Epigenetics: The role histones play leaves researchers “blown away”

_{Denyse O'Leary

October 14, 2015

Epigenetics, Intelligent Design, News}

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Environmental memories transmitted from a father to his grandchildren

… in recent years, scientists have shown that, before his offspring are even conceived, a father’s life experiences involving food, drugs, exposure to toxic products and even stress can affect the development and health not only of his children, but even of his grandchildren.

This group, whose paper was just published in Science, has been studying the role of histones (proteins) in the process.

So, to test their theory about the possible role of histones in guiding embryo development the researchers created mice in which they slightly altered the biochemical information on the histones during sperm cell formation and then measured the results. (It’s a bit like putting a nick in a spool of thread and seeing how it affects the way the thread then loops around the spool.) They then studied the effects on the offspring.

What they discovered was that there were dire consequences for the offspring both in terms of their development e.g. where offspring were prone to birth defects and had abnormal skeletal formation, and in terms of their surviving at all. Moreover, what was most surprising, was that these effects could still be seen two generations later.

“When we saw the decreased survivability across generations and the developmental abnormalities we were really blown away as it was never thought that altering something outside the DNA, i.e. a protein, could be involved in inheritance,” said Sarah Kimmins, from McGill’s Dept. of Animal Science, and one of the lead authors on the paper. Kimmins is also the Canada Research Chair in Epigenetics, Reproduction and Development.

Does anyone remember that Central Dogma? You know, “information flow proceeds from DNA to RNA to proteins” to life form: chunk!

Hey, we were still sweeping up the splinters from the lecterns when

Since chemical modifications on histones are susceptible to environmental exposures, the work opens new avenues of investigation for the possible prevention and treatment of diseases of various kinds, affecting health across generations.” More.

Now, not everything in epigenetics is going to hold up, but it certainly is an open window for fresh air on the subject of genetic inheritance, long cursed by Darwinism and eugenics.

See also: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Abstract

A father’s lifetime experiences can be transmitted to his offspring to affect health and development. The mechanisms underlying paternal epigenetic transmission are unclear. Unlike somatic cells, there are few nucleosomes in sperm and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis reduced H3K4 dimethylation in sperm. KDM1A overexpression in one generation severely impaired development and survivability of offspring. These defects persisted transgenerationally in the absence of KDM1A germ line expression and were associated with altered RNA profiles in sperm and offspring. We show that epigenetic inheritance of aberrant development can be initiated by histone demethylase activity in developing sperm, without changes to DNA methylation at CpG-rich regions. (paywall) – Keith Siklenka, Serap Erkek, Maren Godmann, Romain Lambrot, Serge McGraw, Christine Lafleur, Tamara Cohen, Jianguo Xia, Matthew Suderman, Michael Hallett, Jacquetta Trasler, Antoine H. F. M. Peters, and Sarah Kimmins. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science, 8 October 2015 DOI: 10.1126/science.aab2006

