Meyer’s Hopeless Monster, Part III

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The paperback edition of Stephen Meyer’s book Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design has just been published. It has a new chapter responding to critics of the book – Donald Prothero, Charles Marshall, and yours truly, the blogger the ID guys were dismissing for a year based on the fact that I wrote the review quickly. The largest section of the new chapter responds to me.

The response shows Meyer is finally improving on a few issues like crown/stem group thinking, but rather like a student who flunked the midterm of a phylogenetics course and decided to finally start paying attention, Meyer still makes huge, amateur mistakes. I’ll highlight a few.

(Unfortunately, I have no time to do a detailed rebuttal, so this will just be quick notes. I am frantically trying to finish projects before meeting season starts in, hoo boy, two days. First I am going to SMBE 2014 in Puerto Rico to present this work, and then to Evolution 2014 in Raleigh, NC to present this work.

(By the way, see part of my presentation, cool animations of stochastic mapping of possible biogeographic histories under different models, below…)

Caption: Stochastic mapping of approximately equiprobable alternative histories under each model. Left: DEC model. Right: DEC+J, which includes founder-event speciation. Key: Blue, K=Kauai. Green: O=Oahu. Yellow: M=Maui-Nui. Red: H=Hawaii Big Island. Kauai is the oldest high island (~5.2 Ma), the Big Island is the youngest island (~0.5 Ma).

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Background – previous posts on the Cambrian/Meyer

Alan Gishlick, Nick Matzke, and Wesley R. Elsberry (2004). “Meyer’s Hopeless Monster.” Panda’s Thumb post, August 24, 2004. http://pandasthumb.org/archives/200[…]eless-1.html

The “Meyer 2004” Medley - The Panda’s Thumb – the complete history of the Meyer 2004 craziness.

Matzke, Nicholas (2005). Down with phyla! - The Panda’s Thumb, which reviewed:

Matzke, Nicholas (2005). Down with phyla! (episode II) - The Panda’s Thumb

Matzke, Nicholas (2007). Meet Orthrozanclus (down with phyla!) - The Panda’s Thumb

Matzke, Nicholas (2013). “Meyer’s Hopeless Monster, Part II.” The Panda’s Thumb.

Matzke, Nicholas (2013). “Luskin’s Hopeless Monster.” The Panda’s Thumb.

Matzke, Nicholas (2013). “Meyer on Medved: the blind leading the blind.” The Panda’s Thumb.

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Statistics and Phylogenetics: the Consistency Index (CI)

Meyer discusses – for the first time ever – the Consistency Index (CI), which is a measure of the congruence of characters on a tree, and a standard statistic calculated in cladistic analysis to assess the treelike nature of the data. Meyer cites two CI values from cladistic analyses of Cambrian groups – 0.565 (Legg et al. 2012) and 0.384 (Briggs and Fortey 1989) and declares them “low”. In the case of Briggs and Fortey (1989), Meyer quotes the authors, who call 0.384 “rather low.” Meyer doesn’t mention that this was just about the very first preliminary attempt at cladistics of Cambrian arthropods, but that’s not the most important problem.

The most important problem is that you can’t just eyeball a CI value for a dataset and decide if it is “high” or “low”. Intuitions based on letter grades (70% is a C, 80% is a B, or whatever) are a poor guide to using a technical statistic. Yes, sometimes scientists themselves eyeball a CI and declare it high or low based on intuition, but only when they have not been sufficiently trained on the topic.

Here’s the reality. This is Figure 1.2.1 of Doug Theobald’s Macroevolution FAQ, derived originally from Figure 6 of Klassen et al. 1991:

Figure 1.2.1. A plot of the CI values of cladograms versus the number of taxa in the cladograms. CI values are on the y-axis; taxa number are on the x-axis. The 95% confidence limits are shown in light turquoise. All points above and to the right of the turquoise region are statistically significant high CI values. Similarly, all points below and to the left of the turquoise region are statistically significant low values of CI. (reproduced from Klassen et al. 1991, Figure 6).

What is the expected CI value if there is no phylogenetic signal in the data? This is what creationists are claiming when they claim the data doesn’t support a phylogenetic tree. This null expectation is easy to calculate (as I mentioned in my original review, but which Meyer, incredibly, missed) by reshuffling each character’s data by randomly assigning the character states to species without regard to phylogeny. The resulting dataset will have the exact same percentages of each character state, the same number of states per character, etc., but will have no phylogenetic signal. Parsimony inference of cladograms can be performed, and CI statistics calculated, for these reshuffled datasets.

The result is a null distribution of CI values. The 95% confidence interval of this null distribution is displayed on the plot. As you can see, the null expectation changes somewhat depending on the number of species in the analysis. So, a CI of 0.5 is low if you have only 10 taxa, but it’s high if you have 30. What is key is that if your dataset’s CI is higher than the null, you can statistically reject the hypothesis of no tree structure in the data. With a little more work you could calculate how many standard deviations you are above the mean of the null distribution.

