‘Biodiversity crisis’ is a notion that currently occupies a place in governmental agendas in the developing world. Likewise, awareness of the ‘taxonomic impediment’ now contributes to shape concerns about the sustainability of every-day life in post-industrial societies. Well before that, though, the systematic study of biological diversity had advanced steadily in Europe, particularly during the seventeenth and eighteenth centuries. Historians recognize that biological systematics (in the modern sense of the phrase) derived initially from the incipient work of a multinational, heterogeneous assemblage of ‘naturalists’—the iconic ‘specimen-gatherers’ that were at times passengers in ships bound for long-term expeditions departed from the busiest European commercial ports. In retrospect, it is not difficult to argue that the organization of the ever-increasing amount of information from living beings not previously seen (let alone imagined to exist) that inhabited territories far away from the corresponding centers of colonial expansion was a major interest for those early forgers of ‘the science of biodiversity’.Footnote 1 The establishment of the ‘Linnaean paradigm’ of systematization of biological knowledge was a key component of the many-faceted cultural product we call ‘Natural History’; undoubtedly, it was also one of the predominantly practical endeavors that contributed to the success of the Western project of Modernity. Oddly enough, it is from such cultural platform that statements in direct reference to an imminently endangered species diversity are generated today. As expected, some of these reflections (voiced on occasion by biologists of fame) have an admonitory flavor, as their authors vehemently declare that efforts oriented towards the rational preservation of life on the planet cannot wait.

To talk about systematics in these terms might seem unusual, at least for those not familiar with comprehensive historiographic studies of the Natural Sciences. But the move is perfectly legitimate. It is unavoidable to acknowledge that the importance placed nowadays on the construction of ordered systems of data about living organisms—by contemporary ‘genome curators’ and other molecular bio-informaticians, for instance—is in many ways a continuation of a long-standing tradition of bio-classificatory practices. Such scientific activity, ‘officially’ started by Linnaeus, his students, and later followers, and its results—i.e., the very first ‘universally accepted’ classificatory schemes of biodiversity, expressed in a Latin-based nomenclatural language—played a prominent role in the negotiations that constituted modern Biology. Scholar (or popular, for that matter) narratives of the transition in Western knowledge that created the biological science of today—with its current impressive ability to probe into almost any type of mechanism, in almost any ‘biological kind’ or ‘species’—sometimes focus more on other aspects. However, these accounts can hardly overlook how classification defines the frame of reference to which any biological datum—from the number of stamens of the latest flowering plant species accomodated in a molecular phylogeny to the newest completed vertebrate nuclear genome sequence—must be referred to, if it will ever be meaningful to a/the scientific community that studies the diversity of taxa on the planet. This interest in biodiversity—a genuine ‘biophilia’, to be sure—encompasses its discovery and description, as well as the explanatory accounts of its existence.

Systematic biology is now a highly formalized scientific endeavor that rests on complex computational infrastructures. These include digital databases with information on organismal traits of all sorts, from the macro-morphological to the molecular-genetic, as well as a myriad software programs specifically designed to analyze them. As such, the discipline continues to provide the evidential basis for the increasingly sophisticated explanations of biodiversity that spring from the theoretical body that, according to a large majority, constitutes biology’s most successful general set of principles: contemporary Darwinism. The year 2009 will certainly be full of rapprochements between systematic pattern and evolutionary process. To talk about a conceptual link between the two implies, almost tautologically, their individual, separate place as disciplinary sectors in 21st century’s biology. Interestingly, though, when authors writing from a meta-scientific standpoint have analyzed biology, they have placed unusual emphasis on the theories that explain the patterns, to the expense of the patterns themselves. Some specialists have taken this attitude to the extreme of implying that philosophy of biology cannot be conceived as having (an)other object of analysis besides Darwinism. Indeed, to use the wise terminology already put in place by Winther in the introduction to the opening section of this special issue, philosophy of science’s gaze on comparative biology has often assumed that systematics’ individuality as a research area has either ‘collapsed’, or that the field has been ‘engulfed’ within Evolutionary Biology. As a consequence of this philosophical outlook, systematics’ loss of autonomy reaches such a degree that the field is not easily recognized as ‘independent’ from evolutionary studies, anymore.