Comments

Interesting. Over a year ago someone posted a thread asking what people should research more that would cause challenges for darwinism. I mentioned histones at the time and I stand by that still. Also people should look into histones in the context of dna structure, in particular repetitive DNA sequences and their importance with histones. Which will eventually squash the fallacy of transposons and junk dna. Of course the evo's will play the usual line that histones are encoded by dna and the enzymes that modify them are encoded by dna blah blah so it's still in the central dogma blah blah blah.Dr JDD_{October 15, 2015
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As to the 'membrane issue' raised by Bornagain77. Stephen Meyer:
Many of the biological structures that impart important three-dimensional spatial information—such as cytoskeletal arrays and membrane ion channels—are made of proteins. For this reason, some biologists have insisted that the genetic information in DNA that codes for these proteins does account for the spatial information in these various structures after all. In each case, however, this exclusively “gene-centric” view of the location of biological information—and the origin of biological form—has proven inadequate. First, 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.28 More important, the location of specific sugar molecules on the exterior surface of embryonic cells plays a critical role in the function that these sugar molecules play in intercellular communication and arrangement. Yet their location is not determined by the genes that code for the proteins to which these sugar molecules might be attached. Instead, research suggests that protein patterns in the cell membrane are transmitted directly from parent membrane to daughter membrane during cell division rather than as a result of gene expression in each new generation of cells.29 Since the sugar molecules on the exterior of the cell membrane are attached to proteins and lipids, it follows that their position and arrangement probably result from membrane-to-membrane transmission as well. Consider next the membrane targets that play a crucial role in embryological development by attracting morphogenetic molecules to specific places on the inner surface of the cell. These membrane targets consist largely of proteins, most of which are mainly specified by DNA. Even so, many “intrinsically disordered”30 proteins fold differently depending on the surrounding cellular context. This context thus provides epigenetic information. Further, many membrane targets include more than one protein, and these multiprotein structures do not automatically self-organize to form properly structured targets.31 Finally, it is not only the molecular structure of these membrane targets, but also their specific location and distribution that determines their function. Yet the location of these targets on the inner surface of the cell is not determined by the gene products out of which they are made any more than, for example, the locations of the bridges across the River Seine in Paris are determined by the properties of the stones out of which they are made. Similarly, the sodium-potassium ion pumps in cell membranes are indeed made of proteins. Nevertheless, it is, again, the location and distribution of those channels and pumps in the cell membrane that establish the contours of the electromagnetic field that, in turn, influence embryological development. The protein constituents of these channels do not determine where the ion channels are located. Like membrane targets and ion channels, microtubules are also made of many protein subunits, themselves undeniably the products of genetic information. In the case of microtubule arrays, defenders of the gene-centric view do not claim that individual tubulin proteins determine the structure of these arrays. Nevertheless, some have suggested that other proteins, or suites of proteins, acting in concert could determine such higher-level form. For example, 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.32 Moreover, as several other biologists have shown, the centrioles that compose the centrosomes replicate independently of DNA replication: daughter centrioles receive their form from the overall structure of the mother centriole, not from the individual gene products that constitute them.33 Additional evidence of this kind comes from ciliates, large single-celled eukaryotic organisms. Biologists have shown that microsurgery on the cell membranes of ciliates can produce heritable changes in membrane patterns without altering the DNA.34 This suggests that membrane patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both cases—in membrane patterns and centrosomes—form is transmitted from parent three-dimensional structures to daughter three-dimensional structures directly. It is not entirely contained in DNA sequences or the proteins for which these sequences code.35 Instead, 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.36 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.
[Darwin's Doubt, ch.14]Box_{October 15, 2015
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Bornagain77's examples are very compelling, unlike the case described in the OP.
“When we saw the decreased survivability across generations and the developmental abnormalities we were really blown away as it was never thought that altering something outside the DNA, i.e. a protein, could be involved in inheritance,” said Sarah Kimmins
A histone is not just any ol' floating around protein, it is directly tied to DNA and continually influences its function. It hardly makes sense to say that it is "something outside the DNA". So I don't understand why anyone should be surprised about resulting developmental abnormalities.Box_{October 15, 2015
