Uncommon Descent Serving The Intelligent Design Community

The Image of Pots and Kettles ….

August 6, 2007
Intelligent Design
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I was just reading this fairly-well written article, and came upon one of the last paragraphs.

It’s an interesting take by a, shall we say, “non-scientist”:

“These scientists argue that only ‘rational agents’ could have possessed the ability to design and organise such complex systems.

Whether or not they are right (and I don’t know), their scientific argument about the absence of evidence to support the claim that life spontaneously created itself is being stifled – on the totally perverse grounds that this argument does not conform to the rules of science which require evidence to support a theory.”

You have to like this logic: the scientific community doesn’t want to entertain the idea of ID with its implicit argument that there is no evidence to support RM+NS, since ID is not a scientific theory given that it doesn’t have evidence to support its theory.

Yes, indeed, the “image of pots and kettles”!

Here’s the link.
Arrogance, dogma and why science – not faith – is the new enemy of reason

Comments
Fox’s studies were replicated by many people.
Soap bubbles were replicated by other people too. Fox's protocells are doublespeak. They are nothing like real cells. This is like baking a rectangular piece of clay and suggesting it's like a computer chip by alluding to some superficial similarities. Fox did create something and publish it in peer review. He was rumored on the short list for the Nobel prize. However ID proponents Thaxton, Bradley, and Olsen gave Fox's theories a total thrashing.scordova
August 15, 2007
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art Comments sometimes get eaten for reasons unknown. I have a question regarding the ARN link you gave. Has anyone duplicated Sidney Fox's thermal protein experiment and where is it published? This seems to be the stuff of urban legend but I didn't spend long searching for more.DaveScot
August 15, 2007
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A [Yodaish?] note: A look at the ENV discussion on abiogenesis here, worth taking, it is. Material, indeed, it is . . . GEM of TKIkairosfocus
August 15, 2007
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mg Are ID and methodological naturalism inherently incompatible? Only if you consider intelligent agency to be an unnatural phenomenon. This should be a source of cognitive dissonance for chance & necessity pundits. They purport that human intelligent agents self-assembled over the course of a few billion years from inanimate elements and in the same breath say it's unscientific to propose any precursor intelligence was involved in the process. If intelligence can arise "naturally" then intelligent agency is by definition a force of nature that must be considered as a possible factor. Moreover the Copernican principle of mediocrity implies we should expect intelligent agents to exist elsewhere in time and space (no special creation). It's a good thing for a lot of Darwinists that I'm not the president of the materialist club because I'd revoke a lot their memberships for spitting in the eye of the Copernican paradigm. What should we call that; post-enlightenment or dark age thinking?DaveScot
August 14, 2007
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art Yarus’ work indicates that chemistry in fact does underlie the genetic code, and thus “the arrangement of nucleotide bases”. This is my point in citing Yarus et al., to disabuse readers here of the notion that the genetic code is in some way disconnected from chemistry (as Meyer does). Thus the particular mapping of codons to amino acids (to be more precise). At least for some codon/amino acid mappings there's some sort of chemical affinity. This seems to be a reasonable conclusion if there was no bias introduced by the experimental equipment or procedures. Interpretation is still largely a matter of confirmation bias. Engineered systems exploit properties of materials to best effect. If you see it as an engineered system this is an expected finding. The larger problems for OOL remain untouched. No known natural environment can produce the purified and concentrated homochiral reagent mixture used in the experiment. A fair claim is that Yarus' experiment is further evidence that intelligent agency is required to get these kinds of biochemical reactions to happen.
"An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going." (Crick, Francis H.C. [Co- discoverer of the structure of DNA, Nobel laureate 1962, Professor at the Salk Institute, USA], "Life Itself: Its Origin and Nature," Simon & Schuster: New York NY, 1981, p.88).
This is only more true now than it was when Crick first penned it. I realize this goes beyond your point that there is experimental evidence of chemical affinity between some amino acids and the codons they map to in the universal genetic code. I write it because I don't want readers disabused into thinking this is any significant breakthrough for abiogenesis hypotheses. It's actually more like clutching at straws.DaveScot
August 14, 2007
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Art: 1] Labelling issues as "misconceptions" does not answer them on the merits. In particular, you still have to get TO the first cell with chiral molecules fulfilling a geometrically linked role in a code-based information system, with empirical anchoring. 2] Meyer is saying in effect that there is no universally forced, crystal-like bonded sequence in nucleotides in DNA chains, or of amino acid residues in proteins; otherwise the first would not work well as a storage medium, and the latter would lose its flexibility as the workhorse molecule in the cell. [Hence the comparison to inked glyphs on paper.] 3] Where there is a point, is that the amino acid residues are not evenly distributed in proteins, and that may also be so for dna strands. That is we do not see 5% each for 20 amino acids in every case, and it is possible to deviate from 25% each for G, C, A, T too. 4] And, if the laws of chemistry have "life" written into them, that simply opens up another level of design inference. --> In short for evolutionary materialism to properly prevail, you need to have an empirically credible way to life by chance plus natural regularities that are not themselves also "fishy." --> Let's see you lay it out in summary and link it. [Onlookers cf my always linked, esp. Sections A and B, for a 101 level intro.] GEM of TKI PS: I have no interest in joining ARN's debates.kairosfocus
August 14, 2007
