Nick Matzke and “Clutching in Mid-Air”

_{Barry Arrington

December 9, 2013

Intelligent Design}

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As his recent posts in these pages demonstrate, Nick Matzke loves cladistics, and for reasons that defy explication, he seems to think that cladistics demonstrates – rather than assumes – common descent. It really is a stumper.

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

David Berlinski’s skewering of Matzke is particularly fun to watch:

[P]hylogenetic methods as they exist now,” [Matzke] writes, “can only rigorously detect sister-group relationships, not direct ancestry, and, crucially, … this is neither a significant flaw, nor any sort of challenge to common ancestry, nor any sort of evidence against evolution.” But there can be no sisters without parents, and if cladistic analysis cannot detect their now mythical ancestors, it is hard to see what is obtained by calling them sisters. No challenge to common ancestry? Fine. But no support for common ancestry either. Questions of ancestry go beyond every cladistic system of classification, no matter the character states. . . .

The relationship between cladistics and Darwin’s theory of evolution is thus one of independent origin but convergent confusion. “Phylogenetic systematics,” the entomologist Michael Schmitt remarks, “relies on the theory of evolution.” To the extent that the theory of evolution relies on phylogenetic systematics, the disciplines resemble two biologists dropped from a great height and clutching at one another in mid-air.

Tight fit, major fail.

By the way, I have quoted Berlinski. Matzke’s is always yelling “quote mining!!” whenever he sees a quote with which he disagrees. Let me be clear, then, what I am quoting Berlinski for. I am quoting him for the proposition that Nick Matzke is a fool who cannot see the obvious circularity of attempting to support Darwinian evolution through cladistics methods. I am pretty sure that in context this is what Berlinski means.

