Nick Matzke posted Entry 969 on April 17, 2005 06:27 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/967

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 7:39 PM (e)

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 7:54 PM (e)

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 8:21 PM (e)

Thankyou Mr. Matzke

Comment #25509

Posted by Flint on April 17, 2005 8:36 PM (e)

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)

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 otevidence 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)

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 1:32 AM (e)

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 8:15 AM (e)

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)

(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)

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)

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 3:19 PM (e)

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 4:39 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #25632

Posted by Steve Reuland on April 18, 2005 4:47 PM (e)

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 5:33 PM (e)

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 5:46 PM (e)

We’ll leave that to the wolphins.

Comment #25641

Posted by Steve Reuland on April 18, 2005 5:57 PM (e)

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 6:10 PM (e)

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 6:11 PM (e)

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 6:19 PM (e)

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

Comment #25658

Posted by Pete Dunkelberg on April 18, 2005 7:43 PM (e)

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 7:46 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #25678

Posted by Cassanders on April 19, 2005 4:22 AM (e)

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 8:57 AM (e)

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 9:04 AM (e)

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 9:45 AM (e)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

“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)

“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)

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)

“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)

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)

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)

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 1:26 PM (e)

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 1:30 PM (e)

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 2:05 PM (e)

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 2:07 PM (e)

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 2:11 PM (e)

“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_oreill…

Comment #25762

Posted by Sir_Toejam on April 19, 2005 2:39 PM (e)

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 3:22 PM (e)

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 3:43 PM (e)

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 4:31 PM (e)

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 4:38 PM (e)

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 4:44 PM (e)

…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 4:47 PM (e)

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 4:51 PM (e)

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 4:53 PM (e)

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 4:56 PM (e)

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 5:03 PM (e)

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 5:14 PM (e)

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 is simple; reconstructing that tree correctly is impossible except locally. See Dawkins’s “The Ancestor’s Tale”, where he provides alternative proposed cladograms for some groups. They are quite fundamentally different, yet each is backed by good research and logic.

Comment #25812

Posted by Steve Reuland on April 19, 2005 5:15 PM (e)

Flint wrote:

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!

Let me pick a nit here. To the best of my knowledge, geographical isolation is not considered a sufficient criterion for speciation. The reason being that geographical isolation may be temporary, whereas biological isolation is presumed to be permanent (and as far as I know, it always is.) Of course geographical isolation is thought to be a common precursor to biological isolation (allopatry) but does not itself equal speciation.

Comment #25814

Posted by Sir_Toejam on April 19, 2005 5:42 PM (e)

@flint:

thanks, but um, if you look at the dates on the articles referenced (latest 1991) that was exactly where i left off! in fact, in case you hadn’t noticed, the link you posted was created at berkeley (my alma mater).

funny.

I guess they haven’t posted any new discussions of cladistics using genetics since i left in 91.

I figured someone here would be a bit more up to date on the issue.

nah, cladistics goes much farther than species. part of my thesis was intended to be a more complete cladogram of the Pomacentrids, incorporting arguments for and against using genetics vs. morphology (as it turned out, i was getting a bit ahead of myself :) ).

The issue is a very important one, as we look at the importance of genetic relatedness when looking at evolutionary hypotheses involving genetic drift, for example. some cases of behavior or morphology are insufficiently explained if using purely apparent morphological relatedness.

I could go into a case in point using my own thesis project, if anyone would be interested.

in any case, I appreciate the effort.

thanks

Comment #25817

Posted by Tarc on April 19, 2005 5:52 PM (e)

Syntax Error: mismatched tag 'quote'

Comment #25819

Posted by Scott Davidson on April 19, 2005 5:59 PM (e)

Steve Reuland wrote:
To the best of my knowledge, geographical isolation is not considered a sufficient criterion for speciation.

I believe that Coyne and Orr’s new book on speciation does list geographic isolation as one of the isolating mechanisms for their biological species concept (I don’t have it handy at the moment to check), admittedly it’s only one of the pre-zygotic mechanisms, and I agree it is insufficient to define a species without other facotres being considered. Personally I thought that defining species by shared mating systems (specific mate recognition system) made a great deal of sense, but it seems that’s been adopted into the biological species concept as one of their pre-zygotic mechanisms.

Slightly off topic…

Flint wrote:
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!

There is a case in NZ at the moment where we have an endangered specie, the black stilt (kakï), which hybridises with the Australian Pied stilt (poaka) a migratory species. The Department of Conservation is attempting to restrict this as it would have been an unlikely event in the past (prior to human settlement). Unfortunately due to several causes, such as habitat loss and predation from introduced predators, black stilt numbers have plummeted. A combined effect of the habitat loss and the reduction in numbers is that black stilts will mate with the pied stilts, producing viable hybrids.

So are the black stilts a separate species or a colour (and non-migratory) morph of the Pied Stilts?
The hybridisation is occurring largely due to human actions. And the NZ Dept Of Conservation is making quite a substantial effort to preserve the black stilt.

Kakï will mate and breed with poaka and hybrid stilts, but these pairings only occur when suitable kakï mates are not available. Because there is an almost 3:1 male bias in the kakï population many male kakï are paired inappropriately, and are producing hybrid offspring. MtDNA analyses (maternal lineage only) indicates that kakï have been separated from poaka for around one million years, and remain genetically distinct from poaka today. However, long-term survival of kakï as a species requires that gene flow be less than about 5%. While kakï show strong positive assortative mating, choosing other kakï to mate with whenever possible, gene flow is presently about 15%. Whether similar levels of assortative mating will occur when the population is large and the sex ratio more even is unknown. Successful management of kakï as a distinct species in the long-term will likely require continued management of gene flow. There are several factors that make hybrid management to reduce gene flow feasible. Natural fitness of hybrid offspring is already low (about 50% of pure kakï pairs, probably a result of outbreeding depression that follows Haldanes Rule), kakï already show strong positive assortative mating, hybrids are easy to identify by plumage, and because stilts do not reproduce until they are 2–3 years old there is plenty of opportunity to control inappropriate cross-species matings and resultant progeny.

Comment #25823

Posted by P. Mihalakos on April 19, 2005 6:19 PM (e)

M. Finley wrote:

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.

Actually, enumerating species isn’t as easy as you might think. There are lots and lots of critters to account for, remember. And for such categorization to be useful it would have to avoid superficial morphological comparisons, i.e. you’re looking at cat and chicken “toes,” and in order to know how or to what degree their limbs are related you need to know what it is that identifies digits #3 as a homologous set that exludes the other digits.

Additionally, there are a few open questions concerning morphological evolution that we would want our classification system to address. I’m not sure how the one you are describing would do that, but I am open to your elaboration.

Per Gerd Muller and Stuart Newman, what kind of practical distinctions would the kind of taxonomy that you are suggesting help make when addressing questions arising from Phylogenetics:

Burgess shale effect (Why did metazoan body plans arise in a burst?)

