The Use and Abuse of Sir Karl Popper

Karl Popper has been one of the few philosophers of sciences who has influenced scientists. I evaluate Popper's influence on our understanding of evolutionary theory from his earliest publications to the present. Popper concluded that three sorts of statements in evolutionary biology are not genuine laws of nature. I take him to be right on this score. Popper's later distinction between evolutionary theory as a metaphysical research program and as a scientific theory led more than one scientist to misunderstand his position on evolutionary theory as a scientific theory. In his later work Popper also introduced what he took to be improvements of evolutionary theory. Thus far these improvements have had almost no influence on evolutionary biology. I conclude by examining the influence of Popper on the reception of cladistic analysis.     

Popper,Laws, and the Exclusion of Biology from Genuine Science

The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper--namely, that a genuinely scientific theory is an empirically falsifiable one--is seriously mistaken, that Popper's real view was that genuinely scientific theories have the form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is the best solution to the demarcation problem between genuine science and pseudo- or non-science.     

Bühler and Popper: Kantian therapies for the crisis in psychology

I analyze the historical background and philosophical considerations of Karl Bühler and his student Karl Popper regarding the crisis of psychology. They share certain Kantian questions and methods for reflection on the state of the art in psychology. Part 1 outlines Bühler's diagnosis and therapy for the crisis in psychology as he perceived it, leading to his famous theory of language. I also show how the Kantian features of Bühler's approach help to deal with objections to his crisis diagnosis and to aspects of his linguistic theory. Part 2 turns to Popper's dissertation, completed in 1928 under Bühler. I analyze Popper's disapproval of Schlick's physicalism in psychology, as well as Popper's attempt to extend Bühler's Kantian strategy to the domain of the psychology of thinking. In conclusion, I indicate how these approaches to the crisis in psychology differ from Thomas Kuhn's notions of crisis and revolution, which are still all too popular in current philosophical discussions of psychology.     

The role of comparative morphology and anatomy in interpreting the systematics of fossil gymnosperms

This paper is an analysis of the systematics and phylogeny of gymnosperms as recently proposed by Meyen (Bot. Rev.50(1): 1–111. 1984). Attention is focused on the philosophical approach and on the fundamental concepts that frame the systematic scheme. Morphological interpretations are examined in relation to the concept of homology, and criteria employed for the recognition of whole plants from fossil evidence are evaluated. An examination of fossils from Upper Devonian and Lower Carboniferous strata reveals that only the ovules and ovulate fructifications constitute unequivocal evidence for gymnosperms in these strata. Such examination also reveals that they all can be interpreted as conforming to the same basic structure. If true, there is no evidence for more than one major group of gymnosperms in Devonian and Lower Carboniferous strata. Although many conclusions of Meyen are not accepted, his work plays a valuable role in focusing attention on important, unresolved questions of gymnosperm systematics, and provides a poignant stimulus for the proposal of alternative hypotheses.     

Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics

Practicing phylogenetic systematics as a sophisticated falsification research program provides a basis for claiming increased knowledge of sister species relationships and synapomorphies as evidence for those cladistic propositions. Research in phylogenetic systematics is necessarily cyclic, and the place where the positive shift in understanding occurs is subsequent to discovering the most parsimonious cladogram(s). A priori differential character weighting is inconsistent with seeking the maximally corroborated cladogram (sensu Popper), because weighting adds to background knowledge, the evidence being then less improbable than it would be otherwise. Also, estimating weights from character state frequencies on a cladogram is inconsistent with the view that history is unique. Sophisticated falsification provides the place in the cycle of phylogenetic systematic research where weight of evidence can be evaluated and these inconsistencies do not apply. On balance, phylogenetic systematics appears to achieve greater coherence and generality as a result of focusing on the foundations for claiming increased knowledge and avoiding efforts to differentially weight characters.     

