Down with phyla!

Posted by Nick Matzke on April 17, 2005 06:27 PM

http://www.nysaes.cornell.edu/ent/bcconf/talks/images/nematode.jpgAre phyla “real”?  Is there really a well-defined “number of animal phyla” extant and in the fossil record?  Does the term “bodyplan” or “bauplan” have any consistent definition?  Many paleontologists, notably Stephen Jay Gould (1989, Wonderful Life), have written books that take these concepts for granted, and, observing charts with many animal phyla appearing in the Cambrian, and few appearing afterwards, have reached the conclusion that there was something extra-special and unique about the Cambrian “explosion”.  Creationists, both the traditional and “intelligent design” variety, have been only to happy to put their own spin on this situation, and argue that God, for reasons that remain obscure, engaged in a particularly active period of special creation for a few dozen million years back in the Cambrian.  Recent examples include Stephen Meyer’s hopeless paper “The origin of biological information and the higher taxonomic categories”, the three or so previously-published versions of that paper, and Paul Nelson’s work in general (see a recent powerpoint presentation).

Last week I came across the following paper:

David Fitch and Walter Sudhaus, “One small step for worms, one giant leap for ‘Bauplan?’” Evolution & Development 4:4, 243-246. 

The paper is a frontal attack on the concepts of “phyla” and “bodyplan,” especially as applied to Cambrian fossils.

Nematode mouths

The paper begins with nematodes.  Nematodes are a ubiquitous group of (usually) tiny worms.  They live in the soil, in the ocean, and in and on many other metazoan animals, including you.  There are so many nematodes around that it has been said that if all multicellular life except nematodes were to suddenly vanish, you would still be able to see ghostly images of plants, animals, and humans — made up entirely of nematodes.  Nematodes are bilateral metazoans, recently placed in the ecdysozoa, a group of phyla that molt their cuticles.  Arthropods and sister phyla such as tardigrades and onychophorans are also ecdysozoans. 

Fitch and Sudhaus (2002) begin by noting that in certain lineages of nematodes, the mouth has shifted from a terminal position (“terminal” means that the mouth is at the front tip of the worm, to a “neural” position (twisted to be on the same side of the body as the neural cord) or to an “abneural” position (twisted to be on the opposite side of the neural chord).  See their Figure 1a:

http://www.pandasthumb.org/images/Fitch_Sudhaus_2002_Fig1a.gif

Note: This figure shows three nematode species, Hypodontus macropi (mouth is neural), Gaigeria pachyscelis (mouth is abneural), and Oscheius sp. (mouth is terminal).  Red indicates the appearance of the character change in the phylogeny.

This shift in mouth position is a quite minor change, and has happened independently in various taxa. 

Phyla-level differences

Now, one of the “key differences” separating chordates (deuterostomes) from protostomes is that the chordate mouth is abneural, while the protostome mouth is neural.  Chordates, echinoderms, and some other wormy phyla are deuterostomes, while the other major group of “advanced” bilaterian animals are the protostomes, which include the ecdysozoans we just met as well as the lophotrochozoans (mollusks, annelids, and others).  The differences between protostomes and deuterostomes are supposed to be even “bigger” than the differences between phyla within these groups (after all, each of these groups includes many phyla). The character differences between the phyla are considered to be a fundamental parts of the “bodyplans” of the various phyla. 

Fitch and Sudhaus note, however, that this key character change has occurred many times, in nematodes and elsewhere, and in these contexts it is considered a minor change — perhaps warranting a new family or genus, but certainly not a new “bodyplan” or phylum.  But what is the meaning of “bodyplan” and phylum, if “phylum-level” character changes are going on continually during the history of life, and these changes are considered minor except in the context of the phyla?

Fitch and Sudhaus conclude that — rather like a “language” is a dialect with an army, and the difference between a “religion” and a cult is about 100 years — a “phylum-level difference” is a small set of changes that occurred when animals were first diversifying.  These changes were not particularly “fundamental” or radical at the time, they were just early.  All of the latter changes that accumulated in each lineage were built upon these early changes, producing the appearance — to modern eyes — of these changes being “fundamental differences”.  Among modern organisms, the phyla are fairly distinct now due to accumulated changes and extinction of basal stem groups [1].  But when the phyla were first diverging, the differences were not so large, and many of the stem groups were still around.  This is the reason why many of the Cambrian fossils are difficult to categorize.  If we attempt to shoehorn them into modern taxa, many of them don’t fit, so we have to erect new phyla for them, even though the morphological difference between (say) a lobopod and a basal fossil arthropod or basal fossil onychophoran is not large.

Fitch and Sudhaus show this inconsistency in their Figure 1b:

http://www.pandasthumb.org/images/Fitch_Sudhaus_2002_Fig1b.gif

Note: This figure shows that in Linnaean taxonomy, not all character changes in organisms are treated equally, even if they are identical changes. (Red = new character on the phylogeny)

Linnaean taxonomy works passably well on modern organisms — each modern organism can be put into a natural hierarchy of monophyletic groups [2].  But when applied to fossils, internal contradictions and absurdities begin to appear.  For example, let’s say that we define the class “Aves” as the common ancestor of Archaeopteryx and modern birds, and all of that common ancestor’s descendents.  So far, so good.  However, when we discover a flock of feathered theropod dinosaur fossils, some more closely related to Archaeopteryx than others, we are struck with a quandary.  In order to be self-consistent, the sister group of (Archaeopteryx+modern birds) should itself be ranked as a class.  The sister group of these two classes should get a rank higher than class.  However, these feathered theropods are clearly just one small group of dinosaurs, and if they were all transported to modern times, they are so similar we would put them all in the same small group.  The only ways out of this bind are to (1) give up on the requirement that groups be monophyletic (this is what paleontologists used to do, e.g. with the “mammal-like reptiles”, (2) give up on self-consistency of ranking (leading to problems like having a class within a family, e.g. with the bird-dinosaur example above), or (3) give up on the Linnaean system altogether for fossils, and simply assign a specimen to a species and then determine whether or not it belongs to a crown group (nested within group defined by the common ancestor of a modern monophyletic group) or a stem group (on a branch basal to a crown group).

Option 3, the cladistic option, has taken over much of paleontology, e.g. studies of the origin of birds or the origin of mammals.  Fitch and Sudhaus (2002), and several other papers quoted below in an appendix to this post, represent this view taking over Cambrian paleontology. 

Implications for ID/creationist argumentation

The implications of this conceptual shift within mainstream Cambrian paleontology for ID/creationist argumentation with respect to the Cambrian “explosion” of “phyla” are rather dire.  The entire basis for the ID position is revealed to basically be a mistake — a mistake made by eminent evolutionary biologists, to be sure, but a mistake nonetheless.  The “extinct phyla” that Gould and others cited in support of the idea that the Cambrian phyla appeared in a “phylogenetic lawn” are rapidly being placed as stem groups of modern phyla, showing us how the characters of modern phyla were acquired step-by-step.

There is, of course, zero chance that IDists will just give up on the beloved Cambrian Explosion, but alert creationism watchers might see them move the goalposts.  I suspect we are already seeing some of this when we see IDists waffle on whether or not the Cambrian explosion was really that abrupt, and whether or not any transitional fossils for Cambrian phyla really exist.  It appears that attempts at “in-principle” claims are being substituted — for example, instead of “the Cambrian explosion happened too fast for evolution, too many new body plans with no transitionals”, we are seeing things like “evolution can’t produce new information or new developmental programs, no matter how gradual the Cambrian Explosion was.”  Two examples are quoted below:

Those who think the fossil data provide a more reliable picture of the origin of the Metazoan tend to think these animals arose relatively quickly—that the Cambrian explosion had a “short fuse.” (Conway Morris 2003b:505-506, Valentine & Jablonski 2003). Some (Wray et al. 1996), but not all (Ayala et al. 1998), who think that molecular phylogenies establish reliable divergence times from pre-Cambrian ancestors think that the Cambrian animals evolved over a very long period of time—that the Cambrian explosion had a “long fuse.” This review will not address these questions of historical pattern. Instead, it will analyze whether the neo-Darwinian process of mutation and selection, or other processes of evolutionary change, can generate the form and information necessary to produce the animals that arise in the Cambrian. This analysis will, for the most part, therefore, not depend upon assumptions of either a long or short fuse for the Cambrian explosion, or upon a monophyletic or polyphyletic view of the early history of life.

