• Darwin’s Doubt – Chapter 2 Part 2

    And so we begin our wonderful journey into the world of the Burgess Shale.  Meyer entitles this section “The Bestiary”.  As any good role-playing gamer will tell you, the Bestiary is where we get descriptions of animals.

    I have a minor editing quibble here (and I know this is pot calling the kettle black, because I’m not very good at it), but a further discussion of the discovery of the Burgess Shale should have been in the introduction.  As it is, Meyer talks for another page about the discovery of the shale layer.  He quotes Gould’s Wonderful Life: The Burgess Shale and the Nature of History  … again.

    “Consider the primal character of this tale—the lucky break provided by the slipping horse, . . . the greatest discovery at the very last minute of a field season (with falling snow and darkness heightening the drama of finality), the anxious wait through a winter of discontent, the triumphant return and careful, methodical tracing of errant block to mother lode.”

    Oh for crying out loud.  There’s those damn ellipses again.  Hmmm… this time, they appear to be used correctly.  The missing bit is merely a figure notation.

    Meyer continues on asking why the scientific community would present a fictitious description of the event rather than the majestic beauty of reality.  I ask myself the same question.  I don’t know the answer.  No one knows the answer as the players are all dead by now.  This did happen well over 100 years ago.

    This whole thing is a legend about the discovery of the Burgess Shale.  While moderately entertaining, it’s not really important, other than as an example of the poetic license of people.

    Now, let’s get to it.  One of the reasons that I’ve been delayed on this project is because I’ve found, read, and reviewed almost a dozen peer-reviewed papers on the subject that Meyer is talking about.  [One other reason is I’ve also picked up a new research paper reader and organizer. ] While I have a few minor quibbles with what Meyer reports on page 29, it’s mostly accurate.

    Marrella isn’t always divided into 26 segments, but range from 17-26 (as the paper that Meyer references explains).

    No, the problem I have is in the footnote.  Who reads footnotes right?  In footnote #4 Meyer says:

    A distant relationship between Marrella and chelicerates is the currently favored hypothesis.

    And he provides the two references below (and previously linked to in this post).

    Skimming ahead, we see Meyer complaining about the lack of previous fossils and this attempting to cast doubt on evolution.  Why this is a problem becomes evident when one actually reads the footnote and the paper that is referenced.

    One of the articles that Meyer references for the idea about Marrella is called “Arthropod Origins”.  Which is an interesting choice for Meyer since it describes the origin of arthropods, which Meyer says is impossible without intelligence.  Now Meyer only mentions this in passing, but let me jsut quote from the conclusion of the paper.

    There is strong evidence that lobopodians and arthropods belong to the ecdysozoan branch, but they should have separated before the loss of the characteristic plesiomorphic circulatory system, lacking in all ecdysozoan worms. The compact character of the tree may mean that the “founders” of the four post-flatworm groups were all closely related. Lobopodians and arthropods, representing an early offshoot from ecdysozoans, would therefore also be fairly close to the origins of deuterostomes, bryozoans and lophotrochozoans. This would help explain the extreme difficulties to understand the relationships of arthropods and other animal phyla, whatever method is used.

    I know what you’re thinking… “What.  The.  Fuck??”  A picture is worth a 1000 words, so here is what the authors have done.

    Athropod Cladogram

    This is a cladogram of the origins of arthropods.  The letters are some of the characters shared (or lost) that in all groups after that letter.  For example, both tardigrades (which are awesome) and Arthropods have a full loss of cilia (x in the cladogram).  This chart, based on evidence, on the morphology of the organisms pretty much refutes Meyer’s entire point about the Cambrian phyla.  They didn’t appear fully formed.  The relationships between these groups shows that they are related by common ancestry.

    Rotifera is the phylum of the “wheeled animals” and there are thousands of species in several classes.  These are alive today and first appeared… well, we’re not sure exactly.  These are microscopic creatures and the obviously won’t fossilize well.  However, Rotifers are related to Molluscs and Annelids, and we have very good phylogenetic evidence that rotifers branched off before the common ancestor of molluscs and annelids. Since we see clear fossils of both molluscs and annelids in the Cambrian, we can infer that the line that leads to modern rotifers must also have already branched off by that time.

    I could go on, but this is long, has taken a lot of effort and I could right another 2,000 words just on the groups in that cladogram.  Each one with significant references (see below for a few on rotifers) explaining that these are early or pre-cambrian groupings.

