Epigenetics: DNA distinguishes young vs. old duplicate genes

_{Denyse O'Leary

April 8, 2014

Epigenetics, News}

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Duplicate genes are essential and ongoing sources of genetic material that evolution can act on, yet new duplicates are under constant risk of being inactivated by mutations and subsequently lost. We show that a common heritable epigenetic modifier, DNA methylation, plays an important role in duplicate gene evolution. DNA methylation clearly distinguishes young and old duplicates, and the differences in DNA methylation of duplicate genes are associated with functional differences in expression. Remarkably, for a majority of duplicate gene pairs, a specific duplicate partner is consistently hypo- or hypermethylated across highly divergent tissues. Our results indicate that epigenetic modifications are intimately involved in the regulation and maintenance of duplicate genes.

From the Abstract … Remarkably, many duplicate gene pairs exhibit consistent division of DNA methylation across multiple, divergent tissues: For the majority (73%) of duplicate gene pairs, one partner is always hypermethylated compared with the other. …

Should we tell that guy who is standing athwart epigenetics and yelling “Stop!”?

See also: Richard Dawkins responds to “Die, Selfish Gene, Die”: Mere adversarial journalism

Epigenetics: Inheritance of acquired traits gradually gaining acceptance

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Comments

wd400: You are still evading and equivocating. My simple point is that the regulation of genes requires regulatory procedures, and that those procedures must be written somewhere in some way, if they are transmitted from cell to cell. And we don't know how and where they are written. Of course the regulation of genes cannot be a C(n,k) scenario, because otherwise it could not happen. That's exactly my point. It is not a C(n,k) scenario because it must be controlled by specific procedures, which know exactly what is to be done in different moments, in different cells, and in different circumstances. Call them intelligent or not, as you like. But those procedures must be somewhere. Again, the genome is the same in all cells of one individual. Transcriptomes are many and different, and they must be chosen accurately out of a nearly infinite search space. Only specific algorithmic procedures can ensure that result. Those procedures must be in the genome or somewhere else in the cell. And we know almost nothing of them. That's the simple truth.gpuccio_{April 10, 2014
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You certainly do need methyltransferases...and demethylators (or you cannot switch off from methylated state) and the interpreters of the methylation state. So 3 proteins for the system to work. Chicken or egg? Funny to bring up histones with their huge number of modifications outside just simple methylation as well, increases complexity to an unimaginable degree. It takes great faith to believe this all happened through evolutionary processes as described by current proponents. JDDr JDD_{April 10, 2014
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All I can suggest is that you read a little about gene regulation and development. There's no way the gene regulation of genes, or the evolution ther of, is a C(n,k) scenario, and it's not true that the regulation of genes requires intelligence. As for the Drosophila example, I don't know but I presume this is one of the 'deep sequencing' projects, so it's likely many of the transcripts are aberrant and in very low number. But, in general, alternative splicing is controlled by regulatory proteins that bind to sites in pre-mRNA to prevent (or hinder) the splicing complex. In most cases, aleternatively spliced mRNAs don't make radically different proteins (even in extreme cases like Dropshophila's DScam gene)wd400_{April 10, 2014
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wd400: I am in no "rush to induce outside forces to contol it". I just want to make clear what we know and what we don't know. You seem to be in a rush to state that we understand what we don't understand. It is not simply a problem of regress. Transcriptomes are many and different and functional and appropriate for different cells and conditions. The genome is one, always the same in all the cells of one organism (with the two exceptions I mentioned in a previous thread, immune cells and reproductive cells). Histones, and small RNAs, and proteins, are all made from the same genome, but they are made, or regulated, differently in different cells and in different conditions. To get different ordered transcriptomes from one single genome, you need intelligent procedures. We don't know where those procedures are coded, we don't know how they work. Let's make a very simple example. Let's say, just for the sake of discussion, that as humans we have 20000 protein coding genes (rather accurate), and that we have 1000 different cell types and cell states (just to give a number). Let's assume for a moment (completely hypothetichal) that each different cell type or cell state translates 10000 genes (probably in different isoforms, nut let's ignore that further level of complexity for the moment). Let's ignore also the time sequence in which the genes are translated, and the relative abundance of each gene. Let's simplify. We just define each transcriptome, in this thought experiment, by the simple list of the 10000 genes, out of 20000, which are translated in that cell at that moment. So, we have 1000 different lists (one for each cell type or state) of 10000 genes out of 20000 genes in the common genome. OK. So, how many are the combination of 10000 different genes out of 20000? That is difficult to say, because the statistical program I use (R) cannot give an answer. But I computed the combinations for smaller numbers out of 20000. Here are the results: > choose(20000,10) [1] 2.815526e+36 > choose(20000,20) [1] 4.269216e+67 > choose(20000,30) [1] 3.960858e+96 > choose(20000,40) [1] 1.296003e+124 > choose(20000,50) [1] 3.481789e+150 So, even if only 50 genes have to be sorted out of 20000 as a special combinations, there is a search space of 3.481789e+150. That's about Dembski's universal probability bound, if you remember. For 60 genes, it becomes: > choose(20000,60) [1] 1.268095e+176 Well beyond the bound. Do you understand what I mean when I say that you need definite guiding procedures if you have to select the right genes that have to be translated out of a repertoire of 20000 genes? And remember, we are overlooking the problem of differential transcription/translation of the same gene, of gene chronological sequence and relative abundance, and many others. Remember, in the recent paper about the Drosophila transcriptome they showed that 47 genes were translated with more than 1000 isoforms each, in the central nervous system and in the embryo, some of them with up to 800 different proteins translated for the same gene. So, where are the procedures, and how do they work? My only purpose here is to outline this important, usually overlooked, question. You seem satisfied that "we know a lot more about it than I seem to think". No. the simple fact is that there is a lot lot more that we don't know than you seem to think, a lot lot more than what I know we already know.gpuccio_{April 10, 2014
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wd400: So much for all these posts about the limited power of DNA… It's not that DNA has limited power, it's that DNA has no power. It's like arguing over whether three's more power in a music CD or in a movie DVD or in a software program that arrives on CD or DVD. They all serve equally well as a coaster. More power to them.Mung_{April 9, 2014
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etc..etc.. It is simply impossible for a part to arise in isolation to a prior and meaningful whole existing beforehand. The following book review, using Dawkin's infamous 'Weasel', gets that point across very clearly:
A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Wiker and Witt Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part. (and yet the part is required to convey that meaning) http://www.thinkingchristian.net/C228303755/E20060821202417/
Pastor Joe Boot puts the insurmountable 'context' problem for reductive materialists this way:
"If you have no God, then you have no design plan for the universe. You have no prexisting structure to the universe.,, As the ancient Greeks held, like Democritus and others, the universe is flux. It's just matter in motion. Now on that basis all you are confronted with is innumerable brute facts that are unrelated pieces of data. They have no meaningful connection to each other because there is no overall structure. There's no design plan. It's like my kids do 'join the dots' puzzles. It's just dots, but when you join the dots there is a structure, and a picture emerges. Well, the atheists is without that (final picture). There is no preestablished pattern (to connect the facts given atheism)." Pastor Joe Boot Defending the Christian Faith – 13:20 minute mark of video http://www.youtube.com/watch?v=wqE5_ZOAnKo
And indeed, given reductive materialism, and its insistence that random unguided forces created everything around us, we have no reason to presuppose that the 'form' of the universe to be a circular sphere instead of any number of an infinity of other shapes:
Proverbs 8:26-27 While as yet He had not made the earth or the fields, or the primeval dust of the world. When He prepared the heavens, I was there, when He drew a circle on the face of the deep, Job 26:10 He has inscribed a circle on the face of the waters at the boundary between light and darkness. The Known Universe by AMNH – video - (please note the 'centrality' of the Earth in the 'sphere of the universe' at the 3:36 minute mark in the video) http://www.youtube.com/watch?v=17jymDn0W6U The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole. Dr. Arno Penzias, Nobel Laureate in Physics - co-discoverer of the Cosmic Background Radiation - as stated to the New York Times on March 12, 1978 “Certainly there was something that set it all off,,, I can’t think of a better theory of the origin of the universe to match Genesis” Robert Wilson – Nobel laureate – co-discover Cosmic Background Radiation
