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A simple start?

In case we did not know, New Scientist confirms that at the base of the (postulated) tree of life is an extremely complex life form, much like a modern cell.

“There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.”

It is easy (or not) to imagine something as simple as that arising by natural processes.

here

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333 Responses to A simple start?

  1. a universal genetic code

    I wonder if that should have been listed as the optimized universal genetic code.

    Otherwise, one wouldn’t expect to find a universally optimized genetic code.

    The weight of that problem alone can hardly be underestimated.

  2. The Title says it all:

    Was our oldest ancestor a proton-powered rock?

    LOL, now that title is funny I don’t care who you are,,,

    They should have just went ahead and named the article,,,”Does anybody want to here a really really good fairy-tale?”

    Excerpt from article: In short, then, the last common ancestor of all life looks pretty much like a modern cell.,,,Yet the differences are startling. In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,…Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria which have no nucleus and the archea which have a nucleus).

    They cited this paper in theie article:

    Did DNA replication evolve twice independently? – Koonin
    Excerpt: However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus.

    Yet we don’t even know how it is possible that the “optimal DNA replication” occurred one time much less twice independently.

    God’s Creation – The Coded Language of DNA – video
    http://www.youtube.com/watch?v=hIF_dJVfutE

    i.e. DNA functions exactly as a “devised code”:

    Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell’s Design – 2008 – page 177)

    Ode to the Code – Brian Hayes
    The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.
    https://www.americanscientist.org/issues/pub/ode-to-the-code/4

    Deciphering Design in the Genetic Code
    Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.
    http://www.reasons.org/biology.....netic-code

    The coding system used for living beings is optimal from an engineering standpoint.
    Werner Gitt, – In The Beginning Was Information – p. 95

    Collective evolution and the genetic code – 2006:
    Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.

    Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes…. the present findings support the view that protein-coding regions can carry abundant parallel codes.
    http://genome.cshlp.org/content/17/4/405.full

    The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford – Genetic Entropy

    Human DNA is like a computer program but far, far more advanced than any software we’ve ever created. Bill Gates, The Road Ahead, 1996, p. 188

    To make matters much worse for the materialist the DNA code is not even reducible to the laws of physics or chemistry:

    Life’s Irreducible Structure
    Excerpt: “Mechanisms, whether man-made or morphological, are boundary conditions harnessing the laws of inanimate nature, being themselves irreducible to those laws. The pattern of organic bases in DNA which functions as a genetic code is a boundary condition irreducible to physics and chemistry.” Michael Polanyi – Hungarian polymath – 1968 – Science (Vol. 160. no. 3834, pp. 1308 – 1312)

    “an attempt to explain the formation of the genetic code from the chemical components of DNA… is comparable to the assumption that the text of a book originates from the paper molecules on which the sentences appear, and not from any external source of information.”
    Dr. Wilder-Smith

    i.e. There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequence of nucleotides to exist as they do. In fact as far as the laws of the universe are concerned DNA doesn’t even have to exist at all.

    Stephen Meyer is interviewed about the “information problem” in DNA, Signature in the Cell – video
    http://downloads.cbn.com/cbnne.....f?aid=8497

    Stephen C. Meyer – Signature In The Cell: “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”
    http://www.evolutionnews.org/2.....ligen.html

    As well as coding optimization, DNA is also optimized to prevent damage from light:

    DNA Optimized for Photostability
    Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. http://www.reasons.org/dna-soaks-suns-rays

    The materialist must also account for the overriding complex architectural organization of DNA:

    DNA Wrapping – video
    http://www.youtube.com/watch?v=AF2wwMReTf8

    Dr. Jerry Bergman, “Divine Engineering: Unraveling DNA’s Design”: The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million.

    DNA Packaging: Nucleosomes and Chromatin,,’each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth’s equator 2.5 million times! How is this possible? http://www.nature.com/scitable.....omatin-310

    Well, It turns out that DNA is also optimized for “maximally dense packing” as well:

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/re.....142957.htm

  3. The Title says it all:

    Was our oldest ancestor a proton-powered rock?

    LOL, now that title is funny I don’t care who you are,,,

    They should have just went ahead and named the article,,,”Does anybody want to here a really really good fairy-tale?”

    Excerpt from article: In short, then, the last common ancestor of all life looks pretty much like a modern cell.,,,Yet the differences are startling. In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,…Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria which have no nucleus and the archea which have a nucleus).

    They cited this paper in theie article:

    Did DNA replication evolve twice independently? – Koonin
    Excerpt: However, several core components of the bacterial replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus.

    Yet we don’t even know how it is possible that the “optimal DNA replication” occurred one time much less twice independently.

    God’s Creation – The Coded Language of DNA – video
    http://www.youtube.com/watch?v=hIF_dJVfutE

    i.e. DNA functions exactly as a “devised code”:

    Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell’s Design – 2008 – page 177)

    Ode to the Code – Brian Hayes
    The few variant codes known in protozoa and organelles are thought to be offshoots of the standard code, but there is no evidence that the changes to the codon table offer any adaptive advantage. In fact, Freeland, Knight, Landweber and Hurst found that the variants are inferior or at best equal to the standard code. It seems hard to account for these facts without retreating at least part of the way back to the frozen-accident theory, conceding that the code was subject to change only in a former age of miracles, which we’ll never see again in the modern world.
    https://www.americanscientist.org/issues/pub/ode-to-the-code/4

    Deciphering Design in the Genetic Code
    Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.
    http://www.reasons.org/biology.....netic-code

    The coding system used for living beings is optimal from an engineering standpoint.
    Werner Gitt, – In The Beginning Was Information – p. 95

    Collective evolution and the genetic code – 2006:
    Excerpt: The genetic code could well be optimized to a greater extent than anything else in biology and yet is generally regarded as the biological element least capable of evolving.

    Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes…. the present findings support the view that protein-coding regions can carry abundant parallel codes.

    The data compression of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989). (This is well beyond the complexity of any computer code ever written by man). John Sanford – Genetic Entropy

    Human DNA is like a computer program but far, far more advanced than any software we’ve ever created. Bill Gates, The Road Ahead, 1996, p. 188

    To make matters much worse for the materialist the DNA code is not even reducible to the laws of physics or chemistry:

    Life’s Irreducible Structure
    Excerpt: “Mechanisms, whether man-made or morphological, are boundary conditions harnessing the laws of inanimate nature, being themselves irreducible to those laws. The pattern of organic bases in DNA which functions as a genetic code is a boundary condition irreducible to physics and chemistry.” Michael Polanyi – Hungarian polymath – 1968 – Science (Vol. 160. no. 3834, pp. 1308 – 1312)

    “an attempt to explain the formation of the genetic code from the chemical components of DNA… is comparable to the assumption that the text of a book originates from the paper molecules on which the sentences appear, and not from any external source of information.”
    Dr. Wilder-Smith

    i.e. There are no physical or chemical forces between the nucleotides along the linear axis of DNA (where the information is) that causes the sequence of nucleotides to exist as they do. In fact as far as the laws of the universe are concerned DNA doesn’t even have to exist at all.

    Stephen Meyer is interviewed about the “information problem” in DNA, Signature in the Cell – video
    http://downloads.cbn.com/cbnne.....f?aid=8497

    Stephen C. Meyer – Signature In The Cell: “DNA functions like a software program,” “We know from experience that software comes from programmers. Information–whether inscribed in hieroglyphics, written in a book or encoded in a radio signal–always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source.”

    As well as coding optimization, DNA is also optimized to prevent damage from light:

    DNA Optimized for Photostability
    Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. http://www.reasons.org/dna-soaks-suns-rays

    The materialist must also account for the overriding complex architectural organization of DNA:

    DNA Wrapping – video
    http://www.youtube.com/watch?v=AF2wwMReTf8

    Dr. Jerry Bergman, “Divine Engineering: Unraveling DNA’s Design”: The DNA packing process is both complex and elegant and is so efficient that it achieves a reduction in length of DNA by a factor of 1 million.

    DNA Packaging: Nucleosomes and Chromatin,,’each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth’s equator 2.5 million times! How is this possible?

    Well, It turns out that DNA is also optimized for “maximally dense packing” as well:

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.

  4. Check out the molecular movies here http://www.molecularmovies.com/showcase/index.html

  5. correction to post:,,, archea have no nucleus.

  6. idnet thanks for the link,
    Here are some more cool molecular animations:

    Since evolutionists can’t explain the simplest first replicating cell,, I wonder if they will at least try to explain the formation of ATP synthase:

    Evolution vs ATP Synthase – Molecular Machine – video
    http://www.youtube.com/watch?v=qE3QJMI-ljc

    Or maybe if they can’t explain that they can explain how a non-living virus came to be:

    Virus – Assembly Of A Nano-Machine – video
    http://www.youtube.com/watch?v=Ofd_lgEymto

    Virus – A Nano Lunar Lander – Machine – video
    http://www.seyet.com/t4.html

    That preceding video made me think of the lunar lander of the Apollo program. And when you think about the relative distances, as well as chemical obstacles faced by the virus, the comparison is not without merit.

    here is one more video, this video is interesting for this is now the smallest motor discovered to date (I believe, It is also one of the most powerful discovered):

    Molecular Motor – DNA Packaging Into Virus – Bacteriophage T4 – Video
    http://www.youtube.com/watch?v=wX456hbIouw

  7. Let us not forget that there was no common ancestor. As I have pointed out numerous times, the leading researchers on the phylogenetics of single cell organisms such as Woese and Doolittle have come to the conclusion that there was no common ancestor to life.

  8. @Jehu: Source?

  9. Good to have you back BA! I was really irked to say the least when I found out that they closed the Tangle account. There were so many enlightening videos that you had contributed to the website, and I never got the chance to thank you. Heck it’s like they cut off an entire leg of their ministry if you think about. But regardless, it’s good to see those videos surfacing once again on the youtube account (Where we probably won’t have to waste time deconstructing Raytheon’s tired troll arguments).

  10. bornagain77,

    They should have just went ahead and named the article,,,”Does anybody want to here a really really good fairy-tale?”

    We shouldn’t be comparing this to fairy tales, because there is actually a lot of truth in fairy tales. :)

  11. 11

    The Russell-Martin theory should not be written off as just another tornado in the warm-pond junkyard. It cogently answers the standard objections to abiogenesis as based on factorially low probabilities of assembling RNA and DNA. It is the first to provide a detailed rationale for the origin of cells and viruses, as well as the particular amino acids and elements found in life today.

    Note that the lengthy list of objections posted above by bornagain77 are all aimed at molecular developments subsequent to the Russell-Martin rock-pore protocell, thereby silently giving up on the tornado argument and retreating to later stages of the model, after the protocells have escaped the rocks. This is nothing but the infamous moving of the goalposts, which the Establishment is so often accused to doing.
    Opponents of abiogenesis used to argue the impossibility of any natural process ever producing usable concentrations of nucleic acids or proteins. Now that such a process has been discovered, the argument against abiogenesis has lost huge territory and been forced to retreat a great distance.

    Having lost the tornado argument, bornagain77 has been reduced to arguing against a path from Russell-Martin rock-cells to DNA optimization. He should study the amazing dynamic properties of RNA and its capability of forming intelligent metabolic networks, before he propounds on molecular impossibilities. Such networks are the first appearance of intelligence in the physical world.

    Proponents of emergence and biosemiosis define life as molecular cooperation, which provides an opening for intelligent design to operate from the very beginning of chemical evolution, as soon as RNA appears in those little Hadean-vent pores.

    Finite intelligent entities are the only possible scientific basis of intelligent design. As long as you look for God to do it, you have abandoned science, which is about testability, something we all know God is above.

    Instead of futile carping at abiogenesis, ID needs a conceptual model of how intelligent entities, which are by definition immaterial, can be instantiated in cooperating groups of motile molecules, which are by definition totally physical. Bridging this Cartesian divide is the only way ID can move out of its current pre-scientific status of being a mere outsider critic of atheistic scientism in biology.
    If anybody reads and replies to this post, I could bring up quantum theoretical approaches to bridging this divide. I hope to hear from somebody and that I’m not just typing in the dark.

  12. I’Bill:

    The fundamental problem that any materialistic or naturalistic explanation for life faces is that it has the laws of physics as its ONLY explanatory resource.

    Why is this a problem? Here’s the Cliff notes version. The question of the origin of life is the question of the origin of information. Information is always communicated by means of a language. All languages have symbols and rules. But physics has nothing to say about why the symbols “cat” mean a certain kind of mammal and the symbols “act” mean to do something, something done, or a segment of a play. Neither does physics have anything to say about the rules that make certain arrangements of the symbols (nucleotides) mean something (life). Therefore, a materialist explanation for life is impossible. It will never be forthcoming.

    Information always reduces to mind, not to matter or the laws which govern the behavior of that matter. I really don’t understand the continuing insistence that physics can account for information when clearly it cannot. Maybe you can help.

  13. Such networks are the first appearance of intelligence in the physical world.

    what? I thought evolution was totally devoid of intelligence, just a ‘natural processs’ now apparently evolution is the intelligent designer…

    evolution is all in all…makes giraffes tall and bacteria small…smart enough to direct all things, but with no intelligence at all…evolution is all in all…praise darwin.

  14. 14

    PS – I suggest contemplating the enormous numbers posed by the Russell-Martin model:
    If 2% of the Hadean ocean floor had the proposed vents, those 10 million square kilometers of rock, say at a meter thick, amount to 10 trillion cubic meters of micro-reactors.

    At 10% porosity with 1 micron pores, there would be 10^30 pores, totaling a trillion square kilometers (area of 2000 Earths) of potent catalytic surface. Only one pore has to be lucky, in a hundred million years, or 3 quadrillion seconds. In that huge span of time, events become likely even if their per-second probability is only one in 10^45 pores, each with trillions of molecules. That’s a huge molecular exploration capability, especially at the picosecond level of molecular vibration. At this rate a mere trillion molecules per pore gives 10^70 pecks on the monkeys’ typewriters, looking not for all of Shakespeare but just a few key words.
    Could Dr. Behe please apply his arguments against the utility of random search to these immense numbers?

    The way I look at it, God made all those pores, by arranging the laws of nature, to be sure life would arise with no Divine intervention, in full accordance with compatibilism. The intelligence of ID can only be those of molecules themselves, conferred by God.

  15. 15

    tsmith:
    I’m not somebody with whom Dawkins et al would agree. I think that the intelligence of cooperating molecules transcends the determinism of ‘inanimate’ matter, and that there is no closure problem. The universe is not meaningless and we are spiritual beings who live after our bodies die. Please don’t attribute otherwise to me.

  16. 16

    tgpeeler
    I’m advocating the opposite of the reductionism found in so-called ‘naturalism’. It turns out that the deterministic physical world of reductive physicalism has a tiny crack, in the molecular cooperation of spontaneously generated RNA. Like a root busting up a sidewalk by starting with root hairs pushing into microcracks, this miniscule rare exception to Laplacian determinism is how immaterial mind enters the physical world, as proto-life that begets true life, which goes on to oxygenate the Earth, blueing its once red seas and green skies.

    Being mindful, Russell-Martin proto-life can indeed generate the information now found in DNA.
    You’d never get Dawkins to agree with that.

  17. At this rate a mere trillion molecules per pore gives 10^70 pecks on the monkeys’ typewriters, looking not for all of Shakespeare but just a few key words.

    For lack of a better illustration, it seems a bit like flipping a coin and getting it to land on edge in a windstorm. Overcoming the initial odds is one step. Getting the coin to stay that way is another.

    Life is tentative; countless living things die because their environment does not support their continued existence. So let’s say that after 10^70 attempts, a configuration of molecules appears that resembles a form of life. At last! What happens in the next second? And the one after that? These miraculous molecules don’t “know” that they belong together. They don’t “know” that they should make more of themselves. They don’t “know” that they need to continue being what they are for another moment.

    If it’s even possible that such a once-in-a-billion-year miracle could occur, it seems likely that it would end within seconds. And even that initial possibility is only a hypothesis.

  18. 18

    Scott
    I once saw a friend’s flipped cigarette land standing with coal up, and stay that way in a breeze, which merely helped it burn all the way down and start a fire, to our immense amusement at this spontaneous Rube-Goldberg event. A good analogy, I think, for God watching life start, burning through the whole world.

    Once elemental proto-mind is attained by a group of RNA molecules, such chance arguments are over, and information generation begins. The physical world has been infiltrated by immaterial mind. Probably most pores will do it, once enough RNA is each one. I just raised those large numbers to show that the improbability argument has been answered as never before.

  19. Mr Tgpeeler,

    Neither does physics have anything to say about the rules that make certain arrangements of the symbols (nucleotides) mean something (life).

    I don’t think this is a completely accurate statement.
    RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

  20. Mr ScottAndrews,

    You’ve raised a very important point. A part of the direction and progress of molecular evolution is whether the products of these interactions are degraded back into small feedstock molecules or if they survive for a while to catalyze other molecules. This is where recent OOL theories get a significant boost from mechanisms that trap and concentrate reactants, compared to “warm pond” theories of the past. Ice, mud, ZnS nanoparticles, alkalai vents all have this feature.

  21. Jehu,
    “Woese and Doolittle have come to the conclusion that there was no common ancestor to life.”

    I know you have probably listed the source before but if you don’t mind could you list it again?

  22. I bill,

    Here is how the base line for the universe’s probabilistic resources are calculated:

    Signature in the Cell – Book Review – Ken Peterson
    Excerpt: “there are about 10 to the 80th elementary particles in our observable universe. Assuming a Big Bang about 13 billion years ago, there have been about 10 to the 16th seconds of time. Finally, if we take the time required for light to travel one Plank length we will have found “the shortest time in which any physical effect can occur.” This turns out to be 10 to the minus 43rd seconds. Or turning it around we can say that the most interactions possible in a second is 10 to the 43rd. Thus, the “probabilistic resources” of the universe would be to multiply the total number of seconds by the total number of interactions per second by the total number of particles theoretically interacting. The math turns out to be 10 to the 139th.” http://www.spectrummagazine.or.....ature_cell

    Here is how the probability for the simplest life on earth is calculated:

    Signature in the Cell – Book Review – Ken Peterson
    Excerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions….” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power.
    In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power.
    http://www.spectrummagazine.or.....ature_cell

    In fact years ago Fred Hoyle arrived at approximately the same number, one chance in 10^40,000, for life spontaneously arising. From this number, Fred Hoyle 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”. Fred Hoyle also compared the chance of obtaining just one single functioning protein molecule, by chance combination of amino acids, to a solar system packed full of blind men solving Rubik’s Cube simultaneously.

    Protein Molecules and “Simple” Cells – video
    http://www.youtube.com/watch?v=uFNwStNhHIc

    The Origin of Life – Lecture On Probability – John Walton – Professor Of Chemistry – short video
    http://www.youtube.com/watch?v=VIgQP4RwrqY
    Entire Video:
    http://edinburghcreationgroup.org/originoflife.xml

    Probability’s Nature and Nature’s Probability: A Call to Scientific Integrity – Donald E. Johnson
    Excerpt: “one should not be able to get away with stating “it is possible that life arose from non-life by …” or “it’s possible that a different form of life exists elsewhere in the universe” without first demonstrating that it is indeed possible (non-zero probability) using known science. One could, of course, state “it may be speculated that … ,” but such a statement wouldn’t have the believability that its author intends to convey by the pseudo-scientific pronouncement.” http://www.amazon.com/Probabil.....1439228620

    “Evolution is the only ‘scientific theory’ that needs laws to protect it!” Author Unknown

    The parasitic Mycoplasmal, has between a 0.58-1.38 megabase genome which results in drastically reduced biosynthetic capabilities and explains their dependence on a host. Yet even with this “reduced” complexity we find that:

    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8

    Mycoplasma Genitalium – The “Simplest” Life On Earth – video
    http://www.youtube.com/watch?v=eRoMxpZWR7

    Chance and necessity do not explain the origin of life: Trevors JT, Abel DL.
    Excerpt: Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic–that is, it is programmatically and algorithmically organized and controlled. http://www.ncbi.nlm.nih.gov/pubmed/15563395

    On top of the fact that we now know the genetic code of the simplest organism ever found on Earth is a highly advanced algorithmic code, which far surpasses man’s ability to devise as such, we also know for a fact no operation of logic ever performed by a computer will ever increase the algorithmic code inherent in a computer’s program, i.e. Bill Gates will never use random number generators and selection software to write highly advanced computer codes:

    “… no operation performed by a computer can create new information.”
    Douglas G. Robertson, “Algorithmic Information Theory, Free Will and the Turing Test,” Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34. The Evolutionary Informatics Lab: http://www.evoinfo.org/index.html

    This is also shown to be the case for the infamous “evolutionary algorithms” which modify/refine preexisting information in a computer:

    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. (In these computer simulations)
    http://www.evoinfo.org/Publica.....fo_NoN.pdf

    Thus evolution is soundly defeated at even the most basic level of what we now know for Functional Information generation, specifically it is shown no sequence of events, in any foundational logic known to man, can ever increase complex functional information, though it may refine it.

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.pubmedcentral.nih.g.....id=2662469
    http://mdpi.com/1422-0067/10/1/247/ag

    etc..etc…etc…

  23. 23

    bornagain7
    Thank you for your voluminous reply, much of which I am familiar with though much remains to inspect.
    In my opinion all of these simply ignore the Russell-Martin model and others built on it. Once voluminous RNA generation is a high probability event, all the arguments about amino acids or the number of particles in the universe become irrelevant.
    What I seek to do is provide a theoretical justification for molecular cooperation to be mindful and transcend physics. Dawkins et al are reductionistic Procrustean nihilists, but I am an Aristotelean organicist advocating ontological holism via the quantum mechanical intelligence of macromolecular cooperation.

  24. I Bill, You said something very fanciful of mind arising in that first replicating cell,,, And to give your thought serious consideration,,,do you mind providing the studies which conclusively show a violation of the second law?

    it has been found that our brain processes information in violation of the second law of thermodynamics (entropy). A feat that is not even possible for a “material” computer in the long term since a computer must eventually erase its memory.

    Landauer’s principle
    In 2003 Weiss and Weiss came to the conclusion that information processing by the brain has to be based on Landauer’s principle. In 2008 this has been empirically confirmed by a group of neurobiologists.,,, http://en.wikipedia.org/wiki/L....._principle

  25. bornagain77 (???) 21:

    WOESE, Carl, “The universal ancestor”, Proceedings of the National Academy of Sciences USA 95 (1998): 6854-6859.

    DOOLITTLE, W. F., Sci Am. 2000 Feb;282(2):90-5 “Uprooting the tree of life”, Dalhousie University, Halifax, Nova Scotia.
    PMID: 10710791 [PubMed - indexed for MEDLINE]

  26. Thanks for the references Enezio E. De Almeida Filho

  27. It is easy (or not) to imagine something as simple as that arising by natural processes.

    Argument from incredulity (or not)?

    At least they are trying to work out an explanation of how rather than sitting back lazily content with an assertion of who.

    They have gone to the pathetic level of detail disdained by others to construct a hypothesis which, while it may not be what actually happened, is nonetheless plausible and fascinating.

  28. bornagain77,

    As always, it’s good to see you active again.

    I was wondering what you thought of the Italian professor Luigi Garlaschelli and his claim that he can reproduce the Shroud of Turin without modern technology. I know you’ve talked about the Shroud of Turin on here before.

    I know this is off-topic and I’m sorry if I get banned for this, but I didn’t know of a better way to contact bornagain77

  29. Berceuse, Well, like everything else that materialists/atheists postulate. Their claim turns out to be a deception:

    The Shroud of Turin has NOT been reproduced!
    http://www.youtube.com/watch?v=TjxZFfHVtsE

    This following video is cool because it has John Jackson, who I believe was the leader of the STURP team, talking about why all attempts to replicate the Shroud fail:

    Shroud Of Turin – John Jackson PhD. Talks About Image Formation
    http://www.youtube.com/watch?v=qATmMMvUiUk

  30. 30

    bornagain77
    As long as we’re off topic, please examine the book ‘Caesar’s Messiah’ by Joe Atwill. If the idea of the Shround of Turin being a fake gets you so riled up, then this book will make you apoplectic.

  31. 31

    bornagain77
    Back to abiogenesis.
    You linked to a Wiki entry on Landauer’s principle, but I need the 2008 neurobiology link to make any cogent comments.

    Thank you for the link to the Abel paper. I suggest you peruse the many abiogenesis articles (all FREE) at that same journal.

  32. Here are the references:

    Entropy in thermodynamics and information theory
    Volkmar Weiss and Harald Weiss The golden mean as clock cycle of brain waves. Chaos, Solitons and Fractals 18 (2003) 643-652

    Anita K. Roopun et al. Temporal interactions between cortical rhythms. Frontiers in Neuroscience 2 (2008)145-154
    http://en.wikipedia.org/wiki/E.....ion_theory

    Basically I Bill I draw the line at the second law,,,If you have any proof this law is violated to the degree to violate Abel’s null hypothesis of information generation show it. I am sure you believe it is possible,,,,but believing and proving are two different things,,, so go ahead and give your best example for what you think would violate it…This is science is it not? Not wishful speculation that your great great grand-pappy was a proton powered rock! LOL!!!

  33. Interstellar Bill

    I’ll address your comments on abiogenesis shortly. Before I do that, I’d like to get the off-topic stuff out of the way – i.e. the Shroud of Turin and Joseph Atwill’s book, Caesar’s Messiah.

    1. Caesar’s Messiah has been totally debunked. See this link to Joseph Atwill’s Caesar’s Messiah: A Critique.

    You can read several more devastating reviews of Atwill’s book at http://www.amazon.com/Caesars-.....addOneStar

    I should note in passing that Joseph Atwill’s book has not been discussed in a peer-reviewed journal. Atwill himself is not a scholar but a businessman living in California. So there you have it: one businessman who denies that Jesus existed versus a vast scholarly consensus of believers and non-believers alike, who affirm that Jesus was a real person. Whom to believe? I’d say that’s a no-brainer.

    Here is a link to an article by Paul L. Maier, The Russell H. Seibert Professor of Ancient History at Western Michigan University, entitled Did Jesus Really Exist?

    http://www.4truth.net/site/app.....ct=1740233

    An excerpt:

    In fact, there is more evidence that Jesus of Nazareth certainly lived than for most famous figures of the ancient past. This evidence is of two kinds: internal and external, or, if you will, sacred and secular. In both cases, the total evidence is so overpowering, so absolute that only the shallowest of intellects would dare to deny Jesus’ existence. And yet this pathetic denial is still parroted by “the village atheist,” bloggers on the internet, or such organizations as the Freedom from Religion Foundation.

    2. Regarding the Shroud of Turin, here are some links which explain in detail why Professor Garlaschelli’s claim to have replicated the Shroud of Turin is poorly substantiated:

    http://www.ewtn.com/vnews/gets.....ber=98037#
    http://shroudstory.wordpress.com/
    http://www.shroudofturin4journalists.com/
    http://shroudofturin.wordpress.....elli-fake/

    To cut a long story short: Professor Garlaschelli did a pretty good job of creating a shroud with a negative image, and he deserves credit for that. However, his shroud fails to replicate other key features of the shroud. His shroud has some three-dimensional features, but they are anatomically wrong. The Turin Shroud is much more realistic, and anatomically correct.

    Additionally, scientists can tell that the blood on the Turin Shroud was deposited there before the image was formed. Professor Garlaschelli’s bloodstains were placed on his shroud afterwards, and they fail to replicate key features of the blood on the Turin Shroud.

    I should add that the 1988 dating of the Shroud to A.D. 1260 to 1390 has been called into question in peer-reviewed journals. For further details see http://www.shroudstory.com

  34. My Google-fu has failed me again. I can find no reference other than Abel himself that uses “computational halting” in the same way he does, as in the phrases “acheive computational halting” or “produce computational halting”. But this is a term Abel never defines in his papers. Does anyone have a clue what Abel actually means?

  35. Interstellar Bill (#11, #14, #23)

    I found your remarks on the Russell-Martin hypothesis very interesting. It certainly merits a lot more respect than any other hypothesis that has been proposed to date regarding the origin of life.

    I’ve been having a look at the New Scientist link, How life evolved: 10 steps to the first cells accompanying the article on Rusell & Martin’s pioneering research work.

    I had a problem with Step 5:

    Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA – and providing an ideal setting for their evolution into the world of DNA and proteins.

    I have to say that this sounds a bit like hand-waving. If it really happened that way, well and good. But the point I’d like to make here is that if it did, then the natural chemical pathways leading to the formation of proteins must have been rigged in advance by God, the Author of nature, as mindless processes could never have generated the information in an average protein without some intelligent assistance. Perhaps this is your own position – you write that you believe “God made all those pores, by arranging the laws of nature, to be sure life would arise with no Divine intervention.” Fair enough.

    But I cannot follow you when you write that “[o]pponents of abiogenesis used to argue the impossibility of any natural process ever producing usable concentrations of nucleic acids or proteins.”

    Now, if you are defining “natural process” to include chemical pathways set up by God, then i’d say that’s certainly possible. However, the point I’d like to make here is that there are some pretty solid grounds for believing that an Intelligence was required to account for the emergence of proteins on the primordial earth.

    Instead of linking to a ton of different papers, I’d like to focus on just one: Intelligent Design: Required by Biological Life? by K. D. Kalinsky (2008). Interestingly, the author does not argue that natural selection was incapable of producing the first living things; rather, he argues that if it did so, then the “fitness landscapes” which natural selection presupposes must have been designed by some Intelligence.

    Proteins are one of the central illustrations used by Kalinsky of structures requiring intelligent design. After rigorously defining “functional information,” he examines two particular proteins, SecY and RecA, which are found in all living things, and would therefore be required in a minimal genome. Kalinsky cites calculations estimating that the functional information in the two proteins is 832 bits and 688 bits for RecA and SecY respectively, and concludes that the average 300-amino acid protein has around 700 bits of functional information. He calculates that “ID is 10^155 times more probable than mindless natural processes to produce the average protein,” and concludes that “if natural selection is invoked to explain the origin of proteins, a fitness function will be necessary that requires intelligent design.” He goes on to estimate that the simplest life form would have had 267,000 bits of functional information.

    At the end of his article, he writes:

    If life is the product of natural selection and an extremely complex fitness landscape, then we can conclude that it is extremely likely that intelligent design was required to configure the fitness function… Intelligent design would also be the most probable explanation for any fitness function operative in natural selection that could successfully locate the folding proteins required for life.

    I’d like to know what you think of Kalinsky’s article.

  36. Mr. Nakashima (#34)

    Perhaps this paper might explain what Abel was getting at. (Incidentally, I have absolutely no idea whether the “Abel” referred to in the article is the same Abel as David Abel, who is commonly cited in recent ID literature.)

    A Short Note on the Halting Problem by Kurt van Etten.

    David Abel and Jack Trevors have written an article which explains fairly clearly what they mean by “computational halting,” in my opinion. I suggest you start from page 5:

    http://books.google.com/books?.....38;f=false

    I hope that helps.

  37. 37

    vjtorley
    I’ve seen those anti-Atwill sites and I’m underwhelmed, since they artuflly dodge Atwill’s main points, but this is not the place to discuss it. (Suggestions as to where?)

  38. 38

    BA^77 @ 24

    Landauer’s principle
    In 2003 Weiss and Weiss came to the conclusion that information processing by the brain has to be based on Landauer’s principle. In 2008 this has been empirically confirmed by a group of neurobiologists.,,, http://en.wikipedia.org/wiki/L….._principle

    I’ve seen you (and another poster who also likes using multiple sequential commas for no apparent reason) post this multiple times in the past few days. Here’s the thing: it’s apparently completely untrue. The Wiki article no longer includes that paragraph, the reason given for the edit being “Neither article makes direct reference to this principle.”

    So, checking around, I found a free version of the Weiss and Weiss paper, and also of the paper which supposedly confirms that the “brain processes information in violation of the second law of thermodynamics (entropy)”, as you have put it. Sure enough, neither one has anything to say about Landauer’s Principle. Not a single mention.

    I don’t know where you acquired this notion of the brain violating the laws of thermodynamics from or why you thought these papers supported it, BA^77, especially given that the Wiki article itself clearly states that “Landauer’s principle can be understood to be a simple logical consequence of the second law of thermodynamics” (bolding mine), but it’s utterly unfounded. Probably best to stop posting about it at every opportunity, given the facts.

  39. ScottAndrews @ 17

    If it’s even possible that such a once-in-a-billion-year miracle could occur, it seems likely that it would end within seconds. And even that initial possibility is only a hypothesis.

    Actually, we can demonstrate the results for them. Simialr to what Jonthan Wells proposed, we can take living cells, cut them open and stuff the material into a rock pore. Even eleiminate any harmful radicals that might cause interfering cross reactions, add some nutrients, emerase it back into the water. Come back next year and see how many of the other pores are loaded with “chemical life”. :P

    I know where I’m placing my bets!

  40. I don’t (or maybe I do) understand why the brain consume so much energy? (At least mine, I don’t know about others.)

  41. Doomsday thanks for pointing out the edit,,,should have known better than to trust wiki for a source,,,

    Yet to be honest,,,in looking at the papers,,,whomever originally wrote the wiki article must have seen something in the papers that stood out to him as a violation to the second law (conforming to Landauers principle in that no memory is erased). In fact on closer examination, I think the original author of the wiki article may be on to something, in his hunch of the study conforming to Landauer’s Principle, in that it seems the merging of two rhythms (computational paths) is not performed in the brain to achieve a third rhythm (an answer), (see original ref.)

    specifically this excerpt:

    Temporal Interactions between Cortical Rhythms:
    Excerpt: With a ratio of c.1.6 not only can gamma and beta2 rhythms concatenate to form a beta1 rhythm, but beta2 and beta1 rhythms may concatenate to form an alpha rhythm and alpha and beta1 rhythms concatenate to form a theta rhythm etc. Thus a hierarchical arrangement of frequencies may exist through concatenation in a similar manner to that seen for nested rhythms, but on a finer temporal scale. Such an arrangement fits the hierarchical organisation of network anatomy in the brain very well (Sporns et al., 2004), and has been inferred from the dynamic profile of human EEG data (Weiss and Weiss, 2003). This pattern of inter-relationships between discrete rhythms may provide a possible network dynamic substrate for multi-scale, parallel processing of sensory information over a range of temporal (Wiskott and Sejnowski, 2002) and spatial scales (Smith et al., 2006). However, to date, experimental evidence for such an association is not available.
    http://www.ncbi.nlm.nih.gov/pm.....MC2622758/

    Does such evidence for rhythms maintaining their discreteness (nonerasure of information by a “merging” of paths) qualify as computation based on Landauer’s principle???

    Well the similarity to what would be expected for a “computation in the brain” based on Landauer’s principle is simply uncanny in that regard, and I will have to say the original authors hunch, that the brain processes information based on Landauer’s principle, is not without substantial merit! But as so far as a direct and strict correlation to “bits of information”, as Landauer’s is rigorously defined, I have to side with you on this matter and say that the inference falls far short of a rigid proof that Landauers Principle requires.

    But to defend the main overriding postulation that Mind is a separate entity from brain ,I hold that that particular postulation is indeed shown to be true! I provide this one reference for one proof of many:

    In The Wonder Of Being Human: Our Brain and Our Mind, Eccles and Robinson discussed the research of three groups of scientists (Robert Porter and Cobie Brinkman, Nils Lassen and Per Roland, and Hans Kornhuber and Luder Deeke), all of whom produced startling and undeniable evidence that a “mental intention” preceded an actual neuronal firing – thereby establishing that the mind is not the same thing as the brain, but is a separate entity altogether. http://books.google.com/books?.....8;lpg=PT28

    “Thought precedes action as lightning precedes thunder.”
    Heinrich Heine – in the year 1834

  42. Cabal:

    I don’t (or maybe I do) understand why the brain consume so much energy?

    Your brain is made up of mostly neurons (nerve cells).

    In order to send signals down a neuron pumps have to activated and inactivated in sequence.

    These pumps carry the signal down the neuron.

    After each signal is sent the neuron must be reset in order to be ready for the next.

    Now think of that happening to 100 billion neurons and you will understand where the energy goes/ is required.

  43. Seversky:
    At least they are trying to work out an explanation of how

    I agree, this is progress toward an explanation of undirected abiogenesis, if we assume in advance that some form of undirected abiogenesis is responsible. (When I say “some form” it sounds like there are a few to pick from, when in fact none are known.) There’s a massive assumption factored into your conclusion.

    rather than sitting back lazily content with an assertion of who.

    Leaving aside the “who” which I’m sure you know does not pertain to ID, your use of the term “lazy” is curious. Are you suggesting that, having determined intelligence as the probable cause, one’s work ethic should motivate him to abandon that conclusion in favor of a more challenging one?

  44. Mr Vjtorley,

    Thank you for those references.

    In the blog comment, computational halting is used at is in mathematical discussions of Turing Machines. If Abel is the same as David Abel is unclear from that small sample of his writing.

    The book chapter I had previously found. While it makes the interesting claim that function can be defined as computational halting, it also doesn’t stop to define the term, so we are even worse off than before.

    Obviously, Abel is free to define a technical vocabulary for his own work, a la the Red Queen of Lewis Carroll. But it is a serious problem to equate “function” and “computational halting”. Taking these terms in their common values, a program that computes the digits of pi that halts is not functioning. There are many real time systems in health care and defense applications for which halting = failure, not function. The program inside an iPod, or similar appliance, is probably an infinite loop.

    But in the vocabulary of Abel himself, perhaps these counter-examples are meaningless. Without clear definitions it is hard to tell.

  45. Mr BA^77,

    The quoted text just shows that the firing of some neurons precedes the activation of nerves out to the muscles. That is a better proof that the mind is the brain than the oposite.

  46. Nak, that is gross cherry picking on your part, Are you being intentionally deceptive? Or do you truly think you are right?,,,, please Read the preceding pages of the link carefully.

    Specifically this quote which immediately precedes the link:

    “As I remarked earlier, this may present an “insuperable” for some scientists of materialists bent, but the fact remains, and is demonstrated by research, that non-material mind acts on material brain.” Eccles

  47. correction: should read ,,,,”insuperable” difficulty,,,,

  48. Mr BA^77,

    Eccles’ opinion is neither here nor there. As the previous page quotes Porter and Brinkman, the SMA discharge precedes the voluntary muscle discharge, and the premotor cortex has a discharge that precedes the SMA discharge (that little ‘except’ phrase at the end of the sentence).

    If you’d like to claim that the SMA is connected to nothing, charged by nothing, and yet directs the voluntary muscles to move, then I would admit that you’ve found a locus in the physical brain that may act as a connection point bewtween physical brain and immaterial mind. Alas, that is not the case. The charge of the SMA which is discharged arrives from some other physical part of the brain.

  49. Well Nak, The overriding emphasis of the studies of seems to be The sequence of “firing in the brain” seems to be exactly opposite of what is expected of a materialistic presuppositions…. which forces me to ask “will you ever be fair with anything that supports the independence of mind?”

