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.     

Preparation and heteronuclear 2D NMR spectroscopy of a DNA dodecamer containing a thymidine residue with a uniformly 13C-labeled deoxyribose ring

Summary [¹³C₅]-2-Deoxy-d-ribose, synthesized from [¹³C₆]-d-glucose (98% ¹³C), was coupled with thymine to give [1,2,3,4,5-¹³C₅]-thymidine (T) in an 18% overall yield. The thymidine was converted to the 3-phosphoramidite derivative and was then incorporated into a dodecamer 5-d(CGCGAATTCGCG)-3 by solid-phase DNA synthesis. Preparation of 0.24 mole of the labeled dodecamer, which is sufficient for a single NMR sample, consumed only 25 mg of glucose. By virtue of the ¹³C labels, all of the ¹H-¹H vicinal coupling constants in the sugar moieties were accurately determined by HCCH-E.COSY.     

Mutational specificity of ethyl methanesulfonate in excision-repair-proficient and -deficient strains of Drosophila melanogaster

Summary The vermilion gene was used as a target to determine the mutational specificity of ethyl methanesulfonate (EMS) in germ cells of Drosophila melanogaster. To study the impact of DNA repair on the type of mutations induced, both excision-repair-proficient (exr ⁺) and excision-repair-deficient (exr ^–) strains were used for the isolation of mutant flies. In all, 28 mutants from the exr ⁺ strain and 24 from the exr ^– strain, were characterized by sequence analysis. In two mutants obtained from the exr ⁺ strain, small deletions were observed. All other mutations were caused by single base-pair changes. In two mutants double base-pair substitutions had occurred. Of the mutations induced in the exr ⁺ strain, 22 (76%) were GCAT transitions, 3 (10%) ATTA transversions, 2 (6%) GCTA transversions and 2 (6%) were deletions. As in other systems, the mutation spectrum of EMS in Drosophila is dominated by GCAT transitions. Of the mutations in an exr ^– background, 12 (48%) were GCAT transitions, 7 (28%) ATTA transversions, 5 (20%) GCTA transversions and 1 (4%) was a ATGC transition. The significant increase in the contribution of transversion mutations obtained in the absence of an active maternal excision-repair mechanism, clearly indicates efficient repair of N-alkyl adducts (7-ethyl guanine and 3-ethyl adenine) by the excision-repair system in Drosophila germ cells.     

Evolutionary Morphology, Innovation, and the Synthesis of Evolutionary and Developmental Biology

One foundational question in contemporarybiology is how to `rejoin evolution anddevelopment. The emerging research program(evolutionary developmental biology or`evo-devo) requires a meshing of disciplines,concepts, and explanations that have beendeveloped largely in independence over the pastcentury. In the attempt to comprehend thepresent separation between evolution anddevelopment much attention has been paid to thesplit between genetics and embryology in theearly part of the 20th century with itscodification in the exclusion of embryologyfrom the Modern Synthesis. This encourages acharacterization of evolutionary developmentalbiology as the marriage of evolutionary theoryand embryology via developmental genetics. Butthere remains a largely untold story about thesignificance of morphology and comparativeanatomy (also minimized in the ModernSynthesis). Functional and evolutionarymorphology are critical for understanding thedevelopment of a concept central toevolutionary developmental biology,evolutionary innovation. Highlighting thediscipline of morphology and the concepts ofinnovation and novelty provides an alternativeway of conceptualizing the `evo and the `devoto be synthesized.     

The Philosophy of Donald T. Campbell: A Short Review and Critical Appraisal

Aside from his remarkable studies in psychology and the social sciences, Donald Thomas Campbell (1916–1996) made significant contributions to philosophy, particularly philosophy of science,epistemology, and ethics. His name and his work are inseparably linked with the evolutionary approach to explaining human knowledge (evolutionary epistemology). He was an indefatigable supporter of the naturalistic turn in philosophy and has strongly influenced the discussion of moral issues (evolutionary ethics). The aim of this paper is to briefly characterize Campbells work and to discuss its philosophical implications. In particular, I show its relevance to some current debates in the intersection of biology and philosophy. In fact, philosophy of biology would look poorer without Campbells influence. The present paper is not a hagiography but an attempt to evaluate and critically discuss the meaning of Campbells work for philosophy of biology and to encourage scholars working in this field to read and re-read this work which is both challenging and inspiring.     

