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Junk DNA: Only 20%? All but 8.2%?

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Estimates of how much human DNA is functional: 8.2% to 80%,according to a recent post at ScienceBlogs:

Science and its interpretation is wonderful. Today I saw a post on Twitter from @LAbizar, referencing an @GEN, post that stated 8.2% of Human DNA is Functional with a link to a GEN article: “Surprise: Only 8.2% of Human DNA Is Functional.” The GEN writeup cited a PLoS Genetics article, “8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage,” released today.

In 2012, the ENCODE (Encyclopedia of DNA Elements) project published a landmark summary, “An integrated encyclopedia of DNA elements in the human genome,” from nine years of work measuring the ways in which DNA structure and its interactions with proteins such as transcription factors might contribute to the regulation of genes. In the paper’s abstract the team stated that “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” As a very small fraction of the genome (~1%) encodes for protein sequences, a question in science has been, what does the other 99% do? ENCODE data demonstrated that much of this DNA participates in biochemistry in some way. Many lauded the work for its tour-de-force effort and the resources contributed have been significant.

Not a lot of room between those estimates, is there? Blogger finchtalk says that it all depends on what you count.

Well, if it counts for anything … it’s not junk.

Note: Here’s the referenced 8.2% article. (Public access.)

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Hat tip: Timothy Kershner

31 Replies to “Junk DNA: Only 20%? All but 8.2%?

  1. 1

    I read through the Abstract and the Author Summary part of the paper (parts from which the blog quotes were extracted).
    It seems that their proposed percentage (8%) of functional genome is based mostly on speculations based on the belief in evolution (conserved sequences along hundreds of million years, etc.) while ENCODE percentage resulted more from an empirical, research and measurement approach.
    I found interesting though the readers’ comments. Two such comments notice that “the authors of this work have failed to apply existing nomenclature”. But the most interesting comment is this:

    Nonconserved or fast evolving DNAs are also functional, just for a different purpose
    Posted by ShiHuang on 10 Aug 2014 at 23:27 GMT
    I found the last paragraph of our poster “Testing the infinite sites assumption” recently presented at the “1000 genomes project and beyond” meeting in Cambridge UK to be relevant to this interesting paper. here it is: Sequence conservation per se may not automatically indicate functionality of variants within such sequences as is commonly assumed. Less conserved sequences are more important for adaptation to external environment, while the more conserved ones are important for internal integrity of a system. To a virus or bacteria facing elimination by human medicines, the fast evolving parts of their genome is far more critical/functional to their survival than their more conserved parts. The popular assumption of neutrality/non-functionality for the less conserved parts of the genome overlooks their fundamental function in quick adaptation.

    for a pdf of the poster, please visit this site http://www.sklmg.edu.cn/a

    I followed the above link to professor Shi HUANG’s page where he summarizes his theory: Maximum Genetic Diversity (MGD) which I found interesting. I am quoting it’s main paragraph below:

    We proposed a novel hypothesis of genetic diversity and evolution, the Maximum Genetic Diversity (MGD) hypothesis. It is based on a pair of self-evident intuitions on construction. The first intuitive idea posits that the maximum tolerable level of random variations/errors/noises in building blocks above atom level is inversely related to system complexity. The equivalent of this concept in biology is that MGD is inversely related to epigenetic complexity. The second intuitive idea posits that any system can allow a certain degree of random noises/errors in its building blocks, and such limited degree of random errors may confer zero, negative, or positive values to the functioning/survival of the system under certain environmental circumstances. In biology, this simply means that an organism has a specific level of MGD and that genetic variations within MGD may confer zero, negative, or positive values to the functioning/survival of the organism under certain environmental circumstances. The first idea describes macroevolution where there is change in complexity over time, while the second idea describes microevolution and population genetics where there is no change in system complexity over time. The second idea thus underlies the proven portions of the modern evolution theory composed of Neo-Darwinism and Kimura’s Neutral theory. The novel points of the MGD hypothesis are 1) macroevolution and microevolution are different, and 2) an increase in organismal or epigenetic complexity is associated with a decrease in MGD. This hypothesis has been supported by numerous observations and has yet to meet a contradiction. It has solved a nearly half century old puzzle of biology, the genetic equidistance phenomenon. By studying fundamental mysteries of common diseases, complex traits, and evolution, our goal is to use the MGD hypothesis to solve major real world biomedical problems and to gain novel insights into the past, present and future of life on Earth.