Homoplasy (Why do similar morphologies arise independently and repeatedly?)

Convergence (Why do distantly related lineages produe similar designs?)

Homology (Why do building elements organize as fixed body plans and organ forms?)

Novelty (How are new elements introduced into existing body plans?)

Modularity (Why are design units reused repeatedly?)

Constraint (Why are not all design options of a phenotype space realized?)

Atavisms (Why do characters long absent in a lineage reappear?)

Tempo (Why are the rates of morphological change unequal?)

Now, if you could come up with a classication scheme, i.e. with what you described as a rational taxonomy that merged classical ideas re. telos, but that still imparted real knowledge (predictive power) about the nature of the rules for the organization of form, then it would have immense practical value.

P.S.
ST, I would be interested in reading your thesis. Thank you.

Comment #25825

Posted by Steve Reuland on April 19, 2005 6:21 PM (e)

tarc wrote:

The phylogenetic view indeed won in systematics, but quantitative morphology is a very active field in evolutionary biology and palaeontology … and it is formalist rather than phylogenetic.

You’ll need to explain this for me. I am not familiar with quantitative morphology, altough the name itself seems like it wouldn’t lend itself to formalism.

Comment #25828

Posted by Michael Finely on April 19, 2005 6:45 PM (e)

Scott Davidson wrote:

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?

This problem is not unique to my proposal, right, but is a question for taxonomy in general? I don’t know much about taxonomy, but it seems to me that the criteria for categorization are two: (1) simple similarity of structure or feature, and (2) geneological location (these are related, obviously, but distinguishing them allows for structural similarities that are nonetheless of different categories due to convergence).

Flint wrote:

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.

Well, I am wary of the notion of an “ideal” as well (i.e., of its connotations of perfection and Platonic transcendence). Let’s drop the adjective and talk simply of, e.g., the human “form.” Surely biologists want to say that all humans share a set of structures (genotypic and phenotypic; note the use of “type” in both of these) that differentiates them as a group from other groups of organisms. This sets the stage for the introduction of form.

Part of the problem may be that the classical doctrine of form is thought to involve simple forms, e.g., the form “man” is simple and indivisible, a single entity. Instead, species-forms are complex unities of lower-level forms. “Man,” for example, is a complex form consisting of numerous lower-level forms, e.g., “bipedal,” etc. A change or replacement of a lower-level form would alter the complex.

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.

What of a dog in Canada and a dog in Russia? They do not interbreed, are they different species? For that matter, what about two (wild) dogs in the same pack that happen not to interbreed? Perhaps we might add that they could interbreed, but so can different species (e.g., horse and donkey).

Steve Reuland wrote:

When a population divides and later results in two separate species, at what exact point in time is the new “form” acheived?

Just in case anyone cares, this is called a sorite paradox, e.g., when does a tadpole become a frog, when does red become orange on the spectrum, etc. As with the question concerning which features to emphasize over others, the choice to call a partially changed set of lower-level forms a new form is somewhat conventional, but is nonethless grounded in a real difference.

Biological evolution is defined as the change in allele frequencies in a population over time. But an allele itself doesn’t make a “form”.

I think a place where the concept of form can provide the a significant benefit is the relationship between alleles and their expressions. An allele has a certain structure that produces a macro-structure. An intuitive way to conceptualize this is by appealing to some sort of formal “blue-print” inherent in the allele that leads to the construction of the macro-feature. To put it simply, aren’t body parts prefigured in the genes that give rise to them?

Comment #25831

Posted by Great White Wonder on April 19, 2005 7:04 PM (e)

Finely

I think a place where the concept of form can provide the a significant benefit is the relationship between alleles and their expressions. An allele has a certain structure that produces a macro-structure. An intuitive way to conceptualize this is by appealing to some sort of formal “blue-print” inherent in the allele that leads to the construction of the macro-feature. To put it simply, aren’t body parts prefigured in the genes that give rise to them?

Try to believe that this individual attacked another commenter on this blog with the epithet, “blowhard”.

Comment #25832

Posted by Sir_Toejam on April 19, 2005 7:04 PM (e)

“ST, I would be interested in reading your thesis. Thank you.”

well, for the case under discussion, let me just pull out what i think is a relevant bit.

The primary topic of my thesis was involved with explaining ontogenetic color change (OCC) in fishes, primary among Pomacentridae (damselfishes). As you may be aware, many species within this family exhibit dramatic color shifts from juvenile to adult. This change is so dramatic in some cases that the juvenile and adult forms were at one point considered different species.

To evaluate the several postulated (but poorly tested) hypotheses commonly espoused at the time (back in the 80’s) to explain this phenomenon, I chose an area that had several species within the same genus living in the same area, but where some species exhibited OCC and some did not. I was hoping to tease out what the relative selective pressures might be that would differentiate the appearence of this phenomenon in one species and not the supposedly related species in the same habitat.

alas, what i discovered belatedly was that the phylogenetic relationships of the entire Pomacentridae were in a state of flux, and what i thought were closely related species were being argued from a genetic standpoint to be not so closely related at all (and vice versa in other cases). the consequences of this argument directly relate to whether you can eliminate the possibility that OCC in modern pomacentrids is simpy a result of genetic drift, or just due to a “lack” of any selective pressure against it in various species. In other words, OCC may have evolved in an ancestor of some of the more modern genera (where it might have been favored for some unknown reason), and simply maintained itself as a trait because of a lack of selection pressure to change it.

It was such a confounding factor for me, that I was actually attempting to work with some of the geneticists at berkeley to re-work the cladistics of the family based on their genetic analysis of relatedness, instead of the more common morphological basis, to better tease out how relatedness factored into this.

However, in retrospect I’d have to say that attempting to rework the cladistics of an entire family (with lots of species, no less), along with actually testing hypotheses about the fitness of OCC in the field was a bit much for a PhD student to take on.

I’ve thought about pursuing the matter again, from time to time, hence my interest in seeing what the current status of the arguments for using genetics vs. morphology in determining relatedness.

However, if i started looking at OCC again, i more likely would actually spend my time looking at the new work in fish vision that is being done. Hell, back when i first started, it was thought that UV was not important in underwater vision, but now that is not the case. The most recent issue of Nat Geo even has a nice article on it.

anywho, there ‘tis. thanks for asking.

cheers

Comment #25833

Posted by P. Mihalakos on April 19, 2005 7:04 PM (e)

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Comment #25834

Posted by P. Mihalakos on April 19, 2005 7:10 PM (e)

M. Finley wrote:

To put it simply, aren’t body parts prefigured in the genes that give rise to them?

Even if we were to have firm knowledge of an organism’s genome, it would still be insufficient to compute its form.

Evidence: the same genotypes to not necessarily correspond to the same phenotypes. Also, genetic and developmental pathways can change over evolutionary time even when the morphology remains constant.

