The use of hierarchies as organizational models in systematics

A hierarchy is an abstract organizational model of inter-level relationships among entities. When isomorphic with nature, hierarchies are useful for organizing and manipulating our knowledge. Hierarchies have been used in biological systematics to represent several distinct, but interrelated, facets of the evolution of life with different organizational properties, and these distinctions have been confused by the rubric 'the hierarchy of life'. Evolution, as descent with modification, is inherently dualistic. The organizational structure of a hierarchy can be used to represent dualistic properties as inter-level relationships. Cladistics is monistic, with a singular focus on patterns of descent. Descent has conceptual priority over modification, but the organizational relationship is not exclusive. 'Cladistic classification' is an oxymoron because cladistics lacks the class concepts needed to construct a classification, a point recognized by those who suggest abandoning Linnaean classification in favour of a newly devised monophyletic systematization. Cladistic analysis of descent can be supplemented with an analysis of modification that provides the class concepts needed to construct an evolutionary/phylogenetic classification. When a strong monophyletic pattern of modification is detected (in addition to its monophyletic pattern of descent), the criterion of subsequent modification provides the basis for formally recognizing a certain monophyletic group at a given rank, as opposed to a group that is one node more inclusive or one node less. The criterion of subsequent modification also permits detection of strong paraphyletic patterns of modification, when they exist. By setting standards of evidence needed to recognize paraphyletic groups, one concomitandy strengthens the basis for formally recognizing selective monophyletic groups.     

Parsimony with and without Scientific Justification

Brower's (2000, Cladistics 16, 143–154) pursuit of a nonevolutionary cladistics, like those of others (e.g., Scotland, 2000, Syst. Biol. 49, 480–500), fails for lack of a scientific justification. His operational explication of parsimony does not necessarily rule out the use of other criteria on which to base the identification of a hierarchical branching pattern, nor does he give a compelling reason for why just that one kind of pattern is sought. In the absence of evolutionary theory, such as the descent of species, and the modification of character states, one from another, there is no scientific reason to seek congruence among character hierarchies whose origins, functions, and fates are not necessarily the same. Brower's operational parsimony is no substitute for phylogenetic parsimony, where requirements for ad hoc hypotheses of homoplasy are justifiably minimized, assuming only "descent, with modification." In addition to maximizing explanatory power, that most parsimonious cladogram is the least disconfirmed, most highly corroborated, hypothesis.     

Problems with the use of cladistic analysis in palaeoanthropology

Cladistic analysis is a popular method for reconstructing evolutionary relationships on the human lineage. However, it has limitations and hidden assumptions that are often not considered by palaeoanthropologists. Some researchers who are opposed to its use regard cladistics as the preferred method for taxonomic «splitters» and claim it has lead to a revitalisation of typology. Typology remains a part of human evolutionary studies, regardless of the acceptance or use of cladistics. The assumption/preference for «splitting» over «lumping» in cladistics (alpha) taxonomy and the general failure to evaluate (post-hoc) such taxonomies have served to reinforce this assertion.

Researchers have also adopted a number of practices that are logically untenable or introduce considerable error. The evolutionary trend of human encephalisation, apparently isometric with body size, and concurrent reduction in the gut and masticatory apparatus, suggests continuous cladistic characters are biased by problems of body size.

The method suffers a logical weakness, or circularity, leading to bias when characters with multiple states are used. Coding of such characters can only be done using prior criteria, and this is usually done using an existing phylogenetic scheme. Another problem with coding character states is the handling of variation within species. While this form of variation is usually ignored by palaeoanthropologists, when characters are recognised as varying, their treatment as a separate state adds considerable error to cladograms.

The genetic proximity of humans, chimpanzees and gorillas has important implications for cladistic analyses. It is argued that chimpanzees and gorillas should be treated as ingroup taxa and an alternative outgroup such as orangutans should be used, or an (hypothetical) ancestral body plan developed. Making chimpanzees and gorillas ingroup taxa would considerably enhance the biological utility of anthropological cladograms.

All published human cladograms fail to meet standard quality criteria indicating that none of them may be considered reliable. The continuing uncertainty over the number and composition of fossil human species is the largest single source of error for cladistics and human phylogenetic reconstruction.     

