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Why KeithS’s bomb is a damp squib

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In this short post, I’d like to explain what’s wrong with KeithS’s argument for unguided evolution. The argument, in a nutshell, goes like this:

1. We observe objective nested hierarchies (ONH)
2. Unguided evolution explains ONH
3. A designer explains ONH, but also a trillion alternatives.
4. Both unguided evolution and a designer are capable of causing ONH.
Conclusion: Unguided evolution is a trillion times better at explaining ONH.

The first thing I’d like to point out is that while KeithS, in his post over at TSZ leans heavily on the evidence assembled by Dr. Douglas Theobald in his article, 29+ Evidences of Macroevolution, it is very odd that Dr. Theobald himself does not put forward this argument anywhere in his article. On the contrary, he expressly declares, in his reply to creationist Ashley Camp’s critique:

This is not to say that God could not have created species independently and miraculously, yet gradually. While there currently is absolutely no scientific evidence for such an idea, gradual Divine direction of evolution is indeed consistent and compatible with common descent.

It is possible for a theist to see the theory of common descent, and the hierarchy which it predicts, as a reflection of the Creator’s divine plan—much as Sir Isaac Newton saw his laws of motion, and the ellipses and parabolas which they predict, as evidence of the Creator’s hand in our universe…

In fact, no theological assumptions or arguments are made at all in the essay. The “29 Evidences” is not an argument against creation—it is the scientific argument for common descent, no more, no less…

I personally believe that an omnipotent, omniscient Creator could have created in any manner that he chose. For a theist, the pertinent question is not “what is an omnipotent Creator capable of?” but rather “how exactly did/does the Creator create?”. The first question is purely theological, and as such is left unaddressed in the “29 Evidences”; in contrast, the second question is one that science can answer (given the assumption of a Creator).

The second point I’d like to make – and here I’m basically restating a point that William J. Murray made earlier, in mathematical language – is that KeithS has misapplied Bayes’ Theorem, which states: P(A|B) = P(A).[P(B|A)/P(B)],
where A is a proposition and B is the supporting evidence,
P(A), the prior probability, is the initial degree of belief in A,
P(A|B), the conditional probability, is the degree of belief in A, having taken B into account, and
the quotient P(B|A)/P(B) represents the support B provides for A.

A better way of stating Bayes’ Theorem is to expand the denominator, P(B). We can say that P(B) is equal to [P(B|A).P(A))+(P(B|~A).P(~A)], since if B is true, then either A is also true or A is false (and thus ~A is true). Hence:
P(A|B) = [P(A).P(B|A)]/[P(B|A).P(A))+(P(B|~A).P(~A)]
Where P(~A) is the probability of the initial degree of belief against A, or 1-P(A)
P(B|~A) is the degree of belief in B, given that the proposition A is false.

The problem is that KeithS has conflated two hypotheses: the hypothesis of common descent (which is very well-supported by the evidence that objective nested hierarchies exist in living things), and the hypothesis of unguided design (which he also claims is well-supported by the evidence that objective nested hierarchies exist in living things).

The first hypothesis is indeed well-supported by the evidence, as the only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. The probability that any other process would generate such hierarchies is vanishingly low.

But if KeithS wishes to argue against intelligently guided evolution, then the two alternative hypotheses he needs to consider are not:
A: a branching evolutionary process (also known as a Markov process) generated the objective nested hierarchies we find in living things; and
~A: an Intelligent Designer generated these objective nested hierarchies,

but instead:

A: an unguided process generated the objective nested hierarchies we find in living things; and
~A: an intelligently guided process generated these objective nested hierarchies.

The point KeithS makes in his essay is that on hypothesis ~A, the likelihood of B (objective nested hierarchies in living things) is very low. However, it is also true that on hypothesis A, the likelihood of B is very low, as the vast majority of unguided processes don’t generate objective nested hierarchies.

My third point is that KeithS’s argument assumes that the genetic and morphological features on the basis of which living things are classified into objective nested hierarchies were generated by the same process as the (unguided, Markovian) processes which generates the branches in the hierarchies. This is unlikely, even on a standard evolutionary view: features take time to evolve, and therefore would presumably have appeared at some time subsequent to the branch nodes themselves. Thus it could well be the case that while unguided processes explain the existence of objective nested hierarchies in the living world, guided processes are required to explain some or all of the features in these hierarchies.

