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The Third Way of Evolution was founded in 2014 to make the public aware that contemporary evolution science is not limited to the neo-Darwinian Modern Synthesis of the past century. This was important to do because evolution was challenged as incapable of explaining biological complexity by the Intelligent Design movement. Expounding biological theories like the Modern Synthesis is always subject to limited empirical evidence, fundamental concepts that inevitably change over time, and conceptual preferences that often prove to be misleading. The Modern Synthesis was based on Darwin's preference for the phyletic gradualism necessary to elevate Natural Selection as the sole force determining the direction of evolutionary change. In contradiction to this principle, agricultural crop breeding, direct observation in nature, and genomics have shown that genome change following symbiogenetic cell fusions or interspecific hybridization, not selection, are empirically the most effective methods for originating novel life forms and new species. By asserting that the accumulation of random "slight" variations was the basic mode of both short-term and long-term evolutionary change, the Modern Synthesis also ignored the distinction between (1) microevolutionary change within species by localized mutations and (2) macroevolutionary origination of new species and taxa by genome restructuring. In so doing, the Modern Synthesis failed to recognize the evolutionary importance of cellular capacities to generate large-scale genome changes. By focusing on individual protein-coding genes as the fundamental units of genetic information, the Modern Synthesis did not successfully incorporate either the full non-coding informa tion content in genomes or the major evolutionary potential of mobile DNA elements to generate multisite intragenomic networks necessary for the development of complex organisms. When all of the phenomena overlooked by the Modern Synthesis are taken into consideration, it is not difficult to answer Intelligent Design arguments and show that science is making real progress in understanding the evolution of biological complexity.

All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.

The Modern Synthesis (MS) was based on Darwin’s gradualist view of evolution and early twentieth Century Mendelian and population genetics. Although early results in microbial and molecular genetics seemed to solidify MS views through the Central Dogma of Molecular Biology, accepting their basic concepts as permanent truths blinded MS proponents to the importance of incompatible discoveries in the second half of the 20th and early 21st Centuries. Discoveries based largely on the DNA record have provided a radically different view of genome complexity and biologically-mediated evolutionary change.

Genome change does not occur accidentally. The conventional Modern Synthesis view of gradual evolution guided solely by natural selection fails to incorporate many important lessons from direct examination of genome structure by cytogeneticists and modern genomic sequencers. Among other discoveries is the major role that interspecific hybridization has played in the rapid generation of new species. Interspecific hybrids display altered epigenetic regulation and genome expression, great genome variability (including activation of transposable elements and chromosome rearrangements), and frequently whole genome duplication (WGD) as well. These changes produce novel species with adaptively altered phenotypes and reproductive isolation due to meiotic incompatibility with the progenitor species. Genomics has revealed that hybrid speciation and WGD have been widespread among all types of eukaryotes, from yeast and diatoms to flowering plants and primates. The maintenance of the biological responses to interspecific hybridization across virtually all eukaryotic history indicates that eukaryotes have continuously inheritted a capability for rapid evolutionary change. In other words, the best-documented path to the origin of species we have is an inherited biological process, not a series of accidents.

Simple Summary Cancer genomes can undergo major restructurings involving many chromosomal locations at key stages in tumor development. This restructuring process has been designated “genome chaos” by some authors. In order to examine how chaotic cancer genome restructuring may be, the cell and molecular processes for DNA restructuring are reviewed. Examination of the action of these processes in various cancers reveals a degree of specificity that indicates genome restructuring may be sufficiently reproducible to enable possible therapies that interrupt tumor progression to more lethal forms. Abstract Cancer genomes evolve in a punctuated manner during tumor evolution. Abrupt genome restructuring at key steps in this evolution has been called “genome chaos.” To answer whether widespread genome change is truly chaotic, this review (i) summarizes the limited number of cell and molecular systems that execute genome restructuring, (ii) describes the characteristic signatures of DNA changes that result from activity of those systems, and (iii) examines two cases where genome restructuring is determined to a significant degree by cell type or viral infection. The conclusion is that many restructured cancer genomes display sufficiently unchaotic signatures to identify the cellular systems responsible for major oncogenic transitions, thereby identifying possible targets for therapies to inhibit tumor progression to greater aggressiveness.

