Why the DNA‐containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids (...) the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall‐back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode. (shrink)

The evolution of sex in eukaryotes represents a paradox, given the “twofold” fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favored the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high‐mutation rate across most eukaryote taxa, and several lines of evidence suggest that this high rate is an ancestral character. This seems inexplicable given that mtDNA‐encoded genes underlie the expression of life's most salient functions, including energy conversion. We propose that negative (...) metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA‐induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation. (shrink)

Sexual reproduction is a composite, not a singular, phenomenon and as such can be subdivided into a number of componentsi.e. fusion, recombination, fission, and the male-female phenomenon. These components can evolve independently, though any evolutionary change in one component is likely to influence the future evolution of the other components. The ambiguity that surrounds the term ‘sex’ due to a failure to recognise the composite nature of sexual reproduction has led to considerable confusion in past discussions of the evolution (...) of the phenomenon. This paper considers the possible chronological interaction of the components of sexual reproduction both with each other and with the sequence of selective pressures that seem likely to have acted. This chronological approach is used to consider: the origin of sexual reproduction; the evolution of sexual reproduction in the common ancestor of the procaryotes and eucaryotes; the modification of the ancestral system in the procaryote line following the procaryote-eucaryote dichotomy; and the modification of the ancestral system in the eucaryote line up to the origin of the male-female phenomenon.It is suggested that the fusion and recombination of the first living organisms were chronological continuations of the fusion and recombination of complex organic molecules that led up to the origin of life. The evolution of the third major component of sexual reproductioni.e. fission , by definition coincided with the origin of life. Initial selection on the components of sexual reproduction are likely to have been related to the optimum manifestations of size, complexity, diversity, multiplication, and distribution. Resultant early evolutionary trends are likely to have been: selective fusion between more-similar organisms; increase in number of fissions per fusion; and less recombination.The procaryote-eucaryote dichotomy is argued to have evolved in response to the increasing cellular problems of packing and replicating an increasing amount of hereditary material. The evolution of a single circular hereditary organelle in the procaryote line is argued to have led to the loss of total fusion and the specialisation of individuals into either donors or recipients. The donor-recipient phenomenon of procaryotes is directly analogous to the male-female phenomenon of eucaryotes and leads to parallel evolution due to sexual selection in both groups. In the eucaryote line the ancestral mechanism of sexual reproduction is argued to have persisted through, but to have been greatly modified by, the evolution of complex machinery for the handling of multiple hereditary organelles at cell division and reduction division. The evolutionary modification of the ancestral system of sexual reproduction is suggested to have led in eucaryotes to the evolution of: the species phenomenon; allelic recombination; and the male-female phenomenon. (shrink)

Ideas about the mechanisms that regulate chromosome pairing, recombination, and segregation during meiosis have gained in molecular detail over the last few years. The purpose of this article is to survey briefly the shifts in paradigms and experiments that have generated new perspectives. It has never been very clear what it is that brings together the homologous chromosomes at meiotic prophase. For a while it appeared that the synaptonemal complex might be the nuclear organelle responsible for synapsis, but (...) the supporting evidence has not been entirely convincing. Whatever the mechanism, it has always been assumed that homologous synapsis creates the opportunity for homologous DNA sequences to initiate recombination. At present, alternative ideas are developing. Attractive is the concept that double strand DNA repair mechanisms, that find and use the undamaged homologue for repair, have evolved into a meiotic mechanism for the recognition and pairing of homologous sequences. Subsequent intimate synapsis of homologous chromosomes in the context of the synaptonemal complex may serve later functions in the regulation of interference and segregation at first anaphase. A number of areas that are being tested at present and some that may be investigated in the future are discussed at the end of the review. (shrink)

The doctrine that whatever could exist does exist leads to a proliferation of possibly concrete objects given certain principles of recombination. If, for example, there could have been a large infinite number of concrete objects, then there is at least the same number of possibly concrete objects in existence. And further cardinality considerations point to a tension between the preceding doctrine and the Cantorian conception of the absolutely infinite. This paper develops a parallel problem for a variety of possible (...) worlds accounts of modality which eschew the commitment to a plethora of possibly concrete objects. Moreover, the difficulty is importantly different from more familiar threats of paradox exemplified by certain descendants of Russell's paradox of propositions and Kaplan's paradox. (shrink)

Graphical AbstractOrganelles are reaction vessels containing metabolic pathways. As in a chemical factory, the size of the reaction vessels limits the rate of product formation. Organelle size is tuned to metabolic needs, hence reprogramming organelle size could be a novel therapeutic strategy as well as a new tool for metabolic engineering.