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You have one tough row to hoe, to connect information to chemistry. The work you reference is similar to the amino acid proof of Miller in 1953. It only hints at a very minimum possibility of generating a negligible and very questionable few "words" of CSI if that at all, You do this while ignoring the sheer wall of complexity that has to be scaled to get to a functional life form whose information content is measured in ,at bare minimum, kbits. Plus you ignore the evidence for the interrelated whole of the genome! When you quote such suggestive work then say you have refuted ID, it reveals your bias to the naturalistic/materialistic philosophy, especially considering the overwhelming weight of evidence from the other sciences that conform to the anthropic hypothesis. i.e.,, The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses in complexity any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)! No line of computer code ever written by man approaches that level of data compression (poly-functional complexity). Further evidence for the inherent complexity of the DNA is found in a another study. In June 2007, a international team of scientists, named ENCODE, published a study that indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. This “complex interwoven network” throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. This “interwoven network” finding is extremely bad news for naturalists! Naturalists truly believe you can get such staggering complexity of information in the DNA from some process based on blind chance. They cannot seem to fathom that any variation to a basic component in a species is going to require precise modifications to the entire range of interconnected components related to that basic component. NO natural law based on blind chance, would have the wisdom to implement the multitude of precise modifications on the molecular level in order to effect a positive change from one species to another. Only a “vastly superior intelligence” would have the wisdom to know exactly which amino acids in which proteins, which letters in the DNA code and exactly which repositioning of the 25 million nucleosomes (DNA spools) etc .. etc .. would need to be precisely modified to effect a positive change in a species. For men to imagine blind chance has the inherently vast wisdom to create such stunning interrelated complexity is even more foolish than some pagan culture worshipping a stone statue as their god and creator. Even if evolution of man were true, then only God could have made man through evolution. For only He would have the vast wisdom to master the complexity that would be required to accomplish such a thing. Anyone who fails to see this fails to appreciate the truly astonishing interwoven complexity of life at the molecular level. Even though God could have created us through “directed evolution”, the fossil record (Lucy fossil proven not ancestral in 2007) and other recent “hard” evidence (Neanderthal mtDNA sequenced and proven “out of human range”) indicates God chose to create man as a completely unique and distinct species. But, alas, our naturalistic friend is as blind and deaf as the blind chance he relies on to produce such changes and cannot bring himself to face this truth. Most naturalists I’ve met, by and large, are undaunted when faced with such overwhelming evidence for Divine Intelligence and are convinced they have conclusive proof for naturalistic evolution somewhere. They will tell us exactly what it is when they find it. The trouble with this line of thinking for naturalists is they will always take small pieces of suggestive evidence and focus on them, to the exclusion of the overriding vast body of conclusive evidence that has already been established. They fail to realize that they are viewing the evidence from the wrong overall perspective to begin with. After listening to their point of view describing (with really big words) some imagined evolutionary pathway on the molecular level, sometimes I think they might just be right. Then when I examine their evidence in detail and find it wanting, I realize they are just good story tellers with small pieces of “suggestive” evidence ignoring the overwhelming weight of “hard” evidence that doesn’t fit their naturalistic worldview. Instead of them thinking,” WOW look how God accomplishes life on the molecular level,” they think” WOW look what , dumb and blind chance accomplished on the molecular level.” Naturalists have an all too human tendency to over-emphasize and sometimes even distort the small pieces of suggestive evidence that are taken out of context from the overwhelming body of “conclusive” evidence. This is done just to support their own preconceived philosophical bias of naturalism. This is clearly the practice of very bad science, since they have already decided what the evidence must say prior to their investigation. I could help them find the conclusive proof for evolution they are so desperately looking for if they would just listen to me. For I know exactly where this conclusive proof for evolution is; it is right there in their own imagination. What really amazes me is that most naturalists are people trained in exacting standards of science. Yet, they are accepting such piddling and weak suggestive evidence in the face of such overwhelming conclusive evidence to begin with. This blatant deception; , dumb, blind chance has the inherent wisdom to produce staggering complexity, is surprisingly powerful in its ability to deceive! That it should ensnare so many supposedly rational men and women is remarkable. Then, again, I have also been easily misled by blatant deception many times in my life, so, maybe it is not that astonishing after all. Maybe it is just a painful and all too human weakness we all share that allows us to be so easily deceived.bornagain77
August 14, 2007
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PS: The points for a prebiotic earth also extend to hydrothermal vents etc, as I discuss in my always linked.kairosfocus
August 14, 2007
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All: Several thematic, selective, summary points (insomnia power can do only so much across several threads . . .): 1] Art, 43: Kenyon (and Thaxton), quite frankly, had and hasn’t an inkling of the the work I point to . . . As for homochirality, any system that involves surface-based catalysts is inevitably, inexorably going to move towards a homochiral state. This issue is a non-starter as far as the OOL is concerned. On the contrary, it is you who have to account - without burden of proof shifting or the rhetoric of dismissal -- for getting to a plausible scenario for creating the monomers for proteins and nucleic acids etc in a reasonable pre-boiotic cosmos. If on Earth, you have to account for the credible atmosphere [not the circa 1953 conveniently reducing one for the spark in gas expts etc], and then the resulting chaining in the case of the thermodynamics that supports racemic not chiral soups has to be faced. If in space, you have the further burden of getting to earth through a credible panspermia mechanism and reaching here in time for the first fossils to be there as soon after formation of a crust as we see just above, on the usual timelines. In short, on the evidence in hand, planetary etc systems don't spontaneously form the antecedents to the molecules of life, much less the now partly elucidated information systems including their algorithms and codes. [Onlookers, cf my always linked for more.] 2] “chance” means different things to different people Let's use a simple example to specify a point of reference: heavy objects tend to fall under the natural regularity we call gravity. If the object is a die, the face that ends up on the top from the set {1, 2, 3, 4, 5, 6} is for practical purposes a matter of chance. But, if the die is cast as part of a game, the results are as much a product of agency as of natural regularity and chance. Indeed, the agents in question are taking advantage of natural regularities and chance to achieve their purposes! [From Section A, my always linked.] The relevant point is, that on RM, chance is the prime claimed innovator, as NS only selects from what has been innovated. But, Behe's observed edge of evolution points to the sharp limitation on chance as innovator. Not surprising, in light of say longstanding findings of stat mech and information theory on the creation/ searching out of specified functional complexity by chance-dominated searches across configuration spaces. 