Comment #25836

Posted by Sir_Toejam on April 19, 2005 7:17 PM (e)

“the same genotypes to not necessarily correspond to the same phenotypes. Also, genetic and developmental pathways can change over evolutionary time even when the morphology remains constant”

too true. Just out of curiosity, which do you believe to be the more valuable contribution to phylogentic organization in the context of evolutionary questions then? morphology or genetics?

Comment #25838

Posted by P. Mihalakos on April 19, 2005 7:22 PM (e)

STJ wrote:

In other words, OCC may have evolved in an ancestor of some of the more modern genera (where it might have been favored for some unknown reason), and simply maintained itself as a trait because of a lack of selection pressure to change it.

Hmm… Yes. That’s not terribly uncommon, is it? Or, could it not have arisen as a preadaption, indirectly related to some other selection event?

Comment #25839

Posted by Michael Finley on April 19, 2005 7:23 PM (e)

P. Mihalakos wrote:

This is a modern version of the homunculus fallacy.

In what way?

Genes are insufficient to explain form, i.e. ontogeny…. Even if we were to have firm knowledge of an organism’s genome, it would still be insufficient to compute its form.

Here I am at a loss as I don’t know enough about genetics. Why is this the case, what information is missing that makes the prediction impossible?

Comment #25841

Posted by steve on April 19, 2005 7:39 PM (e)

Maybe you could read a little basic biology before arguing that biologists are wrong?

With creationists, that’s probably too much to ask.

Comment #25842

Posted by Sir_Toejam on April 19, 2005 7:43 PM (e)

“Or, could it not have arisen as a preadaption, indirectly related to some other selection event”

not sure i would use the term “pre-adaptation” as opposed to co-adaptation perhaps (I think the term is linked trait, IIRC), but essentially that is also another [null] hypothesis:

It never affected fitness in any way, ever, but was simply a tag-along with some other trait that did. again, knowing the genetic relatedness in this case would help.

as to the relative measure of “commoness” or not, I can’t say i have a large enough grasp on the literature at this point to make any conjectures. However, if most teleological arguments from an evolutionary standpoint could be demonstrated to be cases of simple genetic drift, I doubt there would still be much interest in pursuing new evolutionary hypotheses. in fact, the whole theory of natural selection wouldn’t be very interesting when you think about it, would it?
OK, OK, a bit over the top, but i think you see my point: in any scientific field of endeavor, if the null hypothesis of any theory was found to be commonly the case, interest would begin to lag a bit after a while. since this is not the case with evolutionary theory, i can reasonablly assume that cases of morphology or behavior expainable via simple genetic drift or linked traits must be fairly uncommon.

cheers

Comment #25843

Posted by Great White Wonder on April 19, 2005 7:50 PM (e)

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Comment #25844

Posted by P. Mihalakos on April 19, 2005 7:51 PM (e)

Well, in early biological theory, the homunculus referred to the fully formed human being that was thought to exist inside an egg or spermatozoon, only in much much smaller form, right? In other words, form was entirely prefigured. Obviously, the question that was begged was then how did the homunculus itself arise?

The same crtique is often extended to the so-called genetic “program.”

M. Finley wrote:

Why is this the case, what information is missing that makes the prediction impossible

You’ve stumbled onto a really good question. The genotype-phenotype relationship is a centeral concern of current (and future) research. The information that is missing depends on the trait you are trying to account for. And it really isn’t that the information is missing, it’s just that it doesn’t reside in one tidy locus, but rather is jointly determined by multiple causes. For lack of a more detailed answer, much research shows that traits are produced by the interaction of numerous developmental resources. The gene/environment dialogue is only one of many ways to divide up the interactants, so that no one type of interactant controls development. These are just a few prominent themes in developmental systems theory (DST) research. One of their main insistences is that current evolutionary theory can predict what will be maintained (via inheritance), but not necessarily what will appear.

Honoring your question in substantial depth would require a long bibliography of research references, but rather than bore others here, I would rather send them off-post. Would that be okay?

Comment #25845

Posted by Sir_Toejam on April 19, 2005 7:53 PM (e)

@finley:
as to your first question about the homunculus fallacy:

“Jean Baptiste Lamarck (publ 1802 or 1809) developed a theory of evolution in which the main points were:
evolution or change within a species is driven by an innate, inner striving toward greater perfection,
use or disuse of various organs made them larger or smaller, accordingly, and
these acquired traits could be inherited or passed on to offspring (inheritance of acquired traits).
A number of subsequent attempts were made to prove or disprove this theory without the benefit of our modern knowledge of genetics. One experiment involved amputation of mouse tails for successive generations, showing that even after twenty generations, there was no effect: baby mice were still born with tails. The Jewish practice of circumcision was also cited as opposing evidence, since obviously it had caused no long-lasting change in the population and still needed to be done to each new boy baby. Lamarck’s theory seemed to make sense in the light of the then-accepted theory of pangenes coming from the body parts to make up the homunculus. The classic example he used was giraffes. He felt that giraffes’ necks got longer because they stretched to reach higher leaves, and this was passed on to their babies. Another example, to make the fallacy of his theory more apparent, would be two people who developed large arm muscles because they were blacksmiths, tennis players, or weight-lifters having a baby who was born with larger than normal arm muscles.”

taken from a basic article that can be found here:

http://www.cartage.org.lb/en/themes/Sciences/Lif…

as to the second, explaining the entire theory of transcription and translation in it’s most modern form would take a bit more space than i would like. suggest you read up on some modern biology or genetic texts.

cheers

Comment #25847

Posted by Sir_Toejam on April 19, 2005 7:59 PM (e)

@ finley:

also go take a look at the archives over at talk.orgins. there are excellent summaries there on many of the issues discussed here.

Comment #25848

Posted by P. Mihalakos on April 19, 2005 8:06 PM (e)

STJ wrote:

However, if most teleological arguments from an evolutionary standpoint could be demonstrated to be cases of simple genetic drift, I doubt there would still be much interest in pursuing new evolutionary hypotheses.  in fact, the whole theory of natural selection wouldn’t be very interesting when you think about it, would it?

You are probably right. But, then again, maybe that’s why so many researchers are currently interested in epigenetic processes.

Comment #25849

Posted by Sir_Toejam on April 19, 2005 8:10 PM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #25850

Posted by Perry Mihalakos on April 19, 2005 8:19 PM (e)

STJ wrote:

…or it could just be where the money is right now for research.

AH ha! I’m sure I wouldn’t know.

Comment #25852

Posted by Mihalakos on April 19, 2005 8:26 PM (e)

STJ wrote:

…or it could just be where the money is right now for research.

AH ha! I’m sure I wouldn’t know.

Comment #25853

Posted by Henry J on April 19, 2005 8:35 PM (e)

Flint,

Re “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!”

Um. And if a researcher captures some of them and takes them to a laboratory for breeding experiments, while in the lab they aren’t interbreeding with the ones in the wild. Taking what you said literally, that would make them a separate species - a conclusion that doesn’t make sense to me.