Briggs & Fortey (1989) had 28 taxa in their analysis. Legg et al. 2012 had 173. Now, consult the figure. I would want to do the randomization myself on the original datasets to be really sure, since conceivably the detailed results could depend e.g. on the number of characters with more than two states, but most morphology datasets are substantially binary characters anyway. As you can see, 28 taxa and a CI of 0.384 is a highly significant rejection of the hypothesis of no cladistic structure, and a CI 0.565 with 173 taxa is an incredibly, mind-bogglingly strong rejection of the null hypothesis. It’s probably hundreds of standard deviations above the random expectation.

Even worse, Meyer should have known about this. Not only has this finding about CI been in the literature since 1991, it’s been prominently available in Theobald’s common ancestry FAQ for 10 years! Meyer himself even cited the FAQ in Darwin’s Doubt, dismissing the entire thing in barely a sentence with “In reality, however, the technical literature tells a different story” (Meyer 2013, p. 122).

The only place where I’ve seen the argument “my gut says that’s a low CI value, therefore cladistics doesn’t support common ancestry” before is from Casey Luskin, Meyer’s “research” assistant for Darwin’s Doubt. Meyer, get a new research assistant! Luskin, get educated before blabbing about technical topics you know nothing about!

Also, regarding Meyer’s argument that a CI of 0.565 means that the 0.435 fraction of the data exhibits homoplasy – the right answer here is “so what”? It is true that the “best characters” are ones that only change state a single time in all of evolutionary history. But character states that evolve twice on a tree still retain a huge amount of phylogenetic signal. Two changes is many fewer changes than you would get if you flipped a coin to place character states at the tips of a tree. Two changes still means that many taxa on the tree share the character state because of common ancestry. If you were going to attempt a classification based on that single character, of course, that wouldn’t work well – but only taxonomists from ancient times, and creationists, think that single-character classifications are how things should work. If you have 100 characters, each of which evolved twice on a tree, the tree would still be readily resolvable.

As usual, creationists make the perfect the enemy of the good. They completely fail understand the difference between “classic homologies” – like the tetrapod limb – and the typical characters used in modern “get as many characters as you can” analyses. In the latter, organisms are atomized as finely as possible while avoiding coding the same character twice under two descriptions. Yes, it would be highly problematic to suggest that the tetrapod limb evolved twice independently. But if you take that limb, and atomize into 100+ individual characters, including the bumps and twists of each bone – is it possible that some of those bumps arose twice independently? Heck yes! If they arose once, they could arise several times, because these highly atomized characters are quite simple (unlike the whole tetrapod limb). Does this homoplasy invalidate the entire enterprise of cladistics and verifying common ancestry? Heck no! Some of those characters might have homoplasy, some might have such high homoplasy that they retain no phylogenetic signal at all (a different thing) – but if you have lots of characters, it doesn’t matter. All that is required is that, on average, most characters retain some phylogenetic signal. Like any measurement of anything in science, you add up many small independent pieces of evidence, some of them noisy or problematic, and yet the final result can be statistically very strong.

This is the typical result of a phylogenetic analysis, and the typical conclusion is that the statistical tree signal is real and quite strong. And this applies to studies of Cambrian taxa (particularly the more recent ones) as much as anywhere else.

Even David Berlinski admitted that the tree structure in cladistic data was real, back in the first round of responses to my review, so I’m not sure where Stephen Meyer thinks he got a leg to stand on on this one. Probably we can just chalk it up to poor research. As usual.

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Ghost lineages and incongruence between cladograms and stratigraphy

Somehow, in his new chapter, Meyer manages to spend pages on ghost lineages and incongruence between cladograms and stratigraphy, without realizing there is a whole literature on statistically measuring this (despite Meyer’s mentions of “statistical paleontology” in the main text, he has almost no familiarity with the field). The typical result of such tests is that there is overall congruence between the two, again a statistically strong pattern.

Again, Theobald covered it thoroughly, and Meyer and Luskin just missed it. I think their brains must just short circuit when they see Theobald’s FAQ:

The most scientifically rigorous method of confirming this prediction is to demonstrate a positive corellation between phylogeny and stratigraphy, i.e. a positive corellation between the order of taxa in a phylogenetic tree and the geological order in which those taxa first appear and last appear (whether for living or extinct intermediates). For instance, within the error inherent in the fossil record, prokaryotes should appear first, followed by simple multicellular animals like sponges and starfish, then lampreys, fish, amphibians, reptiles, mammals, etc., as shown in Figure 1. Contrary to the erroneous (and unreferenced) opinions of some anti-evolutionists (e.g. Wise 1994, p. 225-226), studies from the past ten years addressing this very issue have confirmed that there is indeed a positive corellation between phylogeny and stratigraphy, with statistical significance (Benton 1998; Benton and Hitchin 1996; Benton and Hitchin 1997; Benton et al. 1999; Benton et al. 2000; Benton and Storrs 1994; Clyde and Fisher 1997; Hitchin and Benton 1997; Huelsenbeck 1994; Norell and Novacek 1992a; Norell and Novacek 1992b; Wills 1999). Using three different measures of phylogeny-stratigraphy correlation [the RCI, GER, and SCI (Ghosts 2.4 software, Wills 1999)], a high positive correlation was found between the standard phylogenetic tree portrayed in Figure 1 and the stratigraphic range of the same taxa, with very high statistical significance (P [LESS THAN] 0.0001) (this work, Ghosts input file available upon request).

