Epigenome: Better find a new use for that pocket CD of your genome

_{Denyse O'Leary

January 22, 2011

Intelligent Design}

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Remember when, as sociologist Dorothy Nelkin tells it,

The language used by geneticists to describe the genes is permeated with biblical imagery. Geneticists call the genome the “Bible,” the “Book of Man”and the “Holy Grail.” They convey an image of this molecular structure as more than a powerful biological entity: it is also a mystical force that defines the natural and moral order. And they project an idea of genetic essentialism, suggesting that by deciphering and decoding the molecular text they will be able to reconstruct the essence of human beings, unlock the key to human nature. As geneticist Walter Gilbert put it, understanding our genetic composition is the ultimate answer to the commandment “know thyself.” Gilbert introduces his lectures on gene sequencing by pulling a compact disk from his pocket and announcing to his audience, “This is you.”*

At ScienceDaily (Jan. 14, 2011), we learn that after the complete draft of the human genome was released in 2003, of the growing focus on is on the epigenome:

Whereas the genome is the same in every cell of an organism, the epigenome of every cell type is different. It is because of the epigenome that a liver cell is not a brain cell is not a bone cell.

From the genome, we learned? …

“We learned many things from the Human Genome Project,” Elgin says, “but of course it didn’t answer every question we had!

“Including one of the oldest: We all start life as a single cell. That cell divides into many cells, each of which carries the same DNA. So why are we poor, bare, forked creatures, as Shakespeare put it, instead of ever-expanding balls of identical cells?

“This [epigenome] work,” says Elgin, “will help us learn the answer to this question and to many others. It will help us to put meat on the bones of the DNA sequences.”

You, know, it almost makes one go all religious and say: Re the “Bible,” the “Book of Man”and the “Holy Grail,” worship the creator not the creation. And recycle your CDs.

*Dorothy Nelkin, “Less Selfish Than Sacred? Genes and the Religious Impulse in Evolutionary Psychology,” in Hilary Rose and Steven Rose, eds., Alas, Poor Darwin: Arguments Against Evolutionary Psychology (London: Random House, Vintage, 2001), p. 18. Quoted in Beauregard & O’Leary, The Spiritual Brain, p. 52.

