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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
Off topic: This is the concluding statement of a talk by Alain Aspect on the overturning of Einstein's hidden variable argument: Part 5 - From Bell's Inequalities to Entangled Qubits: A New Quantum Age? http://www.youtube.com/watch?v=Pfg4M5okvxw bornagain77
Dr. Dembski this radio broadcast may be of interest to you: Vaccines & Autism/Climategate http://www.coasttocoastam.com/show/2010/06/09 bornagain77
Just a brief comment about Yockey. While some of the things he says are interesting (and, I would say, very much ID), I was very surprised by this statement: Life originated, but must be taken as an axiom [something we know to be true, but cannot prove]. The problem in the origin of life that science is unable to solve is to explain how information began to govern chemical reactions through the means of a code. I oviously agree with the second part, but what about taking OOL as an axiom? I am always very surprised of how darwinist scientists, or even semi-darwinist scientists (if we can define Yokey that way), so often come out with such epistemological confusion. Darwinists are sadly famous for mixing up theories and facts, as thou thay were two interchangeable categories. And now, Yockey, a phycicist and information theorist, concludes that we have to treat OOL as an axiom. Now, just for clarity, I will paste here a very simple definition of "axiom" which, IMO, is good enough for our discussion: "A statement or formula that is stipulated to be true for the purpose of a chain of reasoning: the foundation of a formal deductive system". The problem is, axioms are a fundamental part of mathematics and logics. They are the basis of formal systems. Formal systems are deductive, and axioms are the only part of them which is accepted without any proof. That's because axioms are "stipulated". We have to remember that mathemathics and logics are the only sciences which are not empirical. They have no relationship with the existence of their "objects" as part of the outer world. The objects of mathematics are purely mental, and need not correspond to anything in the outer world. Therefore, when an axiom is "stipulated", it just means that the relative statement will be held as true in the formal system derived from it. Nothing less, nothing more. But empirical sciences do not work that way. Empirical sciences are interested in what exists in the outer worlds, and in explanations of what exists (finding regularities, building models, and so on). Empirical sciences do not admit "axioms". Empirical sciences start from facts, and build theories and models to explain facts. So, what is Yockey saying when he states that OOL cannot be solved, and must be takes as an axiom? As far as I can see, nothing which has meaning. That life originated is a fact, but that does not make it an axiom. How life originated is the correct question science has to answer. Now, while it is possible (but, I hope, not true) that that specific question will never be answered in a completely satisfying theory based on empirical data (indeed, we have no guarantee in principle that we will be necessarily succesful in explaining everything about reality), there is no possible reason to state that the question cannot find an answer in principle. So, defining it as an "axiom" is senseless, and it means to wrongly apply a concept of deductive abstract sciences to inductive empirical sciences. Empirical sciences allow no axioms. Thet vare only interested in facts, and in the explanation of facts. But I completely agree with Yockey that science is unable "to explain how information began to govern chemical reactions through the means of a code, if instead of "science" we specify "materialistic reductionist science whih refuses a priori to take into consideration consciousness and design as operating parts of reality". In that sense, Yockey's statement is perfectly true. But it simply points to a wrong scientific approach and prejudice, not to an objective impossibility. In the paradigm of design, OOL can and will be satisfactorily explained. gpuccio
the lower limit of functional sequences is IMO completely bogus. It is based on a kind of approach which has deep methodological biases, both in the search method and in the definition of function.
The blog I cited indicated a very broad range of possible values. So research is just beginning. Silly me, having seen several hundred years of science find regularities in phenomena, I'm betting there are more regularities around the next corner. But I admit it's an unknown. We seem to have different expectations about what will be found. I will limit myself to one last slightly snide comment. It is easier to dig and not find a bone than it is to figure out how to increase the probability of finding a bone. It is easier to calculate immense improbabilities than to look for regularities that would reduce the improbability. The first approach simply assumes there are no biases in nature that would make the emergence and evolution of life possible. You calculate odds by assuming complex modern structures must come together all at once. The second approach assumes that there must be an incremental path. If I were to pick an ID proponent who makes sense to me it would be Michael Denton. Petrushka
2)NS. In this kind of GA, the situation is completely different. The environment is completely passive, is not a programmed environment, does not recognize anything and does not promote anything. The selection takes plays because, in a situation of limited resources, the replicators compete one with the other. So, the function which is selected, not being recognized by any fitness function, must have in itself the power to confer a reproductive advantage. IOW, the function selects itself in the replicator, given the environmental resources
1. The "environment is not a single thing, physically or conceptually. The biological selecting environment includes the absolute necessities imposed by biochemistry. The replicator must have the structural elements necessary for metabolism and reproduction. The environment contains active predators and competitors. 2. To use Yockey's analysis, evolution cannot explain first life, but once life exists, replication, fecundity and pruning constitutes an algorithm capable of mining and digitally storing information about what works. 3. It is obvious from this analysis that the environment (in all the aspect listed above) must be permissive enough that some variations are not fatal, and that the mutation rate not overtake fecundity. So it is worthwhile to investigate the gaps argument and the entropy argument. The usual way to investigate such arguments is by research. They don't lend themselves well to axiomatic reasoning. Which is why I asked if anyone can name a species that went extinct through declining fertility associated with genetic entropy. An it's why I ask if there is any specific gap claimed in the last 150 years that has no been narrowed through research. Certainly research into blood clotting has yielded an array of incremental versions of blood clotting, not to mention alternative mechanisms. Pretty much the same is true of flagella and cilia. Many versions using various subcomponents and variations of components. Petrushka
Walter Koover: In darwinian evolution, the environment provides the fitness function. As a semantic issue you may say that the environment does not choose, but from a conceptual point of view I don’t think it matters. It matters, It matters very much. And I definitely don't think I am mistaken. I am pointing to a very specific difference whic is often overlooked. Let's put it this way: 1) Men made GAs: they have a fiteness function which is designed by the programmer. The fitness function recognizes some properties, and, as you say, "determines which ones should be allowed to reproduce in greater numbers". The reproductive bonus is not a direct effect of the independent functionality of the replicator, but a bonus conferred by the system bevause of the recognition of a property which, in itself, would not give any reproductive advantage. So, the reproductive advantage is not spontaneouis, but "assigned" by an environment whose role is active, based on a logical recognition and an active procedure of "promotion". 2)NS. In this kind of GA, the situation is completely different. The environment is completely passive, is not a programmed environment, does not recognize anything and does not promote anything. The selection takes plays because, in a situation of limited resources, the replicators compete one with the other. So, the function which is selected, not being recognized by any fitness function, must have in itself the power to confer a reproductive advantage. IOW, the function selects itself in the replicator, given the environmental resources. This is a big difference, and poses a severe limit to what can be selected and what cannot. gpuccio
OK... and this bears on the truth claims at issue how? Interesting reading, though. Meanwhile, let us not be distracted from you being under the obligation, as an intellectually honest guy (or gal) to show how the laws of physics can explain ANY code. Thanks in advance. tgpeeler
gpuccio:
There are many equivocations about NS, as though something external is selecting, as though some fitness function is evaluating a result. That may be true for human made GAs, but it is not true of the model of darwinian evolution.
