Another One For the “If You Made This Stuff Up No One Would Believe You” File

_{Barry Arrington

December 9, 2013

Intelligent Design}

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What does a “tree of life” purport to show? The obvious answer is a tree of life purports to show the pathways of common descent ASSUMING common descent occurred.

In the combox to a prior post a commenter who goes by wd400 writes:

That we can explain the data so well assuming a tree is evidence for common descent.

Wait just a second, you might say. Doesn’t a tree assume common descent rather than demonstrate it? Of course it does. wd400’s comment might just as well be re-cast as:

That we can explain the data so well assuming a tree is evidence for a tree.

We might be able to say that a tree of life diagram is consistent with common descent, if common descent were true. The diagram cannot be evidence for common descent for the simple reason that it assumes common descent to begin with.

In my last post I said this of Nick Matzke:

One wonders if his faith commitment to metaphysical naturalism renders him unable to see the circularity of his arguments, or if he does see it and just chooses to look the other way. My money is on the former. I think he is literally unable to grasp the obvious question begging that is immediately apparent to those who do not share his faith.

Here we see this same phenomenon again. I am all but certain that wd400 is perfectly sincere. He is not being intentionally provocative, intransigent or obtuse. It seems that it is almost literally impossible for him to see past his faith commitments to the circularity of his arguments.