(Stephen C. Meyer (2004), "The Origin of Biological Information and the Higher Taxonomic Categories")

But the puzzle of the Cambrian Explosion is not really a paleontological (i.e., fossil) problem.

The fossils just make the puzzle more dramatic.

The real problem arises from the way that animals are constructed by the process of development. (emphasis original)

(Paul Nelson (2005). "Why is the Problem of Macroevolution Still Unsolved?" PowerPoint presentation, University of Minnesota-Morris, 6 April 2005.)

In the Appendix below I will quote the relevant bits of some recent articles that make the points I tried to outline in my post above, but in much more authoritative and rigorous fashion.

Notes

1. However, it is worth reading Valentine’s (2004) book The Origin of Phyla and noting every time Valentine says things like “group X is currently placed in phylum A, but it used to be its own phylum B, and before that it was a subphylum in phylum C, but phylum C had to be discarded as a polyphyletic ragbag.”

2. There are some issues with losing phylogenetic resolution (not all of the splits in a phylogenetic tree can be given a rank, even if we start assigning suborders and superclasses) and with the false assumption that taxonomic ranks are going to be comparable (the tree genus Nothofagus is over 60 million years old, the genus Homo is only a few million years old).

3. Well, this note isn’t attached to anything, but I should add that there are some reasons that the origin of the Cambrian phyla is different than the origin of birds or mammals.  First, it was the “mother of all adaptive radiations”, occupying niches that were not just open but completely unoccupied.  Second, there was a major change in the environment for fossil preservation, notably (a) the origin of hard body parts and (b) the origin of burrowing, algae-scraping, and other forms of muck-sucking that mixes up the sediment.  The pre-Cambrian world appears to have been one of undisturbed algal mats, until advanced metazoans came along to eat all of that up.  So calling the Cambrian “explosion” a “myth” — referring to the “phylogenetic lawn” idea — does not exclude the fact that some some very interesting and important things happened at the beginning of the Cambrian.

Appendix — “Down with phyla” excerpts from recent scientific articles

David Fitch and Walter Sudhaus, “One small step for worms, one giant leap for ‘Bauplan?’” Evolution & Development 4:4, 243-246.

[p. 243]

A popular hypothesis about animal diversification is that unique changes occurred in the Precambrian or Cambrian (ca. 700-500 millions of years [Myr] ago) to produce the dis­tinctive features of all animal “Baupläne” (“body plans”) and that such changes have not occurred since (Gould 1989:47). In contrast, we suggest that changes similar to the key innovations initiating the appearance of these distinctive features occur repeatedly during evolution. A major example is the “inversion” of the dorsoventral axis in the evolution of chordates (Arendt and Nübler-­Jung 1994), initiated by a switch in mouth position from the neural to the abneural side. Here we note that similar changes in mouth position evolved <50 Myr ago at least twice in a group of nematodes related to Caenorhabditis elegans. Because this means that such changes were not unique to the Cambrian, they can be stud­ied by experimental approaches in closely related extant or­ganisms. A direct consequence of this focus on studying elemental key changes is that “Bauplan” becomes a less useful concept for understanding how animal diversity evolved.

As a practical approach to understand the origin of differences between currently disparate forms, we can analyze these differences in terms of the suites of apomorphic (derived) evolutionary changes that made one form different from an­ other. Such disparity resulted from many accumulated alterations, novelties, and reductions and the extinction of animals from side lineages with intermediate forms (Sudhaus and Rehfeld 1992:185-188). Retrospectively, some of these changes (which we call “key” changes) might be considered more important than others in initiating a major difference. Even slight changes could provide the important first step (retrospectively recognized as key) in an evolutionary series of events resulting in a major difference between taxa. This approach of identifying key changes relieves us from dealing with Bauplan (body plan), which is typological and has un­ certain ontology. (Bauplan has been defined as a “phylo­typic” organization or archetypal pattern shared by species in a supraspecific taxon and that is distinguishable from other such patterns; e.g., it is unclear how many differences of what grade distinguish Baupläne [Gerhart and Kirschner 1997:296; Raff 1996:33; Sudhaus and Rehfeld 1992:185].) In fact, a break with such typology was the foundation for Darwin’s revolu­tionary conceptual framework (Mayr 1979). Epistemologically, identifying key changes is more likely to give us a practical understanding of the origins of morphological disparity than trying to fit variation into typological concepts like Bauplan.

[…]

[p. 244]

Why is it not recognized more widely that many of the kinds of changes ultimately leading to disparate forms were not unique to the Precambrian/Cambrian? One reason may be that the human mind is so impressed with large differ­ences that it cannot easily conceive origins of such differ­ences in small steps (see Darwin 1859:29). Perhaps focusing on typological Baupläne exacerbates this difficulty? But a more important reason is the common misconception (also sustained by typological terms like “phylum-­level body plan,” “phylotypic stage,” and “phylotypic process”) that the taxonomic level of Phylum is primarily determined by Bau­plan (or developmental stage or spatial pattern of develop­ mental regulatory mechanisms). First, it is tautological to use Bauplan to define a particular taxonomic level if a Bauplan is itself defined as the set of features characteristic of a par­ticular taxon. Second, it has been considered “paradoxical” that “all phyla are old” despite “repeated opportunities for the appearance of new phyla” (Raff 1996:174). This paradox is resolved by noting that the different hierarchical levels of the taxonomic system (Phylum, Class, Order, etc.) are applied arbitrarily. These taxonomic levels reflect relative divergence points in time, as Darwin (1859:420) famously recognized, not particular differences in Bauplan. That is, the groups­-within­-groups hierarchy of taxonomy simply derives from common ancestry at more and more ancient times (Fig. 1B). Phylum divisions represent divergences that occurred earlier than Class or Order divisions within the Phylum, regardless of the grade of difference in Bauplan (Darwin 1859). Even if an identical key innovation as that characterizing a “phylum-level body plan” arose recently from within an Order, a new Phylum could not be erected for it without upsetting the entire taxonomic hierarchy, no matter how distinct the new Bauplan (Fig. 1B). Thus, “all phyla are old” simply because of the hierarchical restrictions of taxonomy, not because fundamental key changes to body plans have not arisen more recently. A paucity of Phyla more recently emerged than the Cambrian is therefore not evidence for lack of recent innovative changes in Bauplan.

Budd, G. E. and S. E. Jensen. 2000. “A critical reappraisal of the fossil record of the bilaterian phyla. Biological Reviews of the Cambridge Philosophical Society 75:253-295.

[p. 253]

ABSTRACT

It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable. A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred in the Early Cambrian or before, the appearance of the modern body plans was in most cases later : very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversification, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the definition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory.

[…]

[p. 255]

II. WHAT, IF ANYTHING, IS A PHYLUM?

Although the debate about the origins of phyla has been vigorously conducted, there has been surprisingly little debate about the very terms of enquiry: how is a phylum defined, and how would variations in its composition change the nature of the debate? (See Valentine & Hamilton, 1997 for a useful exception.) There is, in fact, a difference between those who see a phylum as ‘a group of species sharing a common organization of the body’ (Adoutte et al., 1999, p. 104) and those who see a phylum in phylogenetic terms, although the problem is concealed by the common assumption that members of a phylum are in some way united by a body plan. Nevertheless, in the extant fauna, phyla appear to be used as the largest groupings of taxa that can readily be seen to be more closely related to each other than to any other groups: a primarily taxonomic or phylogenetic usage rather than a morphological, ‘body plan’ based one [for some phyla are recognized to include highly aberrant members, such as the pentastomids (Abele, Kim & Felgenhauer, 1989), or Xenoturbella (Israelsson, 1997; Noren & Jondelius, 1997)], although, critically, such assessments have generally been based on morphology. Claims that the phyla are characterized by particular types of ‘body plan’ features which putative super-phyletic groupings do not possess (e.g. see Table 2-2 in Arthur, 1997) thus seem to be based on an artifact of how we classify groups of animals: if such ‘super-phyletic’ features were readily identifiable, the larger grouping would itself probably be called a phylum, as it would be recognized to be phylogenetically unified. As the level at which this ignorance of relationships becomes important is likely to vary between groups, the cladist’s standard criticism that phyla (and other such ranks) should be positively discouraged on the grounds that they engender spurious comparisons between members of the same ‘rank’ (see e.g. Smith, 1994, and references therein) seems to be valid.

