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This article by a theistic philosopher of science gives a brief account of how the ribosome manufactures proteins, and presents the usual chicken and egg problem for evolution. Does anyone have an answer for his observation?-http://darwins-god.blogspot.com/2010/01/ribosome-checks-for-translation-errors.html-Mine is DNA was pre-coded to make the ribosome.

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This article by a theistic philosopher of science gives a brief account of how the ribosome manufactures proteins, and presents the usual chicken and egg problem for evolution. Does anyone have an answer for his observation?
> 
> http://darwins-god.blogspot.com/2010/01/ribosome-checks-for-translation-errors.html&... 
> Mine is DNA was pre-coded to make the ribosome.-Interesting, he's really tackling an origins question and not one of evolution or natural selection. He's asking "how did ribosomes evolve property 'x,'" when clearly life as we can describe requires ribosomes to function. -That's why his argument spins its wheels here.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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This article by a theistic philosopher of science gives a brief account of how the ribosome manufactures proteins, and presents the usual chicken and egg problem for evolution. Does anyone have an answer for his observation?
> > 
> > http://darwins-god.blogspot.com/2010/01/ribosome-checks-for-translation-errors.html&... > 
> > Mine is DNA was pre-coded to make the ribosome.
> 
> Interesting, he's really tackling an origins question and not one of evolution or natural selection. He's asking "how did ribosomes evolve property 'x,'" when clearly life as we can describe requires ribosomes to function. 
> 
> That's why his argument spins its wheels here.-We're back to the obvious comment. We only know life that comes from life, and we may never know how inorganic chemistry accomplished the switch to organic chemistry, especially when you add up all the necessarily different protein molecules needed to function smoothly with each other in the simplest single cell we know, mycoplasma. Viruses don't count. They must parasitize life to continue 'sort-of living'.

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This article by a theistic philosopher of science gives a brief account of how the ribosome manufactures proteins, and presents the usual chicken and egg problem for evolution. Does anyone have an answer for his observation?
> > > 
> > > http://darwins-god.blogspot.com/2010/01/ribosome-checks-for-translation-errors.html&... > > 
> > > Mine is DNA was pre-coded to make the ribosome.
> > 
> > Interesting, he's really tackling an origins question and not one of evolution or natural selection. He's asking "how did ribosomes evolve property 'x,'" when clearly life as we can describe requires ribosomes to function. 
> > 
> > That's why his argument spins its wheels here.
> 
> We're back to the obvious comment. We only know life that comes from life, and we may never know how inorganic chemistry accomplished the switch to organic chemistry, especially when you add up all the necessarily different protein molecules needed to function smoothly with each other in the simplest single cell we know, mycoplasma. Viruses don't count. They must parasitize life to continue 'sort-of living'.-Right, but that has no bearing at all on evolution. It's an origin of life question and has nothing to do with evolution OR natural selection. We've agreed previously that evolution doesn't need to explain the origin of life in order to explain life. This guy's argument fails because he's attacking evolution by arguing about the origins of life; these are two different topics. -What we really have here is an Einstein moment: Like relativity, we have an awesome explanation for life itself, but have no explanation for how life came to be.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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This is the same theistic philosopher I've presented before. The important point is not his theistic take but his observations about how complex the whole DNA translation process is. Note the comments that disagree with his view of evolution. -http://darwins-god.blogspot.com/2010/01/proteins-that-regulate-protein.html

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Again to the theistic philosopher. It was reported a few days ago that bats and whales use the same protein in their sonar setups. The very large protein is Prestin with a signature nine amino acids in both species. The mechanism of hearing is very complex with marked amplification. Please ignore the theistic side of this fellows remarks. The point I am making is the utter complexity of life, irreducible complexity for some of us.-http://darwins-god.blogspot.com/2010/01/prestin-and-darwins-gardener.html

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One more column from the theistic philosopher. In this column he describes the chicken and egg problem for Darwinists. The current studies show how a complex mechanism is present in current single-celled life, and of course multicellular life, to drive DNA to somatic variation to respond to challenges. It looks pre-planned to allow for evolution once life starts. That has been my observation all along. Evolution is planned for in genetic material and the other mechanisms that influence it. -The problem is: did original life start with these mechanisms in place, or did life 'evolve' really with no way to evolve in the first place? Darwin folks kick this back to 'origin-of-life to escape dealing with the issue. -Please look at the link provided to go to James Shapiro's review from which this philosophic comment derives. The philosopher first:-http://darwins-god.blogspot.com/2010/01/evolution-of-serendipity.html-Shapiro: The whole article is available below the abstract:-http://www.mobilednajournal.com/content/1/1/4-Shapiro's conclusions below:-Conclusion: a 21st century view of evolutionary change
Our ability to think fruitfully about the evolutionary process has greatly expanded,thanks to studies of mobile DNA. Laboratory studies of plasmids, transposons,retrotransposons, NHEJ systems, reverse transcription, antigenic variation in prokaryotic and eukaryotic pathogens, lymphocyte rearrangements and genome reorganization in ciliated protozoa have all made it possible to provide mechanisticexplanations for events documented in the historical DNA record [6]. We know thatprocesses similar to those we document in our experiments have been majorcontributors to genome change in evolution. Using our knowledge of genome restructuring mechanisms, we can generate precise models to account for many duplications, amplifications, dispersals and rearrangements observed at both the genomic and proteomic levels.
The genome DNA record also bears witness to sudden changes that affect
multiple characters at once: horizontal transfer of large DNA segments, cell fusionsand WGDs. These data are not readily compatible with earlier gradualist views on thenature of evolutionary variation. However, we are now able to apply the results offindings on the regulation of natural genetic engineering functions in the laboratoryand in the field to make sense of the DNA record. Cell fusions and WGDs are eventswe know to activate DNA restructuring functions (Tables 3 and 4). Thus, it is notsurprising that bursts of intracellular horizontal transfer, genome reduction andgenome rearrangement follow these initial abrupt changes in the cell's DNA. How anewly symbiotic cell or one with a newly doubled genome manages the transition to astable genome structure that replicates and transfers reliably at cell division is anotherimportant subject for future research. The lessons we learn about silencing mobileDNA by internal deletion [12] and RNA-directed chromatin modification [167] arelikely to prove helpful starting points.
Although there remain many gaps in our knowledge, we are now in a position
to outline a distinctively 21st century scenario for evolutionary change. The scenarioincludes the following elements:
(1) hereditary variation arises from the non-random action of built-in
biochemical systems that mobilize DNA and carry out natural genetic
engineering;
(2) major disruptions of an organism's ecology trigger cell and genome
restructuring. The ecological disruptions can act directly, through stress on
individuals, or indirectly, through changes in the biota that favour unusual
interactions between individuals (cell fusions, interspecific hybridizations).
Triggering events continue until a new ecology has emerged that is filled
with organisms capable of utilizing the available resources;
(3) ecologically-triggered cell and genome restructurings produce organisms
which, at some frequency, will possess novel adaptive features that suit the
altered environment. Novel adaptive features can be complex from the
beginning because they result from processes that operate on pre-existing
functional systems, whose components can be amplified and rearranged in
new combinations. Competition for resources (purifying selection) serves
to eliminate those novel system architectures that are not functional in the
new ecology;
(4) once ecological stability has been achieved, natural genetic engineering
functions are silenced, the tempo of innovation abates, and microevolution
can occur to fine-tune recent evolutionary inventions through successions
of minor changes.
This 21st century scenario assumes a major role for the kind of cellular
sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel
Prize address [1]. Such a cognitive component is absent from conventional
evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. This 21st century viewof evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions.