My fourth point is that KeithS’s exclusion of the origin of life from his argument limits the force of his conclusion. At most, he can argue that objective nested hierarchies are best explained by unguided processes; but that is not the same as saying that living things themselves are best explained by these processes, or that the origin of life is due to an unguided process.

Finally, I’d like to point out that KeithS’s argument against Dr. Douglas Axe is factually mistaken. Nowhere in his paper, “The Case Against a Neo-Darwinian Origin of Protein Folds” does Dr. Axe make the argument KeithS imputes to him.

My time at the Internet cafe is up, so I shall stop here.

Comments
keiths:
Theobald is a methodological naturalist, so guided evolution has no place in his scientific thinking.
Therefore, all his "evidences" for common descent and a single "objective nested hierarchy" are only evidence for unguided evolution. gee. really? how did you reach that conclusion?Mung
November 6, 2014
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keiths:
My point is simply that you needn’t be surprised that Theobald didn’t make the same argument that I do.
So you were quote-mining.Mung
November 6, 2014
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keiths @ 50:
1. Theobald’s stated purpose was to present the evidence for common descent, so that’s what he did.
What was Theobald's position on whether the nested hierarchy was guided or unguided?Mung
November 6, 2014
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Love the title of the OP!Mung
November 6, 2014
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Zach, you don't actually address reality, so as to the Black Knight, 'let's call it a draw shall we?'bornagain77
November 6, 2014
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Interesting that Denyse has closed comments on yet another thread that was going badly for IDers.keith s
November 6, 2014
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Zachriel: The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin’s “long abstract”.
Does this branching principle conform with a top-down tree; as in BA77's question? It seems pretty obvious to me that you refer to the good ol' bottom-up branching pattern.Box
November 6, 2014
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Zachriel 149
lifepsy: How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes? That’s not our position. Theobald shows that branching descent is strongly supported, but says nothing about whether the process is guided or not.
I was responding to Keith S who was adamant about calling it "unguided evolution". Switch out unguided evolution for "branching descent". It is the same problem.
lifepsy: Why should branching common descent necessarily produce a discernible nested hierarchy? It’s a deduction from geometry as grouping leaves by branch and stem form a nested hierarchy. Now consider a tree that grows, but there are occasional mutations that are inherited along a given branch. The end result will be a pattern of traits that form a nested hierarchy. There’s a statistical relationship between the mutation rate, number of traits, and the fit to the nested hierarchy. Here’s a simple example with one mutation* per branch.
I'm aware of the principle. Notice the keyword "discernible". I'm asking you why this nested hierarchy should necessarily be recognizable after the fact, instead of having its signal confounded by a blurring of indistinguishable traits.
lifepsy: Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy? The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin’s “long abstract”.
Your description does not address the problem in any way. You're merely describing the branching principle again, while I'm telling you that whether or not the nested hierarchy is generated in principle, the nested hierarchy signal itself may potentially be masked. Darwin is in accord with my position.
Darwin's Origin p.510 " Extinction has only separated groups: it has by no means made them; for if every form which has ever lived on this earth were suddenly to reappear, though it would be quite impossible to give definitions by which each group could be distinguished from other groups, as all would blend together by steps as fine as those between the finest existing varieties, nevertheless a natural classification, or at least a natural arrangement, would be possible. We shall see this by turning to the diagram: the letters, A to L, may represent eleven Silurian genera, some of which have produced large groups of modified descendants. Every intermediate link between these eleven genera and their primordial parent, and every intermediate link in each branch and sub-branch of their descendants, may be supposed to be still alive; and the links to be as fine as those between the finest varieties. In this case it would be quite impossible to give any definition by which the several members of the several groups could be distinguished from their more immediate parents; or these parents from their ancient and unknown progenitor. Yet the natural arrangement in the diagram would still hold good; and, on the principle of inheritance, all the forms descended from A, or from I, would have something in common. In a tree we can specify this or that branch, though at the actual fork the two unite and blend together. We could not, as I have said, define the several groups; but we could pick out types, or forms, representing most of the characters of each group, whether large or small, and thus give a general idea of the value of the differences between them. This is what we should be driven to, if we were ever to succeed in collecting all the forms in any class which have lived throughout all time and space."