This paper discusses the principle of recombination for possible worlds. It argues that arguments against unrestricted recombination offered by Forrest and Armstrong and by David Lewis fail, but a related argument is a challenge, and recommends that we accept an unrestricted principle of recombination and the conclusion that possible worlds form a proper class.

Science; Ethics; Politics; Beyond recombinant dna.

Camp (2009) distinguishes two varieties of conceptual recombination. One of them is full-blown or (as I prefer to call it) spontaneous recombination. The other is causal-counterfactual recombination. She suggests that while human animals recombine their concepts in a full-blown way, many non-human animals are capable of conceptual recombinability but only of the causal-counterfactual kind. In this paper, I argue that there is conceptual space to draw further sub-distinctions on how different animals may recombine their concepts. More specifically, (...) I propose to differentiate between a) narrow causal-counterfactual recombination; b) broad causal-counterfactual recombination; c) lean spontaneous recombination; d) robust spontaneous recombination. Afterwards, I focus on how these distinctions relate to several previous philosophical ideas on the representational capacities of non-human animals. I also provide several empirical examples suggesting that some animals display one or another of these four ways of recombining concepts, at least in some contexts. (shrink)

In recent years, there has been a growing interest in finding stronger means of securitising identity against the various risks presented by the mobile globalised world. Biometric technology has featured quite prominently on the policy and security agenda of many countries. It is being promoted as the solution du jour for protecting and managing the uniqueness of identity in order to combat identity theft and fraud, crime and terrorism, illegal work and employment, and to efficiently govern various domains and services (...) including asylum, immigration and social welfare. In this paper, I shall interrogate the ways in which biometrics is about the uniqueness of identity and what kind of identity biometrics is concerned with. I argue that in posing such questions at the outset, we can start delimiting the distinctive bioethical stakes of biometrics beyond the all-too-familiar concerns of privacy, data protection and the like. I take cue mostly from Cavarero’s Arendt-inspired distinction between the “what” and the “who” elements of a person, and from Ricoeur’s distinction between the “idem” and “ipse” versions of identity. By engaging with these philosophical distinctions and concepts, and with particular reference to the example of asylum policy, I seek to examine and emphasise an important ethical issue pertaining to the practice of biometric identification. This issue relates mainly to the paradigmatic shift from the biographical story (which for so long has been the means by which an asylum application is assessed) to bio-digital samples (that are now the basis for managing and controlling the identities of asylum applicants). The purging of identity from its narrative dimension lies at the core of biometric technology’s overzealous aspiration to accuracy, precision and objectivity, and raises one of the most pressing bioethical questions vis-à-vis the realm of identification. (shrink)

Camp (2009) distinguishes two varieties of conceptual recombination. One of them is full-blown or (as I prefer to call it) spontaneous recombination. The other is causal-counterfactual recombination. She suggests that while human animals recombine their concepts in a full-blown way, many non-human animals are capable of conceptual recombinability but only of the causal-counterfactual kind. In this paper, I argue that there is conceptual space to draw further sub-distinctions on how different animals may recombine their concepts. More specifically, (...) I propose to differentiate between a) narrow causal-counterfactual recombination; b) broad causal-counterfactual recombination; c) lean spontaneous recombination; d) robust spontaneous recombination. Afterwards, I focus on how these distinctions relate to several previous philosophical ideas on the representational capacities of non-human animals. I also provide several empirical examples suggesting that some animals display one or another of these four ways of recombining concepts, at least in some contexts. (shrink)

Manipulation of physical models such as tangrams and tiles is a popular approach to teaching early mathematics concepts. This pedagogical approach is extended by new computational media, where mathematical entities such as equations and vectors can be virtually manipulated. The cognitive and neural mechanisms supporting such manipulation-based learning—particularly how actions generate new internal structures that support problem-solving—are not understood. We develop a model of the way manipulations generate internal traces embedding actions, and how these action-traces recombine during problem-solving. This model (...) is based on a study of two groups of sixth-grade students solving area problems. Before problem-solving, one group manipulated a tangram, the other group answered a descriptive test. Eye-movement trajectories during problem-solving were different between the groups. A second study showed that this difference required the tangram's geometrical structure, just manipulation was not enough. We propose a theoretical model accounting for these results, and discuss its implications. (shrink)