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PART ONE-David has referred us to several eye-opening articles. The horizontal transfer of genes theory is particularly interesting (How DNA Might Have Developed), especially as Mark Buchanan says there's evidence of it in species that include a frog, lizard, mouse and bushbaby. Could you explain how this process takes place physically?-The James A. Shapiro post is by far the most stimulating, and I'll return to it in a moment, but first let's deal with the "theistic philosopher" Cornelius Hunter. The science is revealing, but the conclusions in his various articles (my quotes are from different ones) seem to me extremely simplistic and even contradictory. He reproduces Antony Flew's garden parable, and uses it to ridicule the "religious beliefs" of the blindly faithful evolutionist to show that there is NO gardener (i.e. evolution is wrong). He doesn't seem to realize that the parable applies equally to his own religious beliefs, and actually finishes this article by saying: "One way or another, there IS a gardener" (my capitals). Orwell would have called this "doublethink". -Hunter rightly, in my view, castigates those evolutionists who believe that "evolution creates the mechanism that evolution requires to work". We've discussed this at length ourselves: evolution and abiogenesis are two different theories. But he uses this to dismiss evolution itself as "a truly silly idea". Is evolution silly just because we don't know what created the mechanisms that set it in motion? In that case, he might as well dismiss his idea that God created the world, since we don't know what created God (Dawkins' favourite non-sequitur). Darwin himself was careful to make the distinction between evolution and origin: "How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated" (Difficulties on Theory). This is not a matter of "turning a blind eye". We don't need to know the origin to believe in the process. Hunter must know perfectly well that not all evolutionists are atheists, and not all evolutionists ascribe the mechanisms to "serendipity". As for evolutionists failing to deliver evidence, even if we know the word is highly adaptable, I don't think I'd be the only one to regard this as a much better example of "turning a blind eye".-Finally, he attempts an aphorism: "Religion drives science, and it matters". An atheist might with equal absurdity claim that atheism drives science. What drives science should be science. And so it is with a sigh of relief that I turn to James A. Shapiro. (See PART TWO.)

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PART TWO-Shapiro's article on "Mobile DNA and evolution in the 21st century" is a model of scientific neutrality, and some of the discoveries are breathtaking, though for a layman like me a lot of it is far too technical. I found a less daunting, and far shorter article called "A Third Way" on: www.bostonreview.net/BR22.1/shapiro.html -I'll quote from both articles, though. It seems to my untrained eye that he disposes once and for all of the gradualism so essential to Darwinism: "We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures." -He thinks the new view of genome restructuring "helps us to formulate reasonable hypotheses about two unresolved questions in evolutionary theory: (i) the connections between evolutionary change and ecological disruption; and (ii) the origin of complex adaptive novelties at moments of macroevolutionary change." This is a huge claim, but he goes into details, with emphasis on the cell as a "multilevel information-processing entity". Matt will be pleased to read this: "Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated."-Linking up with the Buchanan article above, he says: "From countless experiments, we now have overwhelming evidence for horizontal DNA transfer between species and between the three kingdoms of living cells." He also refers to WGD (whole genome doubling) as "another evolutionary process outside the Darwinist perspective that occurs suddenly (that is, within a single generation) and simultaneously affects multiple phenotypic characters." The objection to gradualism that it is "too slow and indeterminate a process to account for natural adaptations" can be met by molecular mechanisms that "utilize the demonstrated capabilities of mobile DNA and other natural engineering mechanisms." One of these is the response to a "genome shock" (e.g. a geological upheaval) as a result of which "novel changes at multiple locations in the genome can arise within a single generation and can produce a progeny expressing all the changes at once. There is no requirement, as in conventional theory, that each individual change be beneficial by itself." But Shapiro does not pretend to have all the answers: "How a newly symbiotic cell or one with a newly doubled genome manages the transition to a stable genome structure that replicates and transfers reliably at cell division is another important subject for future research." And "there remain many gaps in our knowledge."-Let me finish with some quotes that are relevant to our own discussions: -"The potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise." (He includes Dawkins.) -The 21st century view of evolution "answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties." -"Dogmas and taboos may be suitable for religion, but they have no place in science."-Once again, my thanks to David for bringing all of this to our attention. I am now a Shapiro fan!

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> "The potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise." (He includes Dawkins.) 
> 
> The 21st century view of evolution "answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties." 
> 
> "Dogmas and taboos may be suitable for religion, but they have no place in science."
> 
> Once again, my thanks to David for bringing all of this to our attention. I am now a Shapiro fan!-One can summarize Shapiro in one simple expression of his: DNA+0=0. This puts to bed the RNA world concept. Just naked RNA or DNA can do nothing. There must be the whole suite of complex protein molecules to do the translations and productions of proteins that create living cells. This is the chicken-and-egg puzzle that faces those folks who love an automatic 'abiogenesis'. Shapiro offers his opinion that evolution is capable of doing this, of being able to create all of this complex mechanism bit by bit, or in one big jump, driven by what? 'Survival of the fitest" does not apply to molecules. It is his own opinion. There are no facts to follow here. He is an evolutionist at heart, and won't make the jump to accepting my proposal. That is fine with me. He is extremely helpful to my point of view. I think he is proving my point of view, bit by bit. By the way, Shapiro is a practicing Jew while I am not. What does he worship? That is where I struggle. I cannot mouth Jewish litergy, and not beiieve in what is described.

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DAVID: Just naked RNA or DNA can do nothing. There must be the whole suite of complex protein molecules to do the translations and productions of proteins that create living cells. This is the chicken-and-egg puzzle that faces those folks who love an automatic 'biogenesis'. Shapiro offers his opinion that evolution is capable of doing this, of being able to create all this complex mechanism bit by bit, or in one big jump, driven by what? "Survival of the fittest" does not apply to molecules. It is his own opinion. There are no facts to follow here. He is an evolutionist at heart, and won't make the jump to accepting my proposal.-This post comes as a surprise to me. I may have misunderstood Shapiro. The longer article is entitled "Mobile DNA and evolution in the 21st century", and certainly the impression I had from the two articles I read was that he was not starting from scratch, as you are. I thought he was examining existing mechanisms which might explain complex organs, the origin of so-called "novelties", and the relationship between evolutionary change and the environment. NOT that he was explaining how the mechanisms themselves were originally formed. I will, of course, take your word for it, as these two articles are all I've read, but as I like speculating, let me at least offer you a little theory, since you are struggling to reconcile Shapiro's science with his religion.-What had impressed me so much was the absolute neutrality of the two articles. He seems to be presenting the scientific arguments for the different methods by which evolution works (e.g. whole genetic doubling, which may result in multiple changes within a single generation), and from his approach I had actually deduced that he was an agnostic. He certainly criticizes both Creationists and Darwinists for ignoring the latest developments. There is no question that he is, as you say, "an evolutionist at heart", but so are you, aren't you? You reject gradualism and believe in punctuated equilibrium, as he appears to do. The various extremely complex mechanisms that he proposes may well be used to support your point of view ... that it's asking too much to attribute them to chance ... but he doesn't say so. Now, though, since you tell us he is a practising Jew, I can't help wondering if in fact he DOES take your point of view, i.e. that there is a designer responsible for the original mechanisms. Is it possible that he's acting as the model scientist should, and simply separating his scientific research from his faith? As we know of old, evolution is perfectly compatible with theism, and you don't need to taint your scientific research with your subjective beliefs, as Dawkins and Hunter do in their different fundamentalist ways. Just a thought ... and of course you know far more about him than I do.

