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On the impossibility of replicating the cell: A problem for naturalism

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I have sometimes had the idea that the best way for Intelligent Design advocates to make their case would be to build a giant museum replicating the complexity of the cell on a large scale, so that people could see for themselves how the cell worked and draw their own conclusions. Recently I came across an old quote from biochemist Michael Denton’s Evolution: A Theory in Crisis (Adler and Adler, 1985) which put paid to that idea, but which raised an interesting philosophical puzzle for people who adhere to scientific naturalism – which I define here as the view that there is nothing outside the natural world, by which I mean the sum total of everything that behaves in accordance with scientific laws [or laws of Nature]. Here is the first part of the quote from Denton, which I had seen before (h/t Matt Chait):

To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometres in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the portholes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings with find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus of itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell.

We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines. We would notice that the simplest of the functional components of the cell, the protein molecules, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D spatial conformation. We would wonder even more as we watched the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine – that is one single functional protein molecule – would be completely beyond our capacity at present and will probably not be achieved until at least the beginning of the next century. Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.

We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.

What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory which would have one capacity not equalled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle. (pp. 328 ff.)

Reading this passage vindicated my belief that a museum of the cell would be a great way to promote ID. “If we build it, they will come,” I thought. But there was more to follow, which I hadn’t read before. It turns out that we can’t build a replica of the cell, down to the atomic level:

To gain a more objective grasp of the level of complexity the cell represents, consider the problem of constructing an atomic model. Altogether a typical cell contains about ten million million atoms. Suppose we choose to build an exact replica to a scale one thousand million times that of the cell so that each atom of the model would be the size of a tennis ball. Constructing such a model at the rate of one atom per minute, it would take fifty million years to finish, and the object we would end up with would be the giant factory, described above, some twenty kilometres in diameter, with a volume thousands of times that of the Great Pyramid.

Copying nature, we could speed up the construction of the model by using small molecules such as amino acids and nucleotides rather than individual atoms. Since individual amino acids and nucleotides are made up of between ten and twenty atoms each, this would enable us to finish the project in less than five million years. We could also speed up the project by mass producing those components in the cell which are present in many copies. Perhaps three-quarters of the cell’s mass can be accounted for by such components. But even if we could produce these very quickly we would still be faced with manufacturing a quarter of the cell’s mass which consists largely of components which only occur once or twice and which would have to be constructed, therefore, on an individual basis. The complexity of the cell, like that of any complex machine, cannot be reduced to any sort of simple pattern, nor can its manufacture be reduced to a simple set of algorithms or programmes. Working continually day and night it would still be difficult to finish the model in the space of one million years. (Emphases mine – VJT.)

But there’s more, as Matt Chait points out (emphasis mine):

And let me add my two cents to this astounding picture. The model that you would complete a million years later would be just that, a lifeless static model. For the cell to do its work this entire twenty kilometer structure and each of its trillions of components must be charged in specific ways, and at the level of the protein molecule, it must have an entire series of positive and negative charges and hydrophobic and hydrophilic parts all precisely shaped (at a level of precision far, far beyond our highest technical abilities) and charged in a whole series of ways: charged in a way to find other molecular components and combine with them; charged in a way to fold into a shape and maintain that most important shape, and charged in a way to be guided by other systems of charges to the precise spot in the cell where that particle must go. The pattern of charges and the movement of energy through the cell is easily as complex as the pattern of the physical particles themselves.

Also, Denton, in his discussion, uses a tennis ball to stand in for an atom. But an atom is not a ball. It is not even a ‘tiny solar system’ of neutrons, protons and electrons’ as we once thought. Rather, it has now been revealed to be an enormously complex lattice of forces connected by a bewildering array of utterly miniscule subatomic particles including hadrons, leptons, bosons, fermions, mesons, baryons, quarks and anti-quarks, up and down quarks, top and bottom quarks, charm quarks, strange quarks, virtual quarks, valence quarks, gluons and sea quarks…

And let me remind you again, that what we are talking about, a living cell, is a microscopic dot and thousands of these entire factories including all the complexity that we discussed above could fit on the head of a pin. Or, going another way, let’s add to this model of twenty square kilometers of breath taking complexity another one hundred trillion equally complex factories all working in perfect synchronous coordination with each other; which would be a model of the one hundred trillion celled human body, your body, that thing that we lug around every day and complain about; that would, spread laterally at the height of one cell at this magnification, blanket the entire surface of the earth four thousand times over, every part of which would contain pumps and coils and conduits and memory banks and processing centers; all working in perfect harmony with each other, all engineered to an unimaginable level of precision and all there to deliver to us our ability to be conscious, to see, to hear, to smell, to taste, and to experience the world as we are so used to experiencing it, that we have taken it and the fantastic mechanisms that make it possible for granted.

