Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters (sensu Olivier Rieppel) in modern developmental biology’s (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology.     

Out-of-school experience categories influencing interest in biology of secondary school students by gender: exploration on an Abu Dhabi sample

This study employed the international Relevance of Science Education questionnaire to survey the interest in biology and the out-of-school experiences of Abu Dhabi secondary school students (median age 17, mean age 17.53 and mode age of 16) in the third semester of 2014. It included 3100 participants. An exploratory factor analysis was used to categorise the items for both interest in biology and out-of-school experience. Ten interest in biology and 12 out-of-school experience factors were extracted. The summated means for each factor indicated that ‘health and fitness’ and ‘disease control’ enjoyed highest interests among students. For out-of-school experiences, the two factors of ‘digital applications’ and ‘medical treatment’ received the highest scores. Multivariate analysis of variance revealed that all factors for both interest in biology and out-of-school experience exhibited significant differences between boys and girls. More girls than boys were interested in disease control, reproduction (human biology), alternative science, health and fitness, zoology, and applied cosmetic biology. No significant differences were observed for the remaining five other categories. Furthermore, analysis of variance revealed significant differences between boys and girls with regard to individual items comprising each of the factors. The highest correlations were between the two factors of out-of-school experiences of ‘the natural world’ and ‘learning through observation’ and the interest in biology factor related to ‘plant and animal farming and agriculture’. Results suggested that more emphasis must be placed on students’ out-of-school experience and their engagement in informal learning in contextual outdoor environments to enhance their interest in learning more about biology and the living environment in general.     

Gould on Laws in Biological Science

Are there laws in evolutionary biology? Stephen J. Gould has argued that there are factors unique to biological theorizing which prevent the formulation of laws in biology, in contradistinction to the case in physics and chemistry. Gould offers the problem of ’’complexity‘‘ as just such a fundamental barrier to biological laws in general, and to Dollo‘s Law in particular. But I argue that Gould fails to demonstrate: (1) that Dollo‘s Law is not law-like, (2) that the alleged failure of Dollo‘s Law demonstrates why there cannot be laws in biological science, and (3) that ’’complexity‘‘ is a fundamental barrier to nomologicality.     

An attempt to construct a (general) mathematical framework to model biological “context-dependence”

Context-dependent nature of biological phenomena is well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various (particular) facets of biological context-dependence, a formal and general mathematical construct to model the wide spectrum of context-dependence, eludes the students of biology. Such an objective model, from both ‘bottom-up’ as well as ‘top-down’ perspective, is proposed here to serve as the template to describe the various kinds of context-dependence that we encounter in different branches of biology. Interactions between biological contexts was found to be transitive but non-commutative. It is found that a hierarchical nature of dependence among the biological contexts models the emergent biological properties efficiently. Reasons for these findings are provided in a general model to describe biological reality. Scheme to algorithmically implement the hierarchic structure of organization of biological contexts was proposed with a construct named ‘Context tree’. A ‘Context tree’ based analysis of context interactions among biophysical factors influencing protein structure was performed.     

Scientific perspectivism: A philosopher of science's response to the challenge of big data biology

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science to slip into the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena.     

Experiences in Teaching Scientific Writing in the U.S.A.

The origin and intended meaning of the phrase ‘survival of the fittest’ are discussed. The development of the concept of ‘fitness’ in a neo-Darwinian sense is traced, and the use of the term in other contexts is outlined. The treatment of ‘fitness’ in various popular biology texts is considered, and some suggestions about the use of the term in schools are made.

The relationship of interpretations of ‘fitness’ to a broader understanding of evolutionary mechanisms is stressed throughout.     

The influence of genetics on future crop production strategies: from traits to genes, and genes to traits

This paper discusses how a genetical approach to plant physiology can contribute to research underpinning the production of new crop varieties. It highlights the interactions between genetics and plant breeding and how the current advances in genetics and the new science of genomics can contribute to our understanding of the genetical control of key agronomic traits ‐ the process of ‘translating’ traits to identified and mapped genes. Advances in genomics, such as the sequencing of whole genomes and expressed sequence tags, are producing information on genes and gene structures, but without knowing their function. A great deal more biology will be necessary to translate gene structure to function ‐ the process of translating genes to traits. Combining these ‘forward’ and ‘reverse’ genetic approaches will allow us to get comprehensive knowledge of the biology of agronomic traits at the physiological, biochemical and molecular levels, so that the ‘circuitry’ of our crop plants can be elucidated. This will enable plant breeders to manipulate crop phenotype using marker‐assisted breeding or genetic engineering approaches with a precision not previously possible.     

Separating ‘Inquiry Questions’ and ‘Techniques’ to Help Learners Move between the How and the Why of Biology Practical Work

School science practical activities have been criticised for exposing learners to a series of phenomena disconnected from the conceptual frameworks needed to understand them. Such activities are successful in the ‘domain of observables’ but not the ‘domain of ideas’. Few resources exist for classroom teachers wishing to improve the effectiveness of practical activities in the domain of ideas. This report describes an action research project to develop a scaffold for biology practical lessons. This scaffold separates inquiry questions and the techniques needed to address them, and thus combines two approaches to scaffolding in a single tool (‘problematising’ and ‘reducing the degrees of freedom’). Analysis of the speech of 16–17 year olds in the study class (n = 23) was used to assess their engagement in the domain of ideas. Following the scaffold’s introduction, the learners were found to speak more about relevant ideas and concepts during practical activities. When the scaffold was partially faded, the learners continued to demonstrate engagement with the domain of ideas. The approach reported here would seem to have much potential for supporting learning from ‘minds-on’ biology practical work in a variety of contexts.     