This situation is surprising, to say the least. Particularly, in view of a—sometimes ignored—element in the history of the theory of evolution. I specifically refer to Charles Darwin’s clear, lucid opinion on the relationships between systematics and the biological discipline that his outstanding oeuvre gave birth to. Towards the end of The Origin of Species, Darwin included a few lines that reveal that he sat comfortably within the research field responsible for the classification of biological diversity. “When the views advanced by me in this volume (…) are generally admitted”, Darwin wrote, “systematists will be able to pursue their labours as at present (…) (italics added)”. Darwin devoted years to an outstanding reflection on the ontological status of varieties, species and higher taxa. Contextualized in the knowledge of his day—and, of course, accompanied by the explanatory resources he spent so much energy devising—Darwin also described and classified biological entities in the taxonomic groups (the living barnacles, for instance) that he cared for. He did so following the systematic tradition from which his ‘new science’ evolved. Let’s say this even more succinctly: in order to shape evolutionary science the way he did, Darwin had to act as a systematist, first.

The realization of the peculiar relationship that historically has existed between philosophy of science, Darwinism and systematics is one of the main motivations behind this editorial project. As stated in its heading, the second, final section of the volume compiles papers that constitute a ‘biological point of view’ on this tri-partite meta-disciplinary structure. Each of the selected articles represents a peculiar stance, but there is—in my opinion—a significant thread that connects the whole set: the seven authors involved are (primarily) biologists, and all of them have an explicit position on the relevance of philosophical issues in systematics, Darwinism, or the two of them jointly considered. A closing piece, requested ex profeso as a ‘personal reflection’ from a distinguished fellow biologist with a long-term involvement in the philosophy of science, nicely rounds up the volume. As expressed in the other two introductions included, I personally hope that the present volume contributes to that highly satisfying, never-ending habit that many systematists and evolutionary biologists have: discussion about the conceptual foundations of their science. I think that debates on this subject might have special appeal for the international community that celebrates Darwin’s intellectual achievements this year. This will be an international celebration that, to be historically fair, should probably acknowledge also the productions of the many brilliant naturalists filling biology’s scene in 19th century Europe and Anglo-America. That collective work, ultimately, is the reason why ‘evolution’ could finally be articulated in full.

1 From a Biological Stance: 5 (+1) Viewpoints

A rather well-established historiographical fact becomes the natural starting point for the specific topic of this part of the special issue. I refer to the elaborations that led to systematics’ current stage of theoretical maturity, which have spanned a period of intense debate between conflicting points of view, directly or indirectly related to the interplay between systematic pattern and evolutionary process. A useful reformulation of the pattern/process connection is possible through the use of a standard philosophy of science resource. ‘The facts of biodiversity, organized in classifications’ can be construed as embodying an explanandum for which ‘descent with modification’ provides a corresponding explanans. Salient sociological aspects of these debates have been recognized in memorable volumes written by either professional historians and philosophers, or by heavily theory-oriented systematists. Discussions linked to the formalization of “cladistics” have received special attention in all instances, and have been estimated to bear primary importance. For my purposes at this point, it is helpful to insist that authors looking at the events from a decidedly meta-scientific perspective (as professional historians or philosophers) were not the only ones bringing conceptual issues into systematics sensu lato—or cladistics sensu stricto—to make sense of its/their development. The stances that constituted the original matter of dispute were being worked out by full-time scientists (whom, for the most part, had no professional training outside biology), but a sincere engagement in a philosophical mode is easily identifiable in much of the material published over the years. Epistemological, metaphysical and methodological issues pertinent to the inference of relationships evidently stand out as a main subject of interest in this body of biological literature. Consequently, they are constantly present throughout the section.