My question is, “Why don’t we know this?” What Michael Denton has written and I have added to is a perfectly accurate, easily intelligible, non-hyperbolic view of the cell. Why is this not taught in every introductory biology class in our schools?

Based on the foregoing, I think it’s fair to say that we’ll never be able to construct a computer model of the cell either, down to the atomic level: the computing resources required would just be too huge. And in that case, it will never be scientifically possible to model a natural process (or a set of processes) and demonstrate that it could have given rise to the cell – or even show that it had a greater than 50% probability of doing so.

So here’s my question for the skeptics: if we have no hope of ever proving the idea that the cell could have arisen through unguided natural processes, or even showing this idea to be probably true, then how can we possibly be said to know for a fact that this actually happened? Knowledge, after all, isn’t merely a true belief; it has to be a justified true belief. What could justify the claim that abiogenesis actually occurred?

It gets worse. We cannot legitimately be said to know that scientific naturalism is true unless we know that life could have arisen via unguided processes. But if we don’t know the latter, then we cannot know the former. Ergo, scientific naturalism, even if were true, can never be known to be true.

There’s more. Scientific naturalists are fond of claiming that there are only two valid sources of knowledge: a priori truths of logic and mathematics, which can be known through reason alone; and a posteriori empirical truths, which are known as a result of experience and/or scientific inquiry. The statement that abiogenesis occurred without intelligent guidance on the primordial Earth is neither a truth of logic and mathematics nor a truth which can be demonstrated (or even shown to be probable) via experience and/or scientific inquiry. And since we cannot know that scientific naturalism is true unless we know that abiogenesis occurred without intelligent guidance, it follows that the truth of scientific naturalism cannot be known through either of the two avenues of knowledge postulated by the skeptic. So either there must be some third source of knowledge (intuition, perhaps?) that the skeptic has to fall back on. Yeah, right.

And please, don’t tell me, “Well, scientists have explained X, Y and Z, so it’s only a matter of time before they can explain life.” First, that’s illicit reasoning: performing inductive logic over a set of things is problematic enough (black swans, anyone?), but performing it over a set of scientific theories, concocted during a time-span of just 471 years – the Scientific Revolution is commonly held to have begun in 1543 – is absolutely ridiculous. And second, as I’ve argued above, there’s good reason to believe that our computing resources will never be up to the task of showing that the first living cell could have arisen via a natural, unguided process.

One last question: if we cannot know that scientific naturalism is true or even probably true, then why should we believe it?

Checkmate, naturalists? Over to you.

