Harmfulness of Code Duplication - A Structured Review of the Evidence

Duplication of code has long been thought to decrease changeability of systems, but recently doubts have been expressed whether this is true in general. This is a problem for researchers because it makes the value of research aimed against clones uncertain, and for practitioners as they cannot be sure whether their effort in reducing duplication is well-spent. In this paper we try to shed light on this is-sue by collecting empirical evidence in favor and against the nega-tive effects of duplication on changeability. We go beyond the flat yes/no-question of harmfulness and present an explanatory model to show the mechanisms through which duplication is suspected to affect quality. We aggregate the evidence for each of the causal links in the model. This sheds light on the current state of duplication re-search and helps practitioners choose between the available mitiga-tion strategies

Gene duplicability of core genes is highly consistent across all angiosperms

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes

Content based network model with duplication and divergence

We construct a minimal content-based realization of the duplication and divergence model of genomic networks introduced by Wagner [A. Wagner, Proc. Natl. Acad. Sci. {\bf 91}, 4387 (1994)] and investigate the scaling properties of the directed degree distribution and clustering coefficient. We find that the content based network exhibits crossover between two scaling regimes, with log-periodic oscillations for large degrees. These features are not present in the original gene duplication model, but inherent in the content based model of Balcan and Erzan. The scaling exponents $\gamma_1$ and $\gamma_2=\gamma_1-1/2$ of the Balcan-Erzan model turn out to be robust under duplication and point mutations, but get modified in the presence of splitting and merging of strings. The clustering coefficient as a function of the degree, $C(d)$, is found, for the Balcan-Erzan model, to behave in a way qualitatively similar to the out-degree distribution, however with a very small exponent $\alpha_1= 1-\gamma_1$ and an envelope for the oscillatory part, which is essentially flat, thus $\alpha_2= 0$. Under duplication and mutations including splitting and merging of strings, $C(d)$ is found to decay exponentially.Comment: 12 pages, 6 figure

The Duplication of Love's Reasons

If X loves Y does it follow that X has reasons to love a physiologically exact replacement for Y? Can love's reasons be duplicated? One response to the problem is to suggest that X lacks reasons for loving such a duplicate because the reason-conferring properties of Y cannot be fully duplicated. But a concern, played upon by Derek Parfit, is that this response may result from a failure to take account of the psychological pressures of an actual duplication scenario. In the face of the actual loss of a loved one and the subsequent appearance of a duplicate, how could we resist the inclination to love? Drawing upon duplication scenarios from Parfit and from Stanislaw Lem's Solaris, this paper will argue that there could be reasons for X to come to love a duplicate of Y but that these would not be identical with the reasons that X had (and may still have) to love Y. Nor (in the case of an agent with a normal causal history) could they be reasons for a love that violates the requirement that love is a response to a relationship and therefore takes time to emerge.Peer reviewedSubmitted Versio

Duplication, Growth and return

Maintenance consumption is an expense recovered in product prices, yet also a source of taste satisfaction which must be exhausted, rather than reinvested, from the capital affording it. This riddle is solved in the "duplication rules": the cost of maintenance consumption is recovered in pay and prices, but an equal flow is exhausted from the human capital of the worker earning the pay. The rules impact tradition in several ways. If output is defined in principle as value added, then it cannot also be described as consumption plus net investment without double-counting the maintenance consumption recovered in prices. Also rate of return in the stationary state is not zero, but is the rate sufficient to offset the exhaustion of individual human capital. The rules lead to new insights into economic return, and support an argument that all growth at the scale of closure is due to productivity gain rather than to thrift.

Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria

A common and unstable copy number variant is associated with differences in Glo1 expression and anxiety-like behavior

Glyoxalase 1 (Glo1) has been implicated in anxiety-like behavior in mice and in multiple psychiatric diseases in humans. We used mouse Affymetrix exon arrays to detect copy number variants (CNV) among inbred mouse strains and thereby identified a approximately 475 kb tandem duplication on chromosome 17 that includes Glo1 (30,174,390-30,651,226 Mb; mouse genome build 36). We developed a PCR-based strategy and used it to detect this duplication in 23 of 71 inbred strains tested, and in various outbred and wild-caught mice. Presence of the duplication is associated with a cis-acting expression QTL for Glo1 (LOD>30) in BXD recombinant inbred strains. However, evidence for an eQTL for Glo1 was not obtained when we analyzed single SNPs or 3-SNP haplotypes in a panel of 27 inbred strains. We conclude that association analysis in the inbred strain panel failed to detect an eQTL because the duplication was present on multiple highly divergent haplotypes. Furthermore, we suggest that non-allelic homologous recombination has led to multiple reversions to the non-duplicated state among inbred strains. We show associations between multiple duplication-containing haplotypes, Glo1 expression and anxiety-like behavior in both inbred strain panels and outbred CD-1 mice. Our findings provide a molecular basis for differential expression of Glo1 and further implicate Glo1 in anxiety-like behavior. More broadly, these results identify problems with commonly employed tests for association in inbred strains when CNVs are present. Finally, these data provide an example of biologically significant phenotypic variability in model organisms that can be attributed to CNVs.These studies were funded by MH070933, MH79103 and MH020065