Verse and Music:
Genesis 1:1-3 In the beginning God created the heavens and the earth. The earth was without form, and void; and darkness was on the face of the deep. And the Spirit of God was hovering over the face of the waters. Then God said, "Let there be light"; and there was light. Nirvana - Smells Like Teen Spirit https://www.youtube.com/watch?v=hTWKbfoikeg
bornagain77_{April 9, 2014
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wd400 you state:
"this rush to induce outside forces to contol it seems very odd"
Actually what is odd is that reductive materialists/atheists do not see, or refuse to see, the need for 'overall context' in order to make sense of individual things happening in the cell, and in the universe at large. Dr. John Sanford puts the 'context problem' for reductive materialists, and their failure to realize the need for 'contextual meaning', like this:
“it is increasingly clear that the long-reigning neo-Darwinian paradigm is collapsing – and despite many efforts to deny what is obvious – clearly “the emperor has no clothes.” The extremely sophisticated hardware and software systems that enable life simply cannot be built by any trial and error system. In particular – it is very clear that software can never be developed one binary bit at a time. Apart from a fully functional pre-existing hardware/software system, a single bit has absolutely no meaning. I feel that if we are to preserve our scientific integrity, we must acknowledge that we have a major explanatory problem, and we need to go back to the drawing board in terms of understanding the origin of biological information.” John Sanford
Here is an insightful comment:
Intelligent Design Might Be Wrong, But Not the Way You Think by Stephen H. Webb - February 2014 Excerpt: Darwin, like all moderns, believed that matter was something particular, that matter is composed of small bits of stuff called atoms, and thus it can be pushed from behind, as it were, without being pulled from beyond, by form. http://www.firstthings.com/web-exclusives/2014/02/occasionalism-intelligent-design-and-the-myth-of-secondary-causation
Besides the fact that Quantum Mechanics has now falsified reductive materialism as true, it is now known that contextual 'form' is a driving force in molecular biology:
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt:,, when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. http://www.netfuture.org/2012/May1012_184.html#2 What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean The (Electric) Face of a Frog - video https://www.youtube.com/watch?v=0VULjzX__OM The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” Epigenetics and neuroplasticity: The case of the rewired ferrets - April 3, 2014 Excerpt: Like inventive electricians rewiring a house, scientists at the Massachusetts Institute of Technology have reconfigured newborn ferret brains so that the animals’ eyes are hooked up to brain regions where hearing normally develops. The surprising result is that the ferrets develop fully functioning visual pathways in the auditory portions of their brains. In other words, they see the world with brain tissue that was only thought capable of hearing sounds. https://uncommondescent.com/neuroscience/epigenetics-and-neuroplasticity-the-case-of-the-rewired-ferrets/ DNA doesn’t even tell teeth what they should look like - April 3, 2014 Excerpt: A friend writes to mention a mouse experiment where developing tooth buds were moved so that the incisors and the molars were switched. The tooth buds became the tooth appropriate to the switched location, not the original one, in direct contrast to what we would expect from a gene’centric view. “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/ In Embryo Development, Non-DNA Information Is at Least as Important as DNA - Jonathan Wells - May 2012 Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns. http://www.evolutionnews.org/2012/05/in_embryo_devel060031.html How much does DNA influence cell shape? April 2, 2014 Excerpt: We are still far from unravelling the fundamental "engineering”challenges that biology has to overcome in shaping single cells as well as multi-cellular tissues. Yet the rapid development of new theoretical, computational and experimental techniques in these fields, combined with the recent fruitful collaborations between biologists, physicists and engineers, suggest a promising and exciting future. https://uncommondescent.com/genetics/how-much-does-dna-influence-cell-shape/ “The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences
bornagain77_{April 9, 2014
