Intelligent Design, the best explanation of Origins

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Epigenetics

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1 Epigenetics on Thu Jul 16, 2015 6:19 pm

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Epigenetics

http://reasonandscience.heavenforum.org/t2098-epigenetics?highlight=epigenetics

The argument of the genetic piano
1. Dr. Kohzoh Mitsuya [University of Texas Health Science Center] who studies genes says the work of epigenetics “corresponds to a pianist playing a piece of music. Like keys on a piano, DNA is the static blueprint for all the proteins that cells produce.”
2. “Epigenetic information provides additional dynamic or flexible instructions as to how, where and when the blueprint will be used.”
3. After watching the response of mice deficient in the RNA, he said, “It shows how one note is played on the piano. The symphony has only just come into view. We can hear it, but we need to learn how all the parts are being played.”
4. Here the questions are: who’s the pianist and who’s the conductor? 
5. The environment cannot be the musician; it is oblivious to the needs of the organism.  Heredity cannot be the musician; it has no foresight to read or comprehend a collection of processes organized into a work.
6. Thus, this discovery and explanation of Dr. Mitsuya causes trouble for Darwin while it fits precisely into the intelligent design theory.
7. There must be an origin of the information required to produce function.
8. A classical answer to this by the evolutionists is: “this evolved, that’s why it is there.”
9. Answering this we say: “Science is supposed to seek efficient causes, not just-so stories or appeals to chance based on circular reasoning. For example, in his book The Making of the Fittest, Sean Carroll writes “the degree of similarity in DNA is an index of the [evolutionary] relatedness of species.” [98] This can only make sense if we first assume evolution is true. But Carroll’s book is a defense of evolution, intended to demonstrate that the theory is true without first assuming it is true. He seeks to prove evolution is true, but he begins with evolutionary reasoning and interpretations. That is circular reasoning.”
10. The alternative and only explanation is therefore intelligent design with a known cause sufficient to produce functional information: intelligence. Only intelligence can organize atoms or building blocks into order and activities. There is no other experience of anything else putting things into order and motion.
11. Intelligent design means intelligence of the greatest scientist all men call God.
12. God exists.

Reference:
1.  Watanabe, Tomizami, Mitsuya et al, “Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus,” Science, 13 May 2011: Vol. 332 no. 6031 pp. 848-852, DOI: 10.1126/science.1203919.

Humans have only 21,000 genes—the same as a worm—and they are identical in all of the different types of cells. It is not the inherited code of the genes that determines the different cellular functions. Rather, it is way that genes are utilized differently in each type of cell that determines which proteins will produce unique structures. 6

Increasingly, these “epigenetic” mechanisms (that is, mechanisms outside of the simple procedure of assigning an amino acid directly from a code in a gene) are being found to be vastly more complex than ever imagined. This post will describe recent discoveries of dynamic three-dimensional structures in the cell’s nucleus that along with unique localization and packaging of the DNA are vital for every aspect of gene function. Vast complexity of chromatin 3D shapes is another way that DNA is regulated.

Stephen C Meyer , Darwin's doubt pg.218:

Contemporary critics of neo-Darwinism acknowledge, of course, that preexisting forms of life can diversify under the twin influences of natural selection and genetic mutation. Known microevolutionary processes can account for small changes in the coloring of peppered moths, the  acquisition of antibiotic resistance in different strains of bacteria, and cyclical variations in the size of Galápagos finch beaks. Nevertheless, many biologists now argue that neo-Darwinian theory does not provide an adequate explanation for the origin of new body plans or events such as the Cambrian explosion. For example, evolutionary biologist Keith Stewart Thomson, formerly of Yale University, has expressed doubt that large-scale morphological changes could accumulate by minor changes at the genetic level. Geneticist George Miklos, of the Australian National University, has argued that neo- Darwinism fails to provide a mechanism that can produce large-scale innovations in form and structure. Biologists Scott Gilbert, John Opitz, and Rudolf Raff have attempted to develop a new theory of evolution to supplement classical neo-Darwinism, which, they argue, cannot adequately explain large-scale macroevolutionary change. As they note:

Starting in the 1970s, many biologists began questioning its neo-Darwinism's adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but  microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, "the origin of species—Darwin's problem—remains unsolved."

pg. 204

Genes alone do not determine the three-dimensional form and structure of an animal. so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means "above" or "beyond," so epigenetics refers to a source of information that lies beyond the genes. "Detailed information at the level of the gene does not serve to explain form." "epigenetic" or "contextual information" plays a crucial role in the formation of animal "body  assemblies" during embryological development.

Recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all. "the neo-Darwinian paradigm still represents the central explanatory framework of evolution," it has "no theory of the generative." neo-Darwinism "completely avoids the question of the origination of phenotypic traits and of organismal form."
1

Neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information.


FORM AND INFORMATION

Biologists typically define "form" as a distinctive shape and arrangement of body parts. Forms exist in three spatial dimensions and arise in time—in the case of animals during development from embryo to adult. Animal form arises as material constituents are constrained to establish specific arrangements with an identifiable three-dimensional shape , one that we would recognize as the body plan of a particular type of animal. A particular "form," therefore, represents a highly specific arrangement of material components among a much larger set of possible arrangements.

Similarly, animal body plans represent, not only highly improbable, but also highly specific arrangements of matter. Organismal form and function depend upon the precise arrangement of various constituents as they arise during, or contribute to, embryological development. Thus, the specific arrangement of the other building blocks of biological form—cells, clusters of similar cell types,  tissues, and organs—also represent a kind of specified or functional information.

Neo-Darwinists have assumed that genes possess all the information necessary to specify the form of an animal. They have also assumed that mutations in genes will suffice to generate the new information necessary to build a new form of animal life. 2


BEYOND GENES

Many biologists no longer believe that DNA directs virtually everything happening within the cell. Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg.  Biologists now refer to these sources of information as "epigenetic." The information needed to code for complex biological systems vastly outstrips the information in DNA. 3

Once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures.

Distinctive cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. 4

CYTOSKELETAL ARRAYS

Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans.

At a construction site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit

In a similar way, DNA does not by itself direct how individual proteins are assembled into these larger systems or structures—cell types, tissues, organs, and body plans—during animal development.Instead, the three-dimensional structure or spatial architecture of embryonic cells  plays important roles in determining body-plan formation during embryogenesis. Developmental biologists have identified several sources of epigenetic information in these cells.

The structure and location of the microtubules in the cytoskeleton influence the patterning and development of embryos. Microtubule "arrays" within embryonic cells help to distribute essential proteins used during development to specific locations in these cells. Once delivered, these proteins perform functions critical to development, but they can only do so if they are delivered to their correct locations with the help of preexisting, precisely structured microtubule or cytoskeletal arrays.

Thus, the precise arrangement of microtubules in the cytoskeleton constitutes a form of critical structural information. These microtubule arrays are made of proteins called tubulin, which are gene products. Nevertheless, like bricks that can be used to assemble many different structures, the tubulin proteins in the cell's microtubules are identical to one another. Thus, neither the tubulin subunits, nor the genes that produce them, account for the differences in the shape of the microtubule arrays that distinguish different kinds of embryos and developmental pathways. Instead, the structure of the microtubule array itself is, once again, determined by the location and arrangement of its subunits, not the properties of the subunits themselves.

The Centrosome

https://www.youtube.com/watch?v=5rqbmLiSkpk

Another cell structure influences the arrangement of the microtubule arrays and thus the precise structures they form and the functions they perform. In an animal cell, that structure is called the centrosome (literally, "central body"), a microscopic organelle that sits next to the nucleus between cell divisions in an undividing cell. Emanating from the centrosome is the microtubule array that gives a cell its three-dimensional shape and provides internal tracks for the directed transport of  organelles and essential molecules to and from the nucleus. During cell division the centrosome duplicates itself. The two centrosomes form the poles of the cell-division apparatus, and each daughter cell inherits one of the centrosomes; yet the centrosome contains no DNA. Though  centrosomes are made of proteins—gene products—the centrosome structure is not determined by genes alone.

pg 213:

NEO-DARWINISM AND THE CHALLENGE OF EPIGENETIC INFORMATION

These different sources of epigenetic information in embryonic cells pose an enormous challenge to  the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn't wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.

Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion.  

In at least the case of the sugar molecules on the cell surface, gene products play no direct role. Genetic information produces proteins and RNA molecules, not sugars and carbohydrates. Of course, important glycoproteins and glycolipids (sugar-protein and sugar-fat composite molecules) are modified as the result of biosynthetic pathways involving networks of proteins. Nevertheless, the genetic information that generates the proteins in these pathways only determines the function and structure of the individual proteins; it does not specify the coordinated interaction between the  proteins in the pathways that result in the modification of sugars

Some biologists have noted that so-called helper proteins—which are gene products—called "microtubule associated proteins" (MAPs) help to assemble the tubulin subunits in the microtubule arrays. Yet MAPs, and indeed many other necessary proteins, are only part of the story. The locations of specified target sites on the interior of the cell membrane also help to determine the shape of the cytoskeleton. And, as noted, the gene products out of which these targets are made do not determine the location of these targets. Similarly, the position and structure of the centrosome—the microtubule- organizing center—also influences the structure of the cytoskeleton. Although centrosomes are made of proteins, the proteins that form these structures do not entirely determine their location and form.