Whilst phyla are often satisfactory and coherent groupings, an important corollary of this usage is that phyla are defined in such a way that virtually guarantees we are ignorant about their interrelationships. Indeed, morphologically distinct groups of taxa that nevertheless do show clear affinities to one or other of the major phyla (such as the onychophorans, tardigrades, acanthocephalans, pogonophorans or echiurans) present a problem for the phylum concept (Budd, 1998a). Such groups are sometimes referred to as arthropods, rotifers or annelids, and sometimes as phyla in their own right. Such difficulties demonstrate the tensions that arise from trying to think about phyla in both phylogenetic terms and in terms of a group of taxa which share a particular ‘body plan’. Given that the phyla have an evolutionary origin, their characters ± and thus their body plans ± must in broad terms have been assembled in a particular order (Valentine & Hamilton, 1997; Budd, 1996, 1998a). There is thus a logical decoupling between the body plan that the extant members of a phylum share, and their phylogenetic affinities to each other, even when they are tightly correlated with each other in the extant fauna. Early in the history of a clade, when the body-plan features of a group had in the main yet to emerge, members of sister-group lineages of different clades must have been very similar to each other (see e.g. Erwin, Valentine & Jablonski, 1997). This distinction is crucial, because confusion between the phylum considered as a phylogenetic grouping and as a group of taxa that share a body plan has led to considerable misinterpretation of the evolutionary origins of phyla.

[…]

[p. 287]

Indeed, recent emphasis on the Ordovician radiation, which in some accounts is as significant as the Cambrian one (Droser, Fortey & Li, 1996) is entirely in accord with this view. Phyla may be a useful way of viewing the diversity of

[p. 288]

extant taxa, but become a typological hindrance in understanding its origin. Virtually all zoology text books perpetuate this problem by referring to the ‘sudden origin of phyla at the base of the Cambrian’, a misinterpretation of the fossil record based on this sort of typology.

Graham Budd (2001). “Climbing life’s tree.” Nature 412, 487.

[p. 487]

Fossils have always been a bother. Initially, natural philosophers were more impressed by their stony composition and where they were found than by what they looked like. Accordingly, they were compared to gemstones as often as to living organisms - perhaps not the best start for palaeobiology. Even when fossils were recognized as the remains of past life, no one knew how to classify them. Dinosaurs, ammonites and trilobites seemed to be quite like other reptiles, cephalopods and arthropods. But which ones were they like in particular? Conscientious palaeontologists strained sinews trying to force these groups to behave. Surely trilobites were a type of crustacean? Or did those antennae make them insects?

As these efforts at classification often failed, palaeontologists changed tack, creating countless high-level categories for fossils. At best, problematic groups were tagged as, for instance, ‘annelid-like’, given their own class or phylum, and cheerfully connected to the tree of life with dotted lines and question marks. This gave rise to the view that early evolution was different from ‘standard’ microevolution, with living groups of organisms suddenly appearing amid fireworks of excess ‘body plans’. The most popular victim of this muddle has undoubtedly been the origin of animals in the ‘Cambrian explosion’. Yet this amazing pattern - the inspiration for entire books devoted to analyses of its supporting mechanisms - is entirely the consequence of bad systematics.

Jaume Baguñà And Jordi Garcia-Fernàndez (2003). “Evo-Devo: the Long and Winding Road.” Int. J. Dev. Biol. 47: 705-713. PubMed

[p. 708]

Another stumbling block to get a balanced assessment of macroevolution is the excessive, almost mystical, adherence to typological concepts such as Baüplan and phylum which are preformationist and pre-evolutionary. Such concepts muddle and distort the perception of big radiations (the paradigm is the so-called Cambrian Explosion, though it could be extended to the radiation of land plants, mammals, etc,…) leading us to see them as something amazing, exceptional and unique, which they were not, and needing exceptional mechanisms, which likely were not required. Budd (2001b) and Fitch and Sudhaus (2002) have cogently argued (see also Conway-Morris, 2003) that such perceptions are the result of bad systematics (‘stem groups’ or fossils are usually left out) and of not considering that with elapsed time both the disparity among clades and the opportunity for extinctions of intermediate forms increase. Skipping the fossil record removes the ‘stem groups’ (those between the most recent common ancestor of two living groups and that of only one of them), which must comprise, by definition, only fossil organisms. This leaves for comparison only ‘crown groups’ (the most recent common ancestor of a clade plus all of its descendants) which are of little help, especially when comparing high clades (e.g. phyla). This is because lineages diverged from each other in a step-by-step manner which is only documented in the fossil record. In addition, ignoring that elapsed time increases the opportunity for intermediate forms to be extinct, reinforces the mirage that extant

[p. 709]

‘crown groups’ (usually phyla) appeared at once in their present modern form.

Walter Sudhaus (2004). “Radiation within the framework of evolutionary ecology.” Organisms, Diversity & Evolution 4, 127-134.

[p. 128]

For paleontologists radiation is a ‘macroevolutionary’ phenomenon. When looking at fossils, a new bauplan is found to be built up within a relatively short geological period of some tens of millions of years (e.g. high-rank groups of birds and presumably eutherian mammals in the Upper Cretaceous period before the K/T event, and the radiation of these groups after this period of mass extinction). Such data have led to the image of a sudden and “explosive” radiation, the “more or less simultaneous divergence of numerous lines” from an ancestor (Simpson 1953, p. 223), like exploding fireworks that suddenly and simultaneously burst in all directions. This image has become so deeply ingrained in the thinking of evolutionists that nearly no one questions myths like the “Cambrian explosion” (Fitch and Sudhaus 2002).

This last paper is less excited, but does indicate that the nematode mouth change is not unique:

Gonzalo Giribet (2003). “Molecules, development and fossils in the study of metazoan evolution; Articulata versus Ecdysozoa revisited.” Zoology 106: 303-326.

[p. 312]

Most arthropods have mouths that are situated ventrally or subventrally and directed posteriorly, possibly through caudal rotation of the mouth cone (Dewel et al., 1999) independent of that of onychophorans (Eriksson et al., 2003). Primitive arthropods such as Kerygmachela and many lobopodians had terminal mouths, with either unassisted or frontal appendage-assisted feeding. One idea is that arthropods later switched to predatory thoracophagy in some anomalocaridids and most euarthropods (Dewel et al., 1999; Budd, 2002). However, members of the extant Pycnogonida have their mouths located at the terminal end of a proboscis (King, 1973), both as juveniles and as adults. This is indeed interesting because by some authors pycnogonids are considered the sister group of all the remaining extant arthropods (Zrzavy et al., 1998a; Giribet et al., 2001). Considering the information from extinct arthropods and lobopodians, as well as tardigrades and pycnogonids, the putative sister group of the remaining arthropods, it seems that the terminal mouth opening could constitute a plesiomorphic state of panarthropods and an apomorphy of Ecdysozoa. This feature would have been lost in the non-pycnogonid arthropods as well as in modern onychophorans and in certain lineages of nematodes (Fitch and Sudhaus, 2002).

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Comment #25499

Posted by Bayesian Bouffant on April 17, 2005 07:39 PM (e) (s)

Is it a phylum or a class - Isn’t just the sort of mess PhyloCode is intended to do away with?

Comment #25503

Posted by PvM on April 17, 2005 07:54 PM (e) (s)

Excellent. Timely as well since ID and the DI in general have been ‘abusing’ the concept of phyla to argue for a sudden appearance. In fact, often they reference Valentine to support their viewpoints even though Valentine in 2004 clearly stated that he believes that Darwinian mechanisms are sufficient.
Another ‘Icon of ID’ bites the dust.

Comment #25507

Posted by Paul Flocken on April 17, 2005 08:21 PM (e) (s)

Thankyou Mr. Matzke

Comment #25509

Posted by Flint on April 17, 2005 08:36 PM (e) (s)

Mayr speculates that while the fairly rapid radiation of bodyplans was real (but not all THAT rapid, Mayr places it at aroud 60 million years or so, as I recall), it may have been due to the evolution of certain genes like hox genes. Mayr notes that these genes are of critical importance in determining bodyplans because they control development, and supposes that (among multicellular critters, anyway) these genes were themselves being selected out during that period. Most of these genes haven’t changed more than a tiny bit in 450 million years or more. The implication is that bodyplans were wildly experimental while hox genes got “locked in”, after which such genes have been conserved to an astounding degree, and this makes significant morphological variation slow and limited.