Comments

This is an interesting concluding statement from the preceding article by Hameroff: Quantum states in proteins and protein assemblies: The essence of life? Excerpt: "There is some question as to whether centrioles, cilia and flagella (i.e. flagellates) could have evolved purely by natural selection, as they are said to exhibit “irreducible complexity”.58 Darwin said in The Origin of Species: “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Innumerable small, randomly chosen steps of incremental changes in proteins to form tubulin, and tubulin to form microtubules, and microtubules to form centrioles, cilia and flagella would seem to offer no advantages “along the way”. Consequently centrioles, cilia and flagella have been suggested as examples of “intelligent design”.58 Designed by what, or by whom? This question leads some to “Creationism”. But there is also the view that intelligent design reflects the type of Platonic information embedded in the Planck scale suggested by Roger Penrose.59,60 If so, then via quantum states living systems are in touch with a deeper reality. http://www.tony5m17h.net/SHJTQprotein.pdf further notes: The ‘Fourth Dimension’ Of Living Systems https://docs.google.com/document/pub?id=1Gs_qvlM8-7bFwl9rZUB9vS6SZgLH17eOZdT4UbPoy0Ybornagain77_{January 23, 2011
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Here is another article by Hameroff that deals with proteins: Quantum states in proteins and protein assemblies: The essence of life? http://www.tony5m17h.net/SHJTQprotein.pdfbornagain77_{January 23, 2011
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This looks interesting as to trying to get a grip on the 'chemically impossible' massive amounts of information processing that is going on in a cell: Quantum Computing in DNA - Hameroff Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist). Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement. http://www.quantumconsciousness.org/views/QuantumComputingInDNA.htmlbornagain77_{January 22, 2011
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tragic, I think the following article clearly gets the point across for 'information' being infused, and tightly integrated, throughout the entirety of the cell, and the fallacy for one to continue to think in terms of 'genetic reductionism': Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.htmlbornagain77_{January 22, 2011
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tragic, information, transcendent to matter and energy, is infused throughout the genome. It is simply 'chemically impossible' for the unfathomably complex actions we see in a cell to arise from a 'information base'. A information base you contend, erroneously, is situated solely in the DNA.,,, The best way to look at this tragic is to realize that the DNA contains, at best, the complete parts list but that the overriding blueprint is infused throughout the cell. Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video http://www.metacafe.com/watch/4187488/ Shoot after viewing this following video, I am tempted to say that even the whole cell does not contain the entire body plan 'blueprint' information: Fearfully and Wonderfully Made – Glimpses At Human Development In The Womb – video http://www.metacafe.com/watch/4249713 ,,,, though DNA undoubtedly has a very important role in the information processing of the cell, it certainly does not 'all start with DNA'. ,,, I can't stress enough to you the fact that 'transcendent information', more foundational than the 'chemical letter information' encoded on the DNA, is what is actually constraining the cell to be so far out of 'thermodynamic equilibrium' notes: Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/journals.asp?iid=47 Does DNA Have Telepathic Properties?-A Galaxy Insight Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html etc.. etc.. etc..bornagain77_{January 22, 2011
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I looked at some of them and attempted to comment and ask questions, and you responded by posting more links instead of addressing my question. Neo-Darwinism is incorrect. I'm not so sure genetic reductionism is. I've never felt the need to explain evolution since I'm a creationist, so I'm not at all surprised that there's a concrete difference between macro-evolution and micro-evolution. That does nothing to destroy the idea that it all starts with the DNA. It's no different than for instance the lac operon, which we've known about since the 80s, where expression of an enzyme is controlled by the level of its substrate in the cell.tragic mishap_{January 22, 2011
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tragic, in that case all I have to say is that, 'You are severely mistaken if you think the genetic reductionism model of neo-Darwinism is correct', In fact in the links, I presume you did not look at, is very exciting evidence for 'paradigm shifting' in how we look at the 'information' in genomes.bornagain77_{January 22, 2011
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I would like to talk to a person, not a succession of links.tragic mishap_{January 22, 2011