As another specific example, an early analysis published in Science by Mark Norell and Michael Novacek (Norell and Novacek 1992b) examined 24 different taxa of vertebrates (teleosts, amniotes, reptiles, synapsids, diapsids, lepidosaurs, squamates, two orders of dinosaurs, two orders of hadrosaurs, pachycephalosaurs, higher mammals, primates, rodents, ungulates, artiodactyls, ruminants, elephantiformes, brontotheres, tapiroids, chalicotheres, Chalicotheriinae, and equids). For each taxa, the phylogenetic position of known fossils was compared with the stratigraphic position of the same fossils. A positive correlation was found for all of the 24 taxa, 18 of which were statistically significant.

As a third example, Michael Benton and Rebecca Hitchin published a more recent, greatly expanded, and detailed stratigraphic analysis of 384 published cladograms of various multicellular organisms (Benton and Hitchin 1997). Using three measures of congruence between the fossil record and phylogeny (the RCI, SRC, and SCI), these researchers observed values “skewed so far from a normal distribution [i.e. randomness] that they provide evidence for strong congruence of the two datasets [fossils and cladograms].” Furthermore, Benton and Hitchin’s analysis was extremely conservative, since they made no effort to exclude cladograms with poor resolution, to exclude cladograms with very small numbers of taxa, or to use only fossils with reliable dates. Including these types of data will add confounding random elements to the analysis and will decrease the apparent concordance between stratigraphy and cladograms. Even so, the results were overall extremely statistically significant (P [LESS THAN] 0.0005). As the authors comment in their discussion:

”… the RCI and SCI metrics showed impressive left-skewing; the majority of cladograms tested show good congruence between cladistic and stratigraphic information. Cladists and stratigraphers may breathe easy: the cladistic method appears, on the whole, to be finding phylogenies that may be close to the true phylogeny of life, and the sequence of fossils in the rocks is not misleading. … it would be hard to explain why the independent evidence of the stratigraphic occurrence of fossils and the patterns of cladograms should show such striking levels of congruence if the fossil record and the cladistic method were hopelessly misleading.” (Benton and Hitchin 1997, p. 889)

Additionally, if the correlation between phylogeny and stratigraphy is due to common descent, we would expect the correlation to improve over longer geological time frames (since the relative error associated with the fossil record decreases). This is in fact observed (Benton et al. 1999). We also would expect the correlation to improve, not to get worse, as more fossils are discovered, and this has also been observed (Benton and Storrs 1994).

As for Cambrian taxa, I don’t believe this sort of analysis has been done yet (I could do it – if you put me on your grant/paper!). But the available data already indicates the basic result will be the same as the above. The oft-mentioned pattern of “we see mostly stem groups in the early Cambrian” lines up extremely well with the stratigraphy-cladogram congruence pattern discovered elsewhere.

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Other problems with Meyer’s new chapter, briefly mentioned

- Meyer repeats the usual creationist silliness about transitional fossils, claiming that nothing except direct ancestors count, and cladistics can’t provide these, so it’s all meaningless. He even adds a quote from someone with old-school pattern cladist tendencies, in this case Henry Gee. Par for the course, and it completely ignores what the realistic expectations are when you take a phylogeny and sample it with just a few lagerstatten over 10s of millions of years, each of them sampling one narrow time period at one location. This isn’t the late Cenozoic, where we can get pretty continuous and geographically representative samples of some lineages, enough to say that, say, Homo erectus is very likely the species ancestral to Homo sapiens. It’s utterly ridiculous to expect that kind of precision in the Cambrian. Thus we look for familial relationships and collateral ancestry. The methods for determining these sister-group relationships are rigorous and well-tested, as discussed in my original review and in Theobald’s FAQ, all of it completely ignored in Meyer’s response.

- Meyer acts surprised about the term “collateral” ancestry, despite prominent discussions in, say, Prothero’s Evolution: What the Fossils Say and Why it Matters (p. 82), Padian’s testimony in Kitzmiller, or, say, Darwin (1859).

- Meyer repeats his statements about how cladistics doesn’t show how new information and developmental changes come about – No, cladistics shows the major steps that occurred and their order, and that disproves the idea that it had to happen all at once in defiance of Darwinian gradualism, which is a key feature of Meyer’s argument. Once you have the basic steps and their order, then evo-devo and other disciplines can work on each of the steps. Meyer’s tactic of requiring field A to answer question Z’ and field Z to answer question A’, and never putting together the amazing idea that field A might answer A’ and field Z might answer Z’, is widespread with other creationists (e.g. Paul Nelson). It’s a neat trick, but it will only work on people who are uninformed about these fields.