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I guess you misunderstood my comment. I was mentally leap-frogging to origin of life; he makes the statement that evolution can account for the entire complement of supporting molecules to handle the translation of information in DNA. That makes me think that he is presenting a chicken and egg quandry. How does that all appear, if DNA has THE INFORMATION FOR LIFE? DNA cannot translate itself. RNAzymes can only reproduce themselves. So how can it happen? The other mechanisms first and then DNA appears: de novo mechanisms out of the blue? We only know life as it comes from other life. Further research will only intensify this quandry, not clarify it. George, any thoughts?

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While I still have plenty of time to read Shapiro's books, I've been catching up on these posts at a slow rate. -While I'll often argue and play devil on almost all topics, I have to say here that there's a few points I'd like to draw attention to here. -1. I'm perfectly fine with natural selection playing the role it does; a filter. -2. I've no problems with genetic transfers and complexity.-What I'd like to call to attention is a more core notion. -Why is it more reasonable to conclude that life was designed? We all agree its not a scientific claim, so I still wonder why taking an unprovable position is more reasonable? We can't verify anything about a creator, and although there is an analogy to computers often made in the name of biology, it isn't the same thing because we can write programs that can randomly generate other small and useful programs. And there would be no way to determine if these programs were designed by a human or by a computer, thus recreating a similar chicken-and-egg scenario for an outside observer. -Any thoughts?

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

3988 views

While I still have plenty of time to read Shapiro's books, I've been catching up on these posts at a slow rate. 
 
> 
> 1. I'm perfectly fine with natural selection playing the role it does; a filter. -I agree 
> 
> 2. I've no problems with genetic transfers and complexity.-No problem here.
>
> Why is it more reasonable to conclude that life was designed? We all agree its not a scientific claim, so I still wonder why taking an unprovable position is more reasonable? And there would be no way to determine if these programs were designed by a human or by a computer, thus recreating a similar chicken-and-egg scenario for an outside observer. 
> 
> Any thoughts?-Very simply, since we have no concept of how life got here, in the first place, we are left with it was either designed or it arose, somehow, bit by bit by chance. Since it is so complex, and getting more and more complexer by the year, only design seems feasible. Chance is lessened every year as the complexity gets more complex. And you haven't even raised the major point. All of the complex mechanism is needed working together at the same time. DNA needs continuous copy protection. From the beginning. How would you arrange for that?. By chance? No way.

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While I still have plenty of time to read Shapiro's books, I've been catching up on these posts at a slow rate. 
> 
> > 
> > 1. I'm perfectly fine with natural selection playing the role it does; a filter. 
> 
> I agree 
> > 
> > 2. I've no problems with genetic transfers and complexity.
> 
> No problem here.
> >
> > Why is it more reasonable to conclude that life was designed? We all agree its not a scientific claim, so I still wonder why taking an unprovable position is more reasonable? And there would be no way to determine if these programs were designed by a human or by a computer, thus recreating a similar chicken-and-egg scenario for an outside observer. 
> > 
> > Any thoughts?
> 
> Very simply, since we have no concept of how life got here, in the first place, we are left with it was either designed or it arose, somehow, bit by bit by chance. Since it is so complex, and getting more and more complexer by the year, only design seems feasible. Chance is lessened every year as the complexity gets more complex. And you haven't even raised the major point. All of the complex mechanism is needed working together at the same time. DNA needs continuous copy protection. From the beginning. How would you arrange for that?. By chance? No way.-This will kind of be a summary of previous arguments--I just don't find this line of argument compelling. In light of the fact that we don't have a mechanism as to how life arose, your argument of "chance vs. design" is a false dilemma, because we can't reasonably compute the statistic without a known mechanism. At the moment, by your own admission the best expert in the field (Shapiro) has at best a guess that energy cycles was a likely beginning. And from my interpretation of your words, I can't name a single piece of "less-important" decisions I've made essentially using a "negative evidence" argument. -Even more probable (when considering a creator) is chance plus design. If we accept an imperfect creator (which I accepted that possibility long ago) then we have to accept mistakes; and accidents. Probably more informed by my time spent as a musician than as a scientist--I often start with a plan for how a song will be written--and then keep the mistakes. I think it clearly more likely that similar things happen in nature under this meta-physic. -Another thing to think about. What it seems to me that you are arguing, is that since the creator still influences life, then that means that you are arguing that biochemical components are expressing attributes of consciousness. To me this is akin to arguing that molecules are intelligent. Stepping back to the program paradigm, I would never argue that pieces of a program are intelligent. And neither could I truly argue that they were designed, knowing what I know about small programs. -Another thought that just struck my mind. Humans design things to solve problems. If we're ultimately an expression of the creator, then what purpose do we have? What problem do we solve? George Carlin's old bit about the earth and plastic is a great one here. -Doesn't a God that one cannot truly commune with destroy the importance of that question? Even if I accepted a creator such as the one you've discussed, it still is completely devoid of all the benefits one normally associates with a deity.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> This will kind of be a summary of previous arguments--I just don't find this line of argument compelling. In light of the fact that we don't have a mechanism as to how life arose, your argument of "chance vs. design" is a false dilemma, because we can't reasonably compute the statistic without a known mechanism. -But we do understand many of the parts of genome reporduction. We know DNA, RNA, histones, methylation, enzymes, etc. The complexities involve feedback loops and the judgement of proper levels of various molecules that are produced; lets call that chemostats. We know that 20 left-handed amino acids are essential to the manufacture of all this, and right-handed nucleotides. Therefore, we do know that we have to get from A to B to C, and even though we don't know how 20 amino acids appeared, when only 8 are found in meteorites one should be able to calculate the odds against chance from that point. Dembski did it for the flagellum, and he found enormous odds. I just don't know enough math to even try. -But even further is the issue of providing both the code and the decoder, with almost perfect control over the decoding at all times. We can start with the assumption of an already existing single-celled animal, as simple as micoplasma. How did code and decoder arrive together at the same time in development? 
> 
> Even more probable (when considering a creator) is chance plus design. If we accept an imperfect creator (which I accepted that possibility long ago) then we have to accept mistakes; -I accept this approach also. If the mechansim for life included a code for evolution, then natural selection is a filter of influence. Progression of life forms can lead to blind alleys along the way. The next question is: is the evolutionary drive self-correcting or must it try a scattershot approach with natural selection left to sort it out? Both thoughts are feasible.
> 
> Another thing to think about. What it seems to me that you are arguing, is that since the creator still influences life, then that means that you are arguing that biochemical components are expressing attributes of consciousness. -The way the molecules shepherd along the decoding and reproduction process, several authors have said they act like they are thinking. Just a metaphor, of course.
> 
> Another thought that just struck my mind. Humans design things to solve problems. If we're ultimately an expression of the creator, then what purpose do we have? -Back to Frank. If we are created we are fulfilling God's purpose. And then there is the approach of Victor Frankl: "Man's Search for Meaning", in which he gave his life meaning to survive in the concentration camps.
> 
> Doesn't a God that one cannot truly commune with destroy the importance of that question? Even if I accepted a creator such as the one you've discussed, it still is completely devoid of all the benefits one normally associates with a deity.-Those are benefits you imagine from what religions propagandize. To me God only offers the benefit of living a life. Anything else He might provide is lagniappe. As for God's silence, that is where the requirement of faith comes into play. Another book: "A Concealed God", by Stefan Einhorn. I can keep you reading for years. )

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And Dembski solved that problem incorrectly skewing his result by 100 orders of magnitude (against himself, I add). I reiterate that the fact he's not willing to fix an error (that would even work in his own favor) means he's deliberately dishonest. That book's been in print for over 10 years and no errata has appeared on his website to address this. I still don't know why you care to quote him, he is beyond contempt in my view. -All the rest of your post has some good critiques, but I stress that it is all based only on what we know at present, looking at life at present, etc. etc. -There isn't enough certainty in any of this to justify a creator--there's far too little information.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

4002 views


> And Dembski solved that problem incorrectly skewing his result by 100 orders of magnitude (against himself, I add). I reiterate that the fact he's not willing to fix an error (that would even work in his own favor) means he's deliberately dishonest. That book's been in print for over 10 years and no errata has appeared on his website to address this. I still don't know why you care to quote him, he is beyond contempt in my view. -David: "one should be able to calculate the odds against chance from that point. Dembski did it for the flagellum, and he found enormous odds. I just don't know enough math to even try". -I don't care if he made an error. My point was, obviously, he had some way of using necessary proteins to make such a calculation for 'chance',and by your own discussion his odds were more enormous that he stated. The discovery of the error only makes his point stronger, it seems to me, as it increases the odds against 'chance'. You are quite overly emotional about Dembski.