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The problem is: what tells methyl-transferase which genes should be methylated? Histones, mainly. And small RNAs and proteins. You can, of course, keep on regressing deeper, and there is no doubt gene regulation is complex. But we know a lot more about it than you see to think, and this rush to induce outside forces to contol it seems very oddwd400_{April 9, 2014
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wd400: The problem is: what tells methyl-transferase which genes should be methylated? IOWs, protein coding genes produce the effectors (proteins), but where are written the procedures that regulate the expression of different effectors in different cells and situations? We still don't understand that. You may believe that everything is written in the genome. That could be true or not, but at present we don't understand how and where, in the genome or elsewhere, those procedures are coded. The procedures will be, in the end, much more complex than the effectors. As soon as we understand more of how regulatory procedures are coded, a further severe blow will be struck to the myths of neo darwinism.gpuccio_{April 9, 2014
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Epigenetics isn't "above" genetics, not matter what the bits of the word mean. Afterall, without methyl-transferase genes you wont' have methylation...wd400_{April 9, 2014
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WD400 How does that which is above or over that which is not, get controlled by that which is not above or over it? Sometimes you can be really funny.....Andre_{April 9, 2014
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Firstly, what we see here is a real regulation mechanism, I have to ask how does it “know” what is to be regulated? Firstly, what we see here is a real regulation mechanism, I have to ask how does it “know” what is to be regulated? It doesn't, of course. The point I was hoping someone would stumble on, is that this paper shows DNA methylation ('epigenetics') is itself regulated by plain old genetics. So much for all these posts about the limited power of DNA...wd400_{April 9, 2014
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Gpuccio Thank you and very well put on why random can never achieve this type of regulatory system. It is being controlled from becoming random in the first place, but you have to ask this... If it did create itself when did it know when to start regulating itself? Can anybody point me to any ordered system that has ever shown that it can built its own regulation and then also regulate itself? Any system at all?Andre_{April 9, 2014
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wd400 you complain:
Nice try phoodoo, but instead of running the distraction why don’t you answer the question?
Now this, especially the 'running the distraction' part, is a extremely ironic statement for you to make. For I have seen you, instead of ever being honest towards the evidence, constantly 'running the distraction' here on UD. In fact, as I'm sure you well remember, Mr. Arrington recently ran a post featuring your lack of honesty towards the evidence when you were called on a literature bluff (i.e. 'running the distraction'):
Wd400 and his Interlocutors Illuminate the Debate - February 20, 2014 Excerpt: Eric Anderson gets the last word: wd400 “. . . in fact, you set the bar so [high] . . .” The bar has not been set high. No-one is asking for an account of how all of biology actually came about (even though that is what the theory loudly claims to be able to explain). Most of us aren’t even asking for an account of how a complete organism came about. Shoot, the bar has been set so low that most of us would be impressed if the theory could explain a single system, or a single organ, or a single protein complex. Most of us would be impressed if the theory could explain just a fraction of the functional, digitally-specified information that resides in cells. It can’t do any of this, and yet we’re told we must believe the theory anyway, even the grander claims. The bar has been set so low as to be almost embarrassing. It is like being at a track meet and watching all the high jumpers repeatedly fail to clear the bar. The crowd shifts nervously in their seats and glances down uncomfortably at their feet as the meet officials — in a desperate attempt to get someone, anyone, to win the event — keep dropping the bar lower and lower. Yet, the theory can’t seem able to clear the bar. https://uncommondescent.com/intelligent-design/wd400-and-his-interlocutors-illuminate-the-debate/
Now wd400, the following is a very, very, simple point that doesn't take a advanced degree, or advanced mathematics, to understand. In science, empirical evidence has the last word as to whether a theory is true or not. Darwinism has no empirical evidence that it can generate complex novelty of even a trivial kind so as to prove it is true. In fact, the following study surveys four decades of experimental work, and solidly backs up the conclusion that there has never been an observed violation of what is termed 'genetic entropy' by purely material processes:
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Moreover, if you go through the studies in the preceding paper, you will find that the small fraction of 'gain of function' mutations that don't 'degrade the genome to a greater or lesser extent' are found in the experiments where 'compensatory mutations' are allowed to repair a organism after information was subtracted from the organism. Which is all great if you are trying to prove that organisms are ingenuously designed to repair themselves after damage, but is bad news if you are trying to prove that Darwinian processes can generate information over and above what is already present in life! There is even a null hypothesis in place stating that purely material processes can NEVER generate functional information (D. Abel)! Many more notes along the same line, demonstrating the abject failure of Darwinian processes to ever 'deliver the goods' empirically, are gone over here:
Where is the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit
Now wd400, I know you are quite a clever fellow by the way you are continually, to use your words, 'running the distraction', but why do you ignore the empirical elephant in the room? What is your motivation for being so dishonest. This is not a minor point that is going to go away not matter how much you and fellow Darwinists try to obfuscate the matter! You simply have no empirical evidence to give you warrant for your claims that neo-Darwinism can generate the unfathomed levels of integrated complexity being found in life. Moreover, I know that you know that you don't have the evidence! You are simply too smart to think that you do have the evidence, and yet you continually try to 'run the distraction' with your neutral theory gambit, literature bluff, and what not. So wd400 'instead of running the distraction' why don’t you, if not for me at least for yourself personally, answer the (following) question honestly? Why do you sacrifice every ounce of your personal integrity and honor, and trash any respect anyone may have had for you as a scientist here on UD, on the pseudo-science that is Darwinian evolution when you can do so much better than that?
"nobody to date has yet found a demarcation criterion according to which Darwin(ism) can be described as scientific" - Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote was as stated in 1973 LSE Scientific Method Lecture Darwinian Evolution is a Pseudo-Science - Part II https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit
Verse:
Proverbs 22:1 A good name is more desirable than great riches;,,,
bornagain77_{April 8, 2014
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Andre: Very good point. :) The regulation by differential methylation makes no sense under the premise that the duplicated gene is the product of random events, and that its further "evolution" is still the product of random events. Even is random events are implied (which, at this point, is clearly not certain), I would say that there is a name for random events regulated and controlled by definite algorithms: it's "bottom up engineering". IOWs, design.gpuccio_{April 8, 2014
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WD400 I'll give your question a go..... Firstly, what we see here is a real regulation mechanism, I have to ask how does it "know" what is to be regulated? http://www.investorwords.com/7697/regulatory_system.html This is a real example of design in biology it's not even an analogy......Andre_{April 8, 2014
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I think that this is highly intriguing research. If a duplicate gene happens, it is disabled. The darwinian presumption seems to be that this will give it the advantage of floating in the aether of random mutation with the chance of coming up with something wonderful. This is balderdash. In "Edge of Evolution" Behe clearly shows that once two mutations have bombarded the DNA, it is toast! The disabling of duplicate genes, in my opinion, all but eliminates them as a candidate for co-option. This report is bad news for the honest darwinist.Moose Dr_{April 8, 2014
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Nice try phoodoo, but instead of running the distraction why don't you answer the question?wd400_{April 8, 2014
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wd400, How about this for starters: What even remotely realistic proposal do Darwinists have for how in the world did a system which regulates the entire development of the body-through turning on and off switches which decide what genes will do, and is a fundamentally essential structure of the living unit, develop through a step by step series of copying mistakes which accidentally confer small advantages?phoodoo_{April 8, 2014
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Apart from that buzzword "epigenetics", what do you think this research shows? How do you it related to your recent fascinatation with the "limits" of DNA?wd400_{April 8, 2014
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