Uncommon Descent Serving The Intelligent Design Community

Back to School Part VI


Evolutionists are adamant that science must be free of religion or anything that smacks of religion. And while that sounds good, evolutionists are all-the-while driven by religion. They are sure all of biology is a fluke because of their religious convictions. Religion is both the source of evolution’s certainty and the target of its wrath. While not proclaiming that science must be free of religion, evolutionists make a wide spectrum of religious claims that mandate their theory.  Read more

AMW, Gould's 'punctuated equilibrium' model just took a couple of hits also: Fantasy Island: Evolutionary Weirdness Does Not Favor Islands - July 2010 Excerpt: “We concluded that the evolution of body sizes is as random with respect to ‘isolation’ as on the rest of the planet,” he said. “This means that you can expect to find the same sort of patterns on islands and on the mainland.” http://www.creationsafaris.com/crev201007.htm#20100708b Amazing Insects Defy Evolution - October 2010 “India spent tens of millions of years as an island before colliding with Asia. Yet the fossil record contains no evidence that unique species evolved on the subcontinent during this time, http://www.creationsafaris.com/crev201010.htm#20101026a further notes: Ancient Fossils That Have Not Changed For Millions Of Years - video http://www.metacafe.com/watch/4113820 "LIVING" FOSSILS OF MARINE CREATURES - unchanged for millions of years - (Pictures - Including a 500 million year old starfish specimen) http://www.hyahya.org/books/darwinism/atlas_creation_III/atlas_creation_III_03.php THE FOSSILS IN THE CREATION MUSEUM - 1000's of pictures of ancient 'living' fossils that have not changed for millions of years: http://www.fossil-museum.com/fossils/?page=0&limit=30 Fossils Without Evolution - June 2010 Excerpt: New fossils continue to turn up around the world. Many of them have an amazing characteristic in common: they look almost exactly like their living counterparts, despite being millions of years old,,, http://www.creationsafaris.com/crev201006.htm#20100618a Punctuated Equilibrium and Patterns from the Fossil Record - Casey Luskin Excerpt: “The Cambrian Explosion is by no means the only “explosion” in the fossil record. One evolutionist concedes that for the origin of fishes, “this is one count in the creationists’ charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest].” Plant biologists have called the origin of plants an “explosion,” saying, “the … radiation of land (plant) biotas is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” Vertebrate paleontologists believe there was a mammal explosion because of the few transitional forms between major mammal groups: “There are all sorts of gaps: absence of gradationally intermediate ‘transitional’ forms between species, but also between larger groups — between, say, families of carnivores, or the orders of mammals.” Another study, “Evolutionary Explosions and the Phylogenetic Fuse,” found a bird (as well as a mammal) “Early Tertiary ‘explosion’” because many bird and mammal groups appear in a short time period lacking immediately recognizable ancestral forms. Finally, others have called the origin of our own genus Homo, “a genetic revolution” where “no australopithecine (ape) species is obviously transitional” leading one commentator to call it, like others called the Cambrian Explosion, a “big bang theory” of human evolution." http://www.ideacenter.org/contentmgr/showdetails.php/id/1232 The following evolution friendly article was quite honest about the inadequacy of Darwinian evolution to account for novel forms appearing in the fossil record: Saltational Evolution: Hopeful Monsters are Here to Stay - Günter Theißen - 2009 "While we already have a quite good understanding of how organisms adapt to the environment, much less is known about the mechanisms behind the origin of evolutionary novelties, a process that is arguably different from adaptation. Despite Darwin's undeniable merits, explaining how the enormous complexity and diversity of living beings on our planet originated remains one of the greatest challenges of biology." http://www.evolutionnews.org/2010/09/nsf_spends_almost_2_million_of038581.html bornagain77
AMW, The exponent addition per 'prepared generation' works like this: In your paper it states: Although it was shown to be possible for a single arbitrarily chosen polypeptide to evolve infectivity, the evolution stagnated after the 7th generation, which was probably due to the small mutant library size at each generation. Therefore, we have extended in vitro molecular evolution by increasing the library size gradually from 10^2 to 10^6.,,, One generation of our evolutionary study consisted of one cycle of mutation and enrichment processes." ,,,Each time they step in and 'intelligently' enrich a protein sequence they are in fact 'intelligently' increasing the search space they are covering. To properly find sequence space 'effectively' covered they must add the exponent of the last generation to the newly 'enriched' generation. Thus,,,, 10^1 10^1 10^1 10^1 10^1 10^1 10^1 10^2 10^3 10^3 10^3 10^3 10^3 10^4 10^4 10^5 10^5 10^5 10^6 10^6 ------ 10^59 total 'effective' sequence space searched by the experiment AMW you then state: 'I’m not claiming new function. I’m