    But to refute your “the mind is “nothing” deception,,,

    In conjunction with the mathematical necessity of an “Uncaused Cause” to explain the beginning of the universe, in philosophy it has been shown that,,,

    “The ‘First Mover’ is necessary for change occurring at each moment.”
    Michael Egnor – Aquinas’ First Way
    http://www.evolutionnews.org/2......html#more

    I find this centuries old philosophical argument, for the necessity of a “First Mover” accounting for change occurring at each moment, to be validated by quantum mechanics. This is since the possibility for the universe to be considered a “closed system” of cause and effect is removed with the refutation of the “hidden variable” argument. i.e. There must be a sufficient transcendent cause (God/First Mover) to explain the quantum wave collapse to the “uncertain” 3D effect for “each moment” of the universe.

    This following study solidly refutes the “hidden variable” argument that has been used by materialists to try to get around the Theistic implications of this instantaneous “spooky action at a distance” found in quantum mechanics.

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for “spooky” forces, as Einstein termed them—forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    Why, who makes much of a miracle? As to me, I know of nothing else but miracles, Whether I walk the streets of Manhattan,
    Or dart my sight over the roofs of houses toward the sky,,,
    Walt Whitman – Miracles

    Moreover, the transcendent cause must be sufficient to explain the semi-unique effect of 3D centrality witnessed by each individual observer in the universe.

    Quantum Mechanics – The Limited Role Of The Observer – Michael Strauss – video
    http://www.youtube.com/watch?v=elg83xUZZBs

    That the “mind” of a individual observer would play such an integral yet not complete “closed system role”, in the instantaneous quantum wave collapse of the universe to “3D centrality”, gives us clear evidence that our “mind” is a unique entity. A unique entity with a superior quality of existence when compared to the “uncertain 3D particles” of the universe.

    Genesis 2:7
    And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

    Of more importance though, the “effect”, of universal quantum wave collapse to each “central 3D observer”, gives us clear evidence of the extremely special importance that the “cause”, of the “Infinite Mind of God”, places on each of our own individual minds over the “uncertain 3D particles.

    Psalm 139:17-18
    How precious concerning me are your thoughts, O God! How vast is the sum of them!
    Were I to count them, they would outnumber the grains of sand. When I awake, I am still with you.

  50. further notes:

    I find it extremely interesting that quantum mechanics tells us that instantaneous quantum wave collapse to its “uncertain” 3-D state is centered on each individual observer in the universe, whereas, 4-D space-time cosmology tells us each 3-D point in the universe is central to the expansion of the universe. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that I exist?

    Proverbs 15:3
    The eyes of the LORD are in every place,,,

    This is obviously a very interesting congruence in science between the very large (relativity) and the very small (quantum mechanics). A congruence they seem to be having a extremely difficult time “unifying” mathematically (Einstein, Penrose). Yet, a unification which Jesus apparently seems to have joined together with His resurrection:

    The Center Of The Universe Is Life – video
    http://www.youtube.com/watch?v=do2KUiPEL5U

    The End Of Christianity – Finding a Good God in an Evil World – Pg.31 – William Dembski
    Excerpt: “In mathematics there are two ways to go to infinity. One is to grow large without measure. The other is to form a fraction in which the denominator goes to zero. The Cross is a path of humility in which the infinite God becomes finite and then contracts to zero, only to resurrect and thereby unite a finite humanity within a newfound infinity.” http://www.designinference.com.....of_xty.pdf

    Philippians 2: 5-11
    Let this mind be in you, which was also in Christ Jesus: Who, being in the form of God, thought it not robbery to be equal with God: But made himself of no reputation, and took upon him the form of a servant, and was made in the likeness of men: And being found in fashion as a man, he humbled himself, and became obedient unto death, even the death of the cross. Wherefore God also hath highly exalted him, and given him a name which is above every name: That at the name of Jesus every knee should bow, of things in heaven, and things in earth, and things under the earth; And that every tongue should confess that Jesus Christ is Lord, to the glory of God the Father.

    “Miracles do not happen in contradiction to nature, but only in contradiction to that which is known to us of nature.”
    St. Augustine

    Thus, much contrary to the mediocrity of earth, and of humans, brought about by the heliocentric discoveries of Galileo and Copernicus, the findings of modern science are very comforting to Theistic postulations in general, and even lends strong support of plausibility to the main tenet of Christianity which holds Jesus Christ is the only begotten Son of God.

    Matthew 28:18
    And Jesus came up and spoke to them, saying, “All authority has been given to Me in heaven and upon earth.”

    Of related interest, this following article is interesting for it draws attention to the fact that humans “just so happen” to be near the logarithmic center of the universe, between Planck’s length and the cosmic horizon of the cosmic background radiation (10^-33 cm and 10^28 cm respectively) .

    The View from the Centre of the Universe by Nancy Ellen Abrams and Joel R. Primack
    Excerpt: The size of a human being is near the centre of all possible sizes.
    http://www.popularscience.co.u.....feat24.htm

  51. Mr BA^77,

    I’m sorry, you’re tilting at windmills. I don’t hold that the mind is nothing. I don’t even hold that the mind is only the individual’s brain state. I accept the concept of “extended phenotype”.

  52. Nak, I ain’t let you wiggle out of this one after all the work that has gone into refuting “hidden variables,,,explain exactly what you mean by “extended phenotype”

  53. Nak, in trying to understand you reference to “SMA is connected to nothing, charged by nothing, and yet directs the voluntary muscles to move,”

    The mind is held to be transcendent and to have dominion of the “material”:

    To prove this point that “nothing”, in the sense of something non-material, has dominion of the material, I reference quantum teleportation in which transcendent information exercised dominion of material,,,,to the point, I might add, of violating the first law in a controlled manner.

  54. Mr BA^77,

    You could start with the wiki page for “Extended Phenotype”, but the book is the thing to understand the concept.

    As fascinating as I’m sure quantum teleportation is, I’m not sure what it buys you as an explanation. Lets do the experiment and sever all connection between the SMA of these monkeys and the rest of their brains. That should reveal whether the information is arriving at the SMA via quantum teleportation or more conventional means. But lets assume it is arriving mirabile dictu, on the QT.

    A physical state at place A influences a physical state at place B. It could have been through smoke signals and the Pony Express, you started with a physical state, and you ended with a physical state.

    Perhaps you’d like to argue that the information instantiated as a state of being is arriving from something other than another physyical system, not another part of the brain. Lets do the experiment! Start taking out parts of the brain that are disconnected from the SMA. If you can take the whole brain away, and the SMA is still receiving signals from the ether to initiate voluntary actions, get your tuxedo ready for the Nobel ceremony. But I am predicting that is not the outcome you observe.

  55. Mr. Nakashima (#44)

    I see that the topic of computational halting has come up in an earlier thread:

    http://www.uncommondescent.com.....d-article/

    May I make a practical suggestion? If you want to know exactly what David Abel means by computational halting, then why don’t you ask him? I’m sure he wouldn’t mind.

    You can find his contact details here: http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

  56. Take away the brain Nak? I could say something but I’m trying (real hard) to be nice to materialists/atheists,,,

    A Reply to Shermer
    Medical Evidence for NDEs
    Pim van Lommel
    Excerpt: So we need a functioning brain to receive our consciousness into our waking consciousness. And as soon as the function of brain has been lost, like in clinical death or in brain death, with iso-electricity on the EEG, memories and consciousness do still exist, but the reception ability is lost. People can experience their consciousness outside their body, with the possibility of perception out and above their body, with identity, and with heightened awareness, attention, well-structured thought processes, memories and emotions. And they also can experience their consciousness in a dimension where past, present and future exist at the same moment, without time and space, and can be experienced as soon as attention has been directed to it (life review and preview), and even sometimes they come in contact with the “fields of consciousness” of deceased relatives. And later they can experience their conscious return into their body.
    http://www.nderf.org/vonlommel.....sponse.htm

    The Day I Died – Part 4 of 6 – The NDE of Pam Reynolds – video
    http://www.youtube.com/watch?v=WA37uNa3VGU

    It should be noted: All foreign, non-Judeo-Christian, culture NDE studies, I have looked at, have a extreme rarity of encounters with “The Being Of Light”. The following study is shocking for what was found in some non-Judeo-Christian NDE’s:

    Near-Death Experiences in Thailand – Todd Murphy:
    Excerpt: The Light seems to be absent in Thai NDEs. So is the profound positive affect found in so many Western NDEs. The most common affect in our collection is negative. Unlike the negative affect in so many Western NDEs (cf. Greyson & Bush, 1992), that found in Thai NDEs (in all but case #11) has two recognizable causes. The first is fear of ‘going’. The second is horror and fear of hell. It is worth noting that although half of our collection include seeing hell (cases 2,6,7,9,10) and being forced to witness horrific tortures, not one includes the NDEer having been subjected to these torments themselves. http://www.shaktitechnology.com/thaindes.htm

    So Nak,,, What have you got to support your materialistic philosophy??? Nothing!!!

    Summary of paper:
    http://docs.google.com/Doc?doc....._5fwz42dg9

  57. in further note:

    The Brain is Non-Materialistic In Its Organizational Structure thus strongly suggesting the brain is designed by a “living transcendent Being” instead of an accident of the random actions of “dead material particles” of which life supposedly accidentally emerged from:

    Brain Innately Separates Living And Non-living Objects For Processing
    http://www.sciencedaily.com/re.....142430.htm

    Category-Specific Organization in the Human Brain Does Not Require Visual Experience:
    Distinct regions within the ventral visual pathway show neural specialization for nonliving and living stimuli (e.g., tools, houses versus animals, faces). The causes of these category preferences are widely debated.
    http://www.citeulike.org/user/.....le/5443232

    The preceding fact is a very curious thing to know when seeing how people react to statements about the “Living” God:

    To The Brain, God Is Just Another Guy
    Grafman says there were some differences between religious and nonreligious people. Those who said they believed in God had a negative emotional response to statements like, “There is no higher purpose.” Nonbelievers had the same reaction to statements that assumed God exists.
    http://current.com/items/89919.....er-guy.htm

    The Mind and Materialist Superstition – Six “conditions of mind” that are irreconcilable with materialism:
    http://www.evolutionnews.org/2.....super.html

  58. Mr. Nakashima (#45)

    I’m not an out-and-out interactionist dualist, but I would call myself a hylomorphic dualist. I don’t think the soul acts on the brain as a separate substance, but I do think that some of our mental acts (especially acts of reasoning, understanding and free choice) are non-physical acts.

    The fact that the SMA receives input from another part of the brain doesn’t bother me, so long as no-one tries to make the scientifically unsubstantiated claim that this input determines the subsequent activity of the SMA. The neural inputs to the SMA are causes, but not determining causes. It is the individual’s free will that determines how the individual acts, by selecting from a range of available neural pathways. But this selection is done from within, not without. There isn’t a spooky entity 10 centimeters above my head, pushing the neurons around.

    If you had a look at the wiring of a monkey brain and a human brain around the SMA, I’d expect to find qualitative differences in organization between the two, accounting for the fact that the latter is a non-deterministic system. Free will is a hypothesis with testable consequences at the neural level.

    If you want to have a look at some recent scientific articles refuting the claim that all our behavior has to be determined, then I suggest you have a look at my Web page at http://www.angelfire.com/linux.....ul-answers and scroll down to “Refutation of Neurological arguments against the possibility of free will.”

    After that, you might like to have a look here at links to articles refuting materialism:

    http://www.angelfire.com/linux.....-arguments

    Happy hunting.

  59. Here is a poem and a few songs for you Nak,

    Wake Me O Lord

    Wake me O Lord from this sleep of mine
    To the living wonders of creation that are so fine
    With a “Oh, that’s nice” I shall not content
    NO, only when You speak shall my heart be spent
    Others may suffice their cravings of Awe
    With an “Oh Well” shrug of the wonders they saw
    But I know You are in each piece of reality
    Yes, in the wind, the stars, and even the sea
    So this vow to You I make
    No rest in me my heart will take
    Till Your face and hands again I see
    In the many waters of reality
    For the truth be known to You indeed
    That if I see You not with my heart and head
    I’m not really born again, but instead am dead

    Evanescence – “Bring Me To Life” – Video
    http://www.youtube.com/watch?v=K3ORuIBjjBU

    Brooke Fraser- “C S Lewis Song”
    http://www.youtube.com/watch?v=GHpuTGGRCbY

  60. Mr BA^77,

    Thank you for the links to NDE stuff, I know very little about this area. I do think you are sliding too easily from talking about the mind to talking about the soul.

  61. Mr Vjtorley,

    Yes computational halting did come up in that thread, and you can see that my questions were the same back then!

    I will see if Mr Abel will be interested in joining our discussion here.

  62. Nak, you state “I do think you are sliding too easily from talking about the mind to talking about the soul.”

    which made me remember this:

    I think therefore I am.

    i.e. What difference does it make Nak???

    All this intellectual posturing you dance around with is of course pointless to the now established fact that we each do indeed have a soul/mind,,, A soul/mind which must give account to its Creator upon death!!! A truly fearsome event when taking into consideration this Creator created the entire universe with His spoken word!!!! A Creator so holy and powerful that we will be utterly unable to stand before His presence unless we have accepted the sanctification provided before us in Christ,,,I don’t know about you but I take this matter very seriously,,,and have seen enough in this life to KNOW this is no game,,,,and I graciously accept the free gift of Christ’s salvation into my heart so that I may be able to stand in that day I am called to give account to God,,, I can only hope that you would reach out to Him as well,,,

  63. Mr BA^77,

    I accept that you are a devout Christian. Please accept that I am not.

  64. Hello Nakashima,

    It appears that Abel’s use of computational halting refers to a computation which stops and produces a functional output.

    From Abel’s paper:
    “In addition, Prigogine’s dissipative structures do not DO anything formally productive. They possess no ability to achieve computational halting.”

    … but yes it would be great to have Abel himself join the discussion and clarify this point. But, I do believe that since he referred to a structure that DOES something formally productive, he is most likely referring [when he speaks of computational halting] to a computation which stops and provides an output which is functional is the sense of performing an action that contributes to a larger action.

    In fact, it seems that Abel’s “computational halting” is very similar to the “functionally specified organization” that I was referring to on that other thread where we were discussing the difference between order and organization.

  65. Mr CJYman,

    I agree that is the most straightforward interpretation, but then my examples above would be valid criticisms.

  66. Hello Nakashima,

    I’m sorry I haven’t been following this thread the whole way. Which criticisms are you referring to?

  67. Nak, do you truly think you will ever find a natural method of information generation to overturn Abel’s null hypothesis? Especially after all these years of experimentation? Shoot Nak why wasn’t his hypothesis shot down with thousands upon thousands of examples of information generation the first week it was published? It should have been literally crushed by a mountain of evidence! But alas what do we hear for evidence,,,, Silence??? Listen closer??? crickets chirping????

    I’ll give you a big clue where the information came from Nak:

    John 1:1-3
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.

    But alas this answer, though provable through experimentation and solid logic, is, for some personal reason,,, not good enough for you.

    Seeing you so vainly trying to find some kind of loophole in the cohesiveness of the Theistic position reminds me of this verse:

    Psalm 118:22
    The stone which the builders rejected is become the head of the corner.

  68. Mr CJYman,

    I gave some counter-examples @44 such as iPods (not God’s :) ) in which the program running the appliance is an infinite loop, it isn’t designed to stop. Halting is non-function. Similarly a program that calculates digits of pi shouldn’t halt.

  69. Mr BA^77,

    Why hasn’t Abel’s null hypothesis been crushed? I can think of a few reasons.

    No one cares.

    The hypothesis itself is encrusted in terms such as computational halting that are not properly defined.

    Abel may have put together a set of definitions (when teased out) that make falsification logically impossible.

    Abel has added “truly” as in “truly natural”, making him the on;y arbiter in No True Scotsman fashion.

    A single experiment that begins with feedstock chemicals and ends with replicating protocells might take hundreds or thousands of years to run. A true blink of an eye for a natural process, but inordinately long to satisfy most humans.

    Your faith in science eventually creating life on the lab bench is touching, but I think it is more likely that we will have a piecewise explanation long before anyone even tries walking away from an experiment for a millenium. But a piecewise explanation would not satisfy Abel’s call for a falsification of his null hypothesis.

  70. bornagain77 taunts,

    Nak, do you truly think you will ever find a natural method of information generation to overturn Abel’s null hypothesis? Especially after all these years of experimentation? Shoot Nak why wasn’t his hypothesis shot down with thousands upon thousands of examples of information generation the first week it was published?

    There are now two null hypotheses, not just one, you must reject in order to win The Origin-of-Life Prize (r). Do please give succinct statements, in language we ordinarily use here at UD, of the two hypotheses.

  71. #70

    Do please give succinct statements, in language we ordinarily use here at UD

    This, I fear, may be an oxymoron.

  72. Mystic, I wasn’t taunting Nak, I was asking an honest question,,,

    Thanks for the origin of life update,,,I found this link on the page that may be of interest:

    Prescriptive Information (PI)
    4 May 2009 – Dr David L. Abel
    Excerpt: Semantic (meaningful) information has two subsets: Descriptive and Prescriptive. Prescriptive Information (PI) instructs or directly produces nontrivial formal function (Abel, 2009a). Merely describing a computer chip does not prescribe or produce that chip. Thus mere description needs to be dichotomized from prescription. Computationally halting cybernetic programs and linguistic instructions are examples of Prescriptive Information. “Prescriptive Information (PI) either tells us what choices to make, or it is a recordation of wise choices already made.” (Abel, 2009a)
    http://www.us.net/life/index.htm

  73. Nak stated some wishful speculation:

    “A single experiment that begins with feedstock chemicals and ends with replicating protocells might take hundreds or thousands of years to run. A true blink of an eye for a natural process, but inordinately long to satisfy most humans.”

    Number one,,, where are these protocells??? Should we not see some “protocells” hanging around in some nook or cranny on the earth today??? Or is this some type of chemistry that was regulated to a former age of miracles where the second law was magically suspended???

    By the way,,, Water is considered a ‘universal solvent’ which is a very thermodynamic obeying and thus origin of life defying fact.

    Professor Arthur E. Wilder-Smith “Any amounts of polypeptide which might be formed will be broken down into their initial components (amino acids) by the excess of water. The ocean is thus practically the last place on this or any other planet where the proteins of life could be formed spontaneously from amino acids. Yet nearly all text-books of biology teach this nonsense to support evolutionary theory and spontaneous biogenesis … Has materialistic Neo-Darwinian philosophy overwhelmed us to such an extent that we forget or overlook the well-known facts of science and of chemistry in order to support this philosophy? … Without exception all Miller’s amino acids are completely unsuitable for any type of spontaneous biogenesis. And the same applies to all and any randomly formed substances and amino acids which form racemates. This statement is categorical and absolute and cannot be affected by special conditions.”
    http://theevolutioncrisis.org.uk/testimony3.php

    Sea Salt only adds to this thermodynamic problem.

    …even at concentrations seven times weaker than in today’s oceans. The ingredients of sea salt are very effective at dismembering membranes and preventing RNA units (monomers) from forming polymers any longer than two links (dimers). Creation Evolution News – Sept. 2002

    Yet you are being very unfair to, and blatantly ignoring, what evidence we do have available ( just so to appeal to your magical pixie fairy of time)

    Yet when we do look at the evidence available, instead of ignore it, we find:

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-mic.....-evolution

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    The malaria parasite, due to its comparatively enormous population size, has in 1 year more mutation/duplication/selection events than all mammal lineages have had in the entire +100 million years they have been in the fossil record. Moreover, since single cell organisms and viruses replicate, and mutate/duplicate, far more quickly than multi-cellular life-forms can, scientists can do experiments on single celled organisms and viruses to see what we can actually expect to happen over millions of years for mammals with far smaller population sizes. Malaria and AIDS are among the largest real world tests that can be performed to see if evolutionary presumptions are true.

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.” http://www.evolutionnews.org/2....._edge.html

    Behe and Snoke go even further in addressing the Gene Duplication scenario in this following study:

    Simulating evolution by gene duplication of protein features that require multiple amino acid residues: Michael J. Behe and David W. Snoke
    Excerpt: We conclude that, in general, to be fixed in 10^8 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10^9.,,,The fact that very large population sizes—10^9 or greater—are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.

    Waiting Longer for Two Mutations, Part 5 – Michael Behe
    Excerpt: the appearance of a particular (beneficial) double mutation in humans would have an expected time of appearance of 216 million years,
    http://behe.uncommondescent.co.....ns-part-5/

  74. Mystic @70:

    There are now two null hypotheses, not just one, you must reject in order to win The Origin-of-Life Prize (r).

    That’s odd. In the reference to the two null hypotheses given on the page you linked, The Cybernetic Cut, Abel listed three null hypotheses:

    Principles of science must not only be falsifiable, they must provide an historical metanarrative and explanation across a wide range of phenomena. In addition, they should foster verifiable predictions in unrelated fields. What scientific predictions does the Cybernetic Cut afford?

    1) No nontrivial computational function will ever spontaneously arise in any inanimate physicodynamic medium or environment independent of formal intervention and controls.

    2) No sophisticated algorithmic optimization will spontaneously proceed in any inanimate environment upon removal of hidden experimenter choices and steering of iterations.

    3) No nontrivial functional controls of inanimate physical phenomena will be realized independent of the programming of dynamically-inert (dynamically-incoherent) configurable switches that alone instantiate formal agent choices into physical reality.

    A single verifiable occurrence of any of these three null-hypothesis predictions will falsify the Cybernetic Cut.

    (My reformatting and emphasis)

  75. Mr BA^77,

    Number one,,, where are these protocells??? Should we not see some “protocells” hanging around in some nook or cranny on the earth today???

    No, we should not. They’ve been outcompeted and eaten by their children. But we do continue to look in nooks and crannies to make sure of that!

    Prof Wilder-Smith is correct about water breaking down the bonds that hold proteins and RNA together. That is why all modern OOL theories abandon the ‘warm little pond’ of Darwin for more protected environments where rates of formation/preservation exceed rates of degradation, therefore allowing concentrations to rise.

  76. Nakashima:
    “I gave some counter-examples @44 such as iPods (not God’s :) ) in which the program running the appliance is an infinite loop, it isn’t designed to stop. Halting is non-function. Similarly a program that calculates digits of pi shouldn’t halt.”

    I’m sorry I don’t see the problem. If Abel states that law+chance doesn’t produce computation that halts and produces a functional output, then I don’t see how examples of computations that don’t halt (designed or not), is a counter example. A counter example would be showing that law+chance will produce a computation that halts and produces a functional output.

  77. Nak states:
    “They’ve been outcompeted and eaten by their children.”

    And why haven’t the children of protocells, “bacteria”, been eaten by their children?

    Did the moral of “honoring your father and mother finally evolve” so that the children (evolutionary offspring) no longer ate their parents?

  78. Mr CJYman,

    If the definition of function is that it is the outcome of a process that halts, then the origin of the process is irrelevant. My counter examples are of functional, but non-halting processes.

  79. Mr BA^77,

    And why haven’t the children of protocells, “bacteria”, been eaten by their children?

    What makes you think they aren’t? Your question is like the classic “If we descended from apes why are there still apes?” Every bacteria on the planet is the result of the same amount of evolution as we are. If they haven’t changed much it is because their niche hasn’t changed much.

  80. Nakashima,

    It seems that part of the definition of computational halting, as used by Abel, is that it produces a functional output — functional in the sense that the *output does something*. I would interpret that as the output preforms an action that contributes to a larger action (from http://www.m-w.com for “function.”) This says nothing of other systems which function (defined as “operate”) by other means. There are different meanings for the word function, and as long as no one is equivocating we are all good. Yes, according to my understanding of Abel’s use of terms, your examples would not computationally halt, yet that possess no problem for the point being made by Abel — law+chance don’t produce computational halting (among other things).

  81. Nakashima,

    … also, Abel no where states (as far as I can see) that function = “the outcome of a process that halts.” Furthermore, that definition is not needed to make sense of his argument and to me it doesn’t make sense in the first place. His definition would be, if I am correct, that computational halting = a computation that halts and produces a functional output. Then, “functional” would be defined as in my last comment.

  82. Speaking of apes Nak, this fresh off the press,,,and remember you heard it here first, on UD, months ago,,,

    ‘Missing link’ primate isn’t a link after all:
    Excerpt: In fact, Ida is as far removed from the monkey-ape-human ancestry as a primate could be, says Erik Seiffert of Stony Brook University in New York.
    http://www.msnbc.msn.com/id/33.....e-science/

    Missing link? Ida was not even a close relative say fossil experts:
    http://www.dailymail.co.uk/sci.....perts.html

    So Nak, Do you think they will air a retraction documentary on the History Channel, to undo all the brainwashing they have polluted young minds with?

  83. Hey Nak,,,where did bacteria get the foresight to prepare the earth (build a house) for their children?

    Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides. – Paul G. Falkowski – Professor Geological Sciences – Rutgers

    Did the bacteria say “Hey, the children may eat us someday but we still got to take care of them?” LOL!

    I know a lot of parents nowadays who probably feel the same way!!! LOL!

  84. Mr CJYman,

    Look at p5 of the book Mr Vjtorley referenced in a comment above for where Abel ties function to halting.

    I hope Abel will respond to my invitaton for him to participate in the discussion here. I feel we are really groping around blindly, very similar to our conversation on the same topic in the spring.

  85. Mr BA^77,

    Why do you think bacteria have foresight? Do you think they planned to kill themselves off with the Oxygen Catastrophe? A very amusing notion.

  86. Wow Nak,,,they sacrificed themselves so that we might live,,,,sounds very similar to another parent I know!!!

    Really Nak, I don’t think the kids of the bacteria were related to the bacteria. I think they were adopted:

    DNA sequences, and the protein machinery that replicates this DNA, is found to be vastly different in even the most ancient of different single celled organisms:

    Uprooting The Tree Of Life – W. Ford Doolittle
    Excerpt: as DNA sequences of complete genomes have become increasingly available, my group and others have noted patterns that are disturbingly at odds with the prevailing beliefs. http://people.ibest.uidaho.edu.....e_2000.pdf

    Did DNA replication evolve twice independently? – Koonin
    Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus.
    http://nar.oxfordjournals.org/.....27/17/3389

    There simply is no smooth “gradual transition” to be found between these most ancient of life forms, bacteria and archaea, as even this following “evolution friendly” article clearly points out:

    Was our oldest ancestor a proton-powered rock?
    Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,… Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common (between the bacteria and the archea). http://www.newscientist.com/ar.....tml?page=1

    That might explain why they ate there parents,,,LOL!!!

  87. Nak, The very first photosynthetic bacteria found in the geologic and fossil record are shown to have been preparing the earth for more advanced life to appear from the very start of their existence by producing the necessary oxygen for higher life-forms to exist, and by reducing the greenhouse gases of earth’s early atmosphere.

    The Oxygen and Carbon Dioxide Cycle – video
    http://videos.howstuffworks.co.....-video.htm

    Photosynthetic bacteria slowly removed the carbon dioxide, and built the oxygen up, in the earth’s atmosphere primarily by this following photosynthetic chemical reaction:

    6H2O + 6CO2 —–> C6H12O6+ 6O2

    The above chemical equation translates as:

    Six molecules of water plus six molecules of carbon dioxide produce one molecule of sugar plus six molecules of oxygen

    Interestingly, the gradual removal of greenhouse gases corresponded to the gradual 15% increase of light and heat coming from the sun during that time (Ross; Creation as Science). This “lucky” correspondence of the slow increase of heat from the sun with the same perfectly timed slow removal of greenhouse gases from the earth’s atmosphere was necessary for the bacteria to continue to live to do their work of preparing the earth for more advanced life to appear. More interesting still, the by products of the complex biogeochemical processes involved in the oxygen production and greenhouse gas removal by these early bacteria are (red banded) iron formations, limestone, marble, gypsum, phosphates, sand, and to a lesser extent, coal, oil and natural gas (note; though some coal, oil and natural gas deposits are from this early era of bacterial life, most coal, oil and natural gas deposits originated on earth after the Cambrian explosion of higher life forms some 540 million years ago). The resources produced by these early photosynthetic bacteria are very useful, one could even say necessary, for the technologically advanced civilizations of today to exist.

    The following video is good for seeing just how far back the red banded iron formations really go (3.8 billion years ago). But be warned, Dr. Newman operates from a materialistic worldview and makes many unwarranted allusions of the “magical” power of evolution to produce photosynthetic bacteria. Although to be fair, she does readily acknowledge the staggering level of complexity being dealt with in photosynthesis, as well as admitting that no one really knows how photosynthesis “evolved”.

    Exploring the deep connection between bacteria and rocks – Dianne Newman – MIT lecture video
    http://mitworld.mit.edu/video/496

    This following article explores some of the other complex geochemical processes that are also involved in the forming of the red banded iron formations.

    Banded Rocks Reveal Early Earth Conditions, Changes

    Excerpt: Called banded iron formations or BIFs, these ancient rocks formed between 3.8 and 1.7 billion years ago at what was then the bottom of the ocean. The stripes represent alternating layers of silica-rich chert and iron-rich minerals like hematite and magnetite. First mined as a major iron source for modern industrialization, BIFs are also a rich source of information about the geochemical conditions that existed on Earth when the rocks were made. ”

    Interestingly, while the photo-synthetic bacteria were reducing greenhouse gases and producing oxygen, and metal, and minerals, which would all be of benefit to modern man, “sulfate-reducing” bacteria were also producing their own natural resources which would be very useful to modern man. Sulfate-reducing bacteria helped prepare the earth for advanced life by detoxifying the primeval earth and oceans of poisonous levels of heavy metals while depositing them as relatively inert metal ores. Metal ores which are very useful for modern man, as well as fairly easy for man to extract today (mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper to name a few). To this day, sulfate-reducing bacteria maintain an essential minimal level of these heavy metals in the ecosystem which are high enough so as to be available to the biological systems of the higher life forms that need them yet low enough so as not to be poisonous to those very same higher life forms.

    Bacterial Heavy Metal Detoxification and Resistance Systems:
    excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.

    The role of bacteria in hydrogeochemistry, metal cycling and ore deposit formation:
    Textures of sulfide minerals formed by SRB (sulfate-reducing bacteria) during bioremediation (most notably pyrite and sphalerite) have textures reminiscent of those in certain sediment-hosted ores, supporting the concept that SRB may have been directly involved in forming ore minerals.

    Transitional Metals And Cytochrome C oxidase – Michael Denton – Nature’s Destiny
    http://books.google.com/books?.....3&lpg

    As well, geological processes helped detoxify the earth of dangerous levels of metal:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.”

    And on top of the fact that poisonous heavy metals on the primordial earth were brought into “life-enabling” balance by complex biogeochemical processes, there was also an explosion of minerals on earth which were a result of that first life, as well as being a result of each subsequent “Big Bang” of life there afterwards.

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.

    To put it mildly, this minimization of poisonous elements, and “explosion” of useful minerals, is strong evidence for Intelligently Designed terra-forming of the earth that “just so happens” to be of great benefit to modern man.

    Man has only recently caught on to harnessing the ancient detoxification ability of bacteria to cleanup his accidental toxic spills, as well as his toxic waste, from industry:

    What is Bioremediation? – video
    http://www.youtube.com/watch?v=pSpjRPWYJPg

    Clearly many, if not all, of these metal ores and minerals laid down by these sulfate-reducing bacteria, as well as laid down by the biogeochemistry of more complex life, as well as laid down by finely-tuned geological conditions throughout the early history of the earth, have many unique properties which are crucial for technologically advanced life, and are thus indispensable to man’s rise above the stone age to the advanced “space-age” technology of modern civilization.

    Metallurgy
    http://en.wikipedia.org/wiki/Metallurgy

    Inventions: Elements and Compounds – video
    http://videos.howstuffworks.co.....-video.htm

    Mineral
    http://en.wikipedia.org/wiki/Mineral

    As well, many types of bacteria in earth’s early history lived in what are called cryptogamic colonies on the earth’s primeval continents. These colonies dramatically transformed the primeval land into stable nutrient filled soils which were receptive for future advanced vegetation to appear.

    CRYPTOBIOTIC SOIL -
    Excerpt: When moistened, cyanobacteria become active, moving through the soil and leaving a trail of sticky material behind. The sheath material sticks to surfaces such as rock or soil particles, forming an intricate web of fibers throughout the soil. In this way, loose soil particles are joined together, and an otherwise unstable surface becomes very resistant to both wind and water erosion.

    Materialism has no answers for why these different bacterial types, colonies, and processes, would start working in precise concert with each other preparing the earth for future life to appear from the very start of their appearance on earth.

  88. Nakashima,

    I never disputed that function is tied to halting, since Abel’s definition of computational halting seems to rely on functional output.

    However, the point where we are talking past each other is that a computation may halt and not produce a function or may be functional in another sense and not halt. That is fine. If it does not halt and produce a functional output then it is simply not an example of computational halting that *DOES* something, as Abel puts it, and that is what Abel is describing — a computation that halts and produces a functional output (which is what he seemingly means by “computational halting).

    Furthermore, your examples above do nothing to negate his point that law+chance don’t produce what he defines as computational halting.

    And, yes, it would be great if Abel were to join the discussion. However, until then, we only have what he has written to go by. I have shown that he equates *doing* something with the results of computational halting and thus I interpret that as an output that *does* something (is functional). Furthermore, you state that vjtorley has shown above where Abel linked function with his idea of computational halting. So, if it doesn’t halt and produce a functional output, it is not an example of the type of “computational halting” that Abel is discussing.

  89. Mr BA^77,

    Nak, The very first photosynthetic bacteria found in the geologic and fossil record are shown to have been preparing the earth for more advanced life to appear from the very start of their existence by producing the necessary oxygen for higher life-forms to exist, and by reducing the greenhouse gases of earth’s early atmosphere.

    You are conflating their action and intention. (I can, for example, fall off a bicycle without intending to.)

    The whole point of ID is to justify this teleology, not assume it. What you are demonstrating is your hindsight, not bacterial foresight.

  90. Mr CJYman,

    I think it is the other way around, that Abel defines function in terms of (undefined) computational halting.

    The point of my query is why make such a big deal of computational halting (Abel mentions it over and over, and throws it in as a part of his null hypothesis) if it is really not a necessary feature? But if function can only be assessed after halting has happened, my counterexamples are valid criticisms.

    I am in complete agreement that this particular criticism does not negate his thesis. It is just setting the groundwork for further discussion. If we can’t agree on terms, we just talk past each other.

    Again, I suggest reading that passage. Abel is saying there is no function without halting. That is wrong.

  91. So you truly believe all this just happened by accident Nak??? Simply unbelievable Nak,,, You know Nak I was just thinking,,,Do you ever get really happy for just existing??? Sometimes I do,, and I thank God for creating me,,, but for you??,,you know you being a chance-worshiper and all,, whom or what do you thank??? Do you go to Las Vegas, walk into a huge casino, stop in the middle of it all and sing out,,, OH THANK YOU BLIND CHANCE FOR CREATING ALL THIS???? Just what exactly do you do???

  92. What gets lost beneath all the chemical experiments and speculation is that we already have sufficient basis both for deducing an intelligent cause and for rejecting non-intelligent cause.

    Undirected abiogenesis is like a moon made of green cheese. How much math, evidence, or logic do we need to dismiss such a thing? And yet, in the former case, for those who need it spelled out and calculated, it has already been done.

    The burdens of proof for both moons made of cheese and undirected abiogenesis are quite heavy. Chunks of cheddar embedded in meteorites would not suffice. Neither do amino acids and directed experiments that alter the components of existing life.

    The rest is a distraction. The belief in the unintelligent formation of life is merely a quasi-religious commitment to a belief system, endlessly in search of validation, clinging to every straw it grasps. So what if the trend is to call it science? Such things pass.

  93. Nakashima:
    “Again, I suggest reading that passage. Abel is saying there is no function without halting. That is wrong.”

    You’ll have to point me to the passage, please.

    Is Abel stating that there is no such thing as function (according to any definition of function) apart from halting, period? Or is he stating that in this particular case, there is no function because there is no halting? Furthermore, is he actually defining all forms of “function” as necessarily relying on halting, or is he stating that the type of “function” that he is discussing doesn’t arise apart from halting and the output *DOING* something?

  94. Mr CJYman,

    Function is determined by the formal computational halting of the system.

    That is Abel.

  95. Mr BA^77,

    In previous discussions, I’ve given you some insight into my personal beliefs, but in retrospect I don’t think it was helpful. If you continue to frame issues in a personal way, expect no reply.

  96. Mr ScottAndrews,

    What conclusions would you draw from chunks of cheddar embedded in meteorites?

  97. Nakashima,

    In the case of a single meteorite, perhaps it hit a structure containing large amounts of cheese.
    In the case of multiple meteorites I would strongly suspect a hoax. Even more so if articles had begun popping up in science journals suggesting that entire planetary bodies were made of it.
    I would rule out that last possibility because it doesn’t even merit serious consideration.

  98. Well Nak, I am who I am, I don’t know how not to be “personal” as you put it, This is because I tend to see how things are related so as to make a case for design (so this would include how your personal beliefs are distorting your view of reality), and you tend to see only things that would detract from a design inference. Like for instance if I dug a little deeper and found a “life enhancing” properties emerging from the oxygen catastrophe, which surely there are some, you would just ignore that I refuted part of your argument since the evidence did not conform to your “personal” belief,,, Shoot Nak, our personal beliefs color our whole view of reality. You see, I truly believe there is purpose (i.e. design) to be found in every nook and cranny I look at,,, for instance I believe Autumn Leaves have a deeper lesson to teach us than the cyclical chemistry of nutrients:

    Autumn Leafs Laughter
    Oh please do tell us of your secret
    you majestic autumn leaves,of regal red ,and shimmering golden yellow ,
    brilliantly coloring the landscapes of trees .
    Do you dare pass away in a rush of beauty while you are slowly dieing ?
    Pay ye no heed to all the other deaths so solemnly attended with tears and crying?
    or Does the essence in you somehow yearn jealously for a glorious life to come ?
    And you somehow know that death
    shouldn’t be sad but fun?
    For I truly wish I could die like you and that I knew the secret of your story, so that my countenance should light up and glow as my soul is delivered to behold God,s glory.
    So please autumn leaves which mock
    death with such defiant belly laughter,
    Do tell us your secret over death so that we may properly enter the hereafter.

    Autumn Leafs Laughter – Death Where Is Your Sting – video
    http://www.youtube.com/watch?v=OqjN0kAr-Hw

  99. In comment #75, Nakashima-san asserts that there are no “protobionts” in the biosphere today. I strongly suspect that we do not have enough information about the microbiotic composition of the biosphere to make an assertion like this with any confidence.

    As two examples, biologists were almost completely unaware of the existence of an entire domain of living organisms – the Bacteria – until the 18th century, and were unaware of the existence of another of the three domains – the Archaea – until a couple of decades ago. Until the invention of microscopes, the very existence of bacteria was impossible, and until the development of rapid and sophisticated nucleotide sampling and sequencing technology the existence of the domain Archaea was also outside the realm of empirically verified science.

    The relatively recent discovery of these two major domains of living organisms is all the more surprising when one considers that together they make up the vast majority of the total biomass of life on Earth (the global population of Bacteria alone is estimated at 5 X 10 ^30). Bacteria and Archaea also comprise the overwhelming majority of the genetic and metabolic diversity in the biosphere, yet despite a century of looking, we have relatively few tools with which to investigate their biology.

