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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
Box: But none of that is of interest to ID. Very sorry to disappoint you, but ID is strictly about science and does not speculate on the identity, capabilities and options available to a designer. If something is designed, there is a causal connection from the artifact to the art to the artist. In any case, the evidence strongly supports branching descent. Zachriel: If you accept branching descent, it strongly constrains any possible history. Vishnu: Likewise for the nested hierarchies existing as trees out in my backyard. I have no problem with that. That constraint eliminates many creationist claims. Vishnu: Assuming it’s reality It's what the evidence supports. While Theobald's results don't address whether the branching process is guided or not, that all life shares common ancestry is certainly an important finding to biology.Zachriel
November 7, 2014
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Zachriel: That’s why human artifacts don’t form a nested hierarchy.
Some of them do. Airplanes, trains, automobiles, computers, musical instruments, textiles, clothing styles, architecture, just to name a few. Their common root source is "humanity", and each group can be looked at as a branch from that root, with many subgroups, all forming a nested hierarchy. We don't know the extent of the putative designer's options and capabilities. For all we know there could radically different biological trees on a trillion planets out in the universe. But again, as Box said, fascinating religious ideas, but not science. ID (as I understand it) is about inferring to the best explanation, not discovering the options, capabilities and motives of the designer.Vishnu
November 7, 2014
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Box,
What do want Keith?
I'd like a reasoned counterargument, and if you can't provide one, I'd like you to acknowledge that my argument stands unrefuted.
The answer to the question “How many options are available for the designer to order life?” is “at least one”, after ID infers design as best explanation for the ordering of life.
So then we ask, "We know at least one is available, if ID is correct. Which of the options are available, and which aren't?" The answer is "We can't rule any of them out on the design hypothesis". That leaves us with trillions of options that the designer might have been able to choose from. Then we look at unguided evolution of the kind we have been discussing (Hi, lifepsy!). It actually predicts an ONH and rules out the trillions of alternatives. So we have an ID hypothesis that can't eliminate any of the trillions of options, against an unguided evolution hypothesis that actually predicts an ONH over everything else. Unguided evolution is therefore trillions of times better, because it makes a correct prediction that is trillions of times more specific than ID's "prediction" (which is useless since it doesn't rule anything out). If you "follow the evidence where it leads", you cannot honestly continue to believe in ID.keith s
November 7, 2014
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Zachriel: If you accept branching descent, it strongly constrains any possible history.
Likewise for the nested hierarchies existing as trees out in my backyard. I have no problem with that.
The common ancestry of simians and sunflowers is a very profound finding concerning nature,
Assuming it's reality, I don't accept that blind watch maker evolution is soley responsible for ONH. It's a minor player. So I'm unsure of the relevance of your consequent...
...a finding that puts you at odds with much of the ID community.
To the degree that it's true, it's not a concern of mine.Vishnu
November 7, 2014
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Zachriel #253: But a knowledgeable designer creating each organism independently isn’t so constrained, but can mix and match features across lineages.
These are all fascinating religious ideas. But none of that is of interest to ID. Very sorry to disappoint you, but ID is strictly about science and does not speculate on the identity, capabilities and options available to a designer.Box
November 7, 2014
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Vishnu: <II don’t mind straying off the Reservation, if you don’t. We prefer to stay on topic. If you accept branching descent, it strongly constrains any possible history. The common ancestry of simians and sunflowers is a very profound finding concerning nature, a finding that puts you at odds with much of the ID community. Box: if the creator of a mousetrap had only one design option available But a knowledgeable designer creating each organism independently isn't so constrained, but can mix and match features across lineages. That's why human artifacts don't form a nested hierarchy. You would be supposing a designer more limited than humans, and constrained in ad hoc ways.Zachriel
November 7, 2014
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Zachriel @ 248 I think you intended that for someone else.Vishnu
November 7, 2014
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Zachriel, Also, what is the fundamental difference between the information and processes we call a tree genome, and a genetic algorithm that I create towards a certain goal?Vishnu
November 7, 2014
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Box: Such a question, assumes that the designer(s) can choose from several options – which we do not know.