Control mechanisms of diel vertical migration: theoretical assumptions

We explore control mechanisms underlying the vertical migration of zooplankton in the water column under the predator-avoidance hypothesis. Two groups of assumptions in which the organisms are assumed to migrate vertically in order to minimize realized or effective predation pressure (type-I) and to minimize changes in realized or effective predation pressure (type-II), respectively, are investigated. Realized predation pressure is defined as the product of light intensity and relative predation abundance and the part of realized predation pressure that really affects organisms is termed as effective predation pressure. Although both types of assumptions can lead to the migration of zooplankton to avoid the mortality from predators, only the mechanisms based on type-II assumptions permit zooplankton to undergo a normal diel vertical migration (morning descent and evening ascent). The assumption of minimizing changes in realized predation pressure is based on consideration of DVM induction only by light intensity and predators. The assumption of minimizing changes in effective predation pressure takes into account, apart from light and predators also the effects of food and temperature. The latter assumption results in the same expression of migration velocity as the former one when both food and temperature are constant over water depth. A significant characteristic of the two type-II assumptions is that the relative change in light intensity plays a primary role in determining the migration velocity. The photoresponse is modified by other environmental variables: predation pressure, food and temperature. Both light and predation pressure are necessary for organisms to undertake DVM. We analyse the effect of each single variable. The modification of the phototaxis of migratory organisms depends on the vertical distribution of these variables.     

The Descent of Rights and the Descent of Persons

Explication and evaluation of the relative ethnographic and theoretical merits of several constructions of "descent" and "descent groups" (by W. H. R. Rivers, M. Fortes, and W. Goodenough, among others) reveals that relations of descent can have right and duty values only where patri- or matrifiliation is the necessary and sufficient condition for inclusion in a social group. Therefore, only unilineally constituted groups should be described as descent groups.     

Incongruence between cladistic and taxonomic systems

Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases of incongruence, the molecular evidence can be a reliable indicator of taxonomic relationships sometimes, misleading other times, and may afford no clear basis for a systematic decision. In this situation, it is helpful, indeed necessary, to integrate the molecular evidence with the phenetic evidence and bring more characters to bear on the question.     

Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration

Kluge's (2001, Syst. Biol. 50:322-330) continued arguments that phylogenetic methods based on the statistical principle of likelihood are incompatible with the philosophy of science described by Karl Popper are based on false premises related to Kluge's misrepresentations of Popper's philosophy. Contrary to Kluge's conjectures, likelihood methods are not inherently verificationist; they do not treat every instance of a hypothesis as confirmation of that hypothesis. The historical nature of phylogeny does not preclude phylogenetic hypotheses from being evaluated using the probability of evidence. The low absolute probabilities of hypotheses are irrelevant to the correct interpretation of Popper's concept termed degree of corroboration, which is defined entirely in terms of relative probabilities. Popper did not advocate minimizing background knowledge; in any case, the background knowledge of both parsimony and likelihood methods consists of the general assumption of descent with modification and additional assumptions that are deterministic, concerning which tree is considered most highly corroborated. Although parsimony methods do not assume (in the sense of entailing) that homoplasy is rare, they do assume (in the sense of requiring to obtain a correct phylogenetic inference) certain things about patterns of homoplasy. Both parsimony and likelihood methods assume (in the sense of implying by the manner in which they operate) various things about evolutionary processes, although violation of those assumptions does not always cause the methods to yield incorrect phylogenetic inferences. Test severity is increased by sampling additional relevant characters rather than by character reanalysis, although either interpretation is compatible with the use of phylogenetic likelihood methods. Neither parsimony nor likelihood methods assess test severity (critical evidence) when used to identify a most highly corroborated tree(s) based on a single method or model and a single body of data; however, both classes of methods can be used to perform severe tests. The assumption of descent with modification is insufficient background knowledge to justify cladistic parsimony as a method for assessing degree of corroboration. Invoking equivalency between parsimony methods and likelihood models that assume no common mechanism emphasizes the necessity of additional assumptions, at least some of which are probabilistic in nature. Incongruent characters do not qualify as falsifiers of phylogenetic hypotheses except under extremely unrealistic evolutionary models; therefore, justifications of parsimony methods as falsificationist based on the idea that they minimize the ad hoc dismissal of falsifiers are questionable. Probabilistic concepts such as degree of corroboration and likelihood provide a more appropriate framework for understanding how phylogenetics conforms with Popper's philosophy of science. Likelihood ratio tests do not assume what is at issue but instead are methods for testing hypotheses according to an accepted standard of statistical significance and for incorporating considerations about test severity. These tests are fundamentally similar to Popper's degree of corroboration in being based on the relationship between the probability of the evidence e in the presence versus absence of the hypothesis h, i.e., between p(e|hb) and p(e|b), where b is the background knowledge. Both parsimony and likelihood methods are inductive in that their inferences (particular trees) contain more information than (and therefore do not follow necessarily from) the observations upon which they are based; however, both are deductive in that their conclusions (tree lengths and likelihoods) follow necessarily from their premises (particular trees, observed character state distributions, and evolutionary models). For these and other reasons, phylogenetic likelihood methods are highly compatible with Karl Popper's philosophy of science and offer several advantages over parsimony methods in this context.     