3] CS, 4: I think that world-views are very different from theories — and so criteria of theory-choice are different from criteria of world-view choice. I am not so sure of that, as many theories are quite ideological, and at research programme level, deeply embed metaphysical commitments. Further to this, we do have significant power of choice on worldviews as we do on reasoning in general – or else we are back at the point that we have a self-referential frame of thought that discredits all thought. 4] I’ve been trying to steer clear off “materialism vs theism,” Problem is, that through games like imposing the unwarranted concept of methodological naturalism, and even hints at determinism and chance driving the life of the mind, materialism and its fellow travellers are being injected by the power brokers in today's academy. 5] I see this debate as one between competing “research programmes” in Lakatos’ sense. So do I and I see that therein lieth much of the ideological matter and the meta level worldviews and associated epistemology questions. Sometimes I think Feyerabend was right to say in effect that across time and schools, in aggregate, anything goes – as a matter of fact. So we need to sort out the chaos. It might help you to see that I cut my intellectual eye-teeth in the 1970's in a Marxism-dominated intellectual climate as an objector to the ideological hothouse mentality. All the current NCSE, ACLU etc tactics are very very familiar to me – and I predict a very similar outcome probably over the next decade. In short, as the Peloponnesian war showed, “democracies” subjected to Plato's Cave power games and manipulation are on a road to suicide. But that can be very costly to those who try to say “stop the madness” before it is evident to all from its consequences – cf here the literature on group-think. And, even decades after the fact there are still many who are trying to make excuses and to repackage the old empirically discredited notions and agendas. [E.g. too much of environmentalism is Watermelon: green outside, red inside.] 6] CS, 47: I’m concerned that, once the only viable options are starkly posed as “chance” (or “chance” + “necessity”) vs. “design,” too great a chokehold has been placed on our metaphysical imagination. At core level, ever since at least Plato in The Laws, X, ~ 2,400 ya, we do have that interacting trichotomy, as I noted on above. Can you identify a fourth generic alternative that does not reduce to one or more of the three causal forces? Give us a concrete case in point, kindly. However, in concrete situations, the general theme is fleshed out as in e.g my appendix 1 to my always linked, point 6 on the microjets in a vat. Similarly, you can see the debate over Caputo and the Flagellum in that ever so prolonged thread on Padian etc. So, please do not let summary remarks distract from that context of examining what is meant by necessity, chance and agency in specific settings. And I would love to see the fourth alternative, with an example that is concrete. GEM of TKIkairosfocus
August 14, 2007
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Art you state that: As for homochirality, any system that involves surface-based catalysts is inevitably, inexorably going to move towards a homochiral state. Even if you did overcome the homochiral problem, (you sited no study for me to refute) you would still face the insurmountable hurdle of probabilities. i.e. It is commonly presumed in many grade school textbooks that life slowly arose in a primordial ocean of pre-biotic soup. Yet, there is absolutely no hard evidence, such as chemical signatures in the geologic record, indicating that a ocean of this pre-biotic soup ever existed. The hard physical evidence scientists have discovered in the geologic record is stunning in its support of the anthropic hypothesis. The oldest sedimentary rocks on earth, known to science, originated underwater (and thus in relatively cool environs) 3.86 billion years ago. Those sediments, which are exposed at Isua in southwestern Greenland, also contain the earliest chemical evidence (fingerprint) of “photosynthetic” life [Nov. 7, 1996, Nature]. This evidence has been fought by naturalists, since it is totally contrary to their evolutionary theory. Yet, Danish scientists were able to bring forth another line of geological evidence to substantiate the primary line of geological evidence for photo-synthetic life in the earth’s earliest known sedimentary rocks (Indications of Oxygenic Photosynthesis,” Earth and Planetary Science Letters 6907 (2003). Thus we have two lines of hard conclusive evidence for photo-synthetic life in the oldest known sedimentary rocks ever found by scientists on earth! The simplest photosynthetic bacterial life on earth is exceedingly complex, too complex to happen by even if the primeval oceans had been full of pre-biotic soup. The smallest cyano-bacterium known to science has hundreds of millions of individual atomic molecules (not counting water molecules), divided into nearly a thousand different species of atomic molecules; and a genome (DNA sequence) of 1.8 million bits, with over a million individual complex protein molecules which are divided into hundreds of different kinds of proteins. The simplest of all bacteria known in science, which is able to live independent of a more complex host organism, is the candidatus pelagibacter ubique and has a DNA sequence of 1,308,759 bits. It also has over a million individual complex protein molecules which are divided into several hundred separate and distinct protein types. The complexity found in the simplest bacterium known to science makes the complexity of any man-made machine look like child's play. As stated by Geneticist Michael Denton PhD, “Although the tiniest living things known to science, bacterial cells, are incredibly small (10-12 grams), each is a veritable micro-miniaturized factory containing thousands of elegantly designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world”. So, as you can see, there simply is no simple life on earth as naturalism had presumed - even the well known single celled amoeba has the complexity of the city of London and reproduces that complexity in only 20 minutes. Here are a couple of quotes for the complexity found in any biological system, including simple bacteria, by two experts in biology: "Most biological reactions are chain reactions. To interact in a chain, these precisely built molecules must fit together most precisely, as the cog wheels of a Swiss watch do. But if this is so, then how can