Are phyla “real”? Is there really a well-defined “number of animal phyla” extant and in the fossil record? Does the term “bodyplan” or “bauplan” have any consistent definition? Many paleontologists, notably Stephen Jay Gould (1989, Wonderful Life), have written books that take these concepts for granted, and, observing charts with many animal phyla appearing in the Cambrian, and few appearing afterwards, have reached the conclusion that there was something extra-special and unique about the Cambrian “explosion”. Creationists, both the traditional and “intelligent design” variety, have been only to happy to put their own spin on this situation, and argue that God, for reasons that remain obscure, engaged in a particularly active period of special creation for a few dozen million years back in the Cambrian. Recent examples include Stephen Meyer’s hopeless paper “The origin of biological information and the higher taxonomic categories”, the three or so previously-published versions of that paper, and Paul Nelson’s work in general (see a recent powerpoint presentation).
Last week I came across the following paper:
David Fitch and Walter Sudhaus, “One small step for worms, one giant leap for ‘Bauplan?’” Evolution & Development 4:4, 243-246.
The paper is a frontal attack on the concepts of “phyla” and “bodyplan,” especially as applied to Cambrian fossils.
Nematode mouths
The paper begins with nematodes. Nematodes are a ubiquitous group of (usually) tiny worms. They live in the soil, in the ocean, and in and on many other metazoan animals, including you. There are so many nematodes around that it has been said that if all multicellular life except nematodes were to suddenly vanish, you would still be able to see ghostly images of plants, animals, and humans — made up entirely of nematodes. Nematodes are bilateral metazoans, recently placed in the ecdysozoa, a group of phyla that molt their cuticles. Arthropods and sister phyla such as tardigrades and onychophorans are also ecdysozoans.
Fitch and Sudhaus (2002) begin by noting that in certain lineages of nematodes, the mouth has shifted from a terminal position (“terminal” means that the mouth is at the front tip of the worm, to a “neural” position (twisted to be on the same side of the body as the neural cord) or to an “abneural” position (twisted to be on the opposite side of the neural chord). See their Figure 1a:
Note: This figure shows three nematode species, Hypodontus macropi (mouth is neural), Gaigeria pachyscelis (mouth is abneural), and Oscheius sp. (mouth is terminal). Red indicates the appearance of the character change in the phylogeny.
This shift in mouth position is a quite minor change, and has happened independently in various taxa.
Phyla-level differences
Now, one of the “key differences” separating chordates (deuterostomes) from protostomes is that the chordate mouth is abneural, while the protostome mouth is neural. Chordates, echinoderms, and some other wormy phyla are deuterostomes, while the other major group of “advanced” bilaterian animals are the protostomes, which include the ecdysozoans we just met as well as the lophotrochozoans (mollusks, annelids, and others). The differences between protostomes and deuterostomes are supposed to be even “bigger” than the differences between phyla within these groups (after all, each of these groups includes many phyla). The character differences between the phyla are considered to be a fundamental parts of the “bodyplans” of the various phyla.
Fitch and Sudhaus note, however, that this key character change has occurred many times, in nematodes and elsewhere, and in these contexts it is considered a minor change — perhaps warranting a new family or genus, but certainly not a new “bodyplan” or phylum. But what is the meaning of “bodyplan” and phylum, if “phylum-level” character changes are going on continually during the history of life, and these changes are considered minor except in the context of the phyla?
Fitch and Sudhaus conclude that — rather like a “language” is a dialect with an army, and the difference between a “religion” and a cult is about 100 years — a “phylum-level difference” is a small set of changes that occurred when animals were first diversifying. These changes were not particularly “fundamental” or radical at the time, they were just early. All of the latter changes that accumulated in each lineage were built upon these early changes, producing the appearance — to modern eyes — of these changes being “fundamental differences”. Among modern organisms, the phyla are fairly distinct now due to accumulated changes and extinction of basal stem groups [1]. But when the phyla were first diverging, the differences were not so large, and many of the stem groups were still around. This is the reason why many of the Cambrian fossils are difficult to categorize. If we attempt to shoehorn them into modern taxa, many of them don’t fit, so we have to erect new phyla for them, even though the morphological difference between (say) a lobopod and a basal fossil arthropod or basal fossil onychophoran is not large.