Comments
Barry Arrington, I hope you and yours have a calm, happy Thanksgiving full of goodwill and cheer. You seem like you need it.Learned Hand
November 26, 2014
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Alicia Renard
As soon as you postulate a material effect from an immaterial source, you have an observable phenomenon that you can look for.
Exactly! Now I postulate that Alicia Renard wrote a comment on a blog. Are there any observable phenomenon I can look for? Yes, right there at comment 8 is several hundreds bits of complex specified information that could not have been created by chance/law forces from the moment of the big bang until the heat death of the universe. Welcome to the ID camp.
Until then, we are all left with our uncertainty. “I don’t know” is always a possible answer.
Here we are in perfect agreement. I commend you for eschewing the misplaced certainty we seem displayed so often on these pages by materialists.Barry Arrington
November 26, 2014
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Evolve
Scientific naturalism is not an assertion, it is an observation.
That statement is nonsense on a stick. Scientific naturalism asserts a negative: No force “outside” of nature acts within nature. Your fellow Darwinists have been howling for several days about the impossibility of proving a negative. Yours is a classic blunder, which Popper warned against. You have made what Popper called a “universal statement” and asserted it is a scientifically demonstrated fact. Wrong. Popper:
This is the reason why strictly existential statements are not falsifiable. We cannot search the whole world in order to establish that something does not exist [in our case, a non-material phenomenon], has never existed, and will never exist. It is for precisely the same reason that strictly universal statements are not verifiable. Again, we cannot search the whole world in order to make sure that nothing exists which the law forbids.
Evolve
We have never observed any supernatural force tinkering with nature, past or present.
Here you make the same error as Hume, which has been pointed out many times, though materialists refuse to learn: Miracles do not happen. How do we know? Because they are counter to universal human experience. But what about all of the reports of miracles? We can disregard those. Why should we disregard those reports? Because miracles do not happen. Nice tight question begging circle. Your faith commitments appear to be such that you don’t mind making obviously false metaphysical assertions and reasoning in a circle to support them. You might want to think about that.Barry Arrington
November 26, 2014
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LH
No intelligence we have ever observed is capable of it.
That is certainly true. And yet you continue to believe that the accretion of random errors sorted by a fitness function is capable of it. It beggars belief.Barry Arrington
November 26, 2014
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keiths
That realization was one of the things that got me started on the path to deconversion.
And again, the irony of your deconversion is that you traded a worldview that requires a small faith commitment for a worldview that requires staggering levels of blind grit-your-teeth-in-the-face-of-the-plain-evidence “leap against the light” faith. Though I am sure that irony is lost on you.Barry Arrington
November 26, 2014
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Fantastic post VJT. Thank you. How can one continue to insist that blind, unguided natural forces created this wonder of nano-technology after reading this? Learned Hand, keith s, Graham2, and Evolve give you hints in their responses. The staggering levels of blind grit-your-teeth-in-the-face-of-the-plain-evidence faith displayed in those comments is a wonder to behold. I almost called their faith “leap in the dark” faith. But that metaphor is actually just the opposite of the case. The light is glaring and under that light we see a clear path. Their faith requires them to eschew the path revealed by the light and wonder off in the thickets. Instead of a “leap in the dark” faith, it might be called a “leap against the light” faith. And the irony of it all is that they almost certainly think of themselves as skeptical rationalists while they sneer at us benighted faith-bound ID rubes. It is true that my worldview requires a certain level of faith (all worldviews do). But my faith commitments are dwarfed by the faith commitments of those who believe the accretion of random errors sorted by a fitness function can result in the technology VJT describes. Can “leap against the light” fanatics such as these by reasoned with? William J. Murray sums up the prospects for such discourse nicely:
There is no means of rational discourse with a Darwinist when they simply avert their eyes from the blatant, brutal folly of their fanatical religion.
Barry Arrington
November 26, 2014
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The OP reminds me of an article by the unrivaled Stephen Talbott; excerpt:
If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled? (...) how does the cell keep all those “miles of string in the tennis ball” from getting hopelessly tangled? In this case we at least know some of the players addressing the problem. For example, there are enzymes called "topoisomerases", whose task is to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of genes or regions of the chromosome, and prevent a hopeless mass of knots. Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball!) I don't think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts are being made to analyze isolated local forces and “mechanisms”.
Box
November 26, 2014
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All our opponents can offer is their "blah, blah, blah" and they cannot offer any supporting evidence for the claims of their position. Why is that? And why can't any evo find this alleged "theory of evolution"?Joe
November 26, 2014
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There isn't any ToE and how life originated dictates how it evolved. It is only if unguided processes produced life would be infer/ assume unguided processes also produced its diversity. OTOH if the OoL - intelligent design then the inference would be that organisms were designed to evolve and evolved by design. That evos still cannot grasp that simple points says quite a bit about their science-free agenda.Joe
