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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
Quantum theory is doing quite well thank you. The following articles give us a small glimpse as to what it truly means for Leggett's inequality to be confirmed to an order of '120 standard deviations': Standard deviation Excerpt: Particle physics uses a standard of "5 sigma" for the declaration of a discovery.[3] At five-sigma there is only one chance in nearly two million that a random fluctuation would yield the result. http://en.wikipedia.org/wiki/Standard_deviation#Particle_physics SSDD: a 22 sigma event is consistent with the physics of fair coins? - June 23, 2013 Excerpt: So 500 coins heads is (500-250)/11 = 22 standard deviations (22 sigma) from expectation! These numbers are so extreme, it’s probably inappropriate to even use the normal distribution’s approximation of the binomial distribution, and hence “22 sigma” just becomes a figure of speech in this extreme case… https://uncommondescent.com/mathematics/ssdd-a-22-sigma-event-is-consistent-with-the-physics-of-fair-coins/ As to 1+1=2, you might be interested to know that 1+1+2 is considered mathematically 'incomplete'. i.e. the truthfulness of 1+1=2 is not within the equation itself, but to derive the truthfulness for 1+1=2 one is forced appeal to something outside the equation to hold that it is true: Kurt Gödel – Incompleteness Theorem - video https://vimeo.com/96082228bornagain77
December 1, 2014
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Gary, Leggett’s inequality confirmed to 120 standard deviations is hardly speculative as far as empirical science is concerned. As to your concern that ID may no longer be considered scientific if we allow consciousness its rightful place in the scheme of things, exactly how do you propose to rationally do science in the first place if you deny the reality of your own mind and free will?
Leggett’s inequality is not for explaining how consciousness works. I can even do better by algorithmically confirming that 1+1=2 and with zero deviation. But that does not explain how consciousness works either. The equation 1-1=0 indicates that nothing becomes something when it becomes two equal parts. But that does not explain how all the forces in the universe work and their origin. Quantum mechanics theory has plenty of bugs in it, to begin with. It's not reliable enough for this theory.Gary S. Gaulin
December 1, 2014
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Gary, Leggett's inequality confirmed to 120 standard deviations is hardly speculative as far as empirical science is concerned. As to your concern that ID may no longer be considered scientific if we allow consciousness its rightful place in the scheme of things, exactly how do you propose to rationally do science in the first place if you deny the reality of your own mind and free will? Sam Harris's Free Will: The Medial Pre-Frontal Cortex Did It - Martin Cothran - November 9, 2012 Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state -- including their position on this issue -- is the effect of a physical, not logical cause. By their own logic, it isn't logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order. http://www.evolutionnews.org/2012/11/sam_harriss_fre066221.htmlbornagain77
December 1, 2014
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Bornagain77:
Gary, quantum mechanics, with Leggett’s inequality, has now brought us to the point where we can confidently say that matter is derivative from consciousness,,,
I saw the links and the math shown in the video but that's way too speculative. Even where true that does not explain how consciousness works. Or helps explain how intelligence works either. As the theory now stands: the reciprocal cause pathway back to the behavior of matter (all forces, energy) qualifies as a prayer/though path leading back to the source of consciousness, whatever that source may be. One wrong move in how the logic is connected can easily have unintended consequences that lead to contradictions that make the Theory of Intelligent Design a mockery of religion, and no longer be scientific. I must be very careful to avoid that from happening.Gary S. Gaulin
December 1, 2014