Eibi Nevo’s research highlights the complexity of evolutionary responses to ecological parameters. This important work pioneered a growing awareness of the multiple levels of biological activity and organismal interactions that contribute to evolutionary change. In large measure, our current understanding of adaptive innovation is based on the newly acquired ability to track the details of evolutionary processes through genome analysis. Genomics has unambiguously demonstrated the importance of cell fusion, symbiosis, interspecific hybridization, genome restructuring involving mobile DNA elements, and the many forms of infectious heredity all to be major contributors to the appearance of organisms with novel adaptive characteristics. In addition, genomics has confirmed interspecific hybridization as a major stimulus to the rapid emergence of new taxa among sexually reproducing organisms. The work of Eibi and many other scientists has shown that ecology can trigger and influence all these different modes of hereditary change. We must recognize that genomic analyses have provided 21st century evolutionary scientists with such a rich variety of documented paths to inherited novelty that it has become impossible to formulate a comprehensive theory of evolutionary change. Thus an important part of the future in evolution science will be to adapt Eibi’s wisdom by devising synthetic Evolution Canyons as complex experimental microcosms, where we can rigorously study the principles governing ecological and biological interactions in adaptive innovation. Hopefully those interactive principles will make it possible to integrate information from genomic analysis into a coherent picture of evolution as a biological response to ecological change.

Detecting and treating cancer effectively involves understanding the disease as one of somatic cell and tumor macroevolution. That understanding is key to avoid triggering an adverse reaction to therapy that generates an untreatable and deadly tumor population. Macroevolution differs from microevolution by karyotype changes rather than isolated localized mutations being the major source of hereditary variation. Cancer cells display major multi-site chromosome rearrangements that appear to have arisen in many different cases abruptly in the history of tumor evolution. These genome restructuring events help explain the punctuated macroevolutionary changes that mark major transitions in cancer progression. At least two different nonrandom patterns of rapid multisite genome restructuring - chromothripsis ("chromosome shattering") and chromoplexy ("chromosome weaving") - are clearly distinct in their distribution within the genome and in the cell biology of the stress-induced processes responsible for their occurrence. These observations tell us that eukaryotic cells have the capacity to reorganize their genomes rapidly in response to calamity. Since chromothripsis and chromoplexy have been identified in the human germline and in other eukaryotes, they provide a model for organismal macroevolution in response to the kinds of stresses that lead to mass extinctions.

In Genome Chaos: Rethinking Genetics, Evolution, and Molecular Medicine, Henry Heng invites readers to herald a new age in how biologists consider the genome. He reframes the genome’s role in determining the hereditary properties of cells and organisms, while also challenging popular notions of the genotype–phenotype relationship. Reviewer James Shapiro applauds Heng’s novel approach.

Conventional 20th century evolution thinking was based on the idea of isolated genomes for each species. Any possibility of life-history inputs to the germ line was strictly excluded by Weismann's doctrine, and genome change was attributed to random copying errors. Today, we know that many life-history events lead to rapid and nonrandom evolutionary change mediated by specific cellular functions. There are many ways that genomes, viruses, cells, and organisms interact to generate evolutionary variation. These include cell mergers and activation of natural genetic engineering by stress, infection, and interspecific hybridization. In addition, we know molecular mechanisms for transmitting life-history information across generations through gametes. These discoveries require a new agenda for evolutionary theory and novel experimental designs to investigate the genomic impacts of stresses, biotic interactions, and sensory inputs coming from the environment. The review will offer some generic recommendations for enriching evolution experiments to incorporate new knowledge and find answers to previously excluded questions.

The active uptake of exogenous nucleic acids by spermatozoa of virtually all animal species is a well-established phenomenon whose significance has long been underappreciated. A growing body of published data demonstrates that extracellular vesicles released from mammalian somatic tissues pass an RNA-based flow of information to epididymal spermatozoa, thereby crossing the Weismann barrier. That information is delivered to oocytes at fertilization and affects the fate of the developing progeny. We propose that this essential process of epigenetic transmission depends upon the documented ability of epididymal spermatozoa to bind and internalize foreign nucleic acids in their nuclei. In other words, spermatozoa are not passive vectors of exogenous molecules but rather active participants in essential somatic communication across generations.