I think you are seriously mistaken here. In a GA the role of a fitness function is to discriminate among the "organisms" to determine which ones should be allowed to reproduce in greater numbers, isn't it? In darwinian evolution, the environment provides the fitness function. As a semantic issue you may say that the environment does not choose, but from a conceptual point of view I don't think it matters. Walter Kloover
Interesting PDF regarding Yockey: http://www.idnet.com.au/files/pdf/Doubting%20Yockey.pdf Petrushka
Yockey (2005) "The paradox is seldom mentioned that enzymes are required to define or generate the reaction network, and the network is required to synthesize the enzymes and their component amino acids. There is no trace in physics or chemistry of the control of chemical reactions by a sequence of any sort of a code between sequences." tgpeeler
Petruska, since you will not be able to identify the origination of a single protein, nor the transformation of a existing protein, I will give you a easier task. Will you please tell me the natural source of the simple universal ATP energy molecule before the ATP synthase machine was "invented" since ATP molecules are required for the production of proteins. Evolution Vs ATP Synthase - Molecular Machine - video http://www.metacafe.com/watch/4012706 Molecular Machine - The ATP Synthase Enzyme - video http://www.metacafe.com/watch/4380205 This following video will give you a better Idea what I'm looking for: ATP Synthase - Part V http://www.dnatube.com/video/1201/ATP-Synthase--Part-V Now Petruska, I don't want a just so story of how a ATP molecule could have possible formed, I want you to tell me exactly how natural processes form the ATP molecule without the ATP synthase enzymne bornagain77
I see now that anyway BA, with his usual efficiency, has already offered some reference about that. Thank you, BA. That pseudo value of functional sequences is one of the many myths built by darwinists for mere propaganda purposes, like the emergence of nylonase by frameshift mutation, the evolution of the flagellum form the T3SS, the "evolution" of the clotting system (even more ridiculous than the "evolution" of the eye), the various molecular "examples" of cooption (which I have discussed in some detail here with a biologist some time ago), and finally the emergence of the genetic code through supposed biochemical affinities of RNA and aminoacids. All these deserve at best to be treated as vague and very unreliable hypotheses, at worst as explicit lies. gpuccio
Petrushka: the lower limit of functional sequences is IMO completely bogus. It is based on a kind of approach which has deep methodologocal biases, both in the search method and in the definition of fucntion. A se3rious analygsis of the paper which it is based upon would be very interesting, and maybe I will engage in that sooner orn later. But not now. gpuccio
Petruska, this is the second or third time I've seen you appeal to Copernicus and Galileo, and the theory of Gravity. What you don't seem to realize is that both Copernicus and Galileo were devout Christians and were certainly not materialists as you are: "[It is my] loving duty to seek the truth in all things, in so far as God has granted that to human reason." Copernicus http://www.christianitytoday.com/ch/131christians/scholarsandscientists/copernicus.html Mathematics is the language with which God has written the universe. Galileo Galilei As well you seem to be under some delusion that gravity is explained to a material basis: REPORT OF THE DARK ENERGY TASK FORCE The abstract of the September 2006 Report of the Dark Energy Task Force says: “Dark energy appears to be the dominant component of the physical Universe, yet there is no persuasive theoretical explanation for its existence or magnitude. The acceleration of the Universe is, along with dark matter, the observed phenomenon that most directly demonstrates that our (materialistic) theories of fundamental particles and gravity are either incorrect or incomplete. Most experts believe that nothing short of a revolution in our understanding of fundamental physics will be required to achieve a full understanding of the cosmic acceleration. For these reasons, the nature of dark energy ranks among the very most compelling of all outstanding problems in physical science. These circumstances demand an ambitious observational program to determine the dark energy properties as well as possible.” http://jdem.gsfc.nasa.gov/docs/Decadal_Survey-Dark_Energy_Task_Force_report.pdf In fact, when scrutinized for details, the solution for the ultimate source for gravity (Dark Matter) lands squarely in the domain of Theism, so I would very much appreciate it if you would refrain to appealing to gravity to support your unsupportable conjectures for evolution. bornagain77
Petruska please name just one biologically relevant protein to be IDentified with the 10^10 to 10^15 "forward approach" you mentioned: Szostak's 1 in 10^12 work for finding relevant functional proteins in sequence space has now been brought into severe question: 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." http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0007385 Having a randomly generated "protein" stick to the universal ATP molecule and then just calling it functional is a long step away from finding the correct sequence space for a protein that will actually accomplish a specific task as Axe's work does: Even though Axe's work puts the odd at 1 in 10^77 for finding a biologically relevant functional protein in sequence space, the odds are actually much much much worse against the evolutionists: Notes: Proteins have also been shown to have a "Cruise Control" mechanism, which works to "self-correct" the integrity of the protein structure from any random mutations imposed on them. Proteins with cruise control provide new perspective: "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." http://www.princeton.edu/main/news/archive/S22/60/95O56/ Cruise Control?,, 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 algorithmic information must reside in each individual amino acid used in a protein in order to achieve such control. This fact gives us clear evidence that far more functional information resides in proteins than meets the eye. 