such a system develop at all? For if any one of the specific cog wheels in these chains is changed, then the whole system must simply become inoperative. Saying it can be improved by random mutation of one link, is like saying you could improve a Swiss watch by dropping it and thus bending one of its wheels or axis. To get a better watch, all the wheels must be changed simultaneously to make a good fit again." Albert Szent-Györgyi von Nagyrapolt (Nobel prize for Medicine in 1937). "Drive in Living Matter to Perfect Itself," Synthesis I, Vol. 1, No. 1, p. 18 (1977) “Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours" Geneticist Michael Denton PhD. To give an idea how impossible “simple” life is for naturalistic blind chance, Sir Fred Hoyle calculated the chance of obtaining the required set of enzymes for just one of any of the numerous types of “simple” bacterial life found on the early earth to be one in 1040,000 (that is a one with 40 thousand zeros to the right). He compared the random emergence of the simplest bacterium on earth to the likelihood “a tornado sweeping through a junkyard might assemble a Boeing 747 therein”. Sir Fred Hoyle also compared the chance of obtaining just one single functioning protein (out of the over one million protein molecules needed for that simplest cell), by chance combinations of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously. The simplest bacteria ever found on earth is constructed with over a million protein molecules. Protein molecules are made from one dimensional sequences of the 20 different L-amino acids that can be used as building blocks for proteins. These one dimensional sequences of amino acids fold into complex three-dimensional structures. The proteins vary in length of sequences of amino acids. The average sequence of a typical protein is about 300 to 400 amino acids long. Yet many crucial proteins are thousands of amino acids long. Proteins do their work on the atomic scale. Therefore, proteins must be able to identify and precisely manipulate and interrelate with the many differently, and specifically, shaped atoms, atomic molecules and protein molecules at the same time to accomplish the construction, metabolism, structure and maintenance of the cell. Proteins are required to have the precisely correct shape to accomplish their specific function or functions in the cell. More than a slight variation in the precisely correct shape of the protein molecule type will be for the life of the cell. It turns out there is some tolerance for error in the sequence of L-amino acids that make up some the less crucial protein molecule types. These errors can occur without adversely affecting the precisely required shape of the protein molecule type. This would seem to give some wiggle room to the naturalists, but as the following quote indicates this wiggle room is an illusion. "A common rebuttal is that not all amino acids in organic molecules must be strictly sequenced. One can destroy or randomly replace about 1 amino acid out of 100 without doing damage to the function or shape of the molecule. This is vital since life necessarily exists in a "sequence—disrupting" radiation environment. However, this is equivalent to writing a computer program that will tolerate the destruction of 1 statement of code out of 1001. In other words, this error-handling ability of organic molecules constitutes a far more unlikely occurrence than strictly sequenced molecules." Dr. Hugh Ross PhD. It is easily demonstrated mathematically that the entire universe does not even begin to come close to being old enough, nor large enough, to ally generate just one small but precisely sequenced 100 amino acid protein (out of the over one million interdependent protein molecules of longer sequences that would be required to match the sequences of their particular protein types) in that very first living bacteria. If any combinations of the 20 L-amino acids that are used in constructing proteins are equally possible, then there are (20100) =1.3 x 10130 possible amino acid sequences in proteins being composed of 100 amino acids. This impossibility, of finding even one “required” specifically sequenced protein, would still be true even if amino acids had a tendency to chemically bond with each other, which they don’t despite over fifty years of experimentation trying to get amino acids to bond naturally (The odds of a single 100 amino acid protein overcoming the impossibilities of chemical bonding and forming spontaneously have been calculated at less than 1 in 10125 (Meyer, Evidence for Design, pg. 75)). The staggering impossibility found for the universe ever generating a “required” specifically sequenced 100 amino acid protein by would still be true even if we allowed that the entire universe, all 1080 sub-atomic particles of it, were nothing but groups of 100 freely bonding amino acids, and we then tried a trillion unique combinations per second for all those 100 amino acid groups for 100 billion years! Even after 100 billion years of trying a trillion unique combinations per second, we still would have made only one billion, trillionth of the entire total combinations possible for a 100 amino acid protein during that 100 billion years of trying! Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place! The simplest forms of life ever found on earth are exceedingly far more complicated jigsaw puzzles than any of the puzzles man has ever made. Yet to believe a naturalistic theory we would have to believe that this tremendously complex puzzle of millions of precisely shaped, and placed, protein molecules “just happened” to overcome the impossible hurdles of chemical bonding and probability and put itself together into the sheer wonder of immense complexity that we find in the cell. Instead of us just looking at the probability of a single protein molecule occurring (a solar system full of blind men solving the Rubik’s Cube simultaneously), let’s also look at the complexity that goes into crafting the shape of just one protein molecule. Complexity will give us a better indication if a protein molecule is, indeed, the handi-work of an infinitely powerful Creator. In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, that is 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it is estimated it will take one entire year for it to analyze the mechanism by which JUST ONE “simple” protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape. In real life, the protein folds into its final shape in a fraction of a second! The computer would have to operate at least 33 million times faster to accomplish what the protein does in a fraction of a second. That is the complexity found for JUST ONE “simple” protein. It is estimated, on the total number of known life forms on earth, that there are some 50 billion different types of unique proteins today. It is very possible the domain of the protein world may hold many trillions more completely distinct and different types of proteins. The simplest bacterium known to man has millions of protein molecules divided into, at bare minimum, several hundred distinct proteins types. These millions of precisely shaped protein molecules are interwoven into the final structure of the bacterium. Numerous times specific