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with ‘non-coding’ DNA content rather than with protein-coding capacity in the genome. Coincidentally, ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read–Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.

Discoveries in cytogenetics, molecular biology, and genomics have revealed that genome change is an active cell-mediated physiological process. This is distinctly at variance with the pre-DNA assumption that genetic changes arise accidentally and sporadically. The discovery that DNA changes arise as the result of regulated cell biochemistry means that the genome is best modelled as a read–write (RW) data storage system rather than a read-only memory (ROM). The evidence behind this change in thinking and a consideration of some of its implications are the subjects of this article. Specific points include the following: cells protect themselves from accidental genome change with proofreading and DNA damage repair systems; localized point mutations result from the action of specialized trans-lesion mutator DNA polymerases; cells can join broken chromosomes and generate genome rearrangements by non-homologous end-joining (NHEJ) processes in specialized subnuclear repair centres; cells have a broad variety of natural genetic engineering (NGE) functions for transporting, diversifying and reorganizing DNA sequences in ways that generate many classes of genomic novelties; natural genetic engineering functions are regulated and subject to activation by a range of challenging life history events; cells can target the action of natural genetic engineering functions to particular genome locations by a range of well-established molecular interactions, including protein binding with regulatory factors and linkage to transcription; and genome changes in cancer can usefully be considered as consequences of the loss of homeostatic control over natural genetic engineering functions.

The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.

The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read–Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

I am pleased to see that commentators from such disparate backgrounds (genomics, physiology, cancer research, evolutionary computation and physics) agree that there is benefit in rethinking the genome as a RW memory organelle under cell control [1]. This agreement indicates that the RW Genome will prove fruitful and adaptable to many areas of the life sciences and possibly even to the hard and information sciences as well. There are also dissenting interpretations. Let us deal with the dissents first and then move on to further implications of the RW Genome view. While grudgingly acknowledging at the end of his comment that “genomes are indeed read–write”, molecular geneticist Damon Lisch repeats quite a few of the standard (and easily rebutted) objections to the idea that cells actively engage natural genetic engineering (NGE) for useful genome inscriptions to cope with episodes of evolutionary challenge [2]. This is surprising, coming from the author of a paper on the action of maize transposons in “directional modification of genes through biased insertion and DNA acquisition” [3]. A single example will illustrate the limitations of Lisch’s reservations. He characterizes mobile genetic elements (MGEs) as “selfish” “parasitic entities” and states, “it is extremely unlikely that any but a tiny fraction of the insertions contribute to meaningful differences in the morphology of related species”. What Lisch considered “extremely unlikely” is now established genome science. He failed to notice that I indicated where we do have minimum quantitative estimates of the contributions of MGEs to functionally usefully genome elements in mammals. Last year, these stood at 280 000, or 19.1% of all conserved (i.e., positively selected) differences between eutherian mammals and marsupials [4]. Moreover, MGEs have been identified as contributing to between 11 and 20% of human regulatory elements [5]. In a similar dubious vein, Maxim Frank-Kamenetskii argues that the examples of genome RW character do not invalidate the “universal” principles of conventional views about genomic information [6]. I have to disagree strongly on two grounds. In my understanding of the last 60 years of molecular biology, the data show that genome inscriptions are the rule, not the exception. Empirically, the evidence of genome inscriptions needed for progress through the cell cycle, multicellular development, and evolutionary innovation overwhelms any claim that they are exceptional, rather than fundamental, events. From an epistemological perspective, I further find it impossible to accept “universals” where there are well-documented counter-examples [7]. Our job as scientists is to formulate our theories to incorporate

