Epigenetics could be the new “buzzword scienceyness”?

Yes. So? wd400

wd400

You keep saying this, but that doesn’t make it true.

You already admitted that some epigenetic changes are not driven by genetics. Silver Asiatic

BA77

How the Burgeoning Field of Systems Biology Supports Intelligent Design – July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems

True - those features are described in teleological, goal-directed terminology. feedback loops, Timing and synchronization, induce a response, Control and signaling, organizational networks ... it's all top-down Design language. And these are just attempts to describe how the system functions. Evolution has to explain all of that as a blind, unintelligent process - non-goal directed. Silver Asiatic

As I said, evolution is gene-centric. Epigenetics falsifies that. So, evolution is wrong.

You keep saying this, but that doesn't make it true. wd400

wd400

FWIW, I said from the start that most epigenetic states are the result of genetics. There is nothing “selective” in that.

If you think that "some" is equivalent to "all", then you're quite right. There's nothing selective about that. As I said, your theory does not account for the data. "Hey, most of our calculations were correct", said technicians at the Challenger Space Shuttle post-mortem.

What “problems” will epigenetics cause evolution?

As I said, evolution is gene-centric. Epigenetics falsifies that. So, evolution is wrong. Beyond that, you have no explanation for the origin of these mechanisms. You don't even know how the process works. You don't know when it started, how pervasive it is, what impact it has, how it is inherited or not, if it can be selected, how to measure fitness on it and what causes it to change. Adding complexity to organisms is always a problem for evolution.

The implications of the study of Scoville et al.are profound, introducing as it does this additional layer of ecologically relevant epigenetic complexity into considerations of the evolutionary process. Notably, there is variation in the penetrance of epigenetic inheritance among lines, suggesting that the trait of epigenetic inheritance is itself variable and hence potentially visible to selection. In addition, the authors show that there are interactions between line effects and epigenetic effects. While the study offers a fascinating advance in our understanding of the potential ecological and evolutionary significance of epigenetic regulation, it represents just an initial first step, one that raises more questions than provides answers. http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03761.x/pdf

The authors of the above entitled it "The hairy problem of epigenetics in evolution". Silver Asiatic

Thanks for the smile. You think you won some points here by arguing on behalf of “some” epigenetic states. I guess it’s good to see you admitting that your argument that epigenetic states are controlled by genetics was wrong, given that some are not, and you said nothing about that. Your selective argument shows your defensiveness – not that I blame you.

*sigh*. I'm afraid I was being genuine when I said that it was good you'd updated your position. If people can't can be swayed by evidence then there is not hope of dicussion. I see you've regressed. FWIW, I said from the start that most epigenetic states are the result of genetics. There is nothing "selective" in that. What "problems" will epigenetics cause evolution?

A few of the problems include tracing epigenetic changes over the evolutionary timeline and whether the traits are consistently inherited or not and how they are inherited and what the full scope of epigenetic changes on the genome really is — if larger than expected, then it’s a major factor that has been ignored in ‘ordinary genetics’.

So... it's going to take some time to find out if trans-generational epigentics adds up to much at all. But you still haven't told us why it would matter if it turns out t be a big deal. As I said earlier, you are doing a good job of demonstrating the ways in which epigenetics has become a buzzword. You don't know much about the topic, you can't explain why it is a problem but you nevertheless bring the term in to your arguments (presumably to create a veneer of cutting edge science). wd400

Silver Asiatic as to:

Evolutionary explanations on the supposed evolution of ‘ordinary genetics’ are bad enough. Add another layer of code and epigenetic relationships to it and the specificity in the sequence of mutations is inexplicable.

Yes! And I would like to add that Darwinian explanations are useless, even an impediment, in trying understand these higher levels of coding:

"It has become clear in the past ten years that the concept of design is not merely an add-on meta-description of biological systems, of no scientific consequence, but is in fact a driver of science. A whole cohort of young scientists is being trained to “think like engineers” when looking at biological systems, using terms explicitly related to engineering design concepts: design, purpose, optimal tradeoffs for multiple goals, information, control, decision making, etc. This approach is widely seen as a successful, predictive, quantitative theory of biology." David Snoke*, Systems Biology as a Research Program for Intelligent Design podcast: "David Snoke: Systems Biology and Intelligent Design, pt. 1" http://intelligentdesign.podomatic.com/entry/2014-08-11T17_19_09-07_00 podcast: David Snoke: Systems Biology and Intelligent Design, pt. 2 http://intelligentdesign.podomatic.com/entry/2014-08-13T16_30_01-07_00 How the Burgeoning Field of Systems Biology Supports Intelligent Design - July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems: *"Negative feedback for stable operation." *"Frequency filtering" for extracting a signal from a noisy system. *Control and signaling to induce a response. *"Information storage" where information is stored for later use. In fact, Snoke observes: "This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. " *"Timing and synchronization," where organisms maintain clocks to ensure that different processes and events happen in the right order. *"Addressing," where signaling molecules are tagged with an address to help them arrive at their intended target. *"Hierarchies of function," where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order. *"Redundancy," as organisms contain backup systems or "fail-safes" if primary essential systems fail. *"Adaptation," where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, "These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way," and "Only part of the system is allowed to vary randomly, while the rest is highly conserved.",,, Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that "just about everything in the cell does indeed have a role, i.e., that there is very little 'junk.'" He explains, "Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible," and quotes additional authorities who assume that biological systems are optimized.,,, http://www.evolutionnews.org/2014/07/when_biologists087871.html Systems Biology as a Research Program for Intelligent Design - David Snoke - 2014 http://bio-complexity.org/ojs/index.php/main/article/viewArticle/BIO-C.2014.3

bornagain77

BA77 @ 77

They never predicted it, then they denied it could be heritable, and then they denied it could cause lasting change.