claiming new information. Or, rather, increase in functional information.' AMW, It is not an increase of functional information above what was already present in the phage i.e. it is not a violation of the principle of Genetic Entropy! In fact the 'new' protein was slightly less 'functional' than the original one they had removed! Thus if the overall experiment is looked at honestly they have actually lost a little information from what they originally had! Look at this fitness test one more time,,, Is Antibiotic Resistance Evidence For Evolution? – The Fitness Test – video http://www.metacafe.com/watch/3995248/ ,,, AMW that test is the 'gold standard' that you must pass to show a gain in functional information/complexity above what was already present. That is the test that you will have to pass against a 'parent strain' in order to show a violation of the principle of genetic entropy! For you to accept anything less as 'proof of evolution',,, as a 'gain' in functional information is slightly less than forthright on your part to put it mildly! AMW you then state: 'Next, I can notice that lab experiments such as these are conducted over very short timescales, geologically speaking. So even if only modest gains in complexity and fitness can be seen over a year, or decade, or even a human lifetime, those gains are likely to add up when we extend the timescale to millions of years.' AMW The fitness test has NEVER been passed by any 'slight increase' of fitness above the fitness of the parent strain no matter how much time is given. I could use Lenski's long term experiment on e-coli to illustrate this point, but better than Lenski's 'slow slide to genetic meltdown', I will show the results for extremely ancient bacteria that have lived completely in the wilds of nature,,, facing all the glories of neo-Darwinian evolution: Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence. The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 Evolutionists were so disbelieving at this stunning lack of change that they insisted the stunning similarity was due to modern contamination in Vreeland's experiment. Yet the following study laid that objection to rest by verifying that Dr. Vreeland's methodology for extracting ancient DNA was solid and was not introducing contamination because the DNA sequences this time around were completely unique: World’s Oldest Known DNA Discovered (419 million years old) - Dec. 2009 Excerpt: But the DNA was so similar to that of modern microbes that many scientists believed the samples had been contaminated. Not so this time around. A team of researchers led by Jong Soo Park of Dalhousie University in Halifax, Canada, found six segments of identical DNA that have never been seen before by science. “We went back and collected DNA sequences from all known halophilic bacteria and compared them to what we had,” Russell Vreeland of West Chester University in Pennsylvania said. “These six pieces were unique",,, http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland's work: “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961 Dr. Cano's work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated: “After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber." https://uncommondescent.com/intelligent-design/reductionist-predictions-always-fail/comment-page-3/#comment-357693 In reply to a personal e-mail from myself, Dr. Cano commented on the 'Fitness Test' I had asked him about: Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. Here is a revisit to the video of the 'Fitness Test' that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria: Is Antibiotic Resistance evidence for evolution? - 'Fitness Test' - video http://www.metacafe.com/watch/3995248 According to prevailing evolutionary dogma, there 'HAS' to be 'major genetic drift' to the DNA of bacteria within 250 million years, even though the morphology (shape) of the bacteria can be expected to remain exactly the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, has also severely weakened the 'genetic drift' argument of evolutionists: The consequences of genetic drift for bacterial genome complexity - Howard Ochman - 2009 Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria. http://genome.cshlp.org/content/early/2009/06/05/gr.091785.109 I find it interesting that the materialistic theory of evolution expects there to be a significant amount of genetic drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis. AMW as well the overall pattern of the fossil record is completely contrary to the neo-Darwinian model of gradual change. The actual fossil record is consistently characterized by sudden appearance and stagnation. Thus for you to try to cling to the slow gradual model for evolution is really a bit old fashion and does not fit the evidence. bornagain77
