Down with phyla!

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Are 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:

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:

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 less than 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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Nick Matzke has a very good essay on the artificiality of phyletic classifications, and the misuse of the Cambrian explosion by creationists. I'd just like to add to it by pointing out that SJ Gould actually favored the distinction Matzke and his ... Read More

146 Comments

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

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.

Thankyou Mr. Matzke

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.

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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)

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.

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.

(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”.

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.

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

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

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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.

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.

We’ll leave that to the wolphins.

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.

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.

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!)

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

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.

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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

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?

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.

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.

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.

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.

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.

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

Of course, the debate over what is a species is philosophical in nature.

Careful, RPM. Comments like that can call down the thunder around here.

Re “Which is better for phylogeny, genes or morphology? The answer is…wait for it…both.”

Makes sense to me. :) Where data is lacking for one of them, use the other. Where both work, do both and check for disagreement between them.

Re “Is “A and B are the same species” just a way to say “A and B are, in some way, CLOSE”?”

Sounds like it sums it up to me. If the thing isn’t transitive, then it’s not technically a “relation”.

I reckon that’d be “close” in the “space” of dna differences, which might have as many “dimensions” as there are base pairs. If that makes sense.

I conclude that the concept of “fuzzy logic” applies here. :)

Henry

I reckon that’d be “close” in the “space” of dna differences, which might have as many “dimensions” as there are base pairs. If that makes sense.

Well, this is just Z4^3,000,000,000 - not that hard to imagine >:-)

RPM Wrote:

For a good description of species concepts, see Coyne and Orr’s book Speciation. They provide a list of the most commonly used species concepts in the appendix. This should clear up much of the confusion. Of course, the debate over what is a species is philosophical in nature.

John Wilkins, one of our contributors, wrote his PhD thesis on species concepts. I keep waiting for him to make his appearance, but he probably figures we’re too hopelessly confused to warrant wasting his time. :)

M. Finley quoting Dr. Hurlbut Wrote:

… the gene cdx2 is essential for embryogenesis. This gene is expressed immediately after compaction around the 16 to 32-cell stage and is crucial for the differentiation of the trophectoderm, the outer layer of cells that seals the embryo and controls the flow of water and ions into the inner cavity of the cell.

This sounds like a very typical statement, yes. Sounds like cool research. But I don’t think it evinces what you suggest. That is, if you are in fact suggesting that this research provides an example of a “one-to-one” correspondence between a gene and a trait a la “genes as static blueprints for body plans.”

First, let’s keep in mind that this research is calling attention to both the gene’s influence on the cell walls of individual cells, and those same cells’ subsequent differential effects on the induction of a specific kind of germ tissue. Once those cells have differentiated, a whole new cascade of gene-directed products will induce even further differentiation, which will induce additional morphological transformations (perhaps neuroblast segregation, though I’m guessing, because I’m not familiar with this study) and eventually you will begin to notice the embryological precursors of mature nervous tissue. But, where is the one-to-one relationship? Control is not only distributed between different genes at different times, but between different nested levels of morphology, i.e. organelle to cell back to organelle to cell to tissue to tissue, etc. The process is highly iterative.

No, even in this example, it makes much more sense to think of embryogenesis as the interaction of different morphogenetic fields, a hierarchical process, rather than the end result of a simple genetic blueprint. What’s more, as a philosopher you may be interested to know that, to some theoretical biologists who are interested in the mathematical modeling of biological complexity, this suggests that morphogenetic fields may have emergent properties independent of the particular molecular constituents that give rise to the behavior of the field, i.e. they may lead to generic forms. (!!) Hmm … are you getting any hints as to the possible implications such an idea may hold for a philosophical treatment of taxonomy?

You might make a case for more linear relationships among simpler organisms, if that is what you are looking for, but I would wonder what the point would be. Such a gene would still only make functional sense in context of the developmental trajectory of the organism in which it is embedded, i.e. the activity of countless other genes, genes that may be moving around recombining with other genes at different points in development, genes giving rise to products which bind directly to other genes (which may even promote beneficial mutation!), genes that are activated by metabolites released by nearby conspecifics, and the list goes on, believe me.