Genetic exchanges caused by ultraviolet photoproducts in phage λ DNA molecules: The role of DNA replication

Summary Genetic recombination induced by structural damage in DNA molecules was investigated in E. coli K12 () lysogens infected with genetically marked phage . Photoproducts were induced in the phage DNA before infection by exposing them either to 313 nm light in the presence of acetophenone or to 254 nm light. To test the role of the replication of the damaged phage DNA on the frequency of the induced recombination, both heteroimmune and homoimmune crosses were performed.First, samples of a heteroimmune phage imm434 P80 exposed to these treatments were allowed to infect cells lysogenic for prophage cI857 P3. Phage DNA replication and maturation took place, and the resulting progeny phages were assayed for the frequency of P ⁺ recombinants. Recombination was less frequent in infected cells exposed to visible light and in wild type cells able to perform excision repair than in excision-defective lysogens. Therefore, much of the induced recombination can be atributed to the pyrimidine dimers in the phage DNA, the only photoproducts known to be dissociated by photoreactivating enzyme.Second, in homoimmune crosses, samples of similarly treated homoimmune P3 phages were allowed to infect lysogens carrying cI857 P80. Replication of the phage DNA containing ultraviolet photoproducts was repressed by immunity, and was futher blocked by the lack of the P gene product needed for replication. The lysogens were purified and scored for both colony forming ability and for P ⁺ recombinant prophages. The 254 nm photoproducts increased the frequency of recombination in these homimmune crosses, even though phage DNA replication was blocked. Irradiation with 313 nm light and acetophenone M, which produces dimers and unknown photoproducts, was not as effective per dimer as the 254 nm light.It is concluded from these results that certain unidentified 254 nm photoproducts can cause recombination even in the absence of DNA replication. They are not pyrimidine dimers, as they are not susceptible to excision repair or photoreactivation. In contrast, pyrimidine dimers appear to cause recombination only when the DNA containing them undergoes replication.     

Green fluorescent protein (GFP) as a marker during pollen development

The transient expression of three mutant forms of green fluorescent protein (GFP) genes, GFP4, GFP5ER, and GFP4S65C, under several constitutive and pollenspecific promoters throughout pollen development in Nicotianatabacum, thaliana and Antirrhinummajus is described. Immature pollen of tobacco, Arabidopsis and snapdragon, isolated at different developmental stages, were bombarded with plasmids containing the GFP and cultured in vitro for several days until maturity. The expression of GFP was monitored every day during in vitro maturation, germination and pollination, as well as after in situ pollination. The expression pattern of each construct was compared in parallel experiments to that of ßglucuronidase (GUS) constructs expressed by the same promoters. The results show that the expression level of all three GFP mutant forms was dependent on the strength of the promoter used. The strongest promoter was the DC3 promoter, and no notable differences in the intensity and brightness of all three versions of GFP were observed. GFPexpressing pollen from tobacco and snapdragon developed in vitro for several days until maturity and germinated in vitro as well as on the surface of stigmata, strongly suggesting that all three GFPs are not toxic for the development of functional pollen. Furthermore, stably transformed tobacco plants expressing GFP under the control of the strong pollenexpressed DC3 and LAT52 promoters were not impaired in reproductive function, confirming that GFP can be used as a nondestructive marker for plant reproductive biology and development.     

Feeding groups, lifetypes and the global ecology of termites

Two termite functional classifications (Abes lifetypes and Donovans feeding groups) are evaluated, and then synthesized to make a single unified lifeway matrix classification with eight categories. The systematics and biogeography of the lifeway groups are outlined. The lifeways are then tested against other relevant data on termite ecology (stable isotopes, molecular probes, survey data) to show that they consistently reflect real distinctions in termite biology. The advantages and disadvantages of each lifeway are discussed in the context of energy availability, nitrogen balance, foraging and nest-building energetics, and biogeographical dispersal ability. Finally, an ecological evolutionary scheme is outlined for the global ecology of termites using the lifeway classification as a framework.     

