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Michael Yarus and the Thing that Couldn’t Die

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MSTMichael Yarus, an emeritus professor at UColorado,  is one of the leading experts on the RNA World hypothesis, which takes the origin of life as flowing from RNA chemistry. His recent book with Harvard UP, Life from an RNA World, contains lots of material responding to ID, though without basic understanding, to say nothing of nuance.

The reason I bring the book up here, however, is to note his extensive use of Dawkins’ famous METHINKS IT IS LIKE A WEASEL evolutionary computing simulation. Yarus changes the target phrase to NOTHING IN BIOLOGY MAKES SENSE EXCEPT IN THE LIGHT OF EVOLUTION, but the essence of Dawkins’ simulation is nonetheless there in all its glory — indeed, Yarus develops this “instance of evolution” more extensively than Dawkins did. Moreover, Yarus sees this simulation as underwriting the power of evolutionary processes.

Dawkins’ simulation has come under considerable criticism both here at UD and at the Evolutionary Informatics Lab, where we have implemented “WEASEL WARE” (go here). Some internet critics have urged that we are beating a dead horse, that this example was never meant to be taken too seriously, and that if we were “serious scientists,” we would be directing our energies elsewhere. Let me suggest that these critics take up their concerns with Yarus.

The reason we keep bringing up Dawkins’ example is because evolutionists themselves won’t let it die. You can find Yarus’ discussion of it beginning on p. 64 of his book. It is available at Google Books here. Or you can view it below:

Comments
Art, the fact that your comment actually appears here is a good indication of the truth in your sentiments. Whats the matter Art? Is the story of how RNA poofs complexity into existence better told without any critics around?Upright BiPed
June 8, 2010
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notes: Signature In The Cell - Review Excerpt: There is absolutely nothing surprising about the results of these (evolutionary) algorithms. The computer is programmed from the outset to converge on the solution. The programmer designed to do that. What would be surprising is if the program didn't converge on the solution. That would reflect badly on the skill of the programmer. Everything interesting in the output of the program came as a result of the programmer's skill-the information input. There are no mysterious outputs. - Software Engineer - quoted to Stephen Meyer http://www.scribd.com/full/29346507?access_key=key-1ysrgwzxhb18zn6dtju0 A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA – David J D’Onofrio1, Gary An – Jan. 2010 Excerpt: It is also important to note that attempting to reprogram a cell’s operations by manipulating its components (mutations) is akin to attempting to reprogram a computer by manipulating the bits on the hard drive without fully understanding the context of the operating system. (T)he idea of redirecting cellular behavior by manipulating molecular switches may be fundamentally flawed; that concept is predicated on a simplistic view of cellular computing and control. Rather, (it) may be more fruitful to attempt to manipulate cells by changing their external inputs: in general, the majority of daily functions of a computer are achieved not through reprogramming, but rather the varied inputs the computer receives through its user interface and connections to other machines. http://www.tbiomed.com/content/7/1/3 The Capabilities of Chaos and Complexity - David L. Abel - 2009 Excerpt: "A monstrous ravine runs through presumed objective reality. It is the great divide between physicality and formalism. On the one side of this Grand Canyon lies everything that can be explained by the chance and necessity of physicodynamics. On the other side lies those phenomena than can only be explained by formal choice contingency and decision theory—the ability to choose with intent what aspects of ontological being will be preferred, pursued, selected, rearranged, integrated, organized, preserved, and used. Physical dynamics includes spontaneous non linear phenomena, but not our formal applied-science called “non linear dynamics”(i.e. language,information). http://www.mdpi.com/1422-0067/10/1/247/pdf LIFE’S CONSERVATION LAW - William Dembski - Robert Marks - Pg. 13 Excerpt: Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case. http://evoinfo.org/publications/lifes-conservation-law/ and once again Natural Selection is severely intolerant to carrying around functionless junk: Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/content/vp471464014664w8/bornagain77
June 8, 2010
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I must say that there is an unusual absence of darwinist debate on this thread. Anybody wants to defend Yarus and his Weasel revival?