A Review on Cladistics

The theoretical bases and approaches of cladistics and some specific problems that, directly or indirectly, rely on cladistic analysis for their revolution, are outlined and discussed. Seven sections comprise this paper: a ) the philosophical foundation of cladistics; b) the theoretical tenets of cladistics; c) the operational procedure of cladisties; d) three schools of classification; e) cladistics and biogeography; f) cladistics and hybrid recognition; and g) is cladistic systematics a scientific theory ? Considerations of scientific methodology involve philosophical questions. From this point, Popper'falsificationism serves a good foundation. Popper emphasizes that all scientific knowledge is hypothetical-deductive, consisting of general statements (theories) that can never be confirmed or verified but only falsified. The theories, that can be tested most effectively, are preferable. Cladistics, aiming at generating accurately expressed and strictly testable systematic hypotheses, is well compatible with this requirement. The principles central to the cladistic theory and methodology are: the Principle of Synapomorphy; the Principle of Strict Monophyly; and the Principle of Strict Parsimony. The first requires forming nested groups by nesting statements about shared evolutionary novelties (synapomorphy) postulated from observed similarities and is the primary one. The second is mainly methodological, subject to modification and compromise. The principle of strict parsimony specifies the most preferable hypothesis (namely the one exhibiting the most congruence in the synapomorphy pattern). The operational procedure that might be followed in formulating and testing hypotheses of the synapomorphy pattern (the cladogram itself) consists of five steps. The erections of monophyletic groups, to a greater or lesser extent, rely on the hypothesis of the previous systematic studies and is the starting point for cladistic analysis. Character analysis, which focuses on character distribution and determination of the polarities, decides the reconstructed phylogeny. A detailed discussion on the methodological principles for identifying transformation sequence is presented. Many algorithms have been designated to infer the cladogram, and are basically of parsimony techniques and Compatibility techiques. The thus yielded cladograms, with their expected pattern of congruent synapomorphies, are tests of a particular hypothesis of synapomorphy and reciprocally synapomorphies are tests of cladistic hypothesis (cladogram). Such reciprocity is a strong stimulus to profound understanding on phylogenetic process and phyletic relationships. The cladogram and the Linnaean classification have the identical logic structure and the set-membership of the two can be made isomorphic. There are three principal approaches to biological classification : cladistics, phenetics and evolutionary classification. Cladistics is the determination of the branching pattern of evolution, and in the context of classification, the development of nested sets based on cladograms. Phenetics is the classification by overall similarities, without regard to evolutionary considerations. Evolutionary classification attempts to consider all meaningful aspects of phylogeny and to use these for making a classification. The last approach has been done intuitively, without explicit methods. An enumeration of their differences and a discussion on their relative merits are presented. Three theoretical approaches have been proposed for interpreting biogeographical history: the phylogenetic theory of biogeography, classical evolutionary biogeography and vicariance biogeography. The former two show some similarities in that they usually look upon biogeography in terms of centers of origin and dispersal from the centers. But the first puts a strong emphasis on the construction of hypotheses about the phylogenetic relationships of the organisms in question and the subsequent inference of their geographic relationships; the second advocates a theory which does not have a precise deductive link with phylogenetic construction and often results in wildly narratative-type hypotheses. The vicariance approach de-emphasizes the concepts of centers of origin and dispersal and attempts to analyse distribution patterns in terms of subdivision (vicariance) of ancestral biotas. The development of the theory of plate tectonics and its universal acceptance enormously stimulate biogeographers to look at the world's continents and oceans from a mobilist point, which, along with the establishment of the rigorous tool of the phylogenetic analysis (cladistics), profoundly reshapes the above three theories. Hybridization and polyploidy are outstanding features of many plant groups. But hybridization, or reticulate evolution, is inconsistent with the basic concepts of cladistics which is an ever-branching pattern. Cladists have suggested several approaches. One of them analyses all the taxa by a standard cladistic procedure and closely examines the cladograms for polytomies and character conflicts that may indicate possible hybrids. Such generated hypothesis of hybridization can be corroborated or falsified by other forms of data, such as distribution, polyploidy, karyotype and pollen fertility. There are three criteria to justify a theory to be scientific: a) whether it is a theory composed of hypotheses strictly falsifiable; b) whether it has predictive effect; and c) whether it has a explanatory value. Cladistic systematics aims at generating cladograms, which are hypotheses of the nested pattern of synapomorphy, phylogenetic process and phyletic relationships, susceptible to testing by postulated synapomorphies. The predictive effect of systematics relies on the acceptance of hypotheses of congruence about the correlation of characters, which has been well founded. For non-systematic biologists, phylogenetic classification can be used as axiom to form a preliminary and fundamental explanation.     

