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related footnotes on Dr. Axe’s work: Nothing In Molecular Biology Is Gradual – Doug Axe PhD. – video Quote – “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way. – Doug Axe PhD. *******www.metacafe****/watch/5347797/ Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: 2004 Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. *******www.ncbi.nlm.nih.gov/pubmed/15321723 Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. *******www.evolutionnews****/2010/06/doug_axe_knows_his_work_better035561.html The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010 Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.” *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 Not only are functional proteins found to be extremely rare, thus undermining Darwinian presuppositions, but, as Dr. Axe pointed out in the OP video, the transition of any existent functional protein to a protein of a different function, by unguided Darwinian processes, is found to be of extreme, prohibitive, difficulty as well. The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway – Ann K. Gauger and Douglas D. Axe – April 2011 Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1 When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. *******www.biologicinstitute****/post/18022460402/when-theory-and-experiment-collide “Biologist Douglas Axe on Evolution’s (non) Ability to Produce New (Protein) Functions ” – video Quote: It turns out once you get above the number six [changes in amino acids] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth. *******intelligentdesign.podomatic****/entry/2012-10-15T16_05_14-07_00 The Real Barrier to Unguided Human Evolution – Dr. Ann Gauger – April 25, 2012 Excerpt: Their results? They calculated it would take six million years for a single base change to match the target and spread throughout the population, and 216 million years to get both base changes necessary to complete the eight base binding site. Note that the entire time span for our evolution from the last common ancestor with chimps is estimated to be about six million years. Time enough for one mutation to occur and be fixed, by their account. To be sure, they did say that since there are some 20,000 genes that could be evolving simultaneously, the problem is not impossible. But they overlooked this point. Mutations occur at random and most of the time independently, but their effects are not independent. (Random) Mutations that benefit one trait (are shown to) inhibit another (Negative Epistasis; Lenski e-coli after 50,000 generations). *******www.evolutionnews****/2012/04/the_real_barrie058951.html More from Dr. Ann Gauger on why humans didn’t happen the way Darwin said – July 2012 Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. *******www.uncommondescent****/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/ There is also very good, indeed overwhelming, evidence as to why we should expect such severe constraint on the ability of proteins to mutate, step by step, amino acid by amino acid, from one function to another different function. Proteins are shown to be ‘context dependent’, meaning that the entirety of the amino acid sequence of a protein domain is involved in a specific function and is not built up gradually. The following notes flesh this ‘context dependent’ characteristic of proteins out: Why Proteins Aren’t Easily Recombined, Part 2 – Dr. Ann Gauger - May 17, 2012 Excerpt: In other words, even if only 10% of non-matching residues were changed, the resulting hybrid enzyme no longer functioned. Why? Because the substitution of different amino acids into the existing protein structure destabilized the fold, even though those same amino acids worked well in another context. Thus, each protein’s amino acid sequence works as a whole to help generate a proper stable fold, in a context-dependent fashion. *******www.evolutionnews****/2012/05/why_proteins_ar_1059771.html As well, functional proteins have now been shown to have a ‘Cruise Control’ mechanism, along the entirety of a protein structure, which works to ‘self-correct’ the integrity of a entire protein structure from any random mutations imposed on it. Proteins with cruise control provide new perspective: 2008 “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” *******www.princeton.edu/main/news/archive/S22/60/95O56/ Cruise Control permeating the whole of the protein structure??? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced mathematical information must somehow ‘transcendentally permeate’ along the entirety of a protein structure, in order to achieve such control of the overall protein structure. This fact gives us clear evidence that there is far more functional information permeating proteins than meets the eye than simple rarity of amino acid sequences reveals (Szostak). Moreover this ‘oneness’ of cruise control, within the protein structure, can only ‘rationally’ be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism! For a sample of the equations that must be dealt with, to ‘engineer’ even a simple process control loop like cruise control for a single protein, please see this following site: PID controller A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. *******en.wikipedia****/wiki/PID_controller It is in realizing the staggering level of engineering that must be dealt with, i.e. ‘intelligently designed’ beforehand, in order to achieve ‘cruise control’ for each individual protein, along the entirety of the protein structure, that it becomes apparent that Axe’s 1 in 10^77 estimate for rarity of finding specific functional proteins within ‘sequence space’ is, in all likelihood, far, far too generous. In fact the probabilities over various ‘specific’ configurations of amino acids