    As another measure of how much we don’t know about microbiotics in general, consider that we now recognize only four kingdoms of Eukaryotes (protists/protoctists, plants, fungi, and animals), but over 25 taxonomic groupings equivalent to kingdoms of Bacteria (see http://www.ncbi.nlm.nih.gov/Ta.....Eubacteria ), and at least six taxonomic groupings equivalent to kingdoms of Archaea (see http://www.ncbi.nlm.nih.gov/Ta.....wwwtax.cgi ). How confident can we be that there are no protobionts lurking in the biosphere today?

    Bottom Line: It seems reasonable to me to assume that we haven’t observed protobionts today because we haven’t been looking for them, and don’t even have the tools to look if we were (indeed, we don’t even know what such tools might be).

    Absence of evidence is not evidence of absence.

  100. Mr ScottAndrews,

    Does that mean you consider articles written about abiogenesis topics to be a hoax? I’m trying to understand the strength of your analogy, not put words in your mouth.

  101. Re comment #98:

    Not surprisingly, there is an evolutionary hypothesis for the brilliance of fall foliage, first proposed by William D. Hamilton (of inclusive fitness and kin selection fame). You can read about it here:

    http://scienceblogs.com/loom/2.....lliant.php

    There are two other evolutionary hypotheses for this phenomenon as well. You can read about them here:

    http://en.wikipedia.org/wiki/Autumn_leaf_color

    and follow up the references to the primary literature listed at the end of the Wikipedia article.

  102. 102

    Nakashima:

    Does that mean you consider articles written about abiogenesis topics to be a hoax?

    No. The comparison was the far-fetched implausibility of the propositions, neither of should be taken too seriously.

  103. ba77@91:

    “Do you ever get really happy for just existing??? Sometimes I do,, and I thank God for creating me,,, but for you??,,you know you being a chance-worshiper and all,, whom or what do you thank???”

    I’m just grateful that I am here and came into existence since the chances against me were so great.

    Once again, I don’t think we’re that far apart; I just don’t think I was planned. But we both are glad to be here and try to make our existence meaningful. We’ve a lot more in common that we have apart.

  104. ellazimm, I don’t think we have that much in common and I don’t think you are being logically consistent to your worldview,,, i.e. I believe you are ignoring the deeper implications of your philosophy i.e. the utter futility of your existence that your philosophy entails.

    This video will flesh out our differences a little more

    Countering The New Atheism Of Richard Dawkins – Dan Petersen
    http://www.youtube.com/watch?v=yYv_LRQ7ZVg

  105. Nakashima:
    “‘Function is determined by the formal computational halting of the system.’

    That is Abel.”

    Which paper is that? I can’t seem to find that quote and I’d just like to check out the context. So far, though, that doesn’t seem to pose a problem in how he is using the terminology.

    Combined with the quote of his that I provided earlier, he seems to be merely stating that when he is using the term “function,” he is referring to a system which computationally halts and produces and output. If the output itself doesn’t have to be “functional” in the traditional sense of “actions which contribute to a larger action,” then yes, any program which halts and provides an output would be an example of a formally functional system.

    Again, I see no problem.

  106. Allen_MacNeill,,Not surprisingly, there is an evolutionary hypothesis for the brilliance of fall foliage,,,
    Not surprisingly??? That is a huge understatement,,,evolution has a “creation myth” for everything,

    You alluded to undiscovered evidence of “protocells” to deflect from the evidence we do have,,,Number 1 extreme conservation for morphology and molecular makeup for as far back as we can find bacteria! Number 2 a total lack to the variability of bacteria any further than small variations within kind,,,

    It is not the lack of evidence that is so distressing to evolutionists,, it is what the evidence we do have is screaming to us,,,

    By the way Allen, if any “evolution” went on to bring about the sheer beauty of Autumn foliage, it was surely accomplished under the principles of Genetic Entropy!

  107. Mr CJYman,

    The quote is from “More than Metaphor: Genomes are Objective Sign Systems”, a book chapter in Biosemiotic Research Trends. Mr Vjtorley @36 above provides a link. To find this sentence, go back to page 5.

    The problem is that he isn’t saying some functional programs halt, he’s saying that _all_ functional programs halt. But we know some don’t, I gave some examples. So there is a problem either with his definition of “function” or with his definition of “formal computational halting”. Granting for the sake of argument that Abel, you and I agree that “formal computational halting” means “it stops”, the problem is with his definition of function.

  108. A little more on the “origin of life” “problem”:

    Allen alluded to “undiscovered” evidence, yet is there any reason to presuppose that he may be right? I don’t think so. The trend of physical evidence is definitely not tracking for the evolutionists.

    First big blow to evolution?

    First and foremost, we now have recently discovered evidence for photosynthetic life suddenly appearing on earth, as soon as water appeared on the earth, in the oldest sedimentary rocks ever found on earth.

    Scientific Evidence For The First Life On Earth – video
    http://science.discovery.com/v.....dence.html

    Dr. Hugh Ross – Origin Of Life Paradox – video
    http://www.youtube.com/watch?v=HHEl9PZW4hc

    Materialists have tried to get around this crushing evidence for the sudden appearance of life by suggesting life could originate in extreme conditions. Yet they are betrayed once again by the empirical evidence:

    Refutation Of Hyperthermophile Origin Of Life scenario
    Excerpt: While life, if appropriately designed, can survive under extreme physical and chemical conditions, it cannot originate under those conditions. High temperatures are especially catastrophic for evolutionary models. The higher the temperature climbs, the shorter the half-life for all the crucial building block molecules, http://www.reasons.org/LateHea.....iginofLife

    Intense research has not alleviated the complexity being dealt with in any origin of life research but only illuminated it:

    Intelligent Design or Evolution? Stuart Pullen – Book
    The chemical origin of life is the most vexing problem for naturalistic theories of life’s origins. Despite an intense 50 years of research, how life can arise from non-life through naturalistic processes is as much a mystery today as it was fifty years ago, if not more.

    What does the simplest life ever found on earth tell us?

    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8

    Plus it is now known that:

    Chance and necessity do not explain the origin of life: Trevors JT, Abel DL.
    Excerpt: Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic–that is, it is programmatically and algorithmically organized and controlled.

    As well:

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.

    As well:

    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.”

    “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

  109. ellazimm, to further differentiate the drastic differences between your materialistic worldview and my theistic worldview, I would like to point out that materialism has an extremely difficult time assigning proper value to humans in the first place: In fact ignoring all the atrocities conducted by atheistic regimes, just valuing the “material” ingredients in your body you come to figure that you are only worth a dollar:

    How much is my body worth?
    Excerpt: The U.S. Bureau of Chemistry and Soils invested many a hard-earned tax dollar in calculating the chemical and mineral composition of the human body,,,,Together, all of the above (chemicals and minerals) amounts to less than one dollar!
    http://www.coolquiz.com/trivia...../worth.asp

    Whereas Theism tells me the creator of the entire “material” universe values me this much:

    Greater love has no one than this, that he lay down his life for his friends.

    So there really is a very drastic difference between how we ultimately view our lives!!!

  110. ATTENTION:

    Here is a message from Dr. David Abel, in response from an email I sent him, inviting him to join in the discussion on this thread. I have reproduced it in its entirety, without any alterations.

    Vincent,

    I do not have time to participate in blogs. But you may cut and paste this response to your specific question of me IN ITS ENTIRETY ONLY into your blog if you wish.

    I doubt that your lay bloggers would be interested in delving into a technical discussion of “Decision Problems,” “Undecidability,” and “Turing’s computational halting paradox.” Can we know for sure in advance, prior to actually running it, that a program will reach its intended conclusion (FINISH: do what it was written to do)?

    Programmers often distinguish between “halting” and “faulting.” “Halting” tends to imply that the program finishes its computation successfully and does what the program was intended to do rather than just running endlessly, or stopping without achieving the utility for which it was written because of some fault or error in the program.

    For purposes of your lay discussion, it would probably be clearer and easier to just talk in terms of computational or programming “SUCCESS.” Most people are familiar with the expression, “Does not compute!” Computer programmers from the early days often joked about their programming efforts “blue screening.” Instead of getting hung up in technical Turing terminology, your bloggers should concentrate more on the difference between “computational success” vs. “blue-screening” or “running forever in a continuous worthless loop.”

    Nobody wants to buy off-the-shelf software that is full of bugs, let alone one with a fatal computational fault or error in the form of the software repeatedly crashing. Computations must successfully reach their formal “conclusion” to provide the desired utility.

    Ultimately the questions that naturalistic life-origin research is interested in are these:

    1) Can inanimate physicodynamics in a prebiotic environment achieve any form of spontaneous computational success? In other words, can mass/energy interactions alone successfully program or compute formal function? By what mechanism?

    2) HOW would the necessary programming “choices” be made at each decision node by chance and/or necessity so as to steer the computation toward potential formal programming success? As you know, natural selection favors only the fittest already-programmed, already-living phenotypes. Natural selection is nothing more than differential survival and reproduction of the fittest holistic living organisms. Natural selection cannot program linear digital prescription of potential function or life using a representational symbol system at the genetic and genomic level (The GS Principle).

    Remember, the nucleotides must be rigidly bound with covalent bonds into a positive strand sequence before prescribing polyamino acid sequencing. Amino acids must also be rigidly bound together with strong covalent bonds into their primary structure (their linear sequence or string) before any folding occurs into three-dimensional molecular machines. The programmed sequencing is what determines what the free-energy sinks will be. This is turn determines what the string’s average foldings and dynamic motions will be. Programming choices have to be made in advance of any realized physical reality or function. Thus, natural selection is of no help in elucidating the mechanisms of The Genetic Selection Principle of biology, especially at the pre-biotic chemical-evolution level of gene emergence.

    3) Can chance and/or necessity generate a linear, digital, meaningful, prescriptive message using a representational material symbol system (such as we repeatedly observe in genetics, genomics, and in polynucleotide and polycodon messenger molecules? By what natural mechanism?

    4) How did inanimate nature craft such an efficacious Hamming redundancy block code to reduce noise pollution in the Shannon channel?

    5) How did physicality achieve such a sophisticated (very close to conceptually ideal) translation system between two formal languages (the polycodon language and the polyamino acid language)? These sequencings are physicodynamically indeterminate (inert, incoherent with physical cause-and-effect). This means from the standpoint of physics and chemistry they are effectively arbitrary. Arbitrary does not mean random. Arbitrary means uncoerced by physical laws. It means specific sequencing of the positive single informational stand of nucleic acid is free from determinism. No as-of-yet undiscovered law is going to be able to explain the free-from-law selection and sequencing of nucleotides (programming) of prescriptive nucleic acid in a pre RNA or RNA World. All we have to work with is either stochastic ensembles (random strings), or highly ordered strings such as polyadenosines adsorbed onto montmorillonite clay with all the same “letters.” A homopolymer cannot contain prescriptive information because it has no uncertainty (0 bits). So far as the stochastic ensembles of nucleotides are concerned, no one has ever observed a random number generator produce a computationally successful computer program.

    Scientific pursuits tend to center more around “How?” questions that elucidate specific natural-process mechanisms. What are our proposed mechanisms?

    Do those theoretical mechanisms smuggle in artificial selection through the back door? If so, they are not “natural-process mechanisms.”

    Hope this helps to keep your discussion scientific.

    Dave Abel

    P.S.: Don’t forget, if you use any of my response made to you personally in your blogging, use ALL of it. Quote my entire emailed answer to your perfectly reasonable academic question regarding the meaning of a term used in my peer-reviewed science journal publications. Don’t associate me with any of your personal metaphysical persuasions. I am a scientist, not a metaphysician or philosopher. Thanks, Vincent.

    David L. Abel, Program Director
    The Gene Emergence Project(TM)
    An international consortium of scientists investigating primordial biocybernetics and biosemiotics.
    The Origin of Life Science Foundation, Inc
    http://www.lifeorigin.org

    Peer-reviewed publications: http://davidlabel.blogspot.com/

    SciTopics http://www.scitopics.com/Presc.....on_PI.html
    http://www.scitopics.com/The_Cybernetic_Cut.html
    http://www.scitopics.com/The_G.....ciple.html

    Mail to: life @ us.net

  111. Mr Vjtorley,

    I received the same message.

  112. bornagain77 @ 91

    So you truly believe all this just happened by accident Nak??? Simply unbelievable Nak,,, You know Nak I was just thinking,,,Do you ever get really happy for just existing??? Sometimes I do,, and I thank God for creating me,,, but for you??,,you know you being a chance-worshiper and all,, whom or what do you thank???

    Why should we need to thank anyone? Why do you need to thank someone?

    Even within Christian theology it is arguably presumptuous to thank God for creating you. Adam and Eve were directly created by God. You are the child of your parents and all of you are distant descendants of the original couple. Neither you nor anyone else alive today are claimed to be His direct creation.

    By all means be happy to be alive. Those of us who are fortunate enough to enjoy a relatively good life in a wealthy First World country are lucky indeed. Not only are we a tiny minority of all the potential human beings who never made it this far but our lot is a lot better than that of many others on this planet.

    bornagain77 @ 91

    …I would like to point out that materialism has an extremely difficult time assigning proper value to humans in the first place…

    Whereas Christians are lucky enough to have God do all the valuing for them? They don’t have to do any thinking for themselves. God does it all for them. They just have to look it up in the Good Book.

    And just what is “proper value” in the first place?

    Whereas Theism tells me the creator of the entire “material” universe values me this much:

    Greater love has no one than this, that he lay down his life for his friends.

    What makes you think you are one of His valued friends?

    In the Great Flood, God laid down the lives of everyone else for His few “friends”. So much for “greater love”.

    If He exists and if He decides to do it again, the odds are against you being one of the favored few. Yes, I know He promised never to do it again but, right at the beginning, He promised Adam he would die on the day he ate the fruit. That never happened so we have to say that His word is not entirely reliable.

  113. Mr MacNeill,

    I wish I shared your hopefullness over finding new and simpler forms of life that might be related closely to our earliest ancestors. However, as we have scaled down several orders of magnitude in microscopy, each advance has not revealed new vistas of unknown biomass.

    I realize that I should hedge my language more than I did earlier, but reviews such as this on nanobes, nanobacteria and UMB is behind my pessimism for finding “living fossils” that reflect early life of 3.5 billion years ago.

  114. 114

    Seversky,

    Even within Christian theology it is arguably presumptuous to thank God for creating you. Adam and Eve were directly created by God. You are the child of your parents and all of you are distant descendants of the original couple. Neither you nor anyone else alive today are claimed to be His direct creation.

    Even if millions of generations passed since Adam and Eve, all are the result of being created. It is no less true for the last than for the first. And if bornagain77 wants to thank someone for his birthday gift, I don’t blame him, We thank people for the gift of house slippers on our birthday, can we not thank someone for the gift of life on our birthday? Does this really need to be explained? And the world was being judged by God in the flood, do you have it in mind that it was not worthy of judgment? And Adam did die spiritually on the day he ate the fruit, that is why it is important to be “born again” as bornagain77′s name indicates. This is basic stuff really. Maybe you should look it up in the good book yourself, and free yourself from your unwarranted assumptions.

  115. OT: The shifty professor, Allen MacNeill, is making questionable claims about U.D. and its members at another I.D. blog (October 22nd, 2009 at 10:43 pm).

    I don’t want to seem a trouble maker, I just thought you all should be made aware of it.

  116. Hello Nakashima,

    It appears that Abel’s brief explanation of “faulting” and “halting” above should clear up how he defines “function” in relation to computational halting.

    It seems clear now, that if Abel is referring to “function,” then he is referring to computational halting that does indeed halt and provide a useful output. According to his definition, neither your endless looping scenario nor your crashing software scenario would be an example of formal function. You can call your endless loop functional according to another definition of the term and that’s all good and fine. However, for the purpose of what Abel is discussing — the generation of formal function — he seems interested in explaining computations that halt and provide functional (useful and thus functional in the dictionary sense of “actions contributing to a larger action”) output. To simplify the wording, he merely labels that type of system as “formally functioning.” Thus, he differentiates between programs which merely loop infinitely, programs that “blue screen,” and programs that output something useful.

    Does that pretty much sum it up?

  117. I realize that I have a simple mind and much of what is written above is beyond my mathematical ken. HOWEVER, :-) it seems to me that my original assertion still stands and is still fatal to materialism/naturalism.

    If materialism is true then physics is the only thing available for explaining anything and everything. I’m sure no discussion is required for this group. I can do it, but it’s tedious and obvious so I won’t unless someone demands that I do.

    But physics cannot explain information and it will never be able to explain information because information requires language to encode/transmit/decode it and languages consist of symbols and rules for the organizing of those symbols into meaningful phrases – that is – phrases that mean something. In the genetic language, the language of life, meaningful = alive. Certain arrangements of DNA code for living things and others do not.

    But physics has nothing to say about either the symbols or the rules of any language and that includes the genetic language. What law or laws of physics tell us the difference between a noun and a verb and when to use them in a sentence? What law or laws of physics tell us that a certain combination of codons codes for a protein and that others don’t? That’s right, none of them do. That’s because physics deals with quarks, leptons, and forces, not abstract things like information, morality, purpose, design, and so on.

    The typical materialist move at this juncture is to deny the existence of a moral law (although they seem strangely committed to the proposition that it is WRONG to teach ID in schools :-) ) or of design or purpose. Thus we have Dawkins and others saying that things are only “apparently” designed or that they have “apparent” purpose or that there is the “strong illusion” of purpose.

    But the materialist cannot deny the existence of information because the denial involves the use of information. A logical contradiction if there ever was one. Therefore the game is over for the materialist. If you think not, then tell me what law or laws of physics explain any symbol, the representation of one thing for another or any rule of any language, genetic or otherwise.

    I don’t know why, really, that this seems so hard for some people to grasp. Maybe because the implications are so profound. Bernd Olaf-Kuppers says in his book Information and the Origin of Life that the question of the origin of life is the question of the origin of information. I hate to break it to the materialists/naturalists out there but information always reduces to mind, not to physics. Physics cannot explain symbols and rules because it has nothing to say about symbols and rules and it will never have anything to say about symbols and rules because that’s not what physics is about. How many different ways does it have to be said?

    bornagain77 has it right when he cites John 1:1. In the beginning was the Word. In the beginning was Information. In the beginning was the Mind, the Logos, the Reason. This is true not because the Bible says it. The Bible says it because it is true. A distinction that unfortunately many people, including Christians, miss.

  118. Hi everyone:

    I’d like to draw people’s attention to a paper I cited above in #35:

    Intelligent Design: Required by Biological Life? by K. D. Kalinsky (2008).

    Even after making very generous assumptions for an origin-of-life scenario, Kalinsky makes a compelling case that the functional information in a typical 300-amino acid protein is much more likely to have been produced by intelligent design than by mindless natural processes. The odds against such a protein arising as a result of undirected processes are astronomical.

    I find it curious that none of the ID critics on this thread have faulted Kalinsky’s logic. I think that speaks volumes.

    Kalinsky certainly bends over backwards to be generous to the anti-ID camp. Even supposing that the entire mass of the primeval Earth was composed of protein (giving us 10^47 proteins), we would not expect a structure to have arisen with more than about 185 bits of functional information (a term carefully defined in Kalinsky’s paper), over a 500-million year period (which is the maximum amount of time for the formation of life on Earth).

    In #14 above, Interstellar Bill hypothesized the occurrence of picosecond permutations occurring in porous ocean vents on the primeval earth. But even if we allow for the possibility of picosecond permutations of these amino acids instead of annual permutations as Kalinsky supposes, we still only expect natural processes to have generated a structure with about 255 bits of functional information. Kalinsky demonstrates that 300-amno acid proteins have 700 bits of functional information, making their formation by mindless natural processes astronomically unlikely.

    Facts, as Cardinal Newman used to say, are stubborn things. It’s time that opponents of ID faced the facts. There is a very strong case for the common descent of life-forms; but there is an even stronger case for ascribing the origin of life itself to intelligent design. There’s no getting around the math.

  119. #118

    vjtorley

    I am sorry but the maths in this paper is irrelevant. I don’t know of a single scientist who would dispute that if you create a string of amino acids at random the changes of creating a protein that is part of living organism is negligibly small.

    1) A fitness function is not something that is selected to meet a target. It is simply whatever allows that organism to reproduce effectively in that context at that time. It is nonsense to talk about the information content of a fitness function. To talk about its information content is to talk about its probability. But there isn’t a set of fitness functions from which natural selection is choosing. It is just whatever happen to be working for that organism at that moment.

    2) Therefore, you cannot estimate the probability of arriving at a protein that is of using in a living organism by calculating the probability of a string of amino acids chosen at random (where random means any amino acid is equally likely in any position). It is a selection process which vastly increases the probability.

    3) There is real confusion over the likelihood of a functional protein given a mind. Of course, it is possible to imagine an omnipotent mind that is certain to produce any effect we might observe. But that is a specific hypothesis about a specific type of mind – omnipotent minds. But that is quite different from the hypothesis that an unspecified mind created the protein. An unspecified mind would have to include all possible minds – including those with less power than yours and mine and those with immense power but no wish to create life. The probability of an unspecified mind creating a functional protein is certainly not 1 (if you can attach any meaning to such a vague hypothesis).

    The fact that there are one or two human minds that have managed to design parts of a few proteins (making extensive use of existing proteins in doing so). Is quite frankly irrelevant. No one is suggesting that a human mind designed life.

    I am deeply conscious that I have explained this poorly. I strongly recommend Elliott Sober’s book on Evidence and Evolution – particularly chapter 2 on ID – but you may need to read chapter 1 on evidence first.

  120. Mr CJYman,

    Yes, I think that is close enough.

    In terms of Dr Abel’s challenge to falsify his null hypothesis, it is now clearer why no one should care to try. Why bother proving that halting X have property Y, when non-halting X are nore interesting?

    For example, we know that many bacteria have circular genomes. Imagine for a moment a primitive object with a circular RNA genome and a primitive ribosome attached to it. The ribsome loops endlessly around the genome making proteins.
    Abel’s definitions say that this system of genome and ribosome is non-functional, because it never halts. Sorry, that is like saying my heart is non-functional because it doesn’t stop.

    Dr Abel is trying to make a claim about all functioning programs. By including this notion of computational halting, he is limiting himself unintentionally to a subset of function.

  121. To address some of Dr Abel’s points in his message (entered by Mr Vjtorley @110):

    To say that no one wants to buy a program with bugs in it is correct, but hardly an argument against the materialist origin of a genome. We know there are bugs in our genome.

    In his point 2, Dr Abel is correct that the genome is fixed before the cell starts to fight for its place in the universe. He seems to think this is an argument that a cell cannot acheive function. That is not accurate. There is a lag involved, and any one cell may be badly out of tune with its context, and therefore function less well. Another cell may have a similar lag, but function better than expected because the environmental context has shifted favorably in its direction. Dr Abel’s argument is teleological with respect to an individual, ignoring (or vastly understimating) the power of feedback and stochastic variation over a population.

  122. Mark Frank, I watched you dance around with your semantics and I realized after reading what you had wrote that you never gave any real meat, i.e. substance, to the primary question at hand. “Where did the information come from?”,, You never even tried to quote any experiments in which to back up your claims that a fitness function resides in “nature” somewhere. Shoot Lenski, using all his intelligence for coaxing (selecting) E-Coli into greater levels of complexity, has yet to demonstrate to origination of any functional complexity that was not present before, and in fact when his work is scrutinized (Behe Evolution News) it shows that the bacteria are quickly headed towards genetic meltdown:

    New Work by Richard Lenski:
    Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal.
    http://www.evolutionnews.org/2.....enski.html

    If it suffices your curiosity to be placated by such grandiose rhetoric so be it,,,but as for my self show me the exact experiments in which natural processes generated functional information.

    As well I took exception to your remark:
    “it is possible to “imagine” an omnipotent mind that is certain to produce any effect we might observe.”

    But is it possible to prove such a omnipotent Mind exist Mr. Frank?

    I maintain that it is!

    “pure transcendent information” is now shown to be “conserved”. (i.e. it is shown that all transcendent information which can possibly exist, for all possible physical events, past, present, and future, already does exist.)

    Conservation Of Transcendent Information – 2007 – video
    http://www.youtube.com/watch?v=5Hm4lh81r6M

    How Teleportation Will Work -
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://in.geocities.com/info_aruni/tele.htm

    In extension to the preceding video, the following video shows quantum teleportation breakthroughs have actually shed light on exactly what, or more precisely on exactly Whom, has created this universe:

    Scientific Evidence For God Creating The Universe – 2008 – video
    http://www.youtube.com/watch?v=JQhO906v0VM

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) — Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a qubit, an infinite amount of information must be transferred to teleport. http://www.cas.umt.edu/phil/fa.....lPSA2K.pdf

    It is also interesting to note that we can only “destroy” a photon in these quantum teleportation experiments. No one has “created” a photon as of yet. I firmly believe man shall never do as such, since I hold only God is infinite, and perfect, in information/knowledge.

    Reflection on the quantum teleportation experiment:

    That a photon would actually be destroyed upon the teleportation of its “infinite” information to another photon is a direct controlled violation of the first law of thermodynamics. Thus, this is direct empirical validation for the primary tenet of the Law of Conservation of Information (i.e. information cannot be created or destroyed). This conclusion is warranted because information exercises direct dominion of energy, which cannot be created or destroyed by any known material means, yet a photon of energy is destroyed by this transcendent means. Thus, this experiment provides a direct line of logic that transcendent information cannot be created or destroyed. Clearly anything that exercises dominion of the fundamental entity of this physical universe, energy, must of necessity possess the same, as well as greater, qualities. i.e. All information that can exist, for all past, present and future events of energy, already must exist. Another line of evidence, corroborating the primary tenet of the Law of Conservation of Information, is the required mathematical definition for infinite information needed to correctly specify the reality of a photon qubit (Armond Duwell).
    The fact that quantum teleportation shows an exact “location dominion”, of a photon of energy by “a specified truth of infinite information”, satisfies a major requirement for the entity needed to explain the missing Dark Matter. The needed transcendent explanation would have to dominate energy in a very similar “specified location” fashion, as is demonstrated by the infinite information of quantum teleportation, to satisfy what is needed to explain the missing dark matter.

    Colossians 1:17
    He is before all things, and in Him all things hold together.

    Moreover, the fact that simple quantum entanglement shows “coordinated universal control” of entangled photons of energy, by transcendent information, satisfies a major requirement for the entity which must explain the missing Dark Energy. i.e. The transcendent entity, needed to explain Dark Energy, must explain why the entire space of the universe is expanding in such a finely-tuned, coordinated, degree, and would have to employ a mechanism of control very similar to what we witness in the quantum entanglement experiment.

    Job 9:8
    He stretches out the heavens by Himself and walks on the waves of the sea.

    Thus “infinite transcendent information” provides a coherent picture of universal control, and specificity, that could possibly unify all of physics upon further elucidation. It very well may be possible to elucidate, mathematically, the overall pattern God has chosen to implement infinite information in this universe.

    “I discovered that nature was constructed in a wonderful way, and our task is to find out its mathematical structure”
    Albert Einstein

    Further reflections on the “infinite transcendent information” framework:

    Mass becomes infinite at the speed of light, thus mass will never go the speed of light. As well, distance in direction of travel will shrink to zero for mass at the speed of light (i.e. the mass would disappear from our sight if it could go the speed of light.). For us to hypothetically travel at the speed of light, in this universe, only gets us to first base as far as quantum teleportation is concerned. That is to say, traveling at the speed of light only gets us to the place where time, as we understand it, comes to complete stop for light, i.e. gets us to the eternal, “past and future folding into now”, framework/dimension of time. This “eternal” inference for light is warranted because light is not “frozen within time” yet it is shown that time, as we understand it, does not pass for light.

    “I’ve just developed a new theory of eternity.”
    Albert Einstein

    Also, hypothetically traveling at the speed of light in this universe would be instantaneous travel for the person going at the speed of light. This is because time does not pass for them, but, and this is a big but; this “timeless” travel is still not instantaneous and transcendent to our temporal framework/dimension of time, i.e. Speed of light travel, to our temporal frame of reference, is still not completely transcendent of our framework since light appears to take time to travel from our perspective. In information teleportation though the “time not passing”, eternal, framework is not only achieved in the speed of light framework/dimension, but also in our temporal framework/dimension. That is to say, the instantaneous teleportation/travel of information is instantaneous to both the temporal and speed of light frameworks/dimensions, not just the speed of light framework. Information teleportation/travel is not limited by time, nor space, in any way, shape or form, in any frame of reference, as light is seemingly limited to us. Thus “pure information” is shown to be timeless (eternal) and completely transcendent of all material frameworks/dimensions. Moreover, concluding from all lines of evidence we have now examined; transcendent, eternal, infinite information is indeed real and the framework in which It resides is the primary reality (highest dimension) that can exist, (in so far as our limited perception of a primary reality, highest dimension, can be discerned). Logic also dictates “a decision” must have been made, by the “transcendent, eternal, infinite information” from the primary timeless (eternal) reality It inhabits, in order to purposely create a temporal reality with highly specified, irreducible complex, parameters from a infinite set of possibilities in the proper sequential order. Thus this infinite transcendent information, which is the primary reality of our reality, is shown to be alive. The restriction imposed by our physical limitations of us ever accessing complete infinite information to our temporal framework/dimension does not detract, in any way, from the primacy and dominion of the infinite, eternal, transcendent, information framework/dimension that is now established by the quantum teleportation experiment as the primary reality of our reality. Of note: All of this evidence meshes extremely well with the theistic postulation of God being infinite and perfect in knowledge.

    “An illusion can never go faster than the speed limit of reality”
    Akiane – Child Prodigy -
    http://www.youtube.com/watch?v=p_qMuLRq0g4

  123. As has often been the case, Nakashima-san has made a very important point vis-a-vis cellular biochemistry in comments 120 and 121. It is very clear that cellular biochemistry (much less a living organism) does not consist of a series of time-limited genetic programs that terminate (i.e. “halt”) when they are finished. On the contrary, two of the most important characteristics of all biochemical reactions is that they are massively stochastic and recursive. That is, they produce generally similar outputs in generally similar time frames, as a function of cyclic reactions that have no clearly defined “beginning” and “end”.

    The underlying reason for this is that enzyme-substrate interactions (which are the basis for all biochemical reactions) fundamentally depend on dissociation constants, in which the probability of the binding of a substrate to an enzyme’s active site, the probability of the interaction between components of the substrate and the enzyme, and the probability of the release of the catalyzed product from the active site are all less than 1 (and, of course, greater than 0). This means that there is always some irreducible variation in the rate of enzyme-catalyzed reactions (i.e. virtually all of the reactions in biochemistry).

    Furthermore, biochemical reactions almost always happen as part of a cyclic (i.e. recursive) biochemical pathway. That is, virtually all biochemical processes consist of a series of reactions catalyzed by enzymes with different dissociation constants, which cycle almost endlessly. Ergo, the amount of variation in the output rates of the various reactions must be summed over the entire series (indeed, over large sets of interconnected series). This means that there is no firmly established and regulated “halting” function in biochemistry, if by such a function one means that a pre-existing program has a predetermined end point.

    Biochemical reactions are all massively recursive, and are tied together in functional arrays in which nothing ever really “halts” (i.e. ends). Rather, the various inter-related cyclic biochemical pathways continue to function within (and between) cells for as long as the cells continue to exist.

    This also means that there is no point in time that one can identify as the beginning or ending of the operation of a biological program. Given the firmly established cell theory of Schleiden and Schwann, it is quite literally the case that all of biochemistry began at some very remote time in the past (i.e. billions of years ago) and has gone on cycling since then according to the various “laws” of biochemistry in unbroken (i.e. non-”halting”) series ever since. Individual organisms may be mortal (although an argument could be made that this is really only the case for members of the kingdom Animalia), but life itself is immortal (i.e. does not “halt” – is never “finished”), until Sol undergoes gravitational collapse and conversion into large-nuclear core fusion, expanding into a red giant, thereby vaporizing the biosphere.

  124. #122
    Borneagain77

    It is hard to know which parts of your copious comment to respond to. I will confine myself to this request:

    show me the exact experiments in which natural processes generated functional information.

    My background is in philosophy and statistics, not biology. I was responding to a paper which purported to show that intelligent causes were vastly more probably than non-intelligent causes from first principles (without conducting any experiments). My concern was only with the logical and statistical issues in that paper.

  125. Mr. Frank,
    Of what possible use is your philosophical position: “My concern was only with the logical and statistical issues in that paper.” If it does not connect with reality through rigorous experimentation? i.e. you stated the maths are “irrelevant”, yet the maths clearly agree with what reality is telling us through experimentation. The burden is on you to provide “real world” experimentation that shows the model to be incorrect!
    I fail to see how the intellectual posturing, that has given you such warm and fuzzy feelings, has any merit scientifically until you connect it with reality in a meaningful way.

    I agree that a proper philosophical foundation is necessary in order to make accurate postulations in science, but in the end reality is final arbiter of which philosophical position is correct!

    “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”
    William Shakespeare – Hamlet

    Theism Compared To Materialism
    http://docs.google.com/Doc?doc.....#038;hl=en

  126. Nakashima:
    “In terms of Dr Abel’s challenge to falsify his null hypothesis, it is now clearer why no one should care to try. Why bother proving that halting X have property Y, when non-halting X are nore interesting?”

    You mean you don’t find the following null hypothesis interesting: ““Physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic
    optimization, computational halting, and circuit integration.”

    You will notice that Rule 110 is apparently turing complete. Now, I am not an expert by any means on the topic, but from my understanding Rule 110 can be seen as a computation that never halts. Rules 110, as far as I understand is evidence of self order (law) producing non-halting computation. Thus, Abel’s criteria of discovering computational halting is extremely interesting. To date, no system of only law+chance can provide such computational halting.

    Nakashima:
    “For example, we know that many bacteria have circular genomes. Imagine for a moment a primitive object with a circular RNA genome and a primitive ribosome attached to it. The ribosome loops endlessly around the genome making proteins.
    Abel’s definitions say that this system of genome and ribosome is non-functional, because it never halts. Sorry, that is like saying my heart is non-functional because it doesn’t stop.”

    -First of all, you heart isn’t a computation, so it has no bearing on the type of function that Abel is discussing.

    -Second, the ribosome’s action of constantly looping around the RNA would seem to be an example of looping behaviour, however, if it produces a useful output then that means it would have to halt to do so. So, basically, your ribosome is in an endless loop of halting and then starting again. Although the endless loop may not be what Abel is asking an explanation for, the computational halting that occurs is definitely what Abel is asking an explanation for.

    Thus, *you* seem to be the one equivocating here between two definitions of “function.” Abel is only concerned with one of those definitions since it seems to pose a problem for purely physicodynamic systems. Abel isn’t asking for an explanation of heart function, machine function, or enless loop function, since all those systems would “function” according to a different meaning of the term.

    Abel is being very specific about the type of function he is discussing — the type that arises from computational halting. Whether you find his question and null hypothesis interesting or not has no bearing on it relevance.

    Nakashima:
    “Dr Abel is trying to make a claim about all functioning programs.”

    Yes, if by “program” you mean computation involving physicodynamically inert switches, algorithmic optimization, etc, as discussed in aforementioned papers. And, yes, if by “function” you mean the definition of computational halting (as opposed to faulting) producing a useful output.

    Nakashima:
    “By including this notion of computational halting, he is limiting himself unintentionally to a subset of function.”

    No, I’m sure you mean limiting himself *intentionally* to a very specific type of behaviour. This is the type of behaviour that he wishes to discuss. Again, the fact that you may find discussion of that specific type of “function” uninteresting actually amazes me since no system of law+chance has produced such “function” and there are reasons as laid out in Abel’s papers as to why law+chance may not be able to cross the “cybernetic cut” and produce that type of function. Yet, we have those types of systems. I find that a very interesting problem. I can’t help it if you don’t.

  127. Mark Frank (#119)

    Thank you for your thoughtful comments. I’ll address them in reverse order.

    Let’s look at your third point:

    The probability of an unspecified mind creating a functional protein is certainly not 1 (if you can attach any meaning to such a vague hypothesis).

    You are correct, but that’s not the probability that Kalinsky is interested in. When discussing the hypothetical case of a signal from outer space that contains the first 50 prime numbers, Kalinksky writes that “the probability that a mind
    could produce such a signal” needs to be compared with “the probability that mindless natural processes could do it.” Kalinsky continues:

    We know that a mind can generate the first 50 prime numbers, so the probability that a mind could produce that information is 1. If the probability that natural processes could generate the first 50 prime numbers is less than 1, then one can compare the two probabilities to decide how much more likely intelligent design is than mindless natural processes. If it turns out that intelligent design is ten times more likely, or a thousand more times more likely, then it becomes increasingly irrational to invoke mindless natural processes, and increasingly rational to invoke intelligent design.

    The point Kalinsky is making here is not that an unspecified mind would produce such a prime number sequence, but rather that some mind(s) definitely could – for instance, a human mind (and presumably the mind of an advanced alien).

    The same point is relevant for the protein case I discussed above. The question Kalinsky is addressing is not one of motivation, but of capability. Some minds, somewhere, at some time, are capable of making proteins to order, reliably. (Humans will probably be able to do so within the next 100 years, if not sooner; and if there are aliens out there, probably they already can. For an omnipotent mind, as you rightly point out, it would be a snap.)

    Mindless natural processes are able to generate proteins too, but not reliably. It’s much more of a hit-and-miss affair: making a protein is a pretty tall order, even for an intelligent being. A sufficiently advanced mind can make a protein to order; but mindless natural processes don’t take orders. They just produce stuff. Sometimes, as Kalinsky acknowledges, they get lucky:

    Mindless natural processes can accidentally produce effects requiring a low level of functional information.

    Kalinsky now introduces what he/she calls the Intelligence Hypothesis:

    The … Intelligence Hypothesis allows that mindless natural processes can accidentally produce functional information within, say, the background noise of a physical system, but the information will not achieve a significant level.

    It is important to note that for Kalinsky, mindless natural processes proceed randomly:

    A search by mindless natural processes is essentially a random walk, where the search proceeds in no set direction and, for any point in the search, it can be returned to any number of times. This is not to be confused with an evolutionary search that is directed by a fitness function or a fitness landscape, which will be discussed later.

    Which brings us to your second point, which is that “you cannot estimate the probability of arriving at a protein … by calculating the probability of a string of amino acids chosen at random … It is a selection process which vastly increases the probability.”

    Kalinsky, if I read him/her rightly, would answer as follows: “You might well be right. There could be some selection process in the natural world which greatly amplifies the likelihood of arriving at a protein, starting from a set of amino acids. But my point is that proteins contain a measurable amount of functional information – and most proteins have more functional information than that found in the five “watermarks” in Craig Venter’s synthetic genome. My Intelligence Hypothesis states that any process that has the ability to reliably produce significant levels of functional information qualifies as an intelligent process. So if natural selection can do that, then natural selection is an intelligent process – i.e. the work of a mind.”

    Now I shall address your first point:

    A fitness function is not something that is selected to meet a target. It is simply whatever allows that organism to reproduce effectively in that context at that time. It is nonsense to talk about the information content of a fitness function.