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> > And Dembski solved that problem incorrectly skewing his result by 100 orders of magnitude (against himself, I add). I reiterate that the fact he's not willing to fix an error (that would even work in his own favor) means he's deliberately dishonest. That book's been in print for over 10 years and no errata has appeared on his website to address this. I still don't know why you care to quote him, he is beyond contempt in my view. -
The error is 10^65, reducing the odds against chance: 10^-288 to 10^-223, if I remember the numbers correctly. Either way chance has 'no chance' And it appears that Dembski has a giant ego. My source:-http://www.cs.uwaterloo.ca/~shallit/tdr.html

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David
> 
> I don't care if he made an error. My point was, obviously, he had some way of using necessary proteins to make such a calculation for 'chance',and by your own discussion his odds were more enormous that he stated. The discovery of the error only makes his point stronger, it seems to me, as it increases the odds against 'chance'. You are quite overly emotional about Dembski.-The issue is a matter of honesty; he has been publicly confronted about this (and other errors, some of which I've already shown to you and you at least appeared to take them seriously.)-Dembski deliberately misleads through mathematical obfuscation. He does this because its the one thing that the majority of his audience is ignorant to (including yourself, by your own admission!) 
"I just don't know enough math to even try" -The goal of a practitioner of science isn't to obfuscate, but to clarify. -I've gone over exactly why Dembski's premises are wrong, he's calculating the odds of a single linear combination of events, as if there was only a single attempt at each step. This clearly wouldn't be the case with or without a designer. His formula also doesn't talk about time, which is something that he would absolutely need to provide. -I've enumerated a countless number of his fatal mathematical flaws throughout my time here, beginning with your initial probing of Information theory back on my first post.

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> I've gone over exactly why Dembski's premises are wrong, he's calculating the odds of a single linear combination of events, as if there was only a single attempt at each step. This clearly wouldn't be the case with or without a designer. His formula also doesn't talk about time, which is something that he would absolutely need to provide. -
I know he doesn't use time, but that is the "climbing Mt. Improbable" approach, which implies given enough time anything can happen. But Dembski's approach, in which he combines proteins to make a flagellum, involves so many thousands of required units, he comes up with those improbable numbers. The flagellum is very complex and has what I would call bushings and rotors as well as the sliding molecules that make up a wavy flagellum itself. It is in every sense a micro-motor.- I'm not such the one-time shot is such a bad approach in theory, with only 10^18 seconds of history to the universe, and the time for life to work on itself and make a flagellum starts only 3.6 billion years ago (not figuring the available seconds used before the need for a flagellum arose in evolution. We probably had amoebas first). If one 'climbs', what do we get first, a useless rotor, sliding proteins? I see this as irreducible complexity, a la' Behe. The inbetween stages are impossible to imagine if they present no function to help preserve them as time passes.They must develop simultaneously and provide some meaningful use. On the other hand there are exaptations in evolution, which look like pre-planing, hang around useless for as much as 200,000 years and then a use is found. Evolution describes these things with no Darwinian explanation, except from folks like J. Shapiro, who talks about changes driven by environmental challenges. But 200,000 years earlier? (I think I'm right, in my memory, that the human larynx dropped in position, that much earlir before speech developed).

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PART ONE-Matt, you've raised a lot of interesting points in this exchange, and although David has given you a comprehensive answer, I'd like to follow up myself on some of your responses to him and to me. Unfortunately, I'm always chasing you two because of the time lag!-MATT:......we can't reasonably compute the statistic without a known mechanism. -David has responded that a good deal of the mechanism of genome reproduction is known, and our knowledge lengthens the odds against chance. However, I'd just like to add that, as with many of the arguments, the above cuts both ways. Until the mechanism is fully known, it's impossible to say that Chance has a chance! I agree with you that you can't base belief on negative evidence, but nor can you base it on the hope that positive evidence will be found ... and that applies as much to chance as to design. In your latest post you explain why you prefer the materialist approach. That's fair enough, but the fact that we can study chance won't guarantee us any "ultimate truth". It simply gives us something more manageable, which makes us feel better (an argument often used against people's religious beliefs).-MATT: Even more probable (when considering a creator) is chance plus design. -David agrees and so do I. If chance was not built into the whole fabric, it would all be incredibly boring. It would be like knowing the result of every game before it's played. I really like your reference to song-writing. Some authors and composers do plan in advance, but they usually find their plans have to be abandoned: the melody/characters take over. Personally, if I know what's coming, I'm bored and I can't go on. The whole process is a voyage of discovery, and if there is a God, that's how I would imagine his process to be. Your observation about music also raises our old question of where the ideas come from. One set of cells tells you your melody should go in this direction, and another set tells you it should go in another direction? And which set of cells makes the final choice? And what cells bring you the melody in the first place, and why, and how?-MATT: ...since the creator still influences life, then that means that you are arguing that biochemical components are expressing attributes of consciousness.
I would argue the exact opposite. If there is a creator, the biochemical components will be shifted around by HIS intelligence until they can function independently according to the programme HE has built (which allows for the vagaries of chance). If there is no creative intelligence, and the molecules do the work all by themselves, that's when they need to have their own form of consciousness. Then they alone supply codes which require extraordinary intelligence just to understand, let alone create.-Continued in Part Two

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PART TWO-MATT: If we're ultimately an expression of the creator, then what purpose do we have?-If l've understood David correctly, he offers two answers: 1) "If we are created we are fulfilling God's purpose." This is a bit vague, but it sounds like a kind of deism (which I know is not David's belief) ... i.e. whatever we do is part of God's entertainment. In that case, the problem that we solve is God's boredom. 2) Victor Frankl's purpose became to "survive in the concentration camps", which suggests that life's meaning is whatever we think it is. This ties in with: "To me God only offers the benefit of living a life. Anything else He might provide is lagniappe" (I had to look it up. I'd call it a bonus). This is worth a thread all on its own. For those of us who have been privileged to lead a happy and fulfilled life, that surely has to be the most sensible philosophy. Whether God did or didn't give us this life, let's make the most of it and be thankful for anything good that comes our way. Any extras, like a paradisal afterlife, will be a bonus (though not even BBella's period of contemplation followed by a voluntary change of identity really convinces me that eternal life would be such a boon.) The drawback to this restricted approach, as always, is the folk who through no fault of their own have experienced little but suffering. Then, as you say, "such a creator is completely devoid of all the benefits one normally associates with a deity". I have misgivings about the concept of "tough love", especially when it's applied for instance to children killed off before they ever had a chance to be happy. Nor am I too keen on the concept of a deistic God, for much the same reason. But of course the fact that we may not like a particular concept has no bearing on the "truth" ... whatever that may be.-MATT: There is the possibility that our world simply IS with no distinction needed as to whether or not it was or wasn't created.-As you say, this is the Buddhist line, but I don't see it as an alternative. It simply ignores the question of how life arose on Earth. It's a philosophy rather than an explanation.-MATT: At the minimum I can safely make the claim that the universe needed no creator up until the point where abiogenesis is needed.-I'm not so sure. You yourself have pointed out how things are interconnected, and the so-called fine-tuning of the universe ... there are any number of factors without which life would have been impossible ... makes me reluctant to go as far as you. -MATT: You make the mistake of thinking that there's something wrong with being uncertain.-I smiled proudly at your suggestion that agnosticism is "quite possibly the bravest position one can take" ... especially since we agnostics find ourselves in conflict with both sides ... but I'm also constantly aware that in the grand scheme of things, one way or the other I am more of an idiot than a hero!