If you cannot distinguish actual different groups, then you cannot assemble them into branching orders and nested hierarchies. Furthermore, if these finest of intermediate links include heavy losses or reversal of traits, then the nested hierarchy signal is certainly confounded. The conclusion is that the branching pattern of common descent is just as likely (if not more so) to result in a data scenario where traits are so blurred as to make the assembly of nested hierarchies impossible. Thus, as usual, you are accommodating to an outcome that opposes the one you offer as evidence. And lack of a discernible nested hierarchy signal would not falsify a branching descent model. It’s rather unscientific to be promoting "nested hierarchy" as direct evidence for a branching descent model, when "Not-nested hierarchy" could also be accommodated by a branching descent model.
"… But surely no purely random process of extinction would have eliminated so effectively all ancestral and transitional forms, all evidence of the trunk and branches of the supposed tree, and left all remaining groups: mammals, cats, flowering plants, birds, tortoises, vertebrates, molluscs, hymenoptera, fleas and so on, so isolated and related only in a strictly sisterly sense. In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology and not evolution. How much easier it would be to argue the case for evolution if nature’s divisions were blurred and indistinct, if the systema naturae was largely made up of overlapping classes indicative of sequence and continuity… " - Michael Denton
lifepsy
November 6, 2014
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bornagain77: supports the fact that ‘all of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later?’?? Actually, it doesn't address the question.Zachriel
November 6, 2014
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"Nothing in your post rebuts Theobald, which doesn’t address the pattern of branching, whether top-down or bottom-up. You still have a branching pattern. Do you agree? If not, on what basis?" So Theobald, in your ever twisted Darwinian reasoning, supports the fact that 'all of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later?'?? But the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe. So if you are telling me that Theobald supports all of the major differences (i.e. the higher taxonomic categories such as phyla) appearing first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appearing later, then I say welcome to ID Zack and Keith, you guys are both flaming old earth creationists! Darwin's Dilemma - video on the Cambrian Explosion https://www.youtube.com/watch?v=xxh9o32m5c0bornagain77
November 6, 2014
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Zachriel: Hi, happy to see you! I really missed you. :) About the nested hierarchy, my view is very simple. It is a very good argument for common descent, although not necessarily the best. Nothing else.gpuccio
November 6, 2014
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Zachriel:
Theobald shows that branching descent is strongly supported,
No, he doesn't. He shows what he thinks is strong support for branching descent.Joe
November 6, 2014
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LoL! @ keith s- H has to be low in ALL design inferences. That is in the EF and is the way scientific investigation proceeds. CSI exists regardless of what produced it and Dembski never says otherwise.Joe
November 6, 2014
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spamagain77:
Zach, most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize. Why don’t you? You trying to hide in trivialities, instead of admitting you were grossly wrong, is evidence that you are not interested in truth but in pushing a dogma.
Got a mirror handy, sa77?keith s
November 6, 2014
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Box: "What bothers me, is not so much that you won’t respond to my rebuttals, but that you keep repeating your fallacious claim that ID has a trillions-to-one disadvantage with respect to unguided evolution. Can you at least have the courtesy to dispense with this nonsense until you have addressed my refutations?"
Don't. Hold. Breath.Vishnu
November 6, 2014
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bornagain77: Theobald is wrong! Nothing in your post rebuts Theobald, which doesn't address the pattern of branching, whether top-down or bottom-up. You still have a branching pattern. Do you agree? If not, on what basis? bornagain77: most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize. When we pointed out mechanisms of speciation in beetles in response to another poster, you said they were "either unsubstantiated conjecture or trivially true". That's quite funny, but hardly a valid objection.Zachriel
November 6, 2014
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Zach, most people when shown there foundational claims were false would either try to defend them or humbly admit they were wrong and apologize. Why don't you? You trying to hide in trivialities, instead of admitting you were grossly wrong, is evidence that you are not interested in truth but in pushing a dogma.bornagain77
November 6, 2014