    So far, we are four paragraphs into The Bestiary.  I want to spend some effort on the rest of the section as Meyer makes some claims and decisions not for the purpose of advancing science, but to advance a particular notion… which I will attempt to refute and explain why he’s wrong… again.

    Let me add a quick note about creationism and it’s modern interpretation, Intelligent Design, here.  I’ve heard (many, many times) that the appearance of common ancestry is the same as the appearance of common design.  That we can infer common design, basically part-reuse, in organisms that are related by, for example, the characters in the cladogram above.

    In that case, so what?  In that case, if the creationists wish to make that argument, then they have doomed ID.  Why?  Because there are two competing notions; ID and evolution.  In this case, the creationists say that ID predicts the same thing that evolution does.  OK, fine, these common traits are not discriminatory between evolution and design.  This is because both notions predict the exact same thing.  It’s useless to even talk about it and it is certainly not evidence for Intelligent Design.

    However (and you knew this was coming right), evolution has a mechanism for that commonality.  That is, the concept of heredity and speciation.  ID doesn’t have a mechanism (both Behe and Dembski, two leaders of the ID movement, have publicly stated that there is no mechanism for ID).  Since that is the case, there is a difference between evolution and ID.  Evolution predicts a specific mechanism and ID doesn’t.  If that mechanism is found, then evolution is strengthened and ID has to go back to the drawing board.  Even a casual search of peer-reviewed research will yield thousands of speciation events and thousands of instances of proteins, DNA, and RNA sequences changing over time in one species or group and not changing in another species or group (Richard Lenski’s work on E. coli for example).

    So, evolution is supported and ID fails.

    The rest of the series.

    ______________________

    References
    García-Bellido, D.C. & Collins, D.H. A new study of Marrella splendens (Arthropoda, Marrellomorpha) from the Middle Cambrian Burgess Shale, British Columbia, Canada. Canadian Journal of Earth Sciences 43, (2006).

    Bergström, J, and X Hou. “Arthropod origins”, 2003. Available: http://mzp.cz/ris/ekodisk-new.nsf/1a76d1df1a0e29f0c1256e2800520b9d/9a21746463a798e9c125708f002d7766/$FILE/str.%20323-334.pdf.

    Garey, J. R., Schmidt-Rhaesa, A., Near, T. J., Nadler, S. A. 1998. The evolutionary relationships of rotifers and acanthocephalans. Hydrobiologia 387-388: 83-91

    Wirz, A., Pucciarelli, S., Miceli, C., Tongiorgi, P., Balsamo, M. 1999. Novelty in phylogeny of Gastrotricha: Evidence from 18S rRNA gene. Molecular Phylogenetics and Evolution 13(2): 314-318.

    Category: Book ReviewCreationismEvolutionResearch

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    Article by: Smilodon's Retreat

    • Paul King

      I think that it’s even worse for ID than you suggest.

      FIrst, evolution has a mechanism that strongly predicts a nested-tree hierarchy. ID arguably predicts commonalities but not the nested-tree form. And also, by not proposing a designer, evolution is more parsimonious than ID – even if all else were equal ID would lose on that ground.

      Even worse, ID has no theory to replace evolution and probably can’t have a theory that would satisfy all of their supporters. WIth no theory they automatically lose again, unless they can disprove evolution.

      This, I feel, is why Meyer has to try to cover up the evidence of ancestry. An absence of ancestors is one thing that creationism predicts and evolution does not.

    • Doc Bill

      It’s too bad Meyer didn’t spend more time talking with the park ranger on his guided hike to the Burgess Shale or spend some time in the museum in Field where the tour starts. He would have learned that Walcott had spent time on Mt. Stephens, directly behind Field, collecting trilobite specimens from the shale deposits there. Trained in geology, Walcott speculated that the extension of the Mt. Stephens shale deposit may have been preserved on the other side of the valley, perhaps at a similar elevation. It wasn’t by chance that Walcott was examining the area around what was later named Walcott Quarry, but by design. He was looking for fossil shale deposits and found them where he thought they would be. Walcott was using science to guide him, not luck.

      Of course, Meyer doesn’t give a rat’s one way of the other, rather, he’s happy just to trot out a nice story. No need to confuse his readership with pesky things like facts.