    If I understand this MGD theory correctly it claims that the more complex an organism is the more limited is its genetic diversity. Or paraphrasing it, the more complex an organism is, the smaller the number of (random) genetic variations. This make sense logically (and intuitively – as the professor says) because a perfectly functioning, complex organism requires higher precision in its construction and internal biological mechanisms and tolerates (is able to survive with) only reduced number of errors (random variations).
    I would say that this theory sounds like some common sense engineering perspective on complex machinery.

  2. 2
    Andre says:

    Engineering it is indeed….. Blind forces can not create nor solve engineering problems…..

  3. 3
    Axel says:

    ‘Engineering it is indeed….. Blind forces can not create nor solve engineering problems…..’

    That sounds such a simple truism, Andre, that I laughed out loud when I read it, couched, as it is, with such epigrammatic brevity.

    However, since atheists are so desperate for their own world-view not to be proved wrong, it illustrates by courtesy of their good offices, the unfathomable depths human folly is capable of plumbing – and I mean, academically-educated people.

  4. 4
    REC says:

    The two numbers are not mutually exclusive.

    8.2% of the genome is constrained (functional).

    80% of the genome has a Encode biochemical tag associated with it. These can include binding silencing histones or having silencing methylated DNA. Staying quiet and not doing anything is likely not sequence dependent, and is a feature of non-coding DNA.

  5. 5
    gpuccio says:

    I have been arguing for a long time that, while conservation of sequence usually is a sign of function, function does not necessarily require conservation of sequence, indeed often it requires variation.

    That is the main argument is these OP of mine:

    http://www.uncommondescent.com.....-part-one/

    and

    http://www.uncommondescent.com.....-part-two/

    Transcription factors are IMO a good example of that. Their DNA binding motifs are usually highly conserved. Not so the rest of their molecule. Why? IMO, the simple explanation is that the rest of the sequence has regulatory roles, mainly through dynamic interaction with other regulatory elements, TFs or else, and therefore its different, rapidly evolving function requires continuous variations.

    There are many long and very important proteins implied in epigenomic regulation in which conserved motifs are scarcely recognizable in most of the sequence. Does that mean that only a small part of the molecule is functional? I don’t think so. Not at all.

    So, if that is true for well known proteins, how much more it can be for regulatory elements which we are only now beginning to know and understand, like for example long non coding RNAs?

    Equating function with sequence conservation is a very tricky assumption and it can lead to false conclusions. Especially if one is trying so very hard to defend the wrong scientific paradigm of neo darwinism and its poster child of junk DNA.

  6. 6
    REC says:

    “I have been arguing for a long time that, while conservation of sequence usually is a sign of function, function does not necessarily require conservation of sequence, indeed often it requires variation.”

    Durston’s fits are derived from conservation of sequence, no?

  7. 7
    BM40 says:

    Today ENCODE lead scientists are backing away from their ridiculous 80% claim. According to Nature Manolis stated:

    The 80% claim, he says, was misunderstood and misreported.

  8. 8
    gpuccio says:

    REC:

    “Durston’s fits are derived from conservation of sequence, no?”

    Correct. That’s why I said:

    “I have been arguing for a long time that, while conservation of sequence usually is a sign of function, function does not necessarily require conservation of sequence, indeed often it requires variation.”

    Emphasis added.

    IOWs, Durston’s fits probably underestimate functional complexity, and are a lower threshold fot it.

  9. 9
    REC says:

    Gpuccio, your reliance on evolutionary principles, which you then quickly sneer at, is noted.