As Mark McNiven, a molecular biologist at the Mayo Clinic, and cell biologist Keith Porter, formerly of the University of Colorado, have shown, centrosome structure and membrane patterns as a whole convey three-dimensional structural information that helps determine the structure of the cytoskeleton and the location of its subunits.

In each new generation, the form and structure of the cell arises as the result of both gene products and the preexisting three-dimensional structure and organization inherent in cells, cell membranes, and cyto-skeletons. Many cellular structures are built from proteins, but proteins find their way to correct locations in part because of preexisting three-dimensional patterns and organization inherent in cellular structures. Neither structural proteins nor the genes that code for them can alone determine the three-dimensional shape and structure of the entities they build. Gene products provide necessary, but not sufficient, conditions for the development of three-dimensional  structure within cells, organs, and body plans. 5 If this is so, then natural selection acting on genetic  variation and mutations alone cannot produce the new forms that arise in the history of life.

The structures in which epigenetic information inheres—cytoskeletal arrays and membrane patterns, for example—are much larger than individual nucleotide bases or even stretches of DNA. For this reason, these structures are not vulnerable to alteration by many of the typical sources of mutation that affect genes such as radiation and chemical agent. To the extent that cell structures can be altered, these alterations are overwhelmingly likely to have harmful or catastrophic consequences.


1) Müller and Newman, "Origination of Organismal Form,"  Or as Müller also explains, the
question of how "individualized constructional elements" are organized during "the evolution of
organismal form" is "not satisfactorily answered by current evolutionary theories"; Müller, "Homology," 57-58
2) Levinton, Genetics, Paleontology, and Macroevolution, 485
3) Goodwin, "What Are the Causes of Morphogenesis?"; Nijhout, "Metaphors and the Role of Genes in Development"; Sapp, Beyond the Gene; Müller and Newman, "Origination of Organismal Form"; Brenner, "The Genetics of Behaviour"; Harold, The Way of the Cell.
4) Harold, The Way of the Cell, 125.
5) Harold, "From Morphogenes to Morphogenesis," 2767

http://www.microbiologyresearch.org/docserver/fulltext/micro/141/11/mic-141-11-2765.pdf expires=1475512019&id=id&accname=guest&checksum=82B036E71F67093D4C4B4F076E6D8114

Harold, “From Morphogenes to Morphogenesis,” 2774; Moss, What Genes Can’t Do. Of course, many proteins bind chemically with each other to form complexes and structures within cells. Nevertheless, these “self-organizational” properties do not fully account for higher levels of organization in cells, organs, or body plans. Or, as Moss has explained “Neither DNA nor any other aperiodic crystal constitutes a unique repository of heritable stability in the cell; in addition, the chemistry of the solid state does not constitute either a unique or even an ontologically or causally privileged basis for explaining the existence and continuity of order in the living world . . .” Moss, What Genes Can’t Do, 76.

Morphogenesis cannot be orchestrated by the genome, but makes manifest a higher level of order, corresponding to the cellular scale of size and organization. If a single phrase can stand for the whole riddle, it may be ‘ cell polarity ’, The term refers to the visible directionality

6) http://jonlieffmd.com/blog/vast-complexity-of-chromatin-3d-shapes



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2 Re: Epigenetics on Sun Oct 11, 2015 4:26 pm

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Epigenomics: the epigenome is a genome-wide map of reversible chemical modifications to DNA and its associated proteins that determine when genes can be expressed. "By 2004, large-scale genome projects were already indicating that genome sequences, within and across species, were too similar to be able to explain the diversity of life. It was instead clear that epigenetics - those changes to gene expression caused by chemical modification of DNA and its associated proteins - could explain much about how these similar genetic codes are expressed uniquely in different cells, in different environmental conditions and at different times." "Epigenetic coding will be orders of magnitude more complex than genetic coding". (Nature 4 Feb 2010). "The human genome is singular and finite, but the human epigenome is almost infinite - the epigenome changes in different states and different tissues". Every cell in our body has its own epigenome, that is 1015 different epigenomes (Marianne Rots). 1