Homology and errors

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are “homologies” inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character‐state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. © The Willi Hennig Society 2012.     

Models and reality: Doctrine and practicality in classification

Phenetic classification corresponds to no biological model and lacks a sound philosophical basis. Cladistics (ignoring meaningless “transformed cladistics”) assumes divergent evolution and, usually, that best estimates of phylogeny are obtained by parsimony principles, both questionable assumptions at times. It is better than phenetics since more-or-less testable hypotheses are generated, but pitfalls are many, in data selection and interpretation (as to homology), and in commensurability of units and direction of change. Above all we learn: homoplasy is rife in nature. Much bad cladistics has been done. If it is to reflect phylogeny, classification cannot be artificially stabilized, but is its only aim to express (hypothesized) cladistic patterns? And can it do that with any degree of overall assurance? Biologists are legitimately interested in defining grades as well as clades. Recognition of an unequivocal clade-grade frequently leaves a paraphyletic grade residue that cannot itself be unequivocally resolved. This is a real problem that requires attention in formal taxonomy and in applying cladistics. Primarily morphological cladistics will be increasingly supplanted by molecular (nucleotide-sequence) cladistics. The role of evolutionary taxonomy will change accordingly.     

The scientific status of metazoan cladistics: why current research practice must change

Jenner, R. A. (2004). The scientific status of metazoan cladistics: why current research practice must change. —Zoologica Scripta, 33, 293–310. Metazoan phylogenetics is bustling with activity. The use of comprehensive morphological data sets in recent phylogenetic analyses of the Metazoa indicates that morphological evidence continues to play a key role in the reconstruction of metazoan deep history. In this paper I review the scientific status of morphological metazoan cladistics from the perspective of cladistic research cycles. Each research cycle consists of three main steps: (1) the compilation of a data matrix (2) the simultaneous evaluation of all possible cladograms in a character congruence test, and (3) the assessment of the relationship between evidence and hypothesis after finding the optimal tree. I identify a striking discrepancy between the sophistication of the analysis of given data sets (Step 2), and their compilation and the interpretation of the results (Steps 1 and 3). The latter two steps deserve far greater attention than is current practice. Uncritical and nonexplicit character selection, character coding, and character scoring seriously compromise Step 1. Careful comparative morphological study prior to data matrix construction is necessary to remedy this problem in future cladistic analyses. Step 2 is the locus of most recent advances in metazoan cladistics through the increasing availability of computing power, and the development of increasingly efficient phylogenetic software that allows analysis of large data sets. Failure to identify problems and errors generated in Step 1 of the research cycle is testament to the general failure of Step 3. Consequently, recent progress in metazoan cladistics is primarily analytical, while the only empirical anchor of the discipline receives surprisingly little attention. Not surprisingly, the first generation of modern metazoan phylogeneticists used computers principally as a relatively quick and easy means to generate abundant phylogenies from morphological data. The next phase should build on this foundation by critically testing these alternative hypotheses by a thorough qualitative reassessment and elaboration of morphological data matrices, and a more critical approach to data selection. A rigorous research program for metazoan cladistics can only be established when the cladistic research cycle is properly completed, and when subsequent research cycles are effectively linked to previous efforts.     

Über die Beziehung zwischen Systematik und Evolution

The relation between systematics and evolution The theoretical and methodological decoupling of pattern analysis from the causal explanation of the hierarchical order of nature by the hypothesis of descent with modification is defended. This contrasts with the philosophy of phylogenetic systematics which views acceptance of evolutionary theory as a necessary prerequisite for research in systematics.     

