Home » Intelligent Design » “It’s in your genes” theory fading in the wake of epigenetics?

“It’s in your genes” theory fading in the wake of epigenetics?

In “Getting Over the Code Delusion” (The New Atlantis, Summer 2010), Steve Talbott muses on the mystique around the genetic code in past decades, especially in the light of modern findings:

Meanwhile, the epigenetic revolution is slowly but surely making its way into the popular media — witness the recent Time magazine cover story, “Why DNA Isn’t Your Destiny.” The shame of it is that most of the significance of the current research is still being missed. Judging from much that is being written, one might think the main thing is simply that we’re gaining new, more complex insights into how to treat the living organism as a manipulable machine.The one decisive lesson I think we can draw from the work in molecular genetics over the past couple of decades is that life does not progressively contract into a code or any kind of reduced “building block” as we probe its more minute dimensions. Trying to define the chromatin complex, according to geneticists Shiv Grewal and Sarah Elgin, “is like trying to define life itself.” Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate. The explanatory task at the bottom is essentially the same as the one higher up. It’s rather our understanding that all too easily becomes constricted as we move downward, because the contextual scope and qualitative richness of our survey is so extremely narrowed.

The search for precise explanatory mechanisms and codes leads us along a path of least resistance toward the reduction of understanding. A capacity for imagination (not something many scientists are trained for today) is always required for grasping a context in meaningful terms, because at the contextual level the basic data are not things, but rather relations, movement, and transformation.

It could be pared down to a long inscription in marble, and worthy a monument too.

I, for one, believe that the pop gene revolution has been socially harmful. To the extent that people look for the “infidelity gene”, the “violence gene”, the “religion gene”, the “altruism gene”, they are refusing to explore the actual ways they made up their minds about things. Like all junk psychology, it’s way too easy to be true.

I wonder what nonsense will grow from epigenetics. Any guesses?

Also just up at The Mindful Hack, my blog on neuroscience and spirituality:

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14 Responses to “It’s in your genes” theory fading in the wake of epigenetics?

  1. F/N:

    Wiki, as handy 101, on what a “gene” is and what “alleles” are, with further notes on other factors:

    A modern working definition of a gene is “a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions “.[1][2] Colloquial usage of the term gene (e.g. “good genes, “hair color gene”) may actually refer to an allele: a gene is the basic instruction, a sequence of nucleic acid (DNA or, in the case of certain viruses RNA), while an allele is one variant of that gene. Thus, when the mainstream press refers to “having” a “gene” for a specific trait, this is generally inaccurate. In most cases, all people would have a gene for the trait in question, but certain people will have a specific allele of that gene, which results in the trait variant. In the simplest case, the phenotypic variation observed may be caused by a single letter of the genetic code – a single nucleotide polymorphism.

    Notice, the multiple- code, transcription plus regulation view that is emerging, and the use of a very familiar-looking term: FUNCTIONAL SEQUENCE.

    2 –> Protein codes give a description of the molecular bricks used.

    3 –> Cytosine-based, DNA methylation seems to lock off expression, playing a crucial regulatory role:

    DNA methylation involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring (cytosine and adenine are two of the four bases of DNA). This modification can be inherited through cell division. DNA methylation is typically removed during zygote formation and re-established through successive cell divisions during development. DNA methylation is a crucial part of normal organismal development and cellular differentiation in higher organisms. DNA methylation stably alters the gene expression pattern in cells such that cells can “remember where they have been” or decrease gene expression; for example, cells programmed to be pancreatic islets during embryonic development remain pancreatic islets throughout the life of the organism without continuing signals telling them that they need to remain islets. In addition, DNA methylation suppresses the expression of viral genes and other deleterious elements that have been incorporated into the genome of the host over time. DNA methylation also forms the basis of chromatin structure, which enables cells to form the myriad characteristics necessary for multicellular life from a single immutable sequence of DNA. DNA methylation also plays a crucial role in the development of nearly all types of cancer.[1]

    DNA methylation involves the addition of a methyl group to DNA — for example, to the number 5 carbon of the cytosine pyrimidine ring — in this case with the specific effect of reducing gene expression. DNA methylation at the 5 position of cytosine has been found in every vertebrate examined.

    4 –> The spooling of DNA strands seems to also open/hide expression of certain stretches, serving as a further layer of information and regulation.

    5 –> Beyond that, the DNA is expressed in a context of a cell, coming from the maternal line.