Phylogenetic systematics and deductive inference. From a position earned as a veteran author from the period when Hennigian cladistics was formalized, American herpetologist Arnold Kluge offers another chapter in his long-term defense of the adequacy of Popperianism as a conceptual foundation for systematics. Kluge’s place in the history of cladistics is secured, as he has played a major role—along with James S. Farris and a few others, starting in the late 1960’s, up to now—in solidifying the view that it is possible to conceive ‘phylogenetic systematics’ as a deductivism-oriented, fals(ific)ation-based scientific practice. (Other, more recent Klugean contributions to systematic theory include the concept of ‘ideographic’ characters, an idea developed in collaboration with Taran Grant, which is in turn based on the older, Farrisian notion of ‘transformation series’. The ‘ideographic character concept’ is strategically used in Kluge’s text in support of his points.) The paper by Kluge is in itself a brief compendium of Popperiana, an exercise he seems to find fit for fighting against a recent wave of arguments criticizing the validity of deductive inference in cladistics. The opinions of the Swiss paleontologist Olivier Rieppel—the indisputable present leader of the ‘anti-Popperian’ turn in systematics and himself an outstanding bio-philosopher (his paper in this volume appears a few pages upstream)—have received Kluge’s detailed attention. Curiously, though, from his self-confessed Scientific Realist standpoint, Kluge finds Rieppel to be ‘guilty’ of ‘instrumentalism’. (One among other varieties of Empiricism, Instrumentalism is the philosophical stance that conceives of scientific theories as ‘instruments’ for prediction.) For Kluge, systematists should be labelled as instrumentalists whenever they embrace ‘pattern cladistics’ (though the phrase’s meaning is not clear in this context) or positively assimilate Richard Boyd’s notion of ‘homeostatic property cluster kinds’ (HPCKs). As the reader can attest, such assimilation is the case in some of the pieces composing the ‘Philosophical Point of View’ section of the volume! The discussion between Kluge and Rieppel has an extremely intriguing side: two Realist systematists seem to be exchanging mutual accusations of ‘anti-realism’. It can be expected that questions about plurality of realist approaches in comparative biology will be developed in further exchanges between these two indispensable systematists. Kluge’s article can hardly be seen as the end of this debate.

Genomics, Popper, and the ‘Matrix of Life’. Writing also from a Hennigian cladistics tradition, E. Kurt Lienau and Robert DeSalle take, as their starting point, another local, recent discussion with a fellow systematist (Australian conservation biologist Daniel Faith). The DeSalle-Faith exchange had to do specifically with the role Popperianism presumably should have in defining the research agenda of systematic biology—namely, if such intellectual perspective (or the philosophy of science in general) should be the ‘horse’ that pulls the ‘cart of science’, or the other way around. For Lienau and DeSalle, systematics’ goal is unproblematically coherent with an evolutionary, Darwinian interpretation of pattern. In fact, they use the metaphor of the ‘Tree of Life’ (defending it in passim from recent criticisms stemming from prokaryote systematics findings, associated to the mechanism of ‘horizontal gene transfer’) to construe the corresponding notion of ‘Matrix of Life’ (MoL). Roughly, the MoL can be characterized as a truly comprehensive character matrix, that would not only include a dense selection of taxa, but a deep and thorough sampling of molecular information as well. The plausibility of such an enormous matrix depends, evidently, on the application of contemporary genomics technology (DeSalle is currently head of a molecular systematics laboratory at the American Museum of Natural History, where analyses of large amounts of DNA characters for selected taxa are carried out on a daily basis). Lienau and DeSalle argue that construction of the MoL should preoccupy systematists more than the attainment of the ToL. At the same time, they consider that MoL building invites revisiting previous applications of Popperian concepts in systematics. This, inasmuch as complex genomic data could be analyzed according to multiple ‘vantage points’, each of which “tests the content of hypotheses of relationship independently in a total evidence, supermatrix framework”. Mention of ‘supermatrices’ again makes sense as the term contrasts with ‘the supertree approach’. The latter is a practice that Lienau and DeSalle find to lack much merit, due to its bearing on only one of three potential dimensions displayed by Popperian ‘degree of corroboration’ (DOC)—i.e., empirical content (as these systematists explain, the other two dimensions are ‘precision’ and ‘universality’). The paper by Lienau and DeSalle provides additional theoretical basis for work on ‘new metrics’ (carried out elsewhere, mainly by the former author) to assess the DOC of particular ToL hypotheses.

