the direct quote of Nick’s? Is what I said not more close to what Nick said rather than wd400’s statement? Who is struggling with basic reading comprehension?

  23. 23
    bornagain77 says:

    wd400 claims,

    It is known that most molecualr evolution is nuetral,(sic)

    which is interesting claim for him to make since no such thing is established (save for in the imagination of dogmatic Darwinists like wd400)

    To the disbelieving shock of many evolutionary scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence.

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    according to prevailing evolutionary dogma, there ‘HAS’ to be ‘major genetic drift’ to the DNA of modern bacteria from 250 million years ago, even though the morphology (shape) of the bacteria can be expected to remain exactly the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, has also severely weakened the ‘genetic drift’ argument of evolutionists:

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
    http://genome.cshlp.org/conten.....091785.109

    a few more notes that are antagonistic to the fantasy world wd400 lives in:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    In fact it is now strongly suspected that almost all changes in the genome are now found to be ‘designed’ changes that still stay within the overriding principle of Genetic Entropy:

    Revisiting The Central Dogma (Of Evolution) In The 21st Century – James Shapiro – 2008
    Excerpt: Genetic change is almost always the result of cellular action on the genome (not replication errors). (of interest – 12 methods of ‘epigenetic’ information transfer in the cell are noted in the paper)
    http://www.uncommondescent.com.....revisited/

    Scientists Discover What Makes The Same Type Of Cells Different – Oct. 2009
    Excerpt: Until now, cell variability was simply called “noise”, implying statistical random distribution. However, the results of the study now show that the different reactions are not random, but that certain causes (environmental clues) lead to predictable distribution patterns,,,
    http://www.sciencedaily.com/re.....204217.htm

    Bacteria ‘Invest’ (Designed) Wisely to Survive Uncertain Times, Scientists Report – Dec. 2009
    Excerpt: Essentially, variability of bacterial cells appears to match the variability in the environment, thereby increasing the chances of bacterial survival,
    http://www.sciencedaily.com/re.....112102.htm

    etc.. etc.. etc..

  24. 24
    Dionisio says:

    He said, she said, I said, they said, we said,…

    Does this look like a serious discussion?

    We might want to take a break from this never-ending OOL discussion, which is mostly a philosophical confrontation between two irreconcilable opposite worldviews (theistic or materialistic). Better switch to a more productive task, like writing a complete accurate coherent comprehensive detailed description of the mechanisms behind the spindle apparatus that operates on the intrinsic asymmetric ESC divisions during the first few weeks of human embryonic development. This could help us understand the mechanisms behind the cell fate determination, differentiation, migration, as well as the genotype-phenotype association. Once we get that done, those folks who like the philosophical OOL discussion could go back to it.
    😉
    gpuccio and other colleagues here already provided links to very good sources of information about the above mentioned subjects. 🙂

  25. 25
    wd400 says:

    Nick sarted by saying “the fact most molecular evolution is neutral…”

    i.e. the fact neutral theory is so good an explaining so much data makes sense if most of the genome is junk. It doesn’t make much sense otherwise. You bought this argument up while trying to imply that evolutionary biologists are unable to accept a mostly-functional genome because it would do away with neutral theory. That doesn’t really make sense when you consider “most evolution is neutral”.

  26. 26
    PaV says:

    wd400:

    Which illustrates exactly why PaV describing all noncoding DNA as lncDNA is a bad idea?

    You’ve said that three times now. There is no reason in the world for you to make this mistake. None.

    I don’t like the term lncRNA. I consider it redundant and confusing. And I know you can decipher it.

    As to my reaction to my ‘corrected view,’ it changes very little indeed. Why? Because the same problems existed before as after.

    The ENCODE project has been principally criticized for its definition of ‘function,’ a definition that is not tied directly to ‘conserved sequences.’

    I know that it has already been pointed out to you–I think I pointed it out and asked for your reaction: which was a “ho-hum”—that an experiment in which “millions”!!! of “conserved” bases were deleted from the mouse genome produced normal mice! This dismantles and demolishes the primary understanding of population geneticists. In fact, I had just purchased a collection of Kimuras papers in book form and intended to read it when this experiment came out. I put the book away because the experiment mentioned above poked such huge holes in Pop Gen.