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Gary, quantum mechanics, with Leggett's inequality, has now brought us to the point where we can confidently say that matter is derivative from consciousness,,, Do we create the world just by looking at it? - 2008 Excerpt: In mid-2007 Fedrizzi found that the new realism model was violated by 80 orders of magnitude; the group was even more assured that quantum mechanics was correct. Leggett agrees with Zeilinger that realism is wrong in quantum mechanics, but when I asked him whether he now believes in the theory, he answered only “no” before demurring, “I’m in a small minority with that point of view and I wouldn’t stake my life on it.” For Leggett there are still enough loopholes to disbelieve. I asked him what could finally change his mind about quantum mechanics. Without hesitation, he said sending humans into space as detectors to test the theory.,,, (to which Anton Zeilinger responded) When I mentioned this to Prof. Zeilinger he said, “That will happen someday. There is no doubt in my mind. It is just a question of technology.” Alessandro Fedrizzi had already shown me a prototype of a realism experiment he is hoping to send up in a satellite. It’s a heavy, metallic slab the size of a dinner plate. http://seedmagazine.com/content/article/the_reality_tests/P3/ And to further solidify the case that 'consciousness precedes reality' the violation of Leggett's inequalities have been extended. This following experiment verified Leggett's inequality to a stunning 120 standard deviations level of precision: Experimental non-classicality of an indivisible quantum system - Zeilinger 2011 Excerpt: Page 491: "This represents a violation of (Leggett's) inequality (3) by more than 120 standard deviations, demonstrating that no joint probability distribution is capable of describing our results." The violation also excludes any non-contextual hidden-variable model. The result does, however, agree well with quantum mechanical predictions, as we will show now.,,, https://vcq.quantum.at/fileadmin/Publications/Experimental%20non-classicality%20of%20an%20indivisible.pdf The preceding experiment, and the mathematics behind it, are discussed beginning at the 24:15 minute mark of the following video: Quantum Weirdness and God 8-9-2014 by Paul Giem - video https://www.youtube.com/watch?feature=player_detailpage&v=N7HHz14tS1c#t=1449 "As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter." Max Planck - The Father Of Quantum Mechanics - Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944) (from Archiv zur Geschichte der Max-Planck-Gesellschaft, Abt. Va, Rep. 11 Planck, Nr. 1797)bornagain77
December 1, 2014
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Zach, why are you not concerned with the fact that material processes cannot create information? Even when using the brute computational power behind modern computers? If you were honest you would admit this is a fatal blow to your materialistic beliefs. As to computer simulations of population genetics, why not cite any real world evidence to counter Sanford's claim? I cited plenty showing him to be correct! (or why don't you ever cite real references to back up any claim you make instead of just literature bluffs?, am I suppose to take your word for your claims?),,, The reason you refuse to be honest, as you well know, is that you have no substantiating evidence that will withstand scrutiny and yet, for whatever severely misguided reason, you want Darwinism to be true.,,, I don't care what you WANT to be true! I only care for what is actually true! Why not admit what is readily apparent that Darwinism is grossly inadequate to explain the unfathomed complexity we are finding in life???,,,, why all the smoke and mirrors with you? Don't you care for truth in the least? ========== “The computer is not going to generate anything realistic if it uses Darwinian mechanisms.” Dr. David Berlinski: Accounting for Variations - video http://www.youtube.com/watch?v=aW2GkDkimkE On Algorithmic Specified Complexity by Robert J. Marks II - video paraphrase (All Evolutionary Algorithms have failed to generate truly novel information including ‘unexpected, and interesting, emergent behaviors’) - Robert Marks https://www.youtube.com/watch?v=No3LZmPcwyg “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/bornagain77
December 1, 2014
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Bornagain77 this is the illustration being explained in the paragraph: https://sites.google.com/site/intelligenceprograms/Home/Causation.jpg Or optionally: https://sites.google.com/site/intelligenceprograms/Home/Causation.GIF The theory is connecting back to what we are made of, matter.Gary S. Gaulin
December 1, 2014
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bornagain77: all of your intelligently designed evolutionary computer models have the fatal software error of ‘smuggling information’ into them. We're not discussing evolutionary algorithms, but simulations of population genetics. Population genetics explains many important biological phenomena, though it certainly isn't a complete explanation of evolutionary history.Zachriel
December 1, 2014
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More specifically "behavior of" matter:
This behavioral pathway causes all of our complex intelligence related behaviors to connect back to the behavior of matter, which does not need to be intelligent to be source of consciousness.
