Nick Matzke and “Clutching in Mid-Air”

Evolve @42:

Mapou #33 ///There are many instances of horizontal inheritance between species that are in distant branches of the hierarchy.//// Which is why we don’t infer relationships based on one gene, instead we do it from many genes or portions of DNA. Moreover, horizontal gene transfer is much more rampant in microbes than it is in, say, animals.

The important point here is that horizontal genes are found at very high levels in the hierarchy. This breaks the nested hierarchy prediction of common descent. Statistics has nothing to do with it.

////Convergent evolution comes to mind (how evolution can reinvent entire sets of genes is part of the religious “poofery” of Darwinism). //// Similar selection pressures can produce similar genetic/morphological solutions. It’s quite simple actually.

Nonsense. There is absolutely no way random mutations can give rise to the exact same complex DNA sequences in distant species. You are delirious if you believe this hogwash.

///The problem is that common descent does not predict that a subset of the tree of life will be non-nested. This is what intelligent design predicts and this is what is observed. Live with it./// Wrong. ID doesn’t predict any nested hierarchy because we don’t see that in designed objects. If most of the tree agrees with common descent, then what more do you need? Phenomena like HGTs are more of an exception rather than the rule.

You are severely misinformed to the point of absurdity. Intelligent design can produce both nested and non-nested designs over time. I have used the programming language C++ to design both nested and non-nested (multiple inheritance) classes of software objects in the past. Modern languages like Java and C# forbid multiple inheritance so that one is forced to implement only strictly nested class hierarchies. I suggest you get a clue before you come on this forum and act like you have something important to teach us. You're wasting our time with your idiotic nonsense. Mapou

Evolve, "C’mon guys, you can do better than this." Actually, you don't seem to understand the point of the OP either. I hope you can do better too. Go back. Read it again. Think really really hard. It will come to you. (Well, maybe not; the OP does discuss the whole ideological blindness thing) Barry Arrington

Actually, I like the cell phone analogy. - Cell phones are pretty complex (though nowhere near that of a single cell) - They share many common features - They compete in a brutal natural/commercial selection process - They change over time, employing different strategies and technologies as the commercial environment changes - They have the appearance of design, though not nearly as much as a single cell. It would be interesting to challenge a Darwinist to create a phylogenetic tree of these devices. The rules are 1. You must follow the same logic as used for organizing, let's say, the phylum Mollusca (because it's large and offers more flexibility, not to mention the bivalve analogy). 2. You must classify them first ONLY according to their morphology, ordering them in tiny increments, and estimate how many millions of years it took for each of them to evolve. 3. You cannot use any historical market data to order them---that would be cheating! 3. Later, you can pick from several internal similarities to justify some adjustments and argue for convergent evolution, etc. This might get a little technical. What fun! You don't even have to be a Darwinist to join in. -Q Querius

Your feature phone group will have makes such as Samsung, Nokia and Blackberry. Your smartphone group will also have the same. Both groups can feature the same operating systems and/or features. Processors used in one brand will be found in another. Gorilla glass used in one make will be present in another make. Cameras used in one will be found in another. Sensors found in one are present in the other. When it comes to touchscreens, they’re found on everything from information kiosks to phones, tablets, even desktops! In short your tree will be a jumbled mess with no nested arrangement. That’s exactly what one expects with designed objects. Technology used in one category will be used in another too. But this is not the case with living things. Features unique to mammals are found ONLY in mammals. They’re absent in reptiles or birds, each of which have their own unique traits. But all three groups share another set of features that allows you to group them into a larger set -amniotes. Amniotes have unique features not found in amphibians or fishes. But all three of them share traits which allows you to group them into a still larger set – vertebrates. That’s how living things form a groups-within-groups arrangement. This is characteristic of naturally evolved systems.