Next, I predict you might wonder … what if you zeroed in on the very first intracellular genetic products in this particular example? Can we at least assert that this gene provides the “blueprint” for cell wall assembly? Only partially, is the answer. Blueprint metaphors aside, in biology a “partial” role can also be a crucial role. And one feature that does make genes so special is that they do, in fact, specify an enormous range of initial conditions both in context of single cells and embryogenesis as a whole. And we all know that one definitive feature of complex systems is their astounding sensitivity to initial conditions.

Since you asked, I will admit that I don’t know if you are beating a dead horse, but let me repeat that no one ever said that genes weren’t absolutely necessary. In terms of initial conditions, cdx2 appears to provide some crucial developmental resource or set of resources, perhaps in the form of a surface protein that helps stabilize the function of the cell wall. Again, I am not familiar with the details of this example, but that would be typical of this kind of research. So, again, the gene is necessary, but not sufficient, to specify a range of possible modifications that contribute to the emergence of form at a higher level, i.e. the cell walls that influence ion transport and bulk water movement across the cell boundary, which, in turn, influences cell adhesion in some way.

Yet, even at this level the gene is “hijacking” a lot of “free” order, as it were, and we shouldn’t take any order for granted. In fact, the cell wall itself forms mostly spontaneously into a typical configuration reflecting an inevitable shift to lowest energy status, and this is due to the fact that lipids are polar molecules, and thus they are prone to interact with water in a very reliable way, viz. by hiding their hydrophobic ends and exposing their hydrophilic ones. You can witness the same sort of self-assembly by dropping olive oil into vinegar.

I realize that I may not have convinced you that control is not nearly so gene-centered as is commonly repeated in the press. If I haven’t at this point, then I give up. Again, if you are still interested, I can point the way to some relevant literature.

Notwithstanding the fact that the jury is very much “still out” on the usefulness of a theory like morphogenetic fields, I must ask you in all humility at this point in our exchange, Mr. Finley: how can “intelligent design” possibly satisfy your intellect and curiosity when it is compared to the richness of real theorizing, real experimentation, real science? Do you see how absurd it is NOT to derive deep meaning from the study of biological systems and their evolution?

“Mr. Finley: how can “intelligent design” possibly satisfy your intellect and curiosity when it is compared to the richness of real theorizing, real experimentation, real science? Do you see how absurd it is NOT to derive deep meaning from the study of biological systems and their evolution?”

ahh, if only it were as simple as satisfying intellectual curiosity. if that was the case, then there wouldn’t be any argument to sustain ID to begin with, would there.

folks don’t support ID because it satisfies intellectual curiosity. they support it because it supports their religious beliefs. so I guess one could say it satisfies “emotional curiosity” of a sort.

I have to applaud your effort though, it was very eloquent.

cheers

Yes, STJ, you are right.

I suppose my vision of science, after all, is pretty romantic. But I sense something occasionally in some proponents of ID or even New Age “science” that makes me want to just try my very best to make a human connection, even if for a split second, you know? Amidst all the rancor, to share an experience of the sublime, etc., whose creative/evolved status may be in dispute, but whose beauty is not.

My own sense of “spirituality” I suppose.

Oh, and dinnae give up on the ngo just yet. Working folk have to tackle these sorts of ideas step-by-step. There is much to talk about.

“I suppose my vision of science, after all, is pretty romantic. But I sense something occasionally in some proponents of ID or even New Age “science” that makes me want to just try my very best to make a human connection, even if for a split second, you know? Amidst all the rancor, to share an experience of the sublime, etc., whose creative/evolved status may be in dispute, but whose beauty is not. “

no, no. you are right. I’m just a bit too cynical perhaps. I don’t know of anyone who has stayed in science that doesn’t at least share a part of what you are saying.