Or like wd400 who argued that epigenetic states are controlled by genetics and are therefore just 'ordinary genetics'. Oh, he was just talking about "some" of them? Sure, the others are non-genetic but let's not talk about those. It's not clear that they're "important". :-)

“It” in this case is epigenetics and in spite of being wrong, wrong and wrong again, and in spite of the fact that there is no scientific explanation for how epigenetics could have evolved, evolutionists nonetheless insist that it, in fact, must have evolved. Evolution loses every battle but claims to win the war.

Of course, not one word from wd400 or REC on how these relationships evolved, but evolution wins anyway.

Under evolution, the protein machines that attach the epigenetic markers must have fortuitously evolved from random mutations. But placing markers would not have helped if they were not in the right place, and in response to the right environmental signals. In fact, such protein machines could easily wreak havoc if they weren’t working just right.

Can't see "why this would be a problem for evolutionary biology". No need to explain it. Things evolve.

Evolution requires an enormous sequence of random mutations to occur before fitness improvements could be realized.

Evolutionary explanations on the supposed evolution of 'ordinary genetics' are bad enough. Add another layer of code and epigenetic relationships to it and the specificity in the sequence of mutations is inexplicable. Silver Asiatic

wd400

It nice to see you’ve moved from thinking it’s impossible for genotypes to determine epigenetic states to admitting only some such states are not.

Thanks for the smile. You think you won some points here by arguing on behalf of "some" epigenetic states. I guess it's good to see you admitting that your argument that epigenetic states are controlled by genetics was wrong, given that some are not, and you said nothing about that. Your selective argument shows your defensiveness - not that I blame you. I think most IDists accept that some parts of evolutionary theory might be correct. But as indicated, some of it is wrong -- and that's a falsification (claim that cell development is entirely determined by genotype). "Some parts of the theory fit the data". I wouldn't want to build a spacecraft on that kind of science, but I guess it's good enough for evolutionary biology.

But even if it turns out to be, it’s not clear to me why this would be a problem for evolutionary biology.

The review I posted explained why it would be a problem. But beyond this, the gene-centric view is false, as I already said and you denied this.

Such traits are heritable, and if they have fiteness effects they will be subject to natrual selection. Selection of epi-alleles doesn’t seem so different than selection on alleles.

A few of the problems include tracing epigenetic changes over the evolutionary timeline and whether the traits are consistently inherited or not and how they are inherited and what the full scope of epigenetic changes on the genome really is -- if larger than expected, then it's a major factor that has been ignored in 'ordinary genetics'. Silver Asiatic

Chuan He: Evolution Created Epigenetics - Cornelius Hunter - PhD in Biophysics - May 3, 2015 Excerpt: They never predicted it, then they denied it could be heritable, and then they denied it could cause lasting change. “It” in this case is epigenetics and in spite of being wrong, wrong and wrong again, and in spite of the fact that there is no scientific explanation for how epigenetics could have evolved, evolutionists nonetheless insist that it, in fact, must have evolved. Evolution loses every battle but claims to win the war. http://darwins-god.blogspot.com/2015/05/chuan-he-evolution-created-epigenetics.html Tonight’s Feature Presentation: Epigenetics, The Next Evolutionary Cliff - video Excerpt: Just keep this one thing in mind as you watch. For everything you see in this animation, evolutionists have no scientific explanation how it evolved. http://darwins-god.blogspot.com/2013/02/tonights-feature-presentation.html Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html bornagain77

It nice to see you've moved from thinking it's impossible for genotypes to determine epigenetic states to admitting only some such states are not. In the quoted article we land upon a third definition of epigenetics, trans-generational inheritance of such a trait. It's not at all clear if this an important phenomenon. But even if it turns out to be, it's not clear to me why this would be a problem for evolutionary biology. Such traits are heritable, and if they have fiteness effects they will be subject to natrual selection. Selection of epi-alleles doesn't seem so different than selection on alleles. wd400

Some, perhaps many, epigenetic states are not determined by genetic factors and there is clear and abundant evidence of the inheritance of epigenomic states that are independent of genotype.

... multiple examples are known in which variant epigenetic states occur without any genetic variation to account for them (see below). These are considered ‘pure’ epigenetic variants Epigenetic inheritance is the intergenerational transmission of a purely epigenetic variant. There is no question that epigenetic states can be determined by cis- or trans-acting genetic factors: our point is that in some cases, perhaps many cases, they are not. ... there is clear and abundant evidence for multigenerational inheritance of epigenetic states that are independent of genotype. http://rspb.royalsocietypublishing.org/content/280/1771/20130903

Silver Asiatic

The genome does not control the behavior of lactose in changing the shape of the protein

Change the sequence of the proteins' gene and it will no longer change shape when the allolactose binds.

This is why a gene-centric evolutionary explanation (or any at this point) is inadequate. It excludes the influence of non-genetic factors in gene regulation and the function of the genome.