AMW, The exponent addition is simple math. Thus you are incorrect in that regards as to the search space covered. Then I would be much obliged if you would go through that simple math for me, step by step. You seem to be assuming that they start with a population of 1,000, and in each generation they multiply that population by 1,000. That will get you to a population of 10^40. If you're making some other set of assumptions, please let me know. As far as you claiming new function, you are claiming proof for the generation of a completely novel function when clearly some preexistent functionality of lubrication existed prior to the ‘hill climbing’. I'm not claiming new function. I'm claiming new information. Or, rather, increase in functional information. Why in the world are you desiring so badly to say that the highly integrated programming, which we find in the simplest cells on the earth, which far exceeds what man can do in his most advanced computers, can arise from the simple Darwinian RM+NS ‘hill climbing’ scenario? Well, first of all, I can look to experiments like the one I linked to, that show that fitness can improve through mutation and selection, and this fitness improvement can be through increasing complexity to the genome. Next, I can notice that lab experiments such as these are conducted over very short timescales, geologically speaking. So even if only modest gains in complexity and fitness can be seen over a year, or decade, or even a human lifetime, those gains are likely to add up when we extend the timescale to millions of years. Finally, when thinking about unicellular vs. multi-cellular organisms, I can see that expecting simplicity in one and complexity in the other sets up a false dichotomy. If all living organisms share a common ancestor, then they've all been on their own evolutionary paths for about the last 3.5 billion years. If single-celled organisms have been evolving for that long, why wouldn't they be complex? AMW
AMW, may I recommend a book to you that will do a far better job than I of explaining the insurmountable barrier that Darwinism is up against in regards to explaining the information we find in life: Programming of Life - October 2010 Excerpt: "Evolutionary biologists have failed to realize that they work with two more or less incommensurable domains: that of information and that of matter... These two domains will never be brought together in any kind of the sense usually implied by the term ‘reductionism.'... Information doesn't have mass or charge or length in millimeters. Likewise, matter doesn't have bytes... This dearth of shared descriptors makes matter and information two separate domains of existence, which have to be discussed separately, in their own terms." George Williams - Evolutionary Biologist http://scienceintegrity.net/ProgrammingofLife.aspx ----------- notes on finding a truly 'novel protein' and on the complexity of 'simple life': Without enzyme, biological reaction essential to life takes 2.3 billion years: UNC study: In 1995, Wolfenden reported that without a particular enzyme, a biological transformation he deemed “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years.“Now we’ve found a reaction that – again, in the absence of an enzyme – is almost 30 times slower than that,” Wolfenden said. “Its half-life – the time it takes for half the substance to be consumed – is 2.3 billion years, about half the age of the Earth. Enzymes can make that reaction happen in milliseconds.” http://www.med.unc.edu/www/news/2008-news-archives/november/without-enzyme-biological-reaction-essential-to-life-takes-2-3-billion-years-unc-study/?searchterm=Wolfenden "Phosphatase speeds up reactions vital for cell signalling by 10^21 times. Allows essential reactions to take place in a hundreth of a second; without it, it would take a trillion years!" Jonathan Sarfati http://www.pnas.org/content/100/10/5607.abstract 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?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong https://uncommondescent.com/darwinism/media-mum-about-deranged-darwinist-gunman/#comment-363647 bornagain77
AMW, by the way there is a million dollar Origin of Life prize for showing how purely material processes can give rise to genetic instructions (prescriptive information): "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life.' http://www.us.net/life/ bornagain77
AMW, The exponent addition is simple math. Thus you are incorrect in that regards as to the search space covered. As far as you claiming new function, you are claiming proof for the generation of a completely novel function when clearly some preexistent functionality of lubrication existed prior to the 'hill climbing'. Thus you are merely seeing/imagining what you want to see in this example, and are clearly extrapolating far past your basis! But all this is completely beside the point. Why in the world are you desiring so badly to say that the highly integrated programming, which we find in the simplest cells on the earth, which far exceeds what man can do in his most advanced computers, can arise from the simple Darwinian RM+NS 'hill climbing' scenario? It is completely without any basis, or merit, in rationality to hold that such stunning complexity can be had for ALL of life through such a trivially simplistic process!,,, AMW if you want to believe your example of hill climbing proves your point, then by all means go ahead and believe it, but I think I will wait until Abel's null hypothesis is violated until I put any faith whatsoever in material processes generating functional 'prescriptive' information. The main problem, for the secular model of neo-Darwinian evolution to overcome, is that no one has ever seen purely material processes generate functional information. The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009 To focus the scientific community’s 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." A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis. http://www.mdpi.com/1422-0067/10/1/247/pdf Can We Falsify Any Of The Following Null Hypothesis (For Information Generation) 1) Mathematical Logic 2) Algorithmic Optimization 3) Cybernetic Programming 4) Computational Halting 5) Integrated Circuits 6) Organization (e.g. homeostatic optimization far from equilibrium) 7) Material Symbol Systems (e.g. genetics) 8) Any Goal Oriented bona fide system 9) Language 10) Formal function of any kind 11) Utilitarian work http://mdpi.com/1422-0067/10/1/247/ag bornagain77