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"But Darwinism is based on what I call the Genetic Reductionist Model of organisms. It is (based) on the assumption that DNA is the sole carrier of information and heredity and development. And all the characteristics of an organism are encoded in its DNA (DNA as blueprint or recipe). DNA is god and RNA is prophet is how my Biology lecturer at Birmingham University put it.,,, (Darwinism also holds) Mutations in the DNA lead to new organisms and explain the evolutionary descent of all living things.,,, And yet, an unknown secret here, that neo-Darwinian paradigm has been known to be false, unquestionably false, irrefutably false, for over 50 years. I say that the year that the scientific evidence became overwhelming was 1954.,,, It is all to do with what is often called cortical inheritance. Cortex is just the name given to the cell membrane and past the cytoplasmic structure underneath.,,, In fact, until the 1930's it was commonly believe by biologists that the genes do not determine the fundamental features of an organism''s body plan. Many developmental biologist still agree (that genes do not). And the evidence comes from lots of animals but the key organism on which all the key research was done was Ciliates. (Microscopic single celled animals).,,, By the 1950's it was proven beyond doubt that the ciliate cell surface structures and their patterns were inherited independently of genes and DNA. How was this done? Quiet easily. You could perform just a little surgical operation on these animals and remove some structures or replace them, or alter them in some way, carefully remove some cilia and put it in backwards,,, and they would heal very quickly, and then that defect was just reproduced indefinitely. The next generation would produce exactly the same defect. Even though you could show genetically that the DNA had not been changed one iota.,, At first many dismissed this as a quirk of ciliates with their elaborate cell surface structures. (Darwinists called them) a 'rare example' etc..,,, (They claimed) that this is just a unique thing to do with ciliates.,,, But it is clearly universal: 1. Cilate cortex is an elaboration of the cell membrane and cytoskeleton that are universal features of animal and plant cells.,,, 2. Developmental processes are the same,, 3. Some cilates form cysts and then lose all visible surface structures, but cortical inheritance still occurs.,,, So however that cell surface is coded, it is not coded at the molecular, i.e. visible, level. There is clearly another system of heredity operating in cells. And in fact there is plenty of evidence for a wide variety of animals and plants that say this system is there, exists and operates, and is in fact responsible for the main features of the body plan. not the genes (DNA). So the definitive papers were produced back in the 1950s. So we have known since then that genetic paradigm is dead and therefore so is neo-Darwinism.,,, That there is more to heredity than DNA. And yet stubbornly, biologists carry on as if that was not the case. A historian of science has written a history of the whole affair. In fact, his PhD thesis, which was written in the 1980s, and he produced a book about it all in 1987. And in 1987 he concluded this, "Throughout the 1960s and 1970s the evolutionary significance of cortical inheritance was largely ignored by Darwinian evolutionists. Indeed for the most part, it still is. And in 2005 he wrote, "After 20 years it is still ignored and not answered". - Dr. Arthur Jones as quoted at the 56:08 minute mark of the following video Fish, Fossils and Evolution - Dr. Arthur Jones - video https://youtu.be/PtqdZKeyY1Y?t=3368
Of related note:
Biological Information - The Membrane Code 4-4-2015 by Paul Giem https://www.youtube.com/watch?v=_YgXbHvYuBM&index=21&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ
In fact, the 'form' of a body plan, according to the following experiments, is apparently not even reducible to any conceivable mechanism of molecular reductionism, i.e. materialism:
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012 Excerpt: The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately 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 “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.” leodp – UD blogger https://uncommondescent.com/evolution/whats-this-about-the-strange-inevitability-of-evolution/#comment-563451 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. - per UD If DNA really rules (morphology), why did THIS happen? – April 2014 Excerpt: Researchers implanted human embryonic neuronal cells into a mouse embryo. Mouse and human neurons have distinct morphologies (shapes). Because the human neurons feature human DNA, they should be easy to identify. Which raises a question: Would the human neurons implanted in developing mouse brain have a mouse or a human morphology? Well, the answer is, the human neurons had a mouse morphology. They could be distinguished from the mouse ones only by their human genetic markers. If DNA really ruled, we would expect a human morphology." - per UD 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. - per UD
bornagain_{October 15, 2015
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Have these experiments been duplicated in light of criticism of science studies including on UD? It would be a important mechanism for biology change if this was true. In fact it would mean the parent is putting on their genes these memories. no small matter.Robert Byers_{October 14, 2015
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Lamarck is right Darwin is wrong!Andre_{October 14, 2015
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This is probably how finches, guppies and their offsprings adapt to environmental cues. No evidence for Darwinian RM+NS anywhere. Evolution is on its deathbed.Mapou_{October 14, 2015
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