    Now, in regards to what has been said about introns, here are some questions I feel need to be asked: why is there only a portion of the ‘intron’ that is ‘conserved’? Why not all of it, or none of it? What sets the boundary at which the conservation begins and where it ends?

    If these answers cannot be found, then we really don’t know what’s going on.

    In a somewhat analogous vein, DrJDD poses the question above as to why, given ‘neutral evolution,’ there are so many repeated sequences found in the genome since, per neutral theory expectations, regularity over large swaths of sequence should not be appearing—unless, of course, it has function.

    In the first case of the introns, neutral evolution is supposed to be taking place, but yet it stops and starts. Why? In the second case of the repeats, it looks like neutral evolution never really begins. Why?

    gpuccio has stated above that he feels that functional parts of the genome would only have parts of it ‘conserved’. This view has its merits; and, it sounds like the ‘introns,’ in the first place, with their ‘conserved’ areas surrounded by sequences subject to change; and in the second place points to a real problem of neutral evolution and the axiom that conserved sequences are functional, and no more.

    Here’s the problem: if NS is purifying these sequences, then how do they change?

    They can’t, because if they do, the organism won’t, per the axiom, survive. So, now you’re stuck.

    But, wait, the way around this is to simply construct a “just-so” story that says: “purifying selection has been turned off in this area” when dealing with inter-species differences between sequences that both seem to be conserved. IOW, “turning off purifying selection” is not a ‘fact”; it’s an assumption, one that is needed in order to keep the assumed definition of functionality alive. What’s the proof of this other than the utilization of the assumption you want to make?

    If we relax the definition of what constitutes function—as the ENCODE team does—then we have almost 80% of the genome with function, as DrJDD points out above. Well, this is the death-knell of neutral theory. So now what happens? The ENCODE team is berated, beaten up in the academic arena. Will they finally cry “uncle”? I hope not.

    In the meantime, as I’ve already mentioned, every passing day more and more function is being found for so-called “junk DNA.”

    As they say on the stock market watch: “The trend is your friend.”

    So it appears that you are the one on the way to the day of reckoning, and not me.

  27. 27
    wd400 says:

    If you don’t mean all non-coding DNAs are “lncDNAs” then I’m utterly at a loss to understand what you mean by the term. No one thinks lncRNAs are “among the junkiest” of genome elements. I don’t know where you’ve gone off track, but invented your own terminology isn’t going to help anyone trying to decipher your posts.

    But if you are capable of writing an entire post around you own misunderstand of a Wikipedia article, and then incapable of updating your view when you learn that you misunderstood the article, then I really don’t know why anyone would bother.

  28. 28
    Mung says:

    Dr JDD:

    Evolutionists use the terminology “neutral theory makes sense because most of the human genome is junk.” So if we show that most of the genome is NOT in fact junk, where does this theory stand?

    It doesn’t change the theory, because the theory does not depend upon the “junkiness” (or lack thereof) of the genome.

    wd400:

    It is known that most molecular evolution is neutral, this makes sense if most of the genome is junk and is very hard to explain otherwise.

    Is anyone opposed to going back to basics?

    How is it known that most molecular evolution is neutral?

    What does it mean to say that that most molecular evolution is neutral?

    I will attempt an answer to the second question first.

    Most molecular evolution is not under selection. That’s what is meant by most molecular evolution is neutral.

    So then the first question can be re-phrased – How is it that we know that most molecular evolution is not under selection?

    And then, what does any of this have to do with junk?

    If it’s under selection, it must not be junk. It’s not under selection, therefore it must be junk. QED.

  29. 29
    Querius says:

    Bornagain77@23 noted:

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:

    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/…../19/9/1637

    Wow, I didn’t know that!

    It’s not what evolutionists would expect. If there were considerable drift, they would say it “proves” evolution, but if there’s almost no drift, apparently it still “proves” evolution. Oh well, they can call it a paradox and grimly forge ahead, calling anyone who questions evolution “unscientific” or a “kooks.”

    Here’s another example of Monty Python’s Dead Parrot skit revisited. “The parrot is dead!”

    -Q

  30. 30
    Querius says:

    I wonder whether the non-coding (aka “junk”) DNA was also conserved in those bacteria.

    Anyone know?