You still have to add the exponent of the population each time they stepped in to ‘prepare a mutant library’, which even if the population was only 10^2, which it wasn’t, would give a sequence rarity of 10^40, hardly a number to warm a Darwinist heart. No, that's incorrect. The maximum starting population for any generation was 10^6. They didn't increase the population by a factor of 10^2 each generation, which I presume is how you come to a population of 10^40. Even if they started with 10^6 clones in the first generation, that would mean a population of 20*10^6, or 20 million. That's a pretty far cry from 10^40, or ten thousand trillion trillion trillion. the only function of this protein is to provide a ‘lubricating coating’ to better enable infection,,, and clearly the ability to somewhat sufficiently lubricate was apparently already within the random sequence True, fitness was not equal to zero. If it had been, the phages would have gone extinct in the first generation. Evolution doesn't begin at zero fitness. As for the fact that the function was "only" to provide a lubricating coating, I'm not sure what the significance of that is. You've never before specified that certain kinds of functions are impressive, while others are not. Was your original hypothesis that mutation and selection can account for increases in functional information if the function is simple enough? Anyway, the fact remains that they scrambled a gene domain to near uselessness, and it evolved into a new domain that improved the phage's fitness exponentially. The resulting domain was complex, in that it was very unlikely to arise due to chance alone. It was specified in that the experimenter had side information about what the domain should do: assist in infectivity. If that doesn't count as an increase in functional complex specified information, I'd be hard pressed to think of what does. Thus AMW they solved a simple ‘hill climbing problem’ that improved a already existent function That was not a simple hill-climbing problem. The algorithm may have been a simple hill-climbing one, but the landscape it was searching had many local maxima. (See Figure 5 on page 5.) Besides, who said that evolution will always find the global maximum? Clearly this example is a far cry from explaining where the complex functional information for building the phage came from in the first place AMW. That's not the challenge you posed. You said new protein fold or new gene. I daresay some new protein folds occurred when the functionality of the scrambled gene domain improved. And is clearly far short of explaining where completely novel functional proteins come from The resulting protein was novel. The DNA sequences were not the same as the original wild-type, nor were they the same as the randomized sequence. AMW
AMW, You still have to add the exponent of the population each time they stepped in to 'prepare a mutant library', which even if the population was only 10^2, which it wasn't, would give a sequence rarity of 10^40, hardly a number to warm a Darwinist heart.,,, But this is all besides the point, the only function of this protein is to provide a 'lubricating coating' to better enable infection,,, and clearly the ability to somewhat sufficiently lubricate was apparently already within the random sequence,,, or else the phage would most likely have no ability to infect whatsoever as a result.,,, Thus AMW they solved a simple 'hill climbing problem' that improved a already existent function within a population of 10^40 (yet still the improvement was slightly below what the parent coating was),,, Clearly this example is a far cry from explaining where the complex functional information for building the phage came from in the first place AMW. ,,, And is clearly far short of explaining where completely novel functional proteins come from that must do something besides simply lubricate. bornagain77
‘For each generation, we prepared a mutant library from the parental population enriched at the previous generation and continued the iterative enrichment process until the increase in infectivity seemed to cease. We used the enriched population as the parental population for the next generation,’ Thus AMW they were ‘intelligently guiding’ the process for each of the +20 generations of the experiment. The "enrichment process" they refer to appears to be mutation and selection. That doesn't suggest intelligent guidance by normal ID standards. When improvement stagnated, they increased the populations of the clones, but didn't alter their DNA. So all sources of change to the population genome (after the initial scrambling of the one gene domain) were due to mutation and selection. AMW