It is possible to add a qualifier or rephrase it, but believe me, if it at all seems to indicate that atoms and ordinary molecules are intelligent then the Darwinian camp will be all over it.Gary S. Gaulin
December 1, 2014
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Gary, to put the problem for you more simply, besides not having consciousness, computer algorithms do not have free will, and free will is tightly correlated with the creation of new information: Algorithmic Information Theory, Free Will and the Turing Test - Douglas S. Robertson Excerpt: Chaitin’s Algorithmic Information Theory shows that information is conserved under formal mathematical operations and, equivalently, under computer operations. This conservation law puts a new perspective on many familiar problems related to artificial intelligence. For example, the famous “Turing test” for artificial intelligence could be defeated by simply asking for a new axiom in mathematics. Human mathematicians are able to create axioms, but a computer program cannot do this without violating information conservation. Creating new axioms and free will are shown to be different aspects of the same phenomena: the creation of new information. http://cires.colorado.edu/~doug/philosophy/info8.pdfbornagain77
December 1, 2014
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Zach all of your intelligently designed evolutionary computer models have the fatal software error of 'smuggling information' into them. But I guess, given your apparent dishonest nature in dealing with the evidence at hand, smuggling is OK with you as long as it supports Darwinism? :)bornagain77
December 1, 2014
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Gary, you are the one making the extraordinary claim that consciousness can arise from matter. Can you provide evidence for that claim or not? It is not on me to prove your claim impossible, it is on you to prove your claim possible, or even prove it remotely reasonable, which would be an improvement over your present position, ,,, As to providing 'reliable scientific evidence explaining how consciousness works', I will do that as soon as you can tell me how energy 'works': Quantum Mechanics - Double Slit Experiment. Is anything really physical? (Prof. Anton Zeilinger) - video Quote: “The path taken by the photon is not an element of reality. We are not allowed to talk about the photon passing through this or this slit. Neither are we allowed to say the photon passed through both slits. All this kind of language is not applicable.” - Anton Zeilinger http://www.youtube.com/watch?v=ayvbKafw2g0 Double Slit Experiment – Explained By Prof Anton Zeilinger (a leader in quantum mechanics) – video Quote: "We know what the particle is doing at the source when it is created. We know what it is doing at the detector when it is registered, but we do not know what it is doing in-between" - Anton Zeilinger http://www.metacafe.com/watch/6101627/ “Mass-energy is “everything” that constitutes the physical structure of our universe. However, when asked what “that stuff”, which manifests itself in such diverse and mutually intertransformable appearances, really is, science replies with an embarrassed silence. We know how to measure it, but we simply do not know what it is. To quote Richard Feynman, from his legendary The Feynman Lectures on Physics: “It is important to realize that in physics, today, we have no knowledge of what energy is.” – Manfred Eigen of supplemental note: Erwin Schrödinger - "Do Electrons Think?" (BBC 1949) https://www.youtube.com/watch?v=hCwR1ztUXtUbornagain77
December 1, 2014
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Querius: One of them complained about Margulis’ daring to think for herself Why would anyone complain about someone thinking for herself? Margulis was clearly an original thinker who did important work in evolutionary biology. Her ideas concerning endosymbiosis are now a standard part of evolutionary theory. Querius: there was the complaint about a program written in FORTRAN (gasp) as if that made any difference. There's nothing wrong with Fortran. Our comment just pointed out that someone familiar with this common language could understand the problem with the software. By the way, did you have something to say concerning the topic? bornagain77: It is interesting to note that you pick on intelligently designed software to look for a fault whereas Sanford relies on real world evidence to back up his claim that his ‘intelligently designed’ model is correct! The program has a demonstrable error, and therefore doesn't correctly model observed population genetics. Heh. I noticed you again cited the article about Margulis that conflates Darwinism with Neodarwinism.Zachriel
December 1, 2014
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bornagain77:
It is on you to empirically prove that matter can be the source of subjective consciousness.
Unless you can present a testable model or reliable scientific evidence explaining how consciousness works the Theory of Intelligent Design must pertain to intelligence only. Attempting to go beyond what the theory was premised to explain only gets you into speculations that sabotage its scientific integrity. As you can see other than what theory suggests I clearly have no opinion either way, I just stated the possibilities then again made it clear that the theory does not need to explain consciousness.
