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246 Responses to Stephen Meyer’s Book Ranked #1 in Science/Physics/Cosmology at Amazon

1. 241

   kairosfocusAugust 8, 2009 at 8:58 am

   Nakashima-san:

   Evoloops is an intelligently designed and controlled simulation in a computer, not chemistry.

   I note my remarks on how the analogy breaks down:

   ______________

   >> As genes circulate in the loop counterclockwise [note the non-random specificity], copies of them are made [Just how, kindly sir?] and sent [again, just how, and how will these copies just happen to program functional protein chains etc?] toward the tip of the arm. The arm grows through repetition of straight growth and left turning. [How is such "folding" initiated and controlled? Is not Right turning just as probable inherently, in a presumed prebioptic soup, and how are the "right" monomers going to be available in step by step sequence to carry out the info storage and onward metaboliic function etc?]. When the tip reaches its own root after three left turns, they bond together to form a new offspring loop. [an algorithm writes itself out of lucky noise -- or is that by an intelligent programmer's input] Then the connection between parent and offspring disappears [[ That is, we have termination here, a nontrivial issue in algorithm design]]. ( In such a way, the loop reproduces its offspring which has a structure identical to its parent’s in the right area, in 151 updates. >>
   ___________________

   In short,t he functionality of evoloops is crucially dependent on their specific design and coding.

   GEM of TKI

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2. 242

   NakashimaAugust 8, 2009 at 9:04 am

   KF-san,

   (I find it slightly annoying to see you resurrecting an answered matter as though it were not answered; when you did not respond on the merits when I pointed out what was wrong with the latest case being put up.]

   Are you referring to this?

   And then, explain how lucky noise plus blind mechanical necessity somehow spontaneously rearranged dilute racemic organic molecules in a plausible prebiotic soup into a homochiral, functional information storing and processing system. Including inventing along the way: digital information stored in codes [thus also, computer language -- which thus precedes speech, perhaps by 3.8 BY on the conventional timelines], algorithms, data structures, programs, and the executing machinery to implement the hard and software system.

   I do have a proof of materialistic OOL, but it is too long to fit in the margin!

   Really if you take each of the adjectives in your description of the problem, you know that different researchers are working on that aspect of the problem. None of them is a showstopper. Dilute solutions can be concentrated, racemic mixtures sorted, organic molecules created, plausible atmoshperes calculated, and prebiotic environments tested. if you think one of these areas is a showstopper, point it out. If the last paper published in a field was done a few years ago, and it was a review of all the current work up until then which summarized why results had been negative, and the labs had closed and funding wasted away, and no PhD theses were being written in that area, I would certainly agree that the outlook was moribund and pessimistic, similar to Dr Shapiro. However, I don’t see that to be the case.

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3. 243

   kairosfocusAugust 8, 2009 at 9:09 am

   PS: Cf Shapiro’s actual remarks:

   ______________

   RNA’s building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . .

   The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. ["My" NB: Subsequent research has sharply undercut this idea, a point that is unfortunately not accurately reflected in Sci Am's caption on a picture of the Miller-Urey apparatus, which in part misleadingly reads, over six years after Jonathan Wells' Icons of Evolution was published: The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . .] Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

   A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

   To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

   The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

   ______________

   That’s not in the ballpark of 25% support. It’s in the context of lethal defects of speculative theories.

   And, of course, Orgel’s posthumous rebuttal was just as devastating to the metabolism-first model: >> It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . >>

   That’s why evolutionary materialist models and speculations on OOL are in crisis.

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4. 244

   jerryAugust 8, 2009 at 11:10 am

   “You oppose Sanford’s thesis, and you may be right to do so. But the fact of the matter is when ID takes charge of science as opposed to being continually locked in debate with recalcitrant Darwinists, there will be new standards by which we judge whether or not genetic entropy is occurring.”

   I am not sure what you are trying to say. I have no opposition to any type of research at all and am open to any supported conclusions. I just find Sanford’s conclusions not in sync with the world. If all our genomes are crap, I believe like a rusted out car is how Sanford described it, and we still function just fine, then that is a most interesting finding. But I see no indication that the organisms of this world are not functioning well when they have dysfunctional genomes. Some individual members may have problems or the occasional species but in general life is “peachy keen.”

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5. 245

   mad docAugust 8, 2009 at 6:24 pm

   Dave Whisker

   “Actually, mad doc, the authors speculated on the cause, but only in the discussion section”

   I am aware of that and what I was trying to draw attention to was the illogicalities in their speculations: “The authors point out that compensatory epistatic mutations are not the same as “beneficial mutations” (even though they obviously benefit the organism). They postulate these mutations benefit the worst performing organisms the most. (It appears If the organism is mutated then the mutations are good and if the organism is not mutated, mutations are bad).”
   From their results, this is all supposed to have happened within 10 generations in several strains. This is a remarkable achievement for a random process and it puts Dawkin’s “weasel” program to shame.
   Basically I think random mutations are unable to do this in 10 generations. Either their experiment is flawed or there is another explaination. In any event their explaination in the discussion makes no sense for the reasons I have outlined before.
   I am glad that they are doing further investigations. About time too, as that paper is 6 years old. I would be interested to find out the results. I expect the answer will only be found when full genetic mapping of the mutated and non mutated strains can be done and I think you will find a highly efficient data recovery mechanism has been activated in the organism to recover the “lost” information.

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6. 246

   scordovaAugust 9, 2009 at 3:53 pm

   Kairosfocus:

   So, we are justified in reworking the Boltzmann expression to separate clumping/thermal and configurational components:

   S = k ln (Wclump*Wconfig) = k lnWth*Wc . . . [Eqn A.11, cf. TBO 8.2a]

   or, S = k ln Wth + k ln Wc = Sth + Sc . . . [Eqn A.11.1]

   Sth = thermal entropy
   Sc = configurational entropy
   S = total entropy

   Configurational entorpy is a deep subject, and so is amending the notion of “S” to include Sc (configurational entorpy).

   But this seems the most insightful because many creationist still invoke the second law without understanding the important distinctions between Sth( thermal entropy) and Sc (configurationl entropy).

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