P. Mihalakos Wrote:

Finley: how can “intelligent design” possibly satisfy your intellect and curiosity when it is compared to the richness of real theorizing, real experimentation, real science? Do you see how absurd it is NOT to derive deep meaning from the study of biological systems and their evolution?

STJ Wrote:

Folks don’t support ID because it satisfies intellectual curiosity. They support it because it supports their religious beliefs.

A few points: (1) I view the issues we’ve been discussing as independent of those concerning origins. As I said before, I can imagine a version of formalism and teleology that are consistent with limited naturalism (see No.3 below) and Darwinian evolution. And while I can take or leave ID as advocated by the Discovery Institute or more traditional forms of creationism, I have strong philosophical commitments to formalism and teleology that have nothing to do with ID. (2) My religious beliefs, e.g., the belief in a creator-god, do not require “support”; they ground themselves (see the various writings of Alvin Plantinga on the subject, in particular Warrant and Proper Function). My interest in ID is related to those beliefs, but the relation is given by the Scholastic dictum fides quaerens intellectum (“faith seeking understanding”). (3) That said, my religious beliefs are perfectly consistent with Darwinian evolution, indeed, with limited naturalism, i.e., the belief that from its inception the universe has operated according to natural causes (with the obvious exception of miracles; one cannot be a Christian without them, e.g., the resurrection). Some of my friends and relatives view Darwinism as contrary to Christianity. For the life of me I can’t make the connection (there is no valid argument that infers atheism from the truth of Darwinism). I believe in a creator-god, but “creation” could consist of the creation of the cosmos. In which case, as you suggest, we can marvel at the causes of nature as divine instruments. (4) Thus, Darwinism may be my final resting place, but as I am new to the discussion, I am obligated to give the alternatives a fair shake.

Thank you for your help. I think I have a much better grasp of the interplay between genes and environmental conditions.

P. Mihalakos Wrote:

What’s more, as a philosopher you may be interested to know that, to some theoretical biologists who are interested in the mathematical modeling of biological complexity, this suggests that morphogenetic fields may have emergent properties independent of the particular molecular constituents that give rise to the behavior of the field, i.e. they may lead to generic forms. (!!) Hmm … are you getting any hints as to the possible implications such an idea may hold for a philosophical treatment of taxonomy?

Very interesting. I shall have to deepen my understanding of genetics. Stepping back from the details for a moment, I tend to view form as the emergent structure of a combination of parts. In this sense it is synonymous with shape, broadly construed (this, incidentally, is the literal meaning of morphe, one of Plato’s and Aristotle’s words for “form”). A simple example is a bowl - the bowl has a structure, a form, that enables certain functions that cannot be reduced to those of its parts. In this regard, an organism is a fantastically complex bowl.

Underlying this notion of complex forms, is that each simple constituent has a form that consists of its possible combinations with other simple constituents (cf. Wittgenstein’s Tractatus). Eliminative materialism takes it for granted that bits of nature can combine with other bits of nature to make trees, dogs, and neutron stars. The philosophically interesting question is, “How are they able to do that?” It seems to me that this question has to be answered by a doctrine of form.

Mr. Finley,

I understand that you have not officially tossed your hat into the ID ring. I’m sorry for oversimplifying your motives. My goal was to share an appreciation of how complex form (behavioral or morphological) can arise from the simple interactions of simple components, be they biological or otherwise.

Here is why your curiosity about the source of form and the rational basis of formal taxonomy is important, as I see it.

Exhibit A:

Evolving Apeman Wrote:

Oh BTW Flint, what selective advantage is there to the “golden rule” within the human evolutionary framework? Why do I have to obey the “golden rule”? Whether I do or don’t is simply a matter of my genes and environment. Their is no scientific basis for morality. As a Darwinian Fundamentalist you should know better.

Do you see what I mean? Why it is so important not to have misplaced assumptions re. the ultimate directing power of genes? Because it has implications for the generative and directing power of any single source of information.