Fitch and Sudhaus show this inconsistency in their Figure 1b:
Note: This figure shows that in Linnaean taxonomy, not all character changes in organisms are treated equally, even if they are identical changes. (Red = new character on the phylogeny)
Linnaean taxonomy works passably well on modern organisms — each modern organism can be put into a natural hierarchy of monophyletic groups [2]. But when applied to fossils, internal contradictions and absurdities begin to appear. For example, let’s say that we define the class “Aves” as the common ancestor of Archaeopteryx and modern birds, and all of that common ancestor’s descendents. So far, so good. However, when we discover a flock of feathered theropod dinosaur fossils, some more closely related to Archaeopteryx than others, we are struck with a quandary. In order to be self-consistent, the sister group of (Archaeopteryx+modern birds) should itself be ranked as a class. The sister group of these two classes should get a rank higher than class. However, these feathered theropods are clearly just one small group of dinosaurs, and if they were all transported to modern times, they are so similar we would put them all in the same small group. The only ways out of this bind are to (1) give up on the requirement that groups be monophyletic (this is what paleontologists used to do, e.g. with the “mammal-like reptiles”, (2) give up on self-consistency of ranking (leading to problems like having a class within a family, e.g. with the bird-dinosaur example above), or (3) give up on the Linnaean system altogether for fossils, and simply assign a specimen to a species and then determine whether or not it belongs to a crown group (nested within group defined by the common ancestor of a modern monophyletic group) or a stem group (on a branch basal to a crown group).
Option 3, the cladistic option, has taken over much of paleontology, e.g. studies of the origin of birds or the origin of mammals. Fitch and Sudhaus (2002), and several other papers quoted below in an appendix to this post, represent this view taking over Cambrian paleontology.
Implications for ID/creationist argumentation
The implications of this conceptual shift within mainstream Cambrian paleontology for ID/creationist argumentation with respect to the Cambrian “explosion” of “phyla” are rather dire. The entire basis for the ID position is revealed to basically be a mistake — a mistake made by eminent evolutionary biologists, to be sure, but a mistake nonetheless. The “extinct phyla” that Gould and others cited in support of the idea that the Cambrian phyla appeared in a “phylogenetic lawn” are rapidly being placed as stem groups of modern phyla, showing us how the characters of modern phyla were acquired step-by-step.
There is, of course, zero chance that IDists will just give up on the beloved Cambrian Explosion, but alert creationism watchers might see them move the goalposts. I suspect we are already seeing some of this when we see IDists waffle on whether or not the Cambrian explosion was really that abrupt, and whether or not any transitional fossils for Cambrian phyla really exist. It appears that attempts at “in-principle” claims are being substituted — for example, instead of “the Cambrian explosion happened too fast for evolution, too many new body plans with no transitionals”, we are seeing things like “evolution can’t produce new information or new developmental programs, no matter how gradual the Cambrian Explosion was.” Two examples are quoted below:
Those who think the fossil data provide a more reliable picture of the origin of the Metazoan tend to think these animals arose relatively quickly—that the Cambrian explosion had a “short fuse.” (Conway Morris 2003b:505-506, Valentine & Jablonski 2003). Some (Wray et al. 1996), but not all (Ayala et al. 1998), who think that molecular phylogenies establish reliable divergence times from pre-Cambrian ancestors think that the Cambrian animals evolved over a very long period of time—that the Cambrian explosion had a “long fuse.” This review will not address these questions of historical pattern. Instead, it will analyze whether the neo-Darwinian process of mutation and selection, or other processes of evolutionary change, can generate the form and information necessary to produce the animals that arise in the Cambrian. This analysis will, for the most part, therefore, not depend upon assumptions of either a long or short fuse for the Cambrian explosion, or upon a monophyletic or polyphyletic view of the early history of life.
(Stephen C. Meyer (2004), "The Origin of Biological Information and the Higher Taxonomic Categories")
But the puzzle of the Cambrian Explosion is not really a paleontological (i.e., fossil) problem.
The fossils just make the puzzle more dramatic.
The real problem arises from the way that animals are constructed by the process of development. (emphasis original)
(Paul Nelson (2005). "Why is the Problem of Macroevolution Still Unsolved?" PowerPoint presentation, University of Minnesota-Morris, 6 April 2005.)
In the Appendix below I will quote the relevant bits of some recent articles that make the points I tried to outline in my post above, but in much more authoritative and rigorous fashion.
Notes
1. However, it is worth reading Valentine’s (2004) book The Origin of Phyla and noting every time Valentine says things like “group X is currently placed in phylum A, but it used to be its own phylum B, and before that it was a subphylum in phylum C, but phylum C had to be discarded as a polyphyletic ragbag.”