AMW if you want to read it here is one of Dr. Axe's latest papers: 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." http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1 bornagain77
money quote: Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends. bornagain77
AMW, here is a link I just ran across. It seems Doug Axe has had to defend his work against a far higher level of criticism than the paper we are talking about: Shortcuts to new protein folds. - October 2010 http://idintheuk.blogspot.com/2010/10/shortcuts-to-new-protein-folds.html bornagain77
AMW, as well my observation that the information has to be implemented 'top down' instead of 'bottom up', as Darwinists maintain, holds. In fact the necessity of 'top down' implementation should, by all rights, be immediately obvious to you. Please look at the videos of the Bacteriophage that I listed. The first thought I had when I saw the bacteriophage virus is that it looks similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled by the virus, and that the virus must somehow possess, as of yet unelucidated, orientation, guidance, docking, unloading, loading, etc... mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye. The video gives a excellent small glimpse at the intricate, and even humbling, complexity that goes into crafting the "simple" non-living bacteriophage virus. How anyone can not see the need for 'top down' design is beyond me AMW. Especially given the fact that genetic entropy has never been violated by evolutionary processes: Is Antibiotic Resistance Evidence For Evolution? - The Fitness Test - video http://www.metacafe.com/watch/3995248/ bornagain77
I posted comment #86 before I read comment #85. Responding to that one will take some extra time, as I'll have to go back into the paper. AMW
the highly complex preexisting information in the cell is ‘calculating’ a response, and the resultant strain will be slightly less fit than the original parent strain was at the beginning of the experiment. I thought your original argument was that mutation and selection cannot increase information in a genome, no? That appears to be what happened here. Start with a phage, P. Scramble a domain in one of it's genes, and call the resulting phage P'. Through mutation and selection of P', a phage P'' is derived. Now, your argument seems to be that the information content in P'' is less than that in P, so we have a net loss in information at the end of the experiment. But the fact remains that the information content in P'' is greater than that in P'. That means that mutation and selection did indeed increase the information content, as it brought it from a level consistent with P' to a level consistent with P''. Eager to hear your response. Cheers, AMW AMW
AMW, this is why your experiment is not an example of an evolutionary process: from your paper: 'For each generation, we prepared a mutant library from the parental population enriched at the previous generation and continued the iterative enrichment process until the increase in infectivity seemed to cease. We used the enriched population as the parental population for the next generation,' Thus AMW they were 'intelligently guiding' the process for each of the +20 generations of the experiment. As well taking into consideration that the exponent for population size, for each generation, (10^2, 10^4, 10^6 etc..) will add to each of the previous generations per each 'prepared library' of the experiment, then the rarity of functional protein will quickly approach, even surpass, what Doug Axe found in his work. bornagain77
AMW here is a video of the assembly of a phage: The Virus (Bacteriophage) - Assembly Of A Molecular Lunar Landing Machine - Intelligent Design - video http://www.metacafe.com/watch/4023122/ http://www.metacafe.com/watch/4205494/ bornagain77
further note AMW, what they have done is similar to what some evolutionists try to do when they try to claim the immune system is proof of the 'marvel' of 'evolutionary processes': notes: In computer science we recognize the algorithmic principle described by Darwin - the linear accumulation of small changes through random variation - as hill climbing, more specifically random mutation hill climbing. However, we also recognize that hill climbing is the simplest possible form of optimization and is known to work well only on a limited class of problems. Watson R.A. - 2006 - Compositional Evolution - MIT Press - Pg. 272 Response to Kathryn Applegate - Caroline Crocker PhD.- cell biologist and immunologist - October 2010 Excerpt: Diversity of antibodies generated by B cells is due to deliberate, cell-engineered changes in the DNA sequence, not random mutations. In fact, I have never before heard the process whereby functional antibodies are formed (before they encounter antigen) described as mutation. And it is well-known that the appearance of functionality as a result of a mistake-mutation is extremely rare. Of course, after encountering antigen the hypervariable regions of the antibody DNA do undergo somatic hypermutation, but again this is in particular places and is controlled by enzymes.,,, ‘It is possible that mutations occur during this process (Sperm and Egg Meiosis) and these are passed on to the offspring, but note that there is NO deliberate excision and splicing of genetic material, no production of antibodies, in fact virtually no similarity between this process (Meiosis) and that of B cell antibody production. In fact, the only similarity between these processes is that both are marvels of precise engineering and nanotechnology.’ https://uncommondescent.com/intelligent-design/comments-on-kathryn-applegate%E2%80%99s-may-posts-on-biologos/#more-15176 bornagain77