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dhw,
For the first portion, I can safely say I have nothing to debate. 
> MATT: Even more probable (when considering a creator) is chance plus design. 
> 
> .... Your observation about music also raises our old question of where the ideas come from. One set of cells tells you your melody should go in this direction, and another set tells you it should go in another direction? And which set of cells makes the final choice? And what cells bring you the melody in the first place, and why, and how?
> -Part of the answer to this question comes from some experiments on morality talked about by one of the radiolab podcasts I've mentioned before. When asked to kill an innocent, the entire brain flashes (on scans) and the answer was always no. When the question was asked about say, doing the same thing to a criminal, etc., the results weren't as emphatic. What it appeared to show was that some brain cells say yes, and some say no... what was apparent on every scan was that the consensus of cells always won, whatever action the participant chose. This is why some theorists from computing fields are suggesting that consciousness is an emergent phenomenon of cells; that who we are is the result of highly connected cells. -> MATT: ...since the creator still influences life, then that means that you are arguing that biochemical components are expressing attributes of consciousness.
> I would argue the exact opposite. If there is a creator, the biochemical components will be shifted around by HIS intelligence until they can function independently according to the programme HE has built (which allows for the vagaries of chance). If there is no creative intelligence, and the molecules do the work all by themselves, that's when they need to have their own form of consciousness. Then they alone supply codes which require extraordinary intelligence just to understand, let alone create.
> -Untangling a web of intelligences like this is hopeless. I hope it isn't like this!-> Continued in Part Two-[EDIT] I didn't finish my quick explanation on the issue of cellular quorums; in this explanation consciousness itself is still an immaterial thing; it has a physical cause but you cannot study consciousness itself by just studying the cells. I hope I'm not bungling this...

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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MATT: ...some theorists from computing fields are suggesting that consciousness is an emergent phenomenon of cells; that who we are is the result of highly connected cells. [...] in this explanation consciousness itself is still an immaterial thing; it has a physical cause but you cannot study consciousness itself just by studying the cells. I hope I'm not bungling this...-I suspect that the confusion comes from the theories rather than from you! None of these statements bring much clarification, which is not surprising given the complexity of the problem.-1) That "consciousness is an emergent phenomenon of cells" is self-evident, since we know cells are involved in the process. But does the process emerge from the cells, are the cells used by an immaterial identity that controls the process, or is it a mixture of both?-2) That "who we are is the result of highly connected cells" is also self-evident, since the body has an enormous influence on our identity, but this is not enough to describe, explain or account for consciousness or identity, unless we are to regard ourselves as automata.-3) The statement that consciousness is immaterial but has a physical cause could just as well read "consciousness is immaterial but has a physical manifestation". We don't know whether an immaterial element sets the physical element in motion or vice versa, but I have the impression that most of the time "I" make the wheels roll. "I" am of course a collection of highly connected cells, but back we go to 2).-If one day you and your computer buddies build a machine that is conscious, sentient, imaginative, creative etc., the mystery may be solved. I'm aware that such a project is in the pipeline, but you know what a sceptic I am. I'll believe it when...if...

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1) That "consciousness is an emergent phenomenon of cells" is self-evident, since we know cells are involved in the process. But does the process emerge from the cells, are the cells used by an immaterial identity that controls the process, or is it a mixture of both?
> 
> 2) That "who we are is the result of highly connected cells" is also self-evident, since the body has an enormous influence on our identity, but this is not enough to describe, explain or account for consciousness or identity, unless we are to regard ourselves as automata.
> 
> 3) The statement that consciousness is immaterial but has a physical cause could just as well read "consciousness is immaterial but has a physical manifestation". We don't know whether an immaterial element sets the physical element in motion or vice versa, but I have the impression that most of the time "I" make the wheels roll. "I" am of course a collection of highly connected cells, but back we go to 2).
> 
> If one day you and your computer buddies build a machine that is conscious, sentient, imaginative, creative etc., the mystery may be solved. I'm aware that such a project is in the pipeline, but you know what a sceptic I am. I'll believe it when...if...-There's a third option, prompted my Nietzsche and seems to apply to your skepticism:-"There are still harmless self-observers who believe that there are "immediate certainties,"; for example, "I think," or as the superstition of Schopenhauer put it, "I will"; as though knowledge here got hold of its object purely and nakedly as "the thing in itself," without any falsification on the part of either the subject or the object. But that "Immediate certainty" as well as "absolute knowledge" and "the thing in itself," involve a contradictio in adjecto, I shall repeat a hundred times; we really ought to free ourselves from the seduction of words!"-It appears here that you are arguing purely from the realm of abstract theory. I will posit here that your claim in 3 can be rightly thrown out. If I read this correctly, you're stating that if we build a conscious machine that exhibits the same level of creativity as a human, it still wouldn't verify anything about materialism because there would be no way to tell the difference between a consciousness created by the individual processing units and some immaterial force swooping down and making the computer act like a human? -Your skepticism seems to live purely in a theoretical realm; it makes no practical difference whether or not the machine was sparked to life by an outside force or not, because we have no reason to believe that explanation. To me, practicality supersedes the theoretical. We both agree that there would be no way to know if an immaterial force animated the machine (or ourselves.) I say then, this gives us the right to throw it out as a valid explanation--because though it is possible in the realm of theory it isn't testable in the real world, and thus forever beyond our reach. -I see a deeper explanation of my more "Buddhist" perspective is in need--maybe it needs its own thread. In regard to human problems and human conditions; a prime cause is meaningless. The only thing that truly matters is the here in now. In both Buddhism and Nietzsche, they would read this search a fool's game because the current nature and state of humanity is an aberration; In Buddhism the thought "I think" is delusion. If you're familiar with Freud, "I think" comes only from the ID and I think it would be right to say that Buddhism thinks of consciousness similarly to the ID and that is why they practice "here and now." In Nietzsche's terms, all of this is the result of a language based on subject and predicate: our language is necessarily deterministic, this necessarily means that we then try to think of everything as deterministic (even when its not) and according to Nietzsche, the quest for truth (as you appear to be applying it) is tripped up in a pocket of your own creation--language has lead you down a false path. Skepticism is useful, but at the point where skepticism stops being feasible in the here and now we should abandon it. Sometimes you appear to hold to skepticism beyond that which is reasonable. Why would your alternative explanation in 3 be any more reasonable? -David's idea of a creator is akin to simply pointing and saying "I see God," and that's it. To me, even theology must have practical uses; and though I also agree that to a greater or lesser degree man creates his own meanings (even if its taking someone else's) David's view leaves zero practicality. It doesn't actually inform us (because at this state he admits it is faith) nor does it give us any basis to do--anything at all. I can't DO anything with it. In practical terms, it has absolutely zero impact on anything we do. And at least in my terms, I measure the value of an idea in terms of its usefulness.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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I wrote: If one day you and your computer buddies build a machine that is conscious, sentient, imaginative, creative etc., the mystery may be solved. I'm aware that such a project is in the pipeline, but you know what a sceptic I am. I'll believe it when...if...-I won't repeat your immediate comments on this, because I'm afraid they're based on a complete misunderstanding of what I wrote. I'd assumed you would fill in the rest of the clichÃ© for yourself (= I'll believe it when...if...I see it), and my scepticism referred purely to the project of building such a machine. That's why I said the mystery may be solved. In other words, if such a brain is built, I'll believe that the mind is a purely physical phenomenon. Until it is, I'll keep my explanatory options open. But I'm afraid we can't stop there. Although I will then regard the existence of a "soul" as having been disproved, the fact will remain that it took supreme, Nobel-prize-winning intelligence to build that machine. I will therefore still be unable to believe that chance could build it. Whether it's worth bothering about the existence of a God if we're to disappear with all our cells is a different story.-As for the Buddhist perspective, it's entirely up to us whether we think the question of chance v. design, or a prime cause, matters or not. The fact that Buddhists and Nietzsche think it's meaningless is their concern. -I find the remainder of your post rather confusing. You write:-If you're familiar with Freud, "I think" comes only from the ID and I think it would be right to say that Buddhism thinks of consciousness similarly to the ID and that is why they practice "here and now".-Freud's "id", as I'm sure you know, is the UNconscious, (I think, therefore I am asleep?), but I'd have expected even Buddhists to acknowledge that part of us is conscious (ego), part of us is unconscious (id), and part of us consists of unconscious structures formed in our early years (super-ego). Why would this make them practise the here and now?-You continue: "In Nietzsche's terms, all of this is the result of a language based on subject and predicate: our language is necessarily deterministic, this necessarily means that we then try to think of everything as deterministic (even when it's not) [...]"-If I've understood Nietzsche correctly (has anyone?), the idea that you can't separate the subject from the predicate is just another way of saying we are what we are, but I don't see what that has to do with the here and now either. Nor am I sure what you mean by deterministic. Philosophically, determinism boils down to the law of causality, as a result of which there's no such thing as free will. I can see the relevance of this to morality, but what is its relevance to the quest for truth, in the sense of whether there is or is not a God, or whether life did or did not originate by chance? If it's OK for Nietzsche to say God is dead, why shouldn't a Christian say God is alive? This has nothing to do with the subject-predicate structure, and everything to do with belief. -But perhaps by deterministic you mean the fact that language tries to pin reality down to a determinate form. This is certainly true, and is the point I tried to raise in my post on 'Language' (28 January at 11.10). The problem as I see it is less the subject-predicate structure than nouns (particularly in German, which specializes in substantives!). Your Freud example is as good as any. The terms 'id', 'ego' and 'super-ego' are extremely useful categories when it comes to analysing the 'psyche'. And because these names are now established, people refer to them as if they were realities, i.e. as if we knew what they actually were. But if we want to understand the material/immaterial make-up of the psyche, the source of consciousness, how all its different manifestations actually function, what sparks off the electrical discharges and what controls them or is controlled by them, we are totally ignorant. Similarly we refer to memory, the imagination, love etc. as if the words were already an explanation. That's how language can lull us into a false sense of knowledge. But the quest for truth (which can hardly exclude consideration of a prime cause) is impossible without language, so we are all in the same "trap" ... you, me and Nietzsche. If Nietzsche decided that the quest was "a fool's game", I have to admit he was probably right, but only because I don't hold out much chance of getting a result before I shuffle off this mortal coil. It actually gladdens my heart, though, to think that scientists, philosophers, and people like you and me are still searching. That makes me proud to be human. -In spite of the above, however, in the context of chance v. design, material v. immaterial, I really don't think my scepticism is caused by my falling into language traps. On the contrary, I would like to think that it's partly my awareness of the misleading determinacy of language which has brought me to my position of indeterminacy.