Henry

Comment #25855

Posted by Mike Dunford on April 19, 2005 9:00 PM (e)

Michael Finley wrote:

Why is this the case, what information is missing that makes the prediction impossible?

Simply put, there are factors other than genetics that can contribute to the phenotype of the individual. It is possible for a trait to be solely determined by the genotype, it is possible for a trait to be solely determined by the environment, but it is also possible (and common) for a trait to be determined by the combination of the genotype and the environment. This is commonly known as a GxE interaction.

One reason for this is that the expression of many genes is regulated. This means that they are only “turned on” (generating RNA transcripts) under certain circumstances. In some cases, environmental factors can play a role in the activation, inactivation, or degree of activation of various genes. Unless the exact environmental conditions that will prevail throughout development are known, prediction of the precise phenotype is not going to be possible. (Even if the exact environmental conditions can be predicted, it’s likely that random factors would play enough of a role to make phenotype predictions difficult, but that’s a separate issue.)

Comment #25856

Posted by Sir_Toejam on April 19, 2005 9:01 PM (e)

@henry;
that’s why you should have actually read the rest of his post, before “literally” jumping to conclusions:

Flint wrote:

“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.”

tho actually i would argue that if you study population genetics and conservation biology that the question often is worth answering, but that’s another issue.

cheers

Comment #25858

Posted by Michael Finley on April 19, 2005 9:06 PM (e)

Steve wrote:

Maybe you could read a little basic biology before arguing that biologists are wrong?

P. Mihalakos wrote:

The genotype-phenotype relationship is a centeral concern of current (and future) research.

I readily admit that biology, even basic biology, is not my forte, but this doesn’t sound that basic.

P. Mihalakos wrote:

For lack of a more detailed answer, much research shows that traits are produced by the interaction of numerous developmental resources. The gene/environment dialogue is only one of many ways to divide up the interactants, so that no one type of interactant controls development.

We’re not talking about direct interaction of a gene and the environment right, but with some “intermediate” expression of the gene (i.e., midway through otogeny)? I’m imagining, for example, the attaching of a board to infant foreheads to flatten the skull (a cultural pracitce in Africa if memory serves). Yet there must be some level of prediction from genotype to phenotype; e.g., isn’t this involved in screening sperm for genetic defects?

The same crtique is often extended to the so-called genetic “program.”

This is a little more sophisticated than the homunculus position. It is an expression of the principle of sufficient reason. The phenotypic structures, i.e., the “shape” of the parts and the relation of the parts to each other, cannot develop out of thin air, so to speak, the formal component of those structures must be provided somehow. If DNA as the formal carrier is too simplistic, a more complicated account must be found.

Comment #25859

Posted by Michael Finley on April 19, 2005 9:15 PM (e)

Mike Dunford wrote:

It is possible for a trait to be solely determined by the genotype, it is possible for a trait to be solely determined by the environment, but it is also possible (and common) for a trait to be determined by the combination of the genotype and the environment. This is commonly known as a GxE interaction.

One reason for this is that the expression of many genes is regulated. This means that they are only “turned on” (generating RNA transcripts) under certain circumstances. In some cases, environmental factors can play a role in the activation, inactivation, or degree of activation of various genes.

This is very interesting, and thank you for the further clarification. Such instructions to react to the environment in a particular way are completely contained in the genotype, right? If so, then they could simply be incorporated qua form into the genetic “blue-print.”

Functionalism in psychology makes use of formal descriptions like this, functional “states” as they’re called. A hysically instantiated formal system can have a state such that, given input A, then output B. This response is “written” into the formal structure of the system. The same seems to be the case with genes.

Comment #25860

Posted by Great White Wonder on April 19, 2005 9:25 PM (e)

Finley

We’re not talking about direct interaction of a gene and the environment right, but with some “intermediate” expression of the gene (i.e., midway through otogeny)? I’m imagining, for example, the attaching of a board to infant foreheads to flatten the skull (a cultural pracitce in Africa if memory serves).

I’m imagining a troll whose skull is filled with a finite amount of bullcrap.

Comment #25861

Posted by Sir_Toejam on April 19, 2005 9:26 PM (e)

“Such instructions to react to the environment in a particular way are completely contained in the genotype, right? If so, then they could simply be incorporated qua form into the genetic “blue-print.”

not exactly. multiple responses can be regulated via a specific set of genes, but aren’t always directly controlled via the genes themselves, but rather thru specific intereactions with the environment as well.
More like having a genetic “component” to a particular morphology or behavior, but that is then affected by development, environment, or interactions between the two. Hence the whole nature/nuture argument (which is mostly pointless when you realize that traits are on a “sliding scale” wrt to how much they are influenced by genetic “blueprints” vs. environmental interaction.

I hope that helps a bit.

er, you were right when you stated it is a bit more complicated than basic biology. more likely second semester college level biology

:)

Comment #25862

Posted by Sir_Toejam on April 19, 2005 9:30 PM (e)

“A hysically instantiated formal system can have a state such that, given input A, then output B. This response is “written” into the formal structure of the system. The same seems to be the case with genes.”

so with my above input, it would be more like

givent input A, you could get output B, if C was also occuring. however, there is a lesser probability you could get output B2 or even B3.

keeping that in mind, you CAN find cases that are more similar to A in, then B out, but they are more the exception than the rule.

Comment #25865

Posted by Flint on April 19, 2005 9:46 PM (e)

Well, Ernst Mayr at least stakes out the position that if two populations do not interbreed and exchange genes, regardless of the reason they do not interbreed, they are best regarded as different species. Any systemic biological differences may or may not exist (often mere people can’t tell the difference between the populations).

So, does geographic isolation divide an otherwise interbreeding population into a species directly, or does the resulting cessation of gene flow cause the two populations to become “potential” or “incipient” species? There doesn’t seem to be a clean answer to this question.

Finley asks:

What of a dog in Canada and a dog in Russia? They do not interbreed, are they different species? For that matter, what about two (wild) dogs in the same pack that happen not to interbreed? Perhaps we might add that they could interbreed, but so can different species (e.g., horse and donkey).

My reading of Mayr is that the dogs in Canada and Russia would probably be considered separate species, especially if they were wild populations. There are also breeds of dogs that do not interbreed for morphological reasons. The notion that you might be a different species from the woman next door simply because you choose not to breed with her I hope isn’t intended to be taken seriously.

But the interesting distinction is between populations that DO interbreed, and those that CAN interbreed (producing fertile offspring) but do not do so. Mayr discusses the question of just how much gene flow between two populations must take place before they are considered one population? In ring species, there is at least some gene flow from end to end, though the variations at each end are too biologically different to interbreed if they wished. All of which leads to the notion that even the term “species” is to some important degree a term of taxonomic convenience.