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Theobald is wrong! ,,, The tree of life as imagined by Darwinists simply does not exist in either the fossil record or the genetic evidence,,,, “It is hard for us paleontologists, steeped as we are in a tradition of Darwinian analysis, to admit that neo-Darwinian explanations for the Cambrian explosion have failed miserably. New data acquired in recent years, instead of solving Darwin’s dilemma, have rather made it worse. Meyer describes the dimensions of the problem with clarity and precision. His book is a game changer for the study of evolution and points us in the right direction as we seek a new theory for the origin of animals.” -Dr. Mark McMenamin - 2013 Paleontologist at Mt. Holyoke College and author of The Emergence of Animals "The record of the first appearance of living phyla, classes, and orders can best be described in Wright's (1) term as 'from the top down'." (James W. Valentine, "Late Precambrian bilaterians: Grades and clades," Proceedings of the National Academy of Sciences USA, 91: 6751-6757 (July 1994).) “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas." James W. Valentine - On the Origin of Phyla: Interviews with James W. Valentine The unscientific hegemony of uniformitarianism - David Tyler - May 2011 Excerpt: The pervasive pattern of natural history: disparity precedes diversity,,,, The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artifact of sampling. Much the same finding applies to the appearance of classes. These data are presented in Figures 1 and 2 in the paper. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar "Darwin’s prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record." Niles Eldredge and Ian Tattersall, The Myth of Human Evolution (New York: Columbia University Press, 1982), 45-46. Challenging Fossil of a Little Fish "In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution." Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology http://www.fredheeren.com/boston.htm In Explaining the Cambrian Explosion, Has the TalkOrigins Archive Resolved Darwin's Dilemma? - JonathanM - May 2012 Excerpt: it is the pattern of morphological disparity preceding diversity that is fundamentally at odds with the neo-Darwinian scenario of gradualism. All of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later. On the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe. http://www.evolutionnews.org/2012/05/has_the_talk-or059171.html As Roger Lewin (1988) explains in Science, "Several possible patterns exist for the establishment of higher taxa, the two most obvious of which are the bottom-up and the top-down approaches. In the first, evolutionary novelties emerge, bit by bit. The Cambrian explosion appears to conform to the second pattern, the top-down effect." Erwin et al. (1987), in their study of marine invertebrates, similarly conclude that, "The fossil record suggests that the major pulse of diversification of phyla occurs before that of classes, classes before that of orders, orders before that of families. The higher taxa do not seem to have diverged through an accumulation of lower taxa." Indeed, the existence of numerous small and soft-bodied animals in the Precambrian strata undermines one of the most popular responses that these missing transitions can be accounted for by them being too small and too-soft bodied to be preserved. http://www.evolutionnews.org/2012/12/jerry_coynes_c067021.html Scientific study turns understanding about evolution on its head - July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: "This pattern, known as 'early high disparity', turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn't a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.",,, Author Martin Hughes, continued: "Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: "A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,, http://phys.org/news/2013-07-scientific-evolution.html “With the benefit of hindsight, it is amazing that paleontologists could have accepted gradual evolution as a universal pattern on the basis of a handful of supposedly well-documented lineages (e.g. Gryphaea, Micraster, Zaphrentis) none of which actually withstands close scrutiny." Christopher R.C. Paul, “Patterns of Evolution and Extinction in Invertebrates,” K.C. Allen and D.E.G. Briggs, eds., Evolution and the Fossil Record (Washington, D.C., Smithsonian Institution Press, 1989), 105. "It must be significant that nearly all the evolutionary stories I learned as a student from Trueman's Ostrea/Gryphaea to Carruthers' Zaphrentis delanouei, have now been 'debunked'. Similarly, my own experience of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive.' Dr. Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK), 'The nature of the fossil record'. Proceedings of the Geologists' Association, vol.87(2), 1976,p.132. "The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find' over and over again' not gradual evolution, but the sudden explosion of one group at the expense of another." Paleontologist, Derek V. Ager, “The Nature of the Fossil Record,” 87 Proceedings of the British Geological Association 87 (1976): 133. (Department of Geology & Oceanography, University College, Swansea, UK) “It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.” G.G.Simpson - one of the most influential American Paleontologist of the 20th century "A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth's geological formations. This record has never revealed traces of Darwin's hypothetical intermediate variants - instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God." Paleontologist, Mark Czarneckibornagain77