Comments

I don't mean any such cr*p since the probability argument is a red herring, a strawman. Probability has nothing to do with whether or not the common descent hypothesis or the prediction that the tree of life is strictly nested is correct. A single instance of non-nested horizontal sequence sharing between distant branches of the tree breaks it. This has already been found. Therefore common descent is soundly falsified and Darwinism with it. Wake up.Mapou_{December 16, 2013
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You mean if the probability of observing an event, assuming common descent is true, is equal to zero we should discard common descent. How is this different that saying that if the probability of observing data is high, assuming common descent, we should take that as evidence for common descent? Barry's point was this sort of reasoning is circular. I don't think it is.wd400_{December 16, 2013
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wd400 @43, The tree of life is either strictly nested or it is not. Common descent predicts a strictly nested hierarchy. If there is just one case that breaks this prediction, then common descent should thrown into the septic tank of failed hypotheses. Probability has nothing to do with it. Stop acting like you're smarter than everyone else. You are not. Your invocation of probability makes you look like an idiot.Mapou_{December 16, 2013
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What an extraordinary thread. Most commenters here seem to be convinced that I'm an hide-bound idealog who can't see the circularity of my argument. So here's a question for anyone who is still playing. How can you reason probabilistically without calculating the probability of something under a certain assumption? If you want to know the probability of Some Hypothesis given Some Data, then you need to know the probability of the data assuming the hypothesis is true, don't you. Or does the ID movement now deny Bayes Theorem as well as evolutionary biology? Or hypothesis testing for that matter - a p-value is the probability of the data persuming the null hypothesis is true. Is the most basic statistical procedure going circular?wd400_{December 16, 2013
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@Collin 37 Warm blood, Four cavities heart, c´ value are "traits" that violeted the nested hierarchy plus all what you call "convergent evolution". All what need to be explained as LGT.Chesterton_{December 11, 2013
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Take note of what an expert says about the Tree of Life 'explaining' the data: "The genomic revolution did more than simply allow credible reconstruction of the gene sets of ancestral life forms. Much more dramatically, it effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different. Whether the TOL can or should be salvaged—and, if so, in what form—remains a matter of intense debate that is one of the important themes of this book." Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 76-80). Pearson Education (USA). Kindle Edition. Koonin is not an ID enthusiast; he regards ID as 'pernicious nonsense'wsread_{December 11, 2013
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what Darwin expected: Darwin's Dilemma - The Cambrian Explosion - In Darwin's Own Words Excerpt: Consequently, if the theory be true, it is indisputable that, before the lowest Silurian or Cambrian stratum was deposited long periods elapsed, as long as, or probably far longer than, the whole interval from the Cambrian age to the present day; and that during these vast periods the world swarmed with living creatures… To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods, I can give no satisfactory answer… The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained. [emphasis added] —Chapter IX, “On the Imperfection of the Geological Record,” On the Origin of Species, Charles Darwin - fifth edition (1869), pp. 378-381. What the fossil record reveals: Cambrian Explosion Ruins Darwin's Tree of Life (2 minutes in 24 hour day) - video http://www.youtube.com/watch?v=bQKxkUb_AAg and of course the question that is never honestly addressed by Darwinists: Dr. Stephen Meyer: Darwin's Dilemma - Where did the information come from? - video http://www.youtube.com/watch?v=8CTKKrtSc8k Pre-Cambrian Explosion - Jonathan Wells - (How do you change a jellyfish into a trilobite?) - video https://vimeo.com/32428029 footnotes: Instant Body Plans: The Case of Jellyfish - July 26, 2013 Excerpt: Cubomedusae (box jellyfish) are particularly interesting. They have eyes that are almost human-like! "As the name depicts, Cubozoans have a squarish shape with four tentacles and four rhopalia. Each rhopalium contains six eyes of four different types, two of which (the upper lens eye and the lower lens eye) are highly developed image-forming eyes with cornea, pupil, lens, and retina, much like our own...." "The earliest widely accepted animal fossils are rather modern-looking cnidarians, possibly from around 580 million years ago, although fossils from the Doushantuo Formation can only be dated approximately." So it's not clear that the dates are right, but even if they precede the main (Cambrian) explosion by 40 million years, they are already "modern-looking." http://www.evolutionnews.org/2013/07/instant_body_pl074861.html Evolution vs. The Trilobite Eye - Andy McIntosh http://www.metacafe.com/watch/4032589/ The Optimal Trilobite Eye - per Dr. Don Johnson - Programming of Life page 68-66 and appendix F: Trilobites suddenly appeared in the Cambrian (lowest fossil-bearing) stratum with no record of ancestry. The trilobite eye is made of optically transparent calcium carbonate (calcite, the same mineral of its shell) with a precisely aligned optical axis that eliminates double images and two lenses affixed together to eliminate spherical aberrations [McC98, Gal00]. Paleontologist Niles Eldredge observed, “These lenses--technically termed aspherical, aplanatic lenses--optimize both light collecting and image formation better than any lens ever conceived. We can be justifiably amazed that these trilobites, very early in the history of life on earth, hit upon the best possible lens that optical