After our discussion (yours and mine) it is patently obvious to me why Evolving Apeman is wrong. Here he “projects” his own anxiety re. a meaningless amoral universe onto (what he believes is) a typical stance held by “Darwinians.” In fact, it is an atypical stance among all scientists, and certainly no biologist worth her salt would make such an assumption.

He quite literally cannot imagine how or why morality would have any validity outside the framework of a single controlling source of intelligence. God, for him, at least as represented in his posts, functions as a kind of ultimate guarantor of sense, a functional placeholder, very much like the number zero. Therefore, because he wrongly views genes in much the same way, i.e. as putative “controllers” of biological destiny, he cannot help but frame them as a threat (by formal similarity) to his mistaken characteriazation of the message of Christ.

And hence, a mistakenly simplistic view of “determinism” is the source of much of his anger and frustration.

Eliminative materialism takes it for granted that bits of nature can combine with other bits of nature to make trees, dogs, and neutron stars. The philosophically interesting question is, “How are they able to do that?” It seems to me that this question has to be answered by a doctrine of form.

Interesting. It seems to me that this question has to be answered through an analysis of process. Forms emerge from process the way faces in clouds emerge from process of wind, humidity, temperature, etc. So the formalist looks at the cloud and sees a Form (“hey look, there’s a face!”) and the methodologist looks at the cloud and sees the interplay of chaotic meteorological phenomena.

People, like any other living organism, are an epiphenomenon of a process that throws off complex instances like a kaleidoscope throws of complex images. And like the kaleidoscope images, people are only an outcropping of what is potential in the morphospace being “explored” by biological processes in a drunkard’s-walk contingent manner. The probability of any particular organismal form is infinitesimal, the number of possible forms infinite, and the process generating them will never stumble through this neighborhood again. Enjoy life while you have it.

P. Mihalakos Wrote:

I’m sorry for oversimplifying your motives.

Certainly no need to apologize. The bit about my motives was more in answer to TSJ’s remarks than yours. I think religious questions find their way into these discussions for too easily and often. I merely wanted to put my religious cards on the table, and then to point out that they belong to a different game.

He quite literally cannot imagine how or why morality would have any validity outside the framework of a single controlling source of intelligence. God, for him, at least as represented in his posts, functions as a kind of ultimate guarantor of sense, a functional placeholder, very much like the number zero. Therefore, because he wrongly views genes in much the same way, i.e. as putative “controllers” of biological destiny, he cannot help but frame them as a threat (by formal similarity) to his mistaken characteriazation of the message of Christ.

Theoretical ethics is very hard (though I’m not an ethicist by any stretch; philosophy of language and metaphysics are my cup of tea). Yet those of us who derive our ethical beliefs from revelation are not too troubled by its difficulty because we, quite simply, have no use for it (i.e., what do I need ethics for when I have the New Testament). The best systems of secular ethics that I’m familiar with are the natural ethics of Plato and Aristotle. These, however, were roundly rejected by the time of the Renaissance, and with the passing of formalism and teleology have never resurfaced.

I can sympathize with Mr. Apeman. In Darwin’s Dangerous Idea, for example, Dennett takes seriously the charge that Darwinism has let “the worst possible cat out of the bag: nihilism” (p.18) He spends the latter part of the book arguing against that position. It is my own opinion that, though not necessarily incompatible, morality (grounded in oughtness) and thorough-going naturalism are uneasy companions.

Be that as it may, it certaninly has nothing to do with an imagined dichotomy between special creation and Darwinian evolution (or any other version of “creationism”).

What our discussion has made apparent to me is that, if formalism and teleology (not to be confused with Teleology, i.e., the working through of a grand final cause in nature) are to be incorporated into modern biology, the physical bearers of form that contribute to the overall form of an organism will have to include environmental causes as well. It will be an interesting investigation if I ever find the time (I’m merely in the proposal stage of my dissertation).