Testing evolutionary hypotheses for phenotypic divergence using landscape genetics

Understanding the evolutionary causes of phenotypic variation among populations has long been a central theme in evolutionary biology. Several factors can influence phenotypic divergence, including geographic isolation, genetic drift, divergent natural or sexual selection, and phenotypic plasticity. But the relative importance of these factors in generating phenotypic divergence in nature is still a tantalizing and unresolved problem in evolutionary biology. The origin and maintenance of phenotypic divergence is also at the root of many ongoing debates in evolutionary biology, such as the extent to which gene flow constrains adaptive divergence ( Garant et al. 2007 ) and the relative importance of genetic drift, natural selection, and sexual selection in initiating reproductive isolation and speciation ( Coyne & Orr 2004 ). In this issue, Wang & Summers (2010) test the causes of one of the most fantastic examples of phenotypic divergence in nature: colour pattern divergence among populations of the strawberry poison frog (Dendrobates pumilio) in Panama and Costa Rica ( Fig. 1 ). This study provides a beautiful example of the use of the emerging field of landscape genetics to differentiate among hypotheses for phenotypic divergence. Using landscape genetic analyses, Wang & Summers were able to reject the hypotheses that colour pattern divergence is due to isolation‐by‐distance (IBD) or landscape resistance. Instead, the hypothesis left standing is that colour divergence is due to divergent selection, in turn driving reproductive isolation among populations with different colour morphs. More generally, this study provides a wonderful example of how the emerging field of landscape genetics, which has primarily been applied to questions in conservation and ecology, now plays an essential role in evolutionary research.

Figure 1 Open in figure viewer PowerPoint Divergent colour morphs observed among populations of the strawberry poison frog, Dendrobates pumilio. Frogs are from San Cristobal (upper left), Cerro Brujo (upper right), Bastimentos (lower right), and Agua (lower left).     

Reductionism Redux: Computing the Embryo

This paper argues that the consensus physicalist antireductionism in the philosophy of biology cannot accommodate the research strategy or indeed the recent findings of molecular developmental biology. After describing Wolperts programmatic claims on its behalf, and recent work by Gehring and others to identify the molecular determinants of development, the paper attempts to identify the relationship between evolutionary and developmental biology by reconciling two apparently conflicting accounts of bio-function – Wrights and Nagels (as elaborated by Cummins). Finally, the paper seeks a way of defending the two central theses of physicalist antireductionism in the light of the research program of molecular developmental biology, by sharply reducing their metaphysical force.     

Peasants in primitive accumulation: Western Europe and Venezuela compared

Conclusion: The internal market and capitalist development The basic point of this comparison has already been implied. I noted above that primitive accumulation consists of two processes: (1) capital accumulation, and (2) proletarianization. These are, in turn, part of a more general process: the creation of an internal market for capitalism, i. e., a market for means of production and a market for labor power. Yet what is internal and what is external depends on our levels of analysis. When we refer to the development of capitalism in a particular country, e.g. Venezuela or England or Russia, we must examine internal and external markets with reference to the economic formation. But when we are referring to a market for goods, the importance of the distinction between internal and external markets (i.e., intra-state or national market vs. foreign trade) is reduced. When, however, we refer to the development of a market for labor power, the problem takes on special significance. Whereas goods as commodities may flow easily across state boundaries, labor power as a commodity cannot be as free [59]. We must direct our analysis primarily to the market for capital and labor power.It has been argued that a capitalist mode of production developed in England and other countries of Western Europe because an internal market for capitalism emerged within particular economic formations. While these formations depended on foreign markets for goods, they developed an internal market for capital and labor power. Venezuela was part of the internal market of the capitalist system, but its position in that system prohibited the development of an internal market for capital and labor power within the economic formation of Venezuela. This difference can be explained with reference to the respective positions of the formations within the inter-state capitalist system: Western Europe at the center; Venezuela at the periphery.But this study implies another, cognate conclusion which I cannot pursue here, namely, that capitalism cannot be rationalized either as the relatively progressive fate of under-developed peoples, or as an inevitable forerunner of socialism in whatever place the struggle for socialism develops [60].     

The Road from Haeckel: The Jena Tradition in Evolutionary Morphology and the Origins of “Evo-Devo”