There is reciprocal cause in both forward and reverse directions, specifically (for any behavior) behavioral cause or (for intelligent behavior) intelligent cause. This behavioral pathway causes all of our complex intelligence related behaviors to connect back to the behavior of matter, which does not need to be intelligent to be source of consciousness. For sake of theory consciousness is considered to be in addition to intelligence, but not required for intelligence to exist. Otherwise the most rudimentary forms of intelligence even simple algorithm generated computer models of intelligent processes might be expected to be conscious of their existing inside of a personal computer. It is not possible to rule-out electronic or algorithmic consciousness existing, therefore even though consciousness is not expected to exist in a computer model it is still possible that any functioning intelligence system is somehow conscious of their existence. In either case, consciousness is not a requirement for intelligence.
You are welcome to rephrase parts of the paragraph. As long as it briefly states the possibilities without taking sides I'll change the text to that instead.Gary S. Gaulin
December 1, 2014
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Zach you state: "The question concerned the use of computer simulations of population genetics. Computer simulations are models, which are then compared to observations. Many observations are explained by basic processes associated with population genetics.,,,, the problem with the (Sanford's) software is demonstrable. " It is interesting to note that you pick on intelligently designed software to look for a fault whereas Sanford relies on real world evidence to back up his claim that his 'intelligently designed' model is correct!. For instance, his claim about slightly detrimental mutations that are below the power of natural selection to remove from the genome is more than backed up by empirical evidence: Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Moreover, when the Darwinian evolutionary algorithms are analyzed in detail, we find that information is 'smuggled' into them: LIFE’S CONSERVATION LAW - William Dembski - Robert Marks - Pg. 13 Excerpt: (Computer) Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case. http://evoinfo.org/publications/lifes-conservation-law/ You go on about Marguilis being a Darwinist, not a neo-Darwinist, ... SO WHAT! Her quote on population genetics still stands: Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) – Casey Luskin April 12, 2011 Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it–changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get grant money.” - Lynn Margulis – biologist http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html If you disagree with her that the math of population genetics is useless as a predictive tool for telling us how the unfathomed complexity we find in life randomly evolved, then perhaps you can help this guy out: The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology – Bard - 2011 Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation.. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Or perhaps you can help these guys out who took the problem one step further and found the problem with population genetics irresolvable: Biological Information - Overlapping Codes 10-25-2014 by Paul Giem - video https://www.youtube.com/watch?v=OytcYD5791k&index=4&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ Moreover, I can cite empirical studies that back up the claim that detrimental mutations are far more likely to fixate than beneficial mutations,,, Of supplemental note to overlapping codes, (which our best computer programmers can only dream of imitating) At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years: Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637 In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark): "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 'It's becoming extremely problematic to explain how the genome could arise and how these multiple levels of overlapping information could arise, since our best computer programmers can't even conceive of overlapping codes. The genome dwarfs all of the computer information technology that man has developed. So I think that it is very problematic to imagine how you can achieve that through random changes in the code.,,, and there is no Junk DNA in these codes. More and more the genome looks likes a super-super set of programs.,, More and more it looks like top down design and not just bottom up chance discovery of making complex systems.' - Dr. John Sanford Psalm 139:14-15 I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. My frame was not hidden from you when I was made in the secret place, when I was woven together in the depths of the earth. Hillsong - Mighty to Save - With Subtitles/Lyrics http://www.youtube.com/watch?v=-08YZF87OBQbornagain77
December 1, 2014
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Bornagain77, The problem is that a lot of the antagonists here don't seem to be open to any contrary evidence or innovative thinking. Why bother answering a hail of unsupported assertions followed by personal attacks? One of them complained about Margulis' daring to think for herself, and there was the complaint about a program written in FORTRAN (gasp) as if that made any difference. This is hopeless. When they get trapped by evidence or logic, they announce that they've won or resort to personal abuse. Personally, I think they're delusional. Thanks once more for the quotes and vids along with your commentary. I'm sure that vituperation will follow. -QQuerius
