14 thoughts on “The Imprinter of All Maladies

  1. GlenDavidson:
    Disproves evolution, too.

    Somehow, in some way, we don’t know how, but it sure does.

    I have a notion of how it does. If evolution is considered to be the change in allele frequencies within populations, and if the major differences between species are epigenetic rather than genetic, then evolution as defined becomes largely irrelevant to the diversity of life. Of course that requires some serious epigenetic inheritance, which in turn allows for epigenetic evolution. But creationists seem to enjoy getting rid of what we tend to think of as evolution and don’t understand that they’re introducing another sort of evolution to replace it.

    Also, because we don’t quite understand all the details of epigenetic marks, that leaves more room for Jesus.

    Is that it, Sal?

  2. Wait a minute. what do any of these people know? they only know what they see. Watching how genes get inprinted is invisible.
    Well yes epi is used a lot to explain things. yet if this eisen guy is attacking everyone’s competence then creationists can attack too.
    We say there is loads of incompetence in origin subjects/conclusions.
    In fact there is no difference between evolutionist musings and epi folks musings.
    Why suddenly so picky??

    The Indian scientist simply picked some detail and made a whole hypothesis. Now he retreats under attack however its not over.
    I do believe there are triggers in the genes to bring instant biological change and on to the kids.
    Thats the origin for human colour. It never evolved obviously.
    It seems likely to me many animal traits were inprinted on the genes or the memory.
    However these things are complicated and no one can get that upset about someones opinion.
    Especially if one suspects there is a greater, conspiracy, motive to fight anything that opposes old ideas about evolution.
    Keep a eye on everyone.

  3. epigenetics has achieved buzzword status far faster and to a far larger extent than current science justifies, earning the disdain of scientists (like me) who study how information is encoded – See more at: http://www.michaeleisen.org/blog/?p=1894#sthash.zKik1AcX.dpuf

    Oh Really? Epignetics is Nobel Prize winning stuff, man.

    Reprogramming refers to erasure and remodeling of epigenetic marks, such as DNA methylation, during mammalian development.[1] After fertilization some cells of the newly formed embryo migrate to the germinal ridge and will eventually become the germ cells (sperm and oocytes).
    ….
    The first person to successfully demonstrate reprogramming was Sir John Gurdon, who in 1962 demonstrated that differentiated somatic cells could be reprogrammed back into an embryonic state when he managed to obtain swimming tadpoles following the transfer of differentiated intestinal epithelial cells into enucleated frog eggs[4]. For this achievement he received the 2012 Nobel Prize in Medicine alongside Shinya Yamanaka.[1]

    https://en.wikipedia.org/wiki/Reprogramming

  4. epigenetics has achieved buzzword status far faster and to a far larger extent than current science justifies, earning the disdain of scientists (like me) who study how information is encoded

    Oh really? Here is one important sequencing technique used by NIH researchers to deduce epigenetic marks on DNA in various cell lines:

    https://en.wikipedia.org/wiki/Bisulfite_sequencing

    Bisulfite[1] sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA to determine its pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied. In animals it predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the dinucleotide CpG, and is implicated in repression of transcriptional activity.

    Whole Genome Bisulfite Sequencing is one of the staples of the half-billion dollar NIH ENCODE/RoadmapEpigenomic projects.

    https://www.encodeproject.org/news/

    New assays in this phase of ENCODE include:
    •RAMPAGE: Identifies transcriptional start sites with quantification (PMID: 24510412, PMID: 22936248)
    •Shotgun Bisulfite-seq (WGBS): Analyzes DNA methylation at high resolution (PMID: 19829295)

    But Dan Graur hates this sort of science. He call it “excrement” made by “ignoramuses”.

  5. Another experimental technique for experimentally investigating epigenetic marks is Chromatin Immuno Precipitation Sequenction (CHIP-Seq). Here is description of how the ENCODErs perform ChIP-Seq experiments to find histone modifications. This is another example of what Graur hates and refers to as “excrement” made by the ENCODE “ignoramuses”.

    http://genome.cshlp.org/content/22/9/1813.full#aff-19

    ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    ….
    Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells.

    Histone modifications are epigenetic marks.

    Note the listing of where these “ignoramuses” do their epigenetic research for the hated ENCODE consortium:

    1Department of Genetics, Stanford University, Stanford, California 94305, USA;
    2Division of Biology, California Institute of Technology, Pasadena, California 92116, USA;
    3Department of Computer Science, Stanford University, Stanford, California 94305, USA;
    4Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
    5HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
    6Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;
    7Department of Statistics, University of California, Berkeley, California 94720, USA;
    8Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts 02215, USA;
    9Computational Biology & Bioinformatics Program, Yale University, New Haven, Connecticut 06511, USA;
    10Department of Computer Science and Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA;
    11Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
    12Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78701, USA;
    13Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA;
    14Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Boston, Massachusetts 02115, USA;
    15Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60637, USA;
    16Department of Statistics, Penn State University, University Park, Pennsylvania 16802, USA;
    17Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA;
    18National Human Genome Research Institute/National Institutes of Health, Rockville, Maryland 20852, USA;
    19Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
    20Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA;
    21Department of Pathology, Stanford University, Stanford, California 94305, USA;
    22Department of Medicine, University of Washington, Seattle, Washington 98195, USA;
    23University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA;
    24Department of Biochemistry & Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, USA;
    25Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

  6. stcordova: But Dan Graur hates this sort of science. He call it “excrement” made by “ignoramuses”.

    I also hear Darwin beat a puppy just because he could!

  7. Someone help me out here.

    If A–>B–>C

    And A predicts C as well as B predicts C, then B is not an independent predictor or code.

    What am I missing?

  8. stcordova,

    Eisen’s name is not mentioned anywhere in the listing of authors in the textbook on Epigenetics:

    Therefore he’s wrong?

  9. Eisen keeps company with other ENCODE haters like Dan Graur.

    http://mendelspod.com/podcast/debating-encode-with-dan-graur-and-michael-eisen/

    He calls the research project questionable. On what grounds? His ideas about evolutionary theory, not actual physical and chemical experiments which is what ENCODE actually delivers.

    The show that interviewed Graur and Eisen couldn’t get ENCODE researchers to appear. Good for the ENCODE crowd, no need to waste time with Graur and Eisen. Graur hasn’t come up with a single experiment that unequivocally shows ENCODE work is a failure as Graur claims. Eisen and Graur just make noise, not experimental refutations.

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