You can say this as often as you like, it won't become true as a result. As I've already said, it was evolutionary biologists that developed quantitative genetics in the 1920s precisely because gene-environment interaction is key to evolution. wd400

wd400

the whole process depends utterly on the sequence of the E coli genome

To say 'a process depends', is much different than saying 'a process is controlled by'. Given the above, the epigenetic process includes the lactose and protein repressor so that those are incorporated into the genome. But the genome does not change its expression by itself. That is dependent on something external to the genome. The genome does not control the behavior of lactose in changing the shape of the protein. This is why a gene-centric evolutionary explanation (or any at this point) is inadequate. It excludes the influence of non-genetic factors in gene regulation and the function of the genome. It also excludes the effect of environmental factors in changing the epigenome itself and what actually is directing the process. It could just as easily be said that the epigenomic compounds that attach to DNA are what is controlling the genetic process and are directing gene expression. Things like response, control, feedback, directed, confirmation - are all teleological terms from the design world. To use those terms continually and then argue that there's no evidence of design is illogical. Silver Asiatic

If you are still struggling with this, you'd do well to study the lac operon example. In precis: In teh absence of lactose E. coli doesn't express the genes required to metabolise that sugar. That's because a set of protein binds to the DNA upstream of the genes and prevents RNA from being produced. Both the binding sequence in the DNA and the complementary region of the protein are encoded in the E coli genome. When lactose enters the cell it (or actually a derivative molecule) binds to the repressing protein, creating a change in the proteins shape such that it no longer binds to the DNA and now RNA. Again the (allo)-lactose binding domain is encoded in the E coli genome, as is sequence that creates the conformational change that causes the repressor to unbind. Once the repressor is no longer bound there is nothing to prevent transcription so you get RNA and proteins. In other words, you generate change in the expression of genes without ever changing a gene sequence and the whole process depends utterly on the sequence of the E coli genome. wd400

To have a 'genetic basis' for anything should you not have a 'gene' to begin with?

Why the 'Gene' Concept Holds Back Evolutionary Thinking - James Shapiro - 11/30/2012 Excerpt: The Century of the Gene. In a 1948 Scientific American article, soon-to-be Nobel Laureate George Beadle wrote: "genes are the basic units of all living things.",,, This notion of the genome as a collection of discrete gene units prevailed when the neo-Darwinian "Modern Synthesis" emerged in the pre-DNA 1940s. Some prominent theorists even proposed that evolution could be defined simply as a change over time in the frequencies of different gene forms in a population.,,, The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term "gene." In March 2009, I attended a workshop at the Santa Fe Institute entitled "Complexity of the Gene Concept." Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term. The modern concept of the genome has no basic units. It has literally become "systems all the way down." There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other "DNA elements" (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.,,, Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function. http://www.huffingtonpost.com/james-a-shapiro/why-the-gene-concept-hold_b_2207245.html Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 4 http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-4/ In the following podcast, Dr. Sternberg’s emphasis is on ENCODE research, and how that research overturned the ‘central’ importance of the gene as a unit of inheritance. As well he reflects on how that loss of the term ‘gene’ as an accurate description in biology completely undermines the modern synthesis, (i.e. central dogma), of neo-Darwinism as a rational explanation for biology. Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html

also of note to 'genes FOR height':

GIANT study reveals giant number of genes linked to height - Oct. 5, 2014 Excerpt: The largest genome-wide association study (GWAS) to date, involving more than 300 institutions and more than 250,000 subjects, roughly doubles the number of known gene regions influencing height to more than 400. http://medicalxpress.com/news/2014-10-giant-reveals-genes-linked-height.html Gene previously linked to obesity is unrelated - June 29, 2015 Excerpt: … in the real world of careful analysis, scientists are just not finding the “genes” that the headline writers need. British geneticist Steve Jones points out that most human traits are influenced by so many genes that there is no likely systematic cause and effect: "We know of more than 50 different genes associated with height … That has not percolated into the public mind, as the Google search for “scientists find the gene for” shows. The three letter word for — the gene FOR something — is the most dangerous word in genetics." And the craze is not harmless, he warns. … https://uncommondesc.wpengine.com/genetics/gene-previously-linked-to-obesity-is-unrelated/

Neo-Darwinism is impotent to explain any of this integrated complexity that is found to be involved in the trait of height

The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology – Bard - 2011 Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf

bornagain77

That’s why what you said was contradictory. The modifications are caused by molecules, not by the genome

What the... are you serious? Do you similarly think there is no genetic basis to height or eye colour? After all, these traits are the result of molecules encoded by DNA not the DNA molecule itself! wd400

Darwinists can't even demonstrate to origin of a single functional protein,

Stephen Meyer (and Doug Axe) Critique Richard Dawkins's "Mount Improbable" Illustration - video https://www.youtube.com/watch?v=7rgainpMXa8

much less can Darwinists demonstrate the origin of the multi-tiered levels of integrated information that tell proteins what to do once they are created. Stephen Talbott puts the question that Darwinists refuse to answer like this:

HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling... and so on without end. Yet the coherence of the whole is maintained. 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. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: "The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)",,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2

Frank Turek is also quite blunt in laying out the insurmountable problem that atheists refuse to honestly address

Frank Turek Christ Community Church (April 2015) - video - (goal directed embryogenesis 27:10 minute mark) https://youtu.be/iKFfq-IwcrM?t=1629

I think the following quote sums up the atheist's dilemma quite well

"It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident...you have essentially lost your mind." Jay Homnick - senior editor of The American Spectator http://www.evolutionnews.org/2015/04/to_have_a_view095041.html

bornagain77

REC, Evolutionism cannot explain gene regulation nor developmental biology. You cannot use what you cannot explain. Talk about desperation. Virgil Cain

REC

Then any environmental response (say the E. coli Lac operon responding to Lactose and Glucose) could be called epigenetic.

Or, since it's just 'ordinary genetics' then we wouldn't need the term epigenetic.

This reads as a desperate attempt by creationists to sever gene regulation and developmental biology, without knowing the underlying mechanisms one bit.