Comments

I was reading through the fourth paper that Nick cited above (White et al, 2013), under the assumption the most recent would have the best evidence. In the discussion they say:
Our test is based on the expectation that, under evolution, the ancestral sequence of one natural group of taxa will be more similar to the ancestral sequence of a second natural group of taxa, than to any sequence from the first group will be to any sequence from the second. In contrast, a variety of proposed non-evolutionary models either do not make this prediction...
If I understand, what they're doing is basically: 1. Finding proposed ancestral sequences of clade 1 by looking for conserved sequences. 2. Doing the same for clade 2. 3. They find that ancestral Clade 1 is more similar to Ancestral Clade 2 than Modern Clade 1 is to Modern Clade 2 (with very high levels of confidence). But don't we see this same pattern in designed systems? If you the software libraries common android apps and phones (zlib, openssl, opengl, dalvik) and the libraries common IOS apps phones (zlib, openssl, opengl, cocoa) then those two sets will have more in common than if you also include the whole set of all unique software found on both phones. So I don't see how this result is meaningful? And I don't understand at all why they say this wouldn't be predicted by non-evolutionary models.JoeCoder_{December 9, 2013
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Of somewhat related note: Dr Paul Giem has another installment from Darwin's Doubt up: Darwin's Doubt (Part 11) 12-7-2013 by Paul Giem - video http://www.youtube.com/watch?v=xZSqMj8ZHvo&feature=c4-overview&list=UUaBAwmf0uZeTYejbXpXV7VQbornagain77_{December 9, 2013
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Let me lay it out for you in terms adopted to the meanest understanding: Major Premise: In order to support common descent (far less the Darwinian mechanism that purports to account for common descent), a method of investigation would need to detect direct ancestry. Minor Premise: “Phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry.” Conclusion: Phylogenetic methods as they exist now do not support common descent in any rigorous way.
Your/Berlinski's argument is precisely similar to the argument that forensic DNA tests cannot determine that there is some close genetic relationship between samples, because the markers used in a DNA test cannot always tell you if the sample came from a direct ancestor (e.g. grandfather) or a collateral ancestor (e.g. uncle). Over here in reality, such data indicate close relationship, even if the exact relationship might not be determinable with the data/method available. When we have data (DNA etc.) from a bunch of species, the question is -- is there statistically significant tree structure in the data? Stephen Meyer and most of his fans around here seem to deny that there is, that contradictions overwhelm the tree structure, and that the inferred phylogenies are based on nothing rigorous. Berlinski, though, admits that the tree structure in the data is real! Which is it? You tell me.
Yes, yes, you’ve given us your inevitable literature bluff. Do any of those papers purport to suspend the basic laws of logic? If so, please give me a summary of how they do that.
Wow. Such amazing anti-intellectualism! In real scholarship, we read and cite papers, rather than re-writing stuff from scratch each time. Do me a favor, just look at the pictures in those papers. Is the tree hypothesis, i.e. common ancestry, the only hypothesis assumed? Yes or no? I'm actually pretty busy this week, unlike last weekend. I won't reply unless I get direct answers to the questions I asked in this post.NickMatzke_UD_{December 9, 2013
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No, I think what professor Matzke was trying to explain was that phylogenetic changes occur slower than speciation. So one might indeed be able to find an ancestral link between a chihuahua and a grizzly bear, but not between a whale and a dolphin.
No, what I was saying is that transitional fossils between *very* similar sister species are thought to be rare (how rare is debated, Eldredge says very rare, Gingerich says fairly common, actually). Whales and dolphins are not very similar sister species! Duh! Where did this bizarre characterization come from? If anything, the difference between dogs and bears is roughly like the difference between whales and dolphins, in that dogs and bears are quite different from each other, but members of the same order or superfamily, and whales and dolphins are quite different from each other, but members of the same order or superfamily. (I forget what the Linnaean ranks are, because I don't care about Linnaean ranks.) What Eldredge and other strong punctuated equilibria advocates would say are rare, are fossils showing smooth, continuous transitions between very closely-related sister species. E.g., wolves and dire wolves, or wolves and dogs. Or two very similar species of dolphins in the same genus (there are dozens of genera of whales and dolphins, IIRC). I'm not even sure why I am spending time on this. Is there any point, if such basic points cannot be grasped?
Fine, but proteins are not that cooperative as Box @ 6 points out. I still maintain that there’s no legitimate justification for cherry-picking which proteins to compare, ignoring others in order to support a preconceived idea. Even if Darwinism was perfectly correct, a dynamic is missing to explain the anomalies. That dynamic might uncover a new mechanism for DNA change.
This part is all still craziness. It's a simple matter to put in *all* the available proteins into a phylogenetic analysis of a particular group, the fast ones and the slow ones, if you are that worried about it. It's not efficient in terms of genome sequencing money or computational time, but it can be done.
But professor Matzke’s already said he doubts it. I guess it’s more important to portray Science as having All the Answers than to accurately portray our low level of confidence in something only partly understood. A pity. -Q
I am mostly concerned when you guys confidently spout things that are actually straight-up nonsense to anyone who has learned the basics of the field, and done some research in it themselves. Watching you guys talk about evolution is like reading the English-language edition of a Soviet encyclopedia (which I did once) -- wherein the Boy Scouts were described as a paramilitary organization, and the presidential system is described as a short-term dictatorship. It's like looking in a funny-mirror at a circus. Try harder.NickMatzke_UD_{December 9, 2013