Valentino Braitenberg: From neuroanatomy to behavior and back

This article compiles an expose of Valentino Braitenberg’s singular view on neuroanatomy and neuroscience. The review emphasizes his topologically informed work on neuroanatomy and his dialectics of brain-based explanations of motor behavior. Some of his early ideas on topologically informed neuroanatomy are presented, together with some of his more obscure work on the taxonomy of neural fiber bundles and synaptic arborizations. His functionally informed interpretations of neuroanatomy of the cerebellum, cortex, and hippocampus, are introduced. Finally, we will touch on his philosophical views and the inextricable role of function in the explanation of neural behavior.     

Batrachology of Japan and adjacent regions - a systematic review

As is the case with most other organisms, studies of amphibians started with systematics as the basis for many other biological fields, but systematics itself has endured a slower progress than other fields of biology have enjoyed for a long time. Nevertheless, philosophical and methodological 'revolutions' in the past 30 years, combined with more recent progress in biochemical and molecular techniques, have been forcing current systematics into a great change. Stejneger's (1907) monumental book, the first thorough review of amphibians from Japan and adjacent regions, was published nearly a century ago, and since then, the increase in number of areas that have been closely surveyed, together with the application of new theories and methods, have greatly enlarged our knowledge of the amphibian fauna in this region. For example, extensive experiments by the Hiroshima School using artificial hybridization techniques greatly contributed to our understandings of relationships among some groups of amphibians that had been taxonomically confusing. In addition to this, new species discovered by more detailed field surveys in a wider area and cryptic species revealed by analyses of isozymes and acoustic properties have made for a great increment in the number of taxa in this region. Further, analyses of DNA sequences now enable us to infer the affinities of taxa with few phylogenetically informative phenotypic properties, and the resultant phylogenetic hypotheses further contribute to our understandings of biogeography and many other issues on amphibian evolution. From these advances, it has been clarified that the amphibian species diversity is far greater than was previously expected, which in turn means a high endemism within particular regions. It is expected that future studies will also reveal exact systematic relationships of wide-ranging species, both those occurring within this region and those extending outside of it. For that purpose, international and interdisciplinary studies are indispensable. But what is also necessary is to conserve amphibian populations so that they will not disappear before their true relationships are realized. Knowledge of systematics among young amphibian biologists is also a matter of high priority.     

Ronald Brady and the cladists

Ronald Brady was the first philosopher to defend pattern cladistics as an independent scientific field. That independence was achieved through the decoupling of biological systematics from phylogenetics––that is, inferred evolutionary processes (e.g. character transformation). Brady saw parallels between biological systematics and Wolfgang von Goethe's Morphology, an empirical scientific field that incorporates human observation and perception to discover coherent morphological structures. Goethe's Morphology and pre-Darwinian systematics were independent from evolutionary narratives, a tradition that continued into the 20th Century through the work of biologists such as Agnes Arber. Most importantly, Brady provided the philosophical and historical foundations to an independent systematics by demonstrating the links between phenomenology, Goethe's Morphology and comparative biology.     

Is there a direct ontogenetic criterion in systematics?

Much recent literature focuses on whether ontogenetic information can be used as a direct criterion for determining the polarity of character trasformations in systematic analysis. This paper reviews the relevant literature and concludes that the ontogenetic criterion is dependent on parsimony rather than the sequence observed during ontogeny. It is not, therefore, based on the discredited arguments of recapitulation. From the perspective of phyologenetic systematics the ontogenetic criterion is a valid means of polarizing character transformations that represents a special case of a broader methodology involving parsimony. The alternative perspective perspective of patttern cladistics holds that polarity should be contained within the data and not imposed upon it. Thus, ontogeny is not required to polarize characters, but ontogenetic information can generate unequivocal character interpretations in terms of the relative generality of related attributes, and in the sense that absence precedes presence. Furthermore, ontogeny is central to systematics, providing empirical evidence of character transformation, information on the whole life cycle and an escape from systematics being teleologically related to phylogenetic inference and the theory of evolution.     