    Simply asserting that “[a] fitness function is not something that is selected to meet a target” begs the question against Intelligent Design, which seriously puts forward that very hypothesis. It’s a possibility that needs to be discussed.

    Is it nonsense to talk about the information content of a fitness function? Like you, I didn’t major in biology. However, I note that Kalinsky obtained his definition of a fitness function from a text on evolutionary computing. According to the text, a fitness function “defines what improvement means. From the problem-solving perspective, it represents the task to solve in the evolutionary context.” If it describes a problem, then it must have an information content: the requirements to adapt to.

    Natural selection is a non-random search. But if the target is one that requires a large amount of functional information to specify it accurately, then it must be built into the pathway itself. That is, the non-random pathway that gets the evolving components to their target destination must “tell” them which way to go, to get there. In other words, the pathway itself must be a specified one, and if it’s highly specified, then (according to Kalinsky’s Intelligence Hypothesis) it has to be the work of some mind. That’s the point I understood Kalinsky to be making, and it struck me as an interesting perspective on evolution itself.

    I’m not a biologist, and I hope I haven’t badly misunderstood Kalinsky or contemporary evolutionary theory. However, I do have some background in mathematics, and there’s nothing wrong with the mathematics in Kalinsky’s paper. The examples he/she cites are mathematically sound, at least.

    Making a protein of any sort that is stable, folds up and functions properly is a very tall order, if the figures Kalinsky quotes from Axe are correct, since the vast majority of possible proteins are not stable, don’t fold or don’t do anything. If a bunch of amino acids can assemble into a protein that is stable, folds up and functions properly, they need information of some sort to get there. And if every living organism studied to date contains proteins that are not 100 but 300 amino acids long, that is going to be an even more difficult target to reach. Even we can’t do it yet – and we’re intelligent life forms!

    How amino acids reached that target on the primordial earth is a problem that evolutionists haven’t even begun to address. Maybe they could benefit from the insights of other disciplines, which deal with information – such as ID theory.

  128. #126 vjtorley

    As always it is a pleasure to disagree with you. I appreciate your intelligence and good manners.
    I will tackle your responses in the same order you wrote them. I will break my replies into different comments to avoid writing essays as comments. Also I am not sure I will get them all done tonight.

    Before starting I should point out that Kalinsky is implicitly using one model of how observations support hypotheses. He is comparing likelihoods – the probability of the outcome given the hypothesis. There are other approaches e.g. Bayesian which have just as strong a following. But I am sure even his “likelihoodism” doesn’t work. So I am prepared to fight the issue on that basis (with the option of withdrawing to Bayesian high ground if necessary)

    1) The likelihood of creating a functional protein given a mind

    You wrote:
    The point Kalinsky is making here is not that an unspecified mind would produce such a prime number sequence, but rather that some mind(s) definitely could – for instance, a human mind (and presumably the mind of an advanced alien).

    If Kalinsky meant this, then it is not the usual or a reasonable way of comparing the likelihoods. Yes of course it is possible to describe a mind that could create functional proteins. An omnipotent mind can do just that. (With imagination I expect one could come up with a mindless process that was pretty certain to create a functional protein). But that is not very interesting. The ID hypothesis is meant to be a real proposal to be compared to various mindless processes, particularly RM+NS. If the ID hypothesis is to represent a real alternative then it must be proposing not only that a mind could create functional proteins but that a mind did create not only a functional protein but virtually all the functional proteins that have existed on this planet for four billion years. And the hypothesis needs to be clear. Is it that one of a subset of all possible minds led to that result or is it that one of all possible minds led to that result? If a subset, which subset (I hope you can see that it would not be a satisfactory answer to say “that subset which had the ability and motivation to create all functional proteins”)? If it is one of all possible minds, then it is necessary to somehow estimate the mean probability of getting that outcome from all possible minds. It is a pretty meaningless task – but the answer has to be less than one because some of the possible minds are clearly incapable of doing it.

    It may help to compare this to another case. Suppose there is damp patch on my wall. I initially suspect a breach in the damp course. I assess that if there were such a breach there is low chance of it causing the damp but I can see no obvious rival cause. Someone else says –“Ah have you considered a hole in the roof? One could imagine a hole which would result in a 100% chance of creating that damp patch”. But that does not mean that there is a 100% chance that an unspecified hole in the roof would cause the damp patch. To calculate that figure I would have to look at all possible places for holes and average over all possible places. This would be the only reasonable way to compare the generic hypothesis – “caused a by a hole in the roof” with “caused by a breach of the damp course”.

    The fact that some humans can create some proteins four billion years later seems irrelevant. We already accepted that some minds can be imagined that can do the job and no one is proposing that humans did the job. That is like using as evidence the fact that holes it has been observed in other houses on rare occasions that holes in roofs can cause damp patches. We knew that!

  129. Mr. Frank,
    You may find this “experimental evidence” helpful To differentiate which “mind” did the designing of biological life,:

    Physicists find many processes in a cell operate at the “near optimal” capacities allowed in any physical system:

    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

    DNA Optimized for Photostability
    Excerpt: These nucleobases maximally absorb UV-radiation at the same wavelengths that are most effectively shielded by ozone. Moreover, the chemical structures of the nucleobases of DNA allow the UV-radiation to be efficiently radiated away after it has been absorbed, restricting the opportunity for damage. http://www.reasons.org/dna-soaks-suns-rays

    Visible light is also incredibly fine-tuned for life to exist. Though visible light is only a tiny fraction of the total electromagnetic spectrum coming from the sun, it happens to be the “most permitted” portion of the sun’s spectrum allowed to filter through the our atmosphere. All the other bands of electromagnetic radiation, directly surrounding visible light, happen to be harmful to organic molecules, and are almost completely absorbed by the atmosphere. The tiny amount of harmful UV radiation, which is not visible light, allowed to filter through the atmosphere is needed to keep various populations of single cell bacteria from over-populating the world (Ross; reasons.org). The size of light’s wavelengths and the constraints on the size allowable for the protein molecules of organic life, also seem to be tailor-made for each other. This “tailor-made fit” allows photosynthesis, the miracle of sight, and many other things that are necessary for human life. These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe’s entire range of electromagnetic emissions. Like water, visible light also appears to be of optimal biological utility (Denton; Nature’s Destiny).

    Fine Tuning Of Light, Atmosphere, Biological Life, and Water – illustrations
    http://docs.google.com/Doc?doc.....aGh4MmdnOQ

  130. further note:

    Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Gregory S. Engel, Nature (12 April 2007)
    Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated.,,,, This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. —- Conclusion? Obviously Photosynthesis is a brilliant piece of design by “Someone” who even knows how quantum mechanics works.
    http://www.ncbi.nlm.nih.gov/pubmed/17429397

  131. That’s so awesome. I mean, it’s one thing to assume that natural selection works off of pre-existing materials and so creates newer, more complex structures. But it’s quite another to assume that something as complex as a modern cell arose via abiogenesis.

  132. further note:
    U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis
    http://adsabs.harvard.edu/abs/2004E&PSL.217..237R

  133. This following article, that just came out, powerfully backs up my assertion in post 122 that It very well may be possible to elucidate, mathematically, the overall pattern God has chosen to implement infinite transcendent information in this universe.:

    Is Unknown Force In Universe Acting On Dark Matter?
    Excerpt: It is possible that a non-gravitational fifth force is ruling the dark matter with an invisible hand, leaving the same fingerprints on all galaxies, irrespective of their ages, shapes and sizes.” ,,Such a force might solve an even bigger mystery, known as ‘dark energy’, which is ruling the accelerated expansion of the Universe. A more radical solution is a revision of the laws of gravity first developed by Isaac Newton in 1687 and refined by Albert Einstein’s theory of General Relativity in 1916. Einstein never fully decided whether his equation should add an omnipresent constant source, now called dark energy. ,,Dr Famaey added, “If we account for our observations with a modified law of gravity, it makes perfect sense to replace the effective action of hypothetical dark matter with a force closely related to the distribution of visible matter.”
    http://www.sciencedaily.com/re.....154644.htm

  134. Clive Hayden @ 114

    Even if millions of generations passed since Adam and Eve, all are the result of being created. It is no less true for the last than for the first.

    By that argument then the millions who perished in the Flood were also His direct creations; also, according to you and bornagain77, entitled to assume that, as such, they would be looked upon by Him with favor.

    Yet those millions were wiped out. And they were not granted a merciful end. A being of God’s supposed unlimited power could have consigned them to oblivion in an instant. It would have been as if they had never existed. Instead, they were condemned to a slow and terrifying death by drowning.

    And for what? For being flawed? For not turning out as their Creator had intended and expected? Whose fault is that? Certainly not theirs. They had no choice in being made fallible the way they were.

    All of which leads us to the obvious fundamental dilemma. Either God was in error designing human beings with unintended flaws, in which case He cannot be perfect, or He intended us to be flawed beings, in which case He is unjust and inhumane for punishing us for being what He designed us to be.

    Either way, bornagain77 and others who think like him would be unwise to count their chickens too soon.

    And if bornagain77 wants to thank someone for his birthday gift, I don’t blame him, We thank people for the gift of house slippers on our birthday, can we not thank someone for the gift of life on our birthday? Does this really need to be explained?

    No, of course not. By all means, we should say “thank you” to those are kind or compassionate or generous to us. Many of the good things that come to us as children are given to us by our parents or other adults who love us and have our best interests at heart.

    It is hardly surprising therefore that, as adults, we still have a need for such a kindly guardian.

    That doesn’t mean one exists, however.

    And the world was being judged by God in the flood, do you have it in mind that it was not worthy of judgment?

    God judging His own creation and judging it harshly. What does that say about the Creator, though?

    And Adam did die spiritually on the day he ate the fruit, that is why it is important to be “born again” as bornagain77’s name indicates. This is basic stuff really.

    It’s the standard defense.

    But the text does not say he would die spiritually, only that he would die. Are we to assume that God cannot say clearly what He means, that He must hedge His bets by expressing Himself in ambiguous metaphor?

    And if such direct statements are open to interpretation then all the rest must be. So how are we to decide between the different interpretations? And how does that differ from the “moral relativism” of which the atheists are accused?

  135. Mark @ 119

    “I am deeply conscious that I have explained this poorly. I strongly recommend Elliott Sober’s book on Evidence and Evolution – particularly chapter 2 on ID – but you may need to read chapter 1 on evidence first.”

    This book is full of error. I will take one example from chapter 2 to illustrate.

    Elliott says on page 116 of my edition, first published in 2008 by Cambridge University Press, that: “… a random mindless process (presumably ‘natural selection,’ which really means physics, which immediately gets to the heart of the problem if he had the wit to see it) can produce complex and useful devices. It is possible, as we would now say, for monkeys pounding at random on typewriters to eventually produce the works of Shakespeare.”

    Ignoring the fact that Sober cannot begin to account for the existence of the English language or the biological language in which the monkeys are “written,” within his ontology, the one that excludes mind as a causal agent in the universe, he is now going to say that monkeys can produce (random information generators, these monkeys) information. Just for the hell of it, let’s grant Sober the language. Let’s be generous and say that his ontology doesn’t have to account for symbols and rules (language). So how does that play out? What IS the probability of this happening?

    According to “Statistical Reasoning for Everyday Life,” Bennett, Briggs, Triola, Second Edition, Addison Wesley Longman, 2002, “In his complete works, Shakespeare used 31,534 different words and a grand total of 884,647 words counting repetitions.” So, and I have to make an assumption here, if each word averaged 4 letters in length, probably a low number, but it won’t matter, then (ignoring spaces and punctuation marks) the monkeys would have to get 884,647 x 4 letters in a row to duplicate the complete works of Shakespeare. That number is: 3,538,588 letters. Let’s give Sober a break and round it down to 3.5 million. So what are the odds? If we posit lower case letters only, to make it as easy as possible on our monkeys then each letter has a 1 in 26 probability of being selected by our monkeys. Of course, they have to get 3.5 million of them in a row so that looks like 1 over 26^3,500,000. So what is that in scientific notation? If you take the log of both sides (26^3,500,00 = 10^x) you eventually get to x = 3,500,000 x 1.415 or 4,952,500. So the odds, in scientific notation are 1 in 10^4,952,500. Not a bet any of us would want to make.

    If there are 10^80 atoms estimated to exist in the observable universe, and there are, and if the universe has been in existence for, say 10^17 seconds, (I’ve seen 10^16 but what’s a zero among friends, particularly when it will “help” Sober’s case), and if the shortest time for an event to happen is Planck time, 10^-43, then there can be 10^43 events for 10^17 seconds for 10^80 atoms. So that means 10^140 possible events in the history of the universe. (I think Dembski calls this a “universal probability bound” by which I think he means that anything with a probability less than that is essentially impossible.) Since the calculation for a simple probability like this is to take the number of desired outcomes and make that the numerator and the denominator is the number of possibilities, then we have 1 over 10^4,952,500.

    So for fun, let’s assume that there are 10^140 variations of Shakespeare that would count as acceptable outcomes. So now we have 10^140 over 10^4,952,500 or odds of the monkeys banging out Shakespeare of 1 in 10^4,952,360. Remember, I’m not the one who said this was POSSIBLE.

    Clearly, it is not. You’d think a guy that knows so much about statistics (Me, I only had one graduate course 30 years ago, and two or three undergrad, one of which I got a “D” on because I NEVER went to class but that’s another sad story for another time, so who knows how wrong I could be? So I’m counting on this group to keep me straight.) could sort of do a back of the napkin kind of calculation and see that isn’t such a smart claim to make. Makes me wonder about the rest of his assertions and conclusions.

    p.s. With a background in philosophy, perhaps you could comment on my modus tollens argument which I think is decisive concerning naturalism.

    If naturalism is true, then physics must be able to explain life, information, language, and symbols and rules. But physics cannot explain life, information, language, and symbols and rules, therefore, naturalism is not true. I’m obliged.

  136. Seversky, the real argument here is: Does God exist? If so, then there CAN be Acts of God, the Word of God, and the Son of God. If He doesn’t, well then He doesn’t and so much the worse for us, aimless, pointless, amoral, ultimately worthless bags of subatomic particles randomly assembled by physics but remarkably, nonetheless, expressing “apparent” design, intelligence, conscience, purpose, and a desire to know why. So why don’t we have that conversation, it doesn’t have to be here, and depending on how that turns out, go from there.

    We are, all of us, making cosmic “all in” bets here. Make no mistake about that. If I say we live in a “Jesus universe” and you say we do not, then most assuredly one of us is correct. I could almost wish it was you given the consequences for people who get it wrong if it is a “Jesus universe.”

    p.s. Whether you or I personally approve of “how” the universe is or isn’t is irrelevant to the issue of “how” it actually is.

  137. #134

    This book is full of error. I will take one example from chapter 2 to illustrate.

    You ID people have a fondness for calculating very large or very small irrelevant numbers.

    You have shown that the outcome is vastly improbable. Sobers’ point is that there is a difference between the vastly improbable and the impossible. After all every string of 3.5 million characters is just as improbable as the complete works of Shakespeare. If you grant that there is a mechanism for generating 3.5 million characters at random then one of those strings must actually be the result. So being improbable is not at all the same as being impossible. But this is well worn territory and I am surprised you bring it up.

    With a background in philosophy, perhaps you could comment on my modus tollens argument which I think is decisive concerning naturalism.

    I have problems with both of your premises, and there is a danger of writing an essay on “explanation”. However, in essence, I believe that physics can explain life, information, language, and symbols and rules.

  138. #136

    However, in essence, I believe that physics can explain life, information, language, and symbols and rules.

    Can you point me to arguments for how physics could generate information and the mechanisms to process and act upon information in a coordinated manner?

  139. vjtorley

    To continue from my comment #127

    I am going complete my response with this one additional comment. It is an essay, and I do apologise for its length, but I really struggled to make it shorter.

    Estimating the probability of arriving at a protein through mindless processes

    You wrote:

    Kalinsky, if I read him/her rightly, would answer as follows: “You might well be right. There could be some selection process in the natural world which greatly amplifies the likelihood of arriving at a protein, starting from a set of amino acids. But my point is …. states that any process that has the ability to reliably produce significant levels of functional information qualifies as an intelligent process. So if natural selection can do that, then natural selection is an intelligent process – i.e. the work of a mind.”

    Why does Kalinsky claim that such a process would have to be an intelligent process?

    I guess the key sentence is this:

    Natural selection requires a fitness function. If a given protein is a product of natural selection operating within a fitness landscape, then sufficient functional information required to find that protein in an evolutionary search must be encoded within the fitness function.

    To evaluate this sentence we must be clear what is meant by functional information. “Information” notoriously can mean many things in this debate and it is easy to slip between one definition and another. Luckily Kalinsky provides a mathematical definition on page 4. In this context the information content of some outcome (e.g. protein, DNA sequence) is measured by the number of outcomes in that category which correspond to functional proteins divided by the total number of possible outcomes in that category. There is an implicit assumption that all possible outcomes are equally likely and so the “information content” is actually just a convenient way of expressing the improbability that an outcome corresponds to a functional protein.

    So now it is apparent that Kalinsky is essentially repeating Dembski and Mark’s argument that any such process would itself be so improbable that it would more than counter the gain in probability that the process provided.

    Note that, like Dembksi and Marks, Kalinsky is not arguing that a fitness function is vastly unlikely to make functional proteins. He is arguing that if a fitness function is capable of doing this then that fitness function itself must be vastly improbable.

    Kalinsky doesn’t make much of a case for this. As far as I can see this is the only sentence that argues his case.

    Since the fitness function, whether it is found in nature, or in a genetic algorithm, must contain the requirements to adapt to, or that defines the desired outcome, it must contain at least as much functional information as the desired outcome.

    Translating information back into probabilities this becomes:
    Since the fitness function, whether it is found in nature, or in a genetic algorithm, must contain the requirements to adapt to, or that defines the desired outcome, it must be at least as improbable as the desired outcome.

    But how on earth do you give any meaning to the “probability of a fitness function”? What kind of probability are we talking about here? It is hardly a frequentist definition. Maybe it is a classical definition (then we need to enumerate all possible fitness functions and establish that all are equally likely!). It is a meaningless exercise. But in any case the sentence has things backwards. The fitness function (i.e. whatever causes organisms to thrive in that particular context) has no “desired target”. The fitness function comes first with no concept of a target, whether it be size, reproduction rate, or whatever. It emerges from the environment at that time. There is no question of its probability and therefore no question of its information content. It is whatever turns out to work at the time. The only question is what is the probability that such a fitness function will lead to functional proteins.

    When Dembski and Marks paper first came out I tried to illustrate this point with an analogy. I think I can improve on it. Imagine a wide valley with smooth sides and just one bottom – like a bowl. From time to time, through a natural process, stones fall into the valley at completely random (i.e. equally like to fall at any point) locations and then roll. Not surprisingly they all end at the same place. Had it been a flat plain this outcome would have been most surprising and given sufficient stones we could make the improbability of them all ending up in the same place as high as we like. Clearly the combination of the shape of the valley and gravity increases the probability, reduces the information content, of this outcome dramatically. The Dembski/Marks/Kalinsky argument is saying that the valley plus gravity must supply the missing information i.e. the probability of the valley being that shape and gravity working must be sufficiently low to make up for the increase of probability they provide. Besides being utterly meaningless it has the interesting consequence that the more stones fall the greater the information content of the valley+gravity even though they don’t change at all!

  140. Mr. Frank, Here is some more “Real World” experimentation to show that you have no merit in your claims.

    Both the oldest Stromatolite fossils, and the oldest bacterium fossils, found on earth demonstrate an extreme conservation of morphology which, very contrary to evolutionary thought, simply means they look very similar to Stromatolites and bacteria of today.

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.,,,

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart, (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

    Is Antibiotic Resistance evidence for evolution? – “Fitness Test” – video
    http://www.youtube.com/watch?v=_BwWpRSYgOE

    According to prevailing evolutionary dogma, there “HAS” to be “significant genetic/mutational drift” to the DNA of bacteria within 250 million years, even though the morphology (shape) of the bacteria can be expected to remain the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. I find it interesting that the materialistic theory of evolution expects there to be a significant amount of mutational drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis.

    So Mr. Frank,,, the point is is that you must produce evidence for your assertions!!!! NOT EXCUSES, however well articulated for why you have no evidence!

  141. #137

    Can you point me to arguments for how physics could generate information and the mechanisms to process and act upon information in a coordinated manner?

    Happy to have a go at this – but first which of the many definitions of information are you using?

  142. Falsifying this “by experimentation” would suffice Mr. Frank:

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.pubmedcentral.nih.g.....id=2662469
    http://mdpi.com/1422-0067/10/1/247/ag

  143. This may be a better link:

    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily
    falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:
    “Physicodynamics cannot spontaneously traverse The Cybernetic Cut [9]: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization,
    computational halting, and circuit integration.”
    A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    Illustration:
    http://mdpi.com/1422-0067/10/1/247/ag

  144. Mark Frank (#127)

    Thank you very much for your carefully considered responses. I’m afraid I’ll only be able to respond to your first post (#127) tonight.

    I must say I liked your “damp course” analogy. However, there are two significant differences between this case and the evolution of proteins on the primordial earth:

    (i) the disparity between the probabilities of the two rival explanations (damp course vs. hole in the roof) is not immense. A hole in the roof is rather unlikely, but not astronomically so. In the case of the evolution of proteins, however, there is a huge disparity between the plausibility of the two rival explanations, over a 500-million-year time interval: we know that it is astronomically unlikely that random processes could generate even a simple functional folding protein, whereas there is nothing (in principle) to stop an intelligent being from doing so. Kalinsky calculates that “ID is 10^155 times more probable than mindless natural processes to produce the average protein.” 155 orders of magnitude is a huge difference, if his numbers are correct.

    (ii) in the case of the damp course, we can actually estimate the occurrent probabilities of the two rival explanations. A real estate agent could probably tell you what percentage of twenty-year-old houses (say) actually have faulty damp courses and/or leaky roofs. By contrast, in the case of the evolution of proteins, we can only estimate the generative probabilities for the two rival explanations – that is, the probability that an intelligent being could generate a protein within a 500-million-year interval vs. the probability that some random process could do so over the same interval. I agree that it would be nicer to have occurrent probabilities – but if intelligent beings have libertarian freedom, we could never compute such probabilities, in principle.

    Generative probabilities are not very helpful in and of themselves. What makes them useful in this particular case is that the “null” hypothesis, that random processes generated the first proteins, is an enormously implausible one – so much so that we are forced to “think the unthinkable” and consider the possibility of intelligent design. Generative probabilities do not take us very far here, but they do tell us that there is nothing to rule out ID a priori.

    You made a parenthetical observation that “[w]ith imagination I expect one could come up with a mindless process that was pretty certain to create a functional protein,” but you then dismiss this possibility as “not very interesting.” On the contrary: if that were true, and the process were random, it would definitely be Game Over for Kalinsky’s argument. For the whole point of his argument is that over the time interval stipulated (500 million years), no random process is capable of reliably doing the job – whereas an intelligent being is perfectly capable (in principle, at least) of creating proteins reliably, as there is no limit in principle to the amount of functional information that an intelligent being can generate.

    I quite understand your impatience with vague potentialities: you want an actual, specific hypothesis that you can sink your philosophical teeth into. The problem is that it’s early days yet, and our understanding of the Designer’s purposes is extremely limited, at the present time. Nevertheless, I shall speculate. For what it’s worth, I think we need to calculate two numbers: the maximum volume of functional information (call it V1) that the biosphere is capable of storing, if the first living cells were designed by an intelligent being, and the total volume of functional information (call it V2) that human beings will need to keep civilization humming along, and avert any threats to civilization (e.g. ocean acidification) that may arise. Obviously V2 will defend on our level of affluence A: the more complicated our lifestyle, the greater the number of ways in which it could collapse, and hence the more information we will need (e.g. weather forecasting; water pollution monitoring) in order to avoid catastrophe. V2 could conceivably be a simple linear function of A; more alarmingly, it might turn out to be an exponential function of A.

    A far-sighted Intelligent Designer who foresaw the emergence of intelligent life on Earth and who is benevolently disposed towards said life (i.e. a Designer who loves Homo sapiens) should have foreseen the problems we’d face and the technological solutions we’d require, in order to maintain Spaceship Earth. (I’m assuming, by the way, that the Designer doesn’t mind us being affluent – so long as we’re not self-centered.) Such a Designer should have built the answers into the cosmos somewhere – and the biosphere seems to be the only place that is rich enough in functional information to warrant a look. Case in point: here is a link to a TED talk by Craig Venter, Dr. Craig Venter, the man who mapped the human genome. Venter asserts that fourth generation fuels, that is, biofuels made by bacteria from C02, are just 18 months away. (P.S. I’ve just realized that he made that speech in March 2008 – does anyone know if his prediction came true?)
    OK. If V1 (which I assume is more or less constant over time – or is it? What about GM?) is vastly greater than V2 (which is a function of our affluence A), over the foreseeable future, then the Benevolent Design hypothesis remains viable. If not, I guess we’re all up the spout. And on that cheerful note, I shall retire for the evening.

  145. #143

    vjtorley

    Thank you for your reply. I am afraid it was a bit disheartening as it suggests I failed to make my point clearly.

    First a point of definition. I assume that when you talk of occurrent and generative probabilities these are what are referred to in Bayesian terms as prior probabilities and likelihoods.

    All of comment #127 and the analogy were only addressing one aspect of the Kalinsky paper. I wanted to argue that the likelihood of functional proteins given an unspecified mind is not 1 or anything close to 1. If you like I was only interested in the hole in the roof side of things. The damp course was there for background context. I discuss Kalinsky’s statements about natural causes i.e. the damp course in #138.

    Kalinsky’s paper was all about comparing likelihoods. At no point does he even discuss, much less assess, the prior probabilities of an intelligent or mindless cause (this was sensible is it is hard to attach meaning to prior probabilities in this context). It may be that an estate agent may be able to give prior probabilities of faulty damp courses or holes in roofs – but for the purposes of maintaining the analogy I would like to assume that we have no idea what they are.

    You say that the difference between relative likelihoods is vastly greater in the case of functional proteins than in my analogy. As I said above, in this case I was only making a point about the calculation of the likelihood of damp given an unspecified hole in the roof. So this is not really relevant.

  146. #143

    Just looked this paragraph

    You made a parenthetical observation that “[w]ith imagination I expect one could come up with a mindless process that was pretty certain to create a functional protein,” but you then dismiss this possibility as “not very interesting.” On the contrary: if that were true, and the process were random, it would definitely be Game Over for Kalinsky’s argument. For the whole point of his argument is that over the time interval stipulated (500 million years), no random process is capable of reliably doing the job

    With respect I think it is quite easy to think of such a process but it does not address Kalinsky’s main argument. In fact the process exists – it is transcription from DNA. This is a mindless process that produces functional proteins. Of course you will want to say – where did the DNA come from? But when you offer a mind as a cause and we challenge with “but who designed the designer” you say that is irrelevant or we don’t have to know. I plead the same rules.

    I am sure a better chemist than me could suggest a mindless process that produces DNA for functional proteins from some other template and so on – going back in time. Of course it does not address Kalinsky’s paper because he would say the “information” i.e. improbability has been pushed back onto the template. I address that in #138.

  147. # 140

    Happy to have a go at this – but first which of the many definitions of information are you using?

    I’ll take it any sense relevant to the development of life. I don’t know any formal definitions for information so feel free to enlighten me. In the case of single celled life I would assume that the information is mostly specifications for machines which provide function and when and where these machines should be used.

    Machines are always useless unless they are used in the right content and at the right time and usually in harmony with other machines. So I would assume that the biggest challenge any for any naturalistic argument would be the development of communication within the cell which seems to be required from the outset. Or maybe I am mistaken.

  148. #145

    But when you offer a mind as a cause and we challenge with “but who designed the designer” you say that is irrelevant or we don’t have to know. I plead the same rules.

    Not really the same rules at all. The system simply must be looked at as a whole. If one looks at all proteins today they are coded from DNA. You simply cannot separate them. If one takes flint stone, it takes a process i.e. a striking action and the correct context (when fire is wanted) to produce the desired outcome. The consistent use of the the process with flint stone to create a desired outcome is a sign of intelligence.

    Absence of a natural means by which any component i.e. information store, means of production and coordination implies a designer just as an intelligence may be inferred solely by the consistent correct application of a naturally occurring object (flint stone) and a process which could be involuntary (e.g. striking) to produce fire implies that agent causing the fire is intelligent.

  149. #147

    And why shouldn’t the designer alternative be looked at as a whole?

  150. —Mark Frank: “Happy to have a go at this – [how physics can generate information] but first which of the many definitions of information are you using?”

    How about this: “The attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects.”

  151. #148

    And why shouldn’t the designer alternative be looked at as a whole?

    Because in order a designer is responsible for the system we only need to show a one is required for a single aspect of the system. If you wish to show there is a naturalistic explanation for a system then you must explain all the components.

    Who designed the designer is another question entirely. For example if you knew that Joe built a mouse trap you could look at and study Joe to determine how he came to be – this is exactly what we do with all life on earth. We try to use what we know to determine how it came to be. If ever we identify the designer and we are able to study the designer, the nature of the designer etc we could in theory ascertain if the designer was designed or how the designer came to be. But that is a different question and outside the realm of possibility anyway. For the forseeable future at least.

  152. I’m glad to see this discussion is still going strong. I’ll be unavailable pretty much all week, but I’ll be happy to get back in the swing of things next week.

  153. I would like put my two cents in on “who designed the designer?”

    The question is pointless for God has always existed and exists outside of time and space. In fact God created space-time:

    Inflationary spacetimes are not past-complete – Borde-Guth-Vilenkin – 2003
    Excerpt: inflationary models require physics other than inflation to describe the past boundary of the inflating region of spacetime.
    http://arxiv.org/abs/gr-qc/0110012

    “It is said that an argument is what convinces reasonable men and a proof is what it takes to convince even an unreasonable man. With the proof now in place, cosmologists can long longer hide behind the possibility of a past eternal universe. There is no escape, they have to face the problem of a cosmic beginning.” Alexander Vilenkin – Many Worlds In One – Pg. 176

    Every solution to the equations of general relativity guarantees the existence of a singular boundary for space and time in the past.”
    (Hawking, Penrose, Ellis) – 1970

    But of more importance though, in order for you to even be able ask “who designed the designer?” you need to establish, as your basis, that time, as we commonly understand it has always existed and is the only time basis that exists, but all I have to reference, to show your understanding of time is incomplete, is to show that a higher dimensionality/framework of time exists in reality. A “time” that has a “higher quality of existence” than the temporal frame of reference we now live in.

    This is fairly easy to do nowadays since relativity shows that time, as we understand it, comes to a complete stop at the Speed Of Light. Yet light is not “frozen within time” for it still moves in our frame of reference, thus clearly demonstrating a “higher quality” of its existence. A higher “eternal-time” frame of reference in which the past and future fold are required to fold into now so as to maintain the integrity of what we observe in reality with special relativity.

    “The laws of relativity have changed timeless existence from a theological claim to a physical reality. Light, you see, is outside of time, a fact of nature proven in thousands of experiments at hundreds of universities. I don’t pretend to know how tomorrow can exist simultaneously with today and yesterday. But at the speed of light they actually and rigorously do. time does not pass. – Richard Swenson

    “I’ve just developed a new theory of eternity.”
    Albert Einstein

    And since it is shown that this temporal reality ultimately arose from this “higher dimensionality of eternity” by the fact all the material in this temporal universe is ultimately made out of “eternal light” it really is quite pointless for you ask “who designed the designer since it is clear He has always existed in a timeless eternity. How do you create that which has always existed and will always exist?

    I went into a bit more detail of fleshing the “even higher dimensionality” of “information/THE WORD” out in post #122, a post that apparently made no impression.

  154. By the way we have “eye witness” testimony for this “eternal framework” of time:

    A Reply to Shermer – Medical Evidence For NDEs – Pim van Lommel M.D.
    Excerpt: they also can experience their consciousness in a dimension where past, present and future exist at the same moment, without time and space,,,
    http://www.nderf.org/vonlommel.....sponse.htm

    Intelligent Design – The Anthropic Hypothesis
    http://lettherebelight-77.blogspot.com/

  155. #151

    Because in order a designer is responsible for the system we only need to show a one is required for a single aspect of the system. If you wish to show there is a naturalistic explanation for a system then you must explain all the components.

    And if you fail to explain any element of a naturalistic explanation in sufficient detail then the conclusion is that it was designed. Yes – I am familiar with the argument.

  156. Re #141

    I had a go showing how various types of information can be produced by physics. I rather regretted the offer simply because it was so time consuming. But I felt obliged having said I would do it. It was far too long to put in a comment so I put it here.

  157. Mr. Frank, you state in #155:
    “And if you fail to explain ANY element of a naturalistic explanation in sufficient detail then the conclusion is that it was designed. Yes – I am familiar with the argument.”

    Actually, “material”/naturalistic explanations are failing to explain the basis of ALL elements of reality. (Anthropic Principle and violation of the first law in quantum teleportation, for vivid outline of how bankrupt “naturalism is)

    The Fine Tuning Of Dark Energy and The Mass Of The Universe
    http://www.youtube.com/watch?v=7B0t4zSzhjg

    How Teleportation Will Work -
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://in.geocities.com/info_aruni/tele.htm

    As well you seem to think the “information” found in life is fundamentally different from information as we use it:

    How The DNA Code Relates To Human Language
    http://www.youtube.com/watch?v=hIF_dJVfutE

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.youtube.com/watch?v=vUeCgTN7pOo

    Seeing as you worked at IBM I would think this should be obvious to you? And in fact upon reflection I can find absolutely no satisfactory reason for you to “miss this evidence ” except for your philosophical bias of materialism.

    http://docs.google.com/Doc?doc....._5fwz42dg9

  158. further note:

    The materialistic argument essentially appears to be like this:

    Premise One: No materialistic cause of specified complex information is known.

    Conclusion: Therefore, it must arise from some unknown materialistic cause.

    On the other hand, Stephen Meyer, in Signature In The Cell, describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.

    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.

    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

  159. bornagain77

    I am aware that you have been posting a lot of comment directed to me. I apologise for not responding but

    1) they are typically long and include several external references which makes them extremely time consuming

    2) we have such different ideas on almost everything that I feel we will never find enough common ground to make for an interesting debate

    I am sure others will benefit from your comments but I wanted to explain why I am not responding.

  160. Mr. Frank you state:
    “we have such different ideas on almost everything that I feel we will never find enough common ground to make for an interesting debate”

    But that is the whole point Mr. Frank,,, Our ideas are almost completely opposite yet there can only be one truth on these question of human origins (save if you want to compromise to a “lukewarm” a deistic position).

    The overwhelming thrust of my responses to you have been to show you that your materialistic position is thoroughly bankrupt of any rigid empirical validation whatsoever.. i.e. that your materialistic position is NOT TRUE.

    You seem like a fairly smart fellow (You worked at IBM for 30 years),, So
    don’t you care to know what the truth really is? Do you not agree that if reality does not conform to your ideas then your ideas are merely dreams of the imagination that have no place in science proper?
    If so, then why do you not answer the empirics I present with you own empirics and continue to just ignore them?

    Is it that you find the thought of God distasteful to your lifestyle? Surely this can’t be for of what ultimate reward is it to you to be so biased to the point of denying reality? I surely can see no reward in denying the truth of reality (i.e. I would call it being delusional) and in fact in the long run, I deeply believe your stubbornness to face the reality of God dead on very well may lead to you being separated from the living God eternally, Yes, separated from The Living God who is the source of all Life and all that is good! (John 1:1)

    (Romans 1: 19-21
    19since what may be known about God is plain to them, because God has made it plain to them. 20For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that men are without excuse.
    21For although they knew God, they neither glorified him as God nor gave thanks to him, but their thinking became futile and their foolish hearts were darkened.

    Theism Compared to Materialism
    http://docs.google.com/Doc?doc....._5fwz42dg9

  161. –Mark Frank @156: “I had a go showing how various types of information can be produced by physics. I rather regretted the offer simply because it was so time consuming. But I felt obliged having said I would do it.”

    With respect to the information found in a DNA molecule, which is the critical element to be considered, Stephen Meyer has provided this concise definition: “The attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects.”

    Can you explain how physics alone can produce information based on this formulation?

  162. #161

    I am sorry StephenB – you are also on my “do not respond” list. For rather different reasons. I am too weak to handle your very forthright debating style (my fault I am sure). I will stick with vjtorley.

  163. BA77 & StephenB:

    I’m kind of in agreement with Mark here; we’ve gone around and around the central issues so many times that I’m not sure further discussion will get any of us anywhere. I very much respect your willingness to present your views and obviously you know the standard evolutionary paradigm. But it all seems to come down to some of us accepting that a self-replicating molecule that occasionally makes mistakes (including duplicating sections of itself thereby adding to the “code”) will continue to make copies, some of which are better able to exploit the natural resources around them, building more and more complex forms until, molded by the constraints and demands of various environmental niches, a plethora of forms exist. The process is directed by the natural, existing pressures and the “mistakes”/mutations collect “information” in a cumulative fashion.

    But, see, you’ve heard all that. And you can find the arguments. And read books by Dawkins, Miller, Shermer, etc. (I would highly recommend Evolution: What the Fossils Say and Why It Matters by Donald Prothero for anyone interested in the fossil aspect in particular. So many transitional forms . . . ) And those on the other side can read and digest works by Dembski, Behe, Meyer, etc. Perhaps it’s time to agree to disagree and leave it at that?

  164. I only agree to the fact that evolution is a deception, with no foundation in science whatsoever, and that you are delusional to believe in it. If you agree with that then we agree if you don’t then we don’t agree!

  165. I don’t agree with that BUT I will continue to do my best to understand your point of view and occasionally ask sarky questions about it.

    Deal?

  166. —Mark Frank: “I am sorry StephenB – you are also on my “do not respond” list. For rather different reasons. I am too weak to handle your very forthright debating style (my fault I am sure).

    Mark, I am sorry that you find my direct syle so disturbing. Even so, my question @ 150 and 161 was simple enough and there wasn’t even a hint of aggressiveness associated with it. Here is is again: How can physics produce the attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects?

  167. ELL, IF you had truly done your best to understand the evidence so far then you wouldn’t be an evolutionist anymore would you? So why should I trust you anymore than I trust that paradigm of atheistic virtue: the non-debating and blatantly deceptive Dawkins: or even the Eucharist desecrating militant Meyers??
    For you to “so graciously” offer to sit on the sidelines and take potshots at arguments, without ever truly considering the merits of the issue, is a little less than forthright with the matter and has not enhanced my opinion of your debating style, or inherent honesty, in the least.