- Meyer again ignores the voluminous, detailed, published work on the evolution of new genes, with a vague hand wave about how all that biologists can show is merely “reshuffling information.” I addressed the wild unreality of creationist failures to deal with the work and data in the “evolutionary origin of new genes” subfield in my original review. Meyer just ignores this. Again, even David Berlinski and Michael Behe have admitted that normal evolutionary processes can produce new genes. What’s Meyer’s problem? Where’s the line, Stephen Meyer? And don’t say “protein domains”, because you still haven’t shown that new protein domains had much of anything to do with the Cambrian Explosion. Most protein domains go way back to single-celled eukaryotes and to prokaryotes.

- Meyer mentions small shellies briefly – mostly referencing his previous half-baked response online (summary paraphrase: “I briefly mentioned them in passing in a footnote, so I’m good, and Marshall’s diagram draws their diversity separately from the Cambrian phyla, so they must not be connected, so I was right to decide to ignore them, even though it was probably a straight-up mistake rather than a decision.”). In the new chapter, it is apparent that in Meyer’s head, the small shellies are a totally separate event from the Cambrian explosion, as if the gradually increasing diversity and complexity in fossil shells in the 15 million years just before the classic “explosion” was just mere coincidence. It also ignores that some of the small shellies have been taxonomically connected to classic phyla, e.g. when a rare fossil is found showing how the small pieces of “chain mail” body armor assemble together to cover a larger animal. The apparently piecewise evolution of skeletons is, I suppose, also just another coincidence for Meyer.

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Conclusion

A fair bit more could be said, but, as before, this is enough to show that Meyer is not a serious scholar on this issue. He’s still making student-level mistakes.

I am interested in further discussion in the comments, as long as it doesn’t get nasty.

188 Comments

There’s a new edition, with more crap? OK, then I’m done with my multi-chapter breakdown. There’s no point anymore as I have no intention of buying the revised edition and I doubt my annoying benefactor will provide me one.

Still, I wrote 31 blog posts regarding Darwin’s Doubt and probably as many words as Meyer himself. I’ve found dozens of quotemines, many statements that are just flat out wrong and statements that Meyer has used from previous books from a decade ago.

And my mysterious benefactor still absolutely refuses to answer the question, “Why do you take Meyer seriously with all these mistakes?” He also can’t point to anywhere in the book that Meyer actually supports intelligent design. He kept asking me to do this chapter and that chapter and every one is more wrong than the last.

At least I can finally say, “BLEEP it. I’m done.”

Thanks for the comment, but please no cussing, at least not on page 1, comment 1 when people are still reading. PT is in part an educational resource. I bleeped it.

So if a CI of 0.384 means that there is significant phylogenetic signal. Then a Ci of 0.982 means the data is pretty good. So I guess Floyd was wrong again. The SINE insertion data for primate phylogeny is excellent.

Why is it that creationists are always wrong? Is it just chance? No, they would do better than that even if they guessed every time. So the null hypothesis is robustly rejected and there is no information in any creationist blubbering.

Also:

Stephen Meyer, Epilogue: Responses to Critics of the First Edition, pp. 424-425:

“The need to invoke hypothetical ghost lineages commonly arises when evolutionary biologists attempt to use cladistics to infer ancestors otherwise unattested by the fossil record. The reason for this is that the fossil record often reveals so-called stem groups arising contemporaneously with, or even after, crown groups. Theropod dinosaurs provide a classic example of this problem. They first appear in the fossil record millions of years after the birds that allegedly evolved from them.”

Wut.

Archaeopteryx is Late Jurassic, 145 Ma.

Wikipedia: http://en.wikipedia.org/wiki/Theropoda

Theropods first appeared during the Carnian age of the late Triassic period about 230 million years ago (Ma)

Mkay…

Is there any suggestion as to what happened, if it wasn’t evolution?

Anything about why Intelligent Designers would resort to these contrivances, when they are presumably able to do lots of things? Why bother to design things like trilobites and dinosaurs, only to have them go away? Why make animals one way, and then resort to design to improve on the original idea? What would it look like if we were there when one of the designs were implemented?

Sorry Nick. Won’t happen again.

TomS, in the 1st edition, Meyer does make a comment (Chapter 11 I believe) that if evolution can’t do it, then design could. There is an actual chapter (but only two! 17 and 18) on ID but they read like a pamphlet put out by ID. Nothing of substance (big shock).

Here’s the links for my reviews (some partial) of them. http://www.skepticink.com/smilodons[…]bt-a-review/

”… the RCI and SCI metrics showed impressive left-skewing; the majority of cladograms tested show good congruence between cladistic and stratigraphic information. Cladists and stratigraphers may breathe easy: the cladistic method appears, on the whole, to be finding phylogenies that may be close to the true phylogeny of life, and the sequence of fossils in the rocks is not misleading. … it would be hard to explain why the independent evidence of the stratigraphic occurrence of fossils and the patterns of cladograms should show such striking levels of congruence if the fossil record and the cladistic method were hopelessly misleading.” (Benton and Hitchin 1997, p. 889)

Yes, I would certainly like to hear an alternative explanation. How do creationists explain this pattern? Hydrologic sorting? Really? Coincidence? Really?