Six things Popper would like biologists not to ignore: In memoriam, Karl Raimund Popper, 1902–1994

To honour the memory of Sir Karl Popper, I put forward six elements of his philosophy which might be of particular interest to biologists and to philosophers of biology and which I think Popper would like them not to ignore, even if they disagree with him. They are: the primacy of problems; the criticizability of metaphysics (and thus the dubiousness of materialism); how downward causation might be real; how norms should matter to scientists; why dogmatism should be avoided; how genuine science is recognizable. I preface these six things with a brief discussion of Popper's early (but later recanted) mistakes concerning biology.     

浅论性状加权

本文从生物分类学理论的一些基本问题分析入手,论述了性状加权的哲学基础和生物学意义,对不同学派的观点从理论上进行了客观分析,并提出了作者本人的一些新的看法。     

The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference

The philosopher Karl Popper described a concept termed degree of corroboration , C , for evaluating and comparing hypotheses according to the results of their tests. C is, fundamentally, a comparison of two likelihoods: p ( e|hb ), the likelihood of the hypothesis ( h ) in conjunction with the background knowledge ( b ), and p ( e|b ), the likelihood of b alone. C is closely related to the likelihood ratio of nested hypotheses. When phylogenetic analysis is interpreted as an attempt to assess C for a phylogenetic tree (the hypothesis, h ), several interpretations have been given for p ( e|b ). Here I describe a new interpretation that equates p ( e|b ) with the probability of the data in the absence of a hypothesis of phylogenetic resolution, that is with the likelihood of an unresolved or polytomous tree. Under this interpretation, C for a fully or partially resolved phylogenetic tree is the likelihood of that tree minus the likelihood of the corresponding unresolved tree. These same two likelihoods can be used in a likelihood ratio test (LRT) to assess the significance of the degree of corroboration of the hypothesis of phylogenetic resolution. This LRT for resolution is closely related to permutation tests for phylogenetic structure in the data, because data that evolved on a true polytomous tree are expected to be phylogenetically randomized. It therefore reconciles the interpretation of the evidence ( e ) as the distribution of character states among taxa (rather than the score of the optimal tree) with the interpretation of permutation tests as methods for assessing C. Likelihood methods are (contrary to the views of some commentators) central to understanding how Popper's C applies to phylogenetic hypotheses, and they form the foundation of a unified and inclusive philosophy of phylogenetic inference.     

Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration

Advocates of cladistic parsimony methods have invoked the philosophy of Karl Popper in an attempt to argue for the superiority of those methods over phylogenetic methods based on Ronald Fisher's statistical principle of likelihood. We argue that the concept of likelihood in general, and its application to problems of phylogenetic inference in particular, are highly compatible with Popper's philosophy. Examination of Popper's writings reveals that his concept of corroboration is, in fact, based on likelihood. Moreover, because probabilistic assumptions are necessary for calculating the probabilities that define Popper's corroboration, likelihood methods of phylogenetic inference--with their explicit probabilistic basis--are easily reconciled with his concept. In contrast, cladistic parsimony methods, at least as described by certain advocates of those methods, are less easily reconciled with Popper's concept of corroboration. If those methods are interpreted as lacking probabilistic assumptions, then they are incompatible with corroboration. Conversely, if parsimony methods are to be considered compatible with corroboration, then they must be interpreted as carrying implicit probabilistic assumptions. Thus, the non-probabilistic interpretation of cladistic parsimony favored by some advocates of those methods is contradicted by an attempt by the same authors to justify parsimony methods in terms of Popper's concept of corroboration. In addition to being compatible with Popperian corroboration, the likelihood approach to phylogenetic inference permits researchers to test the assumptions of their analytical methods (models) in a way that is consistent with Popper's ideas about the provisional nature of background knowledge.     