Recombination maps of ancestral species can be constructed from comparative analyses of genomes from closely related species, exemplified by a recently published map of the human‐chimpanzee ancestor. Such maps resolve differences in recombination rate between species into changes along individual branches in the speciation tree, and allow identification of associated changes in the genomic sequences. We describe how coalescent hidden Markov models are able to call individual recombination events in ancestral species through inference of incomplete lineage sorting (...) along a genomic alignment. In the great apes, speciation events are sufficiently close in time that a map can be inferred for the ancestral species at each internal branch ‐ allowing evolution of recombination rate to be tracked over evolutionary time scales from speciation event to speciation event. We see this approach as a way of characterizing the evolution of recombination rate and the genomic properties that influence it. (shrink)

The debate over recombinant DNA research is a unique event, perhaps a turning point, in the history of science. For the first time in modern history there has been widespread public discussion about whether and how a promising though potentially dangerous line of research shall be pursued. At root the debate is a moral debate and, like most such debates, requires proper assessment of the facts at crucial stages in the argument. A good deal of the controversy over recombinant DNA (...) research arises because some of the facts simply are not yet known. There are many empirical questions we would like to have answered before coming to a decision-questions about the reliability of proposed containment facilities, about the viability of enfeebled strains of E. coli, about the ways in which pathogenic organisms do their unwelcome work, and much more. But all decisions cannot wait until the facts are available; some must be made now. It is to be expected that people with different hunches about what the facts will turn out to be will urge different decisions on how recombinant DNA research should be regulated. However, differing expectations about the facts have not been the only fuel for controversy. A significant part of the current debate can be traced to differences over moral principles. Also, unfortunately, there has been much unnecessary debate generated by careless moral reasoning and a failure to attend to the logical structure of some of the moral arguments that have been advanced. (shrink)

The nuclear pore complex (NPC) is emerging as a center for recruitment of a class of “difficult to repair” lesions such as double‐strand breaks without a repair template and eroded telomeres in telomerase‐deficient cells. In addition to such pathological situations, a recent study by Su and colleagues shows that also physiological threats to genome integrity such as DNA secondary structure‐forming triplet repeat sequences relocalize to the NPC during DNA replication. Mutants that fail to reposition the triplet repeat locus to the (...) NPC cause repeat instability. Here, we review the types of DNA lesions that relocalize to the NPC, the putative mechanisms of relocalization, and the types of recombinational repair that are stimulated by the NPC, and present a model for NPC‐facilitated repair. (shrink)

The recent development of RNA replicating protocells and capsules that enclose complex biosynthetic cascade reactions are encouraging signs that we are gradually getting better at mastering the complexity of biological systems. The road to truly cellular compartments is still very long, but concrete progress is being made. Compartmentalization is a crucial natural methodology to enable control over biological processes occurring within the living cell. In fact, compartmentalization has been considered by some theories to be instrumental in the creation of life. (...) With the advancement of chemical biology, artificial compartments that can mimic the cell as a whole, or that can be regarded as cell organelles, have recently received much attention. The membrane between the inner and outer environment of the compartment has to meet specific requirements, such as semi‐permeability, to allow communication and molecular transport over the border. The membrane can either be built from natural constituents or from synthetic polymers, introducing robustness to the capsule. (shrink)

This article analyses the patterns underlying debates in sociological theory, using the debate surrounding the distinction between ‘micro’ and ‘macro’ as its case. Although – and indeed because – few authors have attempted explicit definition of the distinction, a number of different distinctions have been subsumed under these labels and research has been shaped by packages of assumptions that have gone largely unexamined in their contradictory nature. The article disaggregates the different distinctions that have been associated with the terms ‘micro’ (...) and ‘macro’ and situates theoretical strategies of the past decades in the grammar of oppositions that makes them possible and innovative. Gap-bridging has been the attempt to bring together aspects of the distinction that have been construed as direct opposites; recombination has been the attempt to release certain aspects of the distinction from their association with one side of the divide. Disaggregating the distinction can help us isolate specific theoretical problems for further work, including work that asks how aspects emphasized by different theoretical approaches vary empirically. (shrink)