AMW, that is not an evolutionary process, and does not violate Genetic Entropy. i.e. the highly complex preexisting information in the cell is 'calculating' a response, and the resultant strain will be slightly less fit than the original parent strain was at the beginning of the experiment. What the experiment did was take advantage of what was already present in the genome to repair itself to solve a fairly simple 'hill climbing' problem, while completely ignoring, and without explaining where the complex multi-tiered correction mechanisms in the genome came from in the first place! bornagain77
bornagain 77, If you're checking into this thread any longer, try checking out the following study. In a lab environment, the authors took biophages and replaced one of their gene domains with random DNA strings 139 amino acids in length (that would be 417 base pairs, I believe). The gene in question codes for a coat protein without which the phages have a lot of difficulty infecting host cells. But with a phage library of 1,000,000, the phage population increased in infectivity by 17,000 times. The gene domain that had been scrambled did not revert to its original DNA code. Instead, it appears to have developed into a novel domain. Read the full article. I'd be interested in your thoughts. Cheers, AMW AMW
bornagain77, I've got a day job and my degree isn't in molecular evolutionary biology, so I don't have an encyclopedic command of the literature. I've seen some links to some promising papers, but haven't had time to pursue them yet. I'll get back to you once I've been able to do so. Stay classy. AMW AMW
AMW, please ask yourself, Why in the world will you not be able to produce even one novel functional protein originating by evolutionary processes??? If evolution were true for why all the amazing diversity of life exist on earth then you should have thousands upon thousands of examples. As well you should have a fairly substantial list of molecular machines arising from evolutionary processes!!! Yet you have none!!! Why is this AMW??? And why in the world do you buy into a theory that has not even met this minimum level of integrity??? Maybe perhaps you thought you had/have evidence??? Could you please present what YOU think is the strongest piece of evidence for Darwinism so that we may see exactly what deception you have bought into??? bornagain77
A molecular machine originating by evolutionary processes would have me over on PZ’s echo chamber talking about all those IDiots on UD. Gee, I sure hope not. In the first place, name-calling never convinces anyone but the choir. And on top of that, PZ is kind of a, well, sphincter cavity. Anyway, it'll probably take me a little time to find an example for your consideration. But just keep checking back here and I'll try to get one for you. Cheers, AMW AMW
AMW, any novel protein will do. A molecular machine originating by evolutionary processes would have me over on PZ's echo chamber talking about all those IDiots on UD. bornagain77
I want actual empirical evidence of ‘vertical’ evolution, not evolutionary ‘just so stories’ saying sequence/protein y came from sequence/protein x Okay, I think I understand. But am I right that what you want is info at the actual genome (or genotype) level? You want to see a new gene or protein fold arising in a population, right? As opposed to a new physical trait (or phenotype) that we might infer comes from a genetic change? AMW
AMW I want actual empirical evidence of 'vertical' evolution, not evolutionary 'just so stories' saying sequence/protein y came from sequence/protein x: notes: For a broad outline of the 'Fitness test', required to be passed to show a violation of the principle of Genetic Entropy (to show vertical evolution), please see the following video and articles: Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Testing the Biological Fitness of Antibiotic Resistant Bacteria - 2008 http://www.answersingenesis.org/articles/aid/v2/n1/darwin-at-drugstore Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009 Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,, A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses. http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html#more This following study recently confirmed the severe limit for evolution found by Dr Behe: Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010 Excerpt: In experimental evolution, the best way to permit various evolutionary alternatives, and assess their relative likelihood, is to avoid conditions that rule them out. Our experiments, like others (e.g. [40]), used populations of cells growing slowly under limiting nutrient conditions, thereby allowing a number of paths to be taken to higher fitness. We engineered the cells to have a two-step adaptive path to high fitness, but they were not limited to that option. Cells could reduce expression of the non-functional trpAE49V,D60N allele in a variety of ways, or they could acquire a weakly functional tryptophan synthase subunit by a single site reversion to trpAD60N, bringing them within one step of full reversion (Figure 6). When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2/BIO-C.2010.2 Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009 Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own. http://www.discovery.org/a/9951 Lenski's e-coli - Analysis of Genetic Entropy Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment. http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria etc.. etc.. etc.. bornagain77