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tragic, it should also be noted that we now have very suggestive evidence that the 'information' in a genome is not so much 'encoded onto a chemical chalkboard', or emerged from a material basis as Darwinists presuppose, as it is that the 'transcendent information' itself, separate from, and foundational to, matter and energy, is constraining the matter and energy to be out of 'thermodynamic equilibrium': Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/journals.asp?iid=47 Quantum entanglement holds together life’s blueprint - 2010 Excerpt: “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/ Quantum entanglement helps keep DNA together - June 2010 Excerpt: As it turns out, the size of the DNA helix corresponds rather well to the wavelength (frequency) of the phonons. This correspondence causes the phonons to stay within this frequency, something called ‘phonon trapping.’ Though the nucleotide phonons in each base pair oscillate in opposite directions they do so in a quantum entangled system – they act together and at the same frequency, ensuring the stability of the pair bond and of the helix itself. http://scitechstory.com/2010/06/29/quantum-entanglement-helps-keep-dna-together/ DNA and quantum entanglement - July 2010 Excerpt: That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size. http://kottke.org/10/07/dna-and-quantum-entanglement Does DNA Have Telepathic Properties?-A Galaxy Insight Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn't be able to. Explanation: None, at least not yet.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html It is important to realize just how far detached our understanding is, for this 'chemical impossibility' of what is happening inside DNA, so that it may be clearly understood that there is another more foundational force at work in the DNA, besides, and independent of, matter and energy. Namely Information: Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm The ‘Fourth Dimension’ Of Living Systems https://docs.google.com/document/pub?id=1Gs_qvlM8-7bFwl9rZUB9vS6SZgLH17eOZdT4UbPoy0Y The ID argument from thermodynamics: Excerpt: "energy cannot create CSI (Complex Specified Information)." https://uncommondescent.com/intelligent-design/the-id-argument-from-thermodynamics/#more-9090 Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ etc.. etc.. etc..bornagain77_{January 22, 2011
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When the effect is inactivation through methylation, then I don't think it's wrongheaded to think of it as still the same letter. Certainly organisms have the ability to change back right? To be de-methylated if circumstances change?tragic mishap_{January 22, 2011
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tragic: Getting Over the Code Delusion Excerpt: Not only is DNA “managed” by the spatial dynamism of the nucleus and the complex structural folding and unfolding of the chromatin matrix, but the DNA sequence itself is subject to continual transformation. It happens, for example, that certain nucleotide bases are subject to “DNA methylation” — the attachment of methyl groups. These small chemical entities are said to “tag” or “mark” the affected bases, a highly significant process that occurs selectively and dynamically throughout the entire genome. Words such as “attach,” “tag,” and “mark,” however, are grossly inadequate, suggesting as they do little more than a kind of binary coding function whereby we can classify every nucleotide base simply according to the presence or absence of a methyl group. What this leaves out is the actual qualitative change resulting from the chemical transaction. Part of the problem lies in the mechanistic mindset that looks for the mere aggregation of parts, as if the methyl group and nucleotide base were discrete Lego blocks added together. But wherever chemical bonds are formed or broken, there is a transformation of matter. The result is not just an aggregation or mixture of the substances that came together, but something new, with different qualities and a different constellation of forces. 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.,, etc.. http://www.thenewatlantis.com/publications/getting-over-the-code-delusionbornagain77_{January 22, 2011
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also of interest is just how similar the basic 'DNA gene set' is across widely divergent species, thus strongly suggesting, when taken in conjunction with the previously cited evidence, that the information for such drastic morphological novelty is completely contrary to the 'central Dogma' of 'original' neo-Darwinian thought: More Questions for Evolutionists - August 2010 Excerpt: First of all, we have 65% of the gene number of humans in little old sponges—an organism that appears as far back as 635 million years ago, about as old as you can get [except for bacteria]. This kind of demolishes Darwin’s argument about what he called the pre-Silurian (pre-Cambrian). 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!). Here’s a quote: “It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” (Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.) I want to know, too! https://uncommondescent.com/intelligent-design/more-questions-for-evolutionists/ Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 of related note, the 98% gene similarity number that evolutionists 'dogmatically' give for Man-chimp similarity is probably the most misleading of all the falsehoods to come out of the 'genetic reductionism model' of neo-Darwinism: Chimpanzee? 