Zachriel #231: That’s fine. That leaves us with a proposition with no entailments, so it is scientifically vacuous.
So, if the creator of a mousetrap had only one design option available, than a ID-proposition has no entailments and is scientifically vacuous.? Can you elucidate your reasoning?Box
November 7, 2014
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Oops. That should have been attributed to lifespy.Zachriel
November 7, 2014
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Vishnu: I see, so you just want to assign some arbitrary magical limit on how distorted the signal could potentially become. Only if you consider statistics to be magic.Zachriel
November 7, 2014
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Zechriel, Regarding the ONH, it would probably be more fair to say that I am comfortable with the overall layout. I do not think it is evidence of a blind watchmaker sort of evolution. And I rather like what gpuccio said, "About the nested hierarchy, my view is very simple. It is a very good argument for common descent, although not necessarily the best."
Vishnu: was the ONH generated by such a system as I described? Zachriel: It’s generated by the branching process.
What is the nature of the branching process? Does it feature the sort of information and processes I mentioned? Is it "forward looking", that is, it is goal oriented?
Zachriel: You haven’t provided any evidence of a “forward-looking” process, but that’s beyond the scope of the thread, which concerns branching descent.
I don't mind straying off the Reservation, if you don't. So then, you don't think a tree genome can be said to have a forward looking process? Perhaps that sort of language is a bit too harsh for your sensibilities. I don't intend to say that a tree genome is consciously thinking about what it's producing. Neither do the genetic algorithms that I create consciously think about that they are doing. So then, what about a goal (as in "goal posts") oriented process? Is it not fair to say that the programmed information and systems of a tree genome is to produce a tree with certain properties within certain limits taking advantage of certain stocastic variables? Do you think "goal" is too strong a word here? If so, why?Vishnu
November 7, 2014
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Zachriel
As we pointed out above, the nested hierarchy is not expected to be perfect for any of a number of reasons, including hybridization, reversals, loss of function, and convergence.
I see, so you just want to assign some arbitrary magical limit on how distorted the signal could potentially become. If the factors you just listed were extensive enough, (and there is no rule of evolution which says they can't be) it could potentially obliterate any substantial signal of a nested hierarchy.
lifepsy: Why are you describing the traits of humans? They’re an example that you might be familiar with. Note the nesting pattern. lifepsy: It’s as if you believe the natural selection fairies were destined to maintain the crania for all time once it had manifested. And yet, there we are, with this highly non-trivial correlation!
ok... Were we debating whether or not humans exist and fall into a nested hierarchy? It appears that, like Keith S, you are simply unwilling to examine what other data your theory can potentially accommodate, but simultaneously you want to claim the current data as a specific prediction of your theory. Both you and Keith S are committing a major fallacy of logic.lifepsy
November 7, 2014
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Vishnu: I am persuaded that it probably did. We're in agreement, then. Vishnu: was the ONH generated by such a system as I described? It's generated by the branching process. Vishnu: However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems. You haven't provided any evidence of a "forward-looking" process, but that's beyond the scope of the thread, which concerns branching descent. By the way, the branching process helps give us the historical context to understand the mechanisms of change. lifepsy: And the simple fact is that unguided evolution as it is believed today on planet Earth also predicts a scenario where the signal of the objective nested hierarchy has been lost. That's clearly not the case. The nested hierarchy has been fundamental to the theory of evolution since Darwin.Zachriel
November 7, 2014
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Keith S 222
Please stop telling me what my argument is.
I'm not. It's on the first post of this thread.
We are talking about actual biological evolution on the planet earth.
We are talking about the potential outcomes biological evolution predicts. That is the whole crux of your "coin/dice" analogy in Post #1. If biological unguided evolution can accommodate opposing outcomes (which it can), then you can not logically use only one of those outcomes as direct evidence. And the simple fact is that unguided evolution as it is believed today on planet Earth also predicts a scenario where the signal of the objective nested hierarchy has been lost. I'm sorry if you don't get that.