November 26, 2014
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But there is more...... Anything that is engineered will always have a major draw back, the more complex the system the more likely that it will fail. That is why engineers build redundancy, fault tolerance stability control and trade-offs into their systems. Biological systems as complex systems have all these mechanisms built in. But believe me they did not build it themselves how can they if they don't know what's critical, vital or what's even needed to sustain itself? The 18 truths about failure of complex systems http://www.zdnet.com/blog/projectfailures/18-truths-the-long-fail-of-complexity/6786Andre
November 26, 2014
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There is no means of rational discourse with a Darwinist when they simply avert their eyes from the blatant, brutal folly of their fanatical religion.William J Murray
November 26, 2014
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This is what it is all about.... "It can be said that reverse engineering begins with the product and works through the design process in the opposite direction to arrive at a product definition statement (PDS). In doing so, it uncovers as much information as possible about the design ideas that were used to produce a particular product."Andre
November 26, 2014
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Why an engineering problem? Because you can only reverse engineer things that are engineered. Ask yourself these reverse engineering questions. Then look at Biomimetics. 1.The original manufacturer of a product no longer produces a product 2.There is inadequate documentation of the original design 3.The original manufacturer no longer exists, but a customer needs the product 4.The original design documentation has been lost or never existed 5.Some bad features of a product need to be designed out. For example, excessive wear might indicate where a product should be improved 6.To strengthen the good features of a product based on long-term usage of the product 7.To analyse the good and bad features of competitors' product 8.To explore new avenues to improve product performance and features 9.To gain competitive benchmarking methods to understand competitor's products and develop better products 10.The original CAD model is not sufficient to support modifications or current manufacturing methods 11.The original supplier is unable or unwilling to provide additional parts 12.The original equipment manufacturers are either unwilling or unable to supply replacement parts, or demand inflated costs for sole-source parts 13.To update obsolete materials or antiquated manufacturing processes with more current, less-expensive technologiesAndre
November 26, 2014
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And I have told you........ The problem is an engineering one...... It should leave you with a clue of what you need to do next but I don't think you want to because I'll bet my salary you're too afraid of what you might find......Andre
November 26, 2014
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Andre writes:
Alicia And hopefully one day you’ll move beyond your wild imagination that chemicals conspired to become alive…….
I don't know exactly how life got started on Earth. No matter how hard we look we can't seem to find that spark, that élan vital that, according to some, we should find in vivo but not in vitro Current research leaves you, me and everyone to speculate as wildly as they wish.Alicia Renard
November 26, 2014
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"He only gives his certainty level as 6 out of 7." How pathetic... And he is the talking head for science.EugeneS
November 26, 2014
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Why o why in the name of the FSM are these people ignoring abiogenesis? It is a cop-out! And why are you forgetting Darwin's warm little pond? If you can't say how life started you can't say anything about how it evolved.... mkay?Andre
November 26, 2014
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TSeriK writes:
No. You are mistaken as that is EXACTLY what the Darwinist is claiming.
Which Darwinist? Remember the theory of evolution makes no prediction about how life on Earth got started, it merely proposes a mechanism (or suite of mechanisms) for how life could have diversified subsequently. Even spawn-of-Satan Richard Dawkins does not rule out the possibility of God's existence. He only gives his certainty level as 6 out of 7.Alicia Renard
November 26, 2014
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Alicia And hopefully one day you'll move beyond your wild imagination that chemicals conspired to become alive.......Andre
November 26, 2014
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A third source of knowledge? Or trillions of sources? So Keith S we actually have true/false/maybe? on/off/dim Really Keith S? Speak for yourself Mr uncertain.... something is either true or it is false or it is on or it is off . No wonder you can't believe yourself. I would struggle too if I was you.Andre
November 26, 2014
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Vincent:
I wasn’t trying to argue for Intelligent Design but against naturalism.
True, but your argument works against ID nevertheless.
Also, my argument is a reductio only for people who accept that there are two and only two sources of knowledge. I don’t.
You evade your own argument only if you can demonstrate the existence and reliability of your third source of knowledge. Merely believing in it is insufficient.keith s
November 26, 2014
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Who is claiming that life on Earth got started via purely physical and chemical processes is a fact?
No. You are mistaken as that is EXACTLY what the Darwinist is claiming.TSErik
November 26, 2014
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Vincent torley asks:
So here’s my question for the skeptics: if we have no hope of ever proving the idea that the cell could have arisen through unguided natural processes, or even showing this idea to be probably true, then how can we possibly be said to know for a fact that this actually happened?