December 1, 2014
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bornagain77: computer simulations are all programmed by intelligence, do you REALLY think that computer simulations that are Intelligently Designed help you in any way, shape, or form, to prove that life was not designed? The question concerned the use of computer simulations of population genetics. Computer simulations are models, which are then compared to observations. Many observations are explained by basic processes associated with population genetics. See Mendel, Experiments in Plant Hybridization, Proceedings of the Natural History Society of Brünn 1865. bornagain77: if you don’t like Sanford’s work, which I consider above reproach As we said, the problem with the software is demonstrable. bornagain77: you repeated the Marguilas question after I had already cited Encyclopedia Britannica on her position The article you cited above concerning Margulis conflated Darwinism and Neodarwinism. That's the problem with relying on polemics for scientific information.Zachriel
December 1, 2014
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Zach, my quotes are accurate in so far as they go. You didn't like them and tried to nitpick on side issues with them,,, thus, ONCE AGAIN, I don't care if you don't like my quotes!,,, Zach, computer simulations are all programmed by intelligence, do you REALLY think that computer simulations that are Intelligently Designed help you in any way, shape, or form, to prove that life was not designed? Moreover, if you don't like Sanford's work, which I consider above reproach, we can always go into Dembski and Mark's work and further expose you as a fraud. LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information http://evoinfo.org/publications/ I asked you if you understood the distinction between lying and telling the truth since you seem to be having such a hard time telling the difference, yet, instead of answering the question honestly, you repeated the Marguilas question after I had already cited Encyclopedia Britannica on her position,,, DUH! Thus I guess you did answer the question on honesty in your own round-a-bout way. Apparently you could care less about truth and are only interested in rhetorical tricks.,,, Too bad. I actually had some hope that you would be a bit different than most Darwinists.bornagain77
December 1, 2014
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bornagain77: I don’t care if you don’t like the quotes I cite! That's fine. No one can require you to support your positions, or answer simple questions. We can, however, point out when you don't. bornagain77: I’ll take Sanford’s word The problem with his software is demonstrable. The usual response at this point is to ask for support, rather than relying on misplaced authority. bornagain77: I understand pretty much exactly what Margulis believed Margulis was an avowed Darwinist, but rejected Neodarwinism. Do you understand the distinction? Dionisio: I don’t understand the distinction. Can you explain it, please? Sure. Neodarwinism is the old synthesis of Darwin's theory with Mendelian genetics. It posits a model of variation where changes are primarily through mutational steps and homologous recombination. It's somewhat outmoded now, but still describes many aspects of population genetics. Margulis was using Darwinism conventionally to refer to the theory that natural selection is the primary mechanism of adaptation. She accepted Darwinism, but she rejected Neodarwinism as an oversimplified model, and she provided important examples of evolutionary change that were not due to mutational steps, including her theory of endosymbiosis. Nonetheless, she realized that endosymbiotes only persist because of natural selection. Margulis proposed her endosymbiotic theory in the early 1970s. (See Margulis, The Origin of Eukaryotic Cells, Yale University Press 1972). That the theory is now a standard part of the theory of evolution shows that naïve Neodarwinism was long ago outmoded. Neodarwinism is still taught as a simplified model in evolutionary biology, just as Newton's Theory is taught as a simplified model in physics. They both explain many phenomena, though they are both limited in their domains.Zachriel
December 1, 2014
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Dionisio, Margulis believed life evolved, but not in the manner held by Neo-Darwinists,,, "Throughout most of her career, Margulis was considered a radical by peers who pursued traditional Darwinian “survival of the fittest” approaches to biology. Her ideas, which focused on symbiosis—a living arrangement of two different organisms in an association that can be either beneficial or unfavourable—were frequently greeted with skepticism and even hostility." http://www.britannica.com/EBchecked/topic/364780/Lynn-Margulis She, begrudgingly accepted, was a constant thorn in the side for neo-Darwinists: "This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn't create.... [N]eo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change -- led to new species. I believed it until I looked for evidence." (Quoted in "Discover Interview: Lynn Margulis Says She's Not Controversial, She's Right," Discover Magazine, p. 68 (April, 2011).) http://www.evolutionnews.org/2014/04/lynn_margulis_e084871.htmlbornagain77
December 1, 2014
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@271 Zachriel
The writer conflates Neodarwinism with Darwinism. Margulis is an avowed Darwinist, but rejects Neodarwinism. Do you understand the distinction?