We know, from actual observations, that mutation rates are low
This isn't much of a constraint since population levels, selection pressures, and specific durations associated with past evolutionary events are hypothetical and extremely plastic to whatever the evolutionist needs to harmonize Evolution theory. The populations of common ancestors of major taxa themselves are essentially imaginary. They have been conjured into being by storytellers.
and that inheritance is primarily vertical, particularly in multicellular life forms.
So what? If vertical inheritance is coupled with a pattern of extensive loss and reversals of traits than it will not necessarily produce a recognizable signal of the objective nested hierarchy. Maybe, like Zachriel, you'd like to appeal to the natural selection fairies which have a friendly predisposition to maintain inherited traits so that there will be a nice orderly typological nested hierarchy for scientists to study after they've evolved.lifepsy
November 7, 2014
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Keith #232: For ID to have a chance, you have to assume a nonzero probability that the designer would produce an ONH. If the probability were zero, then design would be ruled out. Once you assume a nonzero probability, as you must, then the question arises: what value do you assign?
What do want Keith? The answer to the question "How many options are available for the designer to order life?" is "at least one", after ID infers design as best explanation for the ordering of life. What ID does not address is religious questions like "Why would the designer choose a nested hierarchy arrangement rather than some other arrangement?" or questions regarding 'omnipotence' or 'indifference'. That is religion Keith. There is no scientific way of knowing these things. Got it?Box
November 7, 2014
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Zachriel: That’s not part of Theobald’s study, which only concerns whether such a branching process occurred. Do you agree that such a process did occur? If not, why not?
I am persuaded that it probably did. What about you? So, again, was the ONH generated by such a system as I described?Vishnu
November 7, 2014
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Joe @237:
Who has the better hypothesis?
Bob, of course. What's your point?keith s
November 7, 2014
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Vishnu: Was the ONH generated by such a system? That's not part of Theobald's study, which only concerns whether such a branching process occurred. Do you agree that such a process did occur? If not, why not?Zachriel
November 7, 2014
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keith @232, You keep missing the obvious flaw in your equal probabilities argument. There is no problem of assuming that there could have been many different types of design and designers. Who cares? The design hypothesis does not have that assumption. The ID hypothesis is that there was only one type of designer, intelligent ones. We can test this hypothesis because we know how intelligent entities (humans) design things. Objects intelligently designed over a long period of time invariably follow an ONH pattern. This is not an assumption. It is a fact. ONH is such an inescapable consequence of intelligent design that modern software design tools enforce a hierarchical organization in software design. The whole idea behind hierarchical design is that previous designs should be reused as much as possible. It's very simple, really.Mapou
November 7, 2014
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Joe:
Does keith s realize that we do not see an objective nested hierarchy with prokaryotes?
Yes, because of horizontal gene transfer. Does Joe realize that my argument does not depend on the presence of an ONH among the prokaryotes? It depends only on the objective nested hierarchy among the 30 major taxa, illustrated in Theobald's Figure 1. P.S. Joe, you're doing well! It must be really hard for you to lay off the invective. Good job. Keep it up.keith s
November 7, 2014
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keith s, your challenge, like your arguments, is bogus and misleading. Bob is out hunting with a top-notch mainstream geologist. They are deep into the New England woods and the geologist points out different rock formations to pass the time. As they were heading to an unknown area they come across a 3 foot high wall-type structure of stones, millions of stones stretching North to South. The wall top is flat and secure enough to walk on. The sides of the wall are also relatively flat with an occasional protrusion. 1/2 mile North of that position they find another wall exactly perpendicular to the first wall, heading west. It is roughly the same height and also has a flat top and flat sides. Bob says it must have been early pioneers clearing the land and making walls with what they plowed and dug up. The geologist laughed and said there aren’t any houses around, no tools and no human remains. These are just rocks and mother nature produces those in abundance. We know this are was visited by glaciers in the past and this is nothing but a glacial deposit. Who has the better hypothesis?Joe
November 7, 2014
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kairosfocus, The challenge was to answer my questions and justify your answers, if they differed. You didn't even answer my questions. Now step aside and allow some braver IDers to take the challenge, if any are willing. Bydand!keith s
November 7, 2014
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Does keith s realize that we do not see an objective nested hierarchy with prokaryotes?Joe
November 7, 2014
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Zechrial: The branching process is algorithmically simple.