This is a robust and statistically highly significant confirmation of an important prediction of the theory of evolution. Is there any viable alternative? Anything? Anything at all? No. Well then consider the case for evolution closed. Creationism loses once and for all. Again.

TomS said:

Is there any suggestion as to what happened, if it wasn’t evolution?

Anything about why Intelligent Designers would resort to these contrivances, when they are presumably able to do lots of things? Why bother to design things like trilobites and dinosaurs, only to have them go away? Why make animals one way, and then resort to design to improve on the original idea? What would it look like if we were there when one of the designs were implemented?

Trilobites and dinosaurs each had their reign over the seas and land for hundreds of millions of years. Sounds to me like they were the focus of this first half of the marvelous show that is Life on Earth, and we humans (at less than a quarter of a million and already running into some existential problems) are a fleeting, ephemeral afterthought on a trip to the snack bar during the intermission.

Stephen Meyer’s Hopeless Monster?

Please tell me it’s not another Twilight sequel.

“Theropod dinosaurs provide a classic example of this problem. They first appear in the fossil record millions of years after the birds that allegedly evolved from them.”

Here Meyer is misquoting/misunderstanding an old an erroneous argument by the few paleornithologists (Alan Feduccia, Larry Martin, etc.) who thought birds didn’t descend from dinosaurs. The argument was that the most bird-like theropods (e.g. Velociraptor, Deinonychus) lived later than the earliest known bird Archaeopteryx, thus birds couldn’t have evolved from them. The “Birds Are Not Dinosaurs” group has about as much understanding of cladistics as creationists do though, in this case confusing ancestor-descendant relationships with common ancestry. No one ever claimed birds evolved from Velociraptor itself, only that Velociraptor and birds had a common ancestor that was itself a theropod dinosaur.

Of course, the 30 million year gap between Archaeopteryx and Deinonychus has closed completely since the 80s when that argument was first used, and now we have so many intermediates that it’s hard to know if some complete skeletons are on the bird line or the Velociraptor/Deinonychus line. We even have species that lived before Archaeopteryx that seem pretty close to that common ancestor (e,g, Anchiornis, Aurornis, Eosinopteryx).

In 1999, we found out the Velociraptor/Deinonychus line had feathers, and when the Birds Are Not Dinosaurs group eventually accepted that, they accepted them as relatives of Archaeopteryx and modern birds, and suddenly the then 20 million year gap didn’t matter anymore. So not only is Meyer using a terrible argument from a discredited group of scientists, he’s using one even they don’t believe anymore. It really is like a student scanning literature he doesn’t understand.

While I’m here, one relevant thing that wasn’t clear in your discussion of Consistency Indices is that when dealing with morphological studies such as the Cambrian ‘explosion’ examples, the CI is largely an artifact of which characters and taxa the authors chose to include. Sometimes authors will include mostly characters which support their own cladogram, and that results in a ‘high’ CI. Ideally, authors include characters that support rival hypotheses so that their analyses are actual tests of the strength of each competing cladogram. In these cases, the CI is ‘low’, but this is a good thing because more of the known data is being tested. In neither of these cases is the CI an actual value that exists in nature though, since we’re always finding new species and new characters to add to studies. Now molecular studies on the other hand do have real CIs, since their characters are discrete nucleotide differences in a finite genome (though you’ll still get a bit of variation depending on which taxa you use, and of course different parts of the genome have differing levels of noise).

ksplawn said:

TomS said:

Is there any suggestion as to what happened, if it wasn’t evolution?

Anything about why Intelligent Designers would resort to these contrivances, when they are presumably able to do lots of things? Why bother to design things like trilobites and dinosaurs, only to have them go away? Why make animals one way, and then resort to design to improve on the original idea? What would it look like if we were there when one of the designs were implemented?

Trilobites and dinosaurs each had their reign over the seas and land for hundreds of millions of years. Sounds to me like they were the focus of this first half of the marvelous show that is Life on Earth, and we humans (at less than a quarter of a million and already running into some existential problems) are a fleeting, ephemeral afterthought on a trip to the snack bar during the intermission.

My joke has usually been that when the intelligent designer decides to return he is going to be really ticked off at the metazoan condominiums that he designed for his beloved prokaryotes. When he determines that we are using antibiotics and other chemical warfare it will be all over for us. Just think what he will do when he discovers that we pasteurize our milk specifically to cook the poor little guys alive. Probably the only reason he saved Noah and the other animals with the breath of life is so that his bacteria would still have their time share condos. As it is pretty soon PETA will have us anesthetizing the bacteria before pasteurization. That could be our only salvation.