Wait. LOL. What? TSErik

Mapou #33 ///There are many instances of horizontal inheritance between species that are in distant branches of the hierarchy.//// Which is why we don't infer relationships based on one gene, instead we do it from many genes or portions of DNA. Moreover, horizontal gene transfer is much more rampant in microbes than it is in, say, animals. ////Convergent evolution comes to mind (how evolution can reinvent entire sets of genes is part of the religious “poofery” of Darwinism). //// Similar selection pressures can produce similar genetic/morphological solutions. It's quite simple actually. ///The problem is that common descent does not predict that a subset of the tree of life will be non-nested. This is what intelligent design predicts and this is what is observed. Live with it./// Wrong. ID doesn't predict any nested hierarchy because we don't see that in designed objects. If most of the tree agrees with common descent, then what more do you need? Phenomena like HGTs are more of an exception rather than the rule. Evolve

Shader #30 ///It’s really silly to say that smartphones wouldn’t produce a nested hierarchy pattern... For instance, the first cellphone sits on top. Perhaps the tree then branches into the flip-phones and non flip-phones. Then somewhere down the line, the touch-screens form a branch, after which the smartphones emerge./// Your feature phone group will have makes such as Samsung, Nokia and Blackberry. Your smartphone group will also have the same. Both groups can feature the same operating systems and/or features. Processors used in one brand will be found in another. Gorilla glass used in one make will be present in another make. Cameras used in one will be found in another. Sensors found in one are present in the other. When it comes to touchscreens, they're found on everything from information kiosks to phones, tablets, even desktops! In short your tree will be a jumbled mess with no nested arrangement. That's exactly what one expects with designed objects. Technology used in one category will be used in another too. But this is not the case with living things. Features unique to mammals are found ONLY in mammals. They're absent in reptiles or birds, each of which have their own unique traits. But all three groups share another set of features that allows you to group them into a larger set -amniotes. Amniotes have unique features not found in amphibians or fishes. But all three of them share traits which allows you to group them into a still larger set - vertebrates. That's how living things form a groups-within-groups arrangement. This is characteristic of naturally evolved systems. Evolve

Barry #27 and Optimus #34 ////The point that Berlinski made (and which neither you nor Nick has addressed) is that calling two species “sisters” is pointless if you can’t detect direct ancestry. Go back and read the OP. I don’t think you’ve grasped it yet.//// ////However, how did you determine the ‘sisterhood’ of the organisms in the first place? As none of us were present to observe said organisms, we have no empirical knowledge of their relationship. It must be either inferred or assumed. It tends to be assumed./// C'mon guys, you can do better than this. "Sister" here means genetic relationship. Ho do you determine relationship? By comparing DNA sequences, just like you determine paternity. Now, when you say you're related to someone in your family what does that mean? That both of you shared a common ancestor at some point in the past. It's the same for species too. When we detect "sister" relationships between two species, that means they descended from a common ancestor because relatives are known to arise ONLY from a common ancestor. It's the same in your family and it's the same for all species. Barry, you don't have to detect the ancestor to infer sister relationships. All you need to do is detect a relationship which you can by phylogenetic methods. Relatives invariably arise from a common ancestor. You won't get anywhere with this unless you understand this basic point. Evolve

Professor Matzke_UD objected

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.)

I guess I'm surprised. Supposedly bears diverged from a bear-like dog about 27-34 million years ago. Dolphins supposedly evolved about 10 million years ago. If dogs and bears are indeed about as closely related as whales and dolphins, it would would suggest that the family Delphinidae evolved about three times as fast as the Arctoidea/Ursoidea branch. What evidence would you cite to arrive at this conclusion? The context is phylogenetic comparisons.

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).

Ok, let's take Canis lupus familiaris and Canis lupus as you suggest as closely related "sister" species. It doesn't make any sense to me that there should ever exist any "transitional" fossils between "sister" species such as these. In fact, they might actually be the same species. But this is beside the point.

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.

I'm not "worried" about it, but if it's all so simple ("inefficient" as this might be), why are we supposedly more phylogenetically related to cartilaginous fish than they are to other classes of fish?

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.

