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At Biologic Institute, Doug Axe On “Belgian Waffle”

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Over at the Biologic Institute’s blog, Douglas Axe has a new blog post on a recent paper in PLoS Biology:

Under the heading “Reconstruction of prehistoric DNA refutes criticism on theory of evolution,” an article from Ghent University in Belgium claims a recent scientific paper has rescued evolutionary theory by solving the problem of evolutionary innovation. Considering that innovation is the appearance of new things, it would be hard to exaggerate the importance of that problem, or of the rescue (if true).

The article gives the first hint that it might not be true by following the familiar pattern of conceding a problem with Darwinism only to announce that it has now been solved, and then wagging the finger of orthodoxy at those who keep raising it.

Click here to continue reading.

OT: Peter Hitchens is not too shabby in his address either: Peter Hitchens | The God Debate | Oxford Union - video http://www.youtube.com/watch?v=VnIH4gomOqc bornagain77
Well put introduction to this thread as I see it. They admit to a problem only when they think they a answer. Settled that there is a issue here of innovation. Then they point fingers at critics. Again they admit the critics matter. tHis is only since the rise of ID activism. The world is changing before our eyes on origin issues. One could say ID/YEC is leading the agent of change or creativity on ideas about origins. ID/YEc is not just a serious threat but is contributing to investigation even if the investigation is still coming up short of the truth. Robert Byers
Discovering Intelligent Design by Hallie Kemper, Gary Kemper, and Casey Luskin (Forthcoming, 2013). This curriculum presents the scientific evidence for intelligent design in cosmology and biology in an easy-to-understand format. Leading ID-videos are integrated into the textbook. Ideal for home school or private school at the high school level. Scheduled for release in early-2013.
I think I read somewhere that Richard Sternberg is working on a book? Mung
Here’s the concession:
An important unanswered question in Darwin’s theory of evolution is how new characteristics seem to appear out of nowhere.
Hmmm. Yes, I can see how this could be a problem for a theory of biological origins.
/priceless Chance Ratcliff
OT: Professor John Lennox | The God Debate | Oxford Union - video http://www.youtube.com/watch?v=otrqzITuSqE Please note Michael Shermer in the audience bornagain77
OT: More design found in genetic code: A hidden genetic code: Researchers identify key differences in seemingly synonymous parts of the structure - January 21, 2013 Excerpt: (In the Genetic Code) there are 64 possible ways to combine four bases into groups of three, called codons, the translation process uses only 20 amino acids. To account for the difference, multiple codons translate to the same amino acid. Leucine, for example, can be encoded in six ways. Scientists, however, have long speculated whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Harvard researchers have deciphered that second code,,, Under some stressful conditions, the researchers found, certain sequences manufacture proteins efficiently, while others—which are ostensibly identical—produce almost none. "It's really quite remarkable, because it's a very simple mechanism," Subramaniam said. "Many researchers have tried to determine whether using different codons affects protein levels, but no one had thought that maybe you need to look at it under the right conditions to see this.",,, While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological failsafe, allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources. http://phys.org/news/2013-01-hidden-genetic-code-key-differences.html and this from yesterday: 'Quadruple helix' DNA discovered in human cells - January 20, 2013 Excerpt: In 1953, Cambridge researchers Watson and Crick published a paper describing the interweaving 'double helix' DNA structure - the chemical code for all life. Now, in the year of that scientific landmark's 60th Anniversary, Cambridge researchers have published a paper proving that four-stranded 'quadruple helix' DNA structures - known as G-quadruplexes - also exist within the human genome.,,, Physical studies over the last couple of decades had shown that quadruplex DNA can form in vitro - in the 'test tube', but the structure was considered to be a curiosity rather than a feature found in nature. The researchers now know for the first time that they actually form in the DNA of human cells. "This research further highlights the potential for exploiting these unusual DNA structures to beat cancer –,,, "It's been sixty years since its structure was solved but work like this shows us that the story of DNA continues to twist and turn.",,, While quadruplex DNA is found fairly consistently throughout the genome of human cells and their division cycles, a marked increase was shown when the fluorescent staining grew more intense during the 's-phase' - the point in a cell cycle where DNA replicates before the cell divides.,,, It's a philosophical question as to whether they are there by design or not - but they exist and nature has to deal with them.,,, "The 'quadruple helix' DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark." http://phys.org/news/2013-01-quadruple-helix-dna-human-cells.html a few related notes: Synonymous Codons: Another Gene Expression Regulation Mechanism - September 2010 Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,, http://www.creationsafaris.com/crev201009.htm#20100919a Does Life Use a Non-Random Set of Amino Acids? - Jonathan M. - April 2011 Excerpt: The authors compared the coverage of the standard alphabet of 20 amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) drawn randomly from the pool of 50 plausible prebiotic candidates. The results? The authors noted that: "…the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof." http://www.evolutionnews.org/2011/04/does_life_use_a_non-random_set045661.html Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement – 2009 Excerpt: A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. http://pre.aps.org/abstract/PRE/v79/i6/e060901 Deciphering Design in the Genetic Code - Fazale Rana Excerpt: Sixty-four codons make up the genetic code. Because the genetic code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.,,, Genetic code rules incorporate a design that allows the cell to avoid the harmful effects of substitution mutations. For example, six codons encode the amino acid leucine (Leu). If at a particular amino acid position in a polypeptide, Leu is encoded by 5? (pronounced five prime, a marker indicating the beginning of the codon). CUU, substitution mutations in the 3? position from U to C, A, or G produce three new codons, 5? CUC, 5? CUA, and 5? CUG, all of which code for Leu. The net effect produces no change in the amino acid sequence of the polypeptide. For this scenario, the cell successfully avoids the negative effects of a substitution mutation. Likewise, a change of C in the 5? position to a U generates a new codon, 5?UUU, that specifies phenylalanine, an amino acid with similar physical and chemical properties to Leu. A change of C to an A or to a G produces codons that code for isoleucine and valine, respectively. These two amino acids also possess chemical and physical properties similar to leucine. Qualitatively, the genetic code appears constructed to minimize errors that result from substitution mutations.,,, The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution.18 Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of 10^18 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature. http://www.reasons.org/biology/biochemical-design/fyi-id-dna-deciphering-design-genetic-code Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177) The Finely Tuned Genetic Code - Jonathan M. - November 2011 Excerpt: Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: "why is the genetic code the way it is and how did it come to be?," that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology. - Eugene Koonin and Artem Novozhilov http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html "The more we learn about the chemical basis of life and the intricacy of the genetic code, the more unbelievable the standard historical account becomes." - Thomas Nagel - "Mind & Cosmos" Moreover the first DNA code of life on earth had to be at least as complex as the current DNA code found in life: Shannon Information - Channel Capacity - Perry Marshall - video http://www.metacafe.com/watch/5457552/ “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life "A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107." (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.) bornagain77

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