Mitotic recombination is a repair process which is known to repair double strand breaks and to fill double‐strand gaps by copying a homologous sequence. Meiotic recombination is a process of heteroduplex formation which sometimes generates crossovers. Evidence is presented that the later stages of meiotic recombination have some characteristics of mitotic repair recombination, leading to the conclusion that mismatch repair may be a recombinogenic repair process. The evidence suggests that the recombinational repair process generates hetero‐duplex bubbles (...) which can move. Some bubbles become crossovers. Others cease to exist, perhaps because topoisomerase activity breaks them down. (shrink)

Haecceitism and Hume’s Dictum are each controversial theses about necessity and possibility. According to haecceitism, there are qualitatively indiscernible possible worlds that differ only with respect to which individuals occupy which qualitative roles. According to Hume’s Dictum, there are no necessary connections between distinct entities or, as Humeans sometimes put it, reality admits of “free recombination” so any entities can co-exist or fail to co-exist. This paper introduces a puzzle that results from the combination of haecceitism and Hume’s Dictum. (...) This puzzle revolves around the free recombination of non-qualitative properties like being Socrates. After considering several responses to this puzzle, I defend an ideology-driven solution, which dispenses with non-qualitative properties like being Socrates in favour of primitive theoretical ideology while, at the same time, preserving a commitment to both haecceitism and Hume’s Dictum. (shrink)

Recombinant DNA technology is an essential area of life engineering. The main aim of research in this field is to experimentally explore the possibilities of repairing damaged human DNA, healing or enhancing future human bodies. Based on ethnographic research in a Czech biochemical laboratory, the article explores biotechnological corporealities and their specific ontology through dealings with bio-objects, the bodywork of scientists. Using the complementary concepts of utopia and heterotopia, the text addresses the situation of bodies and bio-objects in a laboratory. (...) Embodied utopias are analyzed as material semiotic phenomena that are embodied by scientists in their visions and emotions and that are related to potential bodies and to future, not-yet-actualized embodiments. As a counterpart to this, the text explores embodied heterotopias, which are always the other spaces, like biotechnological bio-objects that are simulated in computers or stored in special solutions. (shrink)

Within feminist literature from the early 1970s to this day, assisted reproductive technologies have been largely known to divide, replace or eliminate biological motherhood. For example, while in the past biological motherhood was considered a continuous experience, in vitro fertilisation (IVF) and IVF using egg donation allowed a split between two biological mothers, one providing eggs (genetic mother) and the other one gestation (gestational mother). This split was considered irreparable: the genetic mother could not be also gestational, and vice versa. (...) On the contrary, this paper aims to show that assisted reproductive technologies may also have a constructive potential towards biological motherhood(s). To explain how it could be possible, two existing techniques are explored: the first is maternal spindle transfer, which allows a double genetic motherhood; the second is reciprocal effortless IVF, which supposedly enables a double gestational motherhood. While in the first part, these techniques are examined singularly, in the second part a feasible combination of them is speculated. The idea is that assisted reproductive technologies could ‘recombine’ genetic and gestational motherhood in two figures that include both, namely in two ‘complete’ biological mothers, both genetic and gestational. (shrink)

A recombinationist like the earlier Armstrong (1989) claims that logically possible worlds are recombinations of items found in the actual world, with some items reduplicated if need be and others deleted. An immediate consequence of this is that if an..

A recombinationist like the earlier Armstrong (1989) claims that logically possible worlds are recombinations of items found in the actual world, with some items reduplicated if need be and others deleted. An immediate consequence of this is that if an alien property is a property that could only be defined in terms of fundamental properties that are actually uninstantiated, then it is logically impossible that an alien property be instantiated as no recombination of the items in the actual world (...) can yield a world with an entity having such a property. Recombinationism immediately implies that S5 is false. To see this, suppose for simplicity, as I will throughout this paper, that electric charge is a fundamental property--otherwise, a different example would have to be used. Then, let w be a possible world lacking any charged objects. At w, then, it is true that it is logically impossible that there be a charged particle since no recombination of the entities in w yields a charged particle. Therefore, contrary to S5, what is possible at w differs from what is possible at the actual world, since charged particles are actual and hence logically possible at the actual world. While this argument may make one sceptical of recombinationism, the recombinationist will say that it is not surprising that if we follow out the Aristotelian intuition that possibility is to be grounded in actually existing entities, then what is possible will depend on what is actual. Henceforth I will no longer assume S5, and so logical possibilities will have to be relativized to worlds if recombinationism is true: it is logically possible at the actual world for charged particles to exist, but at a world at which there are no charged particles it is logically impossible for charged particles to exist... (shrink)