1) http://wasdarwinwrong.com/kortho44.htm

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Stephen C Meyer , Darwin's doubt pg.268:

THE HIERARCHICAL ORGANIZATION OF GENETIC AND EPIGENETIC  INFORMATION

In addition to the information stored in individual genes and the information present in the integrated  networks of genes and proteins in dGRNs, animal forms exemplify hierarchical arrangements or layers of information-rich molecules, systems, and structures. For example, developing embryos require epigenetic information in the form of specifically arranged

(a) membrane targets and patterns,
(b) cytoskeletal arrays,
(c) ion channels, and
(d) sugar molecules on the exterior of cells (the sugar code).


Much of this epigenetic information resides in the structure of the maternal egg and is inherited directly from membrane to membrane independently of DNA.  This three-dimensional structural information interacts with other information-rich molecules and systems of molecules to ensure the proper development of an animal. In particular, epigenetic information influences the proper positioning and thus the function of regulatory proteins (including  DNA-binding proteins), messenger RNAs, and various membrane components. Epigenetic information also influences the function of developmental gene regulatory networks. Thus, information at a higher structural level in the maternal egg helps to determine the function of both whole networks of genes and proteins (dGRNs) and individual molecules (gene products) at a lower level within a developing animal. Genetic information is necessary to specify the arrangement of amino acids in a protein or bases in an RNA molecule. Similarly, dGRNs are necessary to specify the location and/or function of many gene products. And, in a similar way, epigenetic information is necessary to specify the location and determine the function of lower-level molecules and systems of molecules, including the dGRNs themselves.  Furthermore, the role of epigenetic information provides just one of many examples of the hierarchical arrangement (or layering) of information-rich structures, systems, and molecules within animals. Indeed, at every level of the biological hierarchy, organisms require specified and highly improbable (information-rich) arrangements of lower-level constituents in order to maintain their form and function. Genes require specified arrangements of nucleotide bases; proteins require specified arrangements of amino acids; cell structures and cell types require specified arrangements of proteins or systems of proteins; tissues and organs require specific arrangements of specific cell types; and body plans require specialized arrangements of tissues and organs. Animal forms contain information-rich lower-level components (such as proteins and genes). But they also contain information-rich arrangements of those components (such as the arrangement of genes and gene products in dGRNs or proteins in cytoskeletal arrays or membrane targets). Finally, animals also exhibit information-rich arrangements of higher-level systems and structures (such as the arrangements of specific cell types, tissues, and organs that form specific body plans).

The highly specified, tightly integrated, hierarchical arrangements of molecular components and systems within animal body plans also suggest intelligent design. This is, again, because of our experience with the features and systems that intelligent agents—and only intelligent agents— produce. Indeed, based on our experience, we know that intelligent human agents have the capacity to generate complex and functionally specified arrangements of matter—that is, to generate specified complexity or specified information. Further, human agents often design information-rich hierarchies, in which both individual modules and the arrangement of those modules exhibit complexity and specificity—specified information. Individual transistors, resistors, and capacitors in an integrated circuit exhibit considerable complexity and specificity of design. Yet at a higher level of organization, the specific arrangement and connection of these components within an integrated circuit requires additional information and reflects further design (see Fig.below).



Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies. We know of no other causal entity or process that has this capacity. Clearly, we have good reason to doubt that mutation and selection, self-organizational processes, or any of the other undirected processes cited by other materialistic evolutionary theories, can do so. Thus, based upon our present experience of the causal powers of various entities and a careful assessment of the efficacy of various evolutionary mechanisms, we can infer intelligent design as the best explanation for the origin of the hierarchically organized layers of information needed to build the animal forms that arose in the Cambrian period.