    • Joshua Hedlund

      I don’t understand how “this chart” refutes Meyer’s point that “they didn’t appear fully formed” in the fossil record, because it doesn’t tell me where the fossils coincide with that chart. Do we only have fossils at the right end of the graph (i.e. looking like jklm-n, jklm-op-q, jklmn-rs, etc), inferring the ancestry from non-fossil evidence, or do we also have fossils in the middle of the graph (i.e. looking like jklm without n or op yet, etc) For example, the second graph in Matzke’s review shows “known fossil ranges” that *all* occur after the nodes.

      • SmilodonsRetreat

        Which dog breed is the start of a new species?

        That’s the question that’s being asked here. The short answer is that it is effectively impossible to tell which fossil (or modern animal) will be the node for a new species. With modern groups, we can at least see the process over time (if we’re keeping records).

        The fact that transitional fossils exist takes care of the problem. We’ll never know which fossil is the direct ancestor of a particular group. But we know that the ancestor must exist. This is the same as you not being able to identify your direct ancestor that lived 2,000 years ago, but we know that person must have existed, because you exist.

        The only other option is “an unknown and unknowable intelligence did something, somehow, at some point in time” and that has zero supporting evidence.

        • Joshua Hedlund

          I’m sorry, I still don’t understand how that relates. Sure, we can’t tell who will be *at* the node. But we can at least tell if a fossil comes after a node that represented the common ancestry of our modern phyla, right? (At least that’s what Matzke’s graph of Peterson’s “known fossil ranges” seems to show) So, then, can we also tell if a fossil would come *before* those nodes, and is it true that we don’t have fossils along the black lines before those nodes?

          We still may be able to tell if there’s a common ancestor by other means – i.e. your cladogram above – but unless I misunderstand something that doesn’t refute Meyer’s claims that the fossil record doesn’t show ancestry prior to any of those nodes; if anything it’s evidence of ancestry in spite of of the fossil record’s lack of evidence of ancestry.

          Or maybe I misunderstand what you mean by “the fact that transitional fossils exist.” Are you talking about transitionals between the first representatives of modern phyla and today’s representatives (which is not what Meyer is talking about here), or are you talking about transitionals between the Cryogenian nodes and the first representatives of today’s modern phyla? (which would imply that even Matzke’s graph is incorrect, again unless I’m reading it wrong)

          Analogies about dogs do not help me understand what you are saying is wrong or right about either Meyer’s or Matzke’s fossil evidence graphs… unless you are saying that if dog breeds evolved into very distinct species in six hundred million years, they would be able to derive their common ancestry even if they had no fossils of dogs or wolves or any similar mammals of today or the past x million years because all their fossils started showing up in a twenty million year period three hundred million years from now *after* they all looked very different.

          • SmilodonsRetreat

            I’m not getting your point and I think that’s why we’re talking past each other here. If you read the rest of Nick’s review, you’ll see that there are lots and lots of fossil prior to the Cambrian explosion.

            The nodes in Nick’s cladogram are based on molecular data, not fossils. Molecular data (which we will get to later in Meyer’s book (and Larry Moran explains why Meyer is wrong) tells us when these nodes occur. They don’t say what is at the node.

            The thing about ancestry is that we cannot see who was the ancestor of a particular fossil. It’s not going to happen. We make inferences about specific groups based on time, shared characters (and in the case of some fossils), a fossil record showing the transitions (for example, whales).

            I’d like to point out the common misunderstanding of transitional here. Like the common misunderstanding of ‘theory’, transitional means something a little different to what laymen mean and certainly what creationists mean. Transitional is ONLY intermediate characters. There is no ancestry, there is no time in the definition of transitional. Archeopteryx is a transitional fossil between dinosaurs and birds, yet no paleontologist considers Archeopteryx an ancestor of modern birds. Likewise, Tiktaalik is not the ancestor of amphibians, yet it is still transitional between fish and tetrapods.

            Transitional fossils exist, there are millions of them. Yet we cannot say that this animal (or species) was ancestral to any other group. We can say it’s likely, but the odds are very, very poor.

            But that doesn’t stop us from being able to say that common ancestry exists.

            Now, I want to correct something about your “modern phyla”. A phylum is based on a particular characteristic. That characteristic is very common in the lots of classes, orders, families, genera, and species. For example, the notocord. There are possibly millions of species in at least 7 classes (in subphylum vertebrtes alone) with a notocord.

            Arguably, we could say that the first organism with a notocord was in that phylum, indeed, the founding member of that phylum. But there’s no difference between any historical member of that phylum and any modern member of that phylum, in terms of what defines the phylum. The presence of a notocord is the only defining character. That’s all. There’s no transitional between fossil cordates and modern cordates, because (again in terms of the phylum), they all have that character.