Phylogenetic systematics and abductive inference. Specialized in polychaete classification and evolution, Kirk Fitzhugh has developed a keen interest in the conceptual foundations of systematics. The central theme that provides unity to his recent theoretical work in this area is ‘abduction’ or ‘inference to the best explanation’—for Fitzhugh, the correct reasoning mode for phylogenetic inference. Fitzhugh’s elaborations on abduction and systematics imply the articulation of a whole ‘system of methods’ that entails (recommendations of) radical changes to some of systematics’ most cherished routines. In Fitzhugh’s view, these include ‘character coding’, a task that—as usually carried out—does not properly reflect the cognitive, epistemic aspects of systematists’ access to ‘the organism’. Fitzhugh’s ideas on phylogenetic procedures run not only against Popperian falsation in systematics. His views also point out to a ‘vacuity’ in phylogenetic Bayesianism—the approach that in recent date has acquired perhaps the highest popularity among bioinformatics-oriented, molecularized students of genealogical relationships between species. In his paper, Fitzhugh attempts an ‘update’ to his previously published “definition of species as explanatory hypotheses”. Fitzhugh’s piece is, ironically, faithful in many ways to Willi Hennig’s original intention, despite its disagreement with ‘Hennig’s official heirs’ in several aspects. For its originality of approach, Fitzhugh’s work is highly recommended—it might become a classic.

Cladistics’ ‘new historiography’: criticism and counter-criticism. Key systematists of the ‘reflective’ type have traditionally stated that their intellectual commitment legitimately lies not outside, but within the natural sciences. Consider, for example, that one of the liveliest intra-disciplinary arguments in today’s systematics—the one having to do with the ‘relevance’ or ‘irrelevance’ of classification—is a discussion among specialists that very explicitly claim to be neither philosophers nor historians. First-rate systematists David Williams and Malte Ebach have taken one of the sides in that dispute—the other being represented by the equally distinguished Joseph Felsenstein—as part of their on-going construction of some of the most powerful, ‘insider’ historiographical statements on contemporary comparative biology. It is difficult to find a systematics-related issue that has not experimented criticism in the hands of Williams and Ebach. Among them, the confidence placed by younger generations of specialists on the ‘capability’ of molecular data to ‘unravel the true course of phylogenetic history’ (as was believed of paleontological information some decades ago) has probably suffered the most. With characteristic wit, the piece tells the highly significant, anecdotal story behind the inclusion of ‘three-item analysis’ in a well-known cladistics treatise, still in use in systematics courses world-wide. Additionally, Williams and Ebach argue against paraphyly, unexisting central branches in cladograms, and just about anything that—in their view—impedes the appreciation of ‘what cladistics really is’. This includes—paradoxically, for those of us interested in ‘technical’ philosophy of biology—‘scientific explanation’.

In my own contribution to this volume, I have intended to interrogate Williams and Ebach’s reconstruction of the ‘critique of paleontology’—“pattern cladistics’ true name”. My strategy is meta-historiographical: besides the discourse of these authors, I take into account David Hull’s landmark analysis of the associated controversy. In my exploration, I also use a philosophical tool: the Realism-Antirealism contrast. Proceeding in that way, I attempt to sketch a potential ‘new transformation’ of cladistics, where developmental biology could play a prominent role. Through finding great value in Olivier Rieppel’s notion of ‘causal grounding’ to recover Colin Patterson’s concerns about ontogeny, I raise the point that (the core of the) ‘constructive empiricist’ philosophy of Bas Van Fraassen might be profitably considered as a valid conceptual platform for making full sense of pattern cladistics, in the era of molecular developmental genetics. Finally, like Rasmus Winther in his article (included in Section I) and myself, Jeffrey Schwartz also finds worth looking at the relation between ontogeny and systematics. In a hopeful, final note, Schwartz not only consider that studies of epigenetics and development dissolve “the false dichotomy of molecules versus morphology”, but also suggest that seriously paying attention to the mechanisms underlying ‘the origination of form’ might help biologists find a new way to connect systematics and evolution.