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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
That's not true, there are plenty of instances where autophagy fails and an organism continues to survive. As you said, there are many cases of redundancy in cells, and these allow the organims to carry on when certain systems fail.AVS
November 5, 2014
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So my question remains.... How did unguided processes create a guided process to prevent unguided process from happening? Show me!Andre
November 5, 2014
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Vincent, Regarding your second point, you write:
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.
Okay, so we're in agreement on common descent.
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.
That's not true. In reality, mutation rates are low enough and vertical inheritance predominates enough that we can treat unguided evolution as a Markov process. That's why Theobald can write this:
Does Phylogenetic Inference Find Correct Trees? In order to establish their validity in reliably determining phylogenies, phylogenetic methods have been empirically tested in cases where the true phylogeny is known with certainty, since the true phylogeny was directly observed. Bacteriophage T7 was propagated and split sequentially in the presence of a mutagen, where each lineage was tracked. Out of 135,135 possible phylogenetic trees, the true tree was correctly determined by phylogenetic methods in a blind analysis. Five different phylogenetic methods were used independently, and each one chose the correct tree (Hillis et al.1992 ). In another study, 24 strains of mice were used in which the genealogical relationships were known. Cladistic analysis reproduced almost perfectly the known phylogeny of the 24 strains (Atchely and Fitch 1991). Bush et al. used phylogenetic analysis to retrospectively predict the correct evolutionary tree of human Influenza A virus 83% of the time for the flu seasons spanning 1983 to 1994. In 1998, researchers used 111 modern HIV-1 (AIDS virus) sequences in a phylogenetic analysis to predict the nucleotide sequence of the viral ancestor of which they were all descendants. The predicted ancestor sequence closely matched, with high statistical probability, an actual ancestral HIV sequence found in an HIV-1 seropositive African plasma sample collected and archived in the Belgian Congo in 1959 (Zhu et al.1998 ). In the past decade, phylogenetic analyses have played a significant role in successful convictions in several criminal court cases (Albert et al. 1994; Arnold et al. 1995; Birch et al. 2000; Blanchard et al. 1998; Goujon et al. 2000; Holmes et al. 1993; Machuca et al. 2001; Ou et al. 1992; Veenstra et al. 1995; Vogel 1997; Yirrell et al. 1997), and phylogenetic reconstructions have now been admitted as expert legal testimony in the United States (97-KK- 2220 State of Louisiana v. Richard J. Schmidt [PDF]). The legal test in the U. S. for admissibility of expert testimony is the Daubert guidelines (U. S. Supreme Court Case Daubert v. Merrell Dow Pharmaceuticals, Inc., 509 U.S. 579, 587-89, 113 S. Ct. 2786, 2794, 125 L. Ed. 2d 469, 1993). The Daubert guidelines state that a trial court should consider five factors in determining "whether the testimony's underlying reasoning or methodology is scientifically valid": (1) whether the theory or technique in question can be and has been tested; (2) whether it has been subjected to peer review and publication; (3) its known or potential error rate; (4) the existence and maintenance of standards controlling its operation; and (5) whether it has attracted widespread acceptance within the relevant scientific community (quoted nearly verbatim). Phylogenetic analysis has officially met these legal requirements.