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No, I think what professor Matzke was trying to explain was that phylogenetic changes occur slower than speciation. So one might indeed be able to find an ancestral link between a chihuahua and a grizzly bear, but not between a whale and a dolphin. Fine, but proteins are not that cooperative as Box @ 6 points out. I still maintain that there's no legitimate justification for cherry-picking which proteins to compare, ignoring others in order to support a preconceived idea. Even if Darwinism was perfectly correct, a dynamic is missing to explain the anomalies. That dynamic might uncover a new mechanism for DNA change. But professor Matzke's already said he doubts it. I guess it's more important to portray Science as having All the Answers than to accurately portray our low level of confidence in something only partly understood. A pity. -QQuerius_{December 9, 2013
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As to the disconnect between Nick's statement and mine. I don't want to speak for Nick, but I presume when he says "methods as they exist now can ... not direct ancestry " he means if you can't use phylogenetic methods to infer taxonA is ancestral to taxonB. You might infer they are sister species, in which case you are saying that shared a common ancestor. I think it's reasonable to say two species that share a common ancestor are related by direct ancestry in the sense Berlinkski was going on about.wd400_{December 9, 2013
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wd400 states matter of factly:
"And, of course, if you are a “tree-thinker” you don’t need ancestor-descendant relationships to reconstruct evolutionary events."
Yet, from what I've seen of Darwinian 'tree thinkers', it readily appears they don't need any evidence at all but merely just imagine that it is possible:
"The prevailing assumption in evolutionary science," he (Phillip Johnson) wrote, "seems to be that speculative possibilities, without experimental confirmation, are all that is really necessary." This is wrong only to the extent that speculative possibilities without experimental confirmation are often all that is really possible. - Berlinski also of note from the article: "Every paleontologist writing since Darwin published his masterpiece in 1859, has known that the fossil record does not support Darwin's theory." http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html
Further notes:
"Grand Darwinian claims rest on undisciplined imagination" Dr. Michael Behe - 29:24 mark of following video Evidence of Design from Biology. A Presentation by Dr. Michael Behe at the University of Toronto http://www.youtube.com/watch?feature=player_detailpage&v=s6XAXjiyRfM#t=1762s
Essentially the, ahem, 'scientific' argument for Darwinism appears to be like this:
Darwinism Not Proved (Absolutely) Impossible Therefore Its True - Plantinga http://www.metacafe.com/watch/10285716/
What Darwinists are faced with
Probabilities Of Life - Don Johnson PhD. - 38 minute mark of video a typical functional protein - 1 part in 10^175 the required enzymes for life - 1 part in 10^40,000 a living self replicating cell - 1 part in 10^340,000,000 http://www.vimeo.com/11706014
Here is how Darwinists react to probability arguments:
Dumb and Dumber 'There's a Chance' - video http://www.youtube.com/watch?v=KX5jNnDMfxA
bornagain77_{December 9, 2013
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You can also calculate how the probable (or likely, which is slightly different) the data is given a relationship other than common descent, or test how tree-like a given dataset is. That we can explain the data so well assuming a tree is evidence for common descent.wd400_{December 9, 2013
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Matzke:
[P]hylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry .
wd400:
When you infer to species are sister you are, of of course, inferring they shared a common ancestor. So direct ancestry is indeed detected.
wd, look at those two statements. One may be true and the other false. They may both be false. What is absolutely certain is that they cannot both be true. Perhaps I can help you. The key to your comment is the word “infer.” What inference are you making? You are making two actually. You infer that species A is a sister with species B, and you infer that species A and species B are both descended from species C. And upon what do you base those inferences? Your inferences are based on the assumption that common descent and heritable variation are both true. Don’t you see that it is perfectly circular to infer comment descent when you assume it to begin with?Barry Arrington_{December 9, 2013
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Barry, When you infer to species are sister you are, of of course, inferring they shared a common ancestor. So direct ancestry is indeed detected. What Nick means is that if you take 12 taxa and estimate a tree for them, you can't (using existed methods) infer that taxonA is ancestral to taxonB. Since it's pretty unlikely (but not impossible) that at taxa sample in a typical phylogenetic study would have an ancestor-descendant relationship that doesn't strike me as a big problem. And, of course, if you are a "tree-thinker" you don't need ancestor-descendant relationships to reconstruct evolutionary events.wd400_{December 9, 2013
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Hello Nick, I have got a tip for you and Penny D. - since you guys are into comparing phylogenetic trees constructed from protein sequences : Shark and human proteins “stunningly similar”; shark closer to human than to zebrafish' That's gonna shake up some phylogenetic trees!Box_{December 9, 2013
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Nick, I am not asking anyone to believe me. As incredible as it may seem given the shellacking your reputation for veracity has taken here at UD in recent days, I am asking them to believe you. You write:
[P]hylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry . . .”
If what you say is true, and I will accept that provisionally, then Berlinski’s conclusion follows ineluctably:
But there can be no sisters without parents, and if cladistic analysis cannot detect their now mythical ancestors, it is hard to see what is obtained by calling them sisters. No challenge to common ancestry? Fine. But no support for common ancestry either.