proteins in a distinct protein type will have very specific modifications to a few of the amino acids, in their sequence, in order for them to more precisely accomplish their specific function or functions in the overall parent structure of their protein type. To think naturalists can account for such complexity by saying it “happened by chance” should be the very definition of “absurd” we find in dictionaries. Naturalists have absolutely no answers for how this complexity arose in the first living cell unless, of course, you can take their imagination as hard evidence. Yet the “real” evidence scientists have found overwhelmingly supports the anthropic hypothesis once again. It should be remembered that naturalism postulated a very simple "first cell". Yet the simplest cell scientists have been able to find, or to even realistically theorize about, is vastly more complex than any machine man has ever made through concerted effort !! What makes matters much worse for naturalists is that naturalists try to assert that proteins of one function can easily mutate into other proteins of completely different functions by pure chance. Yet once again the empirical evidence we now have betrays the naturalists. Individual proteins have been experimentally proven to quickly lose their function in the cell with random point mutations. What are the odds of any functional protein in a cell mutating into any other functional folded protein, of very questionable value, by pure chance? “From actual experimental results it can easily be calculated that the odds of finding a folded protein (by random point mutations to an existing protein) are about 1 in 10 to the 65 power (Sauer, MIT). To put this fantastic number in perspective imagine that someone hid a grain of sand, marked with a tiny 'X', somewhere in the Sahara Desert. After wandering blindfolded for several years in the desert you reach down, pick up a grain of sand, take off your blindfold, and find it has a tiny 'X'. Suspicious, you give the grain of sand to someone to hide again, again you wander blindfolded into the desert, bend down, and the grain you pick up again has an 'X'. A third time you repeat this action and a third time you find the marked grain. The odds of finding that marked grain of sand in the Sahara Desert three times in a row are about the same as finding one new functional protein structure (from chance transmutation of an existing functional protein structure). Rather than accept the result as a lucky coincidence, most people would be certain that the game had been fixed.” Michael J. Behe, The Weekly Standard, June 7, 1999, Experimental Support for Regarding Functional Classes of Proteins to be Highly Isolated from Each Other “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)bornagain77
August 13, 2007
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I'm concerned that, once the only viable options are starkly posed as "chance" (or "chance" + "necessity") vs. "design," too great a chokehold has been placed on our metaphysical imagination. And yet I'm also fascinated by the need to accept this constraint.Carl Sachs
August 13, 2007
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the notion, often put forth by ID proponents, that the genetic code is an arbitrary mapping of amino acid upon DNA sequence Well I certainly don't agree with that. An arbitrary mapping would be something I'd expect from a random chance mechanism. A mapping that exploits subtle electro-chemical properties to best advantage is something I'd expect in an engineered system.DaveScot
August 13, 2007
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Art you state: chance means different things to different people. I don’t want to deconvolute the term, just note that it is a pretty empty one IMO. Ahh, but chance means a very specific thing on this blog. Since chance is the only viable option to design, chance is rigorously defined and debated on this site. So if you want to say chance did something biologically on this blog, be prepared to rigorously defend your assertion, I assure you, you will be called on it most strenuously.bornagain77
August 13, 2007
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There are several threads going on here, all of which deserve careful examination. One that interests me quite a bit is what seems to me an assumption made by "Bornagain": that our epistemological situation is one of beginning with a "blank slate," as it were, utterly devoid of not only prejudices but seemingly all concepts altogether, and that mere observation alone can determine the correctness of a world-view. Like Bornagain and GEM, I'm interested in how one can compare world-views, and I'm also interested in how one can justify the assertion that one world-view is more rational than another. However, I am skeptical of several assumptions that I think are at work in this discussion. For one thing, I think that world-views are very different from theories -- and so criteria of theory-choice are different from criteria of world-view choice. (If anyone 'chooses' his or her world-view!) For another, I simply do not see the debate between ID and neo-Darwinism as a debate between competing world-views. This is why I've been trying to steer clear off "materialism vs theism," except to offer skeptical challenges to the way in which this opposition is starkly posed. Likewise I'm frankly puzzled by the emphasis on the putative ethical or political consequences of neo-Darwinism or ID. Instead, I see this debate as one between competing "research programmes" in Lakatos' sense. And so I'm puzzled and fascinated by the emotional energy with which 'both' sides (as if there were only two sides to any interesting question!) invest this problem. In a related note, I'm gearing up to teach Plato in a few weeks, so I'm thinking a lot about how 'theoretical' discourses (metaphysics, epistemology) take on practical significance in response to cultural crisis.Carl Sachs
August 13, 2007
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Thanks Dave Scot, Art you stated "Chance whatever that is" Dr. Dembski has set the chance probability bound at 10^150. This number represents far more quantum events than will ever happen in the universe. This number is "violated many times in molecular biology. You cite a very hypothetical interpretation of the RNA world scenario then scoff at me and expect your very superficial treatment of the evidence to carry more weight than what I can produce. Let me suffice it to say that chance "whatever it is" is not a defense of the molecules to man hypothesis!bornagain77
August 13, 2007
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Hi Dave: It seems that Art is raising a "new" version of the old Kenyon Biochemical Predestination thesis. (Of course, DK abandoned it after he saw the evidence and analysis by Bradley et al, and has subsequently become a design thinker.) That is not irrelevant, as Art would have to first answer to the evidence on distributions and interlocking, codes etc. Then, he would need to answer: how it is that written into the chemistry of the various molecules of life, lo and behold, is a natural regularity that is life-promoting? How do you think that nature as we observe it just happened to be in such an interestingly life-promoting state? [You hint at that in 40 . . .] Also, the issue of chirality cannot be dodged so easily: how do you get to a credible prebiotic soup with sufficiently complex ingredients, and the balance of homochiralities that we observe, relative to chance + necessity only on plausible planetary or comet environments etc? [TBO's TMLO has an extensive assessment of this that is a good starting point.] I think Art has some serious analysis and persuasive but fair on the merits summarising to do. GEM of TKI PS: let's see whart Prof Sachs has to say further.kairosfocus