Henry J writes

And if a researcher captures some of them and takes them to a laboratory for breeding experiments, while in the lab they aren’t interbreeding with the ones in the wild. Taking what you said literally, that would make them a separate species - a conclusion that doesn’t make sense to me.

I’m not sure if I’m parsing this correctly. Simply relocating individuals doesn’t change their species. But in the lab, we can (and frequently do) interbreed what are without question distinct species in the wild. Maybe it might be most useful to think of every population of interbreeding individuals as a species on the path of becoming something different (though perhaps imperceptibly, if Gould’s stasis is the norm).

Comment #25866

Posted by P. Mihalakos on April 19, 2005 9:48 PM (e)

M. Finley wrote:

If DNA as the formal carrier is too simplistic, a more complicated account must be found.

Exactly. That’s the state of the science. And, therefore, a more complicated account is emerging every day, though there do appear to be some basic themes. Just a casual glance across the literature will reveal a growing list of normally occuring environmental (and behavioral!) influences on gene activity. The most dramatic and oft-quoted example would be strange life cycle of the slime mold. But that’s not all…

Lessee… our friends the Nematodes, inspiration of this thread: the absence of presence of food results in neuronal daf-7 gene mRNA expression. This is important because it inhibits or provokes laraval development.

Incubation temperature for various reptiles results in sex determination.

Songbirds, when exposed to the songs of their conspecifics undergo an alteration mRNA in the forebrain, but I don’t remember what the result was.

Mice, when exposed to certain acoustic stimulation, undergo tonotopy in their auditory systems, via c-fos expression influencing neuronal activity.

(whew!)

Other influences that have to play into our complicated account? Tactile/visual/acoustic stimulation, light-dark cycles, learning tasks of all sorts, enviromental complexity, prenatal nutrition, and infantile handling. (I’m particularly interested in the last example as my wife is expecting any day now!)

In any case, in terms of sufficient causality, I’m afraid that the best we can say, according to a large number of researchers, is that the developing organism (multicellulars) as a whole in any given point in time functions as a resource for its own further development. DNA provides a “recipe” for a large array of developmental resources, including fundamental regulation processes (Hox genes, etc.), but despite continued blather in the pop press about “genetic blue prints”, there is really no sense in which a subset of developmental resources, DNA or otherwise, contains a “program” or complete set of determining instructions for development.

This is why it makes people here so mad to hear Evolving Apeman and others accuse scientists of invoking aspects of evolution, viz. what he THINKS is “genetic” determinism, to explain our so-called nihilistic embrace of meaninglessness. “If it’s all just genes….blah blah blah, what’s to keep me from just blowing your head off any time I want.”

Now, I recognize you have never made such an argument yourself. I just included it to illustrate a common misunderstanding.

Comment #25867

Posted by Michael Finley on April 19, 2005 10:05 PM (e)

P. Mihalakos wrote:

…there is really no sense in which a subset of developmental resources, DNA or otherwise, contains a “program” or complete set of determining instructions for development.

Isn’t there though. It may not be a self-contained program that, once initiated, it runs complete from start to finish. Instead, perhaps it is akin to a program that runs some applications automatically, but for others requires some sort of input (cf. Windows, video games, PT’s server software, etc.). In which case, the whole range of options exist beforehand, but some require environmental circumstances to be activated.

Comment #25868

Posted by Michael Finley on April 19, 2005 10:10 PM (e)

Flint wrote:

The notion that you might be a different species from the woman next door simply because you choose not to breed with her I hope isn’t intended to be taken seriously.

Granted it cannot be correct, but the reason it cannot must be accounted for in the definition of “species.” If two organisms are different species if, and only if, they do not interbreed, and that’s it, then it seems to follow that “the woman next door” is a different species. That this is unacceptable, suggests that the definition needs to be supplemented somehow.

Comment #25869

Posted by Michael Finley on April 19, 2005 10:13 PM (e)

Great White Wonder,

We’ve disagreed in past threads. Get over it.

Comment #25870

Posted by Sir_Toejam on April 19, 2005 10:17 PM (e)

“The notion that you might be a different species from the woman next door simply because you choose not to breed with her I hope isn’t intended to be taken seriously.”

Well, it’s usually them as chooses not to be a breedin with me, and i do have a tendency to think them alien for not wanting to, but that’s just me

:)

Comment #25871

Posted by Nick (Matzke) on April 19, 2005 10:36 PM (e)

Great White Wonder,

Chill out. I don’t get a chance to read many threads but Finley is not doing anything objectionable in this one.

Comment #25872

Posted by P. Mihalakos on April 19, 2005 10:40 PM (e)

The analogy holds only if you allow the “program” to be periodically and fundamentally rewritten by a changing set of other determining factors, which could also be thought of as “programs.” And what kind of program is that? A massively parallel network? Okay, but this is not what the public thinks of when they consume the soundbite pablum re. “genetic programs.”

The fact is that the more complex the organism, the more distributed (and robust) are the controls that set and maintain developmental parameters. Even highly conserved genes, such as hox, contribute to entirely different traits–depending on the organism in which hox activity is contextualized. This is why many have concluded that knowing how an organism of particular form is produced demands much more than a knowledge of its molecular composition and enviromental conditions.

Here is Brian Goodwin with what I think is a better metaphor than that of a serial digital computer (genotype) and its output (phenotype, software, etc.):

“…Organisms are like fountains: The form remains the same but the material of which it is composed flows through it changing continuously. What does not change in organisms is certain aspects of the organization of the materials, their dynamic relationships, the way they are arranged in space and the patterns of change they undergo in time…. DNA, the heriditary material plays a VERY important role in stabilizing certain aspects of this spatial and temporal order. But it does not generate the order.”

Comment #25873

Posted by Sir_Toejam on April 19, 2005 10:56 PM (e)

nicely explained, P.

Comment #25874

Posted by Nick (Matzke) on April 19, 2005 11:09 PM (e)

Random comments:

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.

Which is better for phylogeny, genes or morphology? The answer is…wait for it…both. A crappy use of a genetic dataset, like using rapidly evolving mitochondrial DNA to resolve distant events like e.g. the branching mammalian orders, does not necessarily overturn a morphology-based phylogeny. An multi-gene set of unsaturated sequences giving good statistical resolution might well override a traditional morphological phylogeny. On the other hand, with fossils all you’ve got is morphology, so you have to use morphology, and because with fossils you often have intermediate forms, sometimes you can resolve branchings that can’t be resolved by looking at modern organisms.

As both the molecular and morphological datasets improve in quality I think we are seeing more and more consilience, e.g. this recent PNAS paper, a morphological phylogeny placed the early “legged whales” as sister group to the hippos, which was a result suggested by molecular results some years ago.

Even apart from recent improvements, the whole “morphology vs. genes” issue in phylogeny is overblown. The correlation was always pretty good in the big-picture statistical sense. For example, morphology and molecules might have disagreed on whether whales belonged within artiodactyls or as a sister group, but there was congruence both above and below this node in the tree: above the node, whales were clearly a group with many well-resolved subgroups, and below this node, whales+artiodactyls were both clearly placentals, mammals, tetrapods, chordates, etc.