November 6, 2014
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bornagain77: The rest of Zach’s post on beetles and birds is either unsubstantiated conjecture or trivially true. Which is it?! Your lack of interest in beetle sex organs is understandable, but not much of an argument.Zachriel
November 6, 2014
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lifepsy: I asked you a simple question. Why should branching common descent necessarily produce a discernible nested hierarchy? Your original question was "If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups?" You seemed to be asking why organisms branch. Your revised question is actually more pertinent. lifepsy: Why should branching common descent necessarily produce a discernible nested hierarchy? It's a deduction from geometry as grouping leaves by branch and stem form a nested hierarchy. Now consider a tree that grows, but there are occasional mutations that are inherited along a given branch. The end result will be a pattern of traits that form a nested hierarchy. This is true as long as the number of traits is large compared to the mutation rate. There's a statistical relationship between the mutation rate, number of traits, and the fit to the nested hierarchy. Here's a simple example with one mutation* per branch. Trunk: plain First branch: plain Second branch: red* First branch first stem: plain, plain First branch second stem: plain, rippled* Second branch first stem: red, plain Second branch second stem: red, serrated* Even at this point, you can see that they nest by traits into groups. It's basic geometry with a bit of statistics involved to account for the degree of mutation. lifepsy: Common descent may also produce a non-discernible nested hierarchy. If you mean branching common descent, then that would happen if the mutation rate is very high compared to the number of traits. Indeed, if the mutation rate were high enough, the entire organism could be reshuffled in each generation. Of course, we know this doesn't happen, and children closely resemble their parents. lifepsy: Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy? The hypothesis is fidelity in reproduction with only occasional mutation among many traits branching descent. We could probably expand on that some more, but then you would end up with something like Darwin's "long abstract". lifepsy: How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes? That's not our position. Theobald shows that branching descent is strongly supported, but says nothing about whether the process is guided or not.Zachriel
November 6, 2014
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Keith S 145 I already dismantled your premise in the other thread: https://uncommondescent.com/ddd/darwinian-debating-tactic-18-the-black-knight-taunt/#comment-525837 To which you have failed to respond.
And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.
Wrong. Unguided evolution also predicts trillions of other patterns where traits are so blurred as to make the nested hierarchy indiscernible. How is unguided evolution trillions of times better at explaining the evidence if it can also explain trillions of other opposing outcomes? (the very criticism you launch at the design inference!) A straight answer, please.lifepsy
November 6, 2014
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Keith #145, Just stop with the nonsense, please. The trillions-claim in your argument and more specifically the trillion-sided die from post #1 have been soundly refuted - in this thread (#122) and in the ‘black-knight-taunt' thread (e.g. post #243). What bothers me, is not so much that you won’t respond to my rebuttals, but that you keep parading the "trillion" around as if it means something. Can you at least have the courtesy to dispense with this nonsense until you have addressed my refutations?Box
November 6, 2014
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The empirical evidence itself shows keith s's' claim to be false! No where is this more clear than in the Cambrian Explosion: What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video – (challenges Universal Common Descent and the Mechanism of Random Variation/Natural Selection) https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ i.e. There is no hope for your theory if it is directly contradicted by the evidence itself!bornagain77
November 6, 2014
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lifepsy, to Zachriel:
Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy?
I keep explaining this to you, lifepsy. From my OP:
What about our third subset of IDers — those who accept the truth of common descent but believe that intelligent guidance is necessary to explain macroevolution? The evidence is a problem for them, too, despite the fact that they accept common descent. The following asymmetry explains why: the discovery of an objective nested hierarchy implies common descent, but the converse is not true; common descent does not imply that we will be able to discover an objective nested hierarchy. There are many choices available to a Designer who guides evolution. Only a tiny fraction of them lead to a inferable, objective nested hierarchy. The Designer would have to restrict himself to gradual changes and predominantly vertical inheritance of features in order to leave behind evidence of the kind we see. In other words, our ‘common descent IDers’ face a dilemma like the one faced by the creationists. They