The Markov model is empirically verified, which means that ID is still at a trillions-to-one disadvantage with respect to unguided evolution.keith s
November 5, 2014
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From the paper and this is important! ", evidence is accumulating that necrotic cell death in some cases can be as well controlled and programmed as caspase-dependent apoptosis. Autophagy is foremost a survival mechanism that is activated in cells subjected to nutrient or obligate growth factor deprivation. When cellular stress continues, cell death may continue by autophagy alone, or else it often becomes associated with features of apoptotic or necrotic cell death, depending on the stimulus and cell type. It is debatable whether autophagic cell death is an alternative way of dying, different from apoptotic and necrotic cell death, or whether failure of autophagy to rescue the cell can lead to cell death by either pathway." These stability control mechanisms work together but each one is independently regulated.Andre
November 5, 2014
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AVS Yes Autophagy is non-apoptotic, but it is one of the pathways, which there are many of..... http://link.springer.com/chapter/10.1007%2F978-1-4020-9293-0_1#page-1 They all work together and when they start failing the organism fails!Andre
November 5, 2014
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Autophagy is not really a back-up system to apoptosis. In some cases it may have a role in apoptosis, but generally autophagy is a mechanism for the cell to breakdown its own macromolecules in order to support regular cellular function.AVS
November 5, 2014
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Did you read those papers? They actually talk about possible mechanisms of the evolution of apoptosis. I agree completely that the ability of nature to solve engineering problems is astounding, but you should really learn more about them and try to understand what they are capable of, before trying to tell people what they are incapable of. Evolution is not an "unguided process" in my opinion, it is guided by environmental conditions.AVS
November 5, 2014
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Autophagy http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990190/ "Autophagy is a self-degradative process that is important for balancing sources of energy at critical times in development and in response to nutrient stress. Autophagy also plays a housekeeping role in removing misfolded or aggregated proteins, clearing damaged organelles, such as mitochondria, endoplasmic reticulum and peroxisomes, as well as eliminating intracellular pathogens. Thus, autophagy is generally thought of as a survival mechanism, although its deregulation has been linked to non-apoptotic cell death." So we not only have apoptosis we also have another backup system to apoptosis called autophagy! If I was stupid I'd also say wow unguided processes sure are smart!Andre
November 5, 2014
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AVS Autophagy is another one of the stability control mechanisms of the cells, as pointed out there are multiple ones...... in normal English, REDUNDANCY........ mmmmmm redundancy just like stability control is another engineering solution to engineering problems....... Sheesh unguided processes sure are smart AVS! They can solve engineering problems without even thinking about it!Andre
November 5, 2014
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AVS I'm not assuming anything, you are the one that assumes that such machinery could build itself..... I'm asking you to show me how! If you are to claim that unguided processes can do this you need to back your claim with evidence!Andre
November 5, 2014
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AVS http://www.ncbi.nlm.nih.gov/pubmed/15527405 http://www.plantphysiol.org/content/132/1/99 It's there it's conserved! But it I must protest it "evolved" and it transferred itself from unicellular organisms to multi cellular organisms by magic! The moment PCD becomes deregulated the organisms, both uni and multi cellular dies! It stops this unguided nonsense in its tracks!Andre
November 5, 2014
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Andre, you are making the fatal flaw of assuming that because today's organisms have complex machinery that cannot function with missing pieces, the evolution of this machinery is impossible. Much simpler systems were the ancestors of current cellular processes and more often than not they are offshoots of other processes that have already developed. The paper mentions autophagy, maybe apoptosis is related to this cellular process. We simply don't know.AVS
November 5, 2014
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So what am I saying to you? Unguided processes are not capable of solving problems! Because to solve a problem you need to know about it! Unguided evolution knows nothing about problems or how to solve them! To think it does makes you a believer in magic!Andre
November 5, 2014
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Keith S I'm not trying to get an OP.... I'm trying to point out that unguided processes can not create guided processes to prevent unguided processes from happening! It is Impossible, these type of systems are engineering solutions......Andre
November 5, 2014
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AVS So let me see, just like Keith S, Rich and Thornton, you believe it just emerged? A Stability control system is an engineering solution that has a very specific function, it can not be created by ANY unguided process...... The mere fact that there are multiple stability control mechanisms make the claim that unguided evolution did it even more dubious........ When the stability control system becomes deregulated unguided processes take over and the organism dies!Andre
November 5, 2014
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Andre, Here's an idea. See if you can convince one of your fellow IDers, with author privileges, that PCD is the whiz-bang evo-killer you say it is. Then they will enthusiastically post an OP on your behalf. Or not. If you can't even convince your fellow IDers that it's worth an OP, then you certainly aren't going to convince anyone else.keith s
November 5, 2014
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Which unicellular organisms exhibit apoptosis?AVS
November 5, 2014
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AVS Please can you demonstrate how unguided processes created a guided process to prevent unguided processes from happening? In addition there are multiple stability control mechanism like PCD........ Disease happens when PCD becomes unregulated, while PCD is optimal diseases are prevented. In addition PCD builds body plans too.... You guys don't seem to understand the issue here, PCD is also evolutionary conserved in unicellular and multi cellular organisms..... it does not evolve! It can not evolve and if it changes organisms Die!Andre