With Carl Gegenbaur and Ernst Haeckel, inspiredby Darwin and the cell theory, comparativeanatomy and embryology became established andflourished in Jena. This tradition wascontinued and developed further with new ideasand methods devised by some of Haeckelsstudents. This first period of innovative workin evolutionary morphology was followed byperiods of crisis and even a disintegration ofthe discipline in the early twentieth century.This stagnation was caused by a lack ofinterest among morphologists in Mendeliangenetics, and uncertainty about the mechanismsof evolution. Idealistic morphology was stillinfluental in Germany, which prevented a fullappreciation of the importance of Darwinstheory of natural selection for comparativemorphology. Evolutionary morphology andembryology failed to contribute significantlyto the modern synthesis of evolutionarybiology, thereby probably delaying theintegration of developmental biology intomodern evolutionary biology. However, Haeckelsstudent Oscar Hertwig, as well as Victor Franzand Alexej N. Sewertzoff from a youngergeneration, all tried to forge their ownsynthetic approaches in which (inspired byHaeckels work) embryology played an importantrole. Important for all three researchers wereattempts to refine, and sometimes redefine, thebiogenetic law, and to find new scientificexplanations for it (and for the manyexceptions to it). Their research was latermore or less forgotten, and had littleinfluence on the architects of the modernsynthesis. As the relationship betweenevolutionary and developmental biology is nowagain rising in importance in the form ofEvo-Devo, we would like to draw attention tohow this earlier research tradition grappledwith similar questions to those now on theagenda, albeit from sometimes quite differentperspectives.     

Unusual prophase structures and multiple nucleoli in male meiosis of Drosophila species of the virilis group

With silver nitrate (Ag-NOR) staining, unusual fibrillar structures, apparently coupled to the nucleolus, were found is several species of the D. virilis group. In D. littoralis, beaded strings appear in connection with these structures, whereas the late prophase is characterized by the appearance of multiple nucleoli in the nucleoplasm. In D. virilis, the nucleus has a prominent pointed protrusion in the region of the nucleolus and often a fibril protrudes from this point. Small nucleoli are budding from the nucleolus during prophase. The multiple nucleoli at late prophase are smaller and fewer. A nucleolar body with black spots appears at prometaphase and persists through metaphase and anaphase. In D. lummei, the nucleolus becomes surrounded by fibrils, which are released into the nucleoplasm and on which multiple nucleoli are synthesized.These phenomena are similar to the events described in oocyte meiosis of many animals, where rDNA amplification, coupled to the synthesis of multiple nucleoli in late prophase, has been established.     

Ubiquitin — protein conjugates

Summary The data available at present indicates there are three distinct functions of ubiquitin, two of which are related to protein conjugation. The first of these has been extensively studied by our laboratory and others interested in nucleosomes and changes in chromatin states. The ubiquitin-histone (Ub-2A, Ub-2B) conjugation reaction now appears to be a very dynamic process. In the deconjugation (lyase) reaction, both the histone 2A and the ubiquitin are left intact and in a form which makes possible ready reconjugation. Accordingly, this may be a mechanism for moment-to-moment control of the genome.The second function in which ubiquitin is conjugated involves proteolytic activity. This activity is correlated with protein turnover. In this process, the ubiquitin-protein conjugate apparently serves as a signal for the protease cleavage of the protein. The released ubiquitin is also intact and is probably available for reconjugation.In the third function, ubiquitin was suggested to serve as hormone. The studies thus far have been carried out primarily on induction of T- and B-lymphocytes, reduction or delay of Coombs' positivity and reduction of spleen weight. The precise physiological role of this reported function is still unclear, particularly because the ubiquitin used was probably not the physiologically active form.     

Structure of tanacetan,a pectic polysaccharide from tansy Tanacetum vulgare L

Tanacetan TVF was found to have a branched structure with a backbone of linear -1,4-D-galacturonan. The ramified regions consist of linear -1,2-L-rhamno--1,4-D-galacturonan as the core. The side chains appear to attach to the 4-position of the L-rhamnopyranose residues. They are present as single -galactopyranose residues or a branching -1,4-galactopyranan bearing 4,6-substituted -D-galactopyranose residues as branched points. In addition, the ramified regions contain side chains of a branched -1,5-arabinofuranan possessing 2,5- and 3,5-substituted -L-arabinofuranose residues as branching points. Some side chains of rhamnogalacturonan appear to be arabinogalactan which contains branched sugar chains of -1,5-arabinofuranan attached to the linear chains of -1,4-galactopyranan by 1,3- and 1,6-linkages. The residues of -L-arabinofuranose seem to occupy the terminal positions of the arabinogalactan side chains.     