    “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

    Ancient Fossils That Evolutionists Don’t Want You To See – video
    http://www.youtube.com/watch?v=eLzqDLZoufQ

    THE FOSSILS IN THE CREATION MUSEUM – 1000′s of pictures of ancient “living” fossils that have not changed for millions of years:
    http://www.fossil-museum.com/f.....8;limit=30

    Fossil Record – No Transitional Fossils – video
    http://www.youtube.com/watch?v=i0ZlcrumE2s

    “The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find’ over and over again’ not gradual evolution, but the sudden explosion of one group at the expense of another.”
    Paleontologist, Derek V. Ager

    “A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth’s geological formations. This record has never revealed traces of Darwin’s hypothetical intermediate variants – instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God.”
    Paleontologist, Mark Czarnecki

    “There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps.”
    Professor of paleontology – Glasgow University, T. Neville George

    “The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists” – Stephen Jay Gould – Harvard

    “Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? … The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record.” Luther D. Sunderland, Darwin’s Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9

    “The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be …. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin’s time … so Darwin’s problem has not been alleviated”.
    David Raup, Curator of Geology at Chicago’s Field Museum of Natural History

    The Fossil Record – Don Patton – in their own words – video
    http://video.google.com/videop.....6900194790

    Let There Be Light
    http://lettherebelight-77.blogspot.com/

  168. Mark Frank (#145, 146)

    Thank you for your posts, in which you attempted to clarify your position.

    I certainly can’t call myself a statistician, although I did do a couple of years of Stats at uni back in the eighties. I would therefore like to apologize in advance, if some of my comments seem wide of the mark. That said, here goes.

    Re-reading Kalinsky’s paper, it strikes me that he/she is really arguing from an ultra-Darwinian position, rather than an anti-Darwinian one. Modern textbooks on evolution take great pains to emphasize that evolution is more than common descent; it is the hypothesis that living things sprang from a common stock as a result of undirected natural processes. “Undirected” is usually taken to mean “lacking foresight; not aimed at any future goal.” Teilhard de Chardin’s theory of evolution would be dismissed as quackery by most modern scientists for precisely this reason: it has an Omega Point.

    Now, Kalinsky takes the “undirected” part of the modern definition of evolution very seriously; indeed, he/she goes further. For Kalinsky, evolution is the hypothesis that living things sprang from a common stock as a result of unbiased natural processes. A biased bowling ball may not be directed at any particular target; but it still shows a preference for a particular direction. If nature itself shows a built-in bias towards left-handed amino acids, or long-chain amino acids, or for that matter, amino acids that fold up neatly, then that bias requires an explanation, too. For Kalinsky, it’s just too pat, too convenient. It is still legitimate to ask: where does this bias come from? One can easily imagine a cosmos having the same low-level physico-chemical laws as our own, but lacking this biological bias.

    When we consider the emergence of functional information, Kalinsky’s point becomes even clearer. If nature itself is predisposed to favor processes that build up such information, then it can hardly be called unbiased. That’s a Teilhardian solution to the problem of origins. It begs the question: why is nature so nice? Only a theist could answer such a question.

    That is why for Kalinsky there are only two rival hypotheses: either life is the result of “mindless natural processes,” defined by Kalinsky as “a random walk, where the search proceeds in no set direction and, for any point in the search, it can be returned to any number of times” or life is the result of a process capable of producing significant levels of functional information. The so-called via media of invoking a natural process that tends to create functional information has already been ruled out as magical, and as invoking God in all but name. Or to use a Dawkinsian metaphor: natural selection is itself a skyhook if it can do that – which means that it doesn’t really explain anything.

    Now I’d like to return to your contention that “the likelihood of functional proteins given an unspecified mind is not 1 or anything close to 1.” I don’t disagree with you. However, I don’t think that’s the question that Kalinsky is addressing. I’d like to cite a comment that he/she makes on page 6 (point #2):

    Our observations indicate that there does not seem to be any known limit to the amount of functional information that intelligence can produce. It seems to be capable of producing anywhere from 0 bits and up.

    It seems to me that Kalinsky is not interested in individual minds, but in processes. What he/she is asking is: is there any kind of process that can reliably generate significant levels of functional information? Yes, there is: intelligence. And in principle, it can generate an unlimited amount of functional information.

    In his/her article, then, Kalinsky is comparing the capabilities of two processes to generate functional information: intelligence (never mind whose), and a random walk. (We’ve already ruled out a non-random walk as “cheating.”) If the latter process is umpteen orders of magnitude (155 in one of Kalinsky’s protein examples) less reliable at generating functional information than the former, then I would agree with Kalinsky that intelligent design would be a rational explanation.

    I hope these comments shed light on Kalinsky’s reasoning.

  169. #156

    Thanks for the effort. I think information is difficult to define but you know it when you encounter it. Comments briefly as I can.

    Kolmogorov complexity
    Something is missing from this definition. Random noise would by this definition contain as much information as say a university lecture.

    Dembski’s information
    This also seems like a useless definition. Its more of a heuristic one can use to determine if something contains information. But it does not describe information just how to detect its presence.

    Definition 3: Natural information
    In this sense everything is information just by its presence. We we think of information we think of it in terms of a representation either in action or as a store. For example a rules of the road book contains information as much as a driver driving while obeying the rules of the road.

    Definition 4: Unnatural information
    I don’t see a definition here. In fact it presupposed DNA is not the product of a mind which is in dispute. Clearly DNA could well be “natural” in the sense that it was very useful for the designer. Just as a computer has a file system which contains among other things the operating system which is full of information. The machine does not require an agent to view or understand the file system or information contained within for its ultimate cause to have been a designer.

    Thanks for time again. It certainly got me thinking about the nature of information and I am sure I will give it more thought especially as to how to differentiate between information and data.

  170. BA77:

    “ELL, IF you had truly done your best to understand the evidence so far then you wouldn’t be an evolutionist anymore would you?”

    What do you think about the endogenous retroviral evidence? I haven’t yet heard anyone here address that, perhaps I’ve missed it.

    “So why should I trust you anymore than I trust that paradigm of atheistic virtue: the non-debating and blatantly deceptive Dawkins: or even the Eucharist desecrating militant Meyers??”

    You don’t have to trust me at all. I’m not trying to affect you in the slightest. I’m just here to learn.

    “For you to “so graciously” offer to sit on the sidelines and take potshots at arguments, without ever truly considering the merits of the issue, is a little less than forthright with the matter and has not enhanced my opinion of your debating style, or inherent honesty, in the least.”

    I am doing my best to consider the merits, that’s why I’m here. David Berlinski frequently takes potshots at things without always offering an alternative. Is it not alright to ask questions?

    It doesn’t matter what you think of me. Thank you for supporting your contentions with your time and effort. That’s why I’m here.

  171. tgpeeler @ 136

    Seversky, the real argument here is: Does God exist? If so, then there CAN be Acts of God, the Word of God, and the Son of God. If He doesn’t, well then He doesn’t and so much the worse for us, aimless, pointless, amoral, ultimately worthless bags of subatomic particles randomly assembled by physics but remarkably, nonetheless, expressing “apparent” design, intelligence, conscience, purpose, and a desire to know why.

    This is where I have a problem with a certain form of belief when it holds we are “aimless, pointless, amoral, ultimately worthless”

    Says who?

    Why is it only God who gets decide what is our purpose or our worth or what is moral?

    What is to prevent us from working these things out for ourselves?

    You assume that only God can give these things but you do not say by what right. Yes, He has the power – if He exists – but I assume that you agree with me that might does not make right?

    I am quite prepared to believe in the existence of such a being if you can provide evidence for it or if He/She/It is prepared to step forward and do the same.

    Simply pointing to the many gaps in current scientific knowledge and exclaiming: “See! Your much-vaunted science can’t explain how that came to be. It must have been designed/created” is not evidence.

    Yes, in the last century millions were killed by regimes that were avowedly atheistic. Over the many centuries before that uncounted millions were killed in the name of religion. The only reasons why less people were killed in any preceding century is that there were fewer people around to kill and less efficient means of doing their killing.

    On the other hand, there are millions of people alive today who would otherwise be dead because of discoveries by secular or atheistic science. And by that I mean that the explaining how diabetes or malaria or poliomyelitis works or the treatment thereof did not require the assumption of the existence of a deity.

  172. Ell, ERV’s ?

    Shoot Ell, let’s take the whole realm of junk DNA while we are at it!

    Amazingly, materialists use to insist that most of the 98.5% of the genome, which did not directly code for proteins, was useless “Junk DNA”. Some materialists have tried to get around the failed prediction of Junk DNA by saying evolution never really predicted Junk DNA. This following site list several studies and quotes by leading evolutionists that expose their falsehood in denying the functionless Junk DNA predictions that were made by leading evolutionists:

    Functionless Junk DNA Predictions By Leading Evolutionists
    http://docs.google.com/View?id=dc8z67wz_24c5f7czgm

    Whereas ID predicted functional “Junk DNA”:

    “Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk the whole argument of this book would collapse. Teleology would be entirely discredited. On any teleological model of evolution, most, perhaps all the DNA in the genomes of higher organisms should have some function.” From Michael Denton’s 1998 book Nature’s Destiny (pages 289-290)

    Junk DNA – Another Failed Prediction Of Evolution – video
    http://www.youtube.com/watch?v=iFNVfCAvrac

    Despite the unfounded disappointment of materialists , a large sampling of recent studies indicates high level regulatory function is to be found for all sorts of previous “Junk DNA” sequences across the entire spectrum of the human genome.

    How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – Oct. 2009 – Excellent Summary
    Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2.....is_ha.html

    Junk DNA Found To Have High Level Function – Lists Of Over 100 Studies
    http://docs.google.com/View?id=dc8z67wz_25gqm4zzfd

    No Such Thing As ‘Junk RNA,’ Say Researchers – Oct. 2009
    Excerpt: Tiny strands of RNA previously dismissed as cellular junk are actually very stable molecules that may play significant roles in cellular processes, http://www.sciencedaily.com/re.....105809.htm

    Here is a detailed refutation of the Vitamin C (GULO) pseudogene argument used by evolutionists for human/chimp common ancestry:

    Excerpt Of Conclusion:
    When examined in detail, the full pseudogene dataset we collected does not lend itself to a reasonable neo-Darwinian interpretation.
    http://creation.com/images/pdf.....18-127.pdf

  173. StephenB @ 161

    With respect to the information found in a DNA molecule, which is the critical element to be considered, Stephen Meyer has provided this concise definition: “The attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects.”

    Meyer’s definition is vacuous. It amounts to saying that information is whatever causes things to be what they are. If he wants to use that definition for the word that is his choice but he and other design proponents need to make sure they are doing all they can to avoid the charge of equivocation by making it clear that their definition is very far from the common usage of the term.

    Can you explain how physics alone can produce information based on this formulation?

    First, can you explain how something called “information” is actually a property of the object or structure being described rather than of the model and language being used to describe it?

  174. cont.

    Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com.....Endogenous

    Endogenous Retroviruses (ERVS) A Case for Common Descent or A Case for Incorrect Presupposition?
    http://www.whoisyourcreator.co.....ruses.html

    How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schauer:
    List Of “Junk DNA discussed:
    Tandem Repeats, Transposons/Retrotransposons, SINE/Alu Sequences, LINES, Endogenous Retroviruses (ERVs) and LTR retrotransposons, Pseudogenes, C-Value Enigma, “Junk DNA” becomes “The Transcriptome”, Human Accelerated Regions (HARs),
    ….What can we conclude from the evidence presented in this essay:
    Every type of “Junk DNA” presented by pro-evolution websites has been found to have functional roles in organisms, which severely undermines the “shared errors” argument; http://www.geocities.com/wade_.....g_Tide.pdf

  175. Seversky,
    Atheism is a “pagan” religion!:

    The “Fruit of Materialism/Atheism”

    Matthew 7:15-17
    “Beware of false prophets who come to you in sheep’s clothing but inwardly are savage wolves. You will know them by their fruit. Grapes aren’t gathered from thorns, or figs from thistles, are they? In the same way, every good tree produces good fruit, but a rotten tree produces bad fruit.”

    The Ancient Pagan Root Of Evolution
    http://www.youtube.com/watch?v=vtC-vU7ufeg

    The Fruit of Evolution – video
    http://edinburghcreationgroup.org/fruit.xml

    From Darwin To Hitler – Richard Weikart – video
    http://www.youtube.com/watch?v=w_5EwYpLD6A

    Stalin’s Brutal Faith
    http://www.icr.org/index.php?m.....038;ID=276

    The Black Book of Communism: Crimes, Terror, Repression:
    Excerpt: Essentially a body count of communism’s victims in the 20th century, the book draws heavily from recently opened Soviet archives. The verdict: communism was responsible for between 85 million and 100 million, non-war related, deaths in the century. (of note: this estimate is viewed as very conservative by many, with some more realistic estimates passing 200 million dead) (Of Note: Atheistic Communism is defined as Dialectic Materialism)
    http://www.amazon.com/Black-Bo.....0674076087

    Atheist Atrocities Frightening Stats About Atheists
    http://www.youtube.com/watch?v=tP1KpNEeRYU

  176. As well Seversky without Christianity there could very well be no “science” as we know it today!

    Christianity and the Birth of Science
    http://www.ldolphin.org/bumbulis/

  177. Seversky are you trying to deny information even exists in life?

    “No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes programmed?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8

    Mycoplasma Genitalium – The “Simplest” Life On Earth – video
    http://www.youtube.com/watch?v=eRoMxpZWR7

    Chance and necessity do not explain the origin of life: Trevors JT, Abel DL.
    Excerpt: Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic–that is, it is programmatically and algorithmically organized and controlled. http://www.ncbi.nlm.nih.gov/pubmed/15563395

  178. Mr BA^77,

    I hope you realize that quote from Abel and Trevors is a statement of opinion, not fact.

    I wonder what the scientific measure of “technical brilliance” is? How do you compare the genome of Mycoplasma to the program codes they use to predict the weather? Anyone know? Anyone? Bueller?

  179. Nak, Are YOU denying information exists in life?

  180. —-seversky: “Meyer’s definition is vacuous. It amounts to saying that information is whatever causes things to be what they are.”

    You had better explain that to Webster’s dictionary from which he draws the definition.

    —-”If he wants to use that definition for the word that is his choice but he and other design proponents need to make sure they are doing all they can to avoid the charge of equivocation by making it clear that their definition is very far from the common usage of the term.”

    Common usage is a function of those formulations found near the top of the dictionary’s listings. Nice try, though.

    That same definition, by the way, applies to code found in a DNA molecule. Your only argument is to deny that information exists, which means, of course, that you have no argument.

    –”First, can you explain how something called “information” is actually a property of the object or structure being described rather than of the model and language being used to describe it?”

    You might as well ask how I know that the binary code in a software program is real—or how I know that the message in a written paragraph is real—or how I know that the alternative sequences of nucleotide bases and the effects produced by them are real–or how I know that the cellular machinery that receives the instructions are real. Instructions are instructions; storage is storage; codes are codes. Hypersubjectivism doesn’t work with science.

    In any case, Mark Frank told us that he was prepared to explain how physics can produce information if only someone would provide a definition on which we could focus. Obviously, he could not support his assertion, so he ignored my question and began to complain about my “direct” style of debating. Would you care to take up his argument for him? Here, once again is the question: How can physics produce the attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects?

  181. Nak,
    The Coding Found In DNA Surpasses Mans Ability to Code – Stephen Meyer
    http://www.youtube.com/watch?v=HavmzWVt8IU

  182. Seversky makes an excellent point:

    Yes, in the last century millions were killed by regimes that were avowedly atheistic. Over the many centuries before that uncounted millions were killed in the name of religion. The only reasons why less people were killed in any preceding century is that there were fewer people around to kill and less efficient means of doing their killing.

    Imagine the death toll of the Thirty Year’s War had the combatants possessed modern weapons and had the population of Europe been what it is today. The whole “atheists have a higher body count” canard is bogus. Our ID friends are in desperate need of a better schtick.

  183. So Dave,
    Do YOU deny the existence of evil?

  184. BA77:

    “Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com…..Endogenous

    Endogenous Retroviruses (ERVS) A Case for Common Descent or A Case for Incorrect Presupposition?
    http://www.whoisyourcreator.co…..ruses.html”

    Interesting and very much to the point. It’s late where I live and I want to read them again before responding. I am going to want to spend sometime considering the argument that some or all ERVs could have inserted themselves in similar places in the genomes of various species by infecting those species seperately. That argument, of course, takes something away from common descent but gives nothing to ID.

    Thanks for the references.

  185. bornagain77 @ 172

    Amazingly, materialists use to insist that most of the 98.5% of the genome, which did not directly code for proteins, was useless “Junk DNA”. Some materialists have tried to get around the failed prediction of Junk DNA by saying evolution never really predicted Junk DNA.

    “Materialists” did not insist on anything as a group.

    Evolutionary biologists found that there were large parts of the human genome that had no apparent function at the time. Putting it simply, in 1972, Dr Susumu Ohno argued that the accumulation of a large amount of “junk DNA” was a necessary consequence of the way genes mutate. This was not immediately accepted as dogma. In fact, the very first question after his presentation described it as “suspect”.

    Yes, some regions of so-called “junk DNA” have been found to have a function. This was suspected from the beginning. That speculation and the research were done by evolutionary biologists. It did not come from creationists or ID proponents sitting on the sidelines taking potshots at the arguments.

    It was also evolutionary biologists who cut out sections of DNA from the genomes of experimental animals and found it had no apparent effect on subsequent generations. In other words, these sections of DNA actually did not appear to do anything, certainly nothing useful. Maybe they did in the past. Maybe they will be co-opted into doing something useful in the future. No one knows. But the evidence is they do not do anything at this time.

    What else would you expect? Mutations happen. Functional genes – like our vitamin C gene – can occasionally get knocked. As long as it does not impose some intolerable burden on the organism, the broken gene will just continue along for the ride. Over sufficient time, it could mutate out of all recognition from its previous function or it might even be re-activated by another mutation.

    The key point is that this will be the case whether it was designed or evolved through natural causes. If a designer was involved then either he chose to use DNA in full knowledge of its vulnerability to mutation or it was used because there was no other choice.

    Either way, “junk DNA” is no challenge to evolutionary theory and no comfort to believers and/or New Paleyists.

  186. BA writes:

    So Dave,
    Do YOU deny the existence of evil?

    What makes you ask that, BA?

  187. #168 vjtorley

    I think you are reading a lot more into Kalinsky’s article then is there. However, whether Kalinsky implied it or not there seems to be a logical flaw in what you have written.

    You go to some pains to explain something can be biased without being directed. Then later on you write that if nature is biased towards life (i.e. there is a natural process which makes life probable) then:

    That’s a Teilhardian solution to the problem of origins. It begs the question: why is nature so nice? Only a theist could answer such a question.

    Surely that would only be true if the solution were directed.

    Any natural process that increases the probability of producing a functional protein is introducing a “bias” towards those results. But that is perfectly legitimate. That is exactly what having a natural explanation is. Clouds introduce a bias towards rain.

    Kalinsky questions the probability of such a natural process arising and that is what I dealt with in #146. It may be easier if you remember the order of events. The functional proteins are the result of a process that existed before they did, not a target for which the process was created. If a process exists which is likely to produce a result X which would otherwise be improbable then that’s just a fact of nature.

    You also write:

    In his/her article, then, Kalinsky is comparing the capabilities of two processes to generate functional information: intelligence (never mind whose), and a random walk. (We’ve already ruled out a non-random walk as “cheating.”)

    You may have ruled out a non-random walk as cheating. I haven’t. “Random walk” is specific probability model that I cannot see how to apply in this situation – but I think my paragraph above covers this.

    You may be right that Kalinsky is only talking about the capabilities of two processes to produce life. By capability I guess you mean the chances of a process producing life given the absolute best assumptions. So in the case of a mind we assume it is omnipotent and motivated. I actually think he confusing capability (in this sense) with likelihood and slipping between the two. In particular he is comparing the capability of a designed process with his (faulty) estimate of the likelihood of a natural process. He makes no “best possible” assumptions about a purely natural process.

    Anyhow I think we have exhausted this. I hope I have at least addressed your concern that no one has faulted Kalinsky’s logic. At a minimum our very discussion shows that his logic is not clear.

  188. #169 Cable

    A pleasure doing business with you. I think you will find that all definitions of information are unsatisfactory in some respects. That’s because it has many meanings and any good definition will inevitably exclude some of those meanings.

  189. Seversky, only in your fertile imagination is finding virtually 100% poly-functional DNA of no concern to materialists. Furthermore your post hoc excuses for evolutionists never really predicting Junk DNA falls on deaf ears considering I have over the years debated several evolutionists about Junk DNA with them consistently maintaining it was Junk,,,even after the ENCODE findings!

    Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome:
    The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active. The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact.
    http://www.sciencedaily.com/re.....131932.htm

    The Unseen Genome, Gems Among the Junk:
    “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003) http://www.evolutionnews.org/

  190. Dave,
    I ask if you believe in evil because I just want to know from which basis you, as a materialist/atheist, are prepared to make a “moral” argument in the first place.

    Does God Exist?
    http://www.youtube.com/watch?v=U1JbHRgNowU

    Thermodynamic Argument Against Evolution Part 1 of 3 – Thomas Kindell
    http://www.youtube.com/watch?v=nI1RiTOQ4do

  191. Dave,
    A little more clarity:

    Theodicy Without God?
    What Ive never understood about theodicy is this: why do atheists ponder the Problem of Evil?
    http://www.evolutionnews.org/2.....t_god.html

    Little do most atheists realize that the existence of evil itself necessitates the existence of Good. i.e. you cannot disprove God by pointing to evil. All a atheist does when he points to evil in this world is to point out the fact that this world is not perfectly good, Yet Christianity never claimed we were in heaven in the first place. i.e. by pointing to evil (the absence of good), the atheist actually affirms the Christian belief that we are in a fallen world.

    William Lane Craig – Moral Argument For The Existence Of God
    http://www.youtube.com/watch?v=HJ1oaBD8xVo

  192. And Of Course Dave, for a fairly strong and cohesive Theodicy you can check out Dr. Dembski’s new book, if you’re interested:

    The End of Christianity: Finding a Good God in an Evil World
    http://www.amazon.com/End-Chri.....038;sr=1-1

    I believe you can check an excerpt of the book here:
    http://www.designinference.com.....of_xty.pdf

  193. —Mark Frank: “Happy to have a go at this –[explaining how physics alone can produce information] but first which of the many definitions of information are you using?

    TRANSLATION 1. I will answer the question provided someone provides a specific definition of information.

    Definition offered [by yours truly]: “The attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects?”

    —-Mark Frank: “I am sorry StephenB – you are also on my “do not respond” list.” [Along with Bornagain 77]

    TRANSLATION 2. I only respond to those who don’t hold my feet to the fire.

    —Mark Frank to a (nice person?) [unlike me]: “A pleasure doing business with you. I think you will find that all definitions of information are unsatisfactory in some respects. That’s because it has many meanings and any good definition will inevitably exclude some of those meanings.”

    TRANSLATION 3: I will not answer the question even if a nice person provides a definition since all definitions are inferior.

  194. Mark Frank (#187)

    It has been a pleasure exchanging views with you, as always. I would just like to comment on a couple of points you raised before I sign off. You wrote:

    In particular he [Kalinsky - VJT] is comparing the capability of a designed process with his (faulty) estimate of the likelihood of a natural process. He makes no “best possible” assumptions about a purely natural process.

    No “best possible” assumptions? What about this?

    Taylor et al. have estimated that the mass of the earth would equal about 10^47 proteins, of 100 amino acids each.[7] If we suppose that the entire set of 10^47 proteins reorganized once per year over a 500 million year interval (about the estimated time period for pre-biotic evolution), then that search permits about 10^55 options to be tried. Using Eqn. (3), I(nat) = (approx.) 185 bits of functional information.

    500 million years, and an entire planet composed of amino acids and nothing else. If that’s not a “best possible” assumption for the evolution of proteins, then I don’t know what is.

    You also write:

    If a process exists which is likely to produce a result X which would otherwise be improbable then that’s just a fact of nature…

    Any natural process that increases the probability of producing a functional protein is introducing a “bias” towards those results. But that is perfectly legitimate. That is exactly what having a natural explanation is. Clouds introduce a bias towards rain.

    Clouds do introduce a bias towards rain, but they do so on the basis of known, low-level physico-chemical laws. As far as we know, there are no laws favoring the emeregence of amino acids, but if there were, they would have to be pretty odd laws: long, detailed and rather specific – cerainly not the concise, back-of-the-T-shirt variety that we all dreamed of back in the eighties when the “theory of everything” was all the rage.

    If there are certain biases in nature favoring the emergence of proteins, and these biases are not predictable from what we know of physics and chemistry, then I certainly think that’s a very odd fact, and I for one would want to explain it.

  195. Mr BA^77,

    Nak, Are YOU denying information exists in life?

    No, for most definitions of life and information. If the definition of information is non-standard, perhaps.

  196. Mr BA^77,

    The Coding Found In DNA Surpasses Mans Ability to Code – Stephen Meyer

    Thank you for more opinions, not facts. This is an often expressed claim, but you are not backing it up with a measurement.

  197. Nak , that is too funny ,,,you want facts and when presented with facts you NEVER listen,,,The truth is you just want pseudo-facts to tickle your materialistic ears with: Well anyway here is some more facts for you to ignore and dance around with superfluous tongue wagging.

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.youtube.com/watch?v=vUeCgTN7pOo
    Entire video:
    http://www.seraphmedia.org.uk/ID.xml

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute.
    http://www.pubmedcentral.nih.g.....id=1208958

    H.P. Yockey also notes in the Journal of Theoretical Biology:
    It is important to understand that we are not reasoning by analogy. The sequence hypothesis applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical:
    “Self Organization Origin of Life Scenarios and Information Theory,” J. Theoret. Biol.

  198. Here are some more facts for you to ignore:

    John Sanford, a leading expert in Genetics, comments on some of the stunning poly-functional complexity found in the genome:

    “There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). (Dr. John Sanford; Genetic Entropy 2005)

  199. Another fact for you to ignore Nak:

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. – 2009
    Excerpt: We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

  200. Mr BA^77,

    Please continue. Quote the paper that says the genetic code measures 6.7 megahilberts (the standard measure of technical brilliance) and the code of the global weather forecasting system only measures 4.5 megahilberts. I haven’t been able to find it with Google Scholar

  201. Nak,
    Here is more stuff for you to pretend that doesn’t matter:

    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). There are about three-billion letters of code on the six feet of DNA curled up in each human cell. If you were to read the code aloud, at a rate of three letters per second for twenty-four hours per day (about one-hundred-million letters a year), it would take you over thirty years to read it. The capacity of a DNA molecule to store information is so efficient all the information needed to specify an organism as complex as man weighs less than a few thousand-millionths of a gram. The information needed to specify the design of all species of organisms which have ever existed (a number estimated to be one billion) could easily fit into a teaspoon with plenty of room left over for every book ever written on the face of the earth. For comparison sake, if mere man were to write out the proper locations of all the protein molecules in just one human body, in the limited mathematical language he now uses, it would take a bundle of CD-ROM disks greater than the size of the moon, or a billion-trillion computer hard drives, and that’s just the proper locations for the protein molecules in one human body, that billion-trillion computer hard-drives would not contain a single word of instruction telling those protein molecules how to self assemble themselves. (The Bit and the Pendulum – Tom Siegfried – Samuel Braunstein)

    “To the skeptic, the proposition that the genetic programmes of higher organisms, consisting of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of 1,000 volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying, and ordering the growth and development of billions and billions of cells into the form of a complex organism, were composed by a purely random process is simply an affront to reason. But to the Darwinist, the idea is accepted without a ripple of doubt – the paradigm takes precedence!” – Michael Denton

    Psalm 139: 14-15
    “I praise you because I am fearfully and wonderfully made;,,, When I was woven together in the depths of the earth, your eyes saw my unformed body.”

  202. Seversky and Dave Wisker:

    I agree with you that the practice (engaged in by some defenders of Christianity) of comparing the tens of millions killed under Stalin with the smaller number of people killed in Christian atrocities is an unfair one, as it fails to take account of world population during the time when Christianity was dominant.

    If you want to bone up on atrocities, then I cannot do better than to recommend a guy named Matthew White, who has done a lot of research on the subject. White is not a Christian – indeed, he does not belong to any religion, as far as I can tell. Neither is he an academic. However, he is an incisive thinker, and he does get right to the heart of the matter, when addressing issues relating to atrocities – numbers, methods of counting, who’s responsible, what the causes are, and what it all means. Here are some links that will help you a lot.

    Which Has Killed More People? Christianity or Gun Control? by Matthew White.
    Essential reading for those who wish to get a balanced perspective on the harm wrought by religion. Matthew White’s Web site on atrocities is extraordinarily thorough, comprehensive and fair-minded.

    Selected Death Tolls for Wars, Massacres and Atrocities Before the 20th Century by Matthew White.

    Selected Death Tolls for Wars, Massacres and Atrocities Before the 20th Century (Page Two) by Matthew White.

    (Possibly) The Twenty (or so) Worst Things People Have Done to Each Other by Matthew White.

    Blame and Responsibility – FAQs by Matthew White.

    An excerpt:

    Q: Is religion responsible for more more violent deaths than any other cause?

    A: No, of course not – unless you define religion so broadly as to be meaningless. Just take the four deadliest events of the 20th Century – Two World Wars, Red China and the Soviet Union – no religious motivation there, unless you consider every belief system to be a religion.

    Q: So, what you’re saying is that religion has never killed anyone.

    A: Arrgh… You all-or-nothing people drive me crazy. There are many documented examples where members of one religion try to exterminate the members of another religion. Causation is always complex, but if the only difference between two warring groups is religion, then that certainly sounds like a religious conflict to me. Is it the number one cause of mass homicide in human history? No. Of the 22 worst episodes of mass killing, maybe four were primarily religious. Is that a lot? Well, it’s more than the number of wars fought over soccer, or sex (The Trojan and Sabine Wars don’t even make the list.), but less than the number fought over land, money, glory or prestige.

    In my Index, I list 41 religious conflicts compared with 27 oppressions under “Communism”, 24 under Colonialism, 2 under “Railroads” and 2 under “Scapegoats”. Make of that what you will.

  203. Seversky and Dave Wisker

    Before assessing whether religion has been a net blessing or curse for humanity, you also need to consider the number of lives saved by religion. In this connection, here is an article which you really should read, detailing how Christianity improved the status of women and saved millions of people in ancient Rome from death by female infanticide and from the plagues which periodically swept the Roman Empire:

    Reconstructing the rise of Christianity: the role of women by sociologist Rodney Stark. In Sociology of Religion, Fall 1995.

    In 1996, Stark followed up with a book, The Rise of Christianity (1996, Princeton University Press), available at Amazon here: http://www.amazon.com/Rise-Chr.....0060677015 . Some of it can be viewed online here: http://books.google.com/books?.....38;f=false .

    Stark is a very fair-minded researcher, and his writing is very lucid and refreshingly free of bombast and polemic. One thing that emerges clearly from his book, however, is that Christianity significantly improved the social status and rights of women in ancient Rome. This is especially evident when we consider female infanticide, which was prevalent in practically every ancient society. Although most world religions condemn infanticide in forthright terms (see the BBC report, What Different Religions Say About Infanticide ), only three actually managed to ban it: Judaism, Christianity and Islam. Here ar some useful links:

    Pagans, Christianity and Infanticide by Christopher Price.

    (Incidentally, it was Bishop Basil of Caesarea who finally convinced Emperor Valentinian (364-375 CE) – a Christian – to outlaw the practice of infanticide in the Roman Empire.)

    Women’s Right in Islam – Modernising or outdated? : Social Rights of Women in Islam by Dr. Zakir Naik. This article narrates how Islam eradicated female infanticide in Arabia.

    Case study: Female Infanticide (Focus on in India and China). This article documents how femae infanticide continues to run rampant in these societies. And the consequences are truly catastrophic: 90 Million Missing Females, and a $45 Trillion Gap , according to this article from Zenit International News Agency (24 July 2004).

    How many lives has religion saved by its prohibition of infanticide? Here’s my calculation. Population of the Roman empire: about 60 million people. Annual number of births (assuming say, 40 births per 1000 people per year): about 2.4 million, or 1.2 million boys and 1.2 million girls, of whom 200,000 were killed through exposure under the Romans. Enter Christianity: up to 200,000 girls’ lives saved per year, or 20 million per century, or 200 million over a period of a millennium. Do the same math in Arab countries as well, and you get even more girls’ lives saved. Still think religion is anti-social?

  204. Hi vj,

    Sorry, but I don’t recall saying anything about religion being a curse or a benefit. I was simply commenting on the inanity of the “body count’ argument.

  205. Mr. Nakashima

    I take it your reference to “megahilberts” was a humorous one, as the term does not show up in Google – except on this thread!

    However, here are two articles that might impress you:

    Astonishing DNA complexity demolishes neo-Darwinism by Alex Williams.

    Astonishing DNA complexity update by Alex Williams.

    Don’t diss DNA.

  206. Seversky @171

    “This is where I have a problem with a certain form of belief when it holds we are “aimless, pointless, amoral, ultimately worthless”

    Says who?”

    Um, naturalism/materialism and thus anyone who is a proponent of those “isms.” I wasn’t aware that I was being controversial here. I hate to quote Dawkins because some young or untrained mind may think he’s on to something instead of on something but it’s a risk I must take here… From River Out of Eden, p. 132.

    “… Such a universe would be neither evil nor good in intention. It would manifest no intentions of any kind. In a universe of blind physical forces and genetic replication, some people are going to get hurt, other people are going to get lucky, and you won’t find any rhyme or reason in it, nor any justice. The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference.”

    Aside from the fact that his reasoning skills are barely detectable, he does grasp the point that if one is a naturalist/materialist (both demonstrably false, I’d love to have that out with you) then there is no point and if there is no point, why then, there is no point.

    “Why is it only God who gets decide what is our purpose or our worth or what is moral?

    What is to prevent us from working these things out for ourselves?”

    This sounds like you are pissed off at God for some reason and therefore have decided to stamp your foot in anger and deny Him. I’m cool with that but I’m not the one you should be concerned about. You are free to work these things out for yourself. If you can do it rationally, you’ll be the first. Go ahead, convince me that in a Godless, purposeless, pointless, amoral universe of quarks, leptons, and forces, that human life has meaning and significance. Yeah, right. In a 14 billion year old (give or take) universe of which you will occupy for 70 years, plus or minus, you matter?? I matter?? Ha. The fact of it is, IF there is no God then there is no point and there is no value, nothing of intrinsic worth. NOTHING. There is no morality. There is no meaning to anything. In the blink of a cosmic eye we appear and disappear (in your alleged universe) and that’s it. No accounting, no judgment, no owning up, nothing but oblivion. I eagerly await your explanation of meaning given your (apparent) naturalism.

    “I am quite prepared to believe in the existence of such a being if you can provide evidence for it or if He/She/It is prepared to step forward and do the same.”

    What would you consider evidence? That’s a serious question. I thought I had a clue but bornagain77 has swamped everyone with evidence, with able assistance from others, and you and Nak and others just will not get it. There is nothing that can convince you. The tragic thing is, deep down inside you know that God exists and if He does, then miracles are possible. Miracles that could confirm truth claims made by His agents. In other words, if there is a God then there can also be a Word of God. If you will read it and ARGUE with my argument I will prove to you that God exists with an exercise in pure reason that will make a prediction that has been empirically confirmed in the last few decades of science. If you are just going to ignore or dodge the argument, then I won’t bother. It’s been done before by better men and minds than me.

    “Simply pointing to the many gaps in current scientific knowledge and exclaiming: “See! Your much-vaunted science can’t explain how that came to be. It must have been designed/created” is not evidence.”

    If it wouldn’t be completely inappropriate, it is right about now that I would say, no “expletive deleted” kidding (it’s an old technical Marine term). Arguments from ignorance. How pathetic. Odd though that the only such arguments I’ve seen out here that qualify by that standard are the ones “you people” make. I don’t argue from ignorance and neither does anyone on the ID side in this thread. Your biases are showing. And by the way, it’s my science too. I love science and what it has done for me and mine. And others too, if that helps make me look compassionate…

    “Yes, in the last century millions were killed by regimes that were avowedly atheistic. Over the many centuries before that uncounted millions were killed in the name of religion. The only reasons why less people were killed in any preceding century is that there were fewer people around to kill and less efficient means of doing their killing.

    On the other hand, there are millions of people alive today who would otherwise be dead because of discoveries by secular or atheistic science. And by that I mean that the explaining how diabetes or malaria or poliomyelitis works or the treatment thereof did not require the assumption of the existence of a deity.”

    Are you sh… kidding me??? The only reason atheists didn’t kill more in the past was because they didn’t have nukes, CBUs, and automatic weapons??? That’s good. No really, it is genuinely funny. I’m LMAO as I type. And your point would be… what?? As to the “secular or atheistic” science, you demonstrate an abysmal ignorance of history. Science is only possible in a universe of rationality and order and your metaphysic has no warrant for postulating either of those things. Many, if not most, of the early scientists were Christians. They saw the evidence of God in His creation and they were doing science almost as a form of worship. Why would you care about millions saved in a pointless universe? Who gives a s… darn. See, this just demonstrates the futility of reasoning with someone who rejects reason. Your worldview doesn’t allow for good and evil but yet you make reference to those things. That’s called a self-contradiction where I come from. You can’t have it both ways. That’s a rule of logic called the law of non-contradiction. There is either evil or there isn’t. No in betweens, either. That’s called the law of the excluded middle. And yes, “Christians” have done very, very bad things and continue to do so. But that’s not really the point. You see, if we had read the Bible and obeyed it, then we wouldn’t have been creating mischief along with our atheist brethren. That’s the key point. You don’t judge a body of doctrine by the abuses of a few. Not if you are rational, that is.

    I’ll go the extra mile here. Tell me what your basic philosophical assumptions are (I’ll give you mine in a minute) and we can figure out what is the correct way to view things.

    My assumptions are as follows:

    1. Reason is the ultimate authority in matters of truth. (To argue against that statement is to use reason to deny the efficacy of reason and therefore irrational.)
    2. There is a way that the universe is. There is a way that “things are.” (This is also undeniable. If I say “God” and you say “no God” then we are both saying that there is a way that things are and one of us is right and the other is wrong.)
    3. Propositional statements (truth claims) that correspond to the way that things are, are true. Those that do not, are false. This is the definition of truth. You may recognize it as the correspondence theory of truth but it is the definition of truth. The other two major theories of truth, coherence and pragmatism, both allege that they represent reality. i.e. that they correspond to the way that things are.)
    4. Since certain abstract things are indisputably real, such as the laws of physics, economics, and logic, mathematics, and information, then I am justified to think, a priori, that it is possible for other abstract things to exist – that is, minds and God.
    5. But this is not an argument so now we must weigh the available evidence to determine who has a better answer for the universe and all it contains, the theist or the atheist.
    6. When a valid deductive argument (the conclusion necessarily follows from the premises) is sound, that is, the premises are true, the conclusion is necessarily true. Not even God could make it not true.
    7. All arguments must begin with first principles or physical laws otherwise “invisible” assumptions get to “sneak in” unannounced and contaminate the argument.
    8. Believing B.S. never got me anywhere. I make an inductive argument from my personal experience to the personal experience of others and I conclude that believing B.S. probably never did others any good either.
    9. I am selfish and want what’s best for me. That’s why I am interested in what’s true.
    10. I am also a coward and IF there is (determined by rigorous reasoning and unflinching examination of the evidence) an Almighty God, Creator of the universe, then I don’t want to be on His bad side come the time when I have to account for myself. This is not an argument for His existence, it is merely my instinct for self-preservation taking the possibility seriously.
    11. There are two ways, three ways an argument can be defeated. It can be invalid. That is the conclusion doesn’t necessarily follow from the premises. In that case, all one has to do is point that out. The second way is that one or more of the premises can be false. This also makes the conclusion false. The third way, my favorite, because my work is already done, (did I mention lazy, too?) is when an argument destroys itself because it contains an internal contradiction of some kind. I have pointed that out re. naturalism/materialism on this thread but for some reason it’s gotten essentially zero traction. It’s either blindingly obvious (my take) or it sucks (I hope not). In any case I will be “happy” to remake it in detail if need be.