More on how and why: cause and effect in biology revisited

In 1961, Ernst Mayr published a highly influential article on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr argued that proximate causes (e.g. physiological factors) and ultimate causes (e.g. natural selection) addressed distinct ‘how’ and ‘why’ questions and were not competing alternatives. That distinction retains explanatory value today. However, the adoption of Mayr’s heuristic led to the widespread belief that ontogenetic processes are irrelevant to evolutionary questions, a belief that has (1) hindered progress within evolutionary biology, (2) forged divisions between evolutionary biology and adjacent disciplines and (3) obstructed several contemporary debates in biology. Here we expand on our earlier (Laland et al. in Science 334:1512–1516, 2011) argument that Mayr’s dichotomous formulation has now run its useful course, and that evolutionary biology would be better served by a concept of reciprocal causation, in which causation is perceived to cycle through biological systems recursively. We further suggest that a newer evolutionary synthesis is unlikely to emerge without this change in thinking about causation.     

Crisis in Biology An Examination of the Deficiencies in the Current Pattern of Expansion in Biological Education

A method of analysing the content of biology curricula, courses, and texts on the basis of the relative emphasis laid on different levels of biological organization, is discussed. It is suggested that this method may have led to unwarranted contrasts between ‘traditional’ and ‘modern’ curricula. A simple modification to this method is proposed.     

Has Grafen formalized Darwin?

One key aim of Grafen’s Formal Darwinism project is to formalize ‘modern biology’s understanding and updating of Darwin’s central argument’. In this commentary, I consider whether Grafen has succeeded in this aim.     

The Age of Angels: spiritualism and evolutionary progressionism in a nineteenth-century geologic time chart

The term ‘Anthropocene’ often carries apocalyptic overtones of environmental devastation, but many nineteenth-century iterations of the ‘Age of Humans’ idea were explicitly optimistic. The current time period was framed as a ‘Psychozoic Era’ or ‘Age of Mind’ in which human beings took their predetermined place at the pinnacle of ‘creation’. Hiram Alvin Reid, an amateur scientist in the midwestern United States, took this line of thinking a step further. He drafted a geologic time chart in which the current ‘Age of Man’ was succeeded by a future ‘Age of Angels’, wherein humans will become higher beings. Reid was a Christian spiritualist who thought that evolution drove both physical and spiritual advancement, including the recent development of a ‘sixth sense’ that allowed humans to perceive ghosts and angels. Reid’s views, while idiosyncratic and coloured by his metaphysical beliefs, drew heavily on mainstream concepts in biology and geology. Prominent geologists like James Dana and Joseph Le Conte argued for an Age of Mind in terms that mixed scientific rigor with religious and progressionist ideas. The Psychozoic was also embraced by many progressive-minded individuals outside the natural sciences, paralleling widespread modern interest in the Anthropocene.     

Secondary galling: a novel feeding strategy among ‘non‐pollinating’ fig wasps from Ficus curtipes

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How was teleology eliminated in early molecular biology?

This paper approaches the issue of the status of teleological reasoning in contemporary biology through a historical examination of events of the 1930s that surrounded Niels Bohr’s efforts to introduce ‘complementarity’ into biological discussions. The paper examines responses of three theoretical physicists who engaged boundary questions between the biological and physical sciences in this period in response to Bohr—Ernst Pascual Jordan (1902–80), Erwin Schrödinger (1887–1961), and Max Delbrück (1906–81). It is claimed that none of these physicists sufficiently understood Bohr’s ‘critical’ teleological arguments, which are traced to the lineage of Kant and Harald Høffding and their respective resolutions of the Antinomy of Teleological Judgment. The positions of these four historical actors are discussed in terms of Ernst Mayr’s distinction of ‘teleological,’ ‘teleomatic,’ and ‘teleonomic’ explanations. A return to some of the views articulated by Bohr, and behind him, to Høffding and Kant, is claimed to provide a framework for reintroducing a ‘critical’ teleology into biological discussions.     

Procedural understanding in biology: the ‘thinking behind the doing’

Several developments in science education aim to improve pupils' ability to ‘think scientifically’. This paper argues for the explicit teaching of the ideas that pupils need to ‘think about’ to do this; ideas related to the design of investigations and the collection, presentation, analysis, and evaluation of the resulting evidence — ideas which are important both for pupils who continue to study or work with biology and for all pupils to become biologically literate. This paper considers some of the concepts of evidence which are particularly important to biology, and discusses how and why the ideas could be taught.     

Advanced-level Biology—A Possible Approach

Teachers' conscious priorities in selecting topics for teaching rarely include the ‘biology/social science interfaces’; neither are many usually aware of the existence and implications of ‘hidden ideologies’ in the curriculum. This paper gives several examples of such interfaces, and stresses the point that only by redirecting the education of teachers can their awareness and priorities be suitably altered.     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

Synthetic biology and its alternatives. Descartes,Kant and the idea of engineering biological machines

The engineering-based approach of synthetic biology is characterized by an assumption that ‘engineering by design’ enables the construction of ‘living machines’. These ‘machines’, as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes’s and Kant’s thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology’s engineering paradigm.