The only place where I’ve seen the argument “my gut says that’s a low CI value, therefore cladistics doesn’t support common ancestry” before is from Casey Luskin, Meyer’s “research” assistant for Darwin’s Doubt. Meyer, get a new research assistant! Luskin, get educated before blabbing about technical topics you know nothing about!

In an ideal world we would have creationists not less qualified than the scientists doing the hard work.

Looking over what I wrote, I wish I had a George Orwell emulator.

Why bother to design things like trilobites and dinosaurs, only to have them go away?

Apparently he needed them for target practice.

all that biologists can show is merely “reshuffling information.”

All of biology and chemistry is just reshuffling atoms.* All of literature is just reshuffling alphabet letters. Consider this post; its information content is made up of “merely reshuffling” 26 characters developed almost 3,000 years ago. I have added no new characters, so how could it possibly contain new information!?! Well, because reshuffling prexisting components IS one the primary methods by which new information is produced.

Meyer’s complaint here is equivalent to some creationist saying “you can’t show evolution, all you can show is merely natural selection operating on inherited traits to change the distribution of alleles in a population over time.” The method is the result; reshuffling is production.

*Excepting, argubly, nuclear and radiochemistry.

ksplawn said: Trilobites and dinosaurs each had their reign over the seas and land for hundreds of millions of years. Sounds to me like they were the focus of this first half of the marvelous show that is Life on Earth,

Going by time-on-earth, its a bad mistake to think those sorts of critters are the focus. Life’s been around for about 3.5-3.7 billion years. In terms of time on planet, the rankings go:

Gold medal winner: anaerobic prokaryotes. Been here 3.7 billion years and still ticking, baby. Humans should consider the fact that these guys are not the dominant form of life on earth any more because they poisoned the atmosphere with their waste products to such an extent, that the planet’s surface became uninhabitable to them. Hmmmmm.

Silver medal winner: aerobic prokaryotes. A distant second in the race, having only been around for about 2.2 billion years.

Bronze medal winner: virtual tie between single-celled eukaryotes (been here about 1.8 billion years) and the earliest multi-celled microorganisms (about 1.7 billion years).

Not even an honorable mention: trilobites, dinosaurs and the like. Heck even “all land plants.” A measly 0.5 billion years on the planet.

Mickey Mortimer said:

“Theropod dinosaurs provide a classic example of this problem. They first appear in the fossil record millions of years after the birds that allegedly evolved from them.”

Here Meyer is misquoting/misunderstanding an old an erroneous argument by the few paleornithologists (Alan Feduccia, Larry Martin, etc.) who thought birds didn’t descend from dinosaurs. The argument was that the most bird-like theropods (e.g. Velociraptor, Deinonychus) lived later than the earliest known bird Archaeopteryx, thus birds couldn’t have evolved from them. The “Birds Are Not Dinosaurs” group has about as much understanding of cladistics as creationists do though, in this case confusing ancestor-descendant relationships with common ancestry. No one ever claimed birds evolved from Velociraptor itself, only that Velociraptor and birds had a common ancestor that was itself a theropod dinosaur.

Of course, the 30 million year gap between Archaeopteryx and Deinonychus has closed completely since the 80s when that argument was first used, and now we have so many intermediates that it’s hard to know if some complete skeletons are on the bird line or the Velociraptor/Deinonychus line. We even have species that lived before Archaeopteryx that seem pretty close to that common ancestor (e,g, Anchiornis, Aurornis, Eosinopteryx).

In 1999, we found out the Velociraptor/Deinonychus line had feathers, and when the Birds Are Not Dinosaurs group eventually accepted that, they accepted them as relatives of Archaeopteryx and modern birds, and suddenly the then 20 million year gap didn’t matter anymore. So not only is Meyer using a terrible argument from a discredited group of scientists, he’s using one even they don’t believe anymore. It really is like a student scanning literature he doesn’t understand.

While I’m here, one relevant thing that wasn’t clear in your discussion of Consistency Indices is that when dealing with morphological studies such as the Cambrian ‘explosion’ examples, the CI is largely an artifact of which characters and taxa the authors chose to include. Sometimes authors will include mostly characters which support their own cladogram, and that results in a ‘high’ CI. Ideally, authors include characters that support rival hypotheses so that their analyses are actual tests of the strength of each competing cladogram. In these cases, the CI is ‘low’, but this is a good thing because more of the known data is being tested. In neither of these cases is the CI an actual value that exists in nature though, since we’re always finding new species and new characters to add to studies. Now molecular studies on the other hand do have real CIs, since their characters are discrete nucleotide differences in a finite genome (though you’ll still get a bit of variation depending on which taxa you use, and of course different parts of the genome have differing levels of noise).

“… from a discredited group of scientists,” You might want to think about rephrasing that. Changing their minds when the evidence became utterly convincing, it seems to me they were operating in the best scientific tradition – quite credibly IOW.

The sort of obvious evidence that comes from phylogenetics has forced the more educated line of YECs into a hard-line “COMMON DESIGN COMMON DESIGN THAT’S THE ANSWER” approach, because they know nothing else will work for them. Conveniently, God common designed his way into creating what looks just like an evolutionary tree. No way to falsify that.