    I look forward to hearing back from you with some of your “first principles” and a shot at mine. If you’ll really play, that is.

  207. born,

    I base my ethical views on my own internal compass, which derives its direction from my sense of empathy. I don’t want to see others suffer because I don’t like suffering myself . Consequently, I prefer to live in a society where the overall level of human misery is kept to a minimum, which to me means choosing to live in a society where the majority consists of like-minded people over issues such as murder, theft, basic civility, etc. Of course, not everyone derives their moral compass the same way. Some derive it internally, as I do, while others base their morality on direction from a god or gods. I couldn’t care less, as long as the majority of the people try to be most excellent to each other, as The Golden Rule states.

  208. “I couldn’t care less, as long as the majority of the people try to be most excellent to each other, as The Golden Rule states.”

    Why couldn’t I care less about what you care about? What is so wrong with that? Why shouldn’t I just take what I want if I am big, strong, smart, well-armed enough to just take it? Why would I care if you don’t like that? I’m just curious as to what is your ultimate basis for not only “being excellent” (hey Dude, Bill and Ted’s Excellent Adventure!!) but justifying it. You say you have an impulse to keep human misery to a minimum. Why? And what if I have the opposite impulse? Who is right and how do we arbitrate that? And what difference does it make anyway in the blink of cosmic time that we are alive?? Really.

  209. —Dave Wisker: “I base my ethical views on my own internal compass, which derives its direction from my sense of empathy. I don’t want to see others suffer because I don’t like suffering myself.”

    So, I gather that you would defend to the death the life of the unborn infant in the womb. Ironically, very few who derive their morality from their “sense of empathy” extend that sentiment to the most helpless and vulnerable among us. Am I to understand that you are the exception?

  210. tgpeeler,

    Why couldn’t I care less about what you care about? What is so wrong with that? Why shouldn’t I just take what I want if I am big, strong, smart, well-armed enough to just take it?

    If you recall, I said I choose to live in a society where the majority feel pretty much the same way about those issues. Human behavioral variation being what it is, there will be some who don’t think that way. But the only way to keep the level of human misery at a minimum within such a society is to codify those agreed-upon issues into a justice system.

  211. Stephen,

    Frankly, I’m not at peace with the abortion issue. I doubt that makes me the exception either.

  212. Mr Vjtorley,

    Nor will I dis Google, if it searched this thread within an hour!

    I read both of the articles you referenced, thank you. DNA (and all of the epigenetic machinery mentioned in those articles) is truly amazing. But then, so is the code to forecast the weather! We aren’t any closer to comparing the two in any meaningful way.

    We also have to be careful to maintain some continuity in the discussion. Mr BA^77, in quoting Abel and Trevors, referred to a mycoplasmic bacterium as surpassing the technical brilliance of any human programming. Follow-up responses have made reference to the ENCODE project and discoveries about th ecomplexity of the mammalian (human/mouse) genetic system. These are quite different.

    An interesting counter example to the arguments about the importance of noncoding RNA is the creation of mice with long stretches of ‘junk DNA’ knocked out of their genome.

  213. Mr BA^77,

    I don’t think Trifonov 1989 has quite the meaning you think it does. This came up previously in a discussion with Mr Cordova, who is also much taken with Dr Sanford’s book. You can arrive at “12 codes” (one for each of the 12 tribes of Israel – THAT’S NOT A COINCIDENCE!!1!) by multiplying 2 strands by 2 directions by 3 reading frames. As such, it is a statement of possibility, not actuality.

    Think about it. If each strand was read in every reading frame, we wouldn’t have diseases caused by reading frame errors. Nylonase would have always existed.

  214. Nak, please tell me of what possible use it would be for me to clarify your distractions since you never listen when corrected?

  215. #194 vj

    I cannot resist a final response.

    500 million years, and an entire planet composed of amino acids and nothing else. If that’s not a “best possible” assumption for the evolution of proteins, then I don’t know what is.

    This is very far from being the best possible because it assuming that the evolution of proteins is done by throwing together amino acids in chains at “random” until you get lucky. We all accept this will not work. There are other conceivable natural processes for generating proteins.

  216. Mr BA^77,

    I am aware that I must be a tiresome conversationalist. Thank you for your patience.

    let’s try again from here”

    No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms.

    Do you agree that this is phrased as a statement of opinion?

  217. —-Dave Wisker: “Frankly, I’m not at peace with the abortion issue. I doubt that makes me the exception either.”

    I have no doubt of it. Aren’t you even a little curious about how I had already figured out your position on abortion? I have had many discussions with those who embrace a morality based on their personal preferences, and those preferences invariably include libertinism and its friendly companion, abortion on demand. Take note: No one person’s subjective morality ever includes the regulatory hard sayings that he does not like and yet needs to hear.

    —”If you recall, I said I choose to live in a society where the majority feel pretty much the same way about those issues. Human behavioral variation being what it is, there will be some who don’t think that way. But the only way to keep the level of human misery at a minimum within such a society is to codify those agreed-upon issues into a justice system.”

    Notice the contradiction. On the one hand, you are positing a civil law which depends on “agreed upon issues.” On the other hand, you acknowledge that “some will not feel that way.” What do we do with the latter group? Subjective morality always leads first to a tyranny of the minority by the majority, followed by a tyranny of everyone by a few.

    It is not possible to establish civil laws based on subjective preferences, because subjective preferences vary, based as they are on the convenience of the one doing the preferring. Civil law can only be grounded in a higher law. There are only two possibilities: [A] The natural moral law, which promotes a well-ordered society and [B] Might makes right, which leads to tyranny. Moral subjectivism always leads to [B].

  218. Nak,
    Is this an opinion or a fact:

    Missed Opportunities

    There they are smiling as they pass you by
    You smile back and wave a courteous hi
    You blink, and they laugh in that peculiar way
    as they melt into the brick wall of yesterday

  219. Mr BA^77,

    (Sorry if this appears twice. UD hiccuped when I sent it the first time.)

    It is a distraction. Try to answer the question. Opinion or fact?

  220. Dave @210

    “If you recall, I said I choose to live in a society where the majority feel pretty much the same way about those issues. Human behavioral variation being what it is, there will be some who don’t think that way. But the only way to keep the level of human misery at a minimum within such a society is to codify those agreed-upon issues into a justice system.”

    No, I get that. What I don’t get is WHY and what’s the basis for that WHY? Doesn’t that require explanation within a Darwinian worldview if that is what you hold to? And what if I move into your neighborhood? And I have a less charitable view of things? Who’s right? Is that a question that even makes sense to ask? What do you do then? How do you defend yourself and on what basis? Am I “wrong” to oppress or try to oppress you or anyone else or am I just being my evolved self??

  221. Mark @ 215

    “There are other conceivable natural processes for generating proteins.”

    So this is what we’ve come to. If there are “conceivable” processes, then that’s good enough. Never mind that no one has demonstrated, found, or thought of one that could actually work. Dawkins frequently references arguments from incredulity as an example of how impoverished the imaginations are of ID proponents. I take the other tack and say the argument from credulity (it’s “possible”) shows how utterly gullible anyone positing naturalistic evolution is. It’s conceivable so I’ll take that over mountains of evidence that show it didn’t happen that way. Hee hee. Good one.

  222. Well Nak let’s look at the context of the statement,

    Three subsets of sequence complexity and their relevance to biopolymeric information
    Excerpt: Bioinformation has been selected algorithmically at the
    covalently-bound sequence level to instruct eventual three-dimensional shape. The shape is specific for a certain structural, catalytic, or regulatory function. All of these functions must be integrated into a symphony of metabolic functions. Apart from actually producing function, “information” has little or no value. No matter how
    many “bits” of possible combinations it has, there is no
    reason to call it “information” if it doesn’t at least have the
    potential of producing something useful. What kind of information produces function? In computer science, we call it a “program.” Another name for computer software
    is an “algorithm.” No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms’ genomes
    programmed?

    FSC is a succession of algorithmic selections leading to function. Selection, specification, or signification of certain “choices” in FSC sequences results only from nonrandom selection. These selections at successive decision
    nodes cannot be forced by deterministic cause-and-effect
    necessity. If they were, nearly all decision-node selections
    would be the same. They would be highly ordered (OSC). And the selections cannot be random (RSC). No sophisticated program has ever been observed to be written by
    successive coin flips where heads is “1″ and tails is “0.”

    We speak loosely as though “bits” of information in computer programs represented specific integrated binary choice commitments made with intent at successive algorithmic decision nodes. The latter is true of FSC, but technically such an algorithmic process cannot possibly be measured by bits (-log2 P) except in the sense of transmission engineering. Shannon [2,3] was interested in signal space, not in particular messages. Shannon mathematics deals only with averaged probabilistic combinatorics. FSC requires a specification of the sequence of FSC choices. They cannot be averaged without loss of prescriptive information (instructions).
    Bits in a computer program measure only the number of
    binary choice opportunities. Bits do not measure or indicate
    which specific choices are made. Enumerating the specific
    choices that work is the very essence of gaining information (in the intuitive sense). When we buy a computer program, we are paying for sequences of integrated specific decision-node choice-commitments that we expect to work for us. The essence of the instruction is the enumeration of the sequence of particular choices. This necessity
    defines the very goal of genome projects. Algorithms are processes or procedures that produce a
    needed result, whether it is computation or the end-products of biochemical pathways. Such strings of decision-node selections are anything but random. And they are
    not “self-ordered” by redundant cause-and-effect necessity. Every successive nucleotide is a quaternary “switch setting.” Many nucleotide selections in the string are not critical. But those switch-settings that determine folding,
    especially, are highly “meaningful.” Functional switch-
    setting sequences are produced only by uncoerced selection pressure. There is a cybernetic aspect of life processes that is directly analogous to that of computer programming. More attention should be focused on the reality and
    mechanisms of selection at the decision-node level of biological algorithms. This is the level of covalent bonding in primary structure. Environmental selection occurs at the level of post-computational halting. The fittest already-computed phenotype is selected.
    We can hypothesize that metabolism “just happened,” independent of directions, in a prebiotic environment billions of years ago. But we can hypothesize anything. The
    question is whether such hypotheses are plausible. Plausibility is often eliminated when probabilities exceed the “universal probability bound” [132]. The stochastic “self-
    organization” of even the simplest biochemical pathways is statistically prohibitive by hundreds of orders of magnitude. Without algorithmic programming to constrain (more properly “control”) options, the number of possible paths in sequence space for each needed biopolymer is enormous. 10^15 molecules are often present in one test tube library of stochastic ensembles. But when multiple biopolymers must all converge at the same place at the
    same time to collectively interact in a controlled biochemically cooperative manner, faith in “self-organization” becomes “blind belief.” No empirical data or rational scientific basis exists for such a metaphysical leap. Certainly no prediction of biological self-organization has been realized apart from SELEX-like bioengineering. SELEX is a
    selection/amplification methodology used in the engineering of new ribozymes [133-135]. Such investigator interference hardly qualifies as “self-organization.” All of the impressive selection-amplification-derived ribozymes
    that have been engineered in the last fifteen years have
    been exercises in artificial selection, not natural selection
    http://74.125.95.132/search?q=.....#038;gl=us

    So Nak, Though it is not cold hard number/fact for precisely “how much more” functional information is present in the Mycoplamal, It is a cold hard fact that more functional/algorythmic information does indeed reside in the Mycoplasmal, Thus it is not an opinion. But of course you knew this and only seek to distract from a design inference. If you actually had any scientific integrity in you, you would seek to clarify exactly how much more functional information is present in life than in computers instead of trying to find a way to deny what is plainly obvious to everyone. Everyone that is save for dogmatic materialists such as yourself who apparently could care less about the truth.

  223. Dave Wisker

    I was impressed by your candid admission that you are not at peace on the abortion issue.

    From a totally non-religious perspective, here are some links you might want to check out.

    Articles by Libertarians for Life.
    Libertarians for Life was founded by an atheist, Doris Gordon, in 1976. The arguments against abortion on this Website are secular, philosophical arguments which do not in any way appeal to religion.

    Was I Ever a Fetus? by Professor Eric Olson.
    Professor Olson is a non-believer, yet he marshalls powerful arguments to utterly discredit the standard view among philosophers, that my life as a person began when I first became sentient (able to feel pleasure or pain), about six months after conception.

    Femninists for Life.
    “Sweeter even than to have had the joy of caring for children of my own has it been for me to help bring about a better state of things for mothers generally, so that their unborn little ones could not be willed away from them.” – Susan B. Anthony, pioneer of the American suffragette movement and an ardent pro-lifer, who once described abortion as “child murder.”

    It may come as a shock to realise that the early feminists, some of whose names are very familiar to you, and others whom you have yet to meet, were overwhelmingly pro-life. This Web site has been created to offer pregnant women a genuine choice.

  224. Mr. Nakashima,

    According to this link, the UK Met Office uses a million lines of code in its model for making weather forecasts. The Met Office’s one-day weather forecasts are right six days out of seven, and today’s four-day forecasts are as accurate as one-day forecasts were 20 years ago.

    Hmm. They’ve still got a way to go before they catch up to the complexity of DNA coding, I’d say.

  225. #221 tgpeeler

    So this is what we’ve come to. If there are “conceivable” processes, then that’s good enough.

    I suggest you read all the comments leading up to my comment. In this context we were talking about what can be conceived not what the evidence suggests.

  226. vjtorley,

    Many thanks for the links.

  227. 227

    #225

    “In this context we were talking about what can be conceived not what the evidence suggests”

    …boing…boing…

    (sorry, couldn’t resist)

  228. bornagain77 @ 189

    Seversky, only in your fertile imagination is finding virtually 100% poly-functional DNA of no concern to materialists. Furthermore your post hoc excuses for evolutionists never really predicting Junk DNA falls on deaf ears considering I have over the years debated several evolutionists about Junk DNA with them consistently maintaining it was Junk,,,even after the ENCODE findings!

    I don’t see “poly-functional DNA” as a problem for materialism. Why don’t you tell us why you do?

  229. #227 LOL

  230. Seversky states:

    “I don’t see “poly-functional DNA” as a problem for materialism. Why don’t you tell us why you do?”

    My first thought is that you, as a dogmatic materialist, don’t/wouldn’t see anything as a problem for evolution even if you witnessed, first hand, almighty God creating a new species/kind from His primary/highest transcendent realm (His heavenly kingdom) right in front of your eyes.

    The primary problem that poly-functional complexity presents for neo-Darwinism is this:

    To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained to random mutations by poly-functionality, I will use a puzzle:

    If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.

    S A T O R
    A R E P O
    T E N E T
    O P E R A
    R O T A S

    Which is translated ;
    THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

    This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation.

    This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations.

    The puzzle I listed is only poly-functional to 4 elements/25 letters of interdependent complexity, the minimum genome is poly-constrained to approximately 500 elements (genes) at minimum approximation of polyfunctionality. For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order!

  231. 231

    Mark Frank,

    I read your comments. I cannot figure out on what grounds we should ignore what the evidence is telling us in favor of what can be imagined (regardless of what the evidence is telling us).

    Quite honestly, when you made the comment in #215 I was wondering “really…what are they?”

    Since, as you suggest, we all agree that random processes cannot build molecular protein machines (and I assume we also agree that those same processes cannot integrate them once they are built) then what exactly is the non-random process at work in their rise and integration?

  232. tgpeeler @ 206

    Seversky @171

    “This is where I have a problem with a certain form of belief when it holds we are “aimless, pointless, amoral, ultimately worthless”

    Says who?”

    Um, naturalism/materialism and thus anyone who is a proponent of those “isms.” I wasn’t aware that I was being controversial here.

    No, not us, I’m afraid. We have no need of the opinion of some deity about what is our aim or purpose or our worth. And we can – and have – worked out morality for ourselves.

    Aside from the fact that his reasoning skills are barely detectable, he does grasp the point that if one is a naturalist/materialist (both demonstrably false, I’d love to have that out with you) then there is no point and if there is no point, why then, there is no point.

    If you think you can demonstrate that naturalism/materialism are false then, by all means, have at it.

    As for Dawkins’ argument, it look perfectly rational to me, although I prefer the the twist put on it by the character of Ranger Marcus Cole in Babylon 5:

    “You know, I used to think it was awful that life was so unfair. Then I thought, wouldn’t it be much worse if life were fair, and all the terrible things that happen to us come because we actually deserve them? So, now I take great comfort in the general hostility and unfairness of the universe.”

    I will grant you this: J Michael Straczynski is a better dialogue writer and story-teller than Richard Dawkins.

    This sounds like you are pissed off at God for some reason and therefore have decided to stamp your foot in anger and deny Him.

    I’m no more pissed of with God than I am with the Evil Emperor from Star Wars or Sauron from Lord of the Rings. You don’t get pissed off with mythical characters.

    All I get pissed off with is people who think their pet mythical character somehow makes them more special than everyone else.

    In a 14 billion year old (give or take) universe of which you will occupy for 70 years, plus or minus, you matter?? I matter?? Ha. The fact of it is, IF there is no God then there is no point and there is no value, nothing of intrinsic worth. NOTHING. There is no morality. There is no meaning to anything. In the blink of a cosmic eye we appear and disappear (in your alleged universe) and that’s it. No accounting, no judgment, no owning up, nothing but oblivion.

    Quite right, that’s pretty much how I see it. It’s a bleak, terrifying and hopeless prospect, isn’t it? What Christianity has to offer is a lot more comforting and hopeful.

    Ever think that maybe that is why such beliefs exist? Ever think that maybe when faced with such a daunting choice many people prefer to hide in a comforting fantasy rather than face harsh reality?

    But then why should we think that the Universe was set up just to suit us?

    “I am quite prepared to believe in the existence of such a being if you can provide evidence for it or if He/She/It is prepared to step forward and do the same.”

    What would you consider evidence? That’s a serious question. I thought I had a clue but bornagain77 has swamped everyone with evidence, with able assistance from others, and you and Nak and others just will not get it.

    As I see it, evidence is data which can be fitted into the framework of an explanation and thus becomes support for the explanation.

    For example, imagine police being called to the scene of a shooting. They find the front door open with a broken lock. Inside, they find a body on the floor with one bullet-hole in it, a spent cartridge case on the floor and a wall-safe open and empty. Those are all items of data. When the detective forms an explanation based on that data, such as that a robber armed with an semi-automatic pistol broke in, forced the owner to open the safe, took the contents and then shot the owner dead, that data becomes evidence for that explanation.

    BA77 has bombarded this thread with mined quotes, yes, but when others have taken the time to look at the papers he is citing they do not always say what he is claiming they say. They also include pieces from sources such as The Journal of Creation, publicity pieces from Creation Ministries International and YouTube videos. As evidence goes, when you look closely at it it’s a pretty mixed bag, to put it mildly.

    In other words, if there is a God then there can also be a Word of God. If you will read it and ARGUE with my argument I will prove to you that God exists with an exercise in pure reason that will make a prediction that has been empirically confirmed in the last few decades of science.

    Go ahead.

    Are you sh… kidding me??? The only reason atheists didn’t kill more in the past was because they didn’t have nukes, CBUs, and automatic weapons??? That’s good. No really, it is genuinely funny. I’m LMAO as I type. And your point would be… what??

    My point would be the one you apparently missed completely. Maybe I didn’t write it clearly enough.

    What I was trying to say was that the only reason believers hadn’t killed many more over the past centuries was because they lacked modern weapons technology and the number of potential targets we have today.

    Your worldview doesn’t allow for good and evil but yet you make reference to those things. That’s called a self-contradiction where I come from. You can’t have it both ways. That’s a rule of logic called the law of non-contradiction. There is either evil or there isn’t.

    Evil being what exactly? What is its ontological status?

    Is it like beauty? Does beauty exist somewhere out there or is it, as the old saying goes, in the eye of the beholder?

    In yet other words, are you thinking of evil as some kind of objective entity out there like an evil spirit or is it rather the judgement we make about the acts of others that exists nowhere but in our minds?

    I’ll go the extra mile here. Tell me what your basic philosophical assumptions are (I’ll give you mine in a minute) and we can figure out what is the correct way to view things.

    My assumptions are as follows:

    1. Reason is the ultimate authority in matters of truth. (To argue against that statement is to use reason to deny the efficacy of reason and therefore irrational.)

    Not quite. Reason is a tool like a computer, a set of rules for manipulating data. But, like a computer, it depends on good data to produce good results or it’s a case of garbage in/garbage out. So, reason, yes, but also good, reliable, replicable observations to work with as well. As Sherlock Holmes warned: “It is a capital mistake to theorize before one has data. Insensibly one begins to twist facts to suit theories, instead of theories to suit facts.”

    2. There is a way that the universe is. There is a way that “things are.

    Okay, yes, there is an objective reality out there of which we have a limited perception.

    3. Propositional statements (truth claims) that correspond to the way that things are, are true. Those that do not, are false. This is the definition of truth. You may recognize it as the correspondence theory of truth but it is the definition of truth.

    I can go along with that.

    4. Since certain abstract things are indisputably real, such as the laws of physics, economics, and logic, mathematics, and information, then I am justified to think, a priori, that it is possible for other abstract things to exist – that is, minds and God.

    This is more problematic since it depends on what you mean by “real” and “exist”.

    To go back to a previous example, a flower like a red rose could be said to have objective existence because it is there, we assume, whether or not we are looking at it or thinking about it. But what of its red color? We now understand that we see it as red because the petals reflect only a very narrow band of visible light frequencies which are represented in our minds as the color red. Does the red color have objective or only subjective existence? The same with beauty, can that be said to exist anywhere outside our minds?

    I am coming to the view, based on arguments by Australian philosopher of science John Wilkins, that information exists only in our minds although that is very much a minority opinion of which mine counts for little.

    For the rest, I am content to go along with it for the present, simply observing that if the omniscient God of Christianity actually exists then He already knows our innermost thoughts and feelings most probably even better than we do, so attempting to flatter or appease Him would seem to be a pointless exercise.

  233. Seversky:

    “simply observing that if the omniscient God of Christianity actually exists then He already knows our innermost thoughts and feelings most probably even better than we do, so attempting to flatter or appease Him would seem to be a pointless exercise.”

    It is a pointless exercise and nothing we could ever offer God would ever “earn” us escape from the curse of death that we are under. That is why God had to offer us the gift of eternal life freely through Christ.

    If you don’t mind a further opinion, the atheists position seems to be no amount of evidence is enough to warrant belief in God, whereas God’s position seems to be, believe in me and will provide you with more than enough evidence.

  234. —-seversky: “We have no need of the opinion of some deity about what is our aim or purpose or our worth. And we can – and have – worked out morality for ourselves.”

    Yes, indeed. The atheist life ethic may be summed up as follows: When we want them, babies may live; when we don’t want them, they must die. Further, because humans have no inherent dignity, their official worth shall be calculated in terms of their potential to provide a return on the money invested by the state. Thus, those between the ages of 0 – 15, and those over 40, are worth far less than those between the ages of 15 and 40.

  235. #231

    To recap. The Kalinsky article was comparing how likely it is that intelligent or mindless processes produced functional proteins.

    My main point was that there is an asymmetry in the comparison. In the case of mindless processes he (I guess it is a he) tried to assess the likelihood of mindless processes in general to produce functional proteins i.e. given an unspecified mindless process what is the probability it would produce a functional protein. He came up with a very low answer.

    In the case of intelligent processes he assumed the best possible case – a mind that was capable and wanted to produce functional proteins. Not surprisingly, the probability of producing functional proteins given this assumption is 1.

    There are two ways to correct this asymmetry – neither very satisfactory. Either consider unspecified intelligent processes and try to produce some reasonable figure for the probability of such a process producing functional proteins (this would mean taking into account all those intelligent processes where the mind was of limited ability or motivation). Or consider the very best assumption for a natural process. The second case is unlikely to produce a probability of 1 but it can do a lot better than keep on throwing amino acids together at random.

    Having said that – both methods of comparison are meaningless. You can only really do a likelihood comparison if you have two well defined, competing hypotheses which you have independent reasons for supposing might be true. All this thrashing about with probabilities based on really loose concepts like “natural process” and “unspecified mind” proves nothing.

    To come back to your question. Other conceivable processes for generating proteins include natural selection and an undiscovered chemical constraint that means amino acids are far more likely to combine in an order that creates a folding protein.

    Of course we have evidence for the first. The second is a fantasy – but no more so than a designer who happened to have the power and motivation to make life from scratch 4 billion years ago.

  236. Mr BA^77,

    So Nak, Though it is not cold hard number/fact for precisely “how much more” functional information is present in the Mycoplamal, It is a cold hard fact that more functional/algorythmic information does indeed reside in the Mycoplasmal, Thus it is not an opinion.

    Thank you for expressing yourself in your own words and with a solid point of view. I really appreciate it.

    I agree that it is not necessary to come down to a precise number (like 6.7 megahilberts) to create a comparison. We estimate all the time, but we still have a scale or unit of measure that we are using. If someone asked you “Which is bigger?” you’d probably use the Mark I eyeball to estimate length or area or volume.

    So I agree with you that Abel and Trevors are supplying an estimate, somewhere between opinion and fact.

    This does lead to the next question, against what scale was the estimate made? M. genitalium has 520 genes and 600,000 base pairs (approx.). As a parasite that lives in the genitals of mammals, it doesn’t do much in terms of function except survive. It depends on the host to give it a warm safe environment full of predigested food, and to pass it on through sex to another host. (For some reason, this is technical brilliance, while the malaria parasite does a lot more to hold onto its niche, and people complain that it hasn’t evolved to write sonnets. Go figure.)

    So where would you like to take the comparison? There are gross measures, such as lines of code vs base pairs. If we compare the undoubtedly compressed and optimized base pairs of M. gen to the tar.gz of a system with free download like ARPS or MM5, the models are much bigger. If we look at the number of outputs, M. gen creates 470 proteins, while the model produces thousands of data points. Of course, the genes that create those proteins are connected together in a complex regulatory system, but the models also have thousands of internal functional units in the form of subroutines and functions, connected together in a complex way.

    If we look at the expected lifetime of a single M. gen, I’m not sure what it actually is, but bacteria don’t live very long as a rule. Also, about 50% of the results of a bacteria surviving to divide will themselves die before dividing in a steady state infection (which is the best the infection can hope for). I’ll guess that M. gen bacteria (the phenotype) live for a day or two. If we call the forecast the phenotype of the model (a big if, but this is just a place to start the discussion after all), then they also last for a day or two before being beaten by another forcast. The M. gen will suffer point mutations in the genome every thousand replications (very approx.), so there are bugs in the bugs, but there are bugs in the models as well.

    Those are most of the measures I can think of to try to compare M. gen and a weather forecast system. I’ve tried to be fair and balanced, striving for the standard set by Fox News. All estimates are open to refinement and debate, but I hope you can see that on this basis, human programming about atmospheric chemistry is approximately equal to M. genitalium’s programming of organic biochemistry in “technical brilliance”.

    (No, that is not an opinion or a fact, it is an estimate! ;) )

  237. Nak, the technical brilliance of the Mycoplasmal, which has suffered much Genetic Entropy I might add, comes from the extreme functionality generated by the information inherent in its genome, as Abel and Trevors clearly pointed out,

    No matter how
    many “bits” of possible combinations it has, there is no
    reason to call it “information” if it doesn’t at least have the
    potential of producing something useful. What kind of information produces function? In computer science, we call it a “program.” Another name for computer software
    is an “algorithm.” No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms.

    The information in mycoplasmal is bursting at the seams with functionality, dynamically and robustly interacting with its environment, The weather forecasting computer (with far more lines of code”, outputs to a single 2 dimensional screen! Even at first approximation it is clear that the programming of the computer program is vastly outclassed in terms of quality of information,,, I suggest that a new measure of information that produces 3-Dimensional functionality may help clarify the issue,,,Perhaps we can call them hilberts!

  238. Mr BA^77,

    Perhaps you missed the part where M. gen is a parasite that was discovered living in the gonads of human males. Rather than bursting at the seams with functionality (which definitely is an opinion!), it lives a quiet life, as quiet as possible in fact, doing just enough to get by. It does nothing it doesn’t have to do. M. gen is a welfare queen. It is of interest exactly because it is small and does nothing, yet survives.

    It might also help if you learned something about weather forecasting systems. They take in thousands of data points on temperature, pressure, humidity, cloud cover and wind velocity from three dimensions and over time in the atmoshpere, and in the ocean use temperature, salinity, currents in three dimensions of the water column. On the surface the inputs include soil and vegetation types over a three dimansional height field.

    The output of the model is not what the weatherman is standing in front of. That is just one slice of the data. The forecast has to include all of the input data variables over the same dimensions, and resolution in time and space, because that is how the forecast is rolled forward for several days.

    I agree with you that Abel and Trevors are focusing on phenotypic measures when estimating technical brilliance. However, I don’t think they (or you) have shown as good a basis for an estimate of ‘far surpassing’ as I have for ‘about equal’.

  239. Nak, when the weather computer replicates itself down to every nut and bolt I’ll be impressed with the functionality of its information content, until then, as usual you are blatantly ignoring what is apparently obvious to everyone else save for dogmatic materialists such as yourself. You know Nak for once I would love to see you be forthright with the evidence instead of doing your damnedest to be deceptive.

  240. 240

    Seversky:

    “We have no need of the opinion of some deity about what is our aim or purpose or our worth. And we can – and have – worked out morality for ourselves.”

    Were you born tabula rasa with respect to morals?

  241. Mark Frank

    Sorry to intrude again, but after reading your post (#235) I thought I would make one last effort to get my point across. I should admit at the outset that biochemistry was not one of my majors at university, so if I make a complete fool of myself in the illustration that follows because of my abysmal ignorance of protein chemistry, so be it. I really don’t care; egg on my face doesn’t bother me. I should add that I have not read Dr. Meyer’s Signature in the Cell yet; I’m just commenting on Kalinsky’s paper.

    It is an axiom of Darwinian theory that nature does not make leaps. According to Kalinsky (p. 10), “Axe has estimated that the frequency of occurrence of stable, folded functional protein domains, a structurally independent component of a protein, is somewhere between 10^(-64) to 10^(-77).” There are 20 different amino acids, so I’ll use the letters a to t to represent them.

    The point I want to get across in my illustration is that if the islands of amino-acid chain stability are sufficently few and far between, selection won’t work, as hopping from one island to the next will require huge leaps, and nature does not make leaps.

    For instance, let’s say you’re trying to build a stable 150-amino-acid chain by some sort of selection process, one step at a time.

    Let’s imagine that so far, you’ve been incredibly lucky: you have somehow managed to generate a 100-amino-acid chain which is stable:
    hgssifgsqpgteicaqegkaecedjdpeobhrggihfgosdftpcfpogieagphtgjtrffaqpcfanikablctchldbkddqnnonhdsrsligdg

    You’re trying to build your way up to a stable 101-amino-acid chain. Unfortunately, the “nearest” stable one looks like this.
    dprgtjscallmgqlqhenfsipdlnrlisekcrfdjncispnlmfabqipfptapoekajbtplkminphftggonffdsqtmmrerrlfmgilbitdqa

    The 101-amino-acid chain looks nothing like your 100-amino-acid chain, so obviously, just adding one extra amino acid won’t work: all of the 101-amino-acid chains formed in this way are unstable and collapse immediately. Your 100-amino-acid chain can undergo successive random changes in its amino acids over time, but remember it has to remain stable while doing so. And when are you going to add the extra amino acid, to make the chain 101 units long? If you add it at the wrong time, the chain will collapse immediately. Obviously, it’s going to take a mighty improbable sequence of events for your 100-amino-acid chain to “mutate” into the stable 101-amino-acid chain that you want. Even if you have a large number of 100-amino-acid chains like the one above, and a lot of time for amino acid “mutations” and “additions,” the vast majority of changes will be catastrophic. It will take you a very long time indeed to get to the 101-amino-acid chain.

    Now consider the odds of being able to build a 150-amino-acid chain, under circumstances like these. Want to give up?

    Now, for all we know there might be some magic pathway that we haven’t discovered yet, that’ll take us to a 150-amino-acid chain, one step at a time. Or there might be a magic sequence of breaks and mutations, followed by additions. For instance, there might be some law of nature which says that when you get to an 87-amino-acid chain like this…

    ctjxsbicozequmbocrjpgfcorjitufqcp fiweynbmfmgcfiqhnmnkrcslkjyymxagzlumhrnrkvvcpiiukkptwq

    … the chain has to split up into one 33-unit chain and one 54-unit chain, like this…

    ctjxsbicozequmbocrjpgfcorjitufqcp and
    fiweynbmfmgcfiqhnmnkrcslkjyymxagzlumhrnrkvvcpiiukkptwq

    … and then the u in the 13th position on the 33-unit chain has to be substituted with an “m,” while the “f” in the 9th position on the 54-unit chain has to be replaced by an “l”, and then the two chains have to meet up and be joined by a “d,” in order to generate a stable 88-unit chain. That would not be too improbable, given the existence of such a law.

    But regardless of whether there is a magic pathway to 150, or a sequence of magic breaks and re-makes that takes us there, it looks like we’ll have to postulate the existence of some very long, very specific, and very ad hoc natural laws to explain how it is possible to build a 150-amino-acid chain one step at a time, in a space of possible chains where all but a very tiny proportion will collapse immediately.

    Now you can go ahead and postulate that nature just happens to have zillions (and yes, you would need zillions) of these quirky little laws which (as it turns out) favor the emergence of life, in order to account for the panoply of biomolecules, organelles and cells that exist in the natural world today. But if you do that, then what you have is a Nature that functions as if She were Herself intelligent – in other words, pantheism. Anything that’s packed with specified information like that (enabling it to make a living being) might as well be called intelligent, if you consider it to be uncreated (as skeptics do), because it is capable of doing the kinds of complicated jobs that an intelligent being can do. But calling Nature Herself intelligent is one form of ID – which means you’re in our camp.

    Now, I understand that you might not like the notion of an invisible, transcendent Designer. It may sound too vague to suit your metaphysical tastes. But I would put it to you that your alternative – a Nature packed with zillions of highly specific rules enabling it to function as if She were intelligent – is even messier. May I be so bold as to suggest that people who live in metaphysical glass houses should not throw stones?

  242. I love when people defend, or even extol, the randomness of the universe as if they weren’t a part of it, making this judgment, instead, as a rational, independent agent. The irony is almost delightful. But then I observe the arrogance of said individuals and I realize, “Oh…they’re actually serious”

  243. #241 vj

    I understand your point. I am afraid I don’t have the biochemical knowledge to respond. I would not be impressed with a theory of evolution that required zillions of ad hoc laws. I believe that experts in this field can trace possible paths at the level of DNA mutation for some major evolutionary developments without requiring ad hoc laws. These may not be the actual paths of mutation but they are plausible hypotheses.

    However, that requires expertise I don’t have. My point is – if we don’t know the natural process we should not therefore conclude any ad hoc solution including an invisible, transcendent Designer. It is easy to dream up sky hooks – be they natural or intelligent.

  244. vjtorley,

    Before accepting Kalinsky’s use of Axe’s calculations, I suggest reading Art Hunt’s very accessible essay on Axe’s paper here:

    http://aghunt.wordpress.com/20...../#more-611

  245. vjtorley, before you swallow any of Wisker’s swamp land you may want to take a closer look at how they obtain a low end probability:

    The 1 in 10^12 estimate for functional proteins (Szostak), though still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario, was arrived at by an in-vitro (out of living organism) binding of ANY random proteins to the “universal” ATP energy molecule. Yet, Axe’s work was on protein of a 150 amino acid sequence, and the 1 in 10^77 odds he found involved looking for a specific type of function. Whereas Szostak looked for any function whatsoever, biological or non-biological. So Szostak’s number of 1 in 10^12 is severely misleading as to finding a protein that will perform a specific function. Szostak also seems to have allowed “slop” in his experiment with “tethered” mRNA’s. Axe’s work also tends to agree with other reputable research that has been conducted in this area (Sauer; MIT; 1 in 10^64). Clearly Axe’s number of 1 in 10^77, for finding a specific type of functional protein within sequence space, carries much more weight of integrity when balanced against Szotak’s questionable work for finding just 1 in 10^12 for any functional protein whatsoever.

    Yet even if Szostak’s 1 in 10^12 (trillion) number were true for biologically functional proteins, it would still be so rare as to present insurmountable mathematical difficulties for any evolutionary scenario. There simply is no vast reservoir of trillions upon trillions of “junk proteins” to be found in nature (proteins don’t even form “naturally”) waiting to accidentally form into a “simple” self replicating molecule. Nor is there any vast reservoir of junk proteins to be found in life, waiting for natural selection to sift through them to find any novel combinations that may be useful.

    In fact, the Ribosome, which makes the myriad of different yet specific types of proteins found in life, is found to be severely intolerant to any “random mutations” occurring to proteins.

    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/re.....134529.htm

    of course Hunt offers wishful speculation about how a pond-scum “may” generate proteins, but when bacteria are put the test to see what has happened over time we find:

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    Thus Hunt is in dreamland with his speculations about how a functional protein possibly could have arisen when compared to what we actually find in reality:

    If we look even closer at ancient bacteria we don’t find evolution but the exact opposite,,, genetic entropy:

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    So Vjtorley, don’t buy into Hunt and Wisker’s swamp land, or more appropriately swamp water in this case, It is totally worthless.

  246. born, if you are going to try to criticize Art’s assessment of the significance of Axe’s work, you would do better to actually address the points Art makes instead of throwing up a handful of random, irrelevant stuff in the vain hope of blinding anybody actually paying attention.

  247. vjtorley,

    Here are a couple of examples of worthless swamp water:

    Axe’s experimental design forced him to examine a variant of the enzyme that had very low activity–far lower than one found in wild-type individuals. In other words, the sequence space Axe was exploring to get his numbers was already significantly restricted from the start.

    Secondly, Art reminds us that the actual potential sequence space for similar activity should not be restricted to the sequence of the one enzyme Axe used. For example, there is a family of enzymes known as the metallo-beta-lactamases that have similar activity but are structurally unrelated to the TEM-1 enzyme. If selection is for function (i.e, an enzyme’s catalytic activity) rather than pure sequence (and if one gives the subject a moment’s thought it should be obvious that this is so), then the numbers Axe derived are shown to be even less applicable in general than some of our ID friends seem to think.