gpuccio, the keepers of this blog actively discourage debate. If you want to discuss this at my blog, I have an essay about Yarus' work. Consider this an invitation for you to stop on by and explore the matter.Arthur Hunt
June 8, 2010
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Petrushka: "Genetic algorithms have found good solutions to traveling salesman problem involving 10,000 “cities.” In fact there’s an ongoing competition for the best solution to a 10,000 city tour." ... and I'm sure the Genetic Algorithm that wins also brags to all his Genetic Algorithm friends about how smart he is ...CJYman
June 8, 2010
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The reason I bring this up is that 100! is approximately 10^157, a number close to one often mentioned here. Genetic algorithms have found good solutions to traveling salesman problem involving 10,000 "cities." In fact there's an ongoing competition for the best solution to a 10,000 city tour.Petrushka
June 8, 2010
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gpuccio @ #28 http://www.lalena.com/AI/Tsp/
Testing every possibility for an N city tour would be N! math additions. A 30 city tour would have to measure the total distance of be 2.65 X 1032 different tours. Assuming a trillion additions per second, this would take 252,333,390,232,297 years. Adding one more city would cause the time to increase by a factor of 31. Obviously, this is an impossible solution. A genetic algorithm can be used to find a solution is much less time. Although it might not find the best solution, it can find a near perfect solution for a 100 city tour in less than a minute.
Petrushka
June 8, 2010
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For me, I am appalled at the consistency to which the neo_Darwinian framework tries to tear down and devalue human life, at the macro level of abortion and the eugenics movement, and at the micro level of declaring us at 95% junk DNA. But this new song has just reminded me of where my true value finds its worth: Francesca Battistelli - Beautiful, Beautiful (Video) http://www.youtube.com/watch?v=JbCfyZHSQbE We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights,bornagain77
June 8, 2010
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gpuccio - well it would seem that they need ID people to try and engender some debate!.aqeels
June 8, 2010
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Yarus states on the page Dr. Dembski has embedded: "To suggest how Darwinian evolution can surf across supposed oceans of improbability" This is not a minor point he wants "surf across".,,,, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,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." 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)." http://www.creationsafaris.com/epoi_c10.htm ,,,In fact it is easily recognized, even by ardent evolutionists, that functionality is surrounded by expansive wildernesses of non-functionality and is indeed the primary reason why evolutionists have clung so tenaciously to their proposition that up to 95% of the genome is junk, as witnessed by the recent exchange between Dr. Sternberg and Moran and Matheson. On the face of it, given the apparent complexity of life, this 95% number is completely unreasonable to start with, But this position of 95% junk becomes all the more indefensible given the recent studies that are steadily revealing deeper levels of complexity that were undreamed of by most people just a few short decades ago. Such as this following study among the many other studies that I could cite: Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html But the one thing that renders the "surfing across the non-functional ocean argument" moot for me is that the one thing Natural Selection is very good at, in "real life", is at removing useless stuff that is not doing anything useful but only consuming energy: Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - May 2010 Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2 Arriving At Intelligence Through The Corridors Of Reason (Part II) - April 2010 Excerpt: In fact the term ‘junk DNA’ is now seen by many an expert as somewhat of a misnomer since much of what was originally categorized as such has turned out to be pivotal for DNA stability and the regulation of gene expression. In his book Nature’s Probability And Probability’s Nature author Donald Johnson has done us all a service by bringing these points to the fore. He further notes that since junk DNA would put an unnecessary energetic burden on cells during the process of replication, it stands to reason that it would more likely be eliminated through selective pressures. That is, if the Darwinian account of life is to be believed. “It would make sense” Johnson writes “that those useless nucleotides would be removed from the genome long before they had a chance to form something with a selective advantage….there would be no advantage in directing energy to useless structures”. https://uncommondescent.com/intelligent-design/arriving-at-intelligence-through-the-corridors-of-reason-part-ii/ Cells simply do not tolerate oceans of non-functionality, as Yarus, Moran and other evolutionists, imagine they do: 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. http://www.sciencedaily.com/releases/2009/01/090107134529.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm i.e. why would "repair crews" go to all that effort to repair the entire genome? Why doesn't it just repair the 5% functional part? Perhaps the entire genome may have functionality that we are just barely beginning to understand? Just an Idea: As far as Yarus's trying to "surf across the ocean", the target phrase is: "Methinks Yarus's Simulated Example Is All Wet Like A Weasel" Further notes: "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 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. http://creationsafaris.com/crev201002.htm#20100226abornagain77