10-10-2008 - Dr Richard Buggs - research geneticist at the University of Florida ...Therefore the total similarity of the genomes could be below 70%. http://www.idnet.com.au/files/pdf/Chimpanzee.pdf Molecular Biologist Dr. Fazale Rana points out the obvious, and unscientific, bias of Darwinists in this following paper: DNA Comparisons between Humans and Chimps - Fazale Rana Excerpt: It is interesting that when evolutionary biologists discuss genetic comparisons between human and chimpanzee genomes, the fact that, again, as much as 25 percent of the two genomes won’t align receives no mention. Instead, the focus is only on the portions of the genome that display a high-degree of similarity. This distorted emphasis makes the case for the evolutionary connection between humans and chimps seem more compelling than it may actually be. http://www.reasons.org/dna-comparisons-between-humans-and-chimps-response-venema-critique-rtb-human-origins-model-part-2 Moreover, the following 'statistical test' found only a 62% similarity between chimp-human genomes rather than the 95%-98.5% similarity touted by many papers of evolutionists: A simple statistical test for the alleged “99% genetic identity” between humans and chimps - September 2010 Excerpt: The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. https://uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/ Moreover, when scientists did a actual Nucleotide by Nucleotide sequence comparison, to find the 'real world' difference between the genomes of chimps and Humans, they found the difference was even more profound than what Dr. Richard Buggs, or the statistical test, had estimated: Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] http://www.apologeticspress.org/articles/2070 Even this more recent evolution friendly article found the differences in the protein coding genes of the Y chromosome between chimps and Humans to 'differ radically': Recent Genetic Research Shows Chimps More Distant From Humans,,, - Jan. 2010 Excerpt: A Nature paper from January, 2010 titled, "Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content," found that Y chromosomes in humans and chimps "differ radically in sequence structure and gene content," showing "extraordinary divergence" where "wholesale renovation is the paramount theme.",,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,," http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html Chimp and human Y chromosomes evolving faster than expected - Jan. 2010 Excerpt: "The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes. http://www.physorg.com/news182605704.html The evolutionary scientists of the preceding paper offered some evolutionary 'just so' stories of 'dramatically sped up evolution' for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes the evolutionists are required to explain. CHROMOSOME STUDY STUNS EVOLUTIONISTS Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry. http://www.reasons.org/interpreting-genesis/adam-and-eve/chromosome-study-stuns-evolutionistsbornagain77_{January 22, 2011
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also of interest is just how similar the basic 'DNA gene set' is across widely divergent species, thus strongly suggesting, when taken in conjunction with the previously cited evidence, that the information for such drastic morphological novelty is completely contrary to the 'central Dogma' of 'original' neo-Darwinian thought: More Questions for Evolutionists - August 2010 Excerpt: First of all, we have 65% of the gene number of humans in little old sponges—an organism that appears as far back as 635 million years ago, about as old as you can get [except for bacteria]. This kind of demolishes Darwin’s argument about what he called the pre-Silurian (pre-Cambrian). 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!). Here’s a quote: “It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” (Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.) I want to know, too! https://uncommondescent.com/intelligent-design/more-questions-for-evolutionists/ Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 of related note, the 98% gene similarity number that evolutionists 'dogmatically' give for Man-chimp similarity is probably the most misleading of all the falsehoods to come out of the 'genetic reductionism model' of neo-Darwinism: Chimpanzee? 10-10-2008 - Dr Richard Buggs - research geneticist at the University of Florida ...Therefore the total similarity of the genomes could be below 70%. http://www.idnet.com.au/files/pdf/Chimpanzee.pdf Molecular Biologist Dr. Fazale Rana points out the obvious, and unscientific, bias of Darwinists in this following paper: DNA Comparisons between Humans and Chimps - Fazale Rana Excerpt: It is interesting that when evolutionary biologists discuss genetic comparisons between human and chimpanzee genomes, the fact that, again, as much as 25 percent of the two genomes won’t align receives no mention. Instead, the focus is only on the portions of the genome that display a high-degree of similarity. This distorted emphasis makes the case for the evolutionary connection between humans and chimps seem more compelling than it may actually be. http://www.reasons.org/dna-comparisons-between-humans-and-chimps-response-venema-critique-rtb-human-origins-model-part-2 Moreover, the following 'statistical test' found only a 62% similarity between chimp-human genomes rather than the 95%-98.5% similarity touted by many papers of evolutionists: A simple statistical test for the alleged “99% genetic identity” between humans and chimps - September 2010 Excerpt: The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. https://uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/ Post of interest refuting 98% similarity claim: https://uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/#comment-364779 Moreover, when scientists did a actual Nucleotide by Nucleotide sequence comparison, to find the 'real world' difference between the genomes of chimps and Humans, they found the difference was even more profound than what Dr. Richard Buggs, or the statistical test, had estimated: Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] http://www.apologeticspress.org/articles/2070 Even this more recent evolution friendly article found the differences in the protein