I can see where your conclusion is true and obvious from your perspective, which is based on an evolutionary paradigm and the detail to which you've committed your time and study (certainly more than I have). However, from an ID paradigm, I'm simply not confident in the credibility of evolution as a viable method for generating new information in comparison to losing information (eyeless fish, for example). I find many Darwinist claims to be "magical" and contrived. The cherry-picking rationalization of phylogenetic anomalies is such an example. Oh, I mostly agree with the Soviet point of view of Lord Baden-Powell's "boy scouts," who were indeed intended to participate in military operations. His original book supposedly included garrotting techniques to be used by boy scouts on enemy guards. And that the president of the U.S. is a short term dictator is generally agreed on by a significant segment of the American voting public. However, which segment seems to depend entirely on whether he is a Republican or Democrat. ;-) -Q Querius

OT BTW for all CSI skeptics - Please check out my comment toward the end of the 'Tragedy of Two CSIs' thread... Optimus

Barry, from the OP:

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.

I think you're right. I think his comments in this thread alone confirm that he in fact cannot see the circularity of his reasoning and that of others who contend that cladistics confirms common descent. In this he is not alone, of course. Most people take their worldview, their fundamental paradigms regarding the nature of reality, as Truth, often unconsciously, without realizing they have done so. It is then not uncommon for someone to make an argument for the truth of some cherished belief in which their unexamined paradigms are hidden premises, just as they will rationalize away or simply ignore any evidence which threatens that worldview. Bruce David

For anyone interested in cladistics I highly recommend Henry Gee's In Search of Deep Time. I read it this past summer, and I was quite struck by his bluntness in criticizing some of the sloppy reasoning evident in pop-science discussions of evolution. He also had a number of interesting things to say about how many evolutionary narratives rely on appeals to authority. He also makes clear that cladograms rest on the presumption of common ancestry. Optimus

Barry @ 32 Beat me to the punch: P Optimus

Evolve @ 26 You have smuggled assumptions into your basic terminology. You asked Barry what alternative explanation he has for 'sisterhood.' You then reasoned to the effect of, 'What besides common descent can account the sisterhood of these groups?' However, how did you determine the 'sisterhood' of the organisms in the first place? As none of us were present to observe said organisms, we have no empirical knowledge of their relationship. It must be either inferred or assumed. It tends to be assumed. Optimus

Evolve @29:

Common descent produces what’s called a nested hierarchy (groups within groups arrangement). Common design does not. Try constructing a phylogenetic tree of smartphones and see if it produces a nested hierarchy pattern. It won’t. Only naturally descended things produce that pattern, designed things do not. The fact that living things fall into nested hierarchies is strong evidence for common descent as opposed to design.

I agree that intelligent design does not produce a nested hierarchy. But this is actually an argument against common descent and Darwinian evolution. We do not observe a nested hierarchy in nature. There are many instances of horizontal inheritance between species that are in distant branches of the hierarchy. This is such a huge problem for evolutionists that they have invented a bunch of cockamamie pseudoscientific arguments to explain it away. Convergent evolution comes to mind (how evolution can reinvent entire sets of genes is part of the religious "poofery" of Darwinism). The latest trend is to pretend that the problem is a statistical one. The argument is that, since most of the hierarchy is nested, therefore common descent is confirmed. The problem is that common descent does not predict that a subset of the tree of life will be non-nested. This is what intelligent design predicts and this is what is observed. Live with it. Mapou

The point that Berlinski made (and which neither you nor Nick has addressed) is that calling two species "sisters" is pointless if you can't detect direct ancestry. Go back and read the OP. I don't think you've grasped it yet. Barry Arrington

For anyone who thinks designed objects cannot be placed into tree-like pattern of relationships: http://www.nytimes.com/2004/03/09/science/scientist-work-niles-eldredge-bursts-cornets-evolution-bring-harmony-night-day.html?pagewanted=all&src=pm Can't we just put this one to rest? Optimus

Evolve @ 29. It's really silly to say that smartphones wouldn't produce a nested hierarchy pattern. If you look at all the phones that have ever existed, they most certainly do. For instance, the first cellphone sits on top. Perhaps the tree then branches into the flip-phones and non flip-phones. Then somewhere down the line, the touch-screens form a branch, after which the smartphones emerge. But if one wanted, they could build a whole branch based only on processor speed. Or cameras. Or virtually anything else. Doing this would probably give you a completely different tree each time. But there is no doubt that you would still have a tree, even though they were designed. shader