    -Q

  31. 31
    PaV says:

    wd400:

    But if you are capable of writing an entire post around you own misunderstand of a Wikipedia article, and then incapable of updating your view when you learn that you misunderstood the article, then I really don’t know why anyone would bother.

    Because my point is the same point that DrJDD was making regarding the repeats. There is an inconsistency between the kind of massive degree of neutral evolution you would posit and the appearance of orderliness within the genome.

    Having said this, let me point out that you seem to make every effort to NOT understand what I’m saying.

    It’s the kind of effort I’ve seen plenty times before when I’ve had dealings with liberals whose positions I began to dismantle. When they feel helpless, then they begin to question every word I utter, forcing me to explain the obvious, so as to render communication almost impossible.

    Why do they do it? Because they don’t have a leg to stand on.

    You point out minor little things, and then run away from the big things.

    As to lncDNA: let me ask you: do they, or do they not speak of “coding” and “non-coding” sections of DNA? Well, unless you want to wrangle about that one, too, you know the answer is: “Yes, they do.”

    Well, then, why talk about “non-coding” RNA? It’s redundant, and leads to confusion. If the DNA is not ‘coding’, then that means the RNA is not translated. Why lump this kind of RNA with other RNAs that are known to be involved with gene regulation?

    And, finally, why then not call it “junk-RNA” instead of “junk-DNA”. Or is this no more than an effort to be obtuse? Is that all there is to all of this?

  32. 32
    Mung says:

    …practically every major prediction of evolution has failed. For example, one of those puzzles was the finding of long stretches of identical, unconstrained DNA in otherwise distant species. Such a finding, an evolutionist had told me years earlier, would falsify evolution, period. His point was that evolution was falsifiable. That was yet another false claim. That finding of identical, unconstrained DNA did not so much as put a dent in the evolutionist’s certainty (and yes, he is still believes in evolution).

    here

  33. 33
    wd400 says:

    here is an inconsistency between the kind of massive degree of neutral evolution you would posit and the appearance of orderliness within the genome.

    The text you quoted, and based this whole article on, doesn’t support this claim. Remember, the article says ~19% of conserved elements live in the ~30% of the genome and that is intronic. That is to say, most of most introns are not conserved.

    For all the gish gallop that has followed, we are still in the position that this whole post is about your own misunderstanding of the article, and yet you fail to climb down.

    Having said this, let me point out that you seem to make every effort to NOT understand what I’m saying.

    THis is not that the case, and if you leave off from political tribalism and diagnosing people’s motives please.

    Well, then, why talk about “non-coding” RNA? It’s redundant, and leads to confusion.

    mRNA exons are coding RNA, and plenty of viruses have RNA genomes. THe elements are called lncRNAs because they are detected in RNA or cDNA sequencing projects and so are known to be expressed (as opposed to lot of non-coding DNA which is only expressed haphazardly). The grander point is that its unhelpful in the extreme to make up your own terminology. I presumed you where using the term to mean any non-coding DNA because you claimed others say”lncDNAs” are among the junkiest of genome elements. I’ve never seen that claim, so gave you the benefit of the doubt you meant something else.

  34. 34
    wd400 says:

    To go some way to explaining why I find it so hard to understand this post if lncDNA = lncRNA

    If lncDNA is ‘junk’, then according to ‘neutral theory’ it shouldn’t be conserved, not even any portion of it. Yet, of the “highly conserved phastCons elements,” 32% appear in unannotated regions…

    No one claims all lncRNAs are junk, so this “not any portion of it” stuff doesn’t seem to apply. lncRNAs are by definition in annotated regions, so why phastCons elements falling in unannotated regions is applicable to anything I don’t know. The same goes for introns (some lncRNAs are in introns at least).

    If it is “junk,” then why aren’t ‘neutral mutations’ found across their entire length?

    If this sentence is meant to mean ‘If it is “junk,” then why aren’t ‘neutral mutations’ found across lncRNAs entire length?’ then it’s seems like a non sequitur. Nothing in this post has talked about the rate of conservation in lncRNAs, just two types of non-coding DNA.

    So, maybe I did misunderstand you, but I think you can see why?

  35. 35
    PaV says:

    wd400:

    A few notes:

    1.) You’ll notice that the title of this post was phrased as a question.