This paper will discuss the philosophical background to evolutionary theory and present multiple counterfactuals to each of the following seven empirically unsustainable but nonetheless widespread assumptions about genomic (DNA-based) evolution: 1. "All heredity transmission occurs from parent to progeny" 2. "Mutations are the result of inevitable replication errors" 3. "Mutations occur at constant low probabilities over time" (= there are "mutation rates") 4. "Virus infection cannot induce genetic changes giving heritable resistance" 5. "Mutations cannot be targeted within the genome" 6. "Spontaneous hereditary changes are localized and limited to those of small effect" 7. "Cells cannot integrate DNA change with biologically useful adaptive needs". The summary take-home lesson is that we have to change from thinking of the genome as a read-only memory (ROM) that dictates the fate of the cell or organism to conceptualizing the genome as a read-write (RW) organelle modified transiently or permanently by the cell at different time scales.

The read-write genome idea predicts that mobile DNA elements will act in evolution to generate adaptive changes in organismal DNA. This prediction was examined in the context of mammalian adaptations involving regulatory non-coding RNAs, viviparous reproduction, early embryonic and stem cell development, the nervous system, and innate immunity. The evidence shows that mobile elements have played specific and sometimes major roles in mammalian adaptive evolution by generating regulatory sites in the DNA and providing interaction motifs in non-coding RNA. Endogenous retroviruses and retrotransposons have been the predominant mobile elements in mammalian adaptive evolution, with the notable exception of bats, where DNA transposons are the major agents of RW genome inscriptions. A few examples of independent but convergent exaptation of mobile DNA elements for similar regulatory rewiring functions are noted.

A career of following unplanned observations has serendipitously led to a deep appreciation of the capacity that bacterial cells have for restructuring their genomes in a biologically responsive manner. Routine characterization of spontaneous mutations in the gal operon guided the discovery that bacteria transpose DNA segments into new genome sites. A failed project to fuse λ sequences to a lacZ reporter ultimately made it possible to demonstrate how readily Escherichia coli generated rearrangements necessary for in vivo cloning of chromosomal fragments into phage genomes. Thinking about the molecular mechanism of IS1 and phage Mu transposition unexpectedly clarified how transposable elements mediate large-scale rearrangements of the bacterial genome. Following up on lab lore about long delays needed to obtain Mu-mediated lacZ protein fusions revealed a striking connection between physiological stress and activation of DNA rearrangement functions. Examining the fate of Mudlac DNA in sectored colonies showed that these same functions are subject to developmental control, like controlling elements in maize. All these experiences confirmed Barbara McClintock's view that cells frequently respond to stimuli by restructuring their genomes and provided novel insights into the natural genetic engineering processes involved in evolution.

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. � 2007 Elsevier Ltd. All rights reserved.

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences (data files) and repetitive sequences (generic formatting signals) contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read‐write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution.

The past five decades of molecular genetics have produced many discoveries about genome structure and function that can only be understood from an informatic perspective: --- distinct sequence codes to mark the individual steps in packaging, expression, replication, transmission, repair and restructuring of DNA molecules; --- modularity of data files for RNA and protein products; --- combinatoric organization of signals to format the genome for differential functioning during cellular and organismal cycles; --- direct participation of DNA in the execution of biological algorithms (formation of highly structured nucleoprotein complexes); --- hierarchical organization of genomic subsystems to form higher level system architectures. This review will discuss aspects of genome organization and genome change that require a more formal computational analysis. We will see how modern results indicate that genome evolution has many similarities to computer system engineering. The ability of cells to control the function of natural genetic engineering systems is central to the genome's potential as a Read---Write information storage system.

There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.

Genomes operate as sophisticated information storage systems. Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals. In this article, we summarize some features of the taxonomic distribution of retroelements, especially mammalian SINEs, tabulate functional roles documented for different classes of retroelements, and discuss their potential roles as genome organizers. In particular, the fact that certain retroelements serve as boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the reversed transcribed component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the “functionalist” perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.

Repetitive DNA elements are major organizational components of the genome involved in replication, in transmission to daughter cells, and controlling expression of genomic coding sequences. Repetitive elements format the genome system architecture characteristic of each taxonomic group. Appreciating the functional significance of repetitive DNA provides new concepts of genome organization and genome reorganization in evolution.