physics has ever been able to formulate” [Eld76]. Notice these lenses weren’t just good as, but were better than anything modern optical physicists have been able to conceive! ,,, “The design of the trilobite’s eye lens could well qualify for a patent disclosure” [Lev93p58].,,, The trilobite lens is particularly intriguing since the only other animal to use inorganic focusing material is man. The lens may be classified as a prosthetic device since it was non-biological, which also means the lens itself, with apparently no DNA inherent within, was not subject to Darwinian evolution. The manufacturing and controlling of the lenses were obviously biological processes, with an unknown number DNA-prescribed proteins (each with a prescriptive manufacturing program) for collecting and processing the raw materials to manufacture the precision lenses and create the refracting interface between the two lenses. The lenses do not decompose as any other animal’s lenses would, so they are subject to rigorous scientific investigation,,, Since no immediate precursors of trilobites have been found, Darwinists are without any evidence as to how an organism with an eye as complex as a trilobite could have arisen,,, especially in,, the lowest multi-cellular fossil-bearing stratum,,, Appendix F: “Trilobites had solved a very elegant physical problem and apparently knew about Fermat’s principle, Abbe’s sine law, Snell’s laws of refraction and the optics of birefringent crystals” [Cla75] “the rigid trilobite doublet lens had remarkable depth of field (near and far focusing) and minimal spherical aberration” [Gon07] Physicist Riccardo Levi-Setti observes: “In fact, this doublet is a device so typically associated with human invention that its discovery comes as something of a shock. The realization that trilobites developed and used such devices half a billion years ago makes the shock even greater. And a final discovery - that the refracting interface between the two elements in a trilobite’s eyes was designed in accordance with optical constructions worked out by Descartes and Huygens in the mid-seventeenth century - borders on sheer science fiction” [Lev93p57]. “The trilobites already had a highly advanced visual system. In fact, so far as we can tell from the fossil record thus far discovered, trilobite sight was far and away the most advanced in Kingdom Animalia at the base of the Cambrian,,, There is no other known occurrence of calcite eyes in the fossil record” [FM-trib]. Fossil Predictions vs. Actual Evidence - Graphs https://docs.google.com/document/d/1VgBf-FQXfMwPMRxJwbEa0W4OKB-6Q2nHVNRtknqGggc/editbornagain77_{December 11, 2013
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Taxonomic nested hierarchies don’t support Darwinism - May 14, 2013 Excerpt: In sum, the nested hierarchies in taxonomy don’t need Darwinism, in fact, Darwinism distorts the ability actually see the nested hierarchies, and finally nested hierachies based on taxonomy are evidence against Darwinism. https://uncommondescent.com/darwinism/taxonomic-nested-hierarchies-dont-support-darwinism/bornagain77_{December 11, 2013
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An assertion that the tree of life (T) is evidence for evolution (E) is criticisable but you have mis-identified the criticism. Take the following argument: 1. If E then T 2. If I then not T 3. I or E 4. T 5. Conclusion: E The argument is valid and in no way circular. We can express an argument about the Tree of Life in the same form: 1. If evolution were true then there would be a nested hierarchy such that the organisms in the world could be arranged assuming that they evolved from a common ancestor. (If E then T) 2. If Intelligent design were true then there would not be a nested hierarchy such that organisms in the world could be arranged assuming that they evolved from a common ancestor. (If I then not T) 3. We are deciding between evolution and intelligent design (I or E) 4. The organisms in the world can be arranged assuming that they evolved from a common ancestor. (T) 5. Conclusion: Evolution is more likely true/more like the truth than intelligent design. No circularity comes in despite the repeated use of the word “assuming” and the argument is valid. Which of the premises do you disagree with? My money is on “2”, that we would expect a nested hierarchy were intelligent design true. You are criticising the wrong bit of the argument. Now, would we expect a hierarchy given intelligent design? It’s certainly compatible with intelligent design, but then so are non-hierarchical populations. Non-hierarchical populations are not compatible with evolution though. We would expect a hierarchy given evolution, certainly more so than given intelligent design. To keep the maths simple let’s guess at by how much. Take the probability of a hierarchy given evolution , P(T/E), to be 1 and the probability of a hierarchy given intelligent design, P(I/E), to be 0.99. Let’s continue to restrict ourselves to a choice between E and I but we’ll give in to you and load the prior probabilities: P(E) = 0.1 and P(I) = 0.9 (before looking at T intelligent design is 9 times as likely as a evolution). Throw the result into Bayes theorem: - P(E/T) [the probability of evolution given T] = [P(T/E) x P(E)] / [(P(E) x P(T/E)) + (P(I) x (P(T/I)) - P(E/T) = (1 x 0.1) / (0.1 x 1) + (0.9 x 0.99) - P(E/T) = 0.1/ 0.1 + 0.891 - P(E/T) = 0.100908174 You’re welcome to try the calculation with different priors and probabilities of the possibility of producing a Tree of Life: so long as the possibility of producing a Tree of Life assuming evolution has a higher probability than the possibility of producing a Tree of Life without assuming evolution then the possibility of producing a tree of life is (non-circular) evidence for evolution.Tony Lloyd_{December 11, 2013
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mapou, can you give me some examples of the nested hierarchy being violated?Collin_{December 10, 2013
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Mark Frank @21:
The tree of life is not arranged according to an assumption of common descent. It is primarily based on features held in common (although later modified as the theory of common descent became accepted – theory and data have always interacted in this way). Common descent just provides a very, very good explanation for that tree.