August 13, 2007
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art The article you reference is interesting but hardly conclusive and far reaching in implication. The gist of it appears to be that amino acid binding sites were clipped out of a ribosome randomly assembled, amplified, and some statistical anomalies were identified in that triplets (2 codon and 6 anticodon) coding for certain amino acids appear more often in the binding site for that residue than pure chance would predict. They then use this sequence bias to suggest there is biochemical rhyme and reason behind the genetic code mapping rather than it merely being some arbitrary result of pure chance that it is what it is. I'd put forward that rhyme and reason is more characteristic of design than chance. What was your point again?DaveScot
August 13, 2007
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DaveScot, the work I cryptically refer to has nothing to do with homochirality. The amino acid-codon correspondence is rather a different ball of wax. The best I can do by way of pointers is a citation that gives a good (if somewhat incomplete, as it's already "old") overview of the experiments and their implications. A cut'n'paste from the pdf: Annu. Rev. Biochem. 2005. 74:179–98 doi: 10.1146/annurev.biochem.74.082803.133119 Copyright c 2005 by Annual Reviews. All rights reserved First published online as a Review in Advance on February 18, 2005 ORIGINS OF THE GENETIC CODE: The Escaped Triplet Theory Michael Yarus,1 J. Gregory Caporaso,2 and Rob Knight2 1Department of Molecular Cellular and Developmental Biology, 2Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0347 As always, enjoy.Art2
August 12, 2007
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Art2 amino acid-codon correspondence - is a manifestation of perfectly normal interactions between RNA and amino acid Wow. Someone solved the problem of homochirality and I missed it. I need to get out more I guess. I hope you can provide a link to this great achievement. FYI DaveScot
August 12, 2007
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bornagain77, the "information" in DNA - namely, the amino acid-codon correspondence - is a manifestation of perfectly normal interactions between RNA and amino acid. Interactions that fall way on this side of "chance" (whatever that is). FYI.Art2
August 12, 2007
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Re Mgarelick, Following Dave Scots excellent response to you. I would like to point out that the information in the DNA had to originate somehow. The options for how the information came to be in DNA is severely limited. Basically there are only two options. Chance or Design. Can you think of any other option? If you can, please do tell. Thus by logic if chance is overwhelmingly ruled out (as it has been repeatedly) that only leaves design as the only viable option.bornagain77
August 12, 2007
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DS - I'll follow you over to the next thread.mgarelick
August 12, 2007
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mgarelick And I would vigorously dispute that it is “identity.” For every member of the set you are designating as “observed to be the product of agency,” the more precise description is “observed to be the product of human agency.” I fail to see how adding "human" to agency changes the identity. Humans are intelligent agents. All the products mentioned are still the result of agency. If you find something that has many of the same properties as an apple, and you have observed apples growing on apple trees, the most reasonable inference is that what you found was produced by something like an apple tree. Indeed, to infer that what you found just spontaneously formed on the ground from inanimate matter would be entirely unsupported. The only abstract coded information processing and manufacturing machinery where the origin can be determined is a product of human intellect. There is one other known instance of this type of machinery, it's found only in living things, and its origin is undetermined. We only have one confirmed producer of these kinds of machines and the producer is human intellect. The only reasonable inference that can be made is that machines of unknown origin were produced by something like a human intellect. I don't see how this isn't a perfectly valid scientific inference. It is exactly the kind of hypothesis that Popper exemplified with white swans. Popper's Hypothesis: All swans are white. ID Hypothesis: All abstract code driven information processing and manufacturing machinery, which isn't simply a replication of prexisting machinery of the same type, was produced by intelligent agency. Popper's hypothesis, he said, could never be proven because there could never, even in principle, be a way of knowing that a black swan doesn't exist somewhere. Popper said the key thing that made it a scientific hypothesis was that it could be falsified in principle by observing a single black swan. ID's hypothesis can never be proven because we can never know, even in principle, that no non-intelligent process is able to design these kinds of machines. ID's hypothesis however can be falsified by observing a single non-intelligent process creating these kinds of machines.DaveScot
August 12, 2007
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5] CS, 27: Suppose it is the case that human beings have “spiritual properties” and “material properties.” Does it follow that they are opposed to one another? A cube made of steel has spatial properties, mass, chemical properties — they are distinct but not opposed. That various complementary properties may be held by a given entity and are interacting and compatible -- cf. here the effect of a large enough dose of say barbituates -- has nothing to do with the essential divergence between mind and matter. Let it stand as a case in point, that if one knows that a given train of thought has credibly been in effect simply physically [etc] caused rather than being anchored in evidence and reasoning, that is usually enough to discredit it. That is why Marxists loved to use dialectical materialism to discredit their class-interested foes, why Freudians were quick to point to potty training of their uptight critics, and why Skinnerians were quick to point to operant conditioning, etc., etc. But in each case, there is a self-reference involved, and it undermines their own case. The problem here is that materialism, in general, as a monistic system open only to chance and necessity as causal forces at origins, credibly runs into insuperable difficulties accounting for the credibility of the mind and morals relative to its premises. [The link is to a 101 level discussion for those new tot he issues; Willard and many more have more technical discussions; some are linked in the just linked.] 