There is another remarkable aspect of the hierarchical organization of information in animal forms.  Many of the same genes and proteins play very different roles, depending upon the larger organismal  and informational context in which they find themselves in different animal groups. For example, the  same gene (Pax-6 or its homolog, called eyeless), helps to regulate the development of the eyes of fruit flies (arthropods) and those of squid and mice (cephalopods and vertebrates, respectively). Yet arthropod eyes exemplify a completely different structure from vertebrate or cephalopod eyes. The fruit fly possesses a compound eye with hundreds of separate lenses (ommatidia), whereas both mice and squid employ a camera-type eye with a single lens and retinal surface. In addition, although the eyes of squid and mice resemble each other optically (single lens, large internal chamber, single retinal surface), they focus differently. They undergo completely different patterns of development and utilize different internal structures and nerve connections to the visual centers of the brain. Yet the Pax-6 gene and its homologs play a key role in regulating the construction of all three of these different adult sensory structures. Moreover, evolutionary and developmental biologists have found that this pattern of "same genes, different anatomy" recurs throughout the bilaterian phyla, for features  as fundamental as appendages, segmentation, the gut, heart, and sense organs




This pattern contradicts the expectations of textbook evolutionary theory. Neo-Darwinism predicts that disparate adult structures should be produced by different genes. This prediction follows directly from the neo-Darwinian assumption that all evolutionary (including anatomical) transformations begin with mutations in DNA sequences—mutations that are fixed in populations by natural selection, genetic drift, or other evolutionary processes. The arrow of causality flows one way from genes (DNA) to development to adult anatomy. Thus, if biologists observe different animal forms, it follows that they should expect that different genes will specify those forms during animal development. Given the profound differences between the fruit-fly compound eye and the vertebrate camera eye, neo-Darwinian theory would not predict that the "same" genes would be involved in building different eyes in arthropods and chordates.

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4 Re: Epigenetics on Sun Dec 20, 2015 3:41 pm

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RNA-mediated epigenetic regulation of gene expression

Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds and then mediating the recruitment of histone and DNA methyltransferases. In addition, recent advances suggest that chromatin-associated long non-coding RNA scaffolds also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.

http://www.nature.com/nrg/journal/v16/n2/full/nrg3863.html

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5 Re: Epigenetics on Wed Jan 13, 2016 6:38 pm

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A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. 
A genetic program is not sufficient for embryogenesis: biological information outside of DNA is needed to specify the body plan of the embryo and much of its subsequent development. Some of that information is in cell membrane patterns, which contain a two-dimensional code mediated by proteins and carbohydrates.

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6 Re: Epigenetics on Wed Jan 27, 2016 6:17 pm

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Epigenome Project Finds Symphony in Cells


If all cells have the same genome, why do they look and act differently? The epigenome conducts each part in the symphony.
Nature’s special issue this week is about epigenomics. The National Institutes of Health (), now that the ENCODE project (a previous effort to understand how many genes are expressed) has reported its findings, has launched the project (Roadmap Epigenomics Consortium). This issue of Nature presents its first findings based on 111 reference epigenomes. seeks to understand what turns genes on and off: i.e., what regulates their behavior.
Every cell expresses about half of the 22,000 genes in the human genome. The others are controlled by “epigenetic factors” (beyond/above the gene) that can amplify them or repress them. These factors include methyl tags on the histone proteins around which is wrapped, acetyl tags, promoters, enhancers, and other processes. PhysOrg put out a summary of the findings. Nature included ten articles and papers, including:

Like ENCODE, this consortium owes little to evolutionary theory. Only 3 of the articles mention evolution, and those speak either of (1) “evolutionarily conserved” elements, or (2) hope that the work will shed light on evolution. Most of the articles seem impressed with the complexity of epigenomics. “The task at hand was, as researchers like to say, not trivial,” the Editors say. At this stage, researchers are still trying to find out what questions to ask.
The most entertaining entry in the issue is “Epigenome: The Symphony in Your Cells” by Kerri Smith. It includes a video of musicians playing excerpts of Beethoven’s 5th, explaining that all the musicians have the same score, but the conductor lets each player know when and what to play. That’s a pithy analogy as far as it goes, but the epigenome is made up of many parts that don’t seem to have an obvious leader, like the single conductor in the video. Is there a conductor? Much more work will be required to answer that question. Smith ends, “Taken together, the work demonstrates how a cell’s epigenome is complex and exquisitely arranged — just like a Beethoven symphony.”
For a lay introduction to epigenetics, see the video by Dr. Tom Woodward and Dr. James Gills, “The Mysterious Epigenome: What Lies Beyond ” on YouTube. Epigenetics is a scientific revolution in the making that may become as big as genetics itself. If you thought genetics pointed to intelligent design, wait till you see what appears to lie in store with epigenetics. It represents layers of informational complexity: codes regulating other codes in ways that will challenge the mutation-selection mechanism of Darwinism possibly to the breaking point. Already, it has been contributing to the demise of the “junk ” myth. Much of the genome that looked incomprehensible or unnecessary to Darwinians may prove to be the key to understanding inheritance, as researchers take the Darwin earplugs out and hear the symphony.


http://crev.info/2015/02/epigenome-project-finds-symphony-in-cells/

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New Epigenetic Modification is Revealed, Major Scientific Breakthrough 1

A New Epigenetic Modification Has Been Revealed that Could Open Up the Field of Epigenetics, Says Research Team from the University of Cambridge
Epigenetic modification research keeps gaining momentum as the revolutionary science is quickly becoming one of the most important fields of research to describe our genetic expressions. But, before we discuss the most recent breakthrough in epigenetic research, we must first set the table for you. So, hang in there and I promise you, it will be well worth it.