Dawkins continues to complain that Cambrian forms are categorized by comparison with modern forms, rather than by comparison to one another of the time. In Dawkins’s view, this year’s new shoots from the huge oak tree out back look just like the shoots from the original acorn during the very first year of the oak’s life. By extension, the phyla are fractal, no different on larger scales except for the passage of time.

Comment #25517

Posted by Henry J on April 17, 2005 10:36 PM (e) (s)

Re “Thus, “all phyla are old” simply because of the hierarchical restrictions of taxonomy, not because fundamental key changes to body plans have not arisen more recently. A paucity of Phyla more recently emerged than the Cambrian is therefore <ot<evidence for lack of recent innovative changes in Bauplan.”

So much for that old “no new phyla since…” claim! :)

The Tree of Life Project Root Page pretty much ignores the “rank” system, too.

Henry

Comment #25522

Posted by Nick (Matzke) on April 17, 2005 11:58 PM (e) (s)

Random fun quotes from Valentine (2004), On the Origin of Phyla:

The phylum Mollusca is composed of a number of classes with such distinctive organizations that it is difficult to decide just what the molluscan bodyplan actually is…

(p. 295)

The adult urochordate bodyplan is sufficiently distinct from those of the other chordates that urochordates are sometimes considered to be a sister to other chordates or to be a phylum of their own.

(p. 406)

At one time taxa of pseudocoelomate grade were considered by many workers to represent a clade, based on their common lack of a “true” coelom.  The entoprocts and tardigrades were often set aside as outliers.  Most of the minute vermiform groups have been lumped together in various combinations — usually including Nematoda, Nematomorpha, Gastrotricha, Rotifera, Kinorhyncha, and Priapulida — as classes in phylum Aschelminthes. In recent years the aschelminthes have usually been considered polyphyletic…

(p. 257)

Onychophora has sometimes been included in Arthropoda and united with insects and myriapods as Uniramia, a taxon that excluded crustaceans and other putatively  biramous forms…

(p. 257 )

[T]he [marine] arthropods may equal or surpass the mollusks in species numbers and exhibit about the same disparity in body types…

(p. 264)

The pentastomids or tongue worms have a bodyplan that is distinctive enough to have been classed as a phylum of its own by many workers.  Pentastomids are obligate parasites and do not have many of the features associated with the arthropod bodyplan…Nevertheless, some workers have developed evidence to suggest that pentastomids are aberrant crustaceans modified for a parasitic lifestyle…

(p. 270)

Although many early arthropods had nonmineralized cuticles, a marvelous diversity of early arthropod body types has come to light, so many and so distinctive as to pose important problems in applying the principles of systematics.  The most diverse of the extinct arthropod groups is the Trilobita, which were chiefly mineralized and are usually treated as equivalent in Linnean rank to the Crustacea and Chelicerata.  However, a large number of nontrilobite fossils, with jointed bodies and appendages, display great disparity in just those features that form defining characteristics of the living higher arthropod taxa

(p. 275)

In addition to the numerous early arthropod forms that cannot be assigned to living classes, there are a few organisms that have many arthropodan features but that may not be arthropod stem groups or even sisters.  The most spectacular of these are the anomalocarids… 

(p. 282)

Morphologically based invertebrate phylogenies have traditionally placed the flatworms as the earliest truly triploblastic living phylum, the Platyhelminthes. […] New morphological and molecular evidence suggests that Platyhelminthes as usually defined is polyphyletic, with two of the orders, Acoela and Nemertodermatida, representing basal bilaterians, a position traditionally assigned to all Platyhelminthes…. [Former Platyhelminthes subgroup] Rhabditophora appears to have arisen, not only after the last protostome/deuterostome ancestor, but also after the last ecdysozoan/eutrochozoan common ancestor, and is far from being a basal bilaterian group.

(p. 291)

The small catenulid flatworms do not belong within Rhabditophora.  They have simple bodyplans and reproductive features that have caused them commonly to be allied with acoels.  Yet unlike acoels, their nervous system includes lobes that may function as a brain.  The relation of catenulids with either acoelomorphs or to rhabditophorans is disputed, and they may not be closely allied to either.

(p. 292)

A centimeter-sized vermiform invertebrate, Xenoturbella,  is known from three free-living species found in the North Sea and northeastern Atlantic; it has been tentatively placed in several different phyla by different workers.

(p. 293)

The status of crown Annelida — whether it is a monophyletic phylum, and what taxa are to be included in it — is uncertain.

(p. 314)

Pogonophora and Echiura are treated here under Annelida, but are discussed more thoroughly than most subtaxa because their bodyplans are so derived that, based only on morphological evidence, they have been treated as phyla by most workers, and the status of Echiura in particular is by no means settled.

(p. 314)

Another rather cylindrical, unsegmented coelomate group, the sipunculans, were long lumped with the echiurans in an abandoned phylum, the Gephyra.

(p. 326)

It has been common for nermerteans [sic] to be regarded as somewhat advanced derivatives of the flatworm, perhaps owing their novel features to their greater size.

(p. 331)

Among the more perplexing of the living metazoan phyla are the parasitic Orthonectida and Rhombozoa.  Orthonectids have not been subdivided into higher taxa, but Stunkard (1982) has separated two rhombozoan species that are bizarre even for rhombozoans, to form the order Heterocyemida, and considers the remaining rhombozoans to form another order, the Dicyemida, Orthonectids and rhombozoans are commonly united as the phylum Mesozoa, but as Hochberg (1982) has emphasized, their anatomies are distinctive and their life cycles lack homologies, so perhaps they should be treated as separate phyla but at a “mesozoan structural grade.” …they are likely to be separate phyla.

(pp. 331-332)

Comment #25530

Posted by Karen on April 18, 2005 01:32 AM (e) (s)

Then there’s the professor (emeritus) who taught me introductory invertebrate paleontology.  He perceives the whole linnean classification scheme as an overly inflexible template, and has seen lots of Paleozoic fossils reclassified multiple times during his tenure; and the whole business of superclasses and suborders and all the other ways of crowbaring modern knowledge into the template are a silly nuisance.  Of course, being a geologist, he sees fossils as primarily being a tool for dating rocks.  All that taxonomy is just a way to organize the Treatise on Invertebrate Paleontology.

Comment #25549

Posted by Katarina on April 18, 2005 08:15 AM (e) (s)

This post is a gem! I am going to e-mail the link to all my ID/creationist friends and relatives. Thank you, Nick Matzke.

Comment #25573

Posted by Tarc on April 18, 2005 10:40 AM (e) (s)

(First of all, I have to apologize for my bad grammar because English is not my mother tongue)

“Thus, “all phyla are old” simply because of the hierarchical restrictions of taxonomy, not because fundamental key changes to body plans have not arisen more recently.”

This is basically the same argument as Dawkins’ one in his critique of Gould’s Wonderful Life. To my mind, it is erroneous and Valentine explains why quite well in On the Origin of Phyla :

One suggestion has been that the lack of new phyla after the Cambrian is entirely an artifact of the tree of life ; that as the main branches have themselves branched, the many features that characterized the main branches are naturally inherited by the new branches, which we therefore simply define as classes, or as some subsidiary taxa, rather than as new phyla. There is certainly an argument to be made as to how distinctive bodyplans must be to qualify as phyla. The phyla were not recognized because they all had evolved at an early date (which wasn’t known), however, but because of their morphological differences - the judgements were not made with reference to the tree of life, but with reference to bioarchitectural disparities. An incidental point about phyla is that in most cases their bodyplans have not evolved one from another but from last common ancestors with different bodyplans. (p. 461)

In fact, phyla were recognized on the same basis - general bodyplan - as vertebrate classes, just at another level. If the argument made here were right, so a pattern similar to the Cambrian explosion should apply to the origin of vertebrate classes : mammals, fish, birds and reptiles should appear simultaneously in the fossil record. In fact, Vertebrate classes turned out to have evolved progressively one from another and to be paraphyletic.

Phyla were also first recognized as Linnean categories - and it was later discovered that there were, in most cases, monophyletic and appeared rapidly in the fossil record with all of their defining features. It was not predictable, since it didn’t happen about Vertebrate classes. I think there is here a particular pattern - not at all a problem for darwinian evolution, but something more than only a product of “the hierarchical restrictions in taxonomy” : one could well see, in the fossil record, Arthropods arising gradually from Onychophorans, for example, over tens of millions of years. There are indeed putative transitional forms between Arthropods and Onychophorans, just as between Molluscs, Annelids and Brachiopods, but they all belong to the Cambrian fauna - and all these phyla appeared quite abruptly in the Cambrian. This is a phenomenom which deserves to be taken seriously as something real and not just as an artifact, even if ID and creationists try to turn it into a “problem for evolution”.