Physicists question whether there are ‘universals’ in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by Natural Genetic Engineering. Genomes are hierarchically organized as systems assembled from DNA modules. Each genome is formatted and integrated by repetitive DNA sequence elements that do not code for proteins, much as a computer drive is formatted. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, there is a computation-ready Genome System Architecture for each species. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs and their non-random operations help explain how novel genome system architectures can arise in evolution.

Proteus mirabilis colonies display striking symmetry and periodicity. Based on experimental observations of cellular differentiation and group motility, a kinetic model has been developed to describe the swarmer cell differentiation-dedifferentiation cycle and the spatial evolution of swimmer and swarmer cells during Proteus mirabilis swarm colony development. A key element of the model is the age dependence of swarmer cell behaviour, in particular specifying a minimal age for motility and maximum age for septation and dedifferentiation to swimmer cells. Density thresholds for collective motility by mature swarmer cells serve to synchronize the movements of distinct swarmer cell groups and thus help provide temporal coherence to colony expansion cycles. Numerical computations show that the model fits experimental data by generating a complete swarming plus consolidation cycle period that is robust to changes in parameters which affect other aspects of swarmer cell migration and colony development. The kinetic equations underlying this model provide a different mathematical basis for a temporal oscillator from reaction-diffusion partial differential equations. The modelling shows that Proteus colony geometries arise as a consequence of macroscopic rules governing collective motility. Thus, in this case, pattern formation results from the operation of an adaptive bacterial system for spreading on solid substrates, not as an independent biological function. Kinetic models similar to this one may be applicable to periodic phenomena displayed by other biological systems with differentiated components of defined lifetimes.

Bacterial evolution is considered in the light of molecular discoveries about genome organization, biochemical mechanisms of genetic change, and cellular control networks. Prokaryotic genetic determinants are organized as modular composites of coding sequences and protein-factor binding sites joined together during evolution. Studies of genetic change have revealed the existence of biochemical functions capable of restructuring the bacterial genome at various levels and joining together different sequence elements. These natural genetic engineering systems can be subject to regulation by signal transduction networks conveying information about the extracellular and intracellular environments. Mu-mediated araB-lacZ coding sequence fusions provide one example of adaptive mutation (increased formation of useful mutations under selection) and illustrate how physiological regulation can modulate the activity of a natural genetic engineering system under specific conditions.

Formation of araB-lacZ coding-sequence fusions is a key adaptive mutation system. Eighty-four independent araB-lacZ fusions were sequenced. All fusions carried rearranged MuR linker sequences between the araB and lacZ domains indicating that they arose from the standard intermediate of the well-characterized Mu DNA rearrangement process, the strand transfer complex (STC). Five non-standard araB-lacZ fusions isolated after indirect sib selection had novel structures containing back-to-back inverted MuR linkers. The observation that different isolation procedures gave rise to standard and non-standard fusions indicates that cellular physiology can influence late steps in the multi-step biochemical sequence leading to araB-lacZ fusions. Each araB-lacZ fusion contained two novel of DNA junctions. The MuR-lacZ junctions showed 'hot-spotting' according to established rules for Mu target selection. The araB-MuR and MuR-MuR junctions all involved exchanges at regions of short sequence homology. More extensive homology between MuR and araB sequences indicates potential STC isomerization a resolvable four-way structure analogous to a Holliday junction. These results highlight the molecular complexity of araB-lacZ fusion formation, which may be thought of as a multi-step cell biology process rather than a unitary biochemical reaction.