The fitness costs of senescence: The evolutionary importance of events in early adult life

Summary The increased mortality caused by ageing represents a fitness cost to organisms. This paper develops techniques for determining the proportions of that cost that accrue at each age. A variety of analyses using several different sources of data on human ageing—palaeodemographic life tables and life tables from more recent societies with high mortality rates—all suggest that the fitness cost of ageing was high during most of our evolutionary history, and was largely due to physiological changes occurring early in adult life. These results imply that predictions about the nature of senescence based on evolutionary theory should be tested using data from middle-aged individuals. They also have implications about the relative importances for human evolution of the pleiotropy and mutation-accumulation theories of the evolution of senescence, and for the validity of Gompertz Law' for the shape of the relationship between mortality and age. An analysis of a life table of the African buffalo suggests that the costs of ageing early in adult life are relatively high in at least one non-human species in its natural environment.     

Protein sorting and expression of a unique soybean cotyledon protein,GmSBP, destined for the protein storage vacuole

The initial biochemical characterization of the soybean sucrose-binding protein, GmSBP, within our lab and others produced several incongruous characteristics that required a re-characterization of GmSBP via sequence homology, cell biology, immunolocalization, and semi-quantitative analysis. The GmSBP proteins share amino acid sequence homology as well as putative structural homology with globulin-like seed storage proteins. A comparison to the major soybean seed storage proteins, glycinin and -conglycinin established several storage protein-like characteristics for GmSBP. All three proteins were present in a prevacuolar compartment and protein storage vacuole. All three proteins increased in expression during seed development and are remobilized during germination. Quantitatively, the relative concentrations of GmSBP, -conglycinin (/ subunits), and glycinin (acidic subunits) indicated that GmSBP contributes 19-fold less to the stored nitrogen. The quantitative differences between GmSBP and glycinin may be attributed to the unconserved order and spacing of cis-acting regulatory elements present within the promoter regions. Ultimately, GmSBP is transported to the mature protein storage vacuole. The biological function of GmSBP within the protein storage vacuole remains uncertain, but its localization is a remnant of its evolutionary link to a globulin-like or vicilin-like ancestor that gave rise to the 7S family of storage proteins.     

Distribution patterns of interstitial freshwater meiofauna over a range of spatial scales,with emphasis on alluvial river-aquifer systems

Spatial distribution patterns of the interstitial meiobenthos are examined across a range of scales. A global interstitial highway model is presented with the alluvial aquifer system as its central core. Spatially discontinuous hypogean entities, such as karstic aquifers, springs, anchialine waters and the psammolittoral, have limited interconnections except through the alluvial aquifer system and are contiguous with epigean waters. The global interstitial highway is viewed as an evolutionary pathway and long-term dispersal route for meiobenthic forms. The distribution of interstitial animals in alluvial river-aquifer systems is examined at longitudinal (altitudinal), reach, floodplain, gravel bar, and vertical (depth) scales. Geomorphic and hydrogeologic features and interactions emerge as major determinants of the spatially heterogeneous nature of alluvial aquifers that structure the patchy distribution patterns of hypogean fauna across a range of scales.Invited summary of Symposium on the Biogeography of Subterranean Crustaceans: the Effects of Different Scales. Prepared for print by D. C. Culver.Invited summary of Symposium on the Biogeography of Subterranean Crustaceans: the Effects of Different Scales. Prepared for print by D. C. Culver.     

Persistent propensities: Portrait of a familiar controversy

Susan Mills and John Beatty's propensity interpretation of fitness encountered very different philosophical criticisms by Alexander Rosenberg and Kenneth Waters. These criticisms and the rejoinders to them are both predictable and important. They are predictable as raisingkinds of issues typically associated with disposition concepts (this is established through a systematic review of the problems generated by Carnap's dispositional interpretation of all scientific terms). They are important as referring the resolution of these issues to the development of evolutionary biology. This historical approach to the propensity interpretation of fitness draws attention to the precarious relation between philosophical clarification of scientific concepts and any given state of the empirical arts.     

Regulation and possible function of the violaxanthin cycle

This paper discusses biochemical and regulatory aspects of the violaxanthin cycle as well as its possible role in photoprotection. The violaxanthin cycle responds to environmental conditions in the short-term and long-term by adjusting rates of pigment conversions and pool sizes of cycle pigments, respectively. Experimental evidence indicating a relationship between zeaxanthin formation and non-photochemical energy dissipation is reviewed. Zeaxanthin-associated energy dissipation appears to be dependent on transthylakoid pH. The involvement of light-harvesting complex II in this quenching process is indicated by several studies. The current hypotheses on the underlying mechanism of zeaxanthin-dependent quenching are alterations of membrane properties, including conformational changes of the light-harvesting complex II, and singlet-singlet energy transfer from chlorophyll to zeaxanthin