Nice job in explaining the evolutionary origins of these processes. Epi-mutations somehow built a relationship between DNA and environmental factors. Operons "respond" and the genome "controls" its own expression - switching off occasionally, preserving a latent function, only to be switched back on under different conditions. I've read enough on this topic to know you guys are bluffing. Biologists struggle just to explain how this works, and nobody has an evolutionary story to tell about it. Silver Asiatic

"The modifications are caused by molecules, not by the genome itself." The modifications are made and removed by genome-encoded proteins. Mutations to those genes can perturb the epigenome. This is frequently observed in cancers and developmental defects. "Genes are expressed differently because of non-genetic factors" Then any environmental response (say the E. coli Lac operon responding to Lactose and Glucose) could be called epigenetic. This reads as a desperate attempt by creationists to sever gene regulation and developmental biology, without knowing the underlying mechanisms one bit. REC

wd400

The modifications ... get placed and removed by molecules like Histone_deacetylases (HDACs)

That's why what you said was contradictory. The modifications are caused by molecules, not by the genome itself. The DNA does not modify itself -- although if you want to argue that it does, that would be interesting. I didn't offer an additional definition of epigenetics, just merely an essential aspect of it. Genes are expressed differently because of non-genetic factors without changes to the DNA sequence. BA77 offered a number of references that you might want to respond to also. Silver Asiatic

podcast - New Book “Debating Darwin’s Doubt” Released on 90th Anniversary of Scopes Trial http://www.discovery.org/multimedia/audio/2015/07/new-book-debating-darwins-doubt-released-on-90th-anniversary-of-scopes-trial/ bornagain77

Some humans think that Something (Natural) emerged from Nothing. But they do NOT believe something supernatural emerged from nothing. They're right about the latter lol. Batting .500 is pretty darn good actually. ppolish

From the OP article: "Epigenetics is fascinating but still in its infancy. It’s not heretical, it won’t upend Darwin, or give you supernatural powers" When supernatural powers ARE discovered/proven, Darwinians will take credit of course. "That's old news. we knew about that". Just watch. ppolish

Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html Quantum no-deleting theorem Excerpt: A stronger version of the no-cloning theorem and the no-deleting theorem provide permanence to quantum information. To create a copy one must import the information from some part of the universe and to delete a state one needs to export it to another part of the universe where it will continue to exist. http://en.wikipedia.org/wiki/Quantum_no-deleting_theorem#Consequence Information Conservation and the Unitarity of Quantum Mechanics Excerpt: “In more technical terms, information conservation is related to the unitarity of quantum mechanics. In this article, I will explain what unitarity is and how it’s related to information conservation.” http://youngsubyoon.com/QMunitarity.htm

Besides providing direct empirical falsification of neo-Darwinian claims as to the generation of information from a material basis (i.e. non-local quantum information refuses to be reduced to a material basis), the implication of finding ‘non-local’, beyond space and time, and ‘conserved’ quantum information in molecular biology on a massive scale is fairly, and pleasantly, obvious. That pleasant implication being the strong validation of the Theist’s contention that we, as distinct ‘persons’, are ‘souls’ that merely live in a material body and that we are not ‘persons’ who are co-terminus with, and/or emergent from, our material bodies:

“You don’t have a soul. You are a soul. You have a body.” George MacDonald – Annals of a Quiet Neighborhood – 1892 Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video https://www.youtube.com/watch?v=iIyEjh6ef_8

Verse, Picture, and Music:

Psalm 139:13-16 For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. Your eyes saw my unformed body; all the days ordained for me were written in your book before one of them came to be. “What power holds off that moment — precisely for a lifetime, and not a moment longer?” – picture – http://cdn-4.spiritscienceandmetaphysics.com/wp-content/uploads/2014/12/harvardd-2.jpg MATT MAHER – Because He Lives (Amen): Song https://www.youtube.com/watch?v=PBvU7arNhQs

bornagain77

The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism - Michael J. Denton - 2013 Excerpt: Cell form ,,,Karsenti comments that despite the attraction of the (genetic) blueprint model there are no “simple linear chains of causal events that link genes to phenotypes” [77: p. 255]. And wherever there is no simple linear causal chain linking genes with phenotypes,,,—at any level in the organic hierarchy, from cells to body plans—the resulting form is bound to be to a degree epigenetic and emergent, and cannot be inferred from even the most exhaustive analysis of the genes.,,, To this author’s knowledge, to date the form of no individual cell has been shown to be specified in detail in a genomic blueprint. As mentioned above, between genes and mature cell form there is a complex hierarchy of self-organization and emergent phenomena, rendering cell form profoundly epigenetic. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.3/BIO-C.2013.3

In fact, it is found that the ‘form/shape’ of DNA itself is determined, in large measure, by 'non-local' quantum information, not by the sequential, discrete, classical information as is presupposed in neo-Darwinism:

Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/

In the following video, Longitudinal Quantum Information running along the entire length of DNA is discussed at the 19:30 minute mark. At the 24:00 minute mark, Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information that has classical information embedded within it.

Classical and Quantum Information in DNA – Elisabeth Rieper – video https://youtu.be/2nqHOnVTxJE?t=1176

As well, the following study found both 'non local' quantum information/entanglement to be encoded in proteins alongside the classical information:

Classical and Quantum Information Channels in Protein Chain – Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija – 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural – amino acids and peptide planes, (2) energy – classical and quantum state, and (3) information – classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491

Here is another fascinating method by which it was clearly demonstrated that form/shape is not reducible to ‘bottom up’ materialistic explanations:

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

But perhaps the best demonstration that ‘form/shape’ is not reducible to the ‘bottom up’ material explanations is by noting the fact that the ‘form/shape’ of an organism is almost immediately lost upon the death of an organism:

Rabbit decomposition time-lapse (higher resolution) – video https://www.youtube.com/watch?v=C6sFP_7Vezg

In the following article, Stephen Talbott asks this very important question about the relatively sudden loss of ‘form’ at the death of an organism. Specifically Talbott asks, “What power holds off that moment — precisely for a lifetime, and not a moment longer?”