A composite species-level phylogeny of the 'Insectivora' (Mammalia: Order Lipotyphla Haeckel, 1866)

The first MRP (matrix representation with parsimony) supertree phylogeny of the Lipotyphla is presented, covering all the families that were considered to make up the traditional mammalian order Insectivora. The phylogeny does not examine relationships within the shrew subfamily Crocidurinae, but all other taxa are considered at the species level, drawing upon 41 years of systematic literature and combining information from 47 published sources. The MRP technique is also critically discussed. This study will be of use to comparative biology studies of the Lipotyphla (or of mammals as a whole) and is a rigorous review of past systematic work, as well as clearly demonstrating our current level of knowledge. The supertree clearly details a strong imbalance in phylogenetic understanding across the taxon: a great deal is known about the hedgehogs and gymnures (Erinaceidae), the New World moles (Talpidae), Palaearctic species of Sorex (subgenus Sorex ) and the relationships between genera of red-toothed shrews (Soricinae). The supertree, however, clearly shows areas where our knowledge is conflicting or non-existent, and these gaps do not always correspond to obscure species: nothing is known about the systematics of Old World mole genera. Also very little is known about golden moles (Chrysochloridae) and the shrew-tenrec genus Microgale , some of the most threatened mammals on Earth.     

Competing views on cancer

Despite intense research efforts that have provided enormous insight, cancer continues to be a poorly understood disease. There has been much debate over whether the cancerous state can be said to originate in a single cell or whether it is a reflection of aberrant behaviour on the part of a ‘society of cells’. This article presents, in the form of a debate conducted among the authors, three views of how the problem might be addressed. We do not claim that the views exhaust all possibilities. These views are (a) the tissue organization field theory (TOFT) that is based on a breakdown of tissue organization involving many cells from different embryological layers, (b) the cancer stem cell (CSC) hypothesis that focuses on genetic and epigenetic changes that take place within single cells, and (c) the proposition that rewiring of the cell’s protein interaction networks mediated by intrinsically disordered proteins (IDPs) drives the tumorigenic process. The views are based on different philosophical approaches. In detail, they differ on some points and agree on others. It is left to the reader to decide whether one approach to understanding cancer appears more promising than the other.     

Value theory and the best interests standard

The idea of a patient's best interests raises issues in prudential value theory–the study of what makes up an individual's ultimate (nonmoral) good or well-being. While this connection may strike a philosopher as obvious, the literature on the best interests standard reveals almost no engagement of recent work in value theory. There seems to be a growing sentiment among bioethicists that their work is independent of philosophical theorizing. Is this sentiment wrong in the present case? Does value theory make a significant difference in interpreting best interests? In pursuing this question, I begin with a quick sketch of broad kinds of value theories, identifying representatives that are plausible enough to count as contenders. I then explore what each account suggests in (1) neonatal treatment decisions, and (2) decisions for patients in persistent vegetative states. I conclude that while these accounts converge somewhat in their interpretations of best interests, they also have importantly different implications.     

Platyhelminth systematics and the emergence of new characters

Since the inclusion of molecular data in modern phylogenetic analyses, significant progress in resolving the origins and radiation of flatworms has been made, although some key problems remain. Here I review developments in the supply and use of systematic characters that provide the basis for diagnosis and phylogeny reconstruction, that in turn have driven systematic revisions and the interpretation of broader evolutionary patterns and processes; focus is placed on the parasitic taxa. Although useful tools have been refined to the point of becoming established systematic markers of broad utility, attention to the need for denser gene and taxon sampling is addressed in the light of unresolved questions and current trends in molecular systematics, from nucleotide to genome. Tradition and the nature of available comparative information tends to dictate the choice of systematic markers, but faced with incongruent phylogenies, the emergence of new technologies and the need for rapid species diagnosis, there is a pressing need to assess and standardize our choice of tools so they are fit for purpose, available to all and used widely. I present a brief review of existing and potential sources of phylogenetic characters and discuss their likely value in the context of the systematics and diagnostics of parasitic flatworms.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”