within sequence space, which have been one of the primary arguments against neo-Darwinism thus far, simply do not even apply, at all, since the ’cause’ for the ‘non-local quantum information effect’ within proteins does not even reside within the material particles in the first place (i.e. falsification of local realism; (Einstein, Bohr, Bell, Wheeler, Aspect, Zeilinger). The following footnotes are further corroborating evidence that ‘protein specific’ quantum information/entanglement resides along/within the entirety of a functional protein amino acid chain constraining the chain to a specific function: Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. ********www.scimednet****/sapphire/main.php?url=/quantum-coherence-living-cells-and-protein/ Myosin Coherence Excerpt: Absorbance (and emission) of frequency specific radiation (e.g. photosynthesis, vision, [biophotons]..), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects. *******www.energetic-medicine****/bioenergetic-articles/articles/63/1/Myosin-Coherence/Page1.html Cellular Communication through Light Excerpt: Information transfer is a life principle. On a cellular level we generally assume that molecules are carriers of information, yet there is evidence for non-molecular information transfer due to endogenous coherent light. This light is ultra-weak, is emitted by many organisms, including humans and is conventionally described as biophoton emission. *******www.plosone****/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005086 The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems – May 2012 Excerpt: From the energy spectra, it was determined that the protein molecules could both radiate and absorb bio-photons with wavelengths of <3??m and 5–7??m, consistent with the energy level transitions of the excitons.,,, *******jap.aip****/resource/1/japiau/v111/i9/p093519_s1?isAuthorized=no Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. *******www.technologyreview****/view/423087/physicists-discover-quantum-law-of-protein/ As to the ‘minor problem' of protein folding itself: “Blue Gene’s final product, due in four or five years, will be able to “fold” a protein made of 300 amino acids, but that job will take an entire year of full-time computing.” Paul Horn, senior vice president of IBM research, September 21, 2000 *******www.news****/2100-1001-233954.html Networking a few hundred thousand computers together has reduced the time to a few weeks for simulating the folding of a single protein molecule: A Few Hundred Thousand Computers vs. A Single Protein Molecule – video *******www.metacafe****/watch/4018233 Not only are amino acid sequences of proteins shown to be ‘context dependent’ on the specific function of the protein, but, it turns out, that the function of the protein itself, in many cases, is context dependent on the specific function of the cell that a protein may be residing in: The Complexity of Gene Expression, Protein Interaction, and Cell Differentiation – Jill Adams, Ph.D. – 2008 Excerpt: it seems that a single protein can have dozens, if not hundreds, of different interactions,,, In a commentary that accompanied Stumpf’s article, Luis Nunes Amaral (2008) wrote, “These numbers provide a sobering view of where we stand in our cataloging of the human interactome. At present, we have identified less than 0.3% of all estimated interactions among human proteins. We are indeed at the dawn of systems biology.” *******www.nature****/scitable/topicpage/the-complexity-of-gene-expression-protein-interaction-34575 Human Genes: Alternative Splicing Far More Common Than Thought: – 2008 Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. *******www.sciencedaily****/releases/2008/11/081102134623.htm Simplest Microbes More Complex than Thought – Dec. 2009 Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes.” *******www.creationsafaris****/crev200912.htm#20091229a Insight into cells could lead to new approach to medicines – 2010 Excerpt: Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web. Dr Victor Neduva, of the University of Edinburgh, who took part in the study, said: “Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought. *******www.physorg****/news196402353.html Supplemental notes: Wheel of Fortune: New Work by Thornton’s Group Supports Time-Asymmetric Dollo’s Law – Michael Behe – October 5, 2011 Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection. *******www.evolutionnews****/2011/10/wheel_of_fortune_new_work_by_t051621.html Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, *******www.ncbi.nlm.nih.gov/pubmed/19765975 Corticosteroid Receptors in Vertebrates: Luck or Design? – Ann Gauger – October 11, 2011 Excerpt: if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start. *******www.evolutionnews****/2011/10/luck_or_design051801.html “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) “A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble.” Problems in Protein Evolution: Here are further notes that support the position that existing functional proteins are severely constrained in their ability to mutate step by step into new functions: 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. *******www.reasons****/articles/fyi-i.d.-in-dna-deciphering-design-in-the-genetic-code As well, the ‘errors/mutations’ that are found to occur in protein sequences are found to be ‘regulated errors’: Cells Defend Themselves from Viruses, Bacteria With Armor of Protein Errors – Nov. 2009 Excerpt: These “regulated errors” comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed, *******www.sciencedaily****/releases/2009/11/091125134701.htm In fact there is little hope of a truly random (i.e. Darwinian) mutation ever making it through the gauntlet of the ribosome: The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.