An attractive admirer of George Bernard Shaw once wrote to him with a not-so modest proposal: ``You have the greatest brain in the world, and I have the most beautiful body; so we ought to produce the most perfect child.'' Shaw replied: ``What if the child inherits my body and your brains?''What if, indeed? Shaw's retort is interesting not because it revealsa grasp of elementary genetics, but rather because it suggests his grasp of an interesting and important principle of axiology. (...) Since the brainy but ugly Shaw and his beautiful but apparently dim admirer both fall short of the ideal, she suggests that the best thing would be to genetically recombine his intelligence with her beauty. But what then would be the value of another genetic possibility: that of recombining his ugliness with her stupidity? Underlining the prompted inference is a fundamental principle of the theory of value which, perhaps surprisingly, has so far gone largely unnoticed in the ethical literature. I will call it the principle of recombinant values. (shrink)

The function of meiotic recombination has remained controversial, despite recent inroads into mechanisms. Ideas concerning a possible role of recombination in the elimination or efficient incorporation of mutations have been backed by theoretical studies but have lacked empirical support. Recent investigations into the basis for local variations in recombination frequency in yeast have uncovered a strong association between recombination initiation sites and transcriptional regulatory sequences. Other recent studies indicate a strong correlation between transcription and mutation rates (...) in yeast genes. Taken together, these data imply that distributions of recombination and mutation frequencies may be strongly correlated. This suggests that recombination may be targeted to genomic sites of high mutation frequency; such a ‘mutation‐tracking’ function would clearly aid in the shuffling of mutations to break up unfavorable and create favorable allelic combinations. Moreover, recent insights into the mechanism of gene conversion in yeast reveal a very strong inherent bias in favor of alleles on the non‐initiating homolog. Combined with mutation tracking, these findings suggest a novel and general mechanism by which allelic gene conversion may act to eliminate mutations. (shrink)

The idea of truthmakers is important for doing serious metaphysics, since a truthmaker principle can give us important guidance in finding out what we would like to include into our ontology. Recently, David Lewis has argued against Armstrong’s argument that a plausible truthmaker principle requires us to accept facts. I would like to take a close look at the argument. I will argue in detail that the Humean principle of recombination on which Lewis relies is not plausible (independently of (...) the issue of facts). Then I will show that the right truthmaker principle that vindicates facts is superior to the modified truthmaker principle that Lewis has proposed. This will lead into the topic of being and existence. It turns out that truthmaking and facts are plausible, well suited for one another, and very coherent with a plausible conception of being. (shrink)

In this paper I argue that warrant for Lewis ' principle of recombination presupposes warrant for a combinatorial analysis of intrinsicality, which in turn presupposes warrant for the principle of recombination. This, I claim, leads to a vicious circularity: warrant for neither doctrine can get off the ground.

Cultural evolutionists typically emphasize the informational aspect of social transmission, that of the learning, stabilizing, and transformation of mental representations along cultural lineages. Social transmission also depends on the production of public displays such as utterances, behaviors, and artifacts, as these displays are what social learners learn from. However, the generative processes involved in the production of public displays are usually abstracted away in both theoretical assessments and formal models. The aim of this paper is to complement the informational view (...) with a generative dimension, emphasizing how the production of public displays both enable and constrain the production of modular cultural recipes through the process of innovation by recombination. In order to avoid a circular understanding of cultural recombination and cultural modularity, we need to take seriously the nature and structure of the generative processes involved in the maintenance of cultural traditions. A preliminary analysis of what recombination and modularity consist of is offered. It is shown how the study of recombination and modularity depends on a finer understanding of the generative processes involved in the production phase of social transmission. Finally, it is argued that the recombination process depends on the inventive production of an interface between modules and the complex recipes in which they figure, and that such interfaces are the direct result of the generative processes involved in the production of these recipes. The analysis is supported by the case study of the transition from the Oldowan to the Early Acheulean flake detachment techniques. (shrink)

Graphical AbstractThe finding that viruses with RNA and DNA genomes can recombine to produce chimeric entities provides valuable insights into the origin and evolution of viruses. It also substantiates the hypothesis that certain groups of DNA viruses could have emerged from plasmids via acquisition of capsid protein-coding genes from RNA viruses.