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. http://en.wikipedia.org/wiki/PID_controller It is in realizing the staggering level of engineering that must be dealt with to achieve "cruise control", for each individual protein, that it becomes apparent even Axe's 1 in 10^77 estimate for finding specific functional proteins within sequence space, may be far to generous, since the individual amino acids themselves are clearly embedded with highly advanced mathematical language in their structures, which adds an additional severe constraint, on top of the 1 in 10^77 constraint, on which of the precise sequences of amino acids in sequence space will perform a specific function. Though the authors of the paper tried to put a evolution friendly spin on the "cruise control" evidence, finding an advanced "Process Control Loop" at such a base molecular level, before natural selection even has a chance to select for any morphological novelty, is very much to be expected as a Intelligent Design/Genetic Entropy feature, and is in fact a very constraining thing to the amount of variation we can expect from a "kind" of animal in the first place. notes: 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 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 Testing Evolution in the Lab With Biologic Institute's Ann Gauger - audio http://www.idthefuture.com/2010/05/testing_evolution_in_the_lab_w.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 - 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) You can dream all you want petruska, but as I said before you have completely left the field of empirical science by refusing to concede materialism is bankrupt. In fact I have an extreme confidence that in the not to distant future the materialists of today will be seen as the flat-earthers of yesteryear. bornagain77
Regarding Dougles Axe and the origin of proteins:
What is interesting is that the forward approach typically yields a “success rate” in the 10^-10 to 10^-15 range — one usually need screen between 10^10 -> 10^15 random sequences to identify a functional polymer. This is true even for mRNA display. These numbers are a direct measurement of the proportion of functional sequences in a population of random polymers, and are estimates of the same parameter — density of sequences of minimal function in sequence space — that Axe is after. 10^-10 -> 10^-63 (or thereabout): this is the range of estimates of the density of functional sequences in sequence space that can be found in the scientific literature. The caveats given in Section 2 notwithstanding, Axe’s work does not extend or narrow the range. To give the reader a sense of the higher end (10^-10) of this range, it helps to keep in mind that 1000 liters of a typical pond will likely contain some 10^12 bacterial cells of various sorts. If each cell gives rise to just one new protein-coding region or variant (by any of a number of processes) in the course of several thousands of generations, then the probability of occurrence of a function that occurs once in every 10^10 random sequences is going to be pretty nearly 1. In other words, 1 in 10^10 is a pretty large number when it comes to “probabilities” in the biosphere.
http://aghunt.wordpress.com/2008/12/26/axe-2004-and-the-evolution-of-enzyme-function/ Petrushka
P @ 79 "It seems odd to me that anyone would advocate abandoning a methodology that has worked so well for so long." Who's advocating that? Reason applied to evidence, that's the key. The problem with materialists is the rampant rejection of reason because reason always forces them to conclusions they detest. People are free to do whatever they will, of course (and answer for it) but it aggravates me to no end to labeled irrational by the irrational. Not that you are doing that in this snippet. I feel better now. tgpeeler
Petrushka @ 78 Can you point to a law of physics, feel free to use all of them, that can explain a code, any code? tgpeeler
Let me make clear my comment on destiny. A statistician looks at a lottery winner and assumes that given enough tickets and enough drawings, the odds favor someone winning. A biologist, looking at an unusual structure, such as the first eukaryotic cell, might wonder if this is an extraordinary event, or if it is as likely as someone eventually winning lotto. The answer to such questions can only be produced by research, some of it hard and perhaps taking generations. Science works by breaking hard problems down into pieces. Sometimes, when the pieces are understood, one can understand complex phenomena involving the pieces. It seems odd to me that anyone would advocate abandoning a methodology that has worked so well for so long. Petrushka
It is interesting that you cannot even explain the origination of a single protein or even the transformation of a single protein for the flagellum...
Nor could Galileo or Copernicus explain gravity or define it mathematically. Sometimes hundreds of years go by before a phenomenon can be adequately described. Sometimes even useful mathematical laws are limited to a range of conditions. Can you point to a law of physics violated by insertions, deletions, frame shifts, inversions, missense, or duplication? Can you point to a law of physics violated by fecundity and differential reproductive success? Can you point to single complex structure in a living thing that does not have component parts used for similar or different purposes? Or a structure that doesn't have simpler versions in different organisms, or alternate versions having similar functionality? Can you describe the science behind a view of destiny that requires flagella to evolve? Did life not exist before flagella? Would it cease if flagella had not evolved? Did life not exist before eukaryotes? If they had not appeared, would life have ceased? I am curious why ID advocates look at what exists, whether the result of common and repeatable processes, or the result of rare or improbable events, and conclude that destiny requires it to exist. I am also curious why anyone would take seriously the argument that a pre-specified chain of mutations should occur, or that a chain that did occur should repeat itself. Petrushka
It is interesting that you cannot even explain the origination of a single protein or even the transformation of a single protein for the flagellum, and yet you act as if pointing to something and "imagining" it transforming in your mind is somehow objective science: You are completely out of the realm of empirical science: Flagellum - Sean D. Pitman, M.D. http://www.detectingdesign.com/flagellum.html Biologist Howard Berg at Harvard calls the Bacterial Flagellum “the most efficient machine in the universe." Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A bornagain77
Petruska was the song in this video written "top down" from a mind or was it written "bottom up" by the machine? The Amazing Music Machine http://www.metacafe.com/watch/178495 Just as with this song or any other song is the flagellum and the blood clotting cascade, they must be implemented top down from a mind. bornagain77
No one has effectively answered Michael Behe’s challenge on the blood clotting system in the form that he presented it.