June 8, 2010
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I must say that there is an unusual absence of darwinist debate on this thread. Anybody wants to defend Yarus and his Weasel revival? (I know, this is a true provocation... :) )gpuccio
June 8, 2010
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JDH: It's as simple as this: 1) William Dembski does understand the theory of probability, and very well indeed. 2) Michael Yarus simply doesn't. Not even the basics. I would like to think that he is simply lying, that he does not really believe in what he writes. But I feel that any sentient being who understands probability would be deeply ashamed in writing that kind of things, even if strongly motivated by other considerations. So, back to the first interpretation: he does not understand anything. Not that that is an excuse, anyway. Many people don't understand probability, but they don't usually write books about it, and they don't spend their time criticizing real experts like Dembski. So, shame on those who behave this way!gpuccio
June 8, 2010
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I don't know about you, but one of the most irritating things in published debate is when someone claims their opponents ( who are not asked beforehand to rebut ) do not understand something. Many, many people do not properly understand probability and how it applies to directed vs. undirected search. I suggest strongly that William Dembski is not one of those people. I do however, suspect that Yarus doesn't quite understand it. At least this publication is a strong indicator of his ignorance.JDH
June 8, 2010
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Only 2 pages later he comes up with this gem... "Organized complexity is the thing that we are having difficulty in explaining. (NO KIDDING!! YA THINK???) Once we are allowed simply to postulate organized complexity, if only the organized complexity of the DNA/protein replicating engine …" I guess the real mistake is to even bother to try and reason with people like this who clearly are irrational even as they say you are the crazy one. If you can't explain it, well then, simply "postulate" it!!! Problem solved!! I wonder if the engineers know about this new technique??? Seems like they could really take advantage of something like this. They'd certainly have more time for golf and fishing... not have to do all that hard work of actually figuring things out...tgpeeler
June 8, 2010
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Richard Dawkins, the hard headed, supremely rational being, in The Blind Watchmaker, on page 139 (paperback) said this: "We can accept a certain amount of luck in our explanations, but not too much. The question is, how much?" ROFLMAO. He doesn't set the bar very high, now does he? Someone could make a career of discussing all of the ignorant, insane, or wicked things this guy says. Granted, it would be a depressing career...tgpeeler
June 8, 2010
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Let me suggest that these critics take up their concerns with Yarus. Excellent suggestion, but they won't. "Leading experts" will continue to use the Weasel simulation as evidence supporting evolutionary theory until someone points out that it latches on to a target phrase and preserves non-functional intermediates in order to reach a presently-unknown future state. Then they will insist that the Weasel "was never meant to be taken seriously" and that critics should be directing attention elsewhere. "Elsewhere", because their problem has been exposed. If the WEASEL is claimed as solid evidence in favor of evolutionary theory, when it is falsified the theory itself falls apart. So, it's only evidence as long as nobody challenges it.Proponentist
June 8, 2010
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(12) aqeels
Playing devils advocate and trying to make sense of the criticisms, could evolutionists not simply respond by stating that the analogy in nature is that there are hitherto uknown solutions that are effectively stumbled upon. The fact that we are using a phrase as a target that is familiar to us allows one to demonstrate the underlying principle of natural selection acting as an efficient filter. The phrase could have been anyone of the possible combinations.
The question is not what is the phrase, but how is the selection performed and what is the minimum amount of "correct" information required before selection can take place? In the Weasel-like programs, and in the cardboard stencil example, intelligence allows any piece of information that is part of the eventual phrase to be selected (whether that's "Me thinks it's like a Weasel" or "doijfas8382hfasdf"). But natural selection acts on function, not eventual function. Before I go any further, I will state that I am not a biologist, so I will not try to make 100% positive statements. I am really asking for answers. Let's say an RNA World existed. Billions of trillions of bits of RNA somehow formed billions of years ago, and they started making strings completely randomly. Until there is some function, there is no realistic way that natural selection can choose anything that will eventually lead to life. When is selectable function achieved? How many genetic symbols does it take? If the first fully functional RNA sequence was, say, 150 "characters" long, what percentage of that was needed before there was some function to select before evolving (hypothetically) to the final 150-character string? 50%? 90%? 99%? To my knowledge (this is where I'm not an expert and not making assertions), most protein-coding sequences fail completely when a very small amount of information is mutated. When genetic code is able to be selected one character at a time, Darwinian evolution is devastatingly efficient at generating the optimal arrangement, as argued in Behe's EOE and in WEASEL programs. But all evidence I'm aware of does not point to this being anywhere close to the reality of molecular biology. And as far as generating the first life, the question is what is the minimum amount of information needed for selectable function? You cannot evolve to this minimum amount - it must be found randomly, at least within the probabilistic resources of the history of the known Universe, and more accurately within the probabilistic resources of early Earth.uoflcard