The Unbearable Wholeness of Beings – Stephen L. Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings

Well, where does the biological information, specifically the quantum information, that was keeping the organism alive for ‘precisely a lifetime’, suddenly go upon the death of an organism? Reductive materialists would hold that the biological/quantum information simply ceases to exist upon the death of an organism, (since they hold information to be ’emergent’ from a material basis). But the fact of the matter is that the quantum information, the information that was/is in fact ‘holding life together’ for precisely a life time, is ‘conserved’, and does not simply disappear from reality:

Black holes don’t erase information, scientists say – April 2, 2015 Excerpt: The research marks a significant step toward solving the “information loss paradox,” a problem that has plagued physics for almost 40 years, since Stephen Hawking first proposed that black holes could radiate energy and evaporate over time. This posed a huge problem for the field of physics because it meant that information inside a black hole could be permanently lost when the black hole disappeared—a violation of quantum mechanics, which states that information must be conserved. http://phys.org/news/2015-04-black-holes-dont-erase-scientists.html+/ .

bornagain77

Here are a few notes that refute wd400's neo-Darwinian assumptions:

Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA - 2014 - Jonathan Wells Excerpt Page 11: Most proteins are not completely specified by DNA sequences: The central dogma (which here includes Crick’s sequence hypothesis) claims that (1) DNA specifies RNA and (2) RNA specifies protein. Yet this claim fails at both steps, because most RNAs are not uniquely specified by DNA sequences, and many proteins are not uniquely specified by RNAs—either in their amino acid sequences or in their final folded forms. After transcription, RNAs from many eukaryotic genes undergo alternative splicing. Recent studies estimate that transcripts from approximately 95% of multi-exon human genes are spliced in more than one way [289?291]. By intervening between transcription and translation, alternative splicing generates RNAs with sequences that differ from DNA sequences [292].,,, http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2 Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html "Physiology Is Rocking the Foundations of Evolutionary Biology": Another Peer-Reviewed Paper Takes Aim at Neo-Darwinism - Casey Luskin March 31, 2015 Excerpt: Noble doesn't mince words: "It is not only the standard 20th century views of molecular genetics that are in question. Evolutionary theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Muller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved." Noble then recounts those assumptions: (1) that "genetic change is random," (2) that "genetic change is gradual," (3) that "following genetic change, natural selection leads to particular gene variants (alleles) increasing in frequency within the population," and (4) that "inheritance of acquired characteristics is impossible." He then cites examples that refute each of those assumptions,,, He then proposes a new and radical model of biology called the "Integrative Synthesis," where genes don't run the show and all parts of an organism -- the genome, the cell, the body plan, everything -- is integrated. http://www.evolutionnews.org/2015/03/physiology_is_r094821.html “The genome is an ‘organ of the cell’, not its dictator” - Denis Noble – President of the International Union of Physiological Sciences 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/ Neurons constantly rewrite their DNA - Apr. 27, 2015 Excerpt: They (neurons) use minor "DNA surgeries" to toggle their activity levels all day, every day.,,, "We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell's identity," says Hongjun Song, Ph.D.,, "This research shows that some cells actually alter their DNA all the time, just to perform everyday functions.",,, ,,, recent studies had turned up evidence that mammals' brains exhibit highly dynamic DNA modification activity—more than in any other area of the body,,, http://medicalxpress.com/news/2015-04-neurons-constantly-rewrite-dna.html How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 James Shapiro on “dangerous oversimplifications” about the cell - August 6, 2013 Excerpt: "Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function. Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4]." https://uncommondesc.wpengine.com/news/james-shapiro-on-dangerous-oversimplifications-about-the-cell/

Also of note: neo-Darwinists have no evidence that 'form/shape' is even reducible to DNA in the first place, much less do they have any evidence that changes to DNA can generate the myriad of different types of lifeforms we see around us:

'No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution' – Jonathan Wells Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Response to John Wise - October 2010 Excerpt: 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/2010/10/response_to_john_wise038811.html

bornagain77

You need to explain how ‘genetic control’ causes “changes in gene activity and expression without alteration in DNA sequence”.

We know have a second definition of epigeneics, even so, I've already given you examples. Here's another, using the example of histone modifications in you quoted text. These modifications variously "open up" or "close" DNA molecules and otherwise promote or inhibit expression of different genes. The modifications don't just jump on an off regions at random, or due to some inscrutable will in the cell. Rather, they get placed and removed by molecules like Histone_deacetylases (HDACs) which are themselves encoded in DNA, and, whats more the expression of different HDAcs is under the control of different (genetically encoded) transcription factors with their own (genetic) binding sites. When I say most epigenetic states are ultimately under genetic control I mean these states are determined mostly by the proteins and RNAs encoded by our genome, and the cis-regulator elements that genome contains. wd400

BA77 @ 24 - thanks. The Stuart Newman quote says it. Epigenetic states are not controlled by genes.

So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.

Silver Asiatic

wd400

OK, so why do you think genetic control of epigenetics is “illogical” and “contradictory”.

You need to explain how 'genetic control' causes "changes in gene activity and expression without alteration in DNA sequence".