The problem is that common descent predicts a strictly nested hierarchy. This is not what is observed in nature. We observe many cases of horizontal transfers high up in the tree. This is not explainable by common descent. Therefore common descent is falsified. A non-nested hierarchy is what is predicted by intelligent design. We commonly observe this in the evolution of designs in such fields as software engineering, architecture, automobile design, video game design, etc. PS. The circularity is that evolutionary biologists try their best to force fit the data so as to conform to a strictly nested hierarchy. When the data does not fit, they invent all sorts of nonsense (e.g., convergent evolution) to explain away the discrepancies. The latest trend is to pretend that common descent is confirmed because most of the hierarchy is nested. Trying to make this seem like a statistical problem is stupid and dishonest. Common descent does not predict that a subset of the hierarchy is non-nested. It predicts that ALL of it nested.Mapou_{December 10, 2013
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Sorry, one last attempt at clarity: A Tree of Life created based on a) morphology and b) fossil history only provides "evidence" for common descent IF it matches a Tree of Life created based solely on some common descent criteria other than morphology and fossil history. Otherwise, you're just reasoning in a circle.drc466_{December 10, 2013
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DRC, I don't know that it does. I took the assertion that it does at face value.Pro Hac Vice_{December 10, 2013
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In other words, if common descent is fully accurate, what we should be able to do is construct a tree based on complexity, like the vehicles analogy. The base of the tree would be simple 2-wheeled carts, and barrows. Then wagons, and cycles, etc. on up to modern machines. But what we find in the fossil record is more like fully modern motorcycles, fully modern airplanes, fully modern automobiles, full modern boats, etc. We arbitrarily put cars after boats, but we have to hypothesize the transitions between them, and the wagons and carts, and say that they're missing from the fossil record. If anything, the problems evolutionists have with creating an agreed-upon Tree of Life is an argument against common descent, not evidence for.drc466_{December 10, 2013
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Re MF @22 and PHV @30 - but does the tree of life evolutionists have attempted to create really assume common descent? By what criteria do you claim that? For example - why do we say that mammals evolved from reptiles? Is it based on some "common descent" criteria such as morphology, genetics, or functional complexity? No, we put them in the tree that way because that's what we think the fossil record shows. So our "tree" is merely a product of the first - grouping by morphology - not a product of the second, where we have some evidence of common descent. There is no biological reason that leads us to place one life form before or after another - this is why dating of fossils is so contentious. Without fossils and fossil dates, evolutionists don't know whether the tree should show birds --> reptiles, or reptiles --> birds, or neither. The tree is truly an arbitrary grouping that neither requires nor provides evidence for common descent. If anything, many Cambrian life-forms are more complex than we see today - if we created a tree based on complexity, it would either be upside-down or a bush w/ every life form at the same level. Are you prepared to argue, for example, that a mammal is "more complex" than a trilobyte? Again, by what criteria?drc466_{December 10, 2013
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I think a better way of describing the relationship between the data and the model (instead of the model "explaining" the data) is that models characterize the data, and that comparatively one characterization maybe be better than the other at generating useful applications and predictions/retrodictions. I think that there are several great failures of the Darwinist characterization of the data, failures that are better characterized under an ID perspective.William J Murray_{December 10, 2013
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I will try one more time. If I arrange a set of data based on an assumption and then claim the arrangement of data validates the assumption I used to arrange it, I have made a circular argument. Why is that so hard to grasp?
Assuming common descent and using that assumption as proof of itself would be circular. Assuming common descent and asking whether the data are more consistent with that assumption than any other is a test of the assumption using external criteria. The external criteria (the closeness of the fit to the data) makes the argument non-circular.Pro Hac Vice_{December 10, 2013
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Eric @ 28: "(i) is OK. (ii) is bad." Just so. wd400, on whose comments this post is based, does not seem to understand the difference.Barry Arrington_{December 10, 2013