DNA Methylation and Histone Modification
The studying of histones that bind to DNA has the primary focus of epigenetic modification research. These histones can be modified, which can result in genes being read or not. There are basically 5 different types of Histone proteins called H2A,H2B, H3 and H4 which form a bead on which the DNA is wrapped (with two molecules each, so a total 8 protein molecules in the bead and one called H1 between two beads). Within the histones, it is actually the amino acids that are modified.

In addition to histone modifications, genes are also known to be regulated by a form of epigenetic modification that directly affects one base of the DNA, namely the base C. This process is referred to as DNA Methylation.

The four bases are namely Adenine, Thymine, Guanine ad Cytosine. It has already been more than 60 years now, since scientists discovered that C can be modified directly. This process is executed as small molecules of carbon and hydrogen bind to this base and allow certain genes to be turned on and off, or to ‘dim’ their activity. It is estimated that roughly 75 million, or one in ten, of the Cs in the human genome are methylated. [1]

However, published on December 21st, 2015 in the journal Nature Structural and Molecular Biology, a major new discovery suggests there exists many more DNA modifications that we did not know about.

Epigenetic Modification – Direct Methylation of the Base A
Discovered by Magdalena J Koziol, Charles R Bradshaw, George E Allen, Ana S H Costa, Christian Frezza, & John B Gurdon at the Wellcome Trust-Cancer Research UK Gurdon Institute and the Medical Research Council Cancer Unit at the University of Cambridge have identified and characterized a new form of direct modification – methylation of the base A – in several species, including frogs, mouse and humans. [2] [3]

Although, methylation of A appears to be far less common that C methylation, occurring on around 1,700, the research team urges that they are very important and spread across the entire genome. Although, it does not seem to occur on sections of our genes known as exons, which provide the code for proteins.

Opening Up the Field of Epigenetics
“These newly-discovered modifiers only seem to appear in low abundance across the genome, but that does not necessarily mean they are unimportant,” says Dr Magdalena Koziol from the Gurdon Institute. “At the moment, we don’t know exactly what they actually do, but it could be that even in small numbers they have a big impact on our DNA, gene regulation and ultimately human health.”

“It’s possible that we struck lucky with this modifier,” says Dr Koziol, “but we believe it is more likely that there are many more modifications that directly regulate our DNA. This could open up the field of epigenetics.”

The field of epigenetic is growing rapidly and has the potential to redefine our interactions with nature and each other. Stay tuned for follow up articles that will explore these findings in greater depth.

That finding helped us to understand the role of RNA methylation. Adenosine methylation is also used widely in bacterial genome.
http://epigenie.com/key-epigenetic-players/important-dna-methylation-factors/n6-methyladenosine-m6a/

m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency
http://www.cell.com/cell-stem-cell/abstract/S1934-5909(15)00017-X


1. http://conceptualrevolutions.com/2015/12/26/epigenetic-modification-revealed-major-scientific-breakthrough/

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8 Re: Epigenetics on Thu Mar 09, 2017 6:12 pm

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Epigenetics and Cellular Metabolism

Living eukaryotic systems evolve delicate cellular mechanisms for responding to various environmental signals. Among them, epigenetic machinery (DNA methylation, histone modifications, microRNAs, etc.) is the hub in transducing external stimuli into transcriptional response. Emerging evidence reveals the concept that epigenetic signatures are essential for the proper maintenance of cellular metabolism. On the other hand, the metabolite, a main environmental input, can also influence the processing of epigenetic memory. Here, we summarize the recent research progress in the epigenetic regulation of cellular metabolism and discuss how the dysfunction of epigenetic machineries influences the development of metabolic disorders such as diabetes and obesity; then, we focus on discussing the notion that manipulating metabolites, the fuel of cell metabolism, can function as a strategy for interfering epigenetic machinery and its related disease progression as well.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038610/

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