Epigenetics is defined as heritable changes in gene activity and expression that occur without alteration in DNA sequence [1, 2]. It is known these non-genetic alternations are tightly regulated by two major epigenetic modifications: chemical modifications to the cytosine residues of DNA (DNA methylation) and histone proteins associated with DNA (histone modifications) [1, 3]. Functionally, the patterns of epigenetic modifications can serve as epigenetic markers to represent gene activity and expression as well as chromatin state [3-6]. http://www.sabiosciences.com/pathway8_Epigenetic.php

You need to explain how "cells carrying identical DNA differentiate into different cell types, and how they maintain differentiated cellular states". Epigenetic changes in gene expression are not encoded in the DNA sequence itself. The epigenetic state is what regulates those aspects of cellular development and activation. If this was "controlled by DNA" (somehow, without observed changes in sequences), then there'd be no need to cite an epigenetic state. It would just be "ordinary genetics". But the modifications in gene expression are caused by factors external to the genome and are not caused by DNA. Silver Asiatic

Tomorrow Eric Metaxas will have Stephen Meyer on his program to discuss the new book "Debating Darwin's Doubt". Listen online or find your station here: http://www.metaxastalk.com/ This is Zach Johnson's Official Twitter Page. Zach and his team will post news, photos, and more. God bless! Practice Hard, Play Hard, Pray Hard = PH3 https://twitter.com/zachjohnsonpga It appears the new Open champion, Zach Johnson, is a man of great faith bornagain77

wd400 claims: "epigentic states are under the control of genetic elements." That claim is false.

“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 Origin of life: A problem in the origin of information - April 2014 Excerpt: A hallmark of life is the way information flows between different levels of organization. In non-living systems, information flows from the bottom up–the properties of the individual parts determine the fate of the system. But with living systems, that flow goes both ways. Not only genes dictate the nature of proteins which in turn affect the functioning of cells, tissues and organisms, but the behavior of proteins, cells, and organisms also control gene expression. This is what Walker calls “top-down control” or “top-down causation.” And to Walker, this transition–from information seeping upward only to information flowing both up and down–is the key to understanding life’s origins. Put differently, the blueprint for building an organism isn’t stored in its DNA only, but it’s distributed in the state of the entire system. Dr. Sara Walker https://uncommondesc.wpengine.com/intelligent-design/origin-of-life-a-problem-in-the-origin-of-information/ The Gene Myth, Part II - August 2010 Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, (intrinsically disoredered proteins), taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html Metamorphic Proteins - 2008 Summary: Proteins that can adopt more than one native folded conformation may be more common than previously thought. http://www.sciencemag.org/content/320/5884/1725.summary Biology's Quiet Revolution - Jonathan Wells - September 8, 2014 Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called "intrinsically disordered proteins," or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,, So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific "fact," as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that "DNA makes RNA makes protein makes us." http://www.evolutionnews.org/2014/09/biologys_quiet_089651.html podcast - Dr. Jonathan Wells: Biology’s Quiet Revolution - September 17, 2014 "We are talking about 1/3 of the proteins in our body, (could be Intrinsically Disordered Proteins)" - Jonathan Wells http://www.discovery.org/multimedia/audio/idtf/2014/09/dr-jonathan-wells-biologys-quiet-revolution/ On this episode of ID the Future, Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains. Podcast - Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 4 - conclusion "Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA." http://intelligentdesign.podomatic.com/entry/2014-06-16T15_41_30-07_00

bornagain77

OK, so why do you think genetic control of epigenetics is "illogical" and "contradictory". When a transcription factor binds to its binding site that's genes (both the site and the genetic sequencing defining the TF) establishing a new pattern of gene expression. Same goes for histones and DNA methylation. For the most part, epigentic states are under the control of genetic elements. wd400

http://www.nature.com/ng/journal/v33/n3s/full/ng1089.html The term 'epigenetics', which literally means 'outside conventional genetics', is now used to describe the study of stable alterations in gene expression potential that arise during development and cell proliferation. Silver Asiatic

What do you think "epigenetics" means? wd400

SA: But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently. WD: In what sense is this new? The influence of environment on phenotypes has been obvious for a long time. It should be no suprise that evolutionary biologists invented quantative genetics o account for the influences of genes and environment on traits… in the 1920s. Similarly, understanding control of gene expression has been core to molecular biology more or less since that field existed.

The fact that it's not new only makes this worse for your side. Notice, you talk about "understanding gene expression". But you said nothing about the evolutionary origin of this mechanism. If you're just learning how the process works, it's clear that you can say nothing significant about how it evolved from some precursors.

If you mean that gene expression differences might be important for explaining the differences between humans and chimps then congratulations: you’ve caught up to where mainstream evolution biology was 30 years ago.

As above, if mainstream biology only knows that epigenetics might explain morphological differences, you've said absolutely nothing about the evolutionary origin of epigenetic changes (and made it clear that modern evolution doesn't know what it is).

Well, most epigenetics changes are in turn the result of genetic changes.

I'd like to see a reference for that. Again, we're looking for the origin of these changes. You're saying that epigenetics, a known a factor in the regulation of gene expression, evolved through genetic changes.

I can’t see how the second sentence follows from the first, even if it was true.

If similar gene sequences cause different morphological changes due to epigenetic factors, then epigenetic responses are driving the changes - and therefore is not traceable through DNA divergence.

Again, you do realize epigenetic states are mostly controlled by plain old genetics, right?

If someone else can explain what you're trying to say here, I would really appreciate it, because as I read it it's illogical and contradictory. And when we're done with the attempt to explain merely how it works, you can go back to explain how it evolved. That's what's missing. Silver Asiatic

BA -- I guess that was wd400's explanation for the origin of epigenetic relationships. As stated, evolutionary theory has nothing to offer on this -- and wd400's response made that quite clear. Silver Asiatic

"epigenetic states are mostly controlled by plain old genetics" Isn't that backwards, WD400? And how can plain old genetics "control"? Control means purposeful and guided. ppolish

Well sorting all the gross mistakes out of wd400's comment should take you a while SA! :) bornagain77

You are doing a fine job of demonstrating how epigenetics is becoming a buzzword -- something for various science-adjacent fields to attempt to attach their normal patter to...