The fact that morphology and molecules tend to agree at many nodes, even if they disagree at a particular controversial point, is often ignored by compulsively perfectionist scientists. See statistics of incongruent phylogenies for an excellent review.

Just to bring this thread back to ID-bashing, the incongruence topic is another one that is routinely abused by IDists. They tend to argue via quote-mine, picking out minor bits of incongruence cited in the literature, and they universally ignore any kind of statistical measurement of congruence between different datasets. Until they take this into account, they are not really even paying attention to the real issues with respect to the argument for common descent.

Comment #25875

Posted by Michael Finley on April 19, 2005 11:09 PM (e)

P. Mihalakos wrote:

The analogy holds only if you allow the “program” to be periodically and fundamentally rewritten by a changing set of other determining factors, which could also be thought of as “programs.”

Brian Goodwin wrote:

DNA, the heriditary material plays a VERY important role in stabilizing certain aspects of this spatial and temporal order. But it does not generate the order.

I like the Goodwin analogy accept on this last point. The definite article before “order” suggests that the sense of the sentence is “But it does not generate any of the order.” This same sentiment seems to be behind your statement that the “program” can be “fundamentally rewritten.”

Does DNA (or some other source of inherent information), unaided by environmental factors, not generate some of the phenotypic organization? Can the “program” be fundamentall rewritten in every respect? Surely some basic structural features come about all by themselves. Humans, for example, in the vast majority of cases, end up with two feet, two hands, a head connected to a neck, etc., etc. The suggestion cannot be that, given the right environmental circumstances, an ear would grow out of an ankle, etc.

Comment #25876

Posted by P. Mihalakos on April 19, 2005 11:35 PM (e)

M. Finley wrote:

Humans, for example, in the vast majority of cases, end up with two feet, two hands, a head connected to a neck, etc., etc. The suggestion cannot be that, given the right environmental circumstances, an ear would grow out of an ankle, etc.

Depends on what you mean by “environment” again. I don’t know about that specific example, but surely you are aware of teratology. Ever visit the Mutter Museum? What about the tragic example of thalidomide?

Or, let’s talk Drosophila. Maintain the genotype, but vary certain environmental conditions, and you will get the fruit-fly version of an “ear” out of an “ankle.” That’s as jargon-free as I can make this example.

Please don’t misunderstand. I’m not denying DNA’s ability to specify a norm of reaction over environments. It’s just that the relationship between gene and trait is repeatedly shown to be nonlinear and radically contingent, not “essential” except in the possible case of generic forms.

I hate to post and run, but I have to get some sleep.

G’night.

Comment #25877

Posted by Sir_Toejam on April 19, 2005 11:41 PM (e)

@nick:

“the whole “morphology vs. genes” issue “

I appreciate your input on the issue. I rarely think about it in terms of the fossil record, so that viewpoint is welcomed.

An multi-gene set of unsaturated sequences giving good statistical resolution might well override a traditional morphological phylogeny.

yup. kinda what i was running into in berkeley; got caught in the middle of an argument between the molecular biologists and the museum of vertebrate zoology. interesting, but terribly unproductive for a grad student to be in the middle of :)

If you run across any references that review the current status, I’d appreciate it.

cheers

Comment #25878

Posted by Jim Harrison on April 20, 2005 12:16 AM (e)

There simply isn’t enough information in the essentially two-dimensional genome to specify a three-dimensional organism. The environment supplies the rest. What must be recognized is that the environment includes the intimate environment of the egg, the mother’s body, or the seed as well as the external environment. We’re not just talking about coarse factors like climate.

The genome of a fetus is simply not a recipe for human beings. Over and beyond the temperature, pH, and salinity range maintained in the womb and the various maternal hormones that effect development , the unfertilized egg already contains messenger RNA that has a lot to do with the early stages of development, RNA that derives from exclusively maternal DNA. Anyhow, human beings can only function in a social world—naked, defenseless, and neotenous babies just don’t survive by themselves unless you’re Romulus and Remus. For our species as for many others, culture, broadly defined, functons as a parallel system of heredity quite as indespensible and determinate as anything in the nucleus.

Comment #25883

Posted by Russell on April 20, 2005 6:02 AM (e)

Does DNA (or some other source of inherent information), unaided by environmental factors, not generate some of the phenotypic organization?

Mr. Finley seems to have a passion for breaking questions/systems into little pieces that make no sense by themselves. DNA is embedded in cells, which are embedded in organisms, which are embedded in the environment. On the organismal level, the system works together, and evolves as a system. DNA constitutes a record of successful responses to the environment. DNA is not a separate entity working its will on an enslaved population of cell structures.

Can the “program” be fundamentall rewritten in every respect? Surely some basic structural features come about all by themselves. Humans, for example, in the vast majority of cases, end up with two feet, two hands, a head connected to a neck, etc., etc. The suggestion cannot be that, given the right environmental circumstances, an ear would grow out of an ankle, etc.

You lost me.

Comment #25888

Posted by Flint on April 20, 2005 8:20 AM (e)

Finley writes

Granted it cannot be correct, but the reason it cannot must be accounted for in the definition of “species.” If two organisms are different species if, and only if, they do not interbreed, and that’s it, then it seems to follow that “the woman next door” is a different species. That this is unacceptable, suggests that the definition needs to be supplemented somehow.

To me, this objection only suggests you are trying to misinterpret for the sake of keeping in practice.

A species is a population of individuals within which there is an exchange of genes. This means its members breed with one another. It does NOT mean that every member must breed with every other member, but that (as an example) a favorable mutation spreads throughout the population within some number of generations (not that many), and spreads to no other population at all.

Somehow, I think you understand both what I said, and how this works. I think you ‘misunderstand’ very carefully and deliberately, to deflect and distract. Since we can demonstrate that species branching happens, that it’s normal, that no mechanism prevents it, the ‘tree of life’ model emerges directly. Do you object to this model so strongly?

Comment #25891

Posted by Russell on April 20, 2005 9:37 AM (e)

RE: the woman next door as separate species.

This would be yet another example of breaking systems into pieces too small to make sense. The concentration of sodium in your blood is probably right around 0.15 moles/liter. But what, you ask, is the concentration of this sodium atom?

Comment #25892

Posted by RPM on April 20, 2005 10:16 AM (e)

Syntax Error: mismatched tag 'quote'

Comment #25894

Posted by Michael Finley on April 20, 2005 10:29 AM (e)

P. Mihalakos wrote:

Please don’t misunderstand. I’m not denying DNA’s ability to specify a norm of reaction over environments. It’s just that the relationship between gene and trait is repeatedly shown to be nonlinear and radically contingent, not “essential” except in the possible case of generic forms.

Thanks for your patience; if the horse is dead, and I’m continuing to beat it, let me know.