June 8, 2010
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Semi-off topic: Jonathan Wells has just posted this at ENV: The Fact-Free “Science” of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence Excerpt: Since Matheson, Hunt and Moran are all tenured professors at institutions of higher learning, one might have expected a discussion based on reason and conducted in a collegial spirit. And since the discussion is about science, one might have expected lots of references to evidence published in the scientific literature. But Matheson, Hunt and Moran have abandoned reason and resorted to ridicule; and instead of citing evidence they expect us to bow to their authority. http://www.evolutionnews.org/2010/06/the_factfree_science_of_mathes035521.htmlbornagain77
June 8, 2010
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Here's the thing. Before we even get to chemical evolution: In Expelled, Micheal Ruse said "...and I don't see any reason why we can't go from simple to more complex to more and more complex..." Well I do: Empirical evidence: Biochemical molecules tend to break down, not build up, when left exposed to nature. In live, the body constantly need to repair itself against degradation, and when we die, we decompose. So, let's be generous and say this RNA does somehow manage to evolve from chemicals naturally, and it does happen to form something significantly complex. What will prevent preserve it? What will prevent it with forming chemical reactions that will lead it away from live? These questions are never addressed. We simply assume the magic of Darwinism will protect and watch over these molecules.hannodb
June 8, 2010
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aqeels: Playing devils advocate and trying to make sense of the criticisms, could evolutionists not simply respond by stating that the analogy in nature is that there are hitherto uknown solutions that are effectively stumbled upon. The fact that we are using a phrase as a target that is familiar to us allows one to demonstrate the underlying principle of natural selection acting as an efficient filter. The phrase could have been anyone of the possible combinations. There is no chance of playing the devil's advocate. It's a lost battle from the beginning. Not even the devil would take it. If you know the solution, you know the solution. Any "evolutionary" game to retrieve a solution which you already know is just that: a game and a waste of time. Nature, as conceived by darwinists, does not know the solution. Indeed, it does not even know that there is a solution. Indeed, it does not even know that there is a problem. The "solution stumbled upon" must have two properties: 1) Must have been found in a random system, by random events. I am afraid that even "METHINK..." would have problems, in an unassisted search. 2) Must be selectable. Indeed, must select itself in a specific environment. That's the point which is misunderstood. NS (I mean positive selection) does not "select", it just defines the environment where the new fucntion selects itself. Therefore, there is a fundamental constraint to what can be selected: only functions which allow a reproductive advantage can be selected. METHINKS... does not have reproductive advantages, unless the environments cna "recognize" it. And only what is already known can be recognized. The "unknown solutions" which can select themselves are just a tiny fraction of all solutions, which are a tiny fraction of all senseless results. And those selectable solutions are complex. A reproductive advantage is not attained simply in macroevolution (microevolution is different, and the reson for that has been discussed many times). So, it's really stunning that someone still has the courage to propose the METHINKS "model". Or to equivocate on probability theory with such blatant arrogance and misunderstanding.gpuccio
June 8, 2010
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About the RNA world: I suppose it was something like that: In the original soup (some very special one) nucleotides got together at high concentrations in very favourable conditions (well, can we deny a little bit of luck? After all, someone does win a lottery). In the same original soup (or some other soup very near) aminoacids were formed. Very tiny rybozimes (let's say 9 nts, just to pay a tribute to Yarus) formed, and those with special activities were selected (who can deny a litthe bit of luck, etc.). Being near to aminoacids, they started joining them in useless short sequences, completely random I suppose. But wait... with a little bit of luck (who can deny...), some of these sequences were functional. Functional for what? Not very clear, but you cannot ask too much... So, now, these first polipetdides are selected... What are you asking? How? Well, their information... What are you asking? Where is their information? Ehm, in RNA, I suppose. Which RNA? Well, probably, in the same pool, some short sequence of RNA was formed which had the information for the tiny sequences of aminoacids which were being formed randomly by the 9 nts rybozyme... That's called cooption, you know? Or perhaps convergent evolution... Or perhaps... I don't know, it has certainly a name. Perhaps sheer luck? And so, now the game is won (like lotteries, you know). We have the rna gene, and we have the small protein. What is lacking? Well, maybe the symbolic code. Maybe the translation apparatus. Just little details. Arguments from ignorance. God of the gaps. Add a membrane of some kind, maybe a trace of metabolism, some help for reproduction, and we have our first RNA world living beings. And then? Then we just have to move everything to DNA and proteins only, and get rid of those uncomfortable rybozimes. It'important that no trace be kept of all this. It will remain our secret. Our theory. And we will be able to spend a lot of money investigating it.gpuccio