            What I’m getting at here, is that the taxonomic system is completely arbitrary. That’s why most paleontologists don’t use it anymore (and curiously, Meyer does).

            At some point, there was an organism that we may or may not have classified as a chordate, because it had something like, but not totally like a notocord. The earliest chordate that we know of is Yunnanozoon lividium from the middle cambrian (525 mya). There must be something that is before that time frame that was something like a chordate and had something like a notocord. We either haven’t found it, or can’t tell (from rocks more than half a billion years old) that it actually is almost a chordate.

            That’s the point about the dogs. We can’t look at modern dogs and say, “this breed will form a new species and in 200 million years will represent a new phyla”. We can’t just pick up a fossil out of the ground and say “this is the ancestor of all chordates”.

          • Christine Janis

            “if anything it’s evidence of ancestry in spite of of the fossil record’s lack of evidence of ancestry.”

            If the fossil record/geological record was perfect, this might be a good point. As the fossil record is highly imperfect, and rarely preserves soft-bodied animals, the lack of fossil evidence is irrelevant. Fossils are great if you have them. Archaeopteryx shows that birds came from dinosaurs. Without any fossil record evidence we’d still know that birds are more closely related to crocodiles (and thus to dinosaurs) than to any other kind of reptile. Fossils are great for showing us how and when things happened. The nested hierarchy of life is the evidence that evolution has happened, and which surviving groups are related to each other.

        • Christine Janis

          Which individual dog is the start of a new breed?

      • Doc Bill

        Forget the charts. There is no scientific evidence for nor theory of “intelligent design” creationism. Meyer, however, is a professional “intelligent design” creationist. It’s his job. He’s the director of the organization, the Discovery Institute, whose main function is to promote “intelligent design” creationism. Furthermore, Joshua, Meyer doesn’t care a rat’s whether you understand what he’s presenting or not. Sorry, Josh, but you don’t figure into the calculations. Meyer’s “Doubt” is a fundraising vehicle designed to encourage donors to continue to support the Disco Tute and pay Meyer’s salary. Pure and simple. I very much doubt that Meyer will make more than a few thousand dollars in royalties over the next decade. True, it’s fiction, but it’s not Harry Potter.

        Meyer writes to confuse clearly. He avoids the obvious: all organisms had parents. Nothing has ever poofed into existence as Meyer implies by his design “inference.” Simply no evidence for it. Meyer avoids research and evidence that would foul his notions of “intelligent design” creationism which is why he avoids discussions of the small shelly fossils, phylogenetic analysis, the full picture of molecular evidence, the complete geological picture of the Cambrian era and the time that preceded it. Paleontologist Charles Marshall, who Meyer misquotes, summarized “Doubt” in a recent issue of Science calling the book “a systematic failure of scholarship.”

        Meyer needs two things to make his thesis work. (And, mind you, this is not “following the evidence wherever it leads” as creationists are fond of saying, but having a conclusion, “intelligent design” and twisting the world to fit.) Meyer needs no Cambrian ancestors and he needs a short time. And, boy howdy, does he twist and shout to make that happen! However, Meyer can’t fool Mother Nature and he can’t fool those scientists who have studied this era for decades. “Systematic failure of scholarship” is a polite way of saying Meyer lies like a dog.

        The bottom line is this: the Cambrian “explosion” was a whole lot longer than the 5 million years Meyer portrays; he’s simply wrong. Period. And, also, there was a very long period of time, several hundred million years of evolution leading up to the Cambrian period. The final nail is that research has demonstrated with statistical precision that the rates of evolution during the “explosion” were no greater or unusual than other periods of biological radiation.

        Second, forget fossils. Yes, they are lots of fun, but the modern theory of evolution can be understood and supported by molecular evidence alone, to a great degree. All other branches of science add support to the theory and to date there is no scientific evidence that runs counter to the theory of evolution. Of course, Meyer relies on fossils because his sub-target audience, besides financial contributors, knows little about fossils but quite a bit less about molecular data. If Meyer can only create confusion about the fossil record that’s good enough to give him a “pass” with his base. But, as you can see with this review alone, all you have to do is scratch the surface a little and Meyer has nothing to show. It’s all over.

    • Christine Janis

      Yay — so glad you’re back on track with this again!