6] Cs, 27: general epistemological problems with strict empiricism. One problem is “the underdetermination of theories by evidence.” In a nutshell, the problem is this: for any set of observations, the data are consistent with more than one theory . . . Beautiful. So you are willing to agree with me that reason and belief are inextricably intertwined in the roots of all of our worldviews, and particfularly our scientific theorising? That ,therefore, we ALL live by faith, whether Christian or Buddhist, atheist, materialist, scientist or mathematician? (Thence, that we should look at comparative difficulties and make warranted though provisional in principle conclusions as to what and why we believe? Thus, too, that we should embrace diversity in thought at the table of serious discussion, including in our teaching and praxis of science in general and of the science of origins in particular? So, also, what have you been doing about NCSE-style, Judge Jones-enforced censorship?) 7] Cs, 28: the lesson I’ve taken from James’ “The Will to Believe” is that Cliffordian evidentialism is appropriate with respect to scientific questions — James’ complaint is that one could not live as a Cliffordian. Actually, the specific lesson James drew relative to strictly scientific issues in general, was that they are not the sort of issues where one is existentially forced to make a momentous commitment, so one can afford to be tentative and non-committal on such. [But note that at research programme level, scientific disciplines often embed implicit and potentially momentous and forced worldview commitments, and may even be held to “warrant” them. As my always linked discusses, what is happening with NDT and associated evolutionary materialism, is that its warrant is being undermined by advances in information theory relevant to the origin of systems exhibiting what I have abbreviated as FSCI, a subset of WD's CSI.] My more direct concern is the later objections, implicated in the sort of claim Sagan popularised: “extraordinary claims require extraordinary evidence.” The first problem being that the claims perceived as requiring more than merely ADEQUATE evidence/warrant are those that happen to cut across one's worldview expectations [cf above], so one is often begging the question. Next, if one claim is only to be believed relative to extraordinary evidence, that evidence with such implications is in turn most extraordinary and so requires even more extraordinary evidence, leading to an infinite regress. Thus, we are also implicated in a self referential inconsistency as the finite and fallible mind cannot handle such a regress. Thence, a better solution is to accept the reality that we live by faith, seek adequate evidence and warrant, being open to comparative difficulties across live options – which sweeps question-begging and selective hyper-skepticism off the table. [And, if one's credible evidence, say, involves personal knowledge of God through encounter in the face of the risen Christ, that of course shifts the balance of the evidence to be addressed rather dramatically!] 8] BA: I’ve debated both materialist and what I call material/spiritual dualist, and all their conjectures for explanations of the evidence fail in crucial areas of logic in key areas of the evidence! You are here pointing to the importance of comparative difficulties-based worldviews analysis, across factual adequacy, coherence and explanatory power: a sound worldview must account for the relevant facts, must hang together logically and dynamically, and must be elegantly simple, not either simplistic or an ad hoc patchwork. This is precisely where science is revealed as a process within the wider discourse of philosophy, and in which it must be reasonably tentative and open-minded to fresh evidence and reasoning. NDT as a research programme, and associated broader evolutionary materialism models for the claimed cascade from hydrogen to humans, is manifestly failing at that bar. GEM of TKIkairosfocus
August 12, 2007
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Prof Sachs and BA (et al), It seems reasonable to pick up the thread of discussions on points, first noting that Prof Willard has a most interesting collection of articles here. On points of interest: 1] CS, 26: If we confine ourselves, initially, to “direct observation,” then the only agents relevant for FSCI are humans. Not at all. First, a bit of a side-note: there are millions who would dispute -- e.g., based on their personal encounter with God in the face of the risen Christ, going back to a certain famous, course- of- history changing Sunday morning just outside Jerusalem's Northern Gate -- any and all claims that the only agents known to exist through direct observation are humans! (I cite this to show that the full scope of evidence and the issues of selectivity and inconsistent, question-begging skepticism are a bit more widespread on this issue than we like to think.) But more directly, we know notoriously that humans are intentional, intelligent agents. Interesting things follow from that that are crucial: --> We therefore credibly know that agents exist, and so we must be open to the possibility that humans do not exhaust the list of existing or possible agents. Then, when we encounter evidence such as a complex digital storage unit functioning in a complex information system based on code-bearing, algorithm-expressing nanotechnologies that are self-replicating, that should be allowed to speak for itself relative to what we know about information systems and their origins. --> All worldviews that claim to give a credible account of reality must be able to account for the existence of agency and associated mentality. That means that we must be able to account for, precisely, the non-material, mental aspects of agency. Things like propositions, truth, implication, moral obligation, intent, one idea in two or more locations at the same time, etc, etc. --> It further means that when a worldview, such as evolutionary materialism, notoriously and on multiple grounds, struggles to account for the credibility of mind and the binding nature of moral obligation then that worldview is plainly seriously factually inadequate and since mentality is a self-referential issue, it is arguably self-refuting as well. [Hence, the previously linked form Willard as one of many phil arguments on those lines.] 