can force guided evolution to match the evidence, but only by making a completely arbitrary assumption about the behavior of the Designer. They must stipulate, for no particular reason, that the Designer restricts himself to a tiny subset of the available options, and that this subset just happens to be the subset that creates a recoverable, objective, nested hierarchy of the kind that is predicted by unguided evolution. Unguided evolution doesn’t require any such arbitrary assumptions. It matches the evidence without them, and is therefore a superior explanation. And because unguided evolution predicts a nested hierarchy of the kind we actually observe in nature, out of the trillions of alternatives available to a Designer who guides evolution, it is literally trillions of times better than ID at explaining the evidence.
Real evolution is gradual, with predominantly vertical inheritance. That kind of evolution produces ONHs, and this is confirmed empirically: see the Theobald quote in this comment. Thus the evidence of the ONH implies not only that common descent is true, but also that evolution is unguided. My comment #1 illustrates why:
Box, It’s astonishing to me that you still don’t get this, but let me try once more. Suppose you have two objects: 1. A coin with ONH stamped on both sides. 2. A trillion-sided die with ONH engraved on one and only one side. A friend of yours takes both objects into another room, out of your sight. She randomly picks one of the two objects and flips it. “I randomly picked one of the objects and flipped it, and it landed with ONH up,” she shouts to you. Your job is to guess which of the objects she flipped — the coin with ONH on both sides, or the trillion-sided die with ONH on only one side. If you can’t figure out the best answer, I’m afraid there’s little hope that you will ever understand my argument.
keith s
November 6, 2014
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as to this claim: "There’s blurry edges between closely related species, especially with regards to bacteria." Yet, different types of bacteria are now found to have a large percentage of ORFan genes, so the claim for 'blurry edges' is false,
,,,”Typical bacterial species. The smallest part of the pie are the genes that all bacteria share. 8% roughly. This second and largest slice (of the pie, 64%) are the genes that are specialized to some particular environment. They call them character genes. By far the biggest number of genes are the ones that are unique. This big green ball here (on the right of the illustration). These are genes found only in one species or its near relatives. Those are the ORFans (i.e. Genes with no ancestry). They said, on the basis of our analysis the genetic diversity of bacteria is of infinite size.” Paul Nelson – quoted from 8:53 minute mark of the following video Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
You can see the pie chart that Dr. Nelson used in his talk here on page 108 (figure 2) of this following article:
Estimating the size of the bacterial pan-genome Excerpt Figure 2 pg. 108: At the genomic level, a typical bacterial genome is composed of _8% of core genes, 64% of character genes and 28% of accessory genes,,, http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found greater than 139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf
As well, no one has ever evolved one bacteria into another bacteria, and the conservation of morphology in bacteria, throughout deep time, is more extreme than in multicellular organisms. Thus, the 'bottom up' branching pattern, once again, is found to only exists in the imagination of Darwinists,,,
Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282 AMBER: THE LOOKING GLASS INTO THE PAST: Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms. http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330
Moreover, bacteria do not act as was predicted by Darwin:
Doubting Darwin: Algae Findings Surprise Scientists - April 28, 2014 Excerpt: One of Charles Darwin's hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists long have accepted this to be true. Thus, three researchers were more than a little shaken to find that their experiments on fresh water green algae failed to support Darwin's theory — at least in one case. "It was completely unexpected," says Bradley Cardinale, associate professor in the University of Michigan's school of natural resources & environment. "When we saw the results, we said 'this can't be."' We sat there banging our heads against the wall. Darwin's hypothesis has been with us for so long, how can it not be right?" The researchers ,,,— were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.,,, The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh water green algae so they could provide conservationists with useful data for decision-making. "We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists," Cardinale says. "When we started coming up with numbers that showed he wasn't right, we were completely baffled.",,, Darwin "was obsessed with competition," Cardinale says. "He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don't grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected. "Maybe species are co-evolving," he adds. "Maybe they are evolving together so they are more productive as a team than they are individually. We found that more than one-third of the time, that they like to be together. Maybe Darwin's presumption that the world may be dominated by competition is wrong." http://www.livescience.com/45205-data-dont-back-up-darwin-in-algae-study-nsf-bts.html