Sounds like weasel words to me. Behe does not get to define reality. The simple fact is that the flagellum and the blood clotting systen are not irreducible in any way that has consequences for theories of evolution. Both have sub-components that appear in other organisms that lack the "complete structure." Both systems occur in orther organisms in simpler form. There are other implementations of the functions. All of these render the concept of irreducibility moot. There are no magic structures that cannot be slightly modified or which cannot exist in slightly different forms, or which do not use sub-components that are found performing different functions in other organisms. What you have is the equivalent of missing links -- a concept that erodes with time and research. Petrushka
Here is a video on the flagellum that is fairly humbling to those who insist that it is "cobbled together" by Darwinian processes: Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Steven Curtis Chapman - Dive (Concept Video) http://www.youtube.com/watch?v=F2v-wZP6I3c bornagain77
Doug Axe has a article up at ENV: 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 1077 (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 1077 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. http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.html bornagain77
Petrushka: The blood clotting system is a formerly irreducible system that has many subsets among living organisms. And the E.coli flagellum is among dozens of flagella and cilia providing motility but having varying subsets genes and proteins. Not only is motility possible with subsets of genes, but there are quite a few varieties of such structures and quite a few different paths to them. First of all, the fact that a function can be implemented in different ways in different species, vith various sets of proteins, has nothing to do with irreducible complexity. We are well aware that different kinds of flagella and cilia exist. Behe just spoke about one type, and that has been enough, it seems, to give it eternal celebrity. But each single type of that machinery is, as far as I can understand, irreducibly complex. As is the ATP synthase, and probably all or almost all the compex biological machines, pathways and cascdes that we abundantly observe in all kind of cells (signaling form membrane to ythe nuclewus, apoptosis, the mytotic cycle, and so on). Regarding pathways, the clot issue is really very simple. Clotting has a common final pathway, with two alternative initiation pathways (intrinsic and extrinsic). Behe, probably for the sake of simplicity, analyzed in his book only the common final pathway. His argument in the book is about that. And, as far as I know, it has never been countered by anybody. About the flagellum, together with the many sources quoted by BA, you can also check, if you want, the "Frequently Raised But Weak Arguments Against Intelligent Design" section here, where we have tried to give our point of view, at point #33. gpuccio
Here are a couple more references refuting on Blood clotting and the Flagellum: Miller's Failure To Refute Behe - Blood Clotting Cascade - Casey Luskin Excerpt: The lesson to be learned here is to always fact-check the claims of supremely confident defenders of Darwin like Dr. Ken Miller. He’s a very smart biologist. However, sometimes looking closely at his citations shows just how weak his arguments are. In this case, it seems very likely that Miller’s authority, Doolittle, had a very weak basis indeed for claiming that the lamprey lacked Factor V or Factor VIII. http://www.evolutionnews.org/2009/09/ken_millers_reliance_on_doolit025341.html The flagellum has steadfastly resisted all attempts to elucidate its plausible origination by Darwinian processes, much less has anyone ever actually evolved a flagellum from scratch in the laboratory; Genetic Entropy Refutation of Nick Matzke's TTSS (type III secretion system) to Flagellum Evolutionary Narrative: Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept... http://mbe.oxfordjournals.org/cgi/content/abstract/msn153v1 "One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later," Howard Ochman - Biochemist - New Scientist (Feb 16, 2008) Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video http://www.vimeo.com/9032112 bornagain77
Petrushka: Blood clotting and flagella. You are simply wrong on both points. No one has effectively answered Michael Behe's challenge on the blood clotting system in the form that he presented it. http://behe.uncommondescent.com/2009/01/miller-vs-luskin-part-1/ And the "paths" you speak about for flaggellar "precursors" are the biological equivalent of vapourware: http://behe.uncommondescent.com/2009/05/letter-to-trends-in-microbiology/ SCheesman
Isn’t the relationship between genotype and phenotype barely understood to this day? Aren’t “alleles” only really useful as a way to begin to teach undergraduates basic genetics?
I understand that at some time in the education of chemists they are told that everything the learned before is wrong. I'm not sure whether this impinges on the status of alchemy. Petrushka
Nonsense. ID presents that as an observation and an inevitable result of chemistry and statistics. All you need to do to prove ID wrong is to fill in the blanks in a single case that has been presented as “irreduceably complex”.
The blood clotting system is a formerly irreducible system that has many subsets among living organisms. And the E.coli flagellum is among dozens of flagella and cilia providing motility but having varying subsets genes and proteins. Not only is motility possible with subsets of genes, but there are quite a few varieties of such structures and quite a few different paths to them. Petrushka
Isn't the idea of the "allele" outdated? Isn't it true that such a simplistic conception of genes and their related traits does not reflect reality? Isn't the relationship between genotype and phenotype barely understood to this day? Aren't "alleles" only really useful as a way to begin to teach undergraduates basic genetics? Phaedros
Petrushka:
But ID has the logically impossible task of proving there are no possible viable organisms with genes or alleles bridging that gap.
Nonsense. ID presents that as an observation and an inevitable result of chemistry and statistics. All you need to do to prove ID wrong is to fill in the blanks in a single case that has been presented as "irreduceably complex". All swans are white. Find me the black one. It's been done with swans. It hasn't been done with biology yet. SCheesman
Moreover, there are lots of very likely d)s: as I have repeatedly said, a few thousands of independent protein domains which cannot have originated by RV...