I don't understand the distinction. Can you explain it, please? Thank you.Dionisio
December 1, 2014
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Pachyaena @258:
I asked William J Murray: “You’re a theist who believes in one creator god and that that god is the source (creator) of all existence, right?” I got this and a lot of other evasive, diversionary gibberish from William in response:
It seems to me you're not really interested in honest dialogue/debate, since you are insisting that all ID views fit into your preconceived box of oversimplified creationism and that anything other than that which conforms to your cartoonish template is, as you put it, "evasive, diversionary gibberish". There exist more interesting and logically robust forms of theism than that which can be gleaned from watching South Park and The Simpsons. I was fortunate enough to run across those views in the midst of my militant atheism a few years ago. Perhaps you will, too. That is, if you can stop dismissing them out of hand long enough to actually evaluate them fairly.William J Murray
December 1, 2014
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Zach , I'm not your puppet, and I don't care if you don't like the quotes I cite! Get over your self importance! If I were you, I would worry about the fact that I have exposed you as a liar several times! as to accuracy, its your deists/atheists' word against Sanford's. I'll take Sanford's word since I have caught you deists/atheists blatantly lying repeatedly about practically every thing of importance in biological science! ,,,Neo-Darwinism is not a good first approximation but is a pseudo-science that is protected by lawsuits issued by atheistic fundamentalists. In fact, state legislatures have to pass legislation protecting teachers from harassment from atheists for teaching valid criticisms against Neo-Darwinism,, for instance,, Scientists Issue Letter Supporting Louisiana Science Education Act http://www.evolutionnews.org/2011/05/scientists_issue_letter_suppor046881.html The tyranny of neo-Darwinists in academia is well known and for you to pretend academic freedom is the norm is delusional at best or an outright lie at worst:,, See EXPELLED the movie and Bergman's Slaughter of Dissidents for proof I understand pretty much exactly what Margulis believed, so what does that have to do with the fact that you have misrepresented (read lied), about the adequacy of Neo-Darwinism and its stranglehold on public education? You do understand the distinction between lying and telling the truth don't you?bornagain77
December 1, 2014
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Z: Second-hand quote mines don’t constitute an argument... If you want to post something, try just posting a single link for discussion rather than a slew of only tangentially related claims and quote-mines. bornagain77: {posts a bunch of links anyway} bornagain77: the computer simulations are accurate to real world data That is incorrect. The program is written in Fortran, and has a demonstrable flaw. bornagain77: Then why is Neo-Darwinism, i.e. the modern synthesis, taught in schools, by force of law, as if it were an unquestioned fact? Neodarwinism is not written into law. Rather, Neodarwinism is taught just like Newton's Theory is taught, because it is a good first approximation according to a consensus of the scientific community. You never answered the question. Margulis is an avowed Darwinist, but rejects Neodarwinism. Do you understand the distinction?Zachriel
December 1, 2014
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Zach, the computer simulations are accurate to real world data. Sanford is certainly no slouch in population genetics having invented the gene gun,,, Moreover, that you would have to appeal to computer simulations, which are intelligently designed by the way, to try to put some type of observational evidence on the table is a joke!bornagain77
December 1, 2014
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Lynn Margulis is far more antagonistic to the neo-Darwinian stranglehold on science than you want to admit: Darwin’s Frog Defies Evolution - July 5, 2013 Excerpt: Lynn Margulis in an interview with Mazur pronounced, "neo-Darwinists are a… religious sect within the sprawling religious persuasion of Anglo-Saxon Biology." http://www.darwinthenandnow.com/2013/07/darwins-frog-defies-evolution/ Lynn Margulis: Evolutionist and Critic of Neo-Darwinism - Stephen C. Meyer - April 25, 2014 Excerpt: in Chapters 15 and 16 of Darwin's Doubt, I addressed six new (that is, post neo-Darwinian) theories of evolution -- theories that proposed new mechanisms to either supplement or replace the reliance upon mutation and natural selection in neo-Darwinian theory.,, I show that, although several of these new evolutionary theories offer some intriguing advantages over the orthodox neo-Darwinian model, they