A computer adding 1 + 1 to get 2 is algorithmically simple. Designing an computer program to produce a two dimensional tree-like structure on the display is not very challenging for a decent programmer. The rules by which living trees actually produce their trunks, branches, limbs and leaves are not difficult for intelligent humans to discern and simulate using computers. However, all of these cases are examples of the operation of sophisticated, extremely information rich, forwarding looking (that is to say, goal oriented), processes and systems. Was the ONH generated by such a system?Vishnu
November 7, 2014
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Zachriel:
For instance, the human male y-chromosome forms a nested hierarchy.
Based on what criteria? Please be specific or retract your claim.Joe
November 7, 2014
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Does anyone else want to step in and try to explain this to Box? It's getting tiring. Box, For ID to have a chance, you have to assume a nonzero probability that the designer would produce an ONH. If the probability were zero, then design would be ruled out. Once you assume a nonzero probability, as you must, then the question arises: what value do you assign? Since you wish to minimize the assumptions you are making about the designer, you cannot assume that the designer is more likely to design with an ONH motif versus the other possibilities. You also cannot assume that the designer is less likely to design with an ONH motif versus the other possibilities. That means you must assign equal probabilities to the ONH and the trillions of other possible outcomes. Once you do that, my argument kicks in, and ID is rejected because it is trillions of times worse at explaining the ONH versus unguided evolution. Think about it for a while, rather than dashing off another ill-considered reply.keith s
November 7, 2014
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Box: Only an omnipotent and indifferent designer would warrant your idea that all trillions of logical possibilities of the ordering of life are equally probable to happen if they are created. Even the artifacts of humans with somewhat limited capabilities don't form nested hierarchies. Because they are intelligent, they borrow rampantly across lines. Box: Such a question, assumes that the designer(s) can choose from several options – which we do not know. That's fine. That leaves us with a proposition with no entailments, so it is scientifically vacuous. lifepsy: Neither does arranging by organic traits that have undergone heavy losses or reversals. Notably, you have ignored our comments. As we pointed out above, the nested hierarchy is not expected to be perfect for any of a number of reasons, including hybridization, reversals, loss of function, and convergence. lifepsy: Why are you describing the traits of humans? They're an example that you might be familiar with. Note the nesting pattern. lifepsy: It’s as if you believe the natural selection fairies were destined to maintain the crania for all time once it had manifested. And yet, there we are, with this highly non-trivial correlation! In any case, the nested hierarchy isn't dependent on single traits, but the sum of traits. See Darwin 1859 for details. lifepsy: advanced tetrapod trackways appear “tens of millions of years” before the fish-a-pod body types they are supposed to nest in. A fossil doesn't typically represent the first instance of an organism. In any case, that doesn't challenge Theobald.Zachriel
November 7, 2014
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KS, predictably, you are in no concessions denial mode per the pomo community disorganiser modus operandi. Onlookers will see for themselves why the case of what a significant design thinker said on record but was strawman caricatured for 150 years is highly relevant. As to you didn't respond, I did so, point by point through the argument, showing it to be successive repeats of the same basic misrepresentations of design thought. Your Bob is a cartoon, not any informed and responsible design thinker. You come across as either willfully and culpably ignorant of the ID design filter or else as willfully misrepresenting it. Game over. KFkairosfocus
November 7, 2014
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keith s:
We know, from actual observations in real time, that evolution produces objective nested hierarchies.
That is incorrect and borders on dishonesty.Joe
November 7, 2014
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