While I’m here, one relevant thing that wasn’t clear in your discussion of Consistency Indices is that when dealing with morphological studies such as the Cambrian ‘explosion’ examples, the CI is largely an artifact of which characters and taxa the authors chose to include. Sometimes authors will include mostly characters which support their own cladogram, and that results in a ‘high’ CI. Ideally, authors include characters that support rival hypotheses so that their analyses are actual tests of the strength of each competing cladogram. In these cases, the CI is ‘low’, but this is a good thing because more of the known data is being tested. In neither of these cases is the CI an actual value that exists in nature though, since we’re always finding new species and new characters to add to studies.

Well, this is like saying that an R^2 showing high correlation between dark clouds and rain isn’t an actual value that exists in nature. It’s possible that data in one region could show it, and data in another region could not. So yeah, CI is a statement about the data, but this is true of all statistics.

I think even the “low” CI values that might come from an “everything and the kitchen sink” approach to gathering data would still typically be high relative to the concerns creationists have – since they think tree structure in the data is just made-up fibbing by evolutionists.

Re: the Cambrian arthropods, my sense of it is that Legg et al. have more characters in their data matrices for Cambrian arthropods than anyone else (although I can’t recall specifically for the 2012 vs. 2013 paper), so they probably are following the everything-plus-the-kitchen-sink strategy.

One other thing Meyer spends a lot of time on in his new chapter is the alleged subjectivity of character selection and character weighting. I just discussed character selection for Cambrian arthropods above, but on weighting, Legg et al. run their analyses with a bunch of different weighting schemes and get basically the same result. And apparently “weighting choice usually doesn’t matter that much for the big picture” is the common result, or so I was told by phylogenetics professors, although of course it can affect details or weak datasets.

Now molecular studies on the other hand do have real CIs, since their characters are discrete nucleotide differences in a finite genome (though you’ll still get a bit of variation depending on which taxa you use, and of course different parts of the genome have differing levels of noise).

You could presumably pick regions that are saturated and get random-noise-like CIs…my preferred approach would actually be likelihood-based, and make a model where you just try to predict the data from the base frequencies and see what your likelihood score is. One weakness of the frequentist null hypothesis approach is that some other correlation in the data could cause you to reject the null, e.g. if a number of character states correlated with environment. This wouldn’t provide *that much* grouping structure in the data, not nearly as much as a tree, but it could provide enough to reject the randomization null. With a likelihood approach you could model each hypothesis.

“… from a discredited group of scientists,” You might want to think about rephrasing that. Changing their minds when the evidence became utterly convincing, it seems to me they were operating in the best scientific tradition – quite credibly IOW.

I don’t believe the BANDits have changed their minds on the main issue, that’s the problem. Strategically dropping stratigraphy when the stratigraphic evidence comes in to support the other side is also part of the probelm…

david.starling.macmillan said:

The sort of obvious evidence that comes from phylogenetics has forced the more educated line of YECs into a hard-line “COMMON DESIGN COMMON DESIGN THAT’S THE ANSWER” approach, because they know nothing else will work for them. Conveniently, God common designed his way into creating what looks just like an evolutionary tree. No way to falsify that.

I must respectfully disagree. I don’t think that common design solves the problem at all. It does nothing to explain the observed pattern. Now of course a god could have done it that way, but there would be no reason to do it that way, except to fool people into thinking that it was evolution not design. At the very least they have to admit that it isn’t a scientific hypothesis. Once they effectively remove themselves from the realm of science, the battle is essentially over.

david.starling.macmillan said:

The sort of obvious evidence that comes from phylogenetics has forced the more educated line of YECs into a hard-line “COMMON DESIGN COMMON DESIGN THAT’S THE ANSWER” approach, because they know nothing else will work for them. Conveniently, God common designed his way into creating what looks just like an evolutionary tree. No way to falsify that.

If “ common design” is the answer.

And if “why is the human body most similar to those of chimps and other apes, out of all the living things?” is the question.

Then why did the Intelligent Designer(s) make that common design?

1) There is no reason to wonder about this complex specified data. It could be just a matter of chance.

2) The Intelligent Designer(s) were constrained by the material that they were given to work with, or the nature of the methods that they worked by.

3) The Intelligent Designer(s) had “common purposes” for humans, chimps, and other apes.

4) The Intelligent Designer(s) were not directly involved with the common design. That was a result of natural processes.

eric said: All of biology and chemistry is just reshuffling atoms.*

*Excepting, argubly, nuclear and radiochemistry.

This is where you need a good textbook on Metaphysical Chemistry. :)

To be a little more serious, lumping “biology and chemistry” together understates your argument. Biology is merely a rather exotic topic in organic chemistry; chemistry is merely a very specialised area in the physics of the electron.

I am, of course, using “merely” sarcastically. In reality, these are nested layers, and it could be argued that CSI, etc, etc, is just an illusion arising from the complexity inherent in the view at the higher level.