JoeCoder #23 ///But it can’t be used to argue against: 3. A single designer who reused designs as necessary. But Nick is using it to argue against #3./// Common descent produces what's called a nested hierarchy (groups within groups arrangement). Common design does not. Try constructing a phylogenetic tree of smartphones and see if it produces a nested hierarchy pattern. It won't. Only naturally descended things produce that pattern, designed things do not. The fact that living things fall into nested hierarchies is strong evidence for common descent as opposed to design. Evolve

////I quote Matzke for the admission that the methods in question do not detect direct ancestry. I take it you disagree with him. That’s interesting. Why do you disagree?/// You can beat around the bush as much as you want and pretend that you didn't get the point. But I said the same thing as Matzke. Phylogenetic analyses may not detect the common ancestor directly, but it does detect sister relationships and such relations are only known to arise from a common ancestor. We see the telltale signatures of common ancestry in such analyses even if we don't see the ancestor itself. Evolve

Evolve @ 26. In the OP I quote Matzke for the admission that the methods in question do not detect direct ancestry. I take it you disagree with him. That's interesting. Why do you disagree? Barry Arrington

Barry #5 ///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./// This is unbelievable. What explanation do you have for sisterhood other than common ancestry? Sisters, or any relatives in any family for that matter, are known to arise from a common ancestor, plain & simple! No circular reasoning is required here. We don't have to pinpoint the common ancestor to prove common ancestry. Common ancestry is expected to produce certain patterns in phylogenetic analyses, which is exactly what we see. Evolve

An interesting piece of trivia related to the ‘credibility bridge’ that Matzke burned long ago with ID proponents:

https://uncommondescent.com/cambrian-explosion/steve-meyer-cambrian-gaps-not-being-filled-in/#comment-482236

,,,,is that the main blog that Matzke posts own is named Panda's Thumb. The term 'Panda's Thumb' is an allusion to the supposedly bad design of the Panda's digit.

Gould argues that the "thumb" of the panda (which really consists of uniquely modified wrist bones) functions much worse for grasping objects, such as bamboo shoots, than does the true opposable thumb found in humans and therefore Gould says it has poor design.

Yet,,,

it turns out that the panda's thumb is NOT poorly designed. The human opposable thumb would actually NOT be a good design to accommodate 12 hours/day of scraping leaves from bamboo branches (which is what pandas do) however the panda's thumb can accomplish this function without a problem. A study published in Nature used MRI and computer tomography to analyze the panda's thumb and concluded the following: "The radial sesamoid bone and the acessory carpal bone form a double pincer-like apparatus in the medial and lateral sides of the hand, respectively, enabling the panda to manipulate objects with great dexterity." (Hideki Endo, Daishiro Yamagiwa, Yoshihiro Hayashi, Hiroshi Koie, Yoshiki Yamaya, Junpei Kimura, "Role of the giant panda’s pseudo-thumb," Nature, Vol: 347:309-310, January 28, 1999, emphasis added). The authors go on to marvel at the functionality of the panda thumb saying, "[t]he way in which the giant panda .. uses the radial sesamoid bone -- its 'pseudo-thumb' -- for grasping makes it one of the most extraordinary manipulation systems in mammalian evolution." http://www.ideacenter.org/contentmgr/showdetails.php/id/1477 From Discovering Intelligent Design: Two Thumbs Up - May 27, 2013 Excerpt: evolutionary paleontologist Stephen Jay Gould argued that "odd arrangements and funny solutions are the proof of evolution -- paths that a sensible God would never tread." Likewise Miller claims that an intelligent designer would have "been capable of remodeling a complete digit, like the thumb of a primate, to hold the panda's food." It turns out that the panda's thumb is not a clumsy design. A study published in Nature used MRI and computer tomography to analyze the thumb and concluded that the bones "form a double pincer-like apparatus" thus "enabling the panda to manipulate objects with great dexterity." The critics' objection is backed by little more than their subjective opinion about what a "sensible God" should have made. http://www.evolutionnews.org/2013/05/from_discoverin_4072531.html