16 Oct 2012
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Evolution vs. Functional Proteins - Doug Axe - Video *******www.youtube****/watch?v=M4FvdOxIDfU Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. *******www.ncbi.nlm.nih.gov/pubmed/15321723 The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009 To focus the scientific communitys attention on its own tendencies toward overzealous metaphysical imagination bordering on wish-fulfillment, we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration. *******www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2662469 *******mdpi****/1422-0067/10/1/247/ag Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/
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Entire video: Wonders of the Cell - Chris Ashcraft *******www.youtube****/watch?v=OQks3COscX4 Electron Microscope Photograph of Flagellum Hook-Basal Body *******www.skeptic****/eskeptic/08-08-20images/figure03.jpg Bacterial Flagellum: Visualizing the Complete Machine In Situ Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus. *******www.sciencedirect****/science?_ob=ArticleURL&_udi=B6VRT-4M8WTCF-K&_user=10&_coverDate=11%2F07%2F2006&_rdoc=1&_fmt=full&_orig=search&_cdi=6243&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=8d7e0ad266148c9d917cf0c2a9d12e82&artImgPref=F Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video *******www.metacafe****/watch/3994630 Biologist Howard Berg at Harvard calls the Bacterial Flagellum “the most efficient machine in the universe." I would like to reiterate, Darwinism postulated a very simple first cell, yet the simplest cell scientists have been able to find on earth, which can't even be seen with the naked eye, is vastly more complex than any machine man has ever made through concerted effort. This is self evident since a cell can self-replicate with seeming ease whereas a machine cannot. This following site has a interactive graph that lets people look into this 'invisible' world of microbes: CELL TO CARBON ATOM - SIZE AND SCALE - Interactive Graph - Move cursor at the bottom of graph to the right to reduce the size: *******learn.genetics.utah.edu/content/begin/cells/scale/ The smallest cyano-bacterium known to science has hundreds of millions of individual atomic molecules (not counting water molecules), divided into nearly a thousand completely distinct atomic molecule types; and a genome (DNA sequence) of 1.8 million bits, with over a million individual protein molecules which are sub-divided into hundreds of distinct protein classes. Once again, the complexity found in the simplest bacterium known to science easily outclasses the complexity of any machine man has made. These following articles and videos make this point clear: "The manuals needed for building the entire space shuttle and all its components and all its support systems would be truly enormous! Yet the specified complexity (information) of even the simplest form of life - a bacterium - is arguably as great as that of the space shuttle." J.C. Sanford - Geneticist - Genetic Entropy and the Mystery Of the Genome 'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica." Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894 of note: The 10^12 bits of information number for a bacterium is derived from entropic considerations, which is, due to the tightly integrated relationship between information and entropy, considered the most accurate measure of the transcendent information present in a 'simple' life form. For calculations please see the following site: Molecular Biophysics – Information theory. Relation between information and entropy: *******www.astroscu.unam.mx/~angel/tsb/molecular.htm Ben Stein - EXPELLED - The Staggering Complexity Of The Cell - video *******www.metacafe****/watch/4227700 “Although the tiniest living things known to science, bacterial cells, are incredibly small (10^-12 grams), each is a veritable micro-miniaturized factory containing thousands of elegantly designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world”. Michael Denton, "Evolution: A Theory in Crisis," 1986, p. 250. Nanoelectronic Transistor Combined With Biological Machine Could Lead To Better Electronics: - Aug. 2009 Excerpt: While modern communication devices rely on electric fields and currents to carry the flow of information, biological systems are much more complex. They use an arsenal of membrane receptors, channels and pumps to control signal transduction that is unmatched by even the most powerful computers. *******www.sciencedaily****/releases/2009/08/090811091834.htm The Cell as a Collection of Protein Machines "We have always underestimated cells. Undoubtedly we still do today,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each which is composed of a set of large protein machines." Bruce Alberts: Former President, National Academy of Sciences; *******www.imbb.forth.gr/people/aeconomou/documents/Alberts98.pdf The Cell - A World Of Complexity Darwin Never Dreamed Of - Donald E. Johnson - video *******www.metacafe****/watch/4139390 Entire video: *******www.ideaclubtcw****/video/DEJohnson.html Bioinformatics: The Information in Life - Donald Johnson - video *******vimeo****/11314902 On a slide in the preceding video, entitled 'Information Systems In Life', Dr. Johnson points out that: * the genetic system is a pre-existing operating system; * the specific genetic program (genome) is an application; * the native language has codon-based encryption system; * the codes are read by enzyme computers with their own operating system; * each enzyme’s output is to another operating system in a ribosome; * codes are decrypted and output to tRNA computers; * each codon-specified amino acid is transported to a protein construction site; and * in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life. Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." *******www.sciencedaily****/releases/2009/06/090616103205.htm 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." *******www.nature****/nature/journal/v460/n7253/full/460415a.html Simulations reveal new information about the gateway to the cell nucleus Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,"... *******www.psc.edu/science/2006/schulten/ Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. *******creationsafaris****/crev201002.htm#20100226a This stunning energy efficiency of a cell is found across all life domains, thus strongly suggesting that all life on earth was Intelligently Design for maximal efficiency instead of accidentally, and gradually, evolved: Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum Excerpt: Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet—from bacteria to elephants, and algae to sapling trees—we show that metabolism displays a striking degree of homeostasis across all of life. *******www.ncbi.nlm.nih.gov/pmc/articles/PMC2572558/ Also of interest is that a cell apparently seems to be successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers: Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, *******www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf Further quotes on the unmatched complexity of the cell: “Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours" Geneticist Michael Denton PhD. Evolution: A Theory In Crisis pg. 329 "To grasp the reality of life as it has been revealed by molecular biology, we must first magnify a cell a thousand million times until it is 20 kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would see then would be an object of unparalleled complexity,...we would find ourselves in a world of supreme technology and bewildering complexity." Geneticist Michael Denton PhD., Evolution: A Theory In Crisis, pg.328 Building a Cell: Staggering Complexity: - Feb. 2010 Excerpt: “All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 10^9 base pairs) of DNA when each cell divides,” “,,,the segregation machinery must function with far greater accuracy than man-made machines and with an exquisitely soft touch to prevent the DNA strands from breaking.” Bloom and Joglekar talked “machine language” over and over. The cell has specialized machines for all kinds of tasks: segregation machines, packaging machines, elaborate machines, streamlined machines, protein translocation machines, DNA-processing machines, DNA-translocation machines, robust macromolecular machines, accurate machines, ratchets, translocation pumps, mitotic spindles, DNA springs, coupling devices, and more. The authors struggle to “understand how these remarkable machines function with such exquisite accuracy.” *******www.creationsafaris****/crev201002.htm#20100202a Here is a good article that came out in GN magazine in Nov. 2009: 10 Ways Darwin Got It Wrong Excerpt: As molecular biologist Jonathan Wells and mathematician William Dembski point out: “It’s true that eukaryotic cells are the most complicated cells we know. But the simplest life forms we know, the prokaryotic cells (such as bacteria, which lack a nucleus), are themselves immensely complex.,,, There is no evidence whatsoever of earlier, more primitive life forms from which prokaryotes might have evolved” (How to Be an Intellectually Fulfilled Atheist (or Not), 2008, p. 4). These authors then mention what these two types of cells share in terms of complexity: • Information processing, storage and retrieval. • Artificial languages and their decoding systems. • Error detection, correction and proofreading devices for quality control. • Digital data-embedding technology. • Transportation and distribution systems. • Automated parcel addressing (similar to zip codes and UPS labels). • Assembly processes employing pre-fabrication and modular construction. • Self-reproducing robotic manufacturing plants. So it turns out that cells are far more complex and sophisticated than Darwin could have conceived of. How did mere chance produce this, when even human planning and engineering cannot? *******www.gnmagazine****/issues/gn85/10-ways-darwin-wrong.htm There simply is no "simple life" on earth as materialism had presumed - even the well known single celled amoeba has the complexity of the city of London and reproduces that complexity in only 20 minutes. The inner life of a cell - Harvard University - video *******www.youtube****/watch?v=mbcWGU8fpxA User's guide to the video *******sparkleberrysprings****/innerlifeofcell.html Here is a fairly simple to understand basic overview of the cell: How the Body Works: The Cell - video *******www.youtube****/watch?v=NiiLS_ovLwM Map Of Major Metabolic Pathways In A Cell - Diagram *******www.sigmaaldrich****/img/assets/4202/MetabolicPathways_6_17_04_.pdf Metabolism: A Cascade of Design Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. *******www.reasons****/metabolism-cascade-design Making the Case for Intelligent Design More Robust Excerpt: ,,, In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites. *******www.reasons****/making-case-intelligent-design-more-robust Wonders of the Cell - 2008 - Christopher Wayne Ashcraft - video *******video.google****/videoplay?docid=-509988235357380896 Primary Cilium As Cellular 'GPS System' Crucial To Wound Repair Excerpt: The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations. "What we are dealing with is a physiological analogy to the GPS system with a coupled autopilot that coordinates air traffic or tankers on open sea," *******www.sciencedaily****/releases/2008/12/081217190330.htm Mere Biochemistry: Cell Division Involves Thousands of Complex, Interacting Parts - September 2010 *******www.creationsafaris****/crev201009.htm#20100925a Astonishingly, actual motors, which far surpass man-made motors in 'engineering parameters', are now being found inside 'simple cells'. Articles and Videos on Molecular Motors *******docs.google****/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Michael Behe - Life Reeks Of Design - 2010 - video *******www.metacafe****/watch/5066181 And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines *******www.metacafe****/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology What I find very persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the 'near optimal' capacities allowed in any physical system: William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," *******www.princeton.edu/~wbialek/wbialek.html Physicists Finding Perfection… in Biology — June 1st, 2009 by Biologic Staff Excerpt: "biological processes tend to be optimal in cases where this can be tested." *******biologicinstitute****/2009/06/01/physicists-finding-perfection-in-biology/ Also of note: There is a fairly substantial economic payoff to be had for presupposing superior 'Intelligent Design' in life, as is testified to by the burgeoning field of Biomimicry: Biomimicry - Superior Designs That Were Found In Life *******docs.google****/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfNDBkZ3Nwcnd0Yw&hl=en Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
8 Jan 2011
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6:05
The Cell - A World Of Complexity Darwin Never Dreamed Of - Donald E. Johnson - video *******www.metacafe****/watch/4139390 Articles and Videos on Molecular Motors *******docs.google****/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." *******www.sciencedaily****/releases/2009/06/090616103205.htm 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." *******www.nature****/nature/journal/v460/n7253/full/460415a.html Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" *******www.biomedcentral****/content/pdf/1742-4682-2-29.pdf Simulations reveal new information about the gateway to the cell nucleus Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,"... *******www.psc.edu/science/2006/schulten/ Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. *******creationsafaris****/crev201002.htm#20100226a “Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours" Geneticist Michael Denton PhD. Evolution: A Theory In Crisis pg. 329 "To grasp the reality of life as it has been revealed by molecular biology, we must first magnify a cell a thousand million times until it is 20 kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would see then would be an object of unparalleled complexity,...we would find ourselves in a world of supreme technology and bewildering complexity." Geneticist Michael Denton PhD., Evolution: A Theory In Crisis, pg.328 Michael Behe - Life Reeks Of Design - 2010 - video *******www.metacafe****/watch/5066181 And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject. James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines *******www.metacafe****/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. *******www.evolutionnews****/2010/06/doug_axe_knows_his_work_better035561.html Evolution vs. Functional Proteins - Doug Axe - Video *******www.metacafe****/watch/4018222 Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