The gas-phase reactivities of W(a5DJ, a7S3) with N2O, SO2, and NO in the temperature range of 295–573 K are reported. Tungsten atoms produced by the photodissociation of W(CO)6. The tungsten atoms were detected by a laser-induced fluorescence technique. The removal rate constants for the 6s25d4 a5Dl states were found to be pressure dependent for all of the reactants. Removal rate constants for the 6s15d5 a7S3 state were found to be fast compared to the a5DJ states and often approached the gas kinetic rate constant. The reaction rates for all the states were found to be pressure independent with respect to the total pressure. Results are discussed in terms of the different electronic configurations of the states of tungsten © 1997 John Wiley & Sons, Inc. Int J Chem Kinet 29: 367–375 1997

The gas phase reactivities of Mo ( a 7 S 3 , a 5 S 2 , a 5 D J , a 5 G J ) with O2 with O2 in the temperature range 297–620 K are reported. Mo atoms were produced by the photodissociation of Mo(CO)6 and MoCl4 and detected by laser-induced fluorescence. The disappearance rates of all states are found to be pressure independent with argon buffer gas. The disappearance rate constants of the s 1 d 5 a 7 S 3 , a 5 S 2 and a 5 G J states are on the order of the gas kinetic rate constant. The s2d4a5DJ states are not as reactive and are found to be temperature dependent. Results are discussed in terms of the different electron configurations of the states.

The araB-lacZ fusion system has been a key case in the 'directed mutation' controversy. Fusions did not occur detectably during normal growth but formed readily after prolonged incubation on selective Ara-Lac medium. To distinguish the roles of starvation stress and selective substrates in coding sequence fusions, we applied sib selection and PCR technologies. Sib selection of the prefusion strain, MCS2, starved under aerobic conditions permitted us to isolate active fusion clones which had never been in contact with arabinose or lactose. Hence, a directive role for selective substrates is not essential. Aerobiosis was necessary for fusions to appear in glucose-starved cultures. The difference in fusion formation between normal and starved conditions is best explained by the response of a signal transduction network to physiological stimuli to activate Mu prophage joining of araB and lacZ sequences. PCR analysis revealed that direct plating on selective Ara-Lac agar yielded mostly a single class of 'standard' fusions, while sib selection yielded a broader spectrum of fusion structures. Standard fusions were found to occur within a narrow 9 bp window in lacZ. The high frequency of standard fusions in glucose-starved cultures suggested efficient and/or specific Mu action.

Program trading and intraday changes in the S&P 500 Index are correlated. Future prices and, to a lesser extent, cash prices lead program trades. Index arbitrage trades are followed by an immediate change in the cash index, which ultimately reverses slightly. No reversal follows nonarbitrage trades. The cumulative index changes associated with buy-and-sell trades and with arbitrage and nonarbitrage trades all are similar. Price decompositions suggest that the results are not due to microstructure effects. Program trades in this 1989-1990 sample do not seem to have created major short-term liquidity problems. The results are stable within the sample. Many practitioners, regulators, and public commentators have expressed concerns about potential destabilizing effects of program trading. They argue that program trades–especially index arbitrage programs–increase intraday volatility and decrease

Bacteriophage Mu, one of the best-characterized mobile genetic elements, can be used effectively to answer fundamental questions about the regulation of biochemical machinery for DNA rearrangement. Previous studies of Mu virulence have implicated the Clp protease in repressor inactivation (V. Geuskens, A. Mhammedi-Alaoui, L. Desmet, and A. Toussaint, EMBO J. 13:5121-5127, 1992). These studies were extended by analyzing the phenotypic consequences of clp alleles in two Escherichia coli systems: (i) the periodic replication of Mudlac transposons in colonies and (ii) the action of a Mu prophage in forming araB-lacZ coding sequence fusions. The clpP::CM mutation, which removes the proteolytic subunit of Clp protease, caused a drastic reduction in Mu activity in both systems. The clpA::Tn10 mutation, which removes a regulatory subunit of Clp protease, altered the timing of Mu activity in both systems. A clpA deletion reduced the extent of Mudlac replication in colonies. These results point to temporal changes in Clp proteolysis of the Mucts62 repressor as a key molecular event in the regulation of one class of genomic change in E. coli.

The term ‘natural genetic engineering’ means viewing genetic change as a coordinated cell biological process, the reorganization of discrete genomic modules, resulting in the formation of new DNA structures. Examples of natural genetic engineering continue to accumulate, and the concept can be used to integrate observations which demonstrate the similarity between in vitro genetic engineering and the action of in vivo agents of genetic change.