*This is my third attempt to post, it’ll probably show up three times as soon as I post it again.

P. Mihalakos Wrote:

I’m sorry for oversimplifying your motives.

Certainly no need to apologize. The bit about my motives was more in answer to TSJ’s remarks than yours. I think religious questions find their way into these discussions for too easily and often. I merely wanted to put my religious cards on the table, and then to point out that they belong to a different game.

He quite literally cannot imagine how or why morality would have any validity outside the framework of a single controlling source of intelligence. God, for him, at least as represented in his posts, functions as a kind of ultimate guarantor of sense, a functional placeholder, very much like the number zero. Therefore, because he wrongly views genes in much the same way, i.e. as putative “controllers” of biological destiny, he cannot help but frame them as a threat (by formal similarity) to his mistaken characteriazation of the message of Christ.

Theoretical ethics is very hard (though I’m not an ethicist by any stretch; philosophy of language and metaphysics are my cup of tea). Yet those of us who derive our ethical beliefs from revelation are not too troubled by its difficulty because we, quite simply, have no use for it (i.e., what do I need ethics for when I have the New Testament). The best systems of secular ethics that I’m familiar with are the natural ethics of Plato and Aristotle. These, however, were roundly rejected by the time of the Renaissance, and with the passing of formalism and teleology have never resurfaced.

I can sympathize with Mr. Apeman. In Darwin’s Dangerous Idea, for example, Dennett takes seriously the charge that Darwinism has let “the worst possible cat out of the bag: nihilism” (p.18) He spends the latter part of the book arguing against that position. It is my own opinion that, though not necessarily incompatible, morality (grounded in oughtness) and thorough-going naturalism are uneasy companions.

Be that as it may, it certaninly has nothing to do with an imagined dichotomy between special creation and Darwinian evolution (or any other version of “creationism”).

What our discussion has made apparent to me is that, if formalism and teleology (not to be confused with Teleology, i.e., the working through of a grand final cause in nature) are to be incorporated into modern biology, the physical bearers of form that contribute to the overall form of an organism will have to include environmental causes as well. It will be an interesting investigation if I ever find the time (I’m merely in the proposal stage of my dissertation).

It is my own opinion that, though not necessarily incompatible, morality (grounded in oughtness) and thorough-going naturalism are uneasy companions.

After some pondering, I’m at a loss as to why you might have this opinion, or what the grounds for unease might possibly be. I certainly see nothing in the real world that might work toward or even be supportive of antisocial behavior.

Perhaps the problem is that I see morality from a game theory perspective – social behaviors leading to the greatest good for the greatest number consistent with minimally acceptable treatment of everyone. I suppose as an intellectual exercise, I might consider morality to be a list of mandatory and prohibited behaviors drawn up by someone else who claims magical inspiration, but I admit I find that approach unfulfilling.

Conversely, the notion that morality is somehow more consistent or meaningful if reality is rejected strikes me as perverse. Surely something is wrong with ANY position that rejects reality.

Hmmm, that’s very interesting, Flint. If the forms are generic, however, it may mean that different kaleidoscopes, viz. different physical substrates, will inevitably “throw off” many of the same morphologies. IF true, it would mean that there are, in fact, natural constrains on the plasticity of form, both in context of phylogeny and ontogeny. Modularity certainly becomes fascinating in this context.

Also, if the “forms” in question are morphogenetic fields, then there is no practical distinction between process and form. There would only be practical distinctions between the levels of interaction, their scales, parameters, etc.

Flint,

Let me stage set a little before attempting to spell out the unease.

From what I can tell (and let me repeat that I have a cursory grasp of theoretical ethics), the problem of ethics is what Hume referred to as the “is/ought” distinction, and what Weber recast as the “fact/value” distinction, i.e., from the way things are, it is impossible to conclude how they should be (the “should” here denoting a moral imperative).