    2.) You’ll notice that at the end of the OP I ended by saying, “Just curious.”

    3.) In the title I had lncDNA/RNA to posit my view that I prefer lncDNA while including the standard RNA.

    I was not stating that the presence of lncDNA/RNA disproved neutral theory, I was wondering if the case could be made. I found the quote from Wikipedia AFTER I started the post. And, I figured that at some point you would enter into the discussion.

    Your admission that you would change your view if ‘function’ was found for most of the genome not only demonstrates a certain open-mindedness on your part, but also makes clear that “junk DNA” and neutral theory are opposed.

    You state: mRNA exons are coding RNA, and plenty of viruses have RNA genomes. THe elements are called lncRNAs because they are detected in RNA or cDNA sequencing projects and so are known to be expressed (as opposed to lot of non-coding DNA which is only expressed haphazardly).

    Two things:

    (1) That viruses have RNA genomes only adds to the confusion of referring to lncDNA as lncRNA since there is now this added RNA realm to which the lncRNA could refer to independently of DNA.
    (2) That the lncRNA is found using RNA sequencing makes a strong case for current usage. I’ll follow that convention.

    Once corrected on the actual, not relative, amount of conservation, there seems—at this point in time—room for both neutral theory and the amount of conservation seen taking place in ‘junkDNA.’ So, that’s part of the answer I’m looking for.

    Nevertheless, my intuition tells me that neutral theory, like Darwinism, is doomed. The ENCODE project is just, I believe, the beginning of the neutral theory’s unraveling. Time will tell; but, again, “The trend is your friend.” Not good for your side.

    What has not happened, and should have happened (although Mung makes this point rather effectively up above) is a good, hard look at what it means for a sequence to be “conserved.” Standard operational meaning of that is that comparing different species to one another, we don’t find much change in the sequence.

    But I think these are areas you don’t care to dip your toe in.

    So be it.

  36. 36
    Piotr says:

    It’s not what evolutionists would expect. If there were considerable drift, they would say it “proves” evolution, but if there’s almost no drift, apparently it still “proves” evolution. Oh well, they can call it a paradox and grimly forge ahead, calling anyone who questions evolution “unscientific” or a “kooks.”

    Or maybe the “Permian bacteria” are not Permian in the first place. Graur and Pupko practically debunked the claim already in 2001:

    http://mbe.oxfordjournals.org/.....3.full.pdf

    More recently, see this discussion:

    http://geology.gsapubs.org/con.....1.full.pdf

  37. 37
    wd400 says:

    Sorry PaV, but I find it very hard to beleive this post, and it’s associated political rants, gish gallop, repeated accusations of bad faith on my behalf my half and even a insuation that you’d “began to dismantle” an evolutionary theory was offered only as a genuine attempt to learn something new.

    Anyway, thanks at least for climbing down. Though I find this kind of odd

    What has not happened, and should have happened (although Mung makes this point rather effectively up above) is a good, hard look at what it means for a sequence to be “conserved.” Standard operational meaning of that is that comparing different species to one another, we don’t find much change in the sequence.

    I’m not sure what “conserved” could mean if not retained in related species. I also hope you might learn a lesson from all these posts, and hold of from grand declarations about what should be happenign in a field of study until you actually understand it.

  38. 38
    Piotr says:

    #36

    P.S. The first link doesn’t work. Let me try again:
    http://mbe.oxfordjournals.org/...../1143.full

  39. 39
    Querius says:

    It’s because the link might have been busy mutating to a different one, such as this letter:
    http://mbe.oxfordjournals.org/...../1637.full

    Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.

    They musta evolved radioresistance for a while and then lost it again. I especially liked this part . . .

    If three synonymous substitutions out of the 1,023 total nucleotides examined (1/619 from recA and 2/404 from splB), thus 0.2% divergence, are representative of the mutation rate since the divergence of 2-9-3 and S. marismortui 250 MYA, then the 121 synonymous substitutions (12% divergence) between B. subtilis and B. cereus would place their last common ancestor at 15 BYA, much longer than the age of the earth.

    Sure, why not? Ya gotta love those LCA calculations, but it would be easier just to label the contemporary ones “living fossils” like all the others and and move on.

    -Q

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