The rest of Zach's post on beetles and birds is either unsubstantiated conjecture or trivially true. i.e. so what! supplemental note:
Darwin 'Wrong': Species Living Together Does Not Encourage Evolution - December 20, 2013 Excerpt: Charles Darwin's theory of evolution set out in the Origin of Species has been proven wrong by scientists studying ovenbirds. Researchers at Oxford University found that species living together do not evolve differently to avoid competing with one another for food and habitats – a theory put forward by Darwin 150 years ago. The ovenbird is one of the most diverse bird families in the world and researchers were looking to establish the processes causing them to evolve. Published in Nature, the research compared the beaks, legs and songs of 90% of ovenbird species. Findings showed that while the birds living together were consistently more different than those living apart, this was the result of age differences. Once the variation of age was accounted for, birds that live together were more similar than those living separately – directly contradicting Darwin's view. The species that lived together had beaks and legs no more different than those living apart,,, ,,,there is no shortage of evidence for competition driving divergent evolution in some very young lineages. But we found no evidence that this process explains differences across a much larger sample of species.,,, He said that the reasons why birds living together appear to evolve less are "difficult to explain",,, http://www.ibtimes.co.uk/darwin-wrong-species-living-together-does-not-encourage-evolution-1429927
bornagain77
November 6, 2014
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Joe:
LoL! @ keith s- If Dembski says that “H” is the relevant chance hypothesis that means what I said is correct and Rich is wrong.
Joe, p(T|H) has to be extremely small in order for CSI to be high. Rich is right. This isn't rocket science.keith s
November 6, 2014
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Zachriel
lifepsy: If unguided evolution is true, why should we necessarily find identifiable distinct groupings of taxa that fall neatly into groups within groups? This doesn’t directly relate to the original study, which only concerns whether or not the evidence supports branching descent. The evidence supports branching descent, even if we didn’t understand the mechanism or reason for this pattern.
That was a dodge. I asked you a simple question. Why should branching common descent necessarily produce a discernible nested hierarchy? The answer, which perhaps you're uncomfortable stating, is that it shouldn't. Common descent may also produce a non-discernible nested hierarchy.
lifepsy: Why don’t we find a dominant pattern of blurred and indistinct character traits that can not be objectively classified into neat distinguishable groups? We do sometimes. There’s blurry edges between closely related species, especially with regards to bacteria. However, the branching pattern is still discernible, even amidst all the other goings-on.
Why do you interpret a discernible hierarchy as evidence for Common Descent, when Common Descent could also result in a non-discernible hierarchy? It's rather unscientific to be promoting X as direct evidence for something, when Not-X would also be acceptable. Wouldn't you agree?lifepsy
November 6, 2014
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"The evidence supports branching descent" The evidence supports "top down' branching descent within distinct morphological kinds, the evidence does not support Darwin's 'bottom up' descent/ascent from a single common ancestor,, Scientific study turns understanding about evolution on its head – July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,, Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,, http://phys.org/news/2013-07-scientific-evolution.html A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html Dollo's law and the death and resurrection of genes ABSTRACT: Dollo's law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or "lost" developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints; http://www.pnas.org/content/91/25/12283.full.pdf+html The Cambrian's Many Forms Excerpt: "It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.""From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,"....(Yet Surprisingly)...."There's hardly any variation in the post-Cambrian," he said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites." University of Chicago paleontologist Mark Webster; article on the "surprising and unexplained" loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago. http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.htmlbornagain77
November 6, 2014
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ID is based on three premises and the inference that follows (DeWolf et al., "Darwinism, Design and Public Education", pg. 92): 1) High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design. 2) Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity. 3) Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity. 4) Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.Joe
November 6, 2014
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LoL! @ keith s- If Dembski says that "H" is the relevant chance hypothesis that means what I said is correct and Rich is wrong. What is wrong with you?Joe
November 6, 2014
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