too fail to offer adequate explanations for the origin of the genetic and epigenetic information necessary to account for new forms of animal life -- such as those that arise in the Cambrian period. http://www.evolutionnews.org/2014/04/lynn_margulis_e084871.html A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology - May 2014 http://www.evolutionnews.org/2014/05/a_group_of_darw086231.html The Third Way “J.A. Shapiro a professor at the University of Chicago, , and other top researchers, is searching for a “third way,” a scientific, non-Darwinian way.” http://www.thethirdwayofevolution.com/people podcast - Non-Religious Skeptics of Darwinian Evolution – Aug 2014 http://intelligentdesign.podomatic.com/entry/2014-08-25T15_07_31-07_00 Darwin's Doubt (Part 9) by Paul Giem - video - The Post Darwinian World and Self Organization Chapter 15 and 16 of Darwin's Doubt in which 6 alternative models to neo-Darwinism, that have been proposed by evolutionists (such as those of the Altenberg 16) to 'make up' for the inadequacy in neo-Darwinism, are discussed and the failings of each model is exposed. http://www.youtube.com/watch?v=iREO1h4h-GU&index=10&list=PLHDSWJBW3DNUaMy2xdaup5ROw3u0_mK8tbornagain77
December 1, 2014
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Z: Keep in mind that Neodarwinism is not current theory, so try to avoid arguing with a strawman. bornagain77 {points to limitations of Neodarwinian models anyway.}
The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program.
Mendel's Accountant has a demonstrable flaw which virtually eliminates the known empirical effects of selection.Zachriel
December 1, 2014
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as to: "Keep in mind that Neodarwinism is not current theory" Then why is Neo-Darwinism, i.e. the modern synthesis, taught in schools, by force of law, as if it were an unquestioned fact? Evidence for Creation now banned from UK religious education classes - July 2012 Excerpt: Recently, evolutionist Suzan Mazur published a book entitled, The Altenberg 16: An Exposé of the Evolution Industry.,, The Altenberg 16 is a group of top university academics who met together at a symposium held at Altenberg in Austria in 2008. According to Mazur, these leading evolutionary scientists ‘recognize that the theory of evolution which most practicing biologists accept and which is taught in classrooms today, is inadequate in explaining our existence.’ Some of the delegates would clearly go further. According to molecular biologist, Professor Antonio Lima-de-Faria, not only is the Darwinian paradigm wrong, but it ‘actually hinders discovery of the mechanism of evolution.’ Professor Massimo Piattelli-Palmarini spoke for a number in stating simply that natural selection ‘is not the way new species and new classes and new phyla originated.’ Professor Jerry Fodor confessed, ‘I don’t think anybody knows how evolution works.’ If scientists can’t point to a natural process that can drive evolution, why should evolution (by force of law) be taught as science, (as a fact), in school classrooms? http://creation.com/creation-religious-education Scientists stunned by the public’s doubt of Darwin - April 22, 2014 Excerpt: (Stephen) Meyer said that view under-represents the real facts being discovered in evolutionary biology. “Very few leading evolutionary biologists today think that natural selection and random mutation are sufficient to produce the new forms of life we see arising in the history of life,” Meyer said. “And then when the public is catching wind of the scientific doubts of Darwinian evolution and expresses them in a poll like this, these self-appointed spokesmen for science say that the public is ignorant. But actually, the public is more in line with what’s going on in science than these spokesmen for science.” http://www.worldmag.com/2014/04/scientists_stunned_by_the_public_s_doubt_of_darwinbornagain77
December 1, 2014
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Zach you claim "Computer simulations provide a much better view of the process." (of population genetics) And the view we get is not conducive to Darwinian explanations in the least: Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013 Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdfbornagain77
December 1, 2014
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bornagain, Here's why you shouldn't use polemic sources.
Amazingly, while materialists who challenge neo-Darwinism are apparently "persona non grata," Margulis explains that scientists who continue to pursue Darwinian explanations will readily receive grants and support even though they admit the paradigm is failing
The writer conflates Neodarwinism with Darwinism. Margulis is an avowed Darwinist, but rejects Neodarwinism. Do you understand the distinction?Zachriel
December 1, 2014
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