You mean they appear not to have a common protein ancestor. I have no way of evaluating that, so I'll pass on commenting. What you call integration I call spaghetti code. If I, as a programmer, write functions that reads differently depending on the entry point or frame shift, I get fired. Or my company eventually goes broke. Eventually programs require maintenance, and density of meaning becomes a problem rather than a sign of cleverness. So if living things do this, they limit their ability to track environmental change. Raise or lower the average temperature five degrees and you get widespread extinctions. Petrushka
Petrushka: The problem with asserting that “d” exists is that neither evolutionists nor ID proponents have an actual history of such an event. The same problem exists with asserting c). Moreover, there are lots of very likely d)s: as I have repeatedly said, a few thousands of independent protein domains which cannot have originated by RV, and for which there is not even a pale theory for a step by step transition, and all possible evidence against it. And remember, science is about best explanations, not about infinite faith that some day perhaps we could find something which can save us from all our present inconsistencies. And I don't agree about the ID "gaps" becoming narrower with research: research is increasing the level of complexity, of integration and of design present in living beings. In the last few decades, known functional complexity in biology has increased of many orders of magnitude. While materialistic explanations for it are still where they were in the beginning: a useless theory which has no internal consistency and no explicatory power. Micorevolution is still the only thing neo-darwinism can explain. gpuccio
Petrushka: Asserting that there are living examples of “d” seems to be at the very heart of the ID movement. The irreducibly complex structure. Something that jumped the unbridgeable gap. Here you understand ID correctly. gpuccio
The problem with asserting that "d" exists is that neither evolutionists nor ID proponents have an actual history of such an event. What you have with structures like the flagellum is a molecular equivalent of a gap in the fossil record. But ID has the logically impossible task of proving there are no possible viable organisms with genes or alleles bridging that gap. The problem gets more difficult with research, because there are dozens of kinds of cilia and flagella, and it turns out there are only a couple of proteins that are both necessary and common to all these organisms. The problem with the gaps argument is that the gaps get narrower with research. Petrushka
Arthur Hunt (#35): I have read your essay and, quickly for the moment, Yarus' paper. I give you some first impressions: 1) I appreciate your essay, although obviously I don't agree on many things. Some of them are evidently due to our different positions, and it would probably be useless to discuss them as such. But a first point I would like to make is that IMO your emphasis about the central role of the origin of the genetic code in Meyer's book is excessive. I have read the book, and if I had to summarize it in a few words, I would say that the central theme is OOL in all its many aspects. The origin of the genetic code is certainly one of them, but not certainly the only one, and not necessarily the most important, neither in reality nor in Meyer's book. 2) About the Yarus paper, while it can be of some interest, I must say that I am not impressed. Its methodology and its analysis and its conclusions are not convincing, deeply artificial, and obviously motivated by a pre-existing ideology: defending the hypothesis of the RNA world. I have already expressed my "perplexities" about this approach, and I confirm them here. 3) Anyway, some more specific comments are due. I think that Yarus has not proved his thesis in any way (and, I believe, you agree with that in some measure). However, you say that Meyer's statement that there is no biochemical law which binds the genetic codons to the corresponding aminoacids has no supporting evidence, but that's simply the truth of what we observe today, of how the genetic code, transcription and translation work in the real world. In the real world, the codon (or anticodon) do not interact with the aminoacid. It's only the complex of tRNA and aminoacil-trna-synthetases which holds the key to the decoding of the genetic information. These are facts. Yarus' hygpotheses are just hypotheses of how the present situation could have had origin through some transitory state where there was some biochemical connection between a minority of the present codons and some aminoacids. A vague and very incomplete scenario, based as usual on very artificial findings. 4) Even taking for good some of Yarus' findings (and I do that with many reservations), many questions remain regarding his interpretation of those results. a)First of all, only a minority of the codons have a special "enrichment" in the population of artificial RNAs and aminoacid binding sites generated by Yarus. He promptly interprets this fact imagining that those were the original codons, and that the rest was added after. That looks like a very ad hoc explanation. The fact remains that the vast majority of the codons of the genetic code for the 8 aminoacids tested had no special relationship with the corresponding aminoacids. b) Only 8 aminoacids were tested, out of 20. Only six had some relation with some of their codons. Yarus promptly infers that 75% of aminoacids "entered the code in this stereochemical era". A very risky inference, for an era which exists only in his imagination, and for numbers which are so small that do not allow any valid inference. If and when he will test all of the 20 AAs, we will know how many of them have the property he describes (not certainly how many of them entered the code in a stereochemical era of which we have no evidence). c) The results he describes can be interpreted in many different ways. There can be a reason why those specific codons are concentrated in those binding sites. There could be a biochemical reason, but that reason could have nothing to do with the code. It is not clear to me if the analysis has been performed for all 64 codons for each aminoacid. The results of such an analysis, if it was done, are not provided in the paper. The table only shows the statistic probability for the codons specific for each aminoacid, and not for all the rest. And, again, only a minor part of these codons have a significant association, And only in six AAs out of eight. There is more. As you certainly know, there are many different attempts, none of them definitive, to find second codes which can influence the overall behaviour of the DNA molecule beyond the simple coding of the primary structure of proteins. And proteins and nucleic acids certainly interact at many other levels other than translation. there may be biochemical reasons for the specific interactions found by Yarus, which have nothing to do with the genetic code. Or which are necessary for these "second codes", or for regulatory mechanisms. It would be interesting to know if the interactions described by Yarus can find some application and occurrence in what really happens today in existing cells, and not only in artificial RNA molecules created in the lab. d) One final note about the statistical analysis. I cannot comment on it in detail, because I have made no serious attempt to analyze it, and probably I will not (I really can't see any reason to give any priority to that). Moreover, papers rarely give you sufficient data to understand if the statistical analysis is credible, and believe me, many times it isn't. Considering how we arrived to this discussion, anyway, I am obliged to mention that, according to the understanding of probability shown by Yarus in the book which originated this thread, I definitely feel not very inclined to give him credibility in this field. But of course, I hope that at least for the paper he was helped by some competent statistician. :) gpuccio
c) Any complex result which can be deconstructed into successive molecular steps, each of which is in the range of RV, and each of which is selectable, can be achieved. d) On the contrary, any complex result which cannot be deconstructed in that way cannot be achieved
All you are saying here is stuff that any biologist would agree with. 1.The standard model of evolution requires an unbroken chain of descent. 2. Since about 1940 the standard model of evolution requires that variations be small. No hopeful monsters. A lot has been learned since 1940 about molecular biology, but it is still true that individuals must find a mate among others of its species, and that limits the "size" of a mutation that can contribute to the gene pool of a population. Asserting that there are living examples of "d" seems to be at the very heart of the ID movement. The irreducibly complex structure. Something that jumped the unbridgeable gap. Petrushka