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dhw,-I apologize for how much time this took, it appears that I had another one of my "episodes" where a line of thought snaked in and I followed it assuming that you could read my brain. How unfortunate that you lost this ability! -Never fear, however as I shall attempt to "fix" you!-First off, you are absolutely correct. Language is (largely) deterministic--it HAS to be deterministic or it wouldn't make much sense. Language is our means of placing symbols on the world so that we can think about them. It gives our world structure. However the danger according to Buddhists/Nietzsche is in mistaking language for reality, hence the N quote warning against the seduction of words. Man tries to "fix" reality in place, however nature isn't something that is readily "fix"-able. -Buddha/Nietzsche has a line of argument that suggests that since language is deterministic, that its very framework shapes out thinking about the world. In Nietzsche's case, he just wants us to be aware that language itself necessarily shapes how we're going to think about the world. As a linguist, I'm sure you're very much aware of this fact. A classic example would be a culture (such as Hawaiian natives) that never developed a word for "Goodbye." What impact would that have on a culture?-Buddhist thought transforms this concept further to claim that language itself fools us into thinking that there is ANY kind of determinism or cause and effect in anything at allâall things we know, if we "learned" them by language, we don't truly know. Knowing only comes from experience. The article "I" is as much an illusion for the self as ascribing the article "you" to another object. Buddhism is especially repellent to the article "I," as selfishness surrounds the "I." This is why I see Buddhism as being opposed to the concept of ID, because at least from my understanding, ID is simply the self-pleasuring and childish part of the psyche, and it is the Super-Ego that is the unconscious drive for perfection. But I'll be the first to admit, my knowledge of Freud is limited to a very, very, small domain, and it is likely that I was burying myself in something I'm far too ignorant on. -To stay on track, I am willing to indulge the Buddhist view that states that all things we view as causes and effects are as such because we built them to appear that way. In many respects this is an extreme form of relativism, but it (obviously) allows us to keep a strong perspective on what we're discussing, and remind us that the objects in a language are never to be considered the same thing as the entity they describe.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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MATT, replying to my post of 11 February at 11.02: I apologize for how much time this took. It appears I had another of my "episodes" where a line of thought snaked in and I followed it assuming that you could read my brain. -I have a similar problem, on which I blame my failure to write the symphonies and concertos the world has been waiting for. -We're in agreement on the subject of determinate language, though I remain puzzled by Nietzsche's cross-eyed focus on subject and predicate when the problem of linguistic determinacy arises out of the whole process of finding words to denote realities. I didn't know the Hawaiians had no word for "goodbye". I thought they used "aloha" for both hello and goodbye (it should be obvious from the situation which is which). There's no special word in my wife's native language either (Urhobo). It would be a lot more significant, though, if a culture had never developed a word for "evil", or "god". Come to think of it, goodbye is actually "God be with you" (a bit like "adieu" and "adiÃ²s"). Yet another example of how terms become established and we forget about their actual meaning. At this rate, atheists should never say goodbye! -I can see that the selfishness surrounding the "I" (a pronoun, by the way, not an article) is a barrier to Buddhist enlightenment, in which case the ego has to exercise control over the id. Re-reading our original posts, though, I think my difficulty was in seeing how you linked this to the philosophy of "here and now". Probably not important. -You say "all things we view as causes and effects are as such because we built them to appear that way". Doesn't that negate about 90% of science? I agree, of course, that "the objects in a language are never to be considered the same thing as the entity they describe", but that's not quite the same argument, is it?