2. There are some issues with losing phylogenetic resolution (not all of the splits in a phylogenetic tree can be given a rank, even if we start assigning suborders and superclasses) and with the false assumption that taxonomic ranks are going to be comparable (the tree genus Nothofagus is over 60 million years old, the genus Homo is only a few million years old).
3. Well, this note isn’t attached to anything, but I should add that there are some reasons that the origin of the Cambrian phyla is different than the origin of birds or mammals. First, it was the “mother of all adaptive radiations”, occupying niches that were not just open but completely unoccupied. Second, there was a major change in the environment for fossil preservation, notably (a) the origin of hard body parts and (b) the origin of burrowing, algae-scraping, and other forms of muck-sucking that mixes up the sediment. The pre-Cambrian world appears to have been one of undisturbed algal mats, until advanced metazoans came along to eat all of that up. So calling the Cambrian “explosion” a “myth” — referring to the “phylogenetic lawn” idea — does not exclude the fact that some some very interesting and important things happened at the beginning of the Cambrian.
Appendix — “Down with phyla” excerpts from recent scientific articles
David Fitch and Walter Sudhaus, “One small step for worms, one giant leap for ‘Bauplan?’” Evolution & Development 4:4, 243-246.
[p. 243]
A popular hypothesis about animal diversification is that unique changes occurred in the Precambrian or Cambrian (ca. 700-500 millions of years [Myr] ago) to produce the distinctive features of all animal “Bauplne” (“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 Nbler-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 Bauplne [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 Bauplne 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 Bagu And Jordi Garcia-Fernndez (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 Baplan 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).
146 Comments
Bayesian Bouffant · 17 April 2005
Is it a phylum or a class - Isn't just the sort of mess PhyloCode is intended to do away with?
PvM · 17 April 2005
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.
Paul Flocken · 17 April 2005
Thankyou Mr. Matzke
Flint · 17 April 2005
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.
Henry J · 17 April 2005
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
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
Nick (Matzke) · 17 April 2005
Karen · 18 April 2005
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.
Katarina · 18 April 2005
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.
Tarc · 18 April 2005
Ken Shackleton · 18 April 2005
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.
Nick (Matzke) · 18 April 2005
I think I deleted the duplicate comments (sorry, the website is sometimes slow to update!).
Michael Finley · 18 April 2005
Does this criticism of the notion of "phylum" have any implications for that of "nested hierarchy"?
RPM · 18 April 2005
Steve Reuland · 18 April 2005
Evolving Apeman · 18 April 2005
fwiffo · 18 April 2005
We'll leave that to the wolphins.
Steve Reuland · 18 April 2005
Russell · 18 April 2005
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.
Steve Reuland · 18 April 2005
Sir_Toejam · 18 April 2005
please tell us EA isn't your kid, Steve!
Pete Dunkelberg · 18 April 2005
Tarc · 18 April 2005
Cassanders · 19 April 2005
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
Evolving Apeman · 19 April 2005
Aureola Nominee · 19 April 2005
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.
David Greenwood · 19 April 2005
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.
Steve Reuland · 19 April 2005
David Heddle · 19 April 2005
Steve Reuland · 19 April 2005
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.
David Heddle · 19 April 2005
Yeah Steve, jokes about having sex with someone's mother, why that is the hallmark of humor. Bravo.
Michael Finley · 19 April 2005
Steve Reuland · 19 April 2005
Flint · 19 April 2005
bill · 19 April 2005
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.
Michael Finley · 19 April 2005
Mike Kelly · 19 April 2005
Sir_Toejam · 19 April 2005
"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.
Sir_Toejam · 19 April 2005
"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.
RPM · 19 April 2005
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.
Sir_Toejam · 19 April 2005
"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
P. Mihalakos · 19 April 2005
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.
Steve Reuland · 19 April 2005
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.
Henry J · 19 April 2005
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)?
bill · 19 April 2005
Michael Finley · 19 April 2005
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.)
P. Mihalakos · 19 April 2005
Steve Reuland · 19 April 2005
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.
Great White Wonder · 19 April 2005
Sir_Toejam · 19 April 2005
you'd almost have to qualify a falafel as a "polyphyletic" organism, wouldn't you?
Michael Finley · 19 April 2005
P. Mihalakos · 19 April 2005
Michael Finley · 19 April 2005
Sir_Toejam · 19 April 2005
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
Michael Finley · 19 April 2005
Scott Davidson · 19 April 2005
Scott Davidson · 19 April 2005
Sir_Toejam · 19 April 2005
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
Flint · 19 April 2005
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.