Let me lay it out for you in terms adopted to the meanest understanding: Major Premise: In order to support common descent (far less the Darwinian mechanism that purports to account for common descent), a method of investigation would need to detect direct ancestry. Minor Premise: “Phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry.” Conclusion: Phylogenetic methods as they exist now do not support common descent in any rigorous way. Yes, yes, you’ve given us your inevitable literature bluff. Do any of those papers purport to suspend the basic laws of logic? If so, please give me a summary of how they do that.Barry Arrington_{December 9, 2013
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Mapou, you are right. Berlinski has a very refined sense of humor. Berlinski has been a favorite author of mine on ENV for several years:
Here is a list of David Berlinski's articles (gems) that have been posted over the years on ENV http://www.discovery.org/scripts/viewDB/index.php?command=submitSearchQuery&orderBy=date&orderDir=DESC&query=David%20Berlinski&searchBy=author&searchType=all&includeBlogPosts=true
Here is a sample of Berlinski's 'biting' humor:
Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski November 20, 2011 Excerpt: Richard Dawkins published The Blind Watchmaker in 1985. The appearance of design in nature, Dawkins argued, is an illusion. Complex biological structures may be entirely explained by random variations and natural selection. Why biology should be quite so vested in illusions, Dawkins did not say. The Blind Watchmaker captured the public's imagination, but in securing the public's allegiance, very little was left to chance. Those critics who believed that living systems appear designed because they are designed underwent preemptive attack in the New York Times. "Such are the thought habits of uncultivated intellects," wrote the biologist Michael Ghiselin, " -- children, savages and simpletons." Comments such as these had the effect of raw meat dropped carelessly among carnivores. A scramble ensued to get the first bite. No one bothered to attack the preposterous Ghiselin. It was Richard Dawkins who had waggled his tempting rear end, and behind Dawkins, fesse à fesse, Charles Darwin. With the publication in 1991 of Darwin on Trial Phil Johnson did what carnivores so often do: He took a bite.,,, http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html
Also, for anyone who is interested, David Berlinski has a collection of essays in his book 'The Deniable Darwin"
Berlinski's Dismantlement of Darwinism "A Virtuoso Recital" - Anika Smith March 27, 2010 Excerpt: The Deniable Darwin collects essays written from 1996 to 2009 mostly on the same general theme: That the insufferable pretensions and aggressive self-certainty of science ideologues prevent us from justly appreciating how much we actually have learned about the natural world, and how wonderfully little that is. He applies his dauntingly well-informed, remorselessly cogent skepticism to several fields of study -- theoretical physics, mathematics, linguistics, molecular biology -- but it's his dismantlement of Darwinism that he takes to center stage for a virtuoso recital. http://www.evolutionnews.org/2010/03/berlinskis_dismantlement_of_da033321.html
I've always liked this video interview of Berlinski as well
David Berlinski: Rebelious Intellectual Defies Darwinism - video http://www.youtube.com/watch?v=S89IskZI740
This interview is pretty good too:
David Berlinski—Atheism and its Scientific Pretensions http://www.youtube.com/watch?v=FyxUwaq00Rc
I found this following written interview last week, in which this gem of a quote was sitting nested in the midst of it:
An Interview with David Berlinski - Jonathan Witt Berlinski: There is no argument against religion that is not also an argument against mathematics. Mathematicians are capable of grasping a world of objects that lies beyond space and time …. Interviewer:… Come again(?) … Berlinski: No need to come again: I got to where I was going the first time. The number four, after all, did not come into existence at a particular time, and it is not going to go out of existence at another time. It is neither here nor there. Nonetheless we are in some sense able to grasp the number by a faculty of our minds. Mathematical intuition is utterly mysterious. So for that matter is the fact that mathematical objects such as a Lie Group or a differentiable manifold have the power to interact with elementary particles or accelerating forces. But these are precisely the claims that theologians have always made as well – that human beings are capable by an exercise of their devotional abilities to come to some understanding of the deity; and the deity, although beyond space and time, is capable of interacting with material objects. http://tofspot.blogspot.com/2013/10/found-upon-web-and-reprinted-here.html
bornagain77_{December 9, 2013
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Previously came up here: https://uncommondescent.com/cambrian-explosion/steve-meyer-cambrian-gaps-not-being-filled-in/#comment-482736NickMatzke_UD_{December 9, 2013
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Unfortunately, Berlinski and his fans don't know what they are talking about. Penny, D., Foulds, L. R. & Hendy, M. D. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297, 197–200 (1982) Penny, D., Hendy, M. D. & Poole, A. M. Testing fundamental evolutionary hypotheses. J. Theor. Biol. 223, 377–385 (2003) Douglas L. Theobald (2010). A formal test of the theory of universal common ancestry. Nature 465, 219–222 (13 May 2010) doi:10.1038/nature09014 White et al. (2013). “Beyond Reasonable Doubt: Evolution from DNA Sequences.” PLOS One, August 08, 2013. DOI: 10.1371/journal.pone.0069924. Why didn't Berlinski even mention this literature, let alone refute it? Why didn't you? Why should any scholar who knows about it take you guys seriously?NickMatzke_UD_{December 9, 2013
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“Phylogenetic systematics,” the entomologist Michael Schmitt remarks, “relies on the theory of evolution.” To the extent that the theory of evolution relies on phylogenetic systematics, the disciplines resemble two biologists dropped from a great height and clutching at one another in mid-air.
Berlinski has a highly refined and biting sense of humor. You just got to love the man. :-DMapou_{December 9, 2013
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