    Eating your cake and having it too.

    “function does not necessarily require conservation of sequence”
    “functional sequences cannot change much and are conserved”

    So conservation=fits (functional sequence complexity), but function=variability?

  10. 10
    mullerpr says:

    I think it is telling us a lot if some functional code achieve the same outcome regardless of both variation and conservation. It might be because of various factors, of which one can be as simple as a slight change in the “compiler” that permeate the variation without changing the content of instructions…

    There might be any number of other reasons, but the effect that needs explanation is, the fact that, even with genetic variability there are no large scale change to the outcomes.

    I am not a specialist in the field but, this looks like a challenge to most of the parsimonious notions of the simple form – variation=adaptation that leads to new species, that explain common descent.

  11. 11
    gpuccio says:

    REC:

    You are an intelligent person, I supposed you could understand.

    But I will make it simpler for you.

    a) We compare A and B. The function remains the same, and the sequence is conserved. “Functional sequences cannot change much and are conserved”.

    b) We compare A and B. The function has varied for some aspects, and the sequence varies. A is functional. B is functional. In different ways. The sequence is less conserved, because function varies.

    This is completely different from neutral variation in non functional parts of the molecule, which also happens.

    I have given the example of transcription factors. In general DBDs are highly conserved. The simple reason is that their function remains the same in different species: DNA binding.

    The rest of the molecule often varies much more. It is the part which is probably implied in regulatory interactions with other TFs or other molecules, and we know that those regulatory interactions, which are an integral part of the epigenome, vary in different species, sometimes a lot.

    Is that clear enough for you?

  12. 12
    gpuccio says:

    mullerpr:

    There are some aspects which are peculiar of how proteins work. In a protein sequence, there are AA positions which are essential to the function. Others can vary, but up to a certain point, especially according to other associated variations which keep the structure and function. Other positions are much more flexible, and can vary rather freely because their variation is essentially neutral.

    That’s exactly what the Durston method tries to measure.

    My concept here is that there are two kinds of variation when we compare the same molecule in distant species:

    a) neutral variation, which is linked to AA positions which are not essential to the function;

    b) functional variation, where the sequence varies because some aspects of the function vary.

    The Durston method will consider all variation as a), therefore underestimating the functional complexity. However, it remains a good estimate of a lower threshold for it.

    For example, proteins can include localization signals in their sequence, which help in dispatching them to the correct cellular context. Those signals, while functional, are not part of the primary biochemical function of the molecule. So, it is possible that the sequence related to the main biochemical function remains the same, while the localization signal changes from species to species. But both are functional. This is just a general concept, to clarify what I mean.

  13. 13
    Joe says:

    REC- No one is relying on blind watchmaker evolutionary principles.

    Grow up

  14. 14
    gpuccio says:

    REC and others:

    I thought this could be pertinent to the brief discussion about conservation and functional divergence here:

    “Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution.”

    Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130022. doi: 10.1098/rstb.2013.0022. Print 2013 Dec 19.

    The abstract:

    “The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis-regulatory elements) in entire genomes. Comparing protein-DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis-regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein-DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.”

    Emphasis mine.

    High divergence of enhancers?

    I quote myself: 🙂

    “b) We compare A and B. The function has varied for some aspects, and the sequence varies. A is functional. B is functional. In different ways. The sequence is less conserved, because function varies.”

  15. 15
    Barry Arrington says:

    Joe @ 13.

    “Grow up.”

    Having been warned repeatedly to stick to the issues and to lay off the personal attacks, this was the straw that broke the camel’s back.

    Joe is no longer with us.

  16. 16
    Mung says:

    ok Barry, Joe is often way out of line. But banning Joe for a post made by Joe on Nov 5 when the “last warning” was issued on Nov 7?

    http://www.uncommondescent.com.....ent-526212

  17. 17
    Mapou says:

    Why is Joe banned and not me? I am just as outspokenly hostile to Darwinists as Joe is and I don’t usually mince my words.