    6 –> So, the array of nanomachines in the existing host cell — here we go to a chicken and egg, life from life dilemma — also plays a regulatory role.

    7 –> IIRC — BA, where was this said fairly recently? — the insertion of alien DNA into a cell, will trigger expression until there is a point where the host cell family cannot express and the developing embryo dies.

    8 –> this ties back to the point that DNA functions as an information-storage unit, in the context of a self-replicating automaton [cf points 9 - 18 here, in the ID Foundations, 2 post of recent days, and here on the significance of embryological feasibility for macroevo], one that is programmed at macro-level, to implement an organism embryologically in a nurturing environment, from a zygote.

    9 –> Going beyond all this, the crucial issue — addressed in the same Found’ns 2 post, here on page 2 — is that if we are genetically determined, this would imply that our minds and volition are fatally undermined.

    10 –> But, our universal experience — including that of the genetic determinists when they urge us to accept their theories as well-founded on facts and logic, not the mere outworking of their genetic programming — is that we are self-moved agents who initiate chains of cause and effect and are responsible for how we think, will and act.
    _____________________

    Thus, the ID revolution is holding out the prospects of a way out of the quicksands of the chance + necessity genetic determinism morass.

    GEM of TKI

  2. Thus, the ID revolution is holding out the prospects of a way out of the quicksands of the chance + necessity genetic determinism morass.

    I don’t believe ID does any such thing. The way out of genetic determinism is free will. And as I recall people posting on this blob are taking great pains to separate ID from free will.

  3. TM:

    Since freedom of the will is a sharply contested point (given dominant ideologies) it makes sense to for the sake of the argument, first explicitly exclude freedom from premises, then examine and show the empirical point that — whatever its nature — intelligent entities are an empirical fact, and often leave equally empirically reliable signs of their action. On this alone, the issue of inference to design as relevant causal factor can be empirically established.

    Then, as a second issue, it makes sense to ask, what can credibly be responsible for such signs, as FSCI. In short, what is required to be able to exert designing intelligence.

    This is second, as the existence and signs of such designing intelligence need to be empirically grounded as credible fact first.

    It turns out that real power of choice is a significant feature of something that has already been empirically shown.

    The insistently hyperskeptical will of course still deny, but they will be in the unenviable situation of denying evident and credible facts.

    GEM of TKI

  4. I’m inclined to agree with TM. Some recent posts come across as being too clever by half. A “revolution” requires laser-like clarity and lightening resolve. Spin merely muddies up the waters.

  5. This article gives us a glimpse of the future; and that future is not a neo-Darwinian one.

    I posted sometime back that I no longer pursue my studies of population genetics. Why? Because they’ve become so utterly irrelevant.

    This article demonstrates quite clearly that it is not the “genes” (“alleles”) that matter (or whether or not they “change with time”), rather it is the context in which genes operate that determines things.

    Here’s one of many great lines to quote:

    So what’s going on? These puzzles turn out to be intimately related. As organisms rise on the evolutionary scale, they tend to have more “junk DNA.” Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our “junk” that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.

    Of course, how many years is it now that the ID community has been saying this? Neo-Darwinism is dead. And the future looks like it’s ID-compatible.

  6. Once again, just because it’s not the genes (or alleles) doesn’t mean it’s not DNA.

    And believing that all the necessary information for physical life is in DNA is not the same as not believing in free will. If “genetic reductionism” means you don’t believe in free will, than obviously I don’t and can’t believe that. But if all “genetic reductionism” means is that you can’t boil down an organism to its genes then of course I’m down with that. But genes do not 100% of DNA make.

    It would do us all good to withold our judgment on what this means for free will, or even what it means for the central dogma, until we have a better understanding of everything that’s going on. Because my money is on DNA as being the sole information carrier.

  7. kf, here is the reference I have;

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50

    kf, It should be noted that Talbott even critiques DNA methylation here,

    To think of a methylated cytosine (the nucleotide base most commonly affected) as still the same letter “C” that it was before its methylation, but merely tagged with a methyl group, is to miss the full reality of the situation. What we are really looking at is a metamorphosis of millions of letters of the genetic code under the influence of pervasive and poorly understood cellular processes. And the altered balance of forces represented by all those transformed letters plays with countless possible nuances into the surrounding chromatin, reshaping its sculptural qualities and therefore its expressive potentials.