Thus, ironically, it turns out that even the very name of the blog that Matzke primarily posts own testifies to Intelligent Design over and against him on Darwinian evolution. Moreover, the 'Panda's Thumb' was not even a 'scientific' argument to begin with, but was a Theologically based 'bad design' argument:

The role of theology in current evolutionary reasoning - Paul A. Nelson - Biology and Philosophy, 1996, Volume 11, Number 4, Pages 493-517 Excerpt: Evolutionists have long contended that the organic world falls short of what one might expect from an omnipotent and benevolent creator. Yet many of the same scientists who argue theologically for evolution are committed to the philosophical doctrine of methodological naturalism, which maintains that theology has no place in science. Furthermore, the arguments themselves are problematical, employing concepts that cannot perform the work required of them, or resting on unsupported conjectures about suboptimality. Evolutionary theorists should reconsider both the arguments and the influence of Darwinian theological metaphysics on their understanding of evolution. http://www.springerlink.com/content/n3n5415037038134/?MUD=MP Dr. Seuss Biology | Origins with Dr. Paul A. Nelson - video http://www.youtube.com/watch?v=HVx42Izp1ek

Also of interest, here is a excellent deconstruction of PZ Myer's favorite Icon Of Evolution: Pharyngula (PZ named his 'science' blog after it!);

Vertebrate Gene Expression and Other Properties Don't Support a "Phylotypic" Stage - Casey Luskin - June 14, 2013 Excerpt: a new article in PLoS Genetics, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates," shows that,, an analysis of the genome based on Darwinian assumptions fails to confirm many predictions of the "phylotypic" stage. ,,, (as they report),,, "During development, vertebrate embryos pass through a "phylotypic" stage, during which their morphology is most similar between different species. This gave rise to the hourglass model, which predicts the highest developmental constraints during mid-embryogenesis. In the last decade, a large effort has been made to uncover the relation between developmental constraints and the evolution of the genome. Several studies reported gene characteristics that change according to the hourglass model, e.g. sequence conservation, age, or expression. Here, we first show that some of the previous conclusions do not hold out under detailed analysis of the data." (Barbara Piasecka, Pawe? Lichocki, Sebastien Moretti, Sven Bergmann, Marc Robinson-Rechavi, "The Hourglass and the Early Conservation Models -- Co-Existing Patterns of Developmental Constraints in Vertebrates Barbara Piasecka," PLoS Genetics, Vol. 9(4) (April, 2013).),,, http://www.evolutionnews.org/2013/06/vertebrate_gene073171.html

And, much like Matzke's "Panda's Thunb', it turns out that embryological development, as is represented by the term 'Pharyngula', supports intelligent Design and not Darwinian evolution:

Haeckel's Embryos - original fraudulent drawing http://www.darwinthenandnow.com/wp-content/uploads/2009/11/Haeckels-Embryos-Cropped-II.jpg There is no highly conserved embryonic stage in the vertebrates: - Richardson MK - 1997 Excerpt: Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, http://www.ncbi.nlm.nih.gov/pubmed/9278154 Actual Embryos - photos (Early compared to Intermediate and Late stages); http://www.ichthus.info/Evolution/PICS/Richardson-embryos.jpg

Thus it turns out that two of the most popular science blogs on the internet defending Darwinian evolution, Panda's Thumb and Pharyngula, are named after things that, in fact, support Intelligent Design instead of Darwinian evolution bornagain77

Matzke claims that his questions aren't being answered which is, as Barry pointed out, a smoke screen tactic he is using to avoid answering Barry's questions to him in the first place. ,,, Moreover, asked a few simple questions of Matzke the other day:

"even if the fossils did provide such a smooth gradual transition as you imagine they do, what empirical evidence can you provide that it (the transition) happened by the purely random, ‘bottom up’, materialistic processes that are postulated by neo-Darwinists? https://uncommondescent.com/cambrian-explosion/steve-meyer-cambrian-gaps-not-being-filled-in/#comment-482487

and,

While you are at it Nick, can you also clear up a few more details so as to make Darwinism ‘scientific’ in the first place? https://uncommondescent.com/cambrian-explosion/steve-meyer-cambrian-gaps-not-being-filled-in/#comment-482492