    I hereby protest Joe’s banishment.

  18. 18
    keith s says:

    It’s true, Barry. The “last straw” occurred before the “final warning”. You forgot to check the timestamp.

    I think that Joe, and all of the ID critics who were banned for far less, should be reinstated. You could call it a “general amnesty”.

    What do you think, Barry? 🙂

  19. 19
    Mung says:

    keiths, there’s no bandwagon here for you to jump on.

    Go back to TSZ and post yet another incompetent critique of ID where you will find a bandwagon.

  20. 20
    Mung says:

    keiths will soon be lobbying for the unbanning of Joe over at TSZ where “everyone is welcome.” Except Joe. Or not.

  21. 21
    Quest says:

    keitch s is boring… he lost his high and now he is going to torment us with his claims about his ” supposed victorious”…

    It is the time to abandon the sinking ship…

  22. 22
    Barry Arrington says:

    The criticisms in 16 and 18 are fair. My apologies to Joe. He is unbanned but still warned.

  23. 23
    DiEb says:

    [Joe] is unbanned but still warned.

    That is such a relief! It’s always helpful that one of Uncommon Descent‘s more outspoken proponents of the quite mathematical ideas of Intelligent Design is the author of articles like A Tale of Two Sets:

    Given 2 sets, A and B, if A contains all of the members of B AND has members B does not, A’s cardinality has to be greater than B’s.

    And the predicted unsupported and cowardly response of “Joe doesn’t understand infinity”, is duly noted.

    Let the flailing begin…

  24. 24
    centrestream says:

    “The criticisms in 16 and 18 are fair. My apologies to Joe. He is unbanned but still warned.”

    What about all the others who were banned who never deviated from civil discourse?

  25. 25
    keith s says:

    centrestream,

    There’s a simple explanation.

    Barry isn’t afraid of Joe. No one is.

    Barry is afraid of ID critics, however. So even though he knows that it makes him look ridiculous, he maintains a double standard — silently banning critics at the drop of a hat, while excusing everything that ID supporters do. He needs friends, after all.

    It’s a tradeoff. UD looks ridiculous either way, but perhaps Barry thinks the double standard looks less ridiculous than the shellacking that ID supporters take when all of the critics are allowed to post freely.

    Meanwhile, Barry continues to run from challenges, such as this one.

    He’s doing us a favor in the long run, by showing that IDers have no confidence in their ability to defend ID in open, uncensored discussion.

    Keep up the good work, Barry!

  26. 26
    centrestream says:

    Keith S, I tend to agree. I have been banned under so many names (Acartia, Acartia_bogart, William Spearshake, Tintinnid, Stenosemella, Sleemantallcan. And many more) that I forget who I am. And at no time were my crimes more sinister than openly disagreeing with Barry or Mr. Mullings.

  27. 27
    Daniel King says:

    centrestream,

    Barry said that you were not banned (you had banned yourself, or or some such) and criticized me severely for suggesting that he was pretending that he hadn’t banned you.

    He got so angry that I apologized for doubting his honesty.

    It looks like one of you has been lying.

  28. 28
    Mung says:

    Barry, my compliments.

  29. 29
    centrestream says:

    DK: “centrestream,

    Barry said that you were not banned (you had banned yourself, or or some such) and criticized me severely for suggesting that he was pretending that he hadn’t banned you.

    He got so angry that I apologized for doubting his honesty.

    It looks like one of you has been lying.”

    Yes, one of us is obviously lying. Unfortunately, you got caught in the middle and was forced to apologize for making an accusation that was truthful. I would have supported you but, big surprise, I was not permitted to post any comments.

  30. 30
    Joe says:

    Obviously keith s is afraid of me because he keeps avoiding my refutations of his arguments. And no one is banning critics. I can defend ID in any open forum. However no one can defend unguided evolution without lying and ignoring all refutations.

  31. 31
    Joe says:

    Earth to DiEB- Any time you want to try to refute the tale of two sets, you are more than welcome to try.

    Good luck with that.

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