2] CS, 26: organisms and machines both exhibit FSCI. And I’m willing to grant that in all cases that we’ve observed, agency is required for FSCI . . . . What, then, does this tell us about the origins of ‘natural organisms’? It tells us, I think, at most that agency could have been involve, not that it was (or is) . . . . from the fact that “chance” + “necessity” have not been observed to produce FSCI, it does not follow that they could not have. First, we are dealing with a specific, common point across both the cell and the computer: digital storage functioning in a code-bearing, algorithm implementing system. We know that agents can create such, but we also have not only the point that chance + necessity have not been observed to produce such, but also an excellent, physically anchored reason why: the configuration spaces involved in creating such systems through “lucky noise” so vastly outstrip opportunities in the observed cosmos, that we can comfortably look at the C + N null hyp and eliminate it. At the same time we know agents routinely produce such systems and components. And, after 2,400+ years of thought on the matter, there is no credible fourth alternative. Thus, relative to the empirical facts and observations, there is excellent inductive/scientific warrant to infer to agency on the origin of the nanotech in the cell. Of course that does not amount to demonstrative proof, but that is a characteristic of all scientific inference of consequence. Besides, post-Godel, not even Mathematics is capable of proof beyond reasonable doubt. (So, the issue4 of selective hyper-skepticism, Cliffordian evidentialism form, again surfaces.) 3] Cs, 26: I also do not think that inquiry can be replaced by a priori considerations about what “chance” or “necessity” o “matter” can or cannot do. The limits on what we may reasonably expect chance and necessity to do, are not a priori, but are a posteriori, in the context of the rise of modern probability and inferential statistics, as well as the related development of modern statistical thermodynamics as an extension of that same reasoning into precisely the world of the molecule and other microparticles. What has been presented is a comparison, and an observationally anchored elimination [of course subject to type I and I errors, as are all such arguments] by exhaustion of observed available probabilistic resources. That is why many worlds interpretations of the cosmos are suddenly popular among physicists of materialistic bent, as they know all too well the force, success and credibility of the underlying reasoning in statistical thermodynamics. [Cf my already linked microjets thought experiment.] 4] Cs, 26: I only find it unreasonable to think that the design inference is sufficient to allow us to answer that question in the affirmative. The warrant for inference to design as the most credible explanation of say the nature and function of DNA, is at least as good as many another warrant in science, pure and applied. The excerpted is, sadly, simply a statement of selective hyper-skepticism. . . .kairosfocus
August 12, 2007
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Re #24:
The key problem here is of course that this misses the point that DNA is a known case of a specific type of entity as discussed above, one which is of course routinely — and only — observed to be the product of agency. That is, a discrete-state, chained, information-storage unit of large capacity. This is not mere analogy, it is identity.
But the very question before us is whether DNA is the product of agency. How can it be persuasive to say that it must be the product of agency because it is the sort of thing that is only the product of agency? And I would vigorously dispute that it is "identity." For every member of the set you are designating as "observed to be the product of agency," the more precise description is "observed to be the product of human agency."mgarelick
August 11, 2007
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Prof. Sachs You stated: For one, the selection of a theory cannot be determined solely by data. For another, what the data are taken to be evidence for is also influenced by theoretical considerations. I do not doubt for a moment that a non-theist could present an interpretation of trans-cranial magnetic stimulation and of near-death experiences which is as consistent with the data as are the interpretations you’ve presented here. Likewise with respect to the origins of life, the “fine-tuning problem,” etc. It is very interesting that you say a theory cannot be selected solely by data, When it is the very basis of the scientific method that says evidence has the primary authority in science to determine which of the competing theories are true. Are you saying that the scientific method is not first and foremost driven by evidence? This seems a blatant practice in obfuscation to me if you do so. Second, the , across the board , interpretation of the evidence from all branches of knowledge (cosmology, biology, etc etc) conform to the theistic postulations best. I've debated both materialist and what I call material/spiritual dualist, and all their conjectures for explanations of the evidence fail in crucial areas of logic in key areas of the evidence! ONLY Theism stays true to the evidence throughout comparative examination. So your assertion that a "non-theists" can come up with rational explanations to explain the evidence across the board is simply false.bornagain77
August 11, 2007
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GEM, Thanks for the link to the Willard article!Carl Sachs
August 11, 2007
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On a closely related note: the lesson I've taken from James' "The Will to Believe" is that Cliffordian evidentialism is appropriate with respect to scientific questions -- James' complaint is that one could not live as a Cliffordian. On the one hand, what works well for us as scientists does not work well for us as human beings. On the other hand, what is necessary for us to live well as human beings does not always make for good science.Carl Sachs
August 11, 2007
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Bornagain77, My principal objections to what you say are epistemological, not metaphysical. In other words, I have nothing to say for or against materialism or theism. Firstly, I do have some skeptical worries about the basis for that opposition as starkly conceived. Suppose it is the case that human beings have "spiritual properties" and "material properties." Does it follow that they are opposed to one another? A cube made of steel has spatial properties, mass, chemical properties -- they are distinct but not opposed. Secondly, there general epistemological problems with strict empiricism. One problem is "the underdetermination of theories by evidence." In a nutshell, the problem is this: for any set of observations, the data are consistent with more than one theory. (The argument for this comes from the philosopher Quine, if you want to look it up.) Several things follow from this. For one, the selection of a theory cannot be determined solely by data. For another, what the data are taken to be evidence for is also influenced by theoretical considerations. I do not doubt for a moment that a non-theist could present an interpretation of trans-cranial magnetic stimulation and of near-death experiences which is as consistent with the data as are the interpretations you've presented here. Likewise with respect to the origins of life, the "fine-tuning problem," etc. The reason why I work in epistemology and ethics, an avoid metaphysics as much as I can, is because, unlike with scientific theories, I have no idea what would count as a reason to think that a given metaphysical view is true. (Although I find metaphysics fascinating and enjoyable!)Carl Sachs
August 11, 2007
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