June 8, 2010
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uoflcard: I like the stencil-sand example. Thank you. Would it be difficult to write in the cardboard something like: "METHINKS IT'S LIKE A WEASEL"?gpuccio
June 8, 2010
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hannodb: Like the more well known Darwinists like Dawkins, Yarus too is forced to make simple logical errors in order to defend Darwinism. That's not completely fair. He is making both simple and complex logical errors... :)gpuccio
June 8, 2010
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"Michael Schermer said that the difference between the skeptic and a believer is that the former one will change his opinion if the facts point in a new direction." Not quite. A "skeptic" is a believer too - in materialism. They refer to themselves as "skeptics" or "atheists", to create the illusion to themselves and to others that they are completely rational, and only believes what the data can prove. Their uncritical unquestioning devotion to the darwinian-materialistic world view, proves otherwise. They will believe that materialistic processes alone are sufficient to produce specified complexity, despite empirical evidence that proves otherwise. It is for this reason that I believe the term "materialist" is more accurate, as it places the emphasis on what the person DOES believe, rather than what he doesn't.hannodb
June 8, 2010
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hannodb: RNA world investigation is the proof of how much time and resources can be spent in pursuing a fairy tale. RNA world is a fairy tale, a hypothesis which is completely imagined, based on no empirical observation, and whose only justification is that all other materialistic OOL theories are completely illogical. While the theory of RNA world is completely illogical, but perhaps only a little bit less. So, to defend a theory born of sheer imagination, bevause it's the only theory of materialistic OOL which can still be defended, all resources go to artificially try to demonstrate that living beings based on RNA information and RNA catalysis are possible, even if they have never been observed in any form, and even if nobody has any idea of what they could have been, or how they could have worked. The only empirical truth is that the simplest autonomous living being ever known are archea and bacteria: living beings of high complexity, with a DNA mass memory, hundreds of DNA genes, hundreds of complex proteins, a DNA symbolic code, A transcription apparatus, and a very complex translation apparatus which is based not only on specific tRNAs, but forst of all on 20 specific complex proteins, the aminoacyl tRNA synthetases. This is what we observe, this is what, according to all evidence, and especially darwinian evidence (such as homology studies of existing proteins), must be already present 4 billion years ago, when the first prokaryote began populating the earth, alredy very much similar to those we observe today. 5 or 9 nucleotide RNAs accurately built in the lab and which happen to have vague and extremely primitive enzymatic activities have no role in natural life, only in the artificial research of an academy which must at all costs defend its undefendable theories.gpuccio
June 8, 2010
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To be clear when I say "The fact is that 'natural selection' is without doubt a natural hill climbing algorithm that is proven in nature." ...what I mean is selection from pre-existing information. No creation of new information which for me is a violation of the 2LOT.aqeels
June 8, 2010
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I have often wondered about the WEASEL program that Mr Dawking devised. The chief criticism I hear often from UD and others is that the program has prior knowledge of the end phrase. Playing devils advocate and trying to make sense of the criticisms, could evolutionists not simply respond by stating that the analogy in nature is that there are hitherto uknown solutions that are effectively stumbled upon. The fact that we are using a phrase as a target that is familiar to us allows one to demonstrate the underlying principle of natural selection acting as an efficient filter. The phrase could have been anyone of the possible combinations. I think that the "beating a dead horse" criticism is unfair as the recent article by Michael demonstrated. However we seem to be getting wound up on such a trivial matter. The fact is that "natural selection" is without doubt a natural hill climbing algorithm that is proven in nature. The quesiton is exactly what can it climb and what are its limits. Those areas are the real ones and the folk at UD have dealt with them rigourously and should continue to do so.aqeels
June 8, 2010