  248. You know Dave, I’ve been lied to so much I really don’t care what evolutionists say anymore it all turns out to be deception when I dig into it (which has been hundreds of times by now,,,, so just cut to the chase Dave,,, show me the money and so me just one experiment where a sub-species bacteria has gained functionality over its parent-species. Or better show some real scientific integrity and falsify Abel’s Null Hypothesis for information generation,,,Shoot you would probably become legendary within scientific circles if you could do that!

    “Physics is the only real science. The rest are just stamp collecting.”

    – Ernest Rutherford

  249. I am sure Doug Axe would love to hear from Art.

    Has Art sent his essay to him?

    If not what is Art afraid of?

  250. Hey Dave Wisker, Michael Behe has, “Coincidentally”, posted a article on protein evolution on ENV that you may be interested in:

    Not So Many Pathways: Response to Carl Zimmer and Joseph Thornton
    http://www.evolutionnews.org/2......html#more

  251. StephenB @ 234

    Yes, indeed. The atheist life ethic may be summed up as follows: When we want them, babies may live; when we don’t want them, they must die.

    For True Believers this life is just a transition stage leading the afterlife which is the ultimate destination. Losing this life is not such a big deal if you believe you are moving on to something much brighter and better afterwards.

    Whereas for atheists the “life ethic” is based on the assumption that this life is all we have which makes it uniquely precious.

    Besides, Christians are in no position to lecture the rest of us about ethics. I am hardly the first to note that while the Ten Commandments include specific proscriptions against taking the Lord’s name in vain or coveting your neighbor’s ass, there is nothing about child abuse, rape or slavery, all of which today we consider to be far more serious offenses than blasphemy or envy.

    Further, because humans have no inherent dignity, their official worth shall be calculated in terms of their potential to provide a return on the money invested by the state. Thus, those between the ages of 0 – 15, and those over 40, are worth far less than those between the ages of 15 and 40.

    You are a doctor with two patients: one is a 40 year-old father of two, the other a widower of 75. Both are suffering from the same life-threatening illness but you only have the resources to treat one. Who do you choose? What would be the good Christian response to that situation?

    As a society, there are hard choices we should be facing. What we prefer to do, as far as possible, is leave it to the doctors to make the hard decisions for us and hope they do it so discreetly that the rest of us can pretend nothing happened.

  252. Clive Hayden @ 240

    Were you born tabula rasa with respect to morals?

    I think we all are.

  253. 253

    Seversky,

    By that argument then the millions who perished in the Flood were also His direct creations; also, according to you and bornagain77, entitled to assume that, as such, they would be looked upon by Him with favor.

    Yet those millions were wiped out. And they were not granted a merciful end. A being of God’s supposed unlimited power could have consigned them to oblivion in an instant. It would have been as if they had never existed. Instead, they were condemned to a slow and terrifying death by drowning.

    And for what? For being flawed? For not turning out as their Creator had intended and expected? Whose fault is that? Certainly not theirs. They had no choice in being made fallible the way they were.

    Are you joking? Seriously, are you kidding? Where do you see that fallen man should sin with no repercussions in scripture? If you’re using scripture as authoritative in the events, then use it also for your authority in the judgments you’re making, otherwise, I have no reason to listen to your own personal fancies. Unless you want to entertain an objective morality, you cannot even get started on making judgments that you expect I should agree with. Come to me with anything authoritative for your standards of judgment other than yourself and your private whims, then we’ll talk.

    Onlookers: This is the difficulty of the atheist, something is objectively wrong, so they imply, while denying the source of objectivity. It gets worse actually when they try to make a moral argument against God, from whom all morality comes; the only weapon they have against God is one they must borrow from Him.

    But the text does not say he would die spiritually, only that he would die. Are we to assume that God cannot say clearly what He means, that He must hedge His bets by expressing Himself in ambiguous metaphor?

    I find it so interesting that you’re a literalist, while you deny that scripture should be taken literally. OF COURSE there are metaphors and figurative phrases, and you being a literalist should literally see what they are and where they are. It’s not all or nothing in the interpretation of scripture or even in plain language, anymore than me saying that you should “see a metaphor” means that you should get the reason employed to discern a metaphor confused with what literally appears before your eyes when you “see” something. Come on Seversky, really.

    I want to know what your real problem is. It can’t be moral, for they don’t really exist outside of you according to you. What is it, really? What causes the reaction that you have?

  254. William Lane Craig – A Good God And The Problem Of Evil
    http://www.youtube.com/watch?v=TR3xtiHf-K4

    this may be of interest

    If God is all-knowing and all-powerful, how was evil able to enter the world?

    On that age-old question, the answer is related to the concept of free will. And this is what the eminent writer CS Lewis has to say:

    “God created things which had free will. That means creatures which can go either wrong or right. Some people think they can imagine a creature which was free but had no possibility of going wrong; I cannot. If a thing is free to be good it is also free to be bad. And free will is what has made evil possible. Why, then, did God give them free will? Because free will though it makes evil possible, is also the only thing that makes possible any love or goodness or joy worth having. A world of automata — of creatures that worked like machines — would hardly be worth creating. The happiness which God designs for His higher creatures is the happiness of being freely, voluntarily united to Him and to each other in an ecstasy of love and delight compared with which the most rapturous love between a man and a woman on this earth is mere milk and water. And for that they must be free.

    “Of course God knew what would happen if they used their freedom the wrong way: apparently He thought it worth the risk. Perhaps we feel inclined to disagree with Him. But there is a difficulty about disagreeing with God. He is the source from which all your reasoning power comes: you could not be right and He wrong any more than a stream can rise higher than its own source. When you are arguing against Him you are arguing against the very power that makes you able to argue at all: it is like cutting off the branch you are sitting on. If God thinks this state of war in the universe a price worth paying for free will — that is, for making a live world in which creatures can do real good or harm and something of real importance can happen, instead of a toy world which only moves when He pulls the strings — then we may take it is worth paying.

    “When we have understood about free will, we shall see how silly it is to ask, as somebody once asked me: ‘Why did God make a creature of such rotten stuff that it went wrong?’ The better stuff a creature is made of — the cleverer and stronger and freer it is — then the better it will be if it goes right, but also the worse it will be if it goes wrong. A cow cannot be very good or very bad; a dog can be both better and worse; a child better and worse still; an ordinary man, still more so; a man of genius, still more so; a superhuman spirit best — or worst — of all.” –

    C.S. Lewis, Mere Christianity

    test strong
    end test

  255. —-seversky: “For True Believers this life is just a transition stage leading the afterlife which is the ultimate destination. Losing this life is not such a big deal if you believe you are moving on to something much brighter and better afterwards.”

    The connection between this life and the next is more direct than you may appreciate. How you behave here determines in large measure how you will fare there. Heaven and hell start here, they just come to completion in the next world. We take our habits, hates, loves, and actions with us. The man who hates God and neighbor for eternity began by hating them in time/space/history, intensified that attitude through the years, and persisted all the way to the end.

    Sew and act, reap a habit

    Sew a habit, reap a character

    Sew a character, reap a destiny.

    —-“Whereas for atheists the “life ethic” is based on the assumption that this life is all we have which makes it uniquely precious.”

    Yes, and that isolated ethic causes the atheist to discount the preciousness of EVERYONE ELSE’S LIFE EXCEPT HIS OWN, except for those who may be of some use to him. Thus, babies, old people, or anyone else who gets in the way must die.

    —-“Besides, Christians are in no position to lecture the rest of us about ethics. I am hardly the first to note that while the Ten Commandments include specific proscriptions against taking the Lord’s name in vain or coveting your neighbor’s ass, there is nothing about child abuse, rape or slavery, all of which today we consider to be far more serious offenses than blasphemy or envy.”

    That is, of course, absolutely false. Christianity declares that all life is sacred from the womb to the grave. The fifth commandment forbids all wanton violence against neighbor, both physical and, as it turns out, verbal. Atheism forbids nothing. On the contrary, as Dostoevsky noted, without God, all things are permissible.

    —-“You are a doctor with two patients: one is a 40 year-old father of two, the other a widower of 75. Both are suffering from the same life-threatening illness but you only have the resources to treat one. Who do you choose? What would be the good Christian response to that situation?”

    For the Christian, both are of equal value, so both receive the same consideration. So, the doctor, and the health care system, takes them as they come in the order presented. For the atheist, the least fit must go—the sooner the better.

    —-“As a society, there are hard choices we should be facing. What we prefer to do, as far as possible, is leave it to the doctors to make the hard decisions for us and hope they do it so discreetly that the rest of us can pretend nothing happened.”

    One faces hard choices only on condition that a real moral ethic exists. If there is no objective standard for morality to provide the dilemma, then there are no hard choices—only pragmatic choices. Hence, atheism, and the attendant pragmatism/utilitarianism are easy: Simply conduct a cost benefit analysis and kill those who can provide no return on the money invested by the state. No moral dilemma there.

  256. Stephen B, I think the ethical problem about the old vs the young in regards to health care is a very interesting one. I personally think that if we want to be able to have universal health care that is of GOOD quality then we need to build ALOT more hospitals beofre we can even consider just injecting more people into an already backed up system. THis is why the universal care is TOTALLY unthical as it stands. All people are not to be treated equally. I understand what you mean SteveB in regards to not discriminating about age- but in reality people who work harder to afford better health care deserve it by and large (not in every case) and people who do not take care of their health (smoking, heaving drinking and drug use, obesity etc) do not DESERVE the same place in line – or PLACES in line because who knows hoe often they will be abusing the system- that the person who takes care of their health needs because of a rare or unexpected illness. I believe in the market system- and we should work to make the market system work more efficiently and fairly. We should to work to remove the market system just because it has some weaknesses to replace it with a totally unethical system that treats ALL people equally. This is the truth. Jesus said to let the spiritually dead care for themselves- that our bodies are our temples, and that those who abuse a system for their own self gratification (money changers) need to be opposed violently, if necessary. Yes we need to take our time to help those who need and want help- but they need to be helped to help themselves- and this is what Jesus taught- that there was a necessary commitment to the narrow path necessary for one to be worthy of salvation. I say this all with peace and love.

  257. Mark Frank, Dave Wisker and bornagain77

    Thank you all very much for your links and your kind comments. With my extremely limited knowledge of biochemistry, I can’t make any constructive comments about the validity of Axe’s work. However, it appears to me evolutionary naturalists will have to use a co-option argument to explain how functional proteins evolved – on their scenario, they would have had many different functions along the way, as their amino acid chains increased in length. While this is theoretically possible, the mind boggles when imagining the sequence of transmogrifications and transmutations of function, and after reading Professor Behe’s response to Carl Zimmer and Joseph Thornton (thanks for the link, bornagain77), I’m inclined to think that this scenario is highly implausible.

    Nevertheless I will take on board Dave Wisker’s point that the calculations for the improbability of a protein evolving on a step-by-step basis are not as straightforward as they might seem, and I would like to thank him for his link to Art Hunt’s article. Clearly, there is more work to be done, and I guess it will take time before scientists can “firm up” the numbers and reduce the uncertainty involved in the estimates.

    Mark Frank, thank you once again for your comments. It has been a pleasure crossing swords, as always.

  258. Seversky

    I can see that the Flood troubles you theologically.

    Yet those millions were wiped out. And they were not granted a merciful end. A being of God’s supposed unlimited power could have consigned them to oblivion in an instant. It would have been as if they had never existed. Instead, they were condemned to a slow and terrifying death by drowning.

    I’m not going to address the problem of why God would make creatures who were going to sin; other contributors to this thread have addressed that point already.

    In what follows, I’m going to assume for argument’s sake that the Flood really occurred, and that it was a global catastrophe, sent by God, which destroyed the great bulk of humanity. I have to say that on the basis of the scientific evidence discussed at http://www.nap.edu/openbook.php?isbn=0309051916 (see pages 187-212) – and see here for an evaluation of the scientific evidence from the point of view of one Catholic apologist – the notion that the population of humanity ever fell to eight people appears untenable, so if there was a global catastrophe of the kind described in Genesis 6 to 8, it would have to have been one which wiped out most but not all humans, barring Noah and his family. The most likely candidates I’ve found for a global catastrophe in recent times are:

    (1) the Toba eruption about 71,000 years ago which wiped out all but a few thousand human beings (but although some died from a tsunami which flooded coastal areas, most died from the cold as the sun was blocked out for months – and besides, 71,000 years is a long time for a story to be handed down);

    (2) a massive comet exploding over southern Canada 12,900 years ago (see http://www.msnbc.msn.com/id/18789488/ ), which allegedly wiped out large numbers of species and 33 mammalian genera (including the mammoth), decimated human populations and triggered a global plunge in temperatures over the next 1,500 years (but this cometary impact did not trigger floods but fires, and there’s considerable doubt that it actually happened; and

    (3) a comet slamming into the Indian Ocean near Madagascar in 2,807 B.C., triggering producing a tsunami at least 600 feet high that would have killed a large proportion of humanity (see http://crowlspace.com/?p=99 for a short summary of the various reviews and see also here for a detailed and somewhat skeptical creationist response).

    (3) would sort of make sense of the Genesis account as a global catastrophe, but it remains a highly speculative hypothesis.

    As a Christian, I am bound to take the words of Christ seriously when He refers to the Flood as a real incident (Matthew 24: 37-42, Luke 17: 23-30), but He nowhere states explicitly that all human beings outside the ark were destroyed.

    In any case, we are dealing with an account which the author of Genesis probably adapted from a Babylonian source for his own theological purposes. Determining exactly what the sacred author intended to teach thereby is difficult for us, as he wrote 3,000 years ago in another language and culture. All we can say is that a catastrophe happened long ago, that it was sent by God, and that it was intended to teach humanity a terrible lesson and correct its wickedness (we don’t know what kind, but Scripture refers to violence), and that some people were specially rescued by God(a few others may also have survived by sheer dumb luck, I suppose).

    Now, it is a fact that God allows innocent people to die terrible, gruesome deaths. However, the notion that God might actually visit such a death upon innocent people – especially children – so that they ended their lives screaming in terror, is, I would agree, theologically scandalous. I don’t personally believe that God could do such a thing.

    My own solution, for what it’s worth, is that God worked what I call a negative intervention – He simply shut down their nervous systems so that they lost consciousness, and therefore died painlessly. Thjis would not have required an act of intervention on His part, as He maintains everything in existence all the time anyway. All that would have been required is for God to have stopped maintaining these innocent children’s nervous systems in His usual (non-miraculous) fashion, with the result that they fell instantly into a state of oblivion. This would be a very easy thing for a Deity to do, and no laws of nature would have been broken.

    I’m sure you’ll want to ask: “Well, in that case, why doesn’t God do this all the time, then, when innocent people are dying?” But that’s another story, and if you want the answer to that, you might want to read Dr. William Dembski’s The End of Christianity (see http://www.amazon.com/End-Chri.....0805427430 for details) for a discussion of the Fall and its consequences (I just got my copy this morning – thanks Denyse).

  259. Frost, I agree with everything that you said. In keeping with your point, I submit that if universal health care translates into government health care, it will be far worse than anything we have now. I was simply commenting on the ethical considerations that inform life/death decisions based solely on the perception that some individuals are worth more than others.

  260. vjtorley, I just remembered, or was reminded, this morning that Dr. Behe has just written a series of post that offers experimental evidence for your solid reasoning that proteins are highly constrained in their ability to evolve.

    Dollo’s law, the symmetry of time, and the edge of evolution:
    Excerpt: Just as for some general laws of physics, there is nothing inherently time-asymmetric about generic random mutation and selection. So there should be nothing particularly special about evolving back in history versus forward. The only thing that would be “special” about going back is that you can (potentially) know which way you had come, so you can see if the steps can be retraced, as Bridgham et al (2009) did. However, the huge roadblock that the authors discovered for one homologous protein converting to another by Darwinian processes did not have to be in the past — the roadblock could as easily have been in the future. If the GR-like protein had come first in history, then no MR-like protein would likely have arisen by Darwinian means. In that case, however, there would have been no question even raised by investigators about the reversibility of that evolutionary path, because the “path” would not exist — it would have been blocked at the start, in the forward direction. Questions do not arise about hypothetical pathways that would have to pass through brick walls.

    The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future, for well-understood reasons: Natural selection fits a protein to a current, not any future (nor any previous), task; thus it tends strongly to restrict other potential structures/functions. The very same considerations (“shifts in protein structure-function relations”, “epistatically interacting substitutions”, and so on) that frustrate the reacquisition of complex molecular features will tend strongly to stymie their acquisition in the first place, because no potential protein component would ever be without a prior history of selection. 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/2.....f_tim.html

  261. “Whereas for atheists the “life ethic” is based on the assumption that this life is all we have which makes it uniquely precious.”

    Or uniquely absurd. For atheists, we are victims of a cosmic lottery, and to pretend like we are grateful for this is disingenuous in the face of a destiny of oblivion.

  262. “Whereas for atheists the “life ethic” is based on the assumption that this life is all we have which makes it uniquely precious.”

    Or uniquely absurd. For atheists, we are victims of a cosmic lottery, and to pretend like we are grateful for this is disingenuous in the face of a destiny of oblivion.

  263. Seversky,
    The main problem I find with your statement:

    Whereas for atheists the “life ethic” is based on the assumption that this life is all we have which makes it uniquely precious.

    Is this:

    Isaiah 22:13 ,,,”Let us eat and drink, for tomorrow we may die.”

    Once again even in this “this life is all that we have, so it is uniquely precious” attitude, there surfaces the deep seeded problem of moral constraint that faces the atheists.

    Again it is the basic, “if it feels good do it” philosophy that is the basis of hedonism.

    Personally I can tell you this philosophy bites it big time. I lost most of my family to death very early and life and basically had the attitude that this life is all that there was so I was going to enjoy it to the fullest of my ability,,,needless to say after many years of this I had acquired many severe problems of habit that this tendency towards excess wrought. Thankfully at one of my low points in my life brought about by such living I reached out to the Lord and He “surprisingly” was there in a way that I had totally not expected. Now my life is vastly improved because of the correct moral guidance, and compass, that I receive from God. Upon reflection of all this, I know for a fact your philosophy is, at its very depths, bankrupt of any solid foundation for a young man to build his life upon. Plus the fact that now I KNOW that there is a eternal paradise awaiting after this life, makes me feel much like the merchant who had found “the pearl of great price” than anyone who may grumble about missing the so called “sinful pleasures” which in fact are nothing more than swill.

    This video may be of interest:

    In this following video Mickey Robinson reflects on the greatest lesson he learned years after his powerful Near Death Experience (NDE).

    Mickey Robinson – The Pearl Of Great Price
    http://www.youtube.com/watch?v=WfWYeKqxRfs

  264. 264

    Seversky,

    Clive Hayden @ 240

    Were you born tabula rasa with respect to morals?

    Seversky: I think we all are.

    That’s what I suspected you would think. If we’re born in an ethical vacuum, having no intrinsic ethical injunctions, then why should we choose any ethical system? And moreover, what compels us to choose between one system of ethics verses another? We cannot have an ethical duty for choosing an ethical system, for we are still in an ethical vacuum. And we have no way to compare between any ethical systems, because that would presuppose that we are recognizing a more ultimate ethical standard as our basis for comparison. What say you? If we were born tabula rasa, we would die tabula rasa.

  265. vjtorley,
    Dr. Behe is in fine form with another post, in a series, to ENV about the limits of protein evolution. This article plays right into your solid reasoning, you had developed earlier in this thread, against protein evolution with empirical:

    Severe Limits to Darwinian Evolution:
    Excerpt: The immediate, obvious implication (which he clearly wants to keep far away from) is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,, Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
    http://www.evolutionnews.org/2......html#more

  266. Mr BA^77,

    Nak, when the weather computer replicates itself down to every nut and bolt I’ll be impressed with the functionality of its information content…

    Please remember we are talking about programs, not computers. Abel and Trevors don’t need to make that qualification, why suddenly do you?

  267. Nak, Tell you what you ol Darwinian propaganda machine, Why don’t you clue me to why chemistry and physics are so well disposed for life to happen by accident in this big ol universe,,, I’m a bit tired of the old multiverse yarn so do please try to be a bit original with something that at least has a shred of believability,,, I really would appreciate a good yarn to put me to sleep tonight,,

    To clearly illustrate the stunning degree of fine-tuning we are dealing with in the universe, Dr. Ross has used the illustration of adding or subtracting a single dime’s worth of mass in the observable universe would have been enough of a change in mass density to make life impossible in this universe. This word picture he uses, with the dime, helps to demonstrate a number used to quantify that fine-tuning of mass for the universe, namely 1 part in 10^60 for mass density. Compared to the total mass of the observable universe, 1 part in 10^60 works out to about a tenth part of a dime, if not smaller.

    Where Is the Cosmic Density Fine-Tuning? – Hugh Ross
    http://www.reasons.org/where-c.....ine-tuning

    Michael Denton – We Are Stardust – Uncanny Balance Of The Elements – Fred Hoyle Atheist to Deist/Theist – video
    http://www.youtube.com/watch?v=zlV3VjunZmU

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/re.....142957.htm

    Physicists find many processes in a cell operate at the “near optimal” capacities allowed in any physical system:

    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, 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

  268. Clive Hayden @ 253

    Are you joking? Seriously, are you kidding? Where do you see that fallen man should sin with no repercussions in scripture? If you’re using scripture as authoritative in the events, then use it also for your authority in the judgments you’re making, otherwise, I have no reason to listen to your own personal fancies. Unless you want to entertain an objective morality, you cannot even get started on making judgments that you expect I should agree with. Come to me with anything authoritative for your standards of judgment other than yourself and your private whims, then we’ll talk.

    It is Christians who cite the Bible as authoritative on questions of morality, not me. I am pointing out that the text is flawed by inconsistencies which, in my view, fatally undermine any claims to inerrancy.

    To start with, do we assume that God’s decisions on questions of morality are simply made up on the spur of the moment or are they based on reason? If they are based on reason, then why plant the Tree of Knowledge of Good and Evil in the Garden and forbid Adam and Eve to eat its fruit without explaining why? Why shouldn’t they have known the difference between good and evil?

    And if we allow, for the sake of argument, that Adam and Eve had committed a cardinal sin by disobeying God then there is at least a case that they should have been punished as the sinners. But by what system of law can it possibly be considered just to punish not just the offenders but all their children a hundred, a thousand a million generations into the future. I challenge anyone here to defend that as just by any reasonable definition of the word.

    And if Adam and Eve were flawed they were made that way. A perfect being like God does not make mistakes, by definition. He must have made them fallible. And an omniscient God, one who knows our innermost thoughts and sees every sparrow fall, must – must – have known what would happen in the Garden. He must also have created the serpent and known what it was likely to do.

    If you want the warrant for your “objective morality” to be vested in the authority of a perfect God then you must abandon any notion of Biblical inerrancy. If you do, you can certainly still cherry-pick those bits of Scripture which suit your purpose but bear in mind that, in so doing, you are implying that your interpretation in these matters is superior to those of the original authors and compilers of the text. Tell us why you think you are better than they were?

    Onlookers: This is the difficulty of the atheist, something is objectively wrong, so they imply, while denying the source of objectivity. It gets worse actually when they try to make a moral argument against God, from whom all morality comes; the only weapon they have against God is one they must borrow from Him.

    Why is God’s morality any more “objective” than one of our own devising? In fact, in what way can it be said to be objective at all? We still face the Euthyphro Dilemma: either there are acts which are intrinsically good or evil, in which case there is at least the chance we can find it out for ourselves without God’s help or good and evil are only what God says they are and thus could simply be arbitrary choices, not objective in any sense at all.

  269. 269

    Seversky,

    It is Christians who cite the Bible as authoritative on questions of morality, not me. I am pointing out that the text is flawed by inconsistencies which, in my view, fatally undermine any claims to inerrancy.

    Oh now we’re discussing inerrancy? I was asking for your consistency, how you could cite the text as authoritative in the events, and what justification of authority you used in your moral judgment, if not also the text. So, what is it? What do you use as your standard?

    And what difference between good and evil are you referring to? You consider morality your own private fancy, like a preference for pancakes and not spam. Are you telling me that personal preference is either good or evil?

    But by what system of law can it possibly be considered just to punish not just the offenders but all their children a hundred, a thousand a million generations into the future. I challenge anyone here to defend that as just by any reasonable definition of the word.

    Because all of the future generations sinned too, it wasn’t just Adam. It is just to punish offenders. I find this interesting from one who doesn’t really think that an objective offense ever actually occurs. Your entire argument, indeed your whole argument depends only on an objective morality, which you reject. Again, get back with me with what you claim for your authority grounding these complaints outside of your personal preference, then we’ll have some form of reference, some standard of comparison, with which we can use to discuss the moral veracity of scripture. Otherwise, stop acting as if I should agree with you and your personal fancy of morality…Really, I want to know on what ground you would even begin to expect me to agree with your subjective morality? It would be like exhorting me, in impassioned tones, to agree with you that blue shirts are good and red shirts evil.

  270. —-seversky: “And if Adam and Eve were flawed they were made that way.”

    They were not made flawed. Rather they were created with the capacity to choose good or evil, and choosing the latter made them flawed.

    —”And if Adam and Eve were flawed they were made that way. A perfect being like God does not make mistakes, by definition.”

    This is an extension of the first error. Adam and Eve were not made flawed.

    —”He must have made them fallible.”

    The same error extended yet again. Whoever claimed that and Eve were made infallible?

    —”And an omniscient God, one who knows our innermost thoughts and sees every sparrow fall, must – must – have known what would happen in the Garden. He must also have created the serpent and known what it was likely to do.”

    Yes, so what? If free will is not allowed to play itself out, it is not free will.

  271. bornagain 77

    Thank you very much for the links to Professor Behe’s blog posts. I was impressed with the case Behe made. Getting proteins to evolve is certainly no easy matter, that’s for sure. It now looks like they are a lot more limited in their capacity to evolve than scientists had previously anticipated.

  272. Seversky (#268)

    You and I have exchanged views in previous posts about the morality of God’s making Adam and Eve in the first place, so I won’t add to that here, except to say that while it would be morally wrong to make a flawed being and then blame it for its flaws, it would not be immoral to make a fallible being and then blame it when it freely failed. The latter option, not the former, describes what God did to Adam.

    (I am taking Adam here to have been the acknowledged leader of the human race, in its original state, regardless of how many human beings there may have been at the beginning of human history.)

    Regarding the tree of the knowledge of good and evil: I should tell you that there are several different interpretations of what it meant. No-one is sure. Even among the Jewish rabbis (who might be expected to have retained an oral tradition of the meaning of the text) there is a great diversity of opinion. I refer you to Genesis and Jewish Thought by Hayim Navon, some of which can be read online at http://books.google.com/books?.....38;f=false . Please have a look at pages 125-136.

    You can read John Wesley’s commentary on Genesis 3 at http://www.christnotes.org/com.....1&c=3

    Your criticism of the seeming arbitrariness of God’s precept hs no force unless you are sure what it meant in the first place. As Adam understood it, it may have been anything but arbitrary.

    The Wikipedia article on the tree of the knowledge of good and evil contains this interesting tidbit:

    Gordon and Rendsburg[1] have suggested that the phrase … translated good and evil, is a merism. This is a figure of speech whereby a pair of opposites are used together to create the meaning all or everything, as in the English phrase, “they came, great and small”, meaning just that they all came. So the tree of the knowledge of good and evil they take to mean the tree of all knowledge. This meaning can be brought out by the alternative translations tree of the knowledge of good and of evil (the word of not being expressed in the Hebrew) or tree of knowledge, both good and evil.

    According to the Jewish tradition God commanded Adam and Eve not to eat from the tree that was to give free choice and allow them to earn, as opposed to receive, absolute perfection and intimate communion with God at a higher level than the one on which they were created. According to this tradition, Adam and Eve would have attained absolute perfection and retained immortality had they succeeded in withstanding the temptation to eat from the Tree. After failing at this task, they were condemned to a period of toil to rectify the fallen universe. Jewish tradition views the serpent, and sometimes the tree of the knowledge of good and evil itself, as representatives of evil and man’s evil inclination.

    As to the injustice of punishing Adam’s descendants: it is inherently unjust to blame one person for another person’s fault, but it is not necessarily unjust to punish someone for another person’s fault – otherwise the State could never justly imprison criminals who had dependants.

    Other factors to consider: the transgression was freely chosen by Adam, not by God; the warning Adam received about eating from the tree would have been much clearer to him than it is to us, with our sin-clouded intellects; and finally, Christians hold that the terrible consequences of the Fall were undone by the sacrifice of Christ on the Cross. We still have to die, but now, at least, we know the Way to eternal life.

  273. Mr BA^77,

    Nak, Tell you what you ol Darwinian propaganda machine, Why don’t you clue me to why chemistry and physics are so well disposed for life to happen by accident in this big ol universe,,,

    You are acting like a chatterbot, once out of your depth on a topic you are forced to change the subject. Are you giving up on defending the technical brilliance of Mycoplasma genitalium?

    I also got the thought while researching weather forecasting systems for our conversation – could you run a genetic algorithm to improve them? It sounds like a fun project! But if such a project had any significant impact on the quality of the forecasts at all, where should that increment in technical brilliance be attributed?

  274. Mr Vjtorley,

    I’m sorry I haven’t responded earlier to your contributions about the Met Office. Thank you for the link.

    I also wanted to follow up with you on the links you had provided earlier to Alex Williams’ articles. For the purposes of the ‘technical brilliance’ discussion, they were not very relevant since they were about the human genetic system, not this tiny bacterium. However, they did raise this interesting question of whether metadata was evolvable.

    I don’t think I agree with his argument. Certainly metadata can’t exist and can’t evolve without data there in the first place. To be grounded in one example, the pattern of histones that might silence a gene cannot exist without the DNA.

    But the DNA for a simpler kind of life can exist without the histones. Bacteria don’t have histones.

    We also can see that histones serve multiple functions, some metadata related, some not. When first discovered, histone was just considered a packing material that helped keep the DNA tightly packed in the nucleus. Later, the regulatory fuctions were discovered. It is easy to argue that the metadata function is built on top of the packing function which was there first.

    Williams’ main argument against metadata evolution seems to be ‘inextricable dependency’, the idea that metadata is inextricably dependent on data for meaning. Well, that’s true, but so what? One cell used histones for packing, but had multiple genes with overlapping functions. A random methylation event on a histone silences one of the genes, and now the cell survives to reproduce more than similar cells without the methylation, and the methylated histone is copied to each daughter cell. Poof, active metainformation has been created. If the information (or meta-information) is physical, variable, and heritable then it is going to evolve through natural selection on the basis of its effect on the phenotype.

  275. Excuse me Nak, Are we even in the same conversation? You haven’t even begun to “prove” the weather computer program comes close to the technical brilliance of the functional/algorithmic information in mycoplasmal!!! By the way the topic of the thread is “A Simple Start”, thus I find my reference the physics and chemistry of the universe to be of direct foundational relevance. And staggering to the overall issue as to WHY ARE YOU so blind to the design inference? That the entire universe would be found to be balanced to within 1 to 10^60 for mass density is screaming design. In fact my back of the envelope calculations reckons it to “A SINGLE GRAIN OF SAND” which is smaller than Ross’s “very conservative” tenth of a dime estimate”. Why is this mind blowing “coincidence” of absolutely no interest to you? Oh that’s right you are a dogmatic atheist who could care less about the truth! That is why YOU seek to change to overall topic of the thread by “getting lost” in technical irrelevance so that YOU may not have to face to primary question of God and His impact on YOUR personal life. All I can say Nak is be a man and deal with it and quit trying to hide in BS!

    That there would be such a profound disconnect between “life friendly” physics and “natural information generation” (Abel Null Hypothesis) only gives a huge roadsign as to Who the designer of life actually is (The Word) as well as ruling out pantheism that many people would be sure to get lost in instead of actually “finding” the living God, though God is surely not the one who is lost.

  276. Mr BA^77,

    I’m trying to hold up my end of the conversation. I offered some different estimates and comparisons of M. gen and weather forecasting codes. Your responses were either misguided, in thinking the 2D projection of a weather map was the output, or irrelevant, in demanding that a supercomputer reproduce.

    I’m not trying to ‘prove’ anything. I’m trying to have a nice, reasonable discussion about one small point in a much referenced paper, a point you brought up.

    In the sense that I’m trying to talk about science, and you’re trying to talk about my eternal soul and its destiny in hellfire without a personal acceptance Jesus Christ and quantum teleportation of the Holy Spirit, no, we are not having the same conversation. But I’m aware of that, and try desperately to compensate.

  277. Nak, And which is of more importance? You getting right with God or you getting the exact degree to which mycoplasmal exceeds our programming ability? I mean really,,,think about it Nak,,if Abel or Trevor’s, or somebody of that caliber, were able to actually “count” all the functional information inherent in the DNA and proteins of the mycoplasmal, and to showed that it exceeded our ability to program by say 10^12th degree, would that really make one Iota difference to you? Would you not just ignore that fact, as you have all others, and move on to some other irrelevant point so as not to face the weightier issue that admitting there actually is a God would have on your life? (which would be a very God thing by the way!)

  278. born,

    You know Dave, I’ve been lied to so much I really don’t care what evolutionists say anymore it all turns out to be deception when I dig into it (which has been hundreds of times by now,,,, so just cut to the chase Dave,,, show me the money and so me just one experiment where a sub-species bacteria has gained functionality over its parent-species. Or better show some real scientific integrity and falsify Abel’s Null Hypothesis for information generation,,,Shoot you would probably become legendary within scientific circles if you could do that!

    Actually, my goal here is far more modest. I’m trying to get you to discuss the actual points made in Art Hunt’s essay, which so far you have steadfastly refused to do. But since you have decided to play the victim card about how all the big bad Darwinists keep lying to you, engaging in further discussion is probably pointless.

    Do svedanya.

  279. You know Dave, You are in the same “leaky boat” as Nak, You would rather be lost in a myriad of obscure detail than to face the truth that admitting there actually is a God would have on your life. Which in my opinion would be a very, very good truth for you to admit and accept.
    But to try, in my very limited ability, to address the information “problem” of proteins let’s consider a few points:

    Michael Behe is playing havoc with evolutionists right now, in a series of essays dealing with protein evolution, on ENV by showing:

    Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.

    This severe limit Behe had previously “supposed” was:

    “The likelihood of developing two binding sites in a protein complex would be the square of of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.” Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Thus fairly strongly indicating, even neglecting novel protein generation, that the proteins present in life are far too functionally complex to evolve into even any simpler or more complex proteins of similar functional complexity,,

    Severe Limits to Darwinian Evolution: Michael Behe
    http://www.evolutionnews.org/2.....n_evo.html

    But this point is totally mute to you as with Nak? Why is this Dave?

    Yet when we look at the proteins in life, instead of Szotaks ” simply sticky proteins”, in terms of functional complexity we see some very weird things,,for instance,,,

    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/...../60/95O56/

    Cruise Control?!?,, Last time I checked, cruise control is a very limiting thing for a car that prevents any change in speed from happening. 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.

    Dave do you know how much much functional information is required to achieve “process control”?? Well lets take a look:

    For a protein to be “complete in its information content”, in its ability to “cruise control” it would have to implement three different algorithmic forms of control: Proportional (P) Integral (I) and Derivative.

    PID controller:
    Excerpt: 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

    The equations involved for getting even this minimal level of “cruise control” for a dynamically interactive protein are staggering to put it mildly. (Page down on the wiki article to get a small taste of what I’m talking about) Several complex equations, which are derived from the basic PID platform of equations, are necessary to achieve different forms of simple process control in different scenarios in chemical industry. Many of these complex equations will surely be found to be integrated and overlapping so as to be utilized in proteins since proteins are so much more “dynamically controlled” from within its own structure (i.e. the information for control must reside within the protein with no recourse to the DNA for correction once the protein is made)), in such a demanding “process” as is found in life it is ludicrous to suppose otherwise, There is simply no other way for a protein to achieve such self control or any control for that matter unless this type of algorithmic information is inherent within its structure… Shoot it is realizing stuff like this that makes me think even the 1 in 10^77 estimate of Axe, is far to generous for finding a specific functional protein within sequence space.

  280. Born,

    Your continual refusal to address the points in Art Hunt’s essay is duly noted.

  281. Dave, as is your refusal to address the points I raised noted:

  282. Born,

    My original post was in reference to Arts discussion of Axe’s conclusions. I am under no obligation to go running after your inky cloud of misdirection away from those points.

  283. 283

    Address the speculative world of Art Hunt?

    “…the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk…Which means that all of this excitement about RNAs encoded by junk DNA is not warranted – unless one tends to get excited at the prospects of junk, junk squared, and garbage disposals. In a nutshell, what looks like junk may not only be junk, it may give rise to even more junk” – Art Hunt Oct. 2007

    - – - – - -

    Science Daily Oct. 2009:

    No Such Thing As ‘Junk RNA,’ Say Researchers
    Tiny strands of RNA previously dismissed as cellular junk are actually very stable molecules that may play significant roles in cellular processes, according to researchers at the University of Pittsburgh School of Medicine and the University of Pittsburgh Cancer Institute (UPCI).
    The findings, published last week in the online version of the Journal of Virology, represent the first examination of very small RNA products termed unusually small RNAs (usRNAs). Further study of these usRNAs, which are present in the thousands but until now have been neglected, could lead to new types of biomarkers for diagnosis and prognosis, and new therapeutic targets.
    In recent years, scientists have recognized the importance of small RNAs that generally contain more than 20 molecular units called nucleotides, said senior author Bino John, Ph.D., assistant professor, Department of Computational Biology, Pitt School of Medicine.

    “But until we did our experiments, we didn’t realize that RNAs as small as 15 nucleotides, which we thought were simply cell waste, are surprisingly stable, and are repeatedly, reproducibly, and accurately produced across different tissue types.” Dr. John said. “We have dubbed these as usRNAs, and we have identified thousands of them, present in a diversity that far exceeds all other longer RNAs found in our study.”

    The team’s experiments began with the observation that the Kaposi sarcoma-associated herpesvirus produces a usRNA that can control the production of a human protein. Detailed studies using both computational and experimental tools revealed a surprisingly large world of approximately 15 nucleotide-long usRNAs with intriguing characteristics. Many usRNAs interact with proteins already known to be involved in small RNA regulatory pathways. Some also share highly specific nucleotide patterns at one end. The researchers wrote that the existence of several different patterns in usRNAs reflects the diverse pathways in which the RNAs participate.
    “These findings suggest that usRNAs are involved in biological processes, and we should investigate them further,” Dr. John noted. “They may be valuable tools to diagnose diseases, or perhaps they could present new drug targets.”

    When faced with the fact that Junk DNA isn’t junk (in 2007 no less), he recoils to the position that not only is it junk, but the fact that it is transcribed only means it codes for Junk RNA.

    Junk begets Junk -or- ideological wild-assed speculation begets more of the same? Which of these is true?

  284. WOW, Thanks Upright,
    Hey Dave, seeing as Hunt ain’t even close to reality, as far as mainstream science is concerned regarding Junk DNA, do you really want to hitch your wagon to his? If you really feel his pseudo-speculations qualify as rigorous science why don’t you send his paper to Axe, who is far more qualified to comment on it than I, and see what he thinks,,,I am sure that Axe will be willing to address any relevant merits that may be there,,, I’m sure Axe may appreciate a good laugh from reading it as well.