Current evolutionary theory is gene-centric. Morphological changes are attributed to alteration in DNA through random errors in transcription which are fixed through selection or genetic drift and then inherited.

Most mutations are from replication, not transcription. But close enough.

But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently.

In what sense is this new? The influence of environment on phenotypes has been obvious for a long time. It should be no suprise that evolutionary biologists invented quantative genetics o account for the influences of genes and environment on traits... in the 1920s. Similarly, understanding control of gene expression has been core to molecular biology more or less since that field existed.

Morphological changes cannot be attributed merely to DNA change.

Correct. But this is Evolution 101 (changes in heritable traits and all that)

Claiming the morphological differences from chimp to human are explained in a 99% similarity in genotype says nothing about epigenetic factors.

I'm not sure exactly what you are saying here (one of the problems caused by the diluted meaning of 'epigenetic). If you mean that gene expression differences might be important for explaining the differences between humans and chimps then congratulations: you've caught up to where mainstream evolution biology was 30 years ago. If you mean the differences between human and chimp are mostly due to environmentally induced changes in gene expression then I look forward to the experiment!

If morphological differences are epigenetic, then genetic divergence is irrelevant to morphology. This alone proves evolutionary theory wrong.

Well, most epigenetics changes are in turn the result of genetic changes. I can't see how the second sentence follows from the first, even if it was true.

But far beyond this, modern evolution says nothing at all about the origin of this epigenetic relationship. It’s not merely a sequential progression of DNA alterations to be explained, but multi-level coding changes which are responsive to the environment and inherited.

Again, you do realize epigenetic states are mostly controlled by plain old genetics, right? wd400

Perhaps you should let Lizzie know that she is arguing for intelligent design evolution. Virgil Cain

I find it curious that Darwinists insist that as Stephanie Keep over at NCSE says: " ... This idea, that evolution is somehow a self-directed march toward complex perfection, is a fundamental misunderstanding. It’s not only wrong, it’s dangerous, because it has potential to feed into a common creationist argument that scientists believe in evolution because they don’t believe in God. ... " Reference: http://ayearningforpublius.wordpress.com/2015/06/15/there-is-no-try-in-evolution/ And yet as this OP indicates: " ... All of your cells contain all of your 22,000 genes, but not all of them need to be active all the time. They need to be turned on or off, in the right tissue, at the right moment, and so we have incredible networks of control systems in our genomes – circuits, programmes, hierarchies. Epigenetics literally means “in addition to genetics” and is one such system – modifications to DNA without altering the gene sequence itself. Think of DNA as an orchestral score, the notes on the page unchanging. But the annotations on the manuscript will dictate how the music sounds, with crescendo and lento and adagio. The conductor and orchestra play their annotated manuscript, and each performance is unique, even when the original scores are identical. ... " And migratory animals, seemingly at or approaching their evolutionary ideal, migrate to very specific places year after year - generation after generation. This seems to show that there is "somehow a self-directed march toward complex perfection." ayearningforpublius

Well Virgil, anyone who is willing to argue that an intelligently designed program can produce ICness can't be all bad. Mung

Mung- Lizzie ignored your link to Sanford's paper. Are you as unsurprised as I am? Virgil Cain

I think I'm about to go epi on you Virgil! Mung

FYI- The Type III Secretory System is also irreducibly complex. Just sayin'... Virgil Cain

Thanks, BA. Now it's wd400's turn. Silver Asiatic

OT: Why the Type III Secretory System Can't Be a Precursor to the Bacteria Flagellum Casey Luskin July 20, 2015 http://www.evolutionnews.org/2015/07/why_the_type_ii097821.html bornagain77

Well said Silver Asiatic! bornagain77

wd400

What about epigenetics proves “Darwin was wrong” (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty).

Current evolutionary theory is gene-centric. Morphological changes are attributed to alteration in DNA through random errors in transcription which are fixed through selection or genetic drift and then inherited. Evolutionary explanations attempt to offer some kind of sequence of steps in DNA modification to explain the massive diversity evident in the earth's biosphere. As it stands, that claim is absurdly improbable and indefensible as we see every day from evolutionary defenders here on UD. But with epigenetic changes, a new level is added, making it a ridiculously complex scenario. Non-genetic factors cause genes to express themselves differently. Morphological changes cannot be attributed merely to DNA change. Claiming the morphological differences from chimp to human are explained in a 99% similarity in genotype says nothing about epigenetic factors. If morphological differences are epigenetic, then genetic divergence is irrelevant to morphology. This alone proves evolutionary theory wrong. But far beyond this, modern evolution says nothing at all about the origin of this epigenetic relationship. It's not merely a sequential progression of DNA alterations to be explained, but multi-level coding changes which are responsive to the environment and inherited.

If the genome consists of multiple levels of coding, if code can be silenced and reactivated, and if the genome can reprogram itself by cues from the environment, then Darwin's 1859 hypothesis, even after its 1930s update, "neo-Darwinism," looks simplistic and antiquated. Clearly, the environment has no ability to cause adaptive effects, let along program or reprogram anything. Instead, the adaptability of the genome appears more like a design feature: a mechanism for the genome to remain robust through environmental perturbations. http://www.evolutionnews.org/2014/03/ghost_of_lamarc083371.html

Again, evolutionary theory has nothing to explain this. As Stephen Meyer puts it:

"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." -- Darwin's Doubt

Silver Asiatic

wd400 asks:

"What about epigenetics proves “Darwin was wrong” (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty)."