Steve Reuland · 19 April 2005
Flint · 19 April 2005
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.
Steve Reuland · 19 April 2005
Sir_Toejam · 19 April 2005
@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
Tarc · 19 April 2005
Scott Davidson · 19 April 2005
P. Mihalakos · 19 April 2005
Steve Reuland · 19 April 2005
Michael Finely · 19 April 2005
Great White Wonder · 19 April 2005
Sir_Toejam · 19 April 2005
"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
P. Mihalakos · 19 April 2005
[author=M. Finley]To put it simply, aren't body parts prefigured in the genes that give rise to them?
No. This is a modern version of the homunculus fallacy.
Genes are insufficient to explain form, i.e. ontogeny.
P. Mihalakos · 19 April 2005
Sir_Toejam · 19 April 2005
"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?
P. Mihalakos · 19 April 2005
Michael Finley · 19 April 2005
steve · 19 April 2005
Maybe you could read a little basic biology before arguing that biologists are wrong?
With creationists, that's probably too much to ask.
Sir_Toejam · 19 April 2005
"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
Great White Wonder · 19 April 2005
P. Mihalakos · 19 April 2005
Sir_Toejam · 19 April 2005
@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/LifeScience/PhysicalAnthropology/HumanGeneticEvolution/EarlyModels/EarlyModels.htm
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
Sir_Toejam · 19 April 2005
@ 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.
P. Mihalakos · 19 April 2005
Sir_Toejam · 19 April 2005
could be.
or it could just be where the money is right now for research.
?
cheers
Perry Mihalakos · 19 April 2005
Mihalakos · 19 April 2005
Henry J · 19 April 2005
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
Mike Dunford · 19 April 2005
Sir_Toejam · 19 April 2005
@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
Michael Finley · 19 April 2005
Michael Finley · 19 April 2005
Great White Wonder · 19 April 2005
Sir_Toejam · 19 April 2005
"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
:)
Sir_Toejam · 19 April 2005
"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.
Flint · 19 April 2005
P. Mihalakos · 19 April 2005
Michael Finley · 19 April 2005
Michael Finley · 19 April 2005
Michael Finley · 19 April 2005
Great White Wonder,
We've disagreed in past threads. Get over it.
Sir_Toejam · 19 April 2005
"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
:)
Nick (Matzke) · 19 April 2005
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.
P. Mihalakos · 19 April 2005
Sir_Toejam · 19 April 2005
nicely explained, P.
Nick (Matzke) · 19 April 2005
Michael Finley · 19 April 2005
P. Mihalakos · 19 April 2005
Sir_Toejam · 19 April 2005
@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
Jim Harrison · 20 April 2005
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.
Russell · 20 April 2005
Flint · 20 April 2005
Russell · 20 April 2005
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?
RPM · 20 April 2005
Michael Finley · 20 April 2005
Flint · 20 April 2005
Michael Finley · 20 April 2005
Michael Finley · 20 April 2005
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.
Michael Finley · 20 April 2005
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.
Henry J · 20 April 2005
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.
Marek14 · 20 April 2005
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"?
Flint · 20 April 2005
Michael Finley · 20 April 2005
RPM · 20 April 2005
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.
Michael Finley · 20 April 2005
Henry J · 20 April 2005
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
Marek14 · 21 April 2005
Steve Reuland · 21 April 2005
P. Mihalakos · 21 April 2005
Sir_Toejam · 22 April 2005
"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.
Sir_Toejam · 22 April 2005
I have to applaud your effort though, it was very eloquent.
cheers
P. Mihalakos · 22 April 2005
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.
P. Mihalakos · 22 April 2005
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.
Sir_Toejam · 22 April 2005
"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.
Michael Finley · 22 April 2005
mihalakos@earthlink.net · 22 April 2005
Flint · 22 April 2005
Michael Finley · 22 April 2005
Michael Finley · 22 April 2005
Flint · 22 April 2005
P. Mihalakos · 22 April 2005
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.
Michael Finley · 22 April 2005
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.
Michael Finley · 22 April 2005
Flint · 22 April 2005
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.
Flint · 22 April 2005
Michael Finley · 22 April 2005
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?
Flint · 22 April 2005
ErikW · 23 April 2005
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?
Henry J · 25 April 2005
Here's an article on talkorigins related to that:
http://www.talkorigins.org/origins/postmonth/dec97.html
joe larson · 25 April 2005
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?