Thanks gpuccio, that was clear and to the point, and I will cite it because of its clarity. bornagain77
Petrushka and others: About NS and GA. GAs can compute and find solutions. Nobody denies that. But NS is a very specific GA. Petrushka says: Evolution is embodied in imperfect replication plus fecundity. That’s it. There’s no code specifying goals. It’s an inevitable outcome of any system that replicates imperfectly and in which offspring have differential reproductive success. I perfectly agree with that statement, provided that for "evolution" we mean darwinian evolution. Pwetrushka's definition is bvery correct. There are many equivocations about NS, as though something external is selecting, as though some fitness function is evaluating a result. That may be true for human made GAs, but it is not true of the model of darwinian evolution. In that model, NS means only: a) we have replicators b) we have random variation in the replicating process c) if and when RV creates a replication advantage, that specific result of RV expands in the population d) when RV creates a sufficient replication disadvantage, that specific result is eliminated. This is the algorithm. Of this we must discuss, to understand what it can do and what it cannot do. Human made GAs are nothing like that. They create fitness functions, evaluate results, define specific searches. Nothing of that is in the original model. In the original model, the replicator selects itself by some real function which exploits the environment. In other words, it is the new function in the replicator which selects itself, in a specific environment, and not the environment which selects anything. That has an important consequence: only new functions which spontaneously give a replication advantage can be selected. Now, if we ask what the model can do or not do, the answer is: a) It can select anything which arises through RV, provided that the emerged result gives some replicatory advantage. b) Selected results can certainly cumulate, provided that each partial result can emerge through RV, and be selected. c) Any complex result which can be deconstructed into successive molecular steps, each of which is in the range of RV, and each of which is selectable, can be achieved. d) On the contrary, any complex result which cannot be deconstructed in that way cannot be achieved, The ID central point is: most complex results we observe in the genomes and proteomes are of the d) kind. Indeed, no single protein domain has ever been shown to be of the c) kind. IOW, GAs come in different flavours. Some, like the weasel, are only ill inspired propaganda. Others are useful and serious computational tools. But no human made GA says anything about the "spontaneous" GA which is modeled in neo-darwinism. So, if darwinists want to show what their model can really do, they should really analyze the RV + NS algorithm, and not others which are completely different. gpuccio
Petrushka (#50): Please, don't put words in my mouth which I have never said. Your reading of Durston is completely wrong. Random proteins can be functional. Durston: "Abel and Trevors have delineated three qualitative aspects of linear digital sequence complexity [2,3], Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC). ... As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality." Protein functionality can increase gradually due to mutation and selection. Here is the phrase in Durston's paper about which you equivocate: "In principle, some proteins may change from a non-functional state to a functional state gradually as their sequences change. Furthermore, iso-enzymes in some cases may catalyze the same reaction, but have different sequences. Also, certain enzymes may demonstrate variations in both their sequence and their function. Finally, a single mutation in a functional sequence can sometimes render the sequence non-functional relative to the original function." Here Durston is simply listing some common concepts which are the background for his work. Please note that he saya "in principle", that is "it is theoretically possible that". Indeed, the first statement, that "some proteins may change from a non-functional state to a functional state gradually as their sequences change", is simply the currebt assumption. Durston states it dutifully as a theorical possibility, exactly because his work has the purpose of trying to verify quantitatively at least some aspects of that assumption. Your reading of these words if incorrect and instrumentaL. Moreover, I must say that I find your use of the quoted material veri unfair. You know very well that I have presented the Durston paper as an essential example of how functional complexity can be really measured, and of what is the appropriate unit. Those were your questions. Durston gives the answers, and I have repeatedly re-formulated those answers for you and others. You have never commented on the sibstance of those answers, just avoiding them saying that you are not impressed by statistical arguments, or something like that. Instead, you continuosly misquote Durston attributing to him statements that he has never made, and which are not part of the pertinent work he has done. Papers, whoever the authors may be or may think, are important for the facts and the objective work they present. If you want to comment on a paper, take the time to understand it and to comment on the substance of what is presented there. Finally, in my post #43 I have given an explicit comment about your previous post. As usual, no comment has come from you on the substance of what I have said. I don't pretend that you agree, I don't pretend that you spend your time in a long discussion, but at least a brief acknowledgement of what others say in response to you, and some brief thought, would be appreciated. gpuccio
One further question, why oh why would clumps of matter need to or want to reproduce in the first place? What is the point? Isn't one carbon atom, or a chain of them, just as meaningless and inert as any other chance arrangement of atoms? Phaedros
Hmm Petrushka I guess you haven't considered all of the systems needed to sustain just one life and how extremely well they must work. Again an example of the extent to which people have to simplify life in order to accept an inadequate and dated theory. Phaedros
"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,,,," William Bialek bornagain77
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." http://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." http://biologicinstitute.org/2009/06/01/physicists-finding-perfection-in-biology/ bornagain77
Petrushka,
The oracle simply grades each individual by total distance traveled.
Please, please, PLEASE do not contribute to the confusion by adopting the "oracle" terminology of Dembski and Marks. A "black box" function (finite domain and codomain) does not explain itself. Observed input-output pairs provide no information whatsoever as to the outputs associated with inputs yet to be supplied to the box. This is precisely why there is "no free lunch" for optimizers. The notion of Dembski and Marks that the black box supplies "warmer-colder" information, as in the child's game, is simply wrong. Sooner Emeritus
Perfection is not an attribute of living things. Reproduction is just about the only attribute common to all living things. I'm not going to debate the origin of life, because neither side has any detailed record of the history of first life. Once there is a replicator, however, the issue of perfection is moot. So long as some descendants are able to survive it does not matter that some variants are non-viable. There are a bunch of possible red herrings. One is the assumption (unnecessary) that evolution is striving or searching for something. The simple fact is that a lineage either survives or it doesn't. If some variants are more successful than others, the population shifts in their favor. But shifting can also occur because the evolutionary algorithm dithers about a level of fitness without any obvious increase or decrease. Petrushka
Information is completely unlike a crytstal, however, and and no genetic algorithm can arrange letters into meaningful sentences because there is no benefit until the sentence is nearly “perfect”.
You'll need to take that up with gpuccio. He presented evidence on a previous thread that: Random proteins can be functional. Protein functionality can increase gradually due to mutation and selection. Durston was one of the sources. Petrushka
Petrushka:
The traveling salesman algorithm would work even if the cities moved or shifted position between trials.