Who is claiming that life on Earth got started via purely physical and chemical processes is a fact? Being only able to detect material processes ourselves we cannot rule out the possibility that something goes on "invisibly", "in other planes of existence", immaterially" of which we are completely unaware. So long as the suggestion is not made that these can impinge on our material universe, they can be the subject of endless discussion and speculation. There are no entailments. As soon as you postulate a material effect from an immaterial source, you have an observable phenomenon that you can look for. If the unmoved mover moves something, at that moment, the physical laws of the universe must be violated - an apparently uncaused cause - a reaction without an action. If an "intelligent designer" acted at some point in the very distant past to guide or bring about aspects of life on Earth 3 to 4 billion years ago, there is little chance of finding evidence now of how this occurred (unless SETI or other space exploration finds evidence suggesting life is not unique to Earth). How is this different from theistic evolution as a viewpoint? If the "intelligent designer" intervenes on a regular basis, then there's something to look for. Perhaps one day, an ID proponent will move beyond the mantra of "I can see no possible physical pathway for this phenomenon to arise, therefore design" to some suggestion of modus operandi. Until then, we are all left with our uncertainty. "I don't know" is always a possible answer.Alicia Renard
November 26, 2014
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Dr Torley Based on the responses from our materialist friends we can say with certainty that they don't really understand the issue involved here :) nice one! P.S. Evolve.... The problem for materialism around the first replicators is an engineering problem...... hint hint.....Andre
November 26, 2014
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The cell is made up of naturally occurring chemical molecules which react and interact by well-known natural mechanisms. Why then should we invoke imaginary supernatural forces to explain it? Just because the cell is complex and we don’t have a step-by-step recipe to make a cell? Or because we can draw some poor analogies to man-made machines? That’s rubbish. We know for a fact that man-made objects are designed because they don't arise or sustain themselves naturally, and we can see and study the designers, their properties, tools and methods. No designer whatsoever is known for nature, let alone identify what it has designed, when and how. The supernatural designer is a purely fictitious, undefined entity. One can fit him into any scenario one wants! Such a designer has zero explanatory power. Scientific naturalism is not an assertion, it is an observation. We have never observed any supernatural force tinkering with nature, past or present. On the contrary, we have copious data supporting naturalistic evolution and the evidence keeps on growing by the day as predictions made by the theory are confirmed by multiple disciplines of science. All supernatural alternatives to evolution, including ID, have spectacularly failed to propose testable hypothesis that can deseat evolution. Natural evolution best explains the data. This is what school kids must be told about in science classes.Evolve
November 26, 2014
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Keith S Your supposed advice is noted, and trashed in the bin. How can we take your word for anything if you don't even believe yourself? You are the last person to dispense advice, of this you can be certain.Andre
November 26, 2014
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Quick comment: I wasn't trying to argue for Intelligent Design but against naturalism. Also, my argument is a reductio only for people who accept that there are two and only two sources of knowledge. I don't. Got to go.vjtorley
November 26, 2014
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You go on at length regarding the difficulty of modelling a cell at the atomic level. Yes, and it would be even harder to model it at the sub-atomic level, and easier at the molecular level, and even easier at some higher (functional) level still. So which is it ? What level should we settle on ? And why do we need a physical model at all ? Perhaps some simulation would work ? And why do we need a full model/simulation ? These aren't needed to demonstrate underlying principles. Straw man perhaps ?Graham2
November 26, 2014
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Learned Hand, I keep offering free advice to IDers that they never accept. I tell them "if you think you've found a whiz-bang argument against your opponent's position, stop for a minute and ask yourself a simple question: Could this argument be used against me?" It's amazing how many IDer mistakes would be caught if they just followed that one rule faithfully. It would be easier for us, too, as we'd end up spending less time correcting their errors. Vincent apparently forgot to apply the rule. I learned this lesson in my early teens. I was an evangelical Christian, and a friend of mine was a Mormon. We discussed religion a lot -- he was the first Mormon I'd met, and I was fascinated -- and I kept coming up with these great arguments against Mormonism, only to realize that with a few modifications, they worked equally well against my own Christianity! That realization was one of the things that got me started on the path to deconversion.keith s
November 26, 2014
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I have sometimes had the idea that the best way for Intelligent Design advocates to make their case would be to build a giant museum replicating the complexity of the cell on a large scale, so that people could see for themselves how the cell worked and draw their own conclusions.
I think it would be more persuasive if, instead of relying on personal incredulity, you demonstrated that ID's design-detection tools actually worked. Perhaps by testing them, so that you could show that ID is able to distinguish between natural and designed objects in a way that mainstream investigators cannot. More broadly, isn't this special pleading? We cannot, after all, model atomic decay precisely, either. Should we all become Intelligent Radiators? Come to think of it, we also can't model an intelligent being creating a cell. No intelligence we have ever observed is capable of it. If we apply your standards, why would we prefer that impossibility over any other?
Checkmate, naturalists?
Betteridge's Law of Headlines applies to postscripts as well.Learned Hand
November 25, 2014
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