coding genes of the Y chromosome between chimps and Humans to 'differ radically': Recent Genetic Research Shows Chimps More Distant From Humans,,, - Jan. 2010 Excerpt: A Nature paper from January, 2010 titled, "Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content," found that Y chromosomes in humans and chimps "differ radically in sequence structure and gene content," showing "extraordinary divergence" where "wholesale renovation is the paramount theme.",,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,," http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html Chimp and human Y chromosomes evolving faster than expected - Jan. 2010 Excerpt: "The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes. http://www.physorg.com/news182605704.html The evolutionary scientists of the preceding paper offered some evolutionary 'just so' stories of 'dramatically sped up evolution' for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes the evolutionists are required to explain. CHROMOSOME STUDY STUNS EVOLUTIONISTS Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry. http://www.reasons.org/interpreting-genesis/adam-and-eve/chromosome-study-stuns-evolutionists I find it extremely interesting that the Y chromosome (male chromosome) would have such a pronounced 'signature of individuality' in the human genome since it is clearly one of the primary chromosomes directly involved in overseeing human reproduction of males. A 'reproductive individuality' for humans which, of course, has direct and severe contradictory implications to the Darwinian scenario of human evolution since only the 'reproductive mutations/variations', that manage to 'slip through' the multiple layers of error correction, actually count in any Darwinian scenario. As well, lest human women feel left out, this 'signature of individuality' for humans is not limited to just the male Y chromosome: More Chimp-Human Genome Problems - Cornelius Hunter Excerpt: Even more interesting, at these locations the chimp's genome is quite similar to other primates--it is the human that differs from the rest, not the chimp. (human accelerated regions (HARs). http://darwins-god.blogspot.com/2009/08/more-chimp-human-genome-problems.html Scientific American: The Banality of Evil(ution) - Cornelius Hunter - March 2010 Excerpt: Furthermore, these typos simultaneously must have altered two other genes which overlap with HAR1. That’s right, HAR1 (human accelerated region) lies in a region of overlapping genes. Imagine typing a paragraph which contains one message when read normally and a different message when read backward. Not only must evolution have created all of biology's genetic information, but it composed the information in overlapping prose. Someday evolutionists will figure out how. http://darwins-god.blogspot.com/2010/03/scientific-american-banality-of-evil.htmlbornagain77_{January 22, 2011
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http://www.metacafe.com/watch/4899469/ On this video they talk about changing the cell just by changing chemical conditions, and the DNA remains the same. The first example is a bacteria that can change from amoeba to flagellar just by changing the concentration of potassium. Are they suggesting that all the information required for flagellar assembly is contained in potassium ions?tragic mishap_{January 22, 2011
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Right and I would have thought information like this, which serves the same function as RAM in a computer, would have been responsible for everything regarding differentiation. But like RAM, it's temporary memory. The hard drive must still have all the necessary info on it. Otherwise where would these proteins come from? I'm not a computer engineer so I don't know exactly how RAM works, but I know proteins have a half life in a living cell, and RNAs half life is even shorter. Where do RNAs come from? Where do proteins come from? Just because they are responsible for some temporary memory doesn't mean the info isn't also in the DNA and doesn't ultimately come from there.tragic mishap_{January 22, 2011
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further note: Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing labora...tory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies Many times evolutionists will mention evo-devo (Evolutionary Developmental Biology) to try to support the Darwinian claim that minor changes/mutations to DNA can drive major morphological novelty, yet, in this following comment, from a 2005 Nature review article, evolutionary geneticist Jerry Coyne expressed strong skepticism at the proposed mechanism of 'gene switches' for evo-devo: "The evidence for the adaptive divergence of gene switches is still thin. The best case involves the loss of protective armor and spines in sticklebacks, both due to changes in regulatory elements. But these elements represent the loss of traits, rather than the origin of evolutionary novelties...We now know that Hox genes and other transcription factors have many roles besides inducing body pattern, and their overall function in development - let alone in evolution - remains murky." http://www.evolutionnews.org/2010/06/scott_f_gilbert_developmental035931.html Here is a more thorough critique of evo-devo: Nature's "Gems": Microevolution Meets Microevolution - Casey Luskin - August 2010 http://www.evolutionnews.org/2010/08/nature_gems_microevolution_mee037171.html#more This following video gives a glimpse of this 'higher level' information in action: Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 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/2010/10/response_to_john_wise038811.html "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 DNA: The Alphabet of Life - David Klinghoffer Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell's building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn't there. Instead, "It is as if the 'idea' of the fly (or any other organism) must somehow permeate the genome that gives rise to it." http://www.evolutionnews.org/2009/07/dna_the_alphabet_of_life.htmlbornagain77_{January 22, 2011