A genetic algorithm finding the solution to the travelling salesman problem is like the formation of a crystal from a fluid. Things are shifted around in a manner which minimizes the energy, and the crystal is the natural and inevitable result. The shortest (or very nearly shortest) route is the inevitable consequence of the genetic algorithms' actions. Information is completely unlike a crytstal, however, and and no genetic algorithm can arrange letters into meaningful sentences because there is no benefit until the sentence is nearly "perfect". There are no short-range advantages to be gained in permuting random strings to other random strings, and the search space is so large that you cannot hope to locate an island of meaning in the sea of meaninglessness. The problem of composing the information in the DNA that undergirds life, indeed the process required to modify the code to achieve real evolutionary change (as opposed to shuffling around existing information, or expressing it differently via epigenetics) is in no way equivalent to the travelling salesman problem, and by extension genetic algorithms are fundamentally unsuited for such a task. Genetic algortithms are great for growing crystals. Only intelligence can create digital code. SCheesman
There's one other possible outcome of a GA that hasn't seen much discussion. In case where there is no reachable target, only gradations of fitness, the algorithm can reach a certain level and stop improving. It simply dithers up and down in fitness. My itatsi program does this. The fitness scores improve dramatically for a while, then level off, bobbing up and down about a relatively high mean. The initial rapid rise in fitness followed by dithering is suggestive. Some of you have argued that in living things, we seldom see beneficial mutations. This is an inevitable outcome when there is goal or target, just levels of fitness. Petrushka
That’s certainly true. No one wants to deny that algorithms can be very efficient in finding solutions to problem according to laws of necessity, and GAs are just a subset of algorithm, which incorporate some random search as part of their working. But still algorithms they are
Algorithms, whether written by programmers or not, are embodied. They have machinery that executes the steps. Evolution is embodied in imperfect replication plus fecundity. That's it. There's no code specifying goals. It's an inevitable outcome of any system that replicates imperfectly and in which offspring have differential reproductive success. It can be observed in simple chemical replicators, such as Spiegelman Monster. There's no program specifying improvement or targets. Petrushka
How can it have no target and no way of knowing which direction it is going, yet also know that some variations are better than others? “Better” according to what standard — what goal?
A GA requires just two components, both of which are blind to goals. It needs a replicator, a component that produces a generation of offspring. And it needs a component to introduce variations. There is a third component, the oracle, which grades individuals in each generation. But the oracle could be written by another programmer. The criteria for scoring fitness could be anything. The replicator is blind to the oracle's criteria. Petrushka
In fact, you contradicted yourself within two sentences. You first state: “It has no target and no way of knowing how close it is to the best possible solution.”
There's no contradiction. There's no way to know the best solution to the TSP. Unlike the Weasel demo, no one knows the target. The oracle simply grades each individual by total distance traveled. The shortest routes are reproduced with random modifications. There is no end point, just gradual improvement. If you take the trouble to write a Weasel program, you'll discover that this is true even of the simplest form. The algorithm has no knowledge of the target. It simply replicates, with modification, the best scoring individual. The Weasel algorithm doesn't need to know that there is a case where further improvement is impossible. Petrushka
Arthr Hunt: strange, I have debated with many darwinists here in perfect serenity. Anyway, thank you for the invitation. Give me some time: I will read your essay and answer you, either here or elsewhere. gpuccio
Petrushka: Thank you for answering my challenge. I can see the meaning of your post. You mean (correct me if I am wrong): even if the Weasel knows the solution, there are other genetic algorithms which can solve very complex problems without knowing the solution in advance. That's certainly true. No one wants to deny that algorithms can be very efficient in finding solutions to problem according to laws of necessity, and GAs are just a subset of algorithm, which incorporate some random search as part of their working. But still algorithms they are. Again, the point here is not simply complexity. It is fucntional complexity (dFSCI). In other words, algorithms, genetic or not, can certainly generate complexity, but they cannot generate dFSCI. Let's take your example. The only dFSCI which I can see in it is the alògorithm itself, the program. It has a function (solving the traveling salesman problem with reasonable approximation), and it is 27.8 KB long (zipped). So, assuming that the functional target is small enough (in computer programs, single bits are probably more strictly specified than in proteins), it is functionally specified (it describes a function), it is complex, it is not significantly compressible (not in the zipped form, at least), it is digital: it is dFSCI, and it was designed. Not so its output. Its output is not dFSCI, it is just data which give the solution to a specific problem in input. It is information, but not functionally specified information. The Weasel output is dFSCI (if we put the threshold not too strict). It is functional (has meaning in English), it is complex, it is digital. That's why no algorithm genetic or not, will be able to output it without having prior information about the solution. gpuccio
Petrushka: "What evolution doesn’t require is a specific target. Just differences in reproductive success." You have yet to support the assertion that evolution requires no target. Petrushka: "The traveling salesman problem has one significant similarity. It has no target and no way of knowing how close it is to the best possible solution. All it knows is that some variations are better than others." ... according to rules which are defined by a goal -- a target. Or is it just a fluke that the whole class of GAs which are brought together in the aforementioned competition just so happen to come close (some more so than others based on the intelligence of the programmer) to solving that specific problem rather than some other arbitrary problem? In fact, you contradicted yourself within two sentences. You first state: "It has no target and no way of knowing how close it is to the best possible solution." and then you state: "All it knows is that some variations are better than others." How can it have no target and no way of knowing which direction it is going, yet also know that some variations are better than others? "Better" according to what standard -- what goal? As I stated above, tongue in cheek of course, "… and I’m sure the Genetic Algorithm that wins also brags to all his Genetic Algorithm friends about how smart he is …" Do you see the significance? CJYman
The traveling salesman algorithm would work even if the cities moved or shifted position between trials. Obviously there is some rate of shifting that would result in zero progress, but that happens to living things also. Petrushka
Don’t believe it? Then find me a genetic algorithm that can produce “Methinks…”, indeed any sentence without a target built-in.