Note that wd400 did not put a question mark in his supposed question of neo-Darwinism. This omission is telling because neo-Darwinists, such as wd400, never actually question neo-Darwinism to find out what is 'wrong' with neo-Darwinism. In other words, they never actually seek to falsify their theory. Instead neo-Darwinists become a sort of 'story telling' apologist who seeks to cover up embarrassing experimental shortcomings for neo-Darwinism. Indeed, there is no strict falsification criteria to be found anywhere within neo-Darwinism that would allow one to test against it to potentially 'scientifically' falsify neo-Darwinism.

“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” - Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003

And in so far as neo-Darwinism lacks a strict falsification criteria that one can test against to potentially falsify the theory, it is not even considered a proper 'science' in the first place but is more realistically considered to be a pseudo-science:

"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD https://www.youtube.com/watch?v=_T1v_VLueGk

In fact, it is interesting to note what J.B.S. Haldane, one of the founders of the modern synthesis, said.

J.B.S. Haldane worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. http://en.wikipedia.org/wiki/Population_genetics#History

When asked what would falsify Darwinism, J. B. S. Haldane, one of the founders of population genetics, did not refer to any laboratory test to perform to test against his mathematical models, but instead stated that a ‘rabbit fossil in pre-Cambrian rocks would do quite nicely’.

Five Questions Evolutionists Would Rather Dodge 5. Testability What evidence would convince you that evolution is false? If no such evidence exists, or indeed could exist, how can evolution be a testable scientific theory?,,, The evolutionist J. B. S. Haldane, when asked what would convince him that evolution was false, replied that finding a rabbit fossil in pre-Cambrian rocks would do quite nicely. Such a fossil would, by standard geological dating, be out of sequence by several hundreds of millions of years. Certainly such a finding, if rigorously confirmed, would overturn the current understanding of the history of life. But it would not overturn evolution. Haldane’s rabbit is easily enough explained as an evolutionary convergence, in which essentially the same structure or life form evolves twice. In place of a common underlying intelligent design, evolutionists invoke evolutionary convergence whenever confronted with similar biological structures that cannot reasonably be traced back to a common evolutionary ancestor. So long as some unknown or unexplored evolutionary pathway might have led to the formation of some biological structure or organism, evolutionists prefer it over alternative explanations such as intelligent design. And since the unknown and unexplored allow for an infinity of loopholes, the committed evolutionist regards Darwinian and other materialist explanations of life’s origin and subsequent development as always trumping alternative explanations, regardless of the evidence. - By William A. Dembski http://www.brianauten.com/Apologetics/Five_Questions_Ev.pdf

That Haldane would appeal to a pre-Cambrian rabbit, instead of a laboratory test to test his mathematical models against is simply ludicrous! Moreover, even a Darwinist admitted that a ‘pre-Cambrian rabbit’ would not falsify Darwinism:

"In 2009, Steve Meyer and I spoke at the Sam Noble Museum of Natural History at the University of Oklahoma. The day before, the museum’s curator of invertebrate paleontology, Dr. Stephen Westrop, made a pre-emptive strike by giving his own talk about why the Cambrian explosion poses no challenge to Darwinian theory. He concluded by taking exception to J.B.S. Haldane’s claim that finding a fossil rabbit in the pre-Cambrian would prove Darwin’s theory wrong. If such a fossil were found, Westrop said, paleontologists would simply revise their reconstruction of the history of life. During the Q&A, one student asked him whether any fossil find could falsify Darwin’s theory, and Professor Westrop said “No,” since Darwin’s theory is really about natural selection, which operates on a much shorter time scale than the fossil record." https://uncommondesc.wpengine.com/darwinism/actually-said-one-darwin-follower-a-rabbit-in-the-cambrian-would-be-no-problem/

As to epigenetic information itself, Dr. Meyer puts the enormous challenge for neo-Darwinism that epigentics presents as such:

"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." Stephen Meyer - Darwin's Doubt (p. 281)

Of related note as to what is 'wrong' with the modern synthesis:

Podcast - Richard Sternberg PhD - On Human Origins: Is Our Genome Full of Junk DNA? Part 5 (emphasis on ENCODE findings and the loss of the term 'gene' as a accurate description in biology and also how that loss undermines the modern synthesis of neo-Darwinism) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/

also see James Shapiro and Denis Noble bornagain77

Yes Wd400, both evolutionary biology and creationists know that Darwin was wrong about this and that. And those. These. Common ground right there. Why can't we just get along? Because it's a battle, that's why. ppolish

What about epigenetics proves "Darwin was wrong" (or actually, that modern evolutionary biology is wrong, since that field is happy to admit Darwin was wrong about plenty). wd400

You're looking at two points and only answering one: 1. Creationists cite epigenetics to assert that Darwin was wrong 2. and that epigenetics may show Lamarckian evolution #1 remains true even if the process isn't Lamarkian and even if the sequence isn't changed. Natural selection doesn't "act" on anything. Certain DNA changes can be preserved or lost, but evolution has to explain the origin and influence of epigenetic changes along with changes to DNA sequences. Neo-Darwinism (in its most contemporary form) is wrong to claim that natural selection acting on DNA sequence modifications alone is a sufficient explanation. Silver Asiatic

I guess the "fronting Darwinism" bit is this passage:

. Creationists cite epigenetics to assert that Darwin was wrong, and that epigenetics may show Lamarckian evolution – that is, acquired during life. It doesn’t, as the changes do not alter the DNA sequence on which natural selection acts

Can anyone tell me why this isn't correct? It's not the whole of the reason that modern epigenetics isn't much like Lamarkian evolution, but it seems accurate enough to me. wd400