31 Jul 2011
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4:57
Design without a Designer? — December 9th, 2009 by Douglas Axe Excerpt: For one protein subjected to this kind of experiment, the conclusion was that working sequences are as rare as one in a trillion trillion trillion trillion trillion trillion. In other words, they are unimaginably rare— far too rare to be stumbled upon by any unguided search, such as a Darwinian search. Notice that this isn't a negative result in the sense of an unsuccessful attempt to measure something. The measurement was successful. Some will still see it as a negative result in that it precludes unguided searches. But since we do in fact encounter meaningful sentences every day, we know that intelligence is fully capable of producing what chance simply cannot produce. So we ought also to see this as a positive result— one that confirms the design explanation just as decisively as it refutes the Darwinian one. *******biologicinstitute****/2009/12/09/design-without-a-designer/ Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005: *******www.ncbi.nlm.nih.gov/pubmed/15716009 John 1:1-3 In the beginning, the Word existed. The Word was with God, and the Word was God. He was with God in the beginning Through him all things were made; without him nothing was made that has been made. (of note: "Word" in Greek is "Logos", and is the root word from which we get our word "Logic") Darwin's Dilemma Trailer - Excellent Cambrian Explosion Movie Now Available On DVD - Sept. 2009 *******www.illustramedia****/ddinfo.htm Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. (of note: the universe only has 10^80 sub-atomic particles) *******www.ncbi.nlm.nih.gov/pubmed/15321723 A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells Excerpt: "Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division." *******www.plosone****/article/info:doi%2F10.1371%2Fjournal.pone.0007385 Evolution vs ATP Synthase - Molecular Machine - video *******www.youtube****/watch?v=qE3QJMI-ljc Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its new duties. It is at this point it will be destroyed - along with the organism carrying it. Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) The Ribosome, which makes the proteins, is found to be severely intolerant to any "random mutations". The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. *******www.sciencedaily****/releases/2009/01/090107134529.htm Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/
9 Feb 2010
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5:59
Evolution vs. Functional Proteins - Doug Axe - Darwin's Dilemma Video Clip *******www.metacafe****/watch/4018222 Here are the papers Dr. Axe speaks of at the end of his video: Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. *******www.ncbi.nlm.nih.gov/pubmed/15321723 Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Suppose a secretive organization has a large network of computers, each secured with a unique 39-character password composed from the full 94-charater set of ASCII printable characters. Unless serious mistakes have been made, these passwords would be much uglier than any you or I normally use (and much more secure as a result). Try memorizing this: C0$lhJ#9Vu]Clejnv%nr&^n2]B!+9Z:n`JhY:21 Now, if someone were to tell you that these computers can be hacked by the thousands through a trial-and-error process of guessing passwords, you ought to doubt their claim instinctively. But you would need to do some math to become fully confident in your skepticism. Most importantly, you would want to know how many trials a successful hack is expected to require, on average. Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. *******www.evolutionnews****/2010/06/doug_axe_knows_his_work_better035561.html The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio *******intelligentdesign.podomatic****/player/web/2010-05-03T11_09_03-07_00 Here is a fairly good defense of the rarity of protein folds, from a blogger called gpuccio, from the best Darwinian objections that could be mustered against it: *******www.uncommondescent****/darwinism/media-mum-about-deranged-darwinist-gunman/#comment-363452 Conservation of Information in Search: Measuring the Cost of Success - Dembski - Marks - 2009 *******evoinfo****/publications/cost-of-success-in-search/ Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’’ (Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘‘is 5 million times larger than the calculation we have just given’’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. *******www.discovery****/a/9461 Stephen Meyer - Functional Proteins And Information For Body Plans - video *******www.metacafe****/watch/4050681 This following video is a bit 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 *******www.metacafe****/watch/4798685 Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
28 Sep 2010
3172
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9:57
This following video is very good, for it uses the mathematical equations used by leading evolutionists themselves, for population genetics, to show that the evolution of whales is impossible even by their own methods of predicting change: Whale Evolution Vs. Population Genetics - Richard Sternberg PhD. in Evolutionary Biology - video *******www.metacafe****/watch/4165203 Perhaps one of the most egregious violations to common sense, by the evolutionists, is the evolutionists claim that whales evolved from a terrestrial (land dwelling) mammal in a mere 10 million years. These following videos and articles expose a few of their violations of logic: Whale Evolution? - Exposing The Deception - Dr. Terry Mortenson - video *******www.metacafe****/watch/4032568 This following study provides solid support for Dr. Terry Mortenson's critique in the preceding video: How Whales Have (NOT) Changed Over 35 Million Years – May 2010 Excerpt: We could have found that the main whale lineages over time each experimented with being large, small and medium-sized and that all the dietary forms appeared throughout their evolution, or