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Actually I have to disagree with tragic mishap, jstanley01, for contrary to tragic's claim that,,, 'The epigenome is similar to the histone code but is a slight chemical modification of the DNA itself. So it is still in the DNA.' and this,, 'So DNA is not less important because of epigenetics. It’s actually more.' ,,, There is actually very strong evidence that much of the 'epigenetic' information arises completely outside of the DNA,,, notes: Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488/ “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.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4FJXNG6-1&_user=10&_coverDate=06%2F30%2F2005&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor&view=c&_searchStrId=1273117547&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bfa74d6bb0937402472343daa6bdef8 The Case Against Molecular Reductionism - Rupert Sheldrake and Bruce Lipton - video http://www.metacafe.com/watch/4899469/ New Insights Into How (Adult) Stem Cells Determine What Tissue to Become - August 2010 Excerpt: Within 24 hours of culturing adult human stem cells on a new type of matrix, University of Michigan researchers were able to make predictions about how the cells would differentiate, or what type of tissue they would become.,,, "Our research confirms that mechanical factors are as important as the chemical factors regulating differentiation," Fu said. "The mechanical aspects have, until now, been largely ignored by stem cell biologists." http://www.sciencedaily.com/releases/2010/08/100801190257.htm The Gene Myth, Part II - August 2010 Excerpt: So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous 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. http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html This following video and article are much more clear for explaining exactly why mutations to the DNA do not control Body Plan morphogenesis, since the mutations are the ‘bottom rung of the ladder’ as far as the 'higher levels of the layered information’ of the cell are concerned: Stephen Meyer on Craig Venter, Complexity Of The Cell & Layered Information http://www.metacafe.com/watch/4798685 Getting Over the Code Delusion (Epigenetics) - Talbot - November 2010 - Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism: http://www.thenewatlantis.com/publications/getting-over-the-code-delusion Hopeful monsters,' transposons, and the Metazoan radiation: Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" render these explanations untenable. Paleobiologists Douglas Erwin and James Valentine “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan)." Michael John Denton ..Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bsbornagain77_{January 22, 2011
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It might be instructive to understand that before the discovery of this mechanism, I would have thought that differentiated cells replicated specifically as liver cells, pancreas cells, brain cells, etc because of proteins or maybe microRNAs or snRNAs in the nucleus as it divides. Instead, we now know that differentiation is carried to daughter cells via the DNA. DNA is the most stable carrier of information in the cell because everything else degrades rapidly. If, as a designer, you want information to stick around, the best place to put it is in DNA. So DNA is not less important because of epigenetics. It's actually more. *rollseyes*tragic mishap_{January 22, 2011
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Here's a decent article on it: http://science.jrank.org/pages/48419/Epigenetics.htmltragic mishap_{January 22, 2011
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Methylation of cytosine does a very simple thing. It appears to inactive genes that are highly methylated. Big deal. We knew something like this had to occur because different genes must be active, and the rest not active, in different tissues.tragic mishap_{January 22, 2011
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jstanley01, the epigenome consists primarily of methylated cytosine. In other words, one nucleotide is methylated. The epigenome is similar to the histone code but is a slight chemical modification of the DNA itself. So it is still in the DNA. This apparently justifies all the hyberbole about the "epigenome" for some people.tragic mishap_{January 22, 2011
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Very interesting. Somehow, as a layman, I always assumed the all the information needed to build an organism was "in the DNA." My question would be, where does the information content of the epigenome reside?jstanley01_{January 22, 2011
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Epigenomics is 'piled on' devastation, to what was already devastating evidence against neo-Darwinism: The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer "Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a ve...ry low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion." http://eyedesignbook.com/ch6/eyech6-append-d.html Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681bornagain77_{January 22, 2011
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