A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case

This paper shows, within the limitations of the assumption stated below, that approximately 27–29 of the unmutated codons which determine the amino acids of cytochrome c are invariant because of biological requirements. A mutation is defined here as the change of a single base in the sequence of a trinucleotide codon, which change alters the amino acid coded for. Codons, if any, in which mutations would be vigorously selected against are termed invariant codons. We assume that, subject to one adjustment, those mutations in the cytochrome c gene which survived in the descent of today's species are randomly distributed among the variable codons. The one adjustment arises from the possibility that a very few codon positions may exhibit frequencies of mutation sufficiently great to justify the exclusion of these codons from the overall distribution on the grounds that the frequency of mutation occurring in these few positions is clearly inconsistent with the assumption of randomness. There are 5 out of the total 110 codons in the cytochrome c structural gene which have clearly sustained an abnormally large number of mutations.This project received support from grants to W.M.F. from the National Institutes of Health (NB-04565) and the National Science Foundation (GB-4017).     

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.     

The monophyletic origin of the Brachiopoda

Although it is commonly acepted that the brachiopods descended from phoronid-like ancestors there is dispute over their origin. Traditionally they have been regarded as a monophyletic group, a clade. More recently it has been claimed that brachiopods are polyphyletic and that several of the orders arose independently from separate phoronid-like stocks. The latter point of view implies that brachiopods are not a taxon but merely a grade of organization. Traditional stratophenetic approaches do little to resolve the problem, which may be outside their domain. It is possible, even probable, that the initial radiation involved organisms that lacked mineralized shells. Cladistic analysis of both living forms and Lower Paleozoic taxa strongly supports the contention that brachiopods are monophytetic and closely related to the phoronids. It suggests, however, that the 'inarticulate' Paterinida and Kutorginida are genealogically more closely related to the Articulata than they are to the remaining Inarticulata. □ Brachiopoda, Lophophorata, cladistics, Cambrian.     

The assembly of Ebola virus nucleocapsid requires virion-associated proteins 35 and 24 and posttranslational modification of nucleoprotein

Ebola virus encodes seven viral structural and regulatory proteins that support its high rates of replication, but little is known about nucleocapsid assembly of this virus in infected cells. We report here that three viral proteins are necessary and sufficient for formation of Ebola virus particles and that intracellular posttranslational modification regulates this process. Expression of the nucleoprotein (NP) and virion-associated proteins VP35 and VP24 led to spontaneous assembly of nucleocapsids in transfected 293T cells by transmission electron microscopy. A specific biochemical interaction of these three proteins was demonstrated, and, interestingly, O-glycosylation and sialation of NP were demonstrated and necessary for their association. This distinct mechanism of regulation for filovirus assembly suggests new approaches for viral therapies and vaccines for Ebola and related viruses.     

Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10

N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m¹G₉ modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m¹G₉ in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m¹G₉ methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m¹G₉ containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wild-type yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing.     

On the validity of using semilogarithmic plots to determine initial velocities of enzyme-catalyzed reactions

It has been proposed (Johnston & Diven, 1969a) that it is valid to use semilogarithmic (first-order) plots of the extent of reaction versus time for graphic determination of initial velocities of enzyme-catalyzed reactions. This proposition suggests the assumption that the initial velocity error expected to be introduced by the proposed procedure is smaller than or comparable to the error introduced by the customary graphic procedure. The latter is based on the assumption that the progress curves of enzyme-catalyzed reactions have an initial linear segment of sufficient duration to permit accurate determination of slope. The validity of the procedure proposed by Johnston and Diven is examined in this report. It is concluded that the procedure is applicable to a very small class of enzyme-catalyzed reactions and only under certain experimental conditions.     

Cladistics and the hominid fossil record

Cladistic methodology has become common in phylogenetic analyses of the hominid fossil record. Even though it has correctly placed emphasis on morphology for the primary determination of affinities between groups and on explicit statements regarding traits and methods employed in making phylogenetic assessments, cladistics nonetheless has limitations when applied to the hominid fossil record. These include 1) the uncritical assumption of parsimony, 2) uncertainties in the identification of homoplasies, 3) difficulties in the appropriate delimitation of samples for analysis, 4) failure to account for normal patterns of variation, 5) methodological problems with the appropriate identification of morphological traits involving issues of biological relevance, intercorrelation, primary versus secondary characters, and the use of continuous variables, 6) issues of polarity identification, and 7) problems in hypothesis testing. While cladistics has focused attention on alternative phylogenetic reconstructions in hominid paleontology and on explicit statements regarding their morphological and methodological underpinnings, its biological limitations are too abundant for it to be more than a heuristic device for the preliminary ordering of complex human paleontological and neonatological data.