that whales started out medium-sized and the largest and smallest ones appeared more recently—but the data show none of that. Instead, we find that the differences today were apparent very early on. *******www.uncommondescent****/education/beacon-comes-home-with-the-bacon/#comment-356170 This following sites is a bit more detailed in their dismantling of the whale evolution myth: Whale Tale Two Excerpt: We think that the most logical interpretation of the Pakicetus fossils are that they represent land-dwelling mammals that didn’t even have teeth or ears in common with modern whales. This actually pulls the whale evolution tree out by the roots. Evolutionists are back to the point of not having any clue as to how land mammals could possibly have evolved into whales. *******www.ridgecrest.ca.us/~do_while/sage/v6i2f.htm "Whales have a long generation time, and they don't have huge populations. They're like the worst-case scenario for trying to evolve structures rapidly," "To fix all the mutations needed to convert a little land mammal into a fully functional whale [in ten million years]--mathematically that's totally not possible." Casey Luskin *******www.evolutionnews****/2009/11/6_bones_of_contention_with_nat.html#more Whale Evolution? Darwinist 'Trawlers' Have Every Reason To Be Concerned: Excerpt: As one review noted: "The anatomical structure, biological function, and way of life of whales are so distinctly different from those of terrestrial mammals that they cannot possibly have evolved from the latter by small genetic changes; aquatics require the simultaneous presence of all their complex features to survive." *******www.arn****/blogs/index.php/2/2009/12/29/whale_evolution_darwinist_trawlers_have This following video takes a honest look at just what evolutionists are up against to satisfactorily explain whale evolution: What Does It take To Change A Cow Into A Whale - David Berlinski - video *******www.youtube****/watch?v=DRqdvhL3pgM Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’’ (Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘‘is 5 million times larger than the calculation we have just given’’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. *******www.discovery****/a/9461 Stephen Meyer - Functional Proteins And Information For Body Plans - video *******www.metacafe****/watch/4050681 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio *******intelligentdesign.podomatic****/player/web/2010-05-03T11_09_03-07_00 Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
28 Sep 2010
3172
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9:53
Stephen Meyer - Functional Proteins And Information For Body Plans - video *******www.metacafe****/watch/4050681 This following video is a bit 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 *******www.metacafe****/watch/4798685 Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video *******www.metacafe****/watch/4187488 This lack of beneficial morphological novelty also includes the highly touted four-winged fruit fly mutations: ...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 *******www.evolutionnews****/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video *******www.youtube****/watch?v=hZJTIwRY0bs Many times evolutionists will mention evo-devo (Evolutionary Developmental Biology), or HOX genes, 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." *******www.evolutionnews****/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 *******www.evolutionnews****/2010/08/nature_gems_microevolution_mee037171.html#more As well, recent 'cloning studies' give evidence against DNA/Genetic reductionism: "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 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio *******intelligentdesign.podomatic****/player/web/2010-05-03T11_09_03-07_00 Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
28 Sep 2010
655
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8:17
Stephen Meyer - Functional Proteins And Information For Body Plans - video *******www.metacafe****/watch/4050681 This following video is a bit 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 *******www.metacafe****/watch/4798685 Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video *******www.metacafe****/watch/4187488 This lack of beneficial morphological novelty also includes the highly touted four-winged fruit fly mutations: ...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 *******www.evolutionnews****/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video *******www.youtube****/watch?v=hZJTIwRY0bs Many times evolutionists will mention evo-devo (Evolutionary Developmental Biology), or HOX genes, 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." *******www.evolutionnews****/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 *******www.evolutionnews****/2010/08/nature_gems_microevolution_mee037171.html#more As well, recent 'cloning studies' give evidence against DNA/Genetic reductionism: "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 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio *******intelligentdesign.podomatic****/player/web/2010-05-03T11_09_03-07_00 Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
28 Sep 2010
866
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6:47
Animators website: Virtual Cell Animation Collection *******vcell.ndsu.edu/animations/home.htm The Cell as a Collection of Protein Machines "We have always underestimated cells. Undoubtedly we still do today,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each which is composed of a set of large protein machines." Bruce Alberts: Former President, National Academy of Sciences; *******www.imbb.forth.gr/people/aeconomou/documents/Alberts98.pdf Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video *******www.metacafe****/watch/4261990/ Simulations reveal new information about the gateway to the cell nucleus Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,"... *******www.psc.edu/science/2006/schulten/ Nuclear pore: Excerpt: Nuclear pores allow the transport of water-soluble molecules across the nuclear envelope. This transport includes RNA and ribosomes moving from nucleus to the cytoplasm and proteins (such as DNA polymerase and lamins), carbohydrates, signal molecules and lipids moving into the nucleus. It is notable that the nuclear pore complex (NPC) can actively conduct 1000 translocations per complex per second. *******en.wikipedia****/wiki/Nuclear_pore#Transport_through_the_nuclear_pore_complex The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video *******www.metacafe****/watch/4060532 "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.) The coding system used for living beings is optimal from an engineering standpoint. Werner Gitt - In The Beginning Was Information - p. 95 Collective evolution and the genetic code - 2006: Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving. *******www.pnas****/content/103/28/10696.full Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes.... the present findings support the view that protein-coding regions can carry abundant parallel codes. *******genome.cshlp****/content/17/4/405.full The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (12 different ways of DNA transcription) (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford - Genetic Entropy Do you believe Richard Dawkins exists? Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives. *******creation****/does-dawkins-exist Journey Inside The Cell (DNA to RNA to Protein)- Stephen Meyer - video *******www.youtube****/watch?v=1fiJupfbSpg BioVisions - The Inner Life of the Cell - video *******vimeo****/14691840 User's guide to the video *******sparkleberrysprings****/innerlifeofcell.html Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” *******www.creationsafaris****/crev200910.htm#20091015a The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. *******www.sciencedaily****/releases/2009/01/090107134529.htm RNA: Protein Regulators Are Themselves Regulated “What was formerly conceived of as a direct, straightforward pathway is gradually turning out to be a dense network of regulatory mechanisms: genes are not simply translated into proteins via mRNA (messenger RNA). MicroRNAs control the translation of mRNAs (messenger RNAs) into proteins, and proteins in turn regulate the microRNAs at various levels.” *******www.sciencedaily****/releases/2009/09/090910084147.htm The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." *******bio-complexity****/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio *******intelligentdesign.podomatic****/player/web/2010-05-03T11_09_03-07_00 A Few Hundred Thousand Computers vs. A Single Protein Molecule - video *******www.metacafe****/watch/4018233 "The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution") Nature Paper,, Finds Darwinian Processes Lacking - Michael Behe - Oct. 2009 Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites) *******www.evolutionnews****/2009/10/nature_paper_finally_reaches_t.html Mitochondria - Molecular Machine - Powerhouse Of The Cell - video *******www.metacafe****/watch/5510941/ Evolution Vs ATP Synthase - Molecular Machine - video *******www.metacafe****/watch/4012706/ The Cell - A World Of Complexity Darwin Never Dreamed Of - Donald E. Johnson - video *******www.metacafe****/watch/4139390 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." *******www.nature****/nature/journal/v460/n7253/full/460415a.html 10 Ways Darwin Got It Wrong Excerpt: As molecular biologist Jonathan Wells and mathematician William Dembski point out: “It’s true that eukaryotic cells are the most complicated cells we know. But the simplest life forms we know, the prokaryotic cells (such as bacteria, which lack a nucleus), are themselves immensely complex.,,, There is no evidence whatsoever of earlier, more primitive life forms from which prokaryotes might have evolved” (How to Be an Intellectually Fulfilled Atheist (or Not), 2008, p. 4). These authors then mention what these two types of cells share in terms of complexity: • Information processing, storage and retrieval. • Artificial languages and their decoding systems. • Error detection, correction and proofreading devices for quality control. • Digital data-embedding technology. • Transportation and distribution systems. • Automated parcel addressing (similar to zip codes and UPS labels). • Assembly processes employing pre-fabrication and modular construction. • Self-reproducing robotic manufacturing plants. So it turns out that cells are far more complex and sophisticated than Darwin could have conceived of. How did mere chance produce this, when even human planning and engineering cannot? *******www.gnmagazine****/issues/gn85/10-ways-darwin-wrong.htm Quantum Mechanics at Work in Photosynthesis: Algae Familiar With These Processes for Nearly Two Billion Years - Feb. 2010 Excerpt: "We were astonished to find clear evidence of long-lived quantum mechanical states involved in moving the energy. Our result suggests that the energy of absorbed light resides in two places at once -- a quantum superposition state, or coherence -- and such a state lies at the heart of quantum mechanical theory.",,, "It suggests that algae knew about quantum mechanics nearly two billion years before humans," says Scholes. *******www.sciencedaily****/releases/2010/02/100203131356.htm Quantum Information/Entanglement In DNA & Protein Folding - short video *******www.metacafe****/watch/5936605/ Further evidence that quantum entanglement/information is found throughout entire protein structures: *******www.uncommondescent****/intelligent-design/rescue-proteins-leave-evolutionists-in-the-ditch/#comment-373214 It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ is completely transcendent of any time and space constraints (Alain Aspect), should be found in molecular biology, for how can quantum entanglement, in molecular biology, possibly be explained by the materialistic framework of neo-Darwinism, a framework which is predicated on the presupposition of being constrained by time and space, when Alain Aspect and company falsified the validity of local realism (reductive materialism) in the first place with quantum entanglement? It is simply ludicrous to appeal to the materialistic framework, which undergirds the entire neo-Darwinian framework, that has been falsified by the very same quantum entanglement effect that one is seeking an explanation to! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! Probability arguments, which have been a staple of the arguments against neo-Darwinism, simply do not apply! Further notes: The ‘Fourth Dimension’ Of Living Systems ********docs.google****/document/pub?id=1Gs_qvlM8-7bFwl9rZUB9vS6SZgLH17eOZdT4UbPoy0Y Astonishingly, actual motors, which far surpass man-made motors in 'engineering parameters', are now being found inside 'simple cells'. Articles and Videos on Molecular Motors/Machines *******docs.google****/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Michael Behe - Life Reeks Of Design - 2010 - video *******www.metacafe****/watch/5066181 And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist Intelligent Design - The Anthropic Hypothesis *******lettherebelight-77.blogspot****/2009/10/intelligent-design-anthropic-hypothesis_19.html
11 Mar 2011
2255
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6:03