Comment #25588

Posted by Ken Shackleton on April 18, 2005 11:39 AM (e) (s)

What strikes me is how long it took for the Cambrian “Explosion” to occur…..more than 50 million years. That is an incredible length of time.

When you say from 543 to 490 million years ago [The Cambrian Period]….the timespan seems relatively brief when described like that…..but that is still 53 million years!

That’s a lot of time for things to develop and change.

Comment #25596

Posted by Nick (Matzke) on April 18, 2005 12:31 PM (e) (s)

I think I deleted the duplicate comments (sorry, the website is sometimes slow to update!).

Comment #25624

Posted by Michael Finley on April 18, 2005 03:19 PM (e) (s)

Does this criticism of the notion of “phylum” have any implications for that of “nested hierarchy”?

Comment #25630

Posted by RPM on April 18, 2005 04:39 PM (e) (s)

Ken Shackleton wrote:

What strikes me is how long it took for the Cambrian “Explosion” to occur…..more than 50 million years. That is an incredible length of time.

When you say from 543 to 490 million years ago [The Cambrian Period]….the timespan seems relatively brief when described like that…..but that is still 53 million years!

Is that time span a confidence interval or a length?  If it’s a length, it probably has a heftly CI associated with it.  I have trouble with point estimates of events that are (nearly) impossible to accurately date.  Any estimate within a geological time frame obtained using radiometric dating should have some sort of error associated with it, right?

Comment #25632

Posted by Steve Reuland on April 18, 2005 04:47 PM (e) (s)

Michael Finely wrote:

Does this criticism of the notion of “phylum” have any implications for that of “nested hierarchy”?

I’m not sure what you mean, but a nested hierarchy, given enough speciation events, produces a massive number of hierarchical categories. One for each speciation in fact.  Much of the problem with “phylum”, as with other taxonomic ranks, is that whether or not you wish to create a taxonomic rank for a recognizable clade is arbitrary.  All that matters is that the group is monophyletic, containing an ancestor and all of its descendents.  But for even a simple phylogenetic tree, there are large numbers of monophyletic clades.  We choose to assign special names to some of them mostly based on history, ease of communication, aesthetic considerations, and perceived uniqueness.  There simply is no “essence” of a phylum or a class, contrary to cre/ID typological reasoning.

Comment #25637

Posted by Evolving Apeman on April 18, 2005 05:33 PM (e) (s)

There simply is no “essence” of a phylum or a class, contrary to cre/ID typological reasoning.

As “proof of concept” why don’t one of you go mate and successfully produce offspring with a gorilla.

Comment #25639

Posted by fwiffo on April 18, 2005 05:46 PM (e) (s)

We’ll leave that to the wolphins.

Comment #25641

Posted by Steve Reuland on April 18, 2005 05:57 PM (e) (s)

tarc wrote:

In fact, phyla were recognized on the same basis - general bodyplan - as vertebrate classes, just at another level.  If the argument made here were right, so a pattern similar to the Cambrian explosion should apply to the origin of vertebrate classes : mammals, fish, birds and reptiles should appear simultaneously in the fossil record. In fact, Vertebrate classes turned out to have evolved progressively one from another and to be paraphyletic.

It’s precisely because vertebrate classes are not shoe-horned into an “explosion” at the first appearance of vertebrates that most classes are paraphyletic.  (Mammals and birds, by the way, are not paraphyletic.  But by assigning them to their own classes, it requires the reptiles and fish to be paraphyletic.)  We could of course try to enforce monophyly among vertebrate classes, but doing so would require that we cram long-recongized distinct groups into the same class, up to the point at which their affinities become obscure and relegated to the earliest branchings.  Just like what’s been done with phyla.

If your point is that phyla, unlike vertebrate classes, were based on “body-plans” and just so happened to be monophyletic, then I think that’s debatable.  The question is, were the phyla really based on body-plans alone, or were they constructed on the basis of enforcing monophyly?  While both are probably true to an extent, I think given that the identified phyla have changed quite a lot, that most of them have been recognized recently, and that most of them are “worms”, the latter is probably true for the most part.  As pointed out above, “body-plans” are a problematic way to assign taxonomic rankings.  Consider that without phylogenetics, all of the “worm” phyla would have likely been crammed into one or a few phyla, just as the “fish” were originally crammed into one class.

Comment #25642

Posted by Russell on April 18, 2005 06:10 PM (e) (s)

fee, fie, faux phylum,
I smell the blood of…
the remnants of typological thinking which, while serviceable for creationists, doesn’t make much sense from an evolutionary standpoint.

Comment #25644

Posted by Steve Reuland on April 18, 2005 06:11 PM (e) (s)

Evolving Apeman wrote:

As “proof of concept” why don’t one of you go mate and successfully produce offspring with a gorilla.

I don’t normally waste time with trolls, but there is an important point to be made here.

“Gorillas” are a species, hence they have nothing to do with what I was talking about, which is higher taxonomic rankings.  Species can indeed be considered real entities based upon reproductive isolation, although even this is problematic.  (E.g. ring species, differential hybrid fertility, asexual species, etc. all cause problems for the biological species concept.)  Higher rankings, however, like classes and families, cannot be considered real entities.  They are arbitary constructs that we’ve invented for communication purposes. 

As for your smartass remark about mating with gorillas, I’ll just give the obligatory smartass reply:  I’ve had your mom, and that’s as close as I care to get.  (Bud-ump-cha!)

Comment #25645

Posted by Sir_Toejam on April 18, 2005 06:19 PM (e) (s)

please tell us EA isn’t your kid, Steve!

Comment #25658

Posted by Pete Dunkelberg on April 18, 2005 07:43 PM (e) (s)

Steve Reuland wrote:

It’s precisely because vertebrate classes are not shoe-horned into an “explosion” at the first appearance of vertebrates that most classes are paraphyletic.  (Mammals and birds, by the way, are not paraphyletic.  But by assigning them to their own classes, it requires the reptiles and fish to be paraphyletic.)  We could of course try to enforce monophyly among vertebrate classes, but doing so would require that we cram long-recongized distinct groups into the same class, up to the point at which their affinities become obscure and relegated to the earliest branchings.  Just like what’s been done with phyla.

A monophyletic fish includes us all.

Comment #25659

Posted by Tarc on April 18, 2005 07:46 PM (e) (s)

Steve Reuland wrote:

If your point is that phyla, unlike vertebrate classes, were based on “body-plans” and just so happened to be monophyletic, then I think that’s debatable.  The question is, were the phyla really based on body-plans alone, or were they constructed on the basis of enforcing monophyly?  While both are probably true to an extent, I think given that the identified phyla have changed quite a lot, that most of them have been recognized recently, and that most of them are “worms”, the latter is probably true for the most part.  As pointed out above, “body-plans” are a problematic way to assign taxonomic rankings.  Consider that without phylogenetics, all of the “worm” phyla would have likely been crammed into one or a few phyla, just as the “fish” were originally crammed into one class.

“Worm” phyla are indeed quite difficult to define and were considerably modified using phylogenetic data, but my point was about the phyla that appear during the Cambrian explosion - and worms generally don’t fossilize. The phyla relevant to the Cambrian explosion problem were, in fact, all recognized following anatomical criteria only : that’s true about Molluscs, Arthropods, Echinoderms, Chordates, Cnidarians… All of them were recognized in the early twentieth century litterature, well before molecular or fossil phylogenetic data were available - just as Vertebrate classes were.

Many of them could have turned out to be paraphyletic ; in fact, it was somehow expected in some cases : for exemple, it was thought for a while that Arthropods had evolved from Annelids. Other theories involved evolution of Vertebrates from Arthropods or, more recently, from Echinoderms : following Jefferies’ “calcichordate hypothesis”, for example, Chordates would have appeared in the Ordivician or in the Devonian. Arthropods could have evolved from Annelids in the Devonian, Chordates in the Ordovician and - why not ? - Brachiopods in the Silurian. But it was not the case and, historically, it clearly was not predictable - since contrary hypotheses were supported for a while. In fact, even when phyla turned out to be effectively paraphyletic (Onychophorans, in a broad meaning including the Cambrian lobopodians which were probably ancestral to Arthropods, for example), this didn’t change anything to their Cambrian abrupt appearance. And it was not necessary : morphological diversification could have been far more progressive.