Now, this problem confronts religious and secular ethical systems alike. For the theist who grounds ethics in the command of God, the is/ought reply is “Why should I obey the command of God.” And with each subsequent answer the “why” question can be asked again (as you can see, the is/ought question is an ethical gloss on the regress of “whys” known by every three-year-old).

The problem could be removed if the distinction between “is” and “ought” could be collapsed. Teleology gets us close to that goal. Plato, through a lengthy argument, is able to argue that happiness requires morality (virtue). Likewise, the Christian telelogical answer states that man is constituted in such a way that obedience to the revealed truth is the only path to complete happiness. And while the is/ought challenge can still be issued - “Why be happy” - it has been robbed of most of its force, i.e., that we should all want to be happy is self-evident.

It seems to me that complete naturalism, as it excludes teleological explanations, has no good answer for the ethical question “why.” I could be wrong, but that’s my take.

Flint Wrote:

It seems to me that this question has to be answered through an analysis of process. Forms emerge from process the way faces in clouds emerge from process of wind, humidity, temperature, etc. So the formalist looks at the cloud and sees a Form (“hey look, there’s a face!”) and the methodologist looks at the cloud and sees the interplay of chaotic meteorological phenomena.

I would first point out that the presence of form does not require the recognition of form by an intelligence. Whether anyone is around to notice it or not, a bowl is able to hold liquids. This is an emergent formal property of the bowl’s molecules.

Alot rests on what is meant by “emerge” here. I would deny that forms can be reduced to process, or even that forms are the result of (ex nihilo, so to speak) process. Forms must exist in some sense (i.e., potentially) before they emerge through a process. Thus, the emergence of a form is the making actual of a potential or pre-existing form. This sounds rather mysterious until we bring it back to mundane contexts: e.g., the structure of the bowl is a emergent formal possibility of the molecules that constitute it. It exists as a possibility even if the molecules have a different arrangement.

Finley:

I guess I lack your background in this material. I can understand (and even agree) with Plato that happiness requires morality. But why does morality need to be revealed truth, rather than social convention? All that seems to me to be required is that certain parameters of behavior be acceptable within the social milieu as “good” or “right” behaviors. WHAT those behaviors are is probably constrained within much wider boundaries, beyond which society itself is impossible.

Ironically, I read that what upsets so many here about Apeman and others like him is that they are profoundly dishonest, and honesty is tacitally regarded as a moral imperative without which science itself would be impossible. Ultimately, we are upset with these people not because they are ignorant or arrogant, but because they are immoral in a way that threatens ANY social order.

I think people understand this at a deep level that requires no explicit recipes, scriptures, or received wisdom. Daily experience with life from birth on make it clear that honesty is a requisite for happiness, and those who cannot be honest, cannot be happy. For the scientifically oriented, honesty largely lies in the correct apprehension of the objective universe; the closer we can come, the happier we are. Knowingly misrepresenting reality is a sin. For many of us, one of the worst.

Finley:

This sounds rather mysterious until we bring it back to mundane contexts: e.g., the structure of the bowl is a emergent formal possibility of the molecules that constitute it. It exists as a possibility even if the molecules have a different arrangement.

Perhaps it’s this kind of stuff that gives philosphy a bad name. I see a process happening. The process produces material instantiations, which are within the capability of the process to generate. Now, you might look at one of these results and say “It has form; a particular shape.” I doubt anyone would disagree. But to say that the particular shape “had to pre-exist” seems meaningless. So I watch some snails laying tracks of slime across a leaf. Those tracks are a “form” in your sense, but why did they need to pre-exist? Yes, I agree that the potential for that particular pattern of trails existed. But it’s equally true that the potential of any chemically possible ordering of molecules “exists” in the sense that it’s not impossible.

But as I said earlier, maybe it’s just a difference of background. My job is writing computer code, which simply controls a process designed to have specific side effects. My education is in administration, which leads me (for example) to see the court system as a mechanism for conflict resolution. The decisions courts make, by contrast, are the emergent properties. What matters is HOW the decisions are made, and not what they are. “Perfect” decisions are undesirable if their recipients (the public) do not accept them.