By “norm of reaction over environments” do you mean that, while some environmental factors must be operative, whatever they happen to be does not affect the normal development of some features? Could you elaborate on “generic forms”?

Consider the following example that I’m familiar with from another context (see the transcript of this discussion by the President’s Council on Bioethics, specifically the proposal by Dr. Hurlbut a third of the way down):

(http://www.bioethics.gov/transcripts/dec04/sessi…)

Dr. Hurlbut wrote:

As well demonstrated in the work of Dr. Janet Rossant at Mount Sinai Hospital in Canada, 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. Without this, there’s just an open space and the cell just can’t form its own integrity of an inside and an outside. [ … ] Studies confirm that a functional trophectoderm is absolutely essential in embryogenesis. In experiments with mouse models when cdx2 is not expressed, there is only a partial and disorganized developmental process resulting in a visibly abnormal blastocyst.

For the purposes of altered nuclear transfer, cxd2 might be deleted from the somatic cell nucleus before transfer. […] This technologically created limited cellular subsystem from which the embryonic stem cells would be obtained would fail to establish even the most basic features of human organismal infrastructure. A deficiency at the first differentiation of cell type, the formation of the trophectoderm, means the absence of the most fundamental order. […] The resulting cells would have no inherent principle of unity — that is, the entity produced […] would have no inherent principle of unity, no coherent drive in the direction of the mature human form….

Isn’t the development of the cell wall a good example of a structure resulting directly from a particular gene? Granted some environmental conditions must be met, e.g., the blastocyst cannot develop in a freezer, etc., nontheless, this appears (to the untrained eye) to be a clear case of one-to-one correspondence between gene and expression.

Russell wrote:

Mr. Finley seems to have a passion for breaking questions/systems into little pieces that make no sense by themselves.

I do have a penchant for reductive analysis. It’s a product of my education that seems to be ill-suited for biology.

Flint wrote:

Somehow, I think you understand both what I said, and how this works. I think you ‘misunderstand’ very carefully and deliberately, to deflect and distract.

You accuse me of playing the sophist (cf. Thrasymachus’ charge against Socrates in Replublic, I: “That’s abominable of you, Socrates; you take the words in the sense which is most damaging to the argument.”), when I’m honestly trying to get a handle on the Darwinian definition of “species.” I don’t know what else to say other than, “No, I’m really asking in earnest.”

A species is a population of individuals within which there is an exchange of genes. This means its members breed with one another. It does NOT mean that every member must breed with every other member, but that (as an example) a favorable mutation spreads throughout the population within some number of generations (not that many), and spreads to no other population at all.

Doesn’t this shift the question concerning membership in a “species” to membership in a “population”? What is the definition of “population”? If the answer is “a group consisting of animals that interbreed with one another,” aren’t we back to questions about the girl next door?

Comment #25896

Posted by Flint on April 20, 2005 11:30 AM (e)

Finley:

Doesn’t this shift the question concerning membership in a “species” to membership in a “population”?

Absolutely. This was Darwin’s conceptual breakthrough. A species IS a population of individuals that interbreeds. That’s all it is.

What is the definition of “population”? If the answer is “a group consisting of animals that interbreed with one another,” aren’t we back to questions about the girl next door?

ONLY if it is impossible that you and the woman next door shared an ancestor, or that any of your future generations might mate with any of hers. The whole idea is (as I wrote and you quoted) that the genetic variation individuals have (in sexual species. I’m not talking prokaryotes here) are in practice spread around among the members of a population of individuals. That population is a species for that very reason and no other.

In practice, the girl next door is the recipient of the same general blend of genetic variation within the population that you are, and that the blending process will continue to mix actively as members of your group breed essentially randomly with each other. I presume you are aware that the range of genetic variation even across an interbreeding population can be fairly large: there’s a bell curve of variation across each characteristic. When a small group (sometimes a single pregnant female) becomes isolated and starts a new population, there is an important “founder effect” as a result. It’s entirely possible that individuals belonging to the population might like at the opposite ends of some important curve and would never choose to mate with one another, in a variable species. Ring species are a degenerate case of this phenomenon.

And this leads to the interesting observation that two individuals can be the same species (as members of the same interbreeding population) yet be genetically more distant from one another than either is to a member of a different population which does not interbreed for some reason (perhaps a different mating ritual, or the like). Once again, we run up against the same conclusion: the boundary encompassing a species is hazy and arbitrary. A specific individual can legitimately belong to more than one species depending on circumstances. Think of a Venn diagram – each species has a hazy boundary due to variability in its population, and similar populations can overlap and still be different species. Mayr speaks in terms of gene flow below some minimum, but not zero. Otherwise, there could be no wolphins.

(As a footnote I find amusing, competitive birders love the splitters and hate the lumpers. Splitters are those ornithologists who find reason to split one species into two, lumpers are those who find reasons to combine species. Ornithologists argue very actively over just how many species of, say, jays, live in the US, since there are at least a dozen species, but any jay can breed with any other, and they sometimes do. And the more species are defined to be distinct, the more species a birder can get on his life list.)

Comment #25911

Posted by Michael Finley on April 20, 2005 12:49 PM (e)

Flint wrote:

ONLY if it is impossible that … any of your future generations might mate with any of hers.

This seems to move us back to the possibility of interbreeding as opposed to the actuality, i.e., we are of the same species if we or our ancestors could interbreed.

If a species is a population, how is it determined whether a particular organism, a, is a member of a particular population, A? Put another way, how is a population defined?

Are two organisms, a and b, members of the same population because they share “the same general blend of genetic variation”? If so, isn’t the criteria for being in a population, i.e., for being of a species, genetic similarity?

Granted the boundary will often be hazy, but even hazy boundaries depend on some objective basis. They cannot be purely conventional.

Comment #25917

Posted by Michael Finley on April 20, 2005 1:38 PM (e)

Flint,

I had previously considered a species to be a class (sets) of organisms, and therefore, I have no difficulty thinking of them as populations. For a population is simply a class or group of organisms.

As far as I can tell, however, the problem of definition remains. To construct a class we need a sortal concept by which to include or exclude members of the class. We need to be able to indentify organism X as possessing feature Y, making it a member of class (set, population, species) Z.

So far we’ve said that two organisms are of the same population if they interbreed. This, by itself, is insufficient because it would make a donkey and horse of the same population (i.e., species) in the event that they mate.

Perhaps two organisms are of the same population if they share “same general blend of genetic variation.” That would make general genetic similarity the criterion of species-membership.

Comment #25919

Posted by Michael Finley on April 20, 2005 1:40 PM (e)

Flint,

Sorry, the first post was lost in internet limbo for a while. Thinking it had been lost for good, I wrote the second post.

Comment #25920

Posted by Henry J on April 20, 2005 1:41 PM (e)

How about this: two organisms are in the same species if some of their recent ancestors are apt to produce a sizable number of descendants in common.