Comment #25678

Posted by Cassanders on April 19, 2005 04:22 AM (e) (s)

Regarding “evolving apemans” comment on mating with a gorilla:
I assume that the issue have been debated earlier, but I wonder if E.A. or anyone could help me out here. How do CR/ID’ers regard natural occurring  cross mating of two different animals both created as “of a kind” in biblical context? Is it a “natural(istic)” trangression? :-) -or a matter erratic taxonomy? Or what?

In the woods of Scandinavia we have the black grouse (_Lyrurus tetrix_) and the much larger capercaillie (_Terato urogallus_). I am fairly sure the allegedly brilliant taxonomist instructing Noah would have recognised them as two different species, (As you can see, they are even different genera) but still they do mate and do produce a significant percentage of fertile offspring.

Cassanders
In Cod we trust

Comment #25684

Posted by Evolving Apeman on April 19, 2005 08:57 AM (e) (s)

As the unofficial CR/ID spokesman/troll I’d be happy to briefly answer your question. 

1. Despite the straw dummys commonly put up at this site, ID doesn’t deny evolution.  It mainly questions the scientific validity of common descent by macroevolution (as an undirected processes).

2. A naturalistic process-only methodology can never explain a supernatural process.  So any arguments regarding how an intelligent designer should have created are philosophical and furthermore, assume we know the teleologic purpose for all aspects of biology. 

Higher rankings, however, like classes and families, cannot be considered real entities.  They are arbitary constructs that we’ve invented for communication purposes.

Tell me Steve, do you think it will be more feasible in the future to get a heart trasplant from a pig or a shark.  Or would the choice just be arbitrary?

Comment #25687

Posted by Aureola Nominee on April 19, 2005 09:04 AM (e) (s)

Evolving Strawman:

Could you please try using some other logical fallacy, for a change? At least once in a while?

Saying that classes and families are not discreet entities with rigid boundaries does not mean that there is just a magmatic everything with no rhyme nor reason.

One would think that even the most ignorant IDer would refrain from uttering such stupidity.

Comment #25688

Posted by David Greenwood on April 19, 2005 09:45 AM (e) (s)

EA,

So common descent (CD) is accepted by ID proponents? I know Behe accepts it, but I thought most did not or won’t take a stand. You have said yourself that since CD can not be observed, it can not be scientificaly validated. So much for ID being science in your view since it occurred in the unobserved past as well.

Comment #25691

Posted by Steve Reuland on April 19, 2005 10:07 AM (e) (s)

Evolving Apeman wrote:

Tell me Steve, do you think it will be more feasible in the future to get a heart trasplant from a pig or a shark.  Or would the choice just be arbitrary?

The degree of relatedness is not arbitrary.  However, the taxonomic ranking, which is what I’ve been talking about this whole time, is indeed arbitary.  It doesn’t matter if you say that humans and pigs are part of the mammalia, or eutheria, or chordata, or whatever.  These are arbitary circles drawn around monophlyetic groups on the tree of life.  You can make many thousands, if not millions of monophlyetic groups that include both humans and pigs.  Which ones should we give special names to?  It doesn’t matter.  We give special names like “class” or “familiy” to some groups not because there’s anything special about these ranks that actually tells us something about their members, but because they’re convenient.  Hence, when creationists try to claim that “kinds” are defined at the family level (except for the hominid familiy of course — it’s impossible for humans and apes to be of the same “kind” you apostate), or they make a big issue out of the status of phyla, they’re taking arbitarily defined categories and pretending as if they have great biological significance.  They don’t.  Biologists could get together tomorrow and completely rearrange the standard taxonomy, and as long as they ended up with monophlyetic groups, the new taxonomy wouldn’t be any less correct than the old.  (Though changing things around like that would be very confusing.)

I must say, that’s the last attempt I’ll make at explaining what I’ve already explained several times now.  Maybe I’m not communicating clearly, but I’m inclined to believe that the real problem lies elsewhere.

Comment #25692

Posted by David Heddle on April 19, 2005 10:09 AM (e) (s)

Steve to EA

I’ll just give the obligatory smartass reply:  I’ve had your mom, and that’s as close as I care to get.  (Bud-ump-cha!)

What a repulsive comment. Once again a PTer displays a level of class that matches his wits.

Comment #25695

Posted by Steve Reuland on April 19, 2005 10:25 AM (e) (s)

Gosh Heddle, not only are you devoid of a sense of humor, you’re quite the hypocrite.  Speaking of poor class, I’m not the one who first told someone to go have sex with a gorilla.  Try taking your blinders off for once.

Comment #25696

Posted by David Heddle on April 19, 2005 10:31 AM (e) (s)

Yeah Steve, jokes about having sex with someone’s mother, why that is the hallmark of humor. Bravo.

Comment #25697

Posted by Michael Finley on April 19, 2005 10:33 AM (e) (s)

Steve Reuland wrote:

Species can indeed be considered real entities based upon reproductive isolation, although even this is problematic. … Higher rankings, however, like classes and families, cannot be considered real entities. They are arbitary constructs that we’ve invented for communication purposes.

Are you saying that every ranking from genera on up is mere arbitrary convention? Without understanding all of the relevant issue involved, this seems too strong even from the perspective of common descent. At the very least wouldn’t the higher categories represent geneological pathways? And therefore, don’t the rankings “carve nature at the joints” in some sense?

Comment #25703

Posted by Steve Reuland on April 19, 2005 11:02 AM (e) (s)

Michael Finely wrote:

Are you saying that every ranking from genera on up is mere arbitrary convention?

Basically, yes.  This isn’t my idea by the way, it’s the standard phylogenetic interpretation.

Without understanding all of the relevant issue involved, this seems too strong even from the perspective of common descent. At the very least wouldn’t the higher categories represent geneological pathways? And therefore, don’t the rankings “carve nature at the joints” in some sense?

Higher categories represent natural groups, i.e. monophlyetic groups (or at least, they’re supposed to).  That means they contain a common ancestor and all of its descendents.  But like I’ve said, every speciation event creates a new monophyletic group.  Working backwards through the phylogenetic tree, there is a massive number of monophyletic groups.  So why are some groups given names like “mammalia” and “carnivora” but not others?  Basically, we do it for historical reasons, or because some groups are distinct due to extinction having wiped out the intermediates.  But had there been no extinction, all organsisms would be linked via a series of slight transitions.  This means that organisms do not differ in kind, only in degrees of relatedness.

Comment #25706

Posted by Flint on April 19, 2005 11:17 AM (e) (s)

At the very least wouldn’t the higher categories represent geneological pathways? And therefore, don’t the rankings “carve nature at the joints” in some sense?

Good question. Morphological, genetic, and molecular analyses don’t particularly agree with one another as to where such joints may really lie. But perhaps that’s not what you’re asking?

Every life form for all biological history has been a species, and the geneaological tree (like your own family tree) consists exclusively of species. Only physical organisms are “real” in this sense. However, we can’t help but notice that there are degrees of similarity between species, and these degrees suggest the distance in time as well as physical difference between the present and the most recent common ancestor between any two species. The more different the species, the longer it has been since they shared an ancestor, as a general rule.

Presumably the tree of life through time can be viewed very much as a physical tree, with branches off of branches off of branches. These branching events were real events. However, there have been probably billions of such branches, each just as real as any other. Which branching points (assuming we could identify them reliably) should we select to maximize taxonomic convenience? And how many?

Nobody is denying that such branching occurred. The claim is that selecting any particular branching event is just as arbitrary as selecting any other. There are so many such events that we could pick (let’s say) a different 30 of them, within the same shouting distance of the treetrunk, every week forever. And call THIS week’s 30 selections “the phyla” with absolutely equal justification.

Comment #25716

Posted by bill on April 19, 2005 11:33 AM (e) (s)

I tried to mate with a sponge once.  Does that qualify for cross-phyla?

Actually, this has been one of the better, more informative threads with data and references presented.  That is until Prancing Apeman brought the proceedings down to my level.