DS said:

david.starling.macmillan said:

The sort of obvious evidence that comes from phylogenetics has forced the more educated line of YECs into a hard-line “COMMON DESIGN COMMON DESIGN THAT’S THE ANSWER” approach, because they know nothing else will work for them. Conveniently, God common designed his way into creating what looks just like an evolutionary tree. No way to falsify that.

I must respectfully disagree. I don’t think that common design solves the problem at all.

Oh, neither do I. But that doesn’t keep them from trying.

How can one discuss Meyer without cussing? That in itself would be a miracle!

I disagree with Nick’s assessment that Meyer exhibits either a poor understanding of the material or mysterious research errors.

No, Meyer is like a skilled race car driver (making Luskin the crash test dummy. bah dum CHING!). Meyer sees the obstacles to his “thesis” as clearly as orange cones in the road and deftly steers around them.

My favorite assessment of Meyer was made by Marshall who observed that Meyer’s work was a “systematic failure of scholarship.”

All of those mined quotes in Doubt (and the rebuttal to critics), and all of the quotes with an ellipsis are mined, are skillfully cut and pasted together, sometimes from many pages apart. That’s not accidental.

Doc Bill said: All of those mined quotes in Doubt (and the rebuttal to critics), and all of the quotes with an ellipsis are mined, are skillfully cut and pasted together, sometimes from many pages apart. That’s not accidental.

So, you’re saying you detect design? :)

eric said:

Doc Bill said: All of those mined quotes in Doubt (and the rebuttal to critics), and all of the quotes with an ellipsis are mined, are skillfully cut and pasted together, sometimes from many pages apart. That’s not accidental.

So, you’re saying you detect design? :)

Absolutely. And the motives and methods of the just barely intelligent designer are abundantly clear.

OK wait- where is the evidence that natural selection and drift can account for the diversity of Cambrian organisms or any organisms? It isn’t in peer-review and it isn’t in biology textbooks, so where is it?

The point being is how can Meyer be wrong when there isn’t any evidence that demonstrates that he is wrong?

Heck natural selection and drift can’t get beyond populations of prokaryotes given populations of prokaryotes. And don’t fool yourselves- endosymbiosis = nothing more than “it looks like it coulda been bacteria”, and it doesn’t explain the nucleus.

BTW Nick, how did you determine that the evolution of new genes was a happenstance event/ via natural selection and/ or drift? You do understand what is being debated, don’t you?

So Nick ignores everything ID says and decides to prattle on regardless.

As for common design, we see that every day with building codes and engineering standards. No need to re-invent the wheel every time you want/ need a different organism.

That means the only people who argue against the concept are the same people who are the most ignorant of design venues.

Hi Joe.

I’ll remind you that it’s not ONE think in ONE paper that shows the evidence for evolution… it’s thousands of things in millions of papers.

It’s an inference, just like what ID claims to use. However, unlike ID, there is actual evidence that evolution occurs and that earlier populations changed into later populations.

Oh and I’ll just add that “If the ID position is true, why does Meyer have to lie so much to support it?” The answer, of course, is that Meyer doesn’t actually support the ID position. He attacks a strawman of evolution of his own creation and defends it with misrepresentations of actual science and taking quotes out of context from actual scientists.

Your last statement is the point. ID doesn’t SAY anything. It’s meaningless. And even if there was a designer… so what? What does that mean to the search for cures for cancer, or pest elimination, or better crops, or anything else that evolution is currently being used to work on and study.

I would really love to hear the ID processes for dealing with cancers.

https://www.google.com/accounts/o8/[…]5cJLbCdN-pWQ said:

As for common design, we see that every day with building codes and engineering standards. But unlike those thing that we know to be designed, there is no need to start only from an organism that already exists every time you want to design a different organism.

That means the only people who argue against the concept of evolution are the same people who are the most ignorant of how evolution works.

There, fixed that for you. Unless of course you would like to explain how common design explains the observed pattern. No? Thought not.

Reminder to Nick and the administrators, Joe has been permanently banned for threatening physical violence. If this is him again, you need to deal with it once and for all.

Robert Byers said:

…the deposition of fossils is easily explained as in the same year by segregated flows in water.

What a dummy you are, Byers.

Geology is study of things in the ground.

Fossils are in the ground.

Duh.

This comment has been moved to The Bathroom Wall.

Geology and biology are both about things on the same planet, made of the same types of atoms and molecules, interacting with each other, and both producing evidence that is relevant to both subjects.

Gods you’re dumb, Byers.

Why was my last comment moved to the hither regions? It was just a plain answer! Is that a hint or something.

I have replied to Robert’s post at the Bathroom Wall.

Robert Byers said:

Why was my last comment moved to the hither regions? It was just a plain answer! Is that a hint or something.

A hint?

Can’t anything hit you upside the head hard enough to make you notice that everyone here knows that you’re an appallingly ignorant, unteachable troll?

Glen Davidson

About this Entry

This page contains a single entry by Nick Matzke published on June 5, 2014 5:45 PM.

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