Comment #25924

Posted by Marek14 on April 20, 2005 2:02 PM (e)

I think that a part of problem is that “species” are thought of as equivalence classes - this is the notion that every organism has exactly one species.

But while we can define relation “Organisms A and B are the same species.”, say, with some form of possible interbreeding or general genetic compatibility, and while this relation obeys two of three conditions for equivalence classes (reflexivity and symmetry), it is not neccessarily transitive, i.e. if you have organisms A, B, and C, such that A and B are the same species, as are B and C, A and C might not (according to our definition).

I visualize this by imagining organisms as points in the plane, and having each organism capable of interbreeding with, say, those less than 1 unit away. If the organisms are concentrated in small blobs, distant from each other, then the usual concept of “species” works well with them. Once any given blob would spread beyond the 1-unit range, some organisms would be unable to breed with others, and this is where the notion of species starts get hazy, as our conceptual blob elongates, and finally, maybe, divides in two.

I wonder - is this analogy true? Is “A and B are the same species” just a way to say “A and B are, in some way, CLOSE”?

Comment #25926

Posted by Flint on April 20, 2005 2:12 PM (e)

Finley:

Granted the boundary will often be hazy, but even hazy boundaries depend on some objective basis. They cannot be purely conventional.

I suspect this is a false dichotomy. Ultimately, the issue of whether organism a is a member of species A must remain largely arbitrary. In the case of humans, this problem doesn’t arise because there are no similar enough species with with which we could interbreed if we wished. The case of the various species of jays is something quite different. When ornithologists consider that a particular individual could be regarded as a member of two (or even three) species, and that if relocated (let’s say to the next isolated mountain chain of suitable elevation) would cheerfully become a breeding member of the jays found there (which all agree are a different species given a different name), then we see that the notion of species is approaching a convention rather than a biologically distinct reality.

Of course members of a breeding population require a minimal degree of genetic similarity if they are to have offspring at all, and perhaps a greater degree if those offspring are to be fertile. But the story of the wolphin recently was an illustration of such fertility. That particular organism could breed with either false killer whales or bottlenose dolphins, and produce offspring that would be fertile with either. So are false killer whales and bottlenose dolphins ‘really’ different species? Yes, we conventionally say they really are.

So let’s go back and consider the ring species (there are quite a few). Can we draw one or more lines somewhere on the ring and say “on this side is species A, on the other is species B”? Yes, of course we can. What we can NOT do is agree on where it makes sense to draw the lines. They are, within some range, a matter of convention. Not “pure” convention – the line is agreed to have to fall within some range. But within that range, it’s conventional.

Genetic variation, the sine qua non of natural selection, necessarily leads to what I think of as the “continuum problem” – the continuous overlap between ‘adjacent’ species makes clean lines between them necessarily arbitrary and misleading. These species could be adjacent in genetic space, or adjacent in time (we know species branch, but from the beginning of the branching event until the branched population has a more-or-less distinct genetic identity, classification of any individual is arbitrary).

You seem (I’m interpreting here, sorry if I get it wrong) to want any given individual to cleanly belong to one species and no other, on unambiguous biological grounds. But the natural world refuses to accommodate the human craving to classify and pigeonhole. All individuals are unique, and the differences matter. These differences are what drives evolution.

Comment #25958

Posted by Michael Finley on April 20, 2005 3:34 PM (e)

Flint wrote:

What we can NOT do is agree on where it makes sense to draw the lines. They are, within some range, a matter of convention. Not “pure” convention — the line is agreed to have to fall within some range. But within that range, it’s conventional.

I think that’s a good statement. If we use the analogy of the color spectrum, where we draw the exact line between orange and red is a matter of convention, but that it must fall within a particular range is not, i.e., it will not do to place the line at the frequency corresponding to “cherry red.”

That said, it seems to me that the possibility (as opposed to the actuality) of sexual reproduction, supplemented by an arbitrary line drawn between a range of similar genotypes, would be the best way to define a species.

Comment #25968

Posted by RPM on April 20, 2005 4:14 PM (e)

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. Coyne and Orr argue that chosing a species concept depends on what one wishes to study. If you would like to understand speciation in sexually reproducing organsisms, then the biological species concept is most appropriate. If you want to study bacterial speciation, the BSC won’t be of much use.

Comment #25971

Posted by Michael Finley on April 20, 2005 4:38 PM (e)

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.

Comment #26012

Posted by Henry J on April 20, 2005 9:48 PM (e)

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

Comment #26028

Posted by Marek14 on April 21, 2005 1:19 AM (e)

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 >:-)

Comment #26059

Posted by Steve Reuland on April 21, 2005 12:15 PM (e)

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. :)

Comment #26182

Posted by P. Mihalakos on April 21, 2005 11:53 PM (e)

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?

Comment #26185

Posted by Sir_Toejam on April 22, 2005 12:10 AM (e)

“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.

Comment #26186

Posted by Sir_Toejam on April 22, 2005 12:12 AM (e)

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

cheers

Comment #26188

Posted by P. Mihalakos on April 22, 2005 12:28 AM (e)

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.

Comment #26189

Posted by P. Mihalakos on April 22, 2005 12:32 AM (e)

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.

Comment #26191

Posted by Sir_Toejam on April 22, 2005 12:36 AM (e)

“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.

Comment #26223

Posted by Michael Finley on April 22, 2005 10:42 AM (e)

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.

Comment #26266

Posted by mihalakos@earthlink.net on April 22, 2005 2:10 PM (e)

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.

Comment #26269

Posted by Flint on April 22, 2005 2:44 PM (e)

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.

Comment #26282

Posted by Michael Finley on April 22, 2005 3:29 PM (e)

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).

Comment #26284

Posted by Michael Finley on April 22, 2005 3:41 PM (e)

*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).

Comment #26292

Posted by Flint on April 22, 2005 4:02 PM (e)

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.

Comment #26293

Posted by P. Mihalakos on April 22, 2005 4:03 PM (e)

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.

Comment #26297

Posted by Michael Finley on April 22, 2005 4:41 PM (e)

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.

Comment #26301

Posted by Michael Finley on April 22, 2005 5:02 PM (e)

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.

Comment #26302

Posted by Flint on April 22, 2005 5:02 PM (e)

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.

Comment #26305

Posted by Flint on April 22, 2005 5:17 PM (e)

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.

Comment #26314

Posted by Michael Finley on April 22, 2005 6:13 PM (e)

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?

Comment #26339

Posted by Flint on April 22, 2005 10:12 PM (e)

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.

Comment #26357

Posted by ErikW on April 23, 2005 4:18 AM (e)

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?

Comment #26665

Posted by Henry J on April 25, 2005 1:41 PM (e)

Here’s an article on talkorigins related to that:

http://www.talkorigins.org/origins/postmonth/dec…

Comment #26667

Posted by joe larson on April 25, 2005 1:46 PM (e)

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?