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MATT, replying to my post of 11 February at 11.02: I apologize for how much time this took. It appears I had another of my "episodes" where a line of thought snaked in and I followed it assuming that you could read my brain. 
> 
> I have a similar problem, on which I blame my failure to write the symphonies and concertos the world has been waiting for. 
> 
> We're in agreement on the subject of determinate language, though I remain puzzled by Nietzsche's cross-eyed focus on subject and predicate when the problem of linguistic determinacy arises out of the whole process of finding words to denote realities. I didn't know the Hawaiians had no word for "goodbye". I thought they used "aloha" for both hello and goodbye (it should be obvious from the situation which is which). There's no special word in my wife's native language either (Urhobo). It would be a lot more significant, though, if a culture had never developed a word for "evil", or "god". Come to think of it, goodbye is actually "God be with you" (a bit like "adieu" and "adiÃ²s"). Yet another example of how terms become established and we forget about their actual meaning. At this rate, atheists should never say goodbye! 
> -I'll admit that in the section I quoted, the chapter in context was dealing with psychologists and philosophers--but specifically Decartes and his Cogito Ergo Sum. In the same chapter he had a similarly vicious attack against physicists and scientists at large. So, although I characterize him fairly--I'm probably moving him a bit out of context in that passage. Regardless, it was a bad idea as your follow-up post shows that I did a bad job in my message. -> I can see that the selfishness surrounding the "I" (a pronoun, by the way, not an article) is a barrier to Buddhist enlightenment, in which case the ego has to exercise control over the id. Re-reading our original posts, though, I think my difficulty was in seeing how you linked this to the philosophy of "here and now". Probably not important. 
> -Never once will I ever say that the knowledge of my own language is even... "good." I'd be honest in saying that I couldn't even conjugate a verb without looking it up. -> You say "all things we view as causes and effects are as such because we built them to appear that way". Doesn't that negate about 90% of science? I agree, of course, that "the objects in a language are never to be considered the same thing as the entity they describe", but that's not quite the same argument, is it?-Yes, I especially mean that for science. Everything we know we know by language. Everything we know by science as well. If we never had language our state would be little changed over the course of the ages, and while I'll always argue for creature comforts, there's something to be said about a hard life.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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MATT: Why is it more reasonable to conclude that life was designed? We all agree it's not a scientific claim, so I still wonder why taking an unprovable position is more reasonable?-Your question makes it sound as if the choice is between one provable and one unprovable hypothesis. Do you think it's possible to prove that life came about by accident? From my position on the fence, the choice is between two unproven, unprovable, and highly unlikely hypotheses. (BBella offers a third option, but it also entails some kind of universal intelligence.) These are:-1) That the first living organisms could not only spontaneously get themselves to replicate, but could also spontaneously manufacture the capability for heritable adaptations and innovations. (David has described the scientific technology required.) All of these mechanisms ... not only unique in our experience, but also proving to be far more complex than was once thought ... are necessary for evolution. You may be able to write a computer programme that randomly generates other programmes, but we're talking here of the FIRST programme, and for that you need a designer. So that's one "unreasonable" hypothesis I can't believe in.-2) That in some unknown dimension, in some unknown form, and from some unknown provenance there exists a universal intelligence of unknown nature which initiated or survived or was inside and outside the Big Bang, and which went on to organize our universe and to create life on Earth. That's the second "unreasonable" hypothesis I can't believe in.-The choice, then, is belief in one of two prime causes, both of which go beyond the limits of my credulity (ultimately it has to be personal). An amazing scientific discovery or a personal revelation could change all that, but we can only base present beliefs on present knowledge. There's nothing to be proud of in my neutrality. One way or another I've got it horribly wrong.

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MATT: Why is it more reasonable to conclude that life was designed? We all agree it's not a scientific claim, so I still wonder why taking an unprovable position is more reasonable?
> 
> Your question makes it sound as if the choice is between one provable and one unprovable hypothesis. Do you think it's possible to prove that life came about by accident? From my position on the fence, the choice is between two unproven, unprovable, and highly unlikely hypotheses. (BBella offers a third option, but it also entails some kind of universal intelligence.) These are:
> -Well, at the risk of sounding condescending (and not meaning to), I'm firmly wearing my agnostic hat here. I realize the propositions cut both ways, but as I've stated before, I lean materialist in all things for the simple reason that materialist methods are universally reliable methods to gain knowledge. Whether or not life got here by chance, we can clearly study nature, but we can't really do that about God. I attack theistic interpretations because they make what I consider to be an unwarranted assumption. Though atheists might have a faith, at the very least they're not positing the existence of something that isn't studyable. We can study chance. We can revel in that we've defied the odds; personally I'd like it better if it came because of us instead of outside help. -I too find a false dilemma here, although in my case I take a more Buddhist view: There is also the possibility that our world simply *IS* with no distinction needed as to whether or not it was or wasn't created. We could be projecting a prime cause because we want there to be. (I'm not refuting the big bang here, only that IT wasn't the true beginning of the universe, if one even exists.) This is another unanswerable question, but it is just as valid as chance or God. It is also utterly bleak by the estimations of most western thinkers. However I find it resonates with me. -> 1) That the first living organisms could not only spontaneously get themselves to replicate, but could also spontaneously manufacture the capability for heritable adaptations and innovations. (David has described the scientific technology required.) All of these mechanisms ... not only unique in our experience, but also proving to be far more complex than was once thought ... are necessary for evolution. You may be able to write a computer programme that randomly generates other programmes, but we're talking here of the FIRST programme, and for that you need a designer. So that's one "unreasonable" hypothesis I can't believe in.
> -This goes back to Seth Lloyd's book... at the minimum I can safely make the claim that the universe needed no creator up until the point where abiogenesis is needed. -> 2) That in some unknown dimension, in some unknown form, and from some unknown provenance there exists a universal intelligence of unknown nature which initiated or survived or was inside and outside the Big Bang, and which went on to organize our universe and to create life on Earth. That's the second "unreasonable" hypothesis I can't believe in.
> 
> The choice, then, is belief in one of two prime causes, both of which go beyond the limits of my credulity (ultimately it has to be personal). An amazing scientific discovery or a personal revelation could change all that, but we can only base present beliefs on present knowledge. There's nothing to be proud of in my neutrality. One way or another I've got it horribly wrong.-Lol, and you make the mistake of thinking that there's something wrong with being uncertain. I told you this before, it's quite possibly the bravest position one can take, when you consider that it goes against the fiber of a human being. Our nature is to judge and be done.

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\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> I too find a false dilemma here, although in my case I take a more Buddhist view: There is also the possibility that our world simply *IS* with no distinction needed as to whether or not it was or wasn't created. We could be projecting a prime cause because we want there to be. (I'm not refuting the big bang here, only that IT wasn't the true beginning of the universe, if one even exists.) -Right. Alan Guth reminds us in his book, The Inflationary Universe, that we have no idea WHAT went bang! 
>
> This goes back to Seth Lloyd's book... at the minimum I can safely make the claim that the universe needed no creator up until the point where abiogenesis is needed. -I don't think you are that safe. We can still argue that the Big Bang was a caused event by a diety. We have no proof the BB was spontaneous. All we can know is that it occurred. the rest is guesswork.