Comment #25718

Posted by Michael Finley on April 19, 2005 11:43 AM (e) (s)

Steve Reuland wrote:

Working backwards through the phylogenetic tree, there is a massive number of monophyletic groups.  So why are some groups given names like “mammalia” and “carnivora” but not others?  Basically, we do it for historical reasons, or because some groups are distinct due to extinction having wiped out the intermediates. But had there been no extinction, all organsisms would be linked via a series of slight transitions. This means that organisms do not differ in kind, only in degrees of relatedness.

If I understand you correctly, a higher category is an “arbitrary convention” because there are others groups that could be emphasized but are not.

Nonetheless, the groups that are named represent actual groups of features, e.g., “warm-blooded.” Therefore, the category “mammalia,” for example, is not completely conventional - it has some basis in nature.

Wouldn’t it be more accurate to say that, e.g., “mammalia” is a natural category (i.e., a category based in natural fact), but that we emphasize it to the exclusion of other, presently nameless cateogries is a matter of arbitrary convention?

Comment #25719

Posted by Mike Kelly on April 19, 2005 11:45 AM (e) (s)

David Heddle wrote:

Yeah Steve, jokes about having sex with someone’s mother, why that is the hallmark of humor. Bravo.

Surely everybody’s mother has had sex with someone?

*=150160

Comment #25721

Posted by Sir_Toejam on April 19, 2005 12:01 PM (e) (s)

“Yeah Steve, jokes about having sex with someone’s mother, why that is the hallmark of humor. Bravo.”

well, I’m not sure it rises to the level of “clever beyond measure” but it did seem an appropriate level of retort.

The level of sniping exhibited by Heddle deserves at least disemvowelment, if not banishment to the BW.

Comment #25722

Posted by Sir_Toejam on April 19, 2005 12:03 PM (e) (s)

“I tried to mate with a sponge once.  Does that qualify for cross-phyla?”

did you manage to produce viable offspring?

uh, the thought of such offspring just put me right off my breakfast.

ugh.

Comment #25725

Posted by RPM on April 19, 2005 12:10 PM (e) (s)

I think the main point in this discussion is that all classifications above the species level (and some species classifications as well) are the products of human subjectivity.  The tree topology is constrained by actual data, and somewhat immune to subjective interpretation.  Topology is, however, dependent on the dataset used to construct the tree as well as the algorithm applied to the data.

The process becomes subjective when we try to deliniate what is a phylum, class, order, family, etc.  We can objectively define species using certain criteria (i.e., using the biological species concept, any populations that can potential interbreed are defined as a species), but what is considered an order in one clade may be called a genus in another clade.  For instance, mammals are considered a class, but the equivalent amount of evolutionary divergence in an insect clade may only be considered a genus.  That is probably because we come from an anthropocentric perspective and tend to oversplit groups that are similar to us and clump together taxa that are distantly related to us.

In conclusion, tree topology (including monophyletic clades) and species level definitions (for the most part) can be objectively defined.  Hierarchical classifications (what we call things) are extremely subjective.

My biggest problem is with paraphyletic taxa that persists in both the literature and general discussion.  As was mentioned earlier, if we require all taxa to be monophyletic, then humans (and all other mammals) would be considered “fishes.”  This problem can be observed in almost all taxa.

Comment #25726

Posted by Sir_Toejam on April 19, 2005 12:17 PM (e) (s)

“Morphological, genetic, and molecular analyses don’t particularly agree with one another as to where such joints may really lie. But perhaps that’s not what you’re asking?”

maybe not what Finley was asking, but I want to ask a related question.

It’s been a while (er, about 15 years, in fact) since I examined the state of cladistics using morphology vs. genetics.  There was a rising argument at Berkeley when I was there as to which would be more efficacious, and no little debate over what the divergence between genetic relatedness and apparent morphology meant in the most notable cases.

Can anyone point to a decent summary of the current state of affairs in this matter?  Or perhaps summarize it here (at least in the most general terms)?

cheers

Comment #25729

Posted by P. Mihalakos on April 19, 2005 12:33 PM (e) (s)

This is a great thread, partly because the bulk of the posts aren’t dedicated to merely squashing ID propaganda.

To our house zoologists, geneticists, etc.: 
If you have the time and are familiar with Brian Goodwin’s research, it would be great to know what you think of the usefulness of his theoretical emphasis on  organisms as developing and dynamic systems. 

I’m thinking, particularly, of the research summarized in Form and Transformation : Generative and Relational Principles in Biology.

P.S.
Mr. Finley, if you are interested in the conceptual structure of taxonomy, the first portion of the book is dedicated entirely to that subject.  I would be curious to know if it does not satisfy some of your discomfort with the way biologists define (or avoid) the concept of a natural kind.

Comment #25730

Posted by Steve Reuland on April 19, 2005 12:35 PM (e) (s)

Michael Finely:

What you say is basically right.  “Mammals” is not an incorrect grouping, it’s just one of a huge number of equally correct groupings.  The reason we recognize “mammals”, and not other groupings, is a matter of convention.  While mammals are defined by a suite of unique characters (synapomorphies), there is no reason why that particular suite of characters, and not some other, had to be what defines “mammals”.  “Mammals” could have been defined in such a way as to exclude the monotremes, for example, and it would be no less correct. 

See also RPM’s commments; he explains it quite well.

Comment #25736

Posted by Henry J on April 19, 2005 12:49 PM (e) (s)

I thought the question wasn’t so much which groupings  or categories were used, as what “ranks” are assigned to the groups. Esp. when the assigned ranks are misleading, as they are with the various vertebrate classes. Are birds a class, or are they a suborder of crocodilia (their nearest living relatives)?

Comment #25748

Posted by bill on April 19, 2005 01:26 PM (e) (s)

My biggest problem is with paraphyletic taxa that persists in both the literature and general discussion.  As was mentioned earlier, if we require all taxa to be monophyletic, then humans (and all other mammals) would be considered “fishes.”

That certainly explains the blind date I had as a sophomore.

Comment #25750

Posted by Michael Finley on April 19, 2005 01:30 PM (e) (s)

P. Mihalakos,

Thanks for the reference; the topic interestes me more than a little, so I’ll be sure and give a look.

My discomfort stems from the general way I view definition by division. I first became interested in the concept, not in a science class, but in a course on Aristotle’s Organon (i.e., the logical treatises). For Aristotle, the definition of a species involves a formal division from the highest categories, summa genera, to the lowest species. Thus, to say what, e.g., a dog is, is to provide a list of specific differences that differentiate the category of substance (animal is high-level species of the category of substance; “genus” and “species” being relative terms that are applicable to the entire scale of divisions, i.e., a species is a genus for the next species and so on.). (Aristotle applies this method in biology and derives the original taxonomic categories; much of Aristotle’s general framework has been adopted by modern biology.)

Thus, I am inclined to view taxa as representing formal features of individuals. Indeed, to even talk about categories beyond individuals, e.g., “dog” as opposed to “that” (with a pointing gesture) seems to involve the recognition of a formal category that is not mere convention. The taxa, it seems to me, are increasingly general orders of these categories.

(By the way, lest someone think my comments drag this discussion into one about ID, questions concerning form and teleology are independent of questions concerning the origin of form and teleology. The latter involves ID, not the former.)

Comment #25756

Posted by P. Mihalakos on April 19, 2005 02:05 PM (e) (s)

M. Finley wrote:

“Is there any objective reason to prefer one group of features to another?”

Such a preference would be made on objectively practical considerations, and those depend entirely on what you were investigating.  For instance, a developmental biologist vs. a paleontologist. 

Again, the philosophical implications are explicitly taken up by Gerry Webster in the Goodwin book I referenced earlier.  I will look forward to your opinion (or that of others) when it is convenient.

Comment #25757

Posted by Steve Reuland on April 19, 2005 02:07 PM (e) (s)

Biologists simply don’t accept Aristotaelian formalism.  You can come up with a list of differences that separate a category of animal, like “dog, but it’s hard to see how this list is anything but arbitrary.  It’s fairly easy to do this and later find out that many dog-like animals would be excluded, or find that many non-dog-like animals would be included.  (Should hyenas be considered dogs?  You’d be surprised what they’re really related to.)  Where you draw the line between dog and non-dog is purely subjective.

One lesson that you learn from biology is that there are always more critters than you ever thought there were.  Formal and distinct categories make sense to the average person because they’re only familiar with a tiny handful of animals anyway.  But when you get out into nature and see zillions of different species, you realize that a lot of groups that once seemed distinct tend to blend into each other.  This is especially true when you take fossils into consideration.