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I think Mark Frank has a valid point that we can put forward (assume) competing hypotheses and see which one best fits the data. That is, in essence, the approach that underlies the inference to the best explanation. Both traditional evolutionary theory and ID rely on this approach to a greater or lesser extent. My issue is more with the assertions that a Darwinian paradigm well explains the data. In some limited cases that may be true: bacterial resistance to antibiotics, finch beaks, etc. However, anything in biology much beyond that stretches the Darwinian paradigm to the breaking point. At those levels we are treated to just so stories, wild speculations, and irresponsible declarations of faith in the power of particles bumping into each other over time. We need to distinguish between (i) starting with a working assumption to see if it is supported by the data, and (ii) thinking that any particular piece of data "proves" our assumption (circular), particularly if we think our conclusion is somehow a necessary logical conclusion. (i) is OK. (ii) is bad. (ii) needs to be replaced with (x) an overall view of the data across the board, rather than one particular example of, say, similarities between two organisms, (y) an acknowledgement that we are inferring an explanation from the data, rather than "proving" anything in a hard sense, and (z) an acknowledgement that, if we are not careful, our a priori background and philosophical assumptions can get in the way of an objective assessment. BTW, I am not saying that MF is guilty of (ii). I suspect he is aware of the limitations of the inference. As a result, I think my primary disagreement with him would be not over the idea of assuming a tree of life in order to see whether it fits the data, but over whether it in fact fits the data.Eric Anderson_{December 10, 2013
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OT: Hooray! Eric Metaxas? and Stephen Meyer's video is finally up! Socrates in the City - "Darwin's Doubt" with Stephen Meyer - video https://vimeo.com/81215936bornagain77_{December 10, 2013
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#25 KF This is about common descent not design. Do you think life is descended from a limited number of simple life-forms or do you think complex life forms appeared fully formed by some undefined process?Mark Frank_{December 10, 2013
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MF: Three thoughts: 1 --> The evolutionary tees are notorious for major missing links (and for circular reasoning). 2 --> the explanation of the tree-like structure has to account for organisation and associated specific functional information, where FSCO/I has but one empirically grounded explanation, design. 3 --> The root of the tree, OOL cannot be explained on chance variation and differential reproductive success leading to descent with unlimited modification in a tree-like branching pattern, as the reproductive mechanism is part of what needs explanation. So, it is highly reasonable to infer that on inference to best empirically grounded explanation, we cannot censor out design a priori as Lewontin and Sagan did by imposing materialism. That begs the question. Inference to best explanation only escapes question begging by open-ended comparative difficulties across all serious candidates. Multiply this by the pattern above and we see that the best explanation of a treelike structure with cross-links etc, is design with a library of key parts. KFkairosfocus_{December 10, 2013
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Q: or maybe it was the other way around. Some bats occasionally enjoyed a minnow that chanced to leap. next, bats followed birds and developed a diving habit. That led to sonar underwater. They got so fat on fish they couldn't fly anymore. natural selection then got them fins and bigger and bigger bat-swimmers with ability to reproduce in a wate3ry context. Voila, whales! KFkairosfocus_{December 10, 2013
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Sorry, off topic and apologies if this has already been posted. Amazing little animation showing the scale of life: http://Twitpic.com/do7o8zsteveO_{December 10, 2013
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Perhaps this can best be explained as two different trees of life. There is one that is based on features of existing organisms(which Linnaeus began) and there is one that hypothesises the development of life over the billions of years. The first is the observed. The second is the explanation of the first (and also explains the fossil record)and does indeed assume common descent. The fact that the second provides such a good explanation for the first is part of the overwhelming evidence for common descent (which I remind you is accepted by many of the more intelligent IDists)Mark Frank_{December 10, 2013
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Barry
If I arrange a set of data based on an assumption and then claim the arrangement of data validates the assumption I used to arrange it, I have made a circular argument. Why is that so hard to grasp?
The tree of life is not arranged according to an assumption of common descent. It is primarily based on features held in common (although later modified as the theory of common descent became accepted - theory and data have always interacted in this way). Common descent just provides a very, very good explanation for that tree.Mark Frank_{December 10, 2013
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PHV @ 19: "What about that is circular?" Your question might as well be, “what about circularity is circular”? I will try one more time. If I arrange a set of data based on an assumption and then claim the arrangement of data validates the assumption I used to arrange it, I have made a circular argument. Why is that so hard to grasp?Barry Arrington_{December 10, 2013
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I don't think that analogy is relevant to my point. If we take two "assumptions," a tree based on common descent and one based on design, we can test each to see which better fits the data. If the common descent tree does, then that is evidence for common descent. What about that is circular?Pro Hac Vice_{December 9, 2013
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PHV, maybe you'll understand if you see drc's analogy in 13.Barry Arrington_{December 9, 2013
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wdr400: “. . . and find the tree-shape that best fits the observed data” given the ASSUMPTION of common descent. You really don’t see the circularity after it has been pointed out to you over and over. Thank you wd400 for demonstrating how faith commitments trump logic and render the faithful blind, just as I pointed out in the OP.
Can you explain in more detail how this is circular? The "tree-shape" is essentially the assumption of common descent, isn't it? In which case the test here is to see whether that assumption fits the data. That doesn't seem to be circular.Pro Hac Vice_{December 9, 2013
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