Nick never did answer these 'simple' questions I put to him, but only put up a smoke screen as he is doing now, but these simple questions are of primary importance that supersede practically any other questions that can be asked.,,, because 1. Since Darwinism has no demonstrated mechanism to generated even trivial levels of functional complexity, then everything postulated beyond that by Darwinists is highly superfluous in importance! and 2. Since Darwinism is not really even scientific in the first place, then, once again, everything postulated beyond that by Darwinists is highly superfluous in importance! bornagain77

Testing - I appear to have been banned . . . UD: No, you have been placed in mod. Keep your comments civil and on topic and they will be released from mod. Pro Hac Vice

selvaRajan @21 If that's the case then the paper can be used to argue against: 1. Multiple independent origins of life 2. Multiple designers who did not share designs. But it can't be used to argue against: 3. A single designer who reused designs as necessary. But Nick is using it to argue against #3. JoeCoder

JoeCoder @ 16, Simply put, the paper compares common ancestry with multiple ancestry and concludes that multiple ancestry is improbable. So, taking your analogy, iOS apps came out of iOS SDK and Android apps came out of Android SDK. It is more likely that both Andorid and iOS SDK have a common ancestor language, than iOS SDK and Android SDK having separate ancestor language. selvaRajan

Frustrated by the animosity in this thread. Hoping I can do better. Nick wrote @14:

is there statistically significant tree structure in the data? Stephen Meyer and most of his fans around here seem to deny that there is,

My understanding of the design position isn't that there's no statistically significant data, but only that it's not significant enough to separate design from descent. Like I wrote @16. With both common design and common descent, the common bits of separate clades will have more in common than any two members of those clades. That's certainly statistically significant--but it's the same thing we see among designed objects. Nick also wrote:

Over here in reality, such data indicate close relationship, even if the exact relationship might not be determinable with the data/method available.

To separate design from descent you would need to be able to always an unambiguously bifurcating pattern of gene flow--which is unexpected under common design. Otherwise you have nothing better than the IOS and Android analysis. This doesn't falsify common descent but it also doesn't favor it over common design. JoeCoder

Uncommon Descent should do some sort of podcast or interviews with famous evolutionists. I would like to see an interview done with this Matzke character (no fighting though) :) TheisticEvolutionist

Matzke @ 14: “I won’t reply unless I get direct answers to the questions I asked in this post.” For the uninitiated, let me translate from Darwinist-speak: “I can’t refute your argument, so unless you allow me to change the subject, I will skulk off and tell all my Darwinist buddies at the Thumb that I was forced to leave because you would not dialogue in good faith." Barry Arrington

Matzke @ 14 goes into full spin mode. Astounding really.

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).

Umm, Nick, I am not the one that asserted that “phylogenetic methods as they exist now can only rigorously detect sister-group relationships, not direct ancestry.” You are. You quote the argument based on your assertion (which, as I said, I am willing to accept provisionally). But then you fail to even address the argument, far less refute it. Let me ‘splain how addressing an argument works. You can either attack its validity or you can attack its soundness. If you want to attack its validity you must show how the conclusion does not follow from the premises. If you want to attack its soundness, you must show how the premises are false. In this case, it will be difficult for you to attack the minor premise unless you want to attack your own assertion. Therefore, for you to attack the soundness of the argument, you must show the major premise is false. So, Nick. Does the conclusion not follow from the premises? Or is the major premise false. Those are your two options if you want to refute the argument. I’ll be waiting. Barry Arrington

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

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=UUaBAwmf0uZeTYejbXpXV7VQ bornagain77

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

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

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. -Q Querius

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

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

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

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

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

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

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

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

Previously came up here: https://uncommondescent.com/cambrian-explosion/steve-meyer-cambrian-gaps-not-being-filled-in/#comment-482736 NickMatzke_UD

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

“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. :-D Mapou