Comment #25758

Posted by Great White Wonder on April 19, 2005 02:11 PM (e) (s)

“I tried to mate with a sponge once.  Does that qualify for cross-phyla?”

Bill O’Reilly proposed something similar as I recall, except with a falafel.

http://www.boingboing.net/2004/10/14/bill_oreillys_allege.html

Comment #25762

Posted by Sir_Toejam on April 19, 2005 02:39 PM (e) (s)

you’d almost have to qualify a falafel as a “polyphyletic” organism, wouldn’t you?

Comment #25780

Posted by Michael Finley on April 19, 2005 03:22 PM (e) (s)

I hope to locate a copy of Form and Transformation : Generative and Relational Principles in Biology and continue this discussion accordingly. But before I do, I have a couple of prelimiary questions/suggestions.

Steve Reuland wrote:

One lesson that you learn from biology is that there are always more critters than you ever thought there were. Formal and distinct categories make sense to the average person because they’re only familiar with a tiny handful of animals anyway. But when you get out into nature and see zillions of different species, you realize that a lot of groups that once seemed distinct tend to blend into each other.

I do not immediately see why this is an objection to classical formalism. All that is needed are more and more formal categories.

Isn’t there room for a merger of classical formalism and common descent? Are the two necessarily antithetical to each other? One concern might be that classical formalism requires immutable species, which are obviously incompatible with common descent. But that is not the case. The concept of form is sophisticated enough to be adapted to changes in form (i.e., changes in the overall form of an organism).

It seems to me that the very notion of biological change involves the idea of form, i.e., a change from what to what? A brand of formalism together with a certain brand of teleology has a tremendous amount of explanatory power. And if it could be made consistent with a fully naturalistic account of evolution, is there any reason not to give it a look? (Too bad I already have a dissertation topic; this sounds like a good one).

Comment #25785

Posted by P. Mihalakos on April 19, 2005 03:43 PM (e) (s)

Again, great discussion.

M. Finley wrote:

I do not immediately see why this is an objection to classical formalism. All that is needed are more and more formal categories.

Yes, but imagine the problem if the number of categories grew to parity with the number of individual species.  It would defeat any practical application.

Comment #25797

Posted by Michael Finley on April 19, 2005 04:31 PM (e) (s)

P. Mihalakos wrote:

Yes, but imagine the problem if the number of categories grew to parity with the number of individual species. It would defeat any practical application.

It would indeed, but I don’t think that there is a real concern of that happening. Consider two species, A and B, that are very similar to each other (say, because they share most of their common ancestors). Their definitions would include most of the same categories. The same can be said of higher taxa that are very similar to each other. Therefore, a large number of distinct species can be definied by a lesser (significantly less) number of categories. True, there will be a specific difference for every species, but it’s no more difficult to enumerate these than it is to enumerate the species themselves, since the species would be ultimately definied (i.e., differentiated from everything else) by their specific differences.

Comment #25799

Posted by Sir_Toejam on April 19, 2005 04:38 PM (e) (s)

uh, before this continues into yet another Finley led philosophical treatise, could someone who knows cladistics please throw me a summary reference as per my earlier request?

thanks

Comment #25800

Posted by Michael Finley on April 19, 2005 04:44 PM (e) (s)

…before this continues into yet another Finley led philosophical treatise….

I don’t mean to hijack every thread I participate in and send it to 300+ posts, so if author of this thread would rather see the direction I am trying to take us in moved to After the Bar Closes, I am content with that.

Comment #25801

Posted by Scott Davidson on April 19, 2005 04:47 PM (e) (s)

Michael Finley wrote:
Their definitions would include most of the same categories. The same can be said of higher taxa that are very similar to each other.

Doesn’t this still leave you with the problem that the higher classifications are still arbitrarily based on some perceived level of similarity?  Using the system that you propose you still need to decide what the criteria for how similar the species are within each classification, and that decision is still going to be fairly arbitrary isn’t it?

Comment #25803

Posted by Scott Davidson on April 19, 2005 04:51 PM (e) (s)

Michael Finley wrote:
Their definitions would include most of the same categories. The same can be said of higher taxa that are very similar to each other.

Doesn’t this still leave you with the problem that the higher order classifications are based on some perceived level of similarity?  You still need to decide what the criteria for how similar the species are within each classification, and that decision is still going to be fairly arbitrary isn’t it?

Comment #25804

Posted by Sir_Toejam on April 19, 2005 04:53 PM (e) (s)

I’d just like to tip my hat to Mr. Finley for acknowledging the thread’s author.

I should clarify and say i have no real objections to continuing in a more philosophical mode, but I just am personally hoping someone will see my request before the thread gets too large.

cheers

Comment #25805

Posted by Flint on April 19, 2005 04:56 PM (e) (s)

Formalistic approaches don’t strike me as particularly useful. Perhaps Darwin’s greatest breakthrough was in his rejection of the notion of a species as an Ideal Form, to which all its members were approximations, in favor of the notion of a population of interbreeding individuals. What’s considered a species today is a population of individuals that (a) breeds among itself; and (b) does NOT interbreed with any other population of interbreeding individuals, whether or not two populations are otherwise identical. The fact that they do not interbreed is what makes them separate species, although forced breeding produces normal fertile individuals.

Reproductive isolation by any mechanism (color, scent, mating ritual, call, geographic isolation) is a difficult characteristic to formalize, because it is dynamic. WHILE two populations do not interbreed, they are different species. WHY they don’t interbreed is irrelevant. However, if the river changes course and the populations regain access to one another and begin interbreeding as a result, then they once again become the same species — even though not a single individual has changed at all!

Formalistic definitions are an attempt to draw lines on a continuum. These lines are so close to arbitrary as to make the formalisms unhelpful. The distinction between similar species is entirely dynamic: if there is no gene flow between populations (even if their *could* be), then the populations are generally in the process of becoming increasingly different. The question of how different is “different enough” to qualify for a formal distinction (perhaps a new name?) probably isn’t worth answering in most situations.

Comment #25808

Posted by Steve Reuland on April 19, 2005 05:03 PM (e) (s)

Michael Finely wrote:

One concern might be that classical formalism requires immutable species, which are obviously incompatible with common descent. But that is not the case. The concept of form is sophisticated enough to be adapted to changes in form (i.e., changes in the overall form of an organism).

But how does one determine when something has gone from one form to the next?  Let’s say that we consider the “species” to be the penultimate “form”.  (As stated earlier, higher taxonomic ranks are defined arbitrarily.)  When a population divides and later results in two separate species, at what exact point in time is the new “form” acheived?  What particular event resulted in this shift?  Is there no intermediate stage when something was half of one form and half of the next?  Keep in mind that speciation, according to the biological species concept, doesn’t actually require any change at all.  All it takes is for an intemediate population to die out, leaving two extremes reproductively isolated.

It seems to me that the very notion of biological change involves the idea of form, i.e., a change from what to what?

Biological evolution is defined as the change in allele frequencies in a population over time.  But an allele itself doesn’t make a “form”.  Rather, species are defined by the sum total of all of their alleles.  And allele frequencies change within species constantly.  It’s not clear therefore where “form” fits into all of this.  If what we recognize as distinct organisms are the result of a very long process of change along a fine continuum, and not radical shifts in form or type, then how do we apply the concept of form? 

A brand of formalism together with a certain brand of teleology has a tremendous amount of explanatory power.

If you say so.  I will contend that formalism was ditched precisely because it cannot explain biological diversity; any attempt at cramming organisms into distinct forms fails as soon as new, unanticipated intermediate forms are found (which happens all the time).  The phylogenetic view has won out for a reason. 

As for teleology, which is a very abused term, biologists look at living things as explicitly teleological.  The telos of living things is survival and reproduction, and this is how the living world is understood.  That was Darwin’s great achievement — showing that living things not only have a telos, but identifying it and explaining why it exists.  What is not considered teleological, however, is the process of change.  Therein lies much of the confusion.

Comment #25811

Posted by Flint on April 19, 2005 05:14 PM (e) (s)

Sir_Toejam:

You might start here. My general take on cladistics is that it doesn’t use any “higher” organization than the species, and perhaps the organism. It regards all organisms as individuals whose parent(s) are individuals. Individuals become increasingly dissimilar the further back their common ancestor. Clades today (I read somewhere) are considered most reliably reconstructed using molecular methods, and morphological similarities are considered suspect.

The major problem with cladistics is, knowing there had to be a family tree