November 5, 2014
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But apoptosis serves an array of functions in multicellular organisms. I don't think it in any way "prevents any other unguided processes from happening"or "prevents any type of tampering with the optimal state of the organism?" Apoptosis simply is the destruction of specific cells for a specific reason. Careful regulation of this process would be expected to evolve, just as careful regulation of every other process in the cell has evolved.AVS
November 5, 2014
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Here is the paper's conclusion..... and Keith S cannot skirt this issue...... "Apoptosis is regarded as a carefully regulated energy-dependent process, characterized by specific morphological and biochemical features in which caspase activation plays a central role. Although many of the key apoptotic proteins that are activated or inactivated in the apoptotic pathways have been identified, the molecular mechanisms of action or activation of these proteins are not fully understood and are the focus of continued research. The importance of understanding the mechanistic machinery of apoptosis is vital because programmed cell death is a component of both health and disease, being initiated by various physiologic and pathologic stimuli. Moreover, the widespread involvement of apoptosis in the pathophysiology of disease lends itself to therapeutic intervention at many different checkpoints. Understanding the mechanisms of apoptosis, and other variants of programmed cell death, at the molecular level provides deeper insight into various disease processes and may thus influence therapeutic strategy." "Carefully regulated" sounds just like the kind of thing unguided processes can accomplish.... NOT!Andre
November 5, 2014
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AVS PCD... http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/Andre
November 5, 2014
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Hey Andre, what "mechanism that will prevent any other unguided processes from happening and tampering" are you referring to?AVS
November 5, 2014
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That is all I ask, Don't point to the OP at TSZ, I really don't care about it, I know what that is just a trap to have me battered with foul language and belittling, you set the tone yourself when you called me a little twerp...... Answer it here and do so honestly.Andre
November 5, 2014
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Do you understand the problem that PCD presents to your argument Keith? If unguided evolution is the reason why everything in the biological world exist, then we have to give this a thought.... At which point did unguided evolution "decide" (and I use this word loosely) to construct a mechanism that will prevent any other unguided processes from happening and prevent any type of "tampering" with the optimal state of the organism? How did unguided processes know the organism is optimal? And further how is it that unguided evolution managed to build not one but multiple stability control mechanisms for this? Was it by sheer dumb luck? Stuff happens? Keith please you need to address this issue if you are to convince me.Andre
November 5, 2014
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And it is ok for you to concede that point, but you can't hammer on about unguided evolution being the best explanation for the diversity of life if we know empirically that unguided processes, first have multiple mechanisms that prevent them from happening and when they fail we know its catastrophic to the organism. So you see Keith your unguided argument just does not fit the evidence we have.Andre
November 5, 2014
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I don't think the lights will go on for Keith S but it is worth talking about it. The problem is right there methodological naturalism. You see Keith naturalism cannot explain PCD. You haver to be able to demonstrate how an unguided process built a guided process that prevents unguided processes from happening. You see Keith once PCD breaks unguided processes do in fact happen and always at the detriment of the organism. We know PCD is evolutionary conserved, we also know its vital for unicellular and multicellular organisms, but how did it get there? By an unguided process? Really?Andre
November 5, 2014
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William, Theobald is a methodological naturalist, so guided evolution has no place in his scientific thinking.keith s
November 5, 2014
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Perhaps he doesn't make the same argument because he cannot vet the process as unguided. "Microevolution creates ONH's" is not the same statement as "unguided microevolution creates ONH's".William J Murray
November 5, 2014
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Hi Vincent, You write:
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.
I don't find it odd at all. Here are a few plausible explanations: 1. Theobald's stated purpose was to present the evidence for common descent, so that's what he did. 2. He is a methodological naturalist, so for him any discussion of a Designer is off-limits. Also, he is not an atheist, so he may not be particularly motivated to pursue an argument with atheistic implications. (See this commentary.) 3. His primary audience is creationists who doubt common descent, so making an explicit anti-designer argument might lead them to reject his argument out of hand. Leaving room for God makes common descent easier for creationists to swallow. 4. He might also wish to avoid alienating believers who see God as involved in the evolutionary process. 5. He may not have realized that the evidence he was presenting could be used to argue against guided evolution. A lot of evolutionists are surprised by my argument when they hear it for the first time. I don't know which, if any, of those explanations is correct. My point is simply that you needn't be surprised that Theobald didn't make the same argument that I do. Read your Theobald quote again, keeping those plausible explanations in mind:
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).
keith s
November 5, 2014
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Moose Dr #46, You may have some points there. BTW I find it questionable to place the designer in our space-time frame. What I had in mind when I asked my question was the designing/creative part of creation. Science cannot know how the designer comes up with molecular machines, body plans etc. Obviously, his muses are out of our reach, so to speak.Box
November 5, 2014
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