The selecting agent must rank individuals by some definition of fitness. For living things it could be the biochemistry necessary to sustain metabolism, or it could be predation or competition for resources. In all cases, including biological evolution, some sort of differential reproduction takes place. The algorithm needs to know absolutely nothing about how a generation will be ranked. The variation generator needs to know absolutely nothing about what will be useful, necessary or successful. It needs to know nothing about targets or whether the target is fixed or changing. Petrushka
Petrushka: Genetic Algorithms. A valiant effort, but genetic algortithms rely on two important prerequisites: 1) the ability to calculate small improvements in a penalty function, the mere existance of which implies an over-arching knowledge of the solution space, i.e. distance from the target, and 2) a relatively dense solution space, where each valid solution is but a short step away by random search.
OK, but that's exactly what's observed in Nature -- tiny, almost imperceptible variations among individuals. That's the way plant and animal breeding works. What evolution doesn't require is a specific target. Just differences in reproductive success. The traveling salesman problem has one significant similarity. It has no target and no way of knowing how close it is to the best possible solution. All it knows is that some variations are better than others. Petrushka
Petrushka: Genetic Algorithms. A valiant effort, but genetic algortithms rely on two important prerequisites: 1) the ability to calculate small improvements in a penalty function, the mere existance of which implies an over-arching knowledge of the solution space, i.e. distance from the target, and 2) a relatively dense solution space, where each valid solution is but a short step away by random search. Neither of these are present for a truly blind evolutionary process to evolve a bunch of letters into an (or any) intelligible sentence, in any language, of any reasonable length, in less time than the universe has been around. Don't believe it? Then find me a genetic algorithm that can produce "Methinks...", indeed any sentence without a target built-in. SCheesman
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
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
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
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
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
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
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
gpuccio - well it would seem that they need ID people to try and engender some debate!. aqeels
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#20100226a bornagain77
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
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
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
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
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
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
(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
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.html bornagain77
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
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
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
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
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
"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
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
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
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
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
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
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#20100302a bornagain77
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
4) Oh, and when another field of science makes statements refuting Darwinism, then it magically does not apply to biology. See, even though living things are completely reducible to pure chemistry, it is somehow also quite different from everything else for some unknown reason. Maybe simply because Darwinism is "THE THING THAT COULDN'T DIE" hannodb
Thank you William, for this post. On a previous article of Uncommon Decent, a Darwinist confronted me with a 24 page technical paper from Yarus, which he claimed refutes Stephen Meyer's SITC argument. As a layman, I'm quite defenceless when being put on the spot with something like this, but he was kind enough to explain to me what Yarus is saying in simple terms. In short, Yarus seems to have found an evolutionary pathway for the formation of tRNA, which he then claimed refutes Stephens argument of the DNA enigma. Though I could not refute the paper, I could refute the idea that the arbitrary nature tRNA is central to Stephen's argument. I would also suspect that the conditions under which Yarus performed his experiments most probably did not resemble a realistic prebiotic environment, and the paper probably was filled with evolutionary assumptions. Ofcause, without the necesary technical knowledge, that is the best I could do. I aslo found an accusation from the Darwinists that ID scientists avoid Yarus. Sure enough, a search on EvolutionNews.org did not render any results. However, I attributed this to the fact that ID is young, and the Darwinists simply outnumber the ID scientists with so much, that it is impossible to reply to each and every one of them. However, this post confirms to me that: 1) ID scientists are not afraid to engage with Yarus, as they are not affraid to engage with anyone else. (Not that I ever doubted it, I have yet to hear a Darwinist argument that even comes close to the reasoned and calculated logic of ID) 2) Like the more well known Darwinists like Dawkins, Yarus too is forced to make simple logical errors in order to defend Darwinism. 3) This just once again confirms my believe that more scientific data just creates larger problems for Darwinism, rather than to solve existing problems. hannodb
Here is a video I recently uploaded from Dr. Fazale Rana that touches on the RNA world and the origin of life. Problems of the RNA World - Origin Of Life - Dr. Fazale Rana http://www.metacafe.com/watch/4564682 bornagain77
Un-believe-able. Spend just a day in statistical analysis. This methodology supports any conclusion whatsoever; its provided from the start. No wonder these educated men are convinced of themselves. Upright BiPed
Oops, I really have problems with the "cite" tag. The quote in the previous post ends at "Mutation and selection achieve adaptive texts (texts that make sense) without any target.", and my comment starts with "In other words". Please, take notice of that. It's very important! gpuccio
I would like to just emphasize the part which, IMO, is the brightest pearl in that sea of creative nonsense, because it really deserves attention: People who wish to take refuge in complexity sometimes claim that this kind of result is faked because we included the target statement in our program and then intelligently chose the intermediates. This objection gets the argument backward. Even our starting statement, as indicated earlier, is one out of 1.5 x 10^90. Or, to put it in other words, by induction we get a similar result no matter which statement we pick as the target. The Chomsky gibberish on the opening page of this chapter-written long before and in complete disregard of our present purposes (in order to faithfully emulate English text, but without any meaning)-is one of the statements of our Dobzhansky system and accordingly could be evolved if we so chose. The point is not that we evolved any one statement but that we might choose any target with similar results - descent with modification and selection clearly will navigate to any and all of the 1.5 x 10^90 strings of characters in our system, our toy genome. The objection that we picked a particular goal cannot be to the point, because any possibility would have given the same result, whether or not it is predefined from our point of view. Furthermore, we can eliminate human choice as a factor: the first English word surrounded by spaces occurs quickly, at the 19th step. We could evolve words and compose sentences without any initial target instead of targeting Dobzhansky's aphorism. Mutation and selection achieve adaptive texts (texts that make sense) without any target. In other words, if we choose any of 1.5 x 10^90 strings (or, I suppose, any string at all), and we include it in this wonderful Yarus program, the program can easily evolve it! Ah, and I forgot, "the first English word surrounded by spaces occurs quickly, at the 19th step". And I suppose that, by just dropping an english dictionary in the system, it can easily be selected! But why am I worrying? "Mutation and selection achieve adaptive texts (texts that make sense) without any target." That's probably how Yarus'book was generated. :) gpuccio
Incredible! That's what believing in an RNA world does to a human mind! :) gpuccio

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