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It's unbelievable that there are professors like Yarus out there who can't see why this proves nothing except that intelligence can create specified, complex strings of information like this. Until it is proven that there are functional, selectable strings of genetic information that are small enough to be randomly selected (COMPLETELY randomly, not intelligently like this and other waste-of-time programs demonstrate) at least within an astronomically optimistic range of probabilistic resources, abiogenesis will remain the most hopeless scientific enterprise since ether. A simple demonstration of how you can cause a random process to seemingly generate CSI by intelligently inputting the information in at the beginning: - Make a stencil out of a piece of cardboard that says a word - Throw sand or dirt randomly all over the board and surrounding area - Carefully remove the board You now have complex specified information that was generated by a random process...except no one will sprint to their computer to log on to Pharyngula to proclaim victory in a major battle for their worldview. Why? Because even the children who do this kind of thing know that they're the ones who really spelled out "Hello" or "kitty" (or both?), not the random distribution of sand, dirt, sparkles or whatever they used. How is it hard for anyone to see that the information was 100% intelligently supplied? Would natural selection be able to select even a 75% complete string from the first fully functional string of genetic information? Yet this professor has selection acting with the very first matching symbol.uoflcard
June 8, 2010
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hannodb, Does the preceding work lab look to be anywhere near a plausible prebiotic route that would be found on the ancient earth? Of course not. As well Yarus's work, despite his vehement protestations to the contrary. has actually highlighted the primary problem facing the origin of life in particular, as well as highlighting the primary problem facing evolution in general. Namely "Where did the information come from?" Stephen Meyer Responds to Fletcher in Times Literary Supplement - Jan. 2010 Excerpt: everything we know about RNA catalysts, including those with partial self-copying capacity, shows that the function of these molecules depends upon the precise arrangement of their information-carrying constituents (i.e., their nucleotide bases). Functional RNA catalysts arise only once RNA bases are specifically-arranged into information-rich sequences—that is, function arises after, not before, the information problem has been solved. http://www.evolutionnews.org/2010/01/stephen_meyer_responds_to_flet.html The DNA Enigma - Where Did The Information Come From? - Stephen C. Meyer http://www.metacafe.com/watch/4125886 Life - Its Sudden Origin and Extreme Complexity - Dr. Fazale Rana http://www.metacafe.com/watch/4287513 The Sudden Appearance Of Photosynthetic Life On Earth - Intelligent Design http://www.metacafe.com/watch/4262918 The Origin Of Life and God - Henry Fritz Schaefer PhD http://www.metacafe.com/watch/4018204 Hannobd, if you need more references and articles in regards to origin of life questions to counter evolutionists with you can click on my handle and about half way down the page you will find several more articles and videos:bornagain77
June 8, 2010
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hannodb: Here is a fairly thorough critique of Yarus's experimental work on the "RNA world: Origin of Life: Claiming Something for Almost Nothing Excerpt: Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.” But does this work support a naturalistic origin of life? A key question is whether the molecule would form under plausible prebiotic conditions. Here’s how the paper described their work in the lab to get this molecule: RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring. Solid was then redissolved in 2 mL pyridine. Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution. Solution was stirred at room temperature for 4 h. All solutions were sequestered from exposure to air throughout. Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation. Remaining solvent evaporated overnight in a vacuum chamber. Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution). Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated. Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU. PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6. Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%. Even more purification and isolation steps under controlled conditions, using multiple solvents at various temperatures, were needed to prevent cross-reactions. It is doubtful such complex lab procedures have analogues in nature. They started with pre-existing ribose, furthermore, and did not state whether it was one-handed. The putative ribozyme function only consisted of one step of a complex multi-step reaction in living organisms: “The small ribozyme initially trans-phenylalanylates a partially complementary 4-nt RNA selectively at its terminal 2’-ribose hydroxyl using PheAMP, the natural form for activated amino acid.” The team’s interpretation of the significance of their work relies heavily on imagination: “The ultimate importance of these observations may lie partly in the unknown number of other reactions that can be accelerated by comparably small RNAs.” They simply assumed that a “geochemical source” would be able to produce a suite of other five-nucleotide ribozymes, including theirs. “On one hand, with this few ribonucleotides to dispose in space, there may not be other similar nucleotide structures that are both stable and capable of catalysis,” they concluded. But then they relied on future work and imagination: http://creationsafaris.com/crev201003.htm#20100302abornagain77
June 8, 2010
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Michael Schermer said that the difference between the skeptic and a believer is that the former one will change his opinion if the facts point in a new direction. Dawkins has also often referred to the self correcting nature of science and the power of peer review. Consequently, in the very near future we will see Dawkins correcting Yarus in this aspect of his work. In reponse to his peer, Yarus will issue an online retraction of this chapter, effectively stating that the weasel machine has nothing to do with Darwinist view of evolution. A few days from now, and true science will again triumph over ID, who have nothing else to support their case other than a few minor oversights that are taken care of by the scientific process.Alex73
June 8, 2010
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