  285. Mr BA^77,

    I can guarantee you that any conversation I want to have about my soul will not be carried out in the comment threads of UD, and won’t be with you. Here, I’d like to talk about ID and its ripples in the world, which is science, not religion. Thank you.

  286. Upright,

    I see you have joined born in avoiding the specific questions Art was addressing about Axe’s paper. Congratulations.

    Any more red herrings you’ like to throw up helping born to save face?

  287. Wow, ultrasmall RNA with significant biological function!

    I guess we don’t have to raise 4 to the 150th power any more when talking about random oligomers having function. 4^15 is still longer than the lifetime of the universe, right?

    Gotta ask Kalinsky about this…

  288. Hmm, Upright quotes Hunt directly on his completely wrong postulations of junk begetting junk and this is a red herring for you??? Hyper selective are we not oh pragmatic Dave?,,,I consider it a direct statement of fact,,that has direct impact on how we should view any postulations coming from Mr. Hunt,,, you are free to chase his ramblings if you want,,, I see no merit in his current postulations since he made blatantly incorrect postulations in the past,, i.e. He needs to pass peer review to redeem himself as far as I’m concerned! Nak as far as you practicing science correctly your atheistic glasses are blinding you to everything! Thus of what point is it to discuss anything in science with you when you can’t even truly see the scientific issue to begin with?

  289. Mr BA^77,

    I’m glad to see you standing up so strongly for the importance of peer review in the matter of Art Hunt’s criticism of Axe. Does this mean you will delete all the non-peer reviewed articles from your database of quotes? Your principled stand is an example to everyone.

  290. Nakashima,

    I’m glad to see you standing up so strongly for the importance of peer review in the matter of Art Hunt’s criticism of Axe. Does this mean you will delete all the non-peer reviewed articles from your database of quotes? Your principled stand is an example to everyone.

    He’s just applying the same criterion to those who tout it.

  291. Still nobody willing to actually take on Art’s essay regarding Axe’s calculations. Lots of irrelevant distractions, however.

  292. Mr. Nakashima (#274)

    Thank you for your response. First, a couple of points about histones.

    You rightly note that bacteria don’t have histones. I should point out, however, that some archaea do. In any case, the fact that bacteria don’t possess histones does not, in and of itself, make their origin any less mysterious.

    I should also like to note that chromosomal histones are one of the most highly conserved protein molecules in eukaryotic cells. Wikipedia comments: “It also appears that the structure of histones has been evolutionarily conserved, as any deleterious mutations would be severely maladaptive.” That tells me that histone evolution is severely constrained, to say the very least.

    Regarding your hypothesis that meta-information was a later function of histones, which piggybacked on top of its original function for packing, I have a couple of questions:

    (1) Have you run your ideas by any reputable biologist in the field?

    (2) Have you thought about how your hypothesis would be tested empirically? For instance, if you’re right, we might expect to find organisms for which histones serve a function for packing, but have no role as repositories of meta-information. Probably the archaea would be the place to look. Are there any answers on that question, yet?

    I should mention that Alex Williams has written an article specifically about meta-information at http://creation.com/meta-information . The problem for your piggybacking hypothesis, as I see it, is that there’s just so much of this meta-information in the human genome. The regulatory meta-information in our cells actually dwarfs the protein-coding information. Meta-information cannot be dismissed as peripheral; it is a defining feature of eukaryotic cells. Here’s a relevant excerpt from Williams’ article:

    The human genome contains an enormous amount of information, far more than we ever (until recently) imagined. But we now know that most of it is not primary information (protein-coding genes) but meta-information —the information that cells need to have in order to turn those protein-coding genes into a functional human being and maintain and reproduce that functional being. This meta-information is stored and used in a variety of ways:

    DNA consists of a double-helix—two long-chain molecules twisted around one another. Each strand consists of a chain of four different kinds of nucleotide molecules (the shorthand symbols are T, A, G and C). About 3% of this in humans consists of protein-coding genes and the other 97% appears to be regulatory meta-information.

    DNA is an information-storage molecule, like a closed book. This stored information is put to use by being copied onto RNA molecules, and the RNA molecules put the DNA information into action in the cell. For every molecule of protein-producing RNA (primary information), there are about 50 molecules of regulatory RNA (meta-information).

    Down the sides of the DNA double-helix, several different kinds of chemical chains are attached in patterns that code meta-information for turning unspecialized embryonic stem cells into the specialized cells that are needed in fingers, feet, toenails and tail-bones etc.

    DNA is a very long thin molecule. If we unwound one set of human chromosomes, the DNA would be about 2 metres long. To pack it up into the very tiny nucleus inside the very tiny human cell, it is coiled up in four different levels of chromatin structure into 46 chromosomes. This coiling chromatin structure also contains yet further levels of meta-information. The first level (the histone code) codes information about the cell’s history (i.e. it is a cell memory). The three further levels of coiling code further information, some of which is described below, and there is no doubt more that we have yet to unravel.

    The amount of meta-information in the human genome is thus truly enormous compared with the amount of primary gene-coding information.

    I should add that your remarks do not touch upon the other major point that Williams makes – namely, that DNA coding is much more efficient than anything human engineers have come up with. As Williams writes:

    DNA information is overlapping-multi-layered and multi-dimensional; it reads both backwards and forwards; and the ‘junk’ is far more functional than the protein code…. No human engineer has ever even imagined, let alone designed an information storage device anything like it.

    Or in the words of the atheist humanitarian and expert software designer, Bill Gates:

    Human DNA is like a computer program but far, far more advanced than any software we’ve ever created.” The Road Ahead, 1996, p. 188.

    I have a healthy respect for designs that are so clever that I couldn’t have figured them out myself. I put it to you that the hypothesis that someone smarter than I am thought them up warrants serious consideration, and should be the default hypothesis until and unless it is shown to be highly unlikely.

  293. Mr Vjtorley,

    Yes, Mr Williams has a particular definition of ‘functional’ – if it is transcribed into RNA, the DNA is functional.

    Interestingly, if there was a stretch of DNA that I didn’t want to use, one way of handling that is to translate both strands into RNA and let them pair back up as double stranded RNA. You could call this transcription “function” I suppose…

    Alas, I have limited biological facilities available here in my supersecret lair on Volcano Island – FedEx refuses to deliver to my address!!1! But I agree that archaea are good place to look. As you point out, such strong conservation would lead to a supposition of high survival value!

  294. Dave Wisker (#291)

    Have you seen this article?

    Scientist Says His Peer-Reviewed Research in the Journal of Molecular Biology “Adds to the Case for Intelligent Design”.

    I realize it’s not as current as the article by Art Hunt which you cited, but at least it tells you where Axe himself feels the data points.

    If you want a technical response to Art Hunt’s article, you might like to email Dr. Stephen Meyer.

  295. born is suddenly concerned about peer review. Well, here is a quote from the peer-reviewed paper on junk RNA that Art was discussing:
    :

    This is consistent with the notion that a large fraction of the intergenic regions containing SAGE tag (more than 10% of the overall genic regions; Velculescu et al 1997) encode genuine transcripts that are normally targeted for degradation

    Wyers F, M Rougemaille, G Badis, J Rousselle, M Dufour J Boulay, B Régnault, F Devaux, ANamane, BSéraphin (2005). Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase. Cell 121(5): 725-737

  296. Hi vjtorley,

    Thanks for the link. It doesn’t surprise me that Dr Axe would have that view of the implications of his work.

    My purpose here, howe ever, is to get people to strat thiunking about the work itself. It may be daunting technically to a layman, but I think Art did a very good job expressing his concerns with Axe’s conclusions in terms understandable to those of us unfamiliar with the arcane world of biochemistry. And I think he focused on the essential issues, which could easily be lost to a layman struggling with the original paper.

  297. Want to match peer review Dave?

    Lets see I’ll match your 2005 paper with:

    How The Junk DNA Hypothesis Has Changed Since 1980 – Richard Sternberg – Oct. 2009 – Excellent Summary
    Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2.....is_ha.html

    Endogenous Retroviruses (ERVs) – Page up for Pseudo-genes refutation
    http://www.detectingdesign.com.....Endogenous

    Endogenous Retroviruses (ERVS) A Case for Common Descent or A Case for Incorrect Presupposition?
    http://www.whoisyourcreator.co.....ruses.html

    How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schauer:
    List Of “Junk DNA discussed:
    Tandem Repeats, Transposons/Retrotransposons, SINE/Alu Sequences, LINES, Endogenous Retroviruses (ERVs) and LTR retrotransposons, Pseudogenes, C-Value Enigma, “Junk DNA” becomes “The Transcriptome”, Human Accelerated Regions (HARs),
    ….What can we conclude from the evidence presented in this essay:
    Every type of “Junk DNA” presented by pro-evolution websites has been found to have functional roles in organisms, which severely undermines the “shared errors” argument; http://www.geocities.com/wade_.....g_Tide.pdf

    Conserved Noncoding Elements: More Contradictory Genetic Data
    http://darwins-god.blogspot.co.....-more.html

    Astonishing DNA complexity update
    Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes.
    http://creation.com/astonishin.....ity-update

  298. InvAluable junk: the cellular impact and function of Alu and B2 RNAs – 2009
    http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

    42 Glinsky GV. 2008. Phenotype-defining functions of multiple non-coding RNA pathways. Cell Cycle 7(11): 1630-1639.

    43 Bond CS, Fox AH. 2008. Paraspeckles: nuclear bodies built on long noncoding RNA. J. Cell Biol. 186(5): 637-644.

    44 Barak M, et al. In press. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res.

    45 Lee JT. 2009. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23(16): 1831-1842.

    46 Guttman M, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235): 223-227.

    47 Faulkner GJ, et al. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 41(5): 563-571.

    48 Tay SK, et al. 2009. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci U S A. 106(29): 12019-12024.

    etc…etc…etc… Dave

    You know what is really weird Dave,,,it is that you will ignore everything I present that is peer reviewed no matter what it says or who wrote it,,,just so you may concentrate on unsubstantiated pseudo speculations of a highly questionable paper coming from a highly questionable character ,,,just so in order to cling ever so tenaciously to a morsel of justification for your atheism,,, Practicing science just in order to protect a bankrupt world view is not science DAVE!!! It would be absolutely hilarious if it were not for the fact you think you are actually being legitimate with your inquiries into reality with the miraculous tool of science!

  299. I have pointed out many times on this blog that atheism is not an intellectual position at all; it is an emotional cry of wrath. The evidence for a creator, or a first cause, are overwhelming, and, in any case, reason dictates that everything that begins to exist [the universe] must have a cause. There is no way around the force of that argument, though many here have tried in vain to avoid its force.

    According to Paul Vitz, a former atheist and professor of psychology at NYU, “the major barriers to belief in God are not rational and can be called, in a general sense, psychological.” He argues that absent or deficient fathers predispose their children to atheism. “The atheists disappointment in and resentment of his own earthly father unconsciously justifies his rejection of God.” Or as someone else once put it, we cannot perceive the heavenly Father in God if we cannot, in any way, perceive God in our earthly father

    Among the many famous atheists who were mistreated by their fathers we can include, Friedrich Nietzche, David Hume, Bertrand Russell, John-Paul Sartre, Albert Camus, and H.G. Wells. Examples of theists from the same period include Blaise Pascal, Edmund Burke, Moses Mendelssohn, Soren Kierkegaard, G. K. Chesterton, and Dietrich Bonhoeffer. In each case, the atheists had weak, bad or absent fathers. By contrast, the theists had good fathers or good father substitutes.

    No doubt a few atheists can claim that they loved and were loved by their fathers, but that simply means is that they have found some other emotional pretext to justify the testimony of reason. Romans 1: 20 got it right: Evidence of God’s handiwork is all over the place. Most atheists are atheists because they prefer to be that way. “The fool has said in his heart [not mind, not brain] that there is no God.”

  300. StephenB: “I have pointed out many times on this blog that atheism is not an intellectual position at all; it is an emotional cry of wrath.”

    Rather presumptuous. It would be just as justified to ascribe belief in God to fear.

    Aside from that, atheism can just as well be considered both an intellectual and an emotional position: that it is better to believe in no God, rather than a God ultimately responsible for the horrendous human condition (ignoring all the evidence for a Creator).

  301. Hey Nak you stated,

    “I’d like to talk about ID and its ripples in the world, which is science, not religion.”

    Well Nak did you know it is very well possible that without Christianity there would be no modern science as we know it.

    “However we may interpret the fact, (sustained) scientific development has only occurred in a Christian culture. The ancients had brains as good as ours. In all civilizations, ancient Babylonia, Egypt, Greece, India, Rome, Persia, China, the Abassid empire and so on, science developed to a certain point and stopped. It is easy to argue speculatively that, perhaps, science might have been able to develop in the absence of Christianity, but in fact it never did.” Robert E. D. Clark – Christian Belief and Science

    Famous (Founding) Scientists Who Believed in God
    http://www.godandscience.org/a.....faith.html

    Christianity and the Birth of Science by Michael Bumbulis, Ph.D
    http://www.ldolphin.org/bumbulis/

  302. Here is a really cool video to that effect Nak:

    Christianity Is The Foundation Of Modern Science – Henry Schaefer PhD. Part 1 of 3
    http://www.youtube.com/watch?v=cI-4aVG0UxI

    Christianity Is The Foundation Of Modern Science – Henry Schaefer PhD. Part 2 of 3
    http://www.youtube.com/watch?v=XlShXV98H3g

    Christianity Is The Foundation Of Modern Science – Henry Schaefer PhD. Part 3 of 3
    http://www.youtube.com/watch?v=TGrBCy_A0CE

  303. @Magnan

    Maybe it was presumptuous, but not entirely uncalled for. Most atheists I’ve seen are either angry, bitter, or arrogant (or some combination of the three) whenever the topic is discussed.

  304. —magnan: “It would be just as justified to ascribe belief in God to fear.”

    —”Aside from that, atheism can just as well be considered both an intellectual and an emotional position: that it is better to believe in no God, rather than a God ultimately responsible for the horrendous human condition (ignoring all the evidence for a Creator).”

    Both are emotional arguments, as you seem to acknowledge in parenthesis.

  305. Another paper to consider:

    Struhl K (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Structural & Molecular Biology 14: 103-105
    From the abstract:

    Eukaryotes transcribe much of their genomes, but little is known about the fidelity of transcriptional initiation by RNA polymerase II in vivo. I suggest that ~90% of transcriptional initiation in yeast represent transcriptional noise, and that the specificity of initiation is comparable to that of DNA-binding proteins and other biological processes. This emphasizes the need to develop criteria that distinguish transcriptional noise from transcription with a biological function.

    Now some questions about the usRNA article to consider:

    1. How are usRNAs formed? Are they transcribed from specific usRNA “genes”? Are they fragments generated by post-transcriptional processing (like intron-splicing), or byproducts of RNA degradation processing that acquired a function secondarily?
    2. If they are individually and specifically transcribed, does each have its own promoter?
    3. What percentage of the genome is talken up by the sequences specific to usRNAs, and how does that compare to, say, the percentage taken up by pseudogenes, inactive retroviral insertions, and other non-coding DNA?
    4. Out of the thousands of usRNAs discovered by the John team, how many were actually found to have a function?

  306. Hmm up to 2007 are we Dave:

    Phenotype-defining functions of multiple non-coding RNA pathways. 2008:
    Our analysis implies that hundreds thousands of non-protein-coding transcripts are contributing to phenotype-defining regulatory and structural features of a cell. Therefore, definitions of genes as structural elements of a genome contributing to phenotypes should be expanded beyond the physical boundaries of mRNA-encoding units. We propose an information-centered model of a cell suggesting that informasomes (the RNP complexes of sncRNAs and Argonaute proteins) represent the intracellular structures which provide the increasingly complex structural framework of genomic regulatory functions in higher eukaryotes to facilitate the stochastic (random and probabilistic) rather than deterministic mode of choices in a sequence of regulatory events defining the phenotype.
    http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

    Hmm Dave… do you still think we should presuppose that if we don’t know the function of Junk DNA fully that we should label it junk before all the facts are known just to placate your atheistic tendencies?

  307. WOW Dave, This following paper blew Dawkins whole selfish DNA scenario clean out of the water,,,there ain’t even a “selfish gene” boat left to be seen anymore.

    Altruistic functions for selfish DNA. – 2009
    Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this “selfish DNA” or “junk DNA” dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.
    http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

  308. bornagain77 @ 307

    WOW Dave, This following paper blew Dawkins whole selfish DNA scenario clean out of the water,,,there ain’t even a “selfish gene” boat left to be seen anymore.

    Just what did you think Dawkins meant by “selfish gene”?

  309. Seversky Why are you asking? Are you feeling the pain as the last vestiges of Junk DNA are crushed along with your ability to be a (ahem it hurts to write this,,,, fingers cramping,,, must write with knuckles) intellectually fulfilled atheist? Whew that was excruciating

    How to be an Intellectually Fulfilled Atheist (Or Not)
    http://www.amazon.com/How-Inte.....1933859849

    The slow, painful death of junk DNA:
    Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work….Junk DNA is a necessary mathematical extrapolation…Without Junk DNA, evolution runs into insurmountable mathematical difficulties. http://creation.com/junk-dna-slow-death

  310. Dave you still in 2007? Here is another 2009 peer review while I’m waiting for you to catch up:

    Long noncoding RNAs: functional surprises from the RNA world.
    Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional “noise” as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell.
    http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

  311. StephenB @ 255

    The connection between this life and the next is more direct than you may appreciate. How you behave here determines in large measure how you will fare there.

    Is you God omniscient or not? If He is then he knows what we will do and why before we do it. So how can what we do make the slightest difference?

    Yes, and that isolated ethic causes the atheist to discount the preciousness of EVERYONE ELSE’S LIFE EXCEPT HIS OWN, except for those who may be of some use to him. Thus, babies, old people, or anyone else who gets in the way must die.

    No, if human life is precious because each one is unique and unrepeatable then none should be taken without a very good reason. I do not need a God to tell me that.

    Christianity declares that all life is sacred from the womb to the grave. The fifth commandment forbids all wanton violence against neighbor, both physical and, as it turns out, verbal. Atheism forbids nothing.

    You must be using a different fifth commandment. I do not get what you said from an injunction to honor your father and mother.

    And, no , atheism neither forbids nor requires anything. It is simply a lack of belief in a god. Atheists and agnostics in society, however, recognize that there are a number of things we should not do if we are to live together in peace and security. It is not so difficult to work out.

    For the Christian, both are of equal value, so both receive the same consideration. So, the doctor, and the health care system, takes them as they come in the order presented. For the atheist, the least fit must go—the sooner the better.

    You are evading the question. The dilemma lies in both patients needing treatment at the same time while there are insufficient resources to treat both; the point being that we are sometimes faced with choices where none of the alternatives are satisfactory. What would the good Christian do in such a situation?

    As for survival of the fittest, it seems by some of the comments here about universal public healthcare that good Christians favor the private option which is much more a survival of the fittest system than the public option.

    If there is no objective standard for morality to provide the dilemma, then there are no hard choices—only pragmatic choices. Hence, atheism, and the attendant pragmatism/utilitarianism are easy: Simply conduct a cost benefit analysis and kill those who can provide no return on the money invested by the state.

    And what do you think private health insurance companies are doing now when they decide not to fund treatments?

    Unlike some Christians, atheists and agnostics do not need a God to tell them that if they want their own right to life to be respected they must do the same for their fellows. They can work that out for themselves. They can also agree that in a just and fair society, access to the necessities of life should be guaranteed to all.

    Those societies that don’t see it that way tend to be those that subscribe to some sort of authoritarian and absolutist belief system, be it political ideology or religion.

  312. Bornagain, you are right one. These people still using the peer review argument are out of their ever loving minds. The bottom line is that you cannot critique a theory, saying it is not scientific because there are no, or now few, peer reviewed papers, while at the same time disallowing ID papers to be published in the first place. It is a self defeating philosophy to say something isn’t sceince because it isn’t peer reviewed, and that it cant be peer reviewed because it isn’t science. Nonsense. ID is moving on whether these sworn enemies want it to or not- and not because of ID’s “political pull”- as ID is disadvantaged politically and institutionally as it stands now- but it is progressing based on it’s own merits and real value- especially regarding the promise of scientific fecundity.

  313. vjtorley @ 258

    Seversky

    I can see that the Flood troubles you theologically.

    It does, because, as you rightly point out:

    However, the notion that God might actually visit such a death upon innocent people – especially children – so that they ended their lives screaming in terror, is, I would agree, theologically scandalous.

    That is putting it mildly. We might bow down before such a being out of fear for our lives but it would not be worthy of our worship.

    I do not believe that there is any evidence of the global flood as described in the Bible but the problem with the God of the Old Testament is that there are too many such incidents which force believers to resort to all manner of shifts and stratagems to find some sort of half-way acceptable way to account for them. Plainly, there is something wrong with that.

  314. Berceuse @ 262

    Or uniquely absurd. For atheists, we are victims of a cosmic lottery, and to pretend like we are grateful for this is disingenuous in the face of a destiny of oblivion.

    That was my point a little while back, that this need for gratitude makes no sense. I’m glad to see we agree on something.

  315. Clive Hayden @ 264

    And moreover, what compels us to choose between one system of ethics verses another? We cannot have an ethical duty for choosing an ethical system, for we are still in an ethical vacuum. And we have no way to compare between any ethical systems, because that would presuppose that we are recognizing a more ultimate ethical standard as our basis for comparison. What say you? If we were born tabula rasa, we would die tabula rasa

    I take a pragmatic even – dare I say it – a scientific approach to ethics or morals,

    First, I look at them and ask what do they actually do? What is their function? What they appear to be are rules of behavior or codes of conduct that regulate the way people behave towards one another in society. The purpose seems to be to promote peace, stability and security – which makes sense regardless of your beliefs.

    And for agnostics and atheists, who believe this one life is all we have as ourselves, the wish is for as long and as enjoyable a life as possible. Respecting that wish in others is one of the best ways of ensuring that our own wish is treated with similar respect.

    In other words, our ethical and moral beliefs are rooted in – and arise from – our common needs as human beings.

  316. Dave Wisker (#296)

    I agree with you that Art Hunt’s paper was an excellent one. Seldom have I seen such a lucid explanation of matters pertaining to biochemistry.

    I’ve just been having a look at Stephen Meyer’s paper, The Cambrian Explosion: Biology’s Big Bang which will be appearing as a chapter in Darwinism and Design soon. Here’s the link:

    http://www.discovery.org/scrip.....038;id=639

    Pages 368 onwards make for interesting reading, as they address OOL issues. The Cambrian explosion is, in any case, orders of magnitude more difficult to account for than the evolution of life.

  317. Art Hunt asked that I post this reply for him since he is still under moderation, and this discussion is preceding too rapidly for his replies to appear in a readable manner:

    Hi all,

    Many thanks to Dave for posting this in a timely manner.

    I’m delighted to see such an interest in the RNA Underworld. There is too much to respond to, so I’ll try to focus on some bookends.

    Upright Biped at #283, the study you point to in an attempt to rebut my essay on junk RNA isn’t particularly relevant to my essay. I was talking about things known as cryptic unstable transcripts. The study you cite was focused on relatively “un-cryptic” tiny RNAs. They are two rather different subjects, and the existence of tiny RNAs has no bearing on the fact that much (most) of the transcription products arising from highly-repetitive and other non-coding DNA end up in the garbage can. You are making an argument of the form: “The Yankess are better than the Phillies because Eli Manning is a better quarterback than Donovan McNabb.” It doesn’t make any sense, once you think about it for more than a second or so.

    ba77, you are throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend, let alone address. One item is interesting, though. Specifically, the study you mention in #306 is actually a clever idea that strikes at the heart of a favorite ID notion -namely, that there is something called CSI (or FCSI) hidden inside of living things. The proposal discussed in the paper you cite explains how phenotype and its control is a decidedly low or zero-CSI proposition. I’m delighted that you would bring this to the attention of the Uncommon Descent crowd. (Of course, the fact that the author’s idea requires that the numerous small RNAs he mentions be expressed at some reasonable steady state level sort of makes the study irrelevant, at least when it comes to my essay on junk RNA. Hopefully, I won’t have to explain what the word “cryptic” means.)

    Finally, vjtorley at #316, thanks for the kind words. Allow me to extend an invitation to you (and any other curious ID proponent) to ask questions about RNA, proteins, and ID at my blog. I’m afraid that the discussion here is moving faster than the SOM (Speed of Moderation).

  318. —-seversky: “Is you God omniscient or not? If He is then he knows what we will do and why before we do it. So how can what we do make the slightest difference?”

    Just because God knows the future doesn’t mean that he impedes the activity of his creatures, or that his creatures cannot “make a difference.” You are confusing omniscience with determinism. God knows whether or not the stock market is going to crash, but that doesn’t mean that he caused it to happen. God’s creatures possess free will, which means, of course, that they are liable to cause a lot of harm through dishonesty and greed, or, for that matter, they may do great things. God allows it all to play out.

    —–“No, if human life is precious because each one is unique and unrepeatable then none should be taken without a very good reason. I do not need a God to tell me that.”

    If that is the case, why do you hesitate to provide an unqualified condemnation of the destruction of innocent life in the womb? Indeed, why do you avoid the issue? The moral code that you have “worked out” doesn’t seem to be up to the task.

    —–“You must be using a different fifth commandment. I do not get what you said from an injunction to honor your father and mother.”

    I was referring to “Thou Shalt Not Kill,” which is the fifth commandment in my Bible.

    —–“And, no ,atheism neither forbids nor requires anything. It is simply a lack of belief in a god. Atheists and agnostics in society, however, recognize that there are a number of things we should not do if we are to live together in peace and security. It is not so difficult to work out.”

    I once asked you to submit your moral code as a parallel to my moral code and proposed that you and I work out a integrated morality. You chose not to indulge me. If even two people cannot work out a moral code, how can six billion people work one out? They answer is that they can’t. The moral code must precede them.

    —-“You are evading the question. The dilemma lies in both patients needing treatment at the same time while there are insufficient resources to treat both; the point being that we are sometimes faced with choices where none of the alternatives are satisfactory. What would the good Christian do in such a situation?”

    Quite the contrary, I provided a specific, easy to understand answer. I said we take them as they come. What is it about taking them in order that you do not understand? If they come into the emergency room at exactly the same time, then the one whose life is in greatest danger gets priority, even if that person is old. For the atheist, the answer is equally clear—if there is a conflict of interest, then the old person must die. Here is a hint, by the way: Conflicts of interest always exist. That is why we need an objective moral code that transcends those conflicts. Our moral codes are different, which means that one of us must be right and one of us must be wrong. Indeed, everyone’s self-styled morality is different from e everyone else’s self styled morality, which is yet another reason for the need of a natural moral law that binds everyone, regardless of personal preferences.

    —“As for survival of the fittest, it seems by some of the comments here about universal public healthcare that good Christians favor the private option which is much more a survival of the fittest system than the public option.”

    Incorrect. For what it is worth, there are two moral principles that apply to health care: The advanced principles of solidarity and subsidiarity, both of which are based on the basic moral law. But we have not yet elevated the discussion to that level as you don’t even believe in the natural moral law to begin with. So, you are not ready to discuss its more subtle corollaries.

    —-“Unlike some Christians, atheists and agnostics do not need a God to tell them that if they want their own right to life to be respected they must do the same for their fellows.

    —–“They can work that out for themselves. They can also agree that in a just and fair society, access to the necessities of life should be guaranteed to all.”

    But they haven’t worked it out as is evident from the fact that they kill babies without a qualm and are, as we correspond, planning to let old people die who are getting in their way. In a fair and just society, babies and seniors are not assassinated for the convenience of the ruling class. Indeed, you cannot even comment on the issue. So, clearly, you have not really “worked things out.”

    Indeed, when atheists “work out a morality,” they conceive one that is congenial with their individual inclinations, which means that they condemn sins they don’t commit and ignore sins they do commit. Hence, the atheist who steals will condemn violence; the atheist who fornicates will condemn cruelty of speech; and the atheist who slanders will condemn laziness—and so it goes. Also, as Clive has pointed out, atheists cannot provide a rational justification even for those things that he does condemn. If a man doesn’t conform his behavior to a moral code, he will find a moral code that conforms to his behavior.

    —-“Those societies that don’t see it that way tend to be those that subscribe to some sort of authoritarian and absolutist belief system, be it political ideology or religion.”

    Most societies all throughout history have been characterized by a master/slave relationship between the ruling class and its subjects. Political freedom is a rarity and the conditions that foster it are well known. Both atheists and religious fanatics militate against those conditions. If you are curious about the moral principles necessary for a well-ordered society, you can begin with “On Ordered Liberty,” by Samuel Gregg.

  319. Correction: Also, as Clive has pointed out, atheists cannot provide a rational justification even for those things that they do condemn.

  320. Dave Wisker (#317)

    Please convey my thanks to Art Hunt for his kind invitation to comment on his blog. I may do so, when I get a free moment.

    I was, however, intrigued by a comment which Art Hunt directed at bornagain77:

    ba77, you are throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend, let alone address. One item is interesting, though. Specifically, the study you mention in #306 is actually a clever idea that strikes at the heart of a favorite ID notion – namely, that there is something called CSI (or FCSI) hidden inside of living things. The proposal discussed in the paper you cite explains how phenotype and its control is a decidedly low or zero-CSI proposition. I’m delighted that you would bring this to the attention of the Uncommon Descent crowd. (Emphases mine – VJT.)

    Here’s the link once again.

    Glinsky G.V. Phenotype-defining functions of multiple non-coding RNA pathways. 2008. Cell Cycle 7(11): 1630-1639.

    What puzzles me is that the same paper was cited by Dr. Richard Sternberg recently to support a very different conclusion. Sternberg is no fool, as I think everyone will acknowledge. In an article entitled How The Junk DNA Hypothesis Has Changed Since 1980 at http://www.evolutionnews.org/2009/10/ (scroll down to October 8, 12:39 p.m.), Sternberg writes:

    Instead of 90% of the human or fly genome being junk, it seems that 90% or more of chromosomal DNA has some kind of specific developmental function, given the available data. Indeed, the emerging picture is that the species-specific nonprotein-coding regions encode numerous RNAs that help to shape the phenotype in ways that we are only beginning to understand.42 43 44 45 46 This is especially true for the transposable element fraction of human chromosomes—about 50% of our DNA—much of which is arranged and expressed in a taxon-specific manner. 33 47 48 49 Part of the reason for why a human is not a chimp is not a cow is not a whale, then, is that each species has its own set of sui generis “genes” — genomic texts specifying unique RNAs or even proteins that are used in embryogenesis.

    To put everything into perspective, I’ll mine another quote from a paper worth reading:

    We now know that more of the DNA in eukaryotic cells is copied into RNA than previously had been thought. Many of these transcripts serve regulatory instead of template functions in gene readout. Some of these newly recognized RNAs come from regions of the genome that had heretofore been deemed “junk DNA,” yet no one could answer the obvious question: if “junk,” then why still around? Before memory fades, we should note that there were some reasonably well articulated ideas 30-40 years ago that anticipated these recent discoveries.1

    Indeed, those were the very same well-articulated ideas that the selfish DNA hypothesis was supposed to have dispensed with, once and for all.

    How things have changed since 1980. (Emphases mine – VJT.)

    (The reference to Glinsky is #42.)

    “Zero-CSI”? Dr. Sternberg doesn’t seem to agree. Hmmm….

  321. Mr BA^77,

    Want to match peer review Dave?

    Lets see I’ll match your 2005 paper with:

    There follows six links to non-peer reviewed web pages. So I’m not quite sure what ‘match’ means in your opening sentence.

  322. Well Dave,
    Apparently Art thinks he has got all this figured out, so once again I ask why don’t you guys send his paper to Axe? or at least get it published in peer-review? I saw a passing reference to me in which Art so graciously said I was “throwing a whole lot of irrelevant stuff at an argument that you have yet to comprehend,” Well that is quite a statement from someone who failed to comprehend the fact that Junk DNA was not Junk nearly two years after ENCODE,,, As well I noticed that he flippantly blew off the staggering level of information inherent in a protein by trying ever so subtly to imply information could be had on the cheap,,, (nearly in one sentence did he ever so softly combine the two deceptions). Well now I guess that you guys will also have to send his paper to Abel since it seems our Mr. Hunt thinks he has found a way to falsify Abel’s null Hypothesis for information generation,,, (If you want I will personally send it to Abel, so he made get a good laugh, and since you guys don’t seem willing to let Hunt’s paper get the scrutiny it truly deserves though you both jump up and down that it is “the truth” and primarily relevant, ignoring all contradictory evidence, just so to justify your atheism) I also would like to refocus on this I posted previously. that Mr. Hunt so graciously blew off by referencing my ignorance on the matter (as if he has a clue how this information generation occurs):

    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.”

    Dave (and now the condescending Hunt) do you realize how much functional information is required to achieve a simple “process control loop” such as the dynamic cruise control loo we find in the proteinp?? Well lets take a look:

    For a protein to be “complete in its information content”, in its ability to “dynamically cruise control” it would have to implement three different algorithmic forms of information: Proportional (P) Integral (I) and Derivative.

    PID controller:
    Excerpt: 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

    The equations involved for getting even this minimal level of “cruise control” for a dynamically interactive protein are staggering to put it mildly. (Page down on the wiki article to get a small taste of the equations I’m talking about) Several complex equations, which are derived from the basic PID platform of equations, are necessary to achieve different forms of simple process control, in different scenarios, in chemical industry. Many of these complex equations will surely be found to be integrated and overlapping. within the protein structure itself, so as to be utilized by the proteins in its “dynamic environment”(i.e. the information for “cruise control” must reside within the protein with no recourse to the DNA for correction once the protein is made). In such a demanding “process” as is found in life it is simply ludicrous to suppose the equations implemented within the protein structures themselves will be anything less than “tailor-made” for each individual protein. There is simply no other way for a protein to achieve such “sufficient” self-control, or any control at all for that matter, unless this type of specific “tailor made” algorithmic information is inherent within the structure of each individual protein… (I do have a college degree in process control so, contrary to Hunt’s insinuation, I do have a clue what I’m talking about in this matter!) Shoot it is in realizing the staggering amount of engineering to individual proteins that this would require that I realize even the 1 in 10^77 estimate of Axe may be far to generous for finding a specific functional protein within sequence space.
    So Dave (And now Dave’s hero Mr. Hunt), to prove me wrong all you have to do is falsify Abel’s null hypothesis, which brings us back to square one does it not Dave?

  323. Look at the 49 peer reviews on the bottom of the first link NAK!

  324. born,

    Art isn’t my ‘hero’, but a longtime personal friend. I also happen to respect his professional work with RNA (which is the main focus of his lab).

  325. Mr BA^77,

    So I can write a web page about how the moon is made of green cheese, and links to 49 peer reviewed papers makes mine the equivalent of peer reviewed?

    But I see that in your next few messages, you are only quoting peer reviewed papers. Thank you.

  326. Actually Nak, since you claim to not believe in a Creator, you would have to write a paper of how the moon evolved into green cheese, instead of how it was “made” out of green cheese. LOL

  327. vjtorley @ #320:

    When I call regulation by microRNA a low CSI proposition, I am following this outline of reasoning:

    1. microRNAs (miRNAs for short) act by base-pairing to other target RNAs.

    2. Target recognition is a matter of as few as seven nucleotides (see this essay for some more on this).

    3. Some simple math shows that any seven-nt sequence will occur, randomly and by chance, fairly often in a eukaryotic genome, and that many, many more sequences are but one or two mutational steps away from being the target of a given miRNA.

    4. If, as many (such as Glinsky) are assuming or claiming, miRNAs have a large impact on phenotype, it stands to reason that phenotype and phenotypic variation is well within the reach of random natural processes.

    5. “Random, natural processes” seems to be the antithesis of CSI. Hence my assertion.

    I don’t know why Sternberg might hold up microRNAs as examples of high-information moieties (if that is what he is doing – I haven’t read his essay). If that is really where he is going, then he is wrong.

  328. Mr BA^77,

    I’m sure that if radio-telescopes ever detect lactic acid or lactose molecules floating in space, we will never hear the end of the stories like this! ;)

  329. born,

    So Dave (And now Dave’s hero Mr. Hunt), to prove me wrong all you have to do is falsify Abel’s null hypothesis, which brings us back to square one does it not Dave?

    Actually, it doesn’t. Square one is addressing Art’s assessment of Axe’s work, from which, since you steadfastly refuse to address them, we have never left.

  330. Well Dave, you know as I reflect on this, I realize that highly advanced algorithmic math must be “built” into every single amino acid used in life (a rather surprising finding which is staggering evidence for Design in and of itself), and to actually get the precise level of “algorithmic PID process control” that is conclusively shown to exist within the structure of the protein itself, the proteins must be “precisely sequenced” per each correct algorithmic amino acid to achieve the “specific algorithmic process function” of optimal functionality that we find in the individual proteins. I can assure you in the math exams I took using PID equations to solve process control problems, that using a “close” equation to solve a specific process control problem was not an option and was not an answer the instructor would accept. The answer was either exactly correct or it was completely wrong. So as it is in life, for instead of failing a test as I did a few times, the life-form most often dies for not being completely correct. And as Behe has elaborated on this week on ENV, there is now evidence that shows, that this “specificness” of process functionality, is present in “more and less” complex proteins of similar specific function. Thus supporting the strong inference that the “equations of algorithmic amino acids” must be specifically sequenced to achieve specific process control functionality. There simply is no other way to “engineer” this precise level of functionality.
    Now if Hunt actually wanted to do something of worth instead of chase his tail in a circle, he should try to figure out exactly which piece of algorithmic information is inherent in each amino acid so that we may actually try to construct correct mathematical models of protein functionality. That would be something I would buy him a beer for!

  331. Thank you ladies and gentlemen. It is so good to have at least one thread going strong.

    Interestingly, the discussion demonstrates one of the basic tenents of Christianity. God does not force Himself on anyone. You will never find an absolute proof of God. What you find is just enough evidence if you are willing to believe, and not enough evidence if you do not want to.

    As one who made the transition from anti Christian to Christian at age 49 I can tell you how accurate that is. Not one thing in the universe changed when I opened myself to the possibility that Christ is God, but for the first time I saw how it all fits together. It really is a simple system composed of extradinarily complex parts and it works so well. We can find joy in the simplicity of the overall system and likewise enjoy delving into the most complex depths. But they all work because they are designed to work.

    My sympathies are with the deniers. Accepting Christ does mean accepting the need to change and act in a very specific manner (even though we usually have a difficult time living up to it). I did not want to accept that “control” either.

    Interestingly, the opposite has occurred. I am freer, happier, and more in control of my life.

    God Bless You All,

    Gesualdo

  332. vjtorley,

    Many thanks for the link to the Cambrian article– I have read Meyer’s original article on information and the Cambrian Explosion, and it was nice to have another. I have done some thinking about the Cambrian Explosion, and will post it later when I have time.

  333. born,

    I actually appreciated your thoughts in that last post–it gives us something to hang a potentially interesting discussion on. I’ll be replying later whenb I have time. Probably the weekend.

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