Neo-Darwinism isn’t ‘science’ because, besides its stunning failure at establishing empirical validation in the lab, it has no mathematical basis, and furthermore neo-Darwinism can have no mathematical basis because of the atheistic insistence for the ‘random’ variable postulate at the base of its formulation: Evolution and the Illusion of Randomness – Talbott – Fall 2011 Excerpt: In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” *******www.thenewatlantis****/publications/evolution-and-the-illusion-of-randomness “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109. Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism - Casey Luskin - February 27, 2012 Excerpt: "In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) - *******www.evolutionnews****/2012/02/nobel_prize-win056771.html “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote as stated in 1973 LSE Scientific Method Lecture “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) Dr. David Berlinski: Head Scratching Mathematicians – video *******www.youtube****/watch?v=hEDYr_fgcP8 quote from preceding video: “John Von Neumann, one of the great mathematicians of the twentieth century, just laughed at Darwinian theory, he hooted at it!” Dr. David Berlinski Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013 Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? *******www.uncommondescent****/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/ Moreover Darwinism isn’t science because math, as far as math is able to be put to Darwinian claims through population genetics, and probability, falsifies Darwinian claims,,, Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. *******www.icr****/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf The Universal Plausibility Metric (UPM) & Principle (UPP) - Abel - Dec. 2009 Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes.",,, cΩu = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108 cΩg = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96 cΩs = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85 cΩe = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70 *******www.tbiomed****/content/6/1/27 Programming of Life - Probability - Defining Probable, Possible, Feasible etc.. - video *******www.youtube****/user/Programmingoflife#p/c/AFDF33F11E2FB840/8/kckv0wVBYpA Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." *******www.creationsafaris****/epoi_c10.htm Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 *******www.vimeo****/11706014 "The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!" (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University) Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number: DID LIFE START BY CHANCE? Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias) *******members.tripod****/~Black_J/chance.html “The statistical probability that organic structures and the most precisely harmonized reactions that typify living organisms would be generated by accident, is zero.” Ilya Prigogine, Gregoire Nicolis, and Agnes Babloyantz, Physics Today 25, pp. 23-28. (Sourced Quote) “The formation within geological time of a human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field, is as unlikely as the separation by chance of the atmosphere into its components.” Kurt Gödel, was a preeminent mathematician/logician who is considered one of the greatest to have ever lived. Of Note: Godel was a Christian Theist! In Barrow and Tippler's book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God. William Lane Craig William Lane Craig - If Human Evolution Did Occur It Was A Miracle - video *******www.youtube****/watch?v=GUxm8dXLRpA ,,, Yet Darwinists refuse to accept falsification through mathematics.,,, “However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is.” – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years. Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012 Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD. *******www.evolutionnews****/2012/07/thou_shalt_not062351.html Michael Behe on the theory of constructive neutral evolution – February 2012 Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. – Michael Behe “No human investigation can be called true science without passing through mathematical tests.” Leonardo Da Vinci Accounting for Variations – Dr. David Berlinski: – video *******www.youtube****/watch?v=aW2GkDkimkE Moreover neo-Darwinism isn’t science because the random variable postulate at the base of its formulation, when it is pushed to the limits of its explanatory power for our ability to comprehend reality through science, winds up driving the entire enterprise of science into epistemological failure: BRUCE GORDON: Hawking’s irrational arguments – October 2010 Excerpt: What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse – where it is alleged that anything can spontaneously jump into existence without cause – produces a situation in which no absurdity is beyond the pale. For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science. *******www.washingtontimes****/news/2010/oct/1/hawking-irrational-arguments/ The Absurdity of Inflation, String Theory and The Multiverse – Dr. Bruce Gordon – video *******vimeo****/34468027 This ‘lack of a guarantee’, for trusting our perceptions and reasoning in science to be trustworthy in the first place, even extends into evolutionary naturalism (neo-Darwinism) itself; Scientific Peer Review is in Trouble: From Medical Science to Darwinism – Mike Keas – October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga’s nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: “Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not.” Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. *******blogs.christianpost****/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/ Alvin Plantinga – Evolutionary Argument against Naturalism – video *******www.youtube****/watch?v=r34AIo-xBh8 God = ? NYU Questions World-class Philosopher Alvin Plantinga on Science & Religion - March 2012 - video *******www.youtube****/watch?v=7Sp7U9Es3yw Philosopher Sticks Up for God Excerpt: Theism, with its vision of an orderly universe superintended by a God who created rational-minded creatures in his own image, “is vastly more hospitable to science than naturalism,” with its random process of natural selection, he (Plantinga) writes. “Indeed, it is theism, not naturalism, that deserves to be called ‘the scientific worldview.’” *******www.nytimes****/2011/12/14/books/alvin-plantingas-new-book-on-god-and-science.html?_r=1&pagewanted=all “Modern science was conceived, and born, and flourished in the matrix of Christian theism. Only liberal doses of self-deception and double-think, I believe, will permit it to flourish in the context of Darwinian naturalism.” ~ Alvin Plantinga Why No One (Can) Believe Atheism/Naturalism to be True - video Excerpt: "Since we are creatures of natural selection, we cannot totally trust our senses. Evolution only passes on traits that help a species survive, and not concerned with preserving traits that tell a species what is actually true about life." Richard Dawkins - quoted from "The God Delusion" *******www.youtube****/watch?v=N4QFsKevTXs The Unreasonable Effectiveness of Mathematics in the Natural Sciences – Eugene Wigner – 1960 Excerpt: ,,certainly it is hard to believe that our reasoning power was brought, by Darwin’s process of natural selection, to the perfection which it seems to possess.,,, *******www.dartmouth.edu/~matc/MathDrama/reading/Wigner.html
15 Apr 2013
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