A major barrier to recombination between bacterial species lies in the mismatch repair system, a complex of proteins that has evolved to proof‐read freshly replicated DNA. It now appears that a second system, involving an inducible DNA recombination, repair and mutagenesis pathway, also regulates interspecies recombination, but in a positive way, being required for recombination between Escherichia coli and Salmonella typhimurium(1). Thus the rate at which newly emerging species of bacteria diverge can be seen as a (...) balance between a permissive state associated with inducible repair and recombination, and the proof‐reading of intermediates in the recombination pathway by the mismatch correction system. (shrink)

The recent finding of a role for the recA gene in DNA replication restart does not negate previous data showing the existence of recA‐dependent recombinational DNA repair, which occurs when there are two DNA duplexes present, as in the case for recA‐dependent excision repair, for postreplication repair (i.e., the repair of DNA daughter‐strand gaps), and for the repair of DNA double‐strand breaks. Recombinational DNA repair is critical for the survival of damaged cells. BioEssays 26:1322–1326, 2004. © 2004 Wiley Periodicals, Inc.

In On the Plurality of Worlds (Lewis 1986), David Lewis imposes a condition on realist theories of modality which he calls ‘plenitude’. Lewis apparently assigns this condition considerable importance, and uses it to motivate his Humean principle of recombination, but he never says exactly what plenitude amounts to. This chapter first sets aside some obvious ways of reconstructing the plenitude criterion which do not fit with the textual evidence. An objection to modal realism due to John Divers and Joseph (...) Melia (Divers and Melia 2002) is diagnosed as equivocating between an overly-demanding plenitude constraint and a weaker constraint which fails to establish their conclusion. An alternative deflationary interpretation of the plenitude condition has it following from an application of standard theoretical virtues to a modal realist’s total theory; Lewis’ correspondence provides new evidence in support of this interpretation. The deflationary plenitude criterion also has broader application, beyond Lewisian modal realism. (shrink)

Much of the appeal of Armstrong’s combinatorial theory of possibility depends on the theory’s principle of recombination. Despite its centrality, the principle has received little attention in the critical literature on combinatorialism. In this paper, I first set out to discuss how to exactly formulate the principle; then, I show that some notable criticisms of combinatorialism are in fact criticisms to the principle of recombination that allegedly sustains the theory. I focus in particular on Sider’s ‘trickle down’ objection (...) concerning the recombination of mereologically complex wholes and on the objection that combinatorialism cannot account for so-called alien possibilities. The combinatorialist – I contend – can rebut both objections by fine-tuning the principle of recombination. (shrink)

The rapid evolution of drug resistance remains a major obstacle for HIV therapy. The capacity of the virus for recombination is widely believed to facilitate the evolution of drug resistance. Here, we challenge this intuitive view. We develop a population genetic model of HIV replication that incorporates the processes of mutation, cellular superinfection, and recombination. We show that cellular superinfection increases the abundance of low fitness viruses at the expense of the fittest strains due to the mixing of (...) viral proteins during virion assembly. Moreover, we argue that whether recombination facilitates the evolution of drug resistance depends critically on how resistance mutations interact to determine viral fitness. Contrary to the commonly held belief, we find that, under the most plausible biological assumptions, recombination is expected to slow down the rate of evolution of multi‐drug‐resistant virus during therapy. BioEssays 26:180–188, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

CONJECTURE: Alongside the innate physical sucking reflex for obtaining milk to be digested, decomposed and used all over the body for growth, repair, and energy, there is a genetically determined information-sucking reflex, which seeks out, sucks in, and decomposes information, which is later recombined in many ways, growing the information-processing architecture and many diverse recombinable competences.