Flint,

At the end of the day, what we are really talking about is possibility. When we call something a “real possibility,” what exactly are we talking about? To say, for example, that different arrangements are real possibilities of molecules, what is the ontological status of these arrangements? These questions are paradigmatic metaphysical questions.

We want to say that a particular arrangement (i.e., a shape, a form) exists as a possibility, but what kind of existence is this? This is a hard question. Possibilities certainly exist in some sense and do not exist in another sense. Defining these senses is difficult work.

One line of approach can be illustrated by considering two puzzle pieces that fit together. Suppose they are not presently combined. What does it mean to say that they could be combined, that their combination is possible? Perhaps it means that their combination, the shape or form of the combined whole, is “written into” the shape of the pieces. Therefore, by closely examining one piece, it can be seen to fit with another piece of a particular shape. To say, then, that one piece could combine with another, is to say that the shape (form) of the one complements the form of the other.

Your appeal to process, it seems to me, does not address the question. To say of a process that it could bring a certain form about, does not explain how the form is possible in the first place; i.e., what about atoms floating in the void allows for them to combine as the result of processes?

Finley:

Your appeal to process, it seems to me, does not address the question. To say of a process that it could bring a certain form about, does not explain how the form is possible in the first place; i.e., what about atoms floating in the void allows for them to combine as the result of processes?

We may be addressing different questions. A form is possible if a viable process can bring it about. Atoms floating in the void can combine in certain ways because of their chemical properties (at the atomic level, physics and chemistry blendc). Are you asking, why are these chemical properties the way they are? To be honest, I don’t see any utility in exploring this question. The physical properties of the universe are what they are. Whether they could have been different (and still result in a sustainable universe) is thin entertainment. Like asking what life might have been like if you’d been born to different parents or in the third world or whatever. I find little of value in pondering what things might have been like if they had been different.

I think you are manufacturing a question whose answer is of little real interest to anyone, even assuming any answer is meaningful. I find your example of the puzzle pieces frustrating, because it works so backwards. Puzzle makers START with the answer, the completed puzzle, and make the pieces from the solution. By design, the solution is “written into” the pieces that were cut from the solution to begin with. But biological processes have no final solution, and can only work forwards. Seeing biological processes as “fitting together” pieces cut from some kind of Final Solution is a conceptual error. Biological processes have no long-term goal at all. You might as well say that the “goal” of water is to reach the bottom of the hill. But water lacks any such goals, it simply follows the gravitational path of least resistance, a dynamic process. The human instinct to project our own goals and intents onto natural processes is a conceptual blunder, easy to make and often difficult to recognize. And so we project “people equivalents” into things like evolution, the weather, earthquakes, volcanos, draughts, and other natural processes and “see” “people equivalents” (gods) directing these processes for some long-term purposeful goal.

But natural feedback processes (complex adaptive systems) are NOT people, and our projections are self-serving and misleading. We should recognize this and guard against it, not wallow in error.

Molecular estimates consistently puts the diversification times of phyla further back than the cambrian. Does anyone know what the state is of the fossil record before the cambrian?

Here’s an article on talkorigins related to that:

http://www.talkorigins.org/origins/[…]h/dec97.html

i wonder if the Vendian period (when the earth froze over for a few undred million years, right before the Cambrian era) was the cheif driver of the apparent diversification in the cambrian explosion. Imagine, all across earth, small isolated lakes in the ice, all evolving different variations of creatures, probably mostly softbodied and perhaps harder to fossilize in the icy conditions, and then, relatively rapidly, they all get mixed together in a thawed worldwide ocean. And then, the arms race starts with everything evolving hard parts. The diversification happened in the soft, ice surrounded stage… has this idea been proposed before?

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This page contains a single entry by Nick Matzke published on April 17, 2005 6:27 PM.

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