    We are now learning about the consequences of these metamorphoses. In the first place, the transformations of structure brought about by methylation can render DNA locations no longer accessible to the protein transcription factors that would otherwise bind to them and activate the associated genes. Secondly, and perhaps more fundamentally, there are many proteins that do recognize methylated sites and bind specifically to them, recruiting in turn other proteins that restructure the chromatin — typically condensing it and resulting in gene repression.

    It would be difficult to overstate the profound role of DNA methylation in the organism. In humans, distinctive patterns of DNA methylation are associated with Rett syndrome (a form of autism) and various kinds of mental retardation. Stephen Baylin, a geneticist at Johns Hopkins School of Medicine, says that the silencing, via DNA methylation, of tumor suppressor genes is “probably playing a fundamental role in the onset and progression of cancer. Every cancer that’s been examined so far, that I’m aware of, has this (pattern of) methylation.”[4] In an altogether different vein, researchers have reported that “DNA methylation is dynamically regulated in the adult nervous system” and is a “crucial step” in memory formation.[5] It also seems to play a key role in tissue differentiation.

    Some patterns of DNA methylation are heritable, leading (against all conventional expectation) to a kind of Lamarckian transmission of acquired characteristics. According to geneticist Joseph Nadeau at the Case Western Reserve University School of Medicine, “a remarkable variety of factors including environmental agents, parental behaviors, maternal physiology, xenobiotics, nutritional supplements and others lead to epigenetic changes that can be transmitted to subsequent generations without continued exposure.”[6]

    But by no means are all methylation patterns inherited. For the most part they are not, and for good reason. It would hardly do if tissue-specific patterns of methylation — for example, those in the heart, kidney, or brain — were passed along to the zygote, whose undifferentiated condition is so crucial to its future development. In general, the slate upon which the developmental processes of the adult have been written needs to be wiped clean in order to clear a space for the independent life of the next generation. As part of this slate-cleaning, a restructuring wave of demethylation passes along each chromosome shortly after fertilization of an egg, and is completed by the time of embryonic implantation in the uterus. Immediately following this, a new methylation occurs, shaped by the embryo itself and giving it a fresh epigenetic start. When, in mammals, the stage of embryonic methylation is blocked artificially, the organism quickly dies.

    This structuring and restructuring of DNA by the surrounding life processes is fully as central to a developing organism as the code-conforming DNA sequence.
    http://www.thenewatlantis.com/.....e-delusion

  8. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins.

    This implies that the effect of removing DNA must be immediate otherwise “there’s something else going on.” Rubbish. Effects moving down the causal chain don’t have to be immediate. Why do you think the spring equinox, the longest day of the year, occurs before the hottest temperatures of the year? All summer long the days are getting shorter as they are getting hotter. The effect of longer days is delayed by several months, as is the effect of shorter days.

  9. tragic???? and your point is????

  10. 10

    That heat comes from the sun and gets stored in the ground for a period of time before it begins to change the temperature.

    Likewise, information comes from DNA and gets stored in RNA and protein for a period of time before it has its effect on the cell.

  11. 11

    I should say “ground and water” with the emphasis on water. Water has a notoriously high specific heat which means it takes a lot of energy to change its temperature. This is the reason why seasonal temperature changes lag so far behind the solar cycle. The earth is 75-80% water.

    But the point is the same.

  12. tragic you simply do not have the evidence to back up your claim. Surely if DNA is the be and end all, as you would like to maintain it to be, then ‘saturation mutagenesis’ should have picked it up:

    Response to John Wise – October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.

    http://www.evolutionnews.org/2.....38811.html

  13. 13

    I’m tired of this. Why does some mutagenesis study prove that developmental information is not in the DNA and is coming from some magical faraway place? This study shows that no developmental mutations benefit the fruit fly. It does not show developmental information is not in the DNA. Quite the contrary, it shows that developmental information IS in the DNA by systematically removing information from the DNA and observing detrimental results.

  14. tragic mishap:

    No one denies that “developmental information” resides in DNA. The question, rather, is how determinative is this information.

    You can “reprogram” a cell by changing the protein mixture found within a cell. There is some sort of feedback mechanism (probably quite a number of interdependent such loops) at work between cell and DNA. What epigenetics highlights is the role of other factors, factors found within the cell, in the ultimate phenotype of cell and organism.

    All of this undermines the ‘gene-centric’ view of biology, and, by extension, the neo-Darwinian mechanism built upon this view. IMO, that’s what at issue in this thread.

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