In the organelles of plants and mammals, recent evidence suggests that genomic instability stems in large part from template switching events taking place during DNA replication. Although more than one mechanism may be responsible for this, some similarities exist between the different proposed models. These can be separated into two main categories, depending on whether they involve a single‐strand‐switching or a reciprocal‐strand‐switching event. Single‐strand‐switching events lead to intermediates containing Y junctions, whereas reciprocal‐strand‐switching creates Holliday junctions. Common features in all the (...) described models include replication stress, fork stalling and the presence of inverted repeats, but no single element appears to be required in all cases. We review the field, and examine the ideas that several mechanisms may take place in any given genome, and that the presence of palindromes or inverted repeats in certain regions may favor specific rearrangements. (shrink)

The developing neuromuscular junction has provided an important paradigm for studying synapse formation. An outstanding feature of neuromuscular differentiation is the aggregation of acetylcholine receptors (AChRs) at high density in the postsynaptic membrane. While AChR aggregation is generally believed to be induced by the nerve, the mechanisms underlying aggregation remain to be clarified. A 43‐kD protein (43k) normally associated with the cytoplasmic aspect of AChR clusters has long been suspected of immobilizing AChRs by linking them to the cytoskeleton. In recent (...) studies, the AChR clustering activity of 43k has, at last, been demonstrated by expressing recombinant AChR and 43k in non‐muscle cells. Mutagenesis of 43k has revealed distinct domains within the primary structure which may be responsible for plasma membrane targeting and AChR binding. Other lines of study have provided clues as to how nerve‐derived (extracellular) AChR‐cluster inducing factors such as agrin might activate 43k‐driven postsynaptic membrane specialization. (shrink)

The introduction of recombinant DNA technology into the field of genetics has led to a rapid advancement of our knowledge of genes and genome structure. Such technology, applied to the human genome, has provided valuable information concerning the nature and possible treatment of inherited disorders. The possibility that this knowledge will pave the way for the correction of at least some of these disorders has captured the imagination of the informed public. In this review we look at the accomplishments of (...) molecular pathologists to date and how new techniques are being applied to the study of inherited disease. (shrink)

In eukaryotes, RNA trans‐splicing is an important RNA‐processing form for the end‐to‐end ligation of primary transcripts that are derived from separately transcribed exons. So far, three different categories of RNA trans‐splicing have been found in organisms as diverse as algae to man. Here, we review one of these categories: the trans‐splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. Trans‐spliced exons can be predicted from DNA sequences derived from a large number of (...) sequenced organelle genomes. Further molecular genetic analysis of mutants has unravelled proteins, some of which being part of high‐molecular‐weight complexes that promote the splicing process. Based on data derived from the alga Chlamydomonas reinhardtii, a model is provided which defines the composition of an organelle spliceosome. This will have a general relevance for understanding the function of RNA‐processing machineries in eukaryotic organelles. (shrink)

Chi sites are examples of special sites enhancing homologous recombination in their region of the chromosome. Chi, 5′ G‐C‐T‐G‐G‐T‐G‐G3′, is a recognition site for the RecBC enzyme, which nicks DNA near Chi as it unwinds DNA. A molecular model of genetic recombination incorporating these features is reviewed.

Examining the concepts of ‘security’ and ‘sustainability’, as they are employed in contemporary environmental discourses, the paper argues that, although the importance of the environment has been increasingly acknowledged since the 1970s, there has been a failure to incorporate other discourses surrounding ‘nature’. The implications of the ‘new genetics’, prompted by research into recombinant DNA, suggest that future approaches to sustainability need to be more cognisant of changes in ‘our’ nature, as well as those of ‘external’ nature, the environment. This (...) broadening of the compass of ‘security’ and ‘sustainability’ discourses would help provide greater insight into human security, from an environmental perspective. (shrink)

Cells are the fundamental building blocks of organisms and their organization holds the key to our understanding of the processes that control Development and Physiology as well as the mechanisms that underlie disease. Traditional methods of analysis of subcellular structure have relied on the purification of organelles and the painstaking biochemical description of their components. The arrival of high‐throughput genomic and, more significantly, proteomic technologies has opened hereto unforeseen possibilities for this task. Recently two reports(1,2) show how much can be (...) gleaned from the combination of analytical centrifugation, mass spectrometry and advanced statistical techniques focused on a high‐throughput analysis of the content and organization of plant and animal cells. The results reveal intriguing possibilities for the future and the possibility of mapping much of the known proteome onto our current map of the cell. BioEssays 28: 780–784, 2006. © 2006 Wiley Periodicals, Inc. (shrink)