Oh, and the above means you want to see changes in a protein coding portion of a genome or changes in a non-coding portion such that a section of it starts coding for a protein. Correct? AMW
Hi, all. Like AussieID, I teach classes, and today is my busiest of the week. So I won't be able to respond until sometime tomorrow or Friday. bornagain77, you say: I would consider the origination of a new protein fold, or a new gene, as origination of new functional information So I can assume you want genetic data, correct? A new structure/pathway/behavior/etc. isn't enough. You want to see an example where a genome either gets a new gene or the genome changes such that a new protein fold is coded for in the organism. Is that correct? AMW
AMW you are right, Darwinism is NOT a religion. It is a Cult. "...you don't get to use the influence of government to help promote your cult." http://www.evolutionnews.org/2010/10/you_dont_get_to_use_the_influe039541.html Misrepresentation of the First Amendment, which was intended to prohibit government enforcement of orthodoxy and to protect free inquiry, has been atheists' primary cudgel to suppress challenges to their cult in public schools. (promote their own orthodoxy and suppress free inquiry) bornagain77
Mornin' AMW: Just a few footnotes . . . 1 --> The threshold of functional complexity that would be relevant to falsifying the design inference in the biological world would be the empirically observed spontaneous -- blind chance plus necessity only -- of say 500 - 1,000 bits worth [about 250 - 500 bases, or at the upper end about 150 codons] of novel functional genetic information. 2 --> Creation of a novel protein fold domain would fill the bill nicely. 3 --> Underlying, life on evo mat theses, had to originate by such material causal factors, and had to fulfill the requisites of a Von Neumann self-replicating entity from chemicals mixing in whatever warm little pond or other scenario. Codes [i.e. language], algorithms, storage media, processing machinery, functional organisation all had to be there at once or there would be no self-reproducing life relevant to what we observe today. (So-called self-replicating reaction sets or the like do not count. Dawkins' replicator is still a just-so story. And, the underlying chemical environment has to be physically reasonable.) 4 --> Novel varieties of life at body plan level have to have much the same, and require that the new architecture is embryologically feasible. To jump from unicellular organisms to get the sort of body plans in and around the Cambrian life revo, we are looking at 10's - 100's+ millions of new bases. Dozens of times over, and in a narrow window of time of dozens of MY, on just one planet of 6*10^24 kg, most of which is not accessible for that evo. 4 --> By now you should be familiar with why we point out that just 1,000 bits implies 1.07*10^301 possible configs, and the observed universe accounts for ~10^150 Planck-time states [~10^-44 s or so] across its thermodynamically credible lifespan, ~ 50 mn times the 13.7 BY said to have elapsed since the singularity. So the whole observed cosmos cannot sample 1 in 10^150 of the states specified by 1,000 bits. On very generous measures! 4 --> That is why we focus so strongly on the need to account for complex functional organisation and associated information, especially digitally coded, algorithmically functional information. There is but one known and credible, empirically warranted source for such dFSCI: intelligence. So, we infer that dFSCI is a signature of intelligence, and we have a right to infer to intelligent cause when we see it. 5 --> As to the common descent issue, a name does not make much, especially when it is an act of wit. When I wear a SD hat, I know that Cuba [700 mi long] is a Small Island Developing State, and so are countries that are actually coastal continental states, like Belize. Behe, for instance, believes in universal common descent and is a leading design theorist. here at UD, GP is much like that. (I am pretty agnostic on such matters, even trending skeptical about the possible degree of warrant we can have: we weren't there, we cannot observe what actually happened, and we had better be humbly provisional in our inference- to- best- explanation- of- what- we- can- observe- in- the- present knowledge claims. I find Job 38:1 - 4 a stunning rebuke to our intellectual pride on origins.) 6 --> No need for crazy pills, just an awareness that movements of very independent-minded people are not that easy to buttonhole. When you got a Paul Nelson, a Jonathan Wells, a Mike Gene, A Michael Behe and a David Berlinsky in much the same fold, it will not be neatly categorisable. _____________ Back to constitutional crises; at least this will get me in a writing frame of thought. GEM of TKI kairosfocus
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