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> Shapiro's conclusions below:
> The genome DNA record also bears witness to sudden changes that affect
> multiple characters at once: horizontal transfer of large DNA segments, cell fusionsand WGDs. These data are not readily compatible with earlier gradualist views on thenature of evolutionary variation. Although there remain many gaps in our knowledge, we are now in a position
 to outline a distinctively 21st century scenario for evolutionary change. This 21st century scenario assumes a major role for the kind of cellular
> sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel
> Prize address [1]. Such a cognitive component is absent from conventional
> evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. This 21st century viewof evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions.-The following article about a flying reptile definitely supports James Shapiro's theory and findings. Sudden change for half an animal.-http://news.bbc.co.uk/2/hi/science/nature/8306060.stm

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The thoughts that James Shapiro have developed, involving the complexity of what might be called (and in fact has been) the epigenome, continues to raise chicken and egg problems for neo-Darwinsim. DNA requires a complex mechanism to translate the code, produce proteins and create a living organization of those proteins. Now a recent report in Science describes the rDNA mechanisms that protect against error copies, to preserve the original code. Chicken and egg: if DNA arose first, when did the protective copy rDNA arrive? Did DNA produce its own protection? If rDNA appeared later, what protected initial DNA from error translation?? Irreducible complexity appears to be present, with both aspects of the genome needing to arrive at the same time.-http://www.sciencemag.org/cgi/content/abstract/327/5966/693

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> Irreducible complexity appears to be present, with both aspects of the genome needing to arrive at the same time.
> 
> http://www.sciencemag.org/cgi/content/abstract/327/5966/693 -Here is a more complete discussion of the article itself, covering how DNA copying is protected from error:-How were RNA gene repeats, "essential" to DNA repair, formed?
DLH
RNA replications have now been discovered to be "essential" to DNA error correction systems. If they are "essential", how could they arrive by random mutation and "selection"? On what basis does neoDarwinism predict error correction in the first place? 
From Intelligent Design, methodology one expects to see evidence of design in complex biochemical systems. From engineering design, I posit a foundational ID principle to be:
"Design systems to protect their design"
Protection: The first level is to protect the design. e.g. we provide protective coating and protective enclosures to protect hard drives, CDs, and DVDs. We provide transient surge protection to preserve electronic power systems. 
"Repair": The next level of preservation design is to provide systems to repair damage that is likely to occur. e.g. Computer systems use Reed Solomon error correcting codes. Similarly Redundant Array of Inexpensive Disks (RAID) systems are used to provide redundance and error correction in computer systems. 
By inference such design preservation methodology would be expected in designs by other intelligent beings. Thus, ID practitioners expect to see design preservation methods in biochemical systems. e.g., including redundant copies and error correction. 
A fascinating recent discovery is that a certain amount of redundance is essential to DNA repair. See: This Week in Science which reports on:
Protective Abundance
Massively repeated sequences are generally dangerous to genomes because they promote recombination and, potentially, genome instability. Eukaryotic ribosomal RNA genes (rDNA), which are highly transcribed, are organized into large arrays of repeats and have a system that actively maintains these large arrays. In getting to the bottom of this apparent contradiction, Ide et al. (p. 693) found that reducing the number of rDNA repeats in yeast resulted in a marked sensitivity to DNA damage, owing to heavy rDNA transcription preventing repair of compromised DNA replication forks. It appears that the additional copies of rDNA both reduce the ability of transcription to interfere with DNA repair and provide, through the action of condensin, templates for the recombination-based repair of replication-induced damage.
On what foundational principle does neoDarwinism predict such "essential" design repair components and functionality? What detailed step by step method is there to provide any rationally significant probability for such to occur? By contrast, the fact that this specific repetition ... error correction system is "essential" suggests that it is also irreproducibly complex. (See Michael Behe on irreproducible complexity). This fits ideally within an ID perspective.
See the article: Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity Satoru Ide, Takaaki Miyazaki, Hisaji Maki, Takehiko Kobayashi Science 5 February 2010: Vol. 327. no. 5966, pp. 693 ... 696 DOI: 10.1126/science.1179044
Abstract
The ribosomal RNA (rDNA) gene repeats are essential housekeeping genes found in all organisms. A gene amplification system maintains large cluster(s) of tandemly repeated copies in the chromosome, with each species having a specific number of copies. Yeast has many untranscribed rDNA copies (extra copies), and we found that when they are lost, the cells become sensitive to DNA damage induced by mutagens. We show that this sensitivity is dependent on rDNA transcriptional activity, which interferes with cohesion between rDNA loci of sister chromatids. The extra rDNA copies facilitate condensin association and sister-chromatid cohesion, thereby facilitating recombinational repair. These results suggest that high concentrations of heavily transcribed genes are toxic to the cells, and therefore amplified genes, such as rDNA, have evolved. 
Note that Ide et al. further observe "each species having a specific number of copies". Combining species specific rDNA copies with rDNA repeat number being "essential" suggests that this minimum rDNA repeat number forms part of the species barrier. On what basis does neoDarwinism predict such species barriers and the steps to form them?
By contrast, in highly competitive environments, design engineers try to differentiate their systems to prevent use of competitive or generic products. e.g., hardware or software "locks" etc. Thus, from the foundational ID principle of ""Preserving the design", one would expect designs by other intelligent agents to provide methods to preserve designs uniqueness. 
How well are rDNA repeats as essential to DNA error correction predicted by neoDarwinism or ID principles. How can these be tested or differentiated?
(Any corrections to these inferences from reading this news and abstract would also be welcome.)

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In 2001, Michael Behe wrote: "[T]here is an asymmetry between my current definition of irreducible complexity and the task facing natural selection. I hope to repair this defect in future work." Behe specifically explained that the "current definition puts the focus on removing a part from an already functioning system", but the "difficult task facing Darwinian evolution, however, would not be to remove parts from sophisticated pre-existing systems; it would be to bring together components to make a new system in the first place". [33] In the 2005 Kitzmiller v. Dover Area School District trial, Behe testified under oath that he "did not judge [the asymmetry] serious enough to [have revised the book] yet."[34]-Four years isn't enough, eh?-Another excerpt:-The judge in the Dover trial wrote "By defining irreducible complexity in the way that he has, Professor Behe attempts to exclude the phenomenon of exaptation by definitional fiat, ignoring as he does so abundant evidence which refutes his argument. Notably, the NAS has rejected Professor Behe's claim for irreducible complexity..."-What's a good refutation of exaptation that DOESN'T try to remove it via definition?

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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> Behe testified under oath that he "did not judge [the asymmetry] serious enough to [have revised the book] yet."[34]
> 
> Four years isn't enough, eh?-
I don't think that the asymmetry problem is serious. I've been aware of the parallel approaches for quite a while, and they mirror each other. From my book experience I doubt the publisher wants to put in a minor correction, unless the book is under major revision.
> 
> The judge in the Dover trial wrote "By defining irreducible complexity in the way that he has, Professor Behe attempts to exclude the phenomenon of exaptation by definitional fiat, ignoring as he does so abundant evidence which refutes his argument. Notably, the NAS has rejected Professor Behe's claim for irreducible complexity..."
> 
> What's a good refutation of exaptation that DOESN'T try to remove it via definition?-The problem is that the entire phenomenon of exaptation is totally unexplained by Darwin. Why should a morphologic change appear 100,000 years before it is finally used? Why is it maintained if it provides no function at the time? The judge in his final opinion quoted up to 2/3rds of the winning side's brief. I am sure he didn't have the background knowledge to raise the questions I've raised. And finally exaptation is not a refutation of Behe. To me it has always looked like pre-planning in the genome.

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David,-Maybe I'm just arguing via ignorance, but I remember exaptation being a Gould idea, not a Darwin idea? (and what difference would it make?) What's the textbook view of exaptation?

--
\"Why is it, Master, that ascetics fight with ascetics?\"

\"It is, brahmin, because of attachment to views, adherence to views, fixation on views, addiction to views, obsession with views, holding firmly to views that ascetics fight with ascetics.\"

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>What's the textbook view of exaptation?-I don't know whose term it was, but it is as I described. A morphologic entity that arrives with no usefulness tothe organism and then many many years later is used in an advancement.

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Tandem repeats is the term used for 'junk' DNA's ability to push rapid genomic change. The more we learn about junk DNA the more complexity appears, and the pre-planning may have been previously inserted into the genome.-http://www.physorg.com/news162753069.html -Another example of the ability to have rapid change is in Darwin finches. This fits a mathematical formula. As Matt and I have pointed out, nature does math all the time: -http://news.sciencemag.org/sciencenow/2010/02/did-darwins-finches-do-math.html

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