One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and (...) will argue, using examples of what many would call ‘superorganisms’, that the emergence of symbiotic individuals revives the importance of functional and adaptationist thinking in how we conceptualize the lineages of biological individuals. The consequence of the argument is that, if we really want to hold onto tree of life thinking, we had better accept that new saplings appear and disappear all the time. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and (...) computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

In a recent BioEssays paper [W. F. Martin, BioEssays 2017, 39, 1700115], William Martin sharply criticizes evolutionary interpretations that involve lateral gene transfer into eukaryotic genomes. Most published examples of LGTs in eukaryotes, he suggests, are in fact contaminants, ancestral genes that have been lost from other extant lineages, or the result of artefactual phylogenetic inferences. Martin argues that, except for transfers that occurred from endosymbiotic organelles, eukaryote LGT is insignificant. Here, in reviewing this field, we seek to (...) correct some of the misconceptions presented therein with regard to the evidence for LGT in eukaryotes. A recent paper dismisses claims of lateral gene transfer into eukaryotic genomes. We counter the arguments made in that paper and discuss the extensive evidence for LGT in eukaryotes. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we (...) judge networks by fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the (...) latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.Editor's suggested further reading in BioEssays Linguistic evidence supports date for Homeric epics Abstract. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), (...) and their associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)

Imāmiyya holds that the theory of imāmate must rely on scriptural evidence and designation and that the Imām, the successor to Muḥammad, is in charge of all political and religious issues. The authority of the Imām includes some religious and social duties such as executing the legal punishments, collecting almsgiving, sustaining social order and declaring holy war. The fulfillment of these duties requires actual leadership of the Imām or his deputy. With the beginning of the great occultation in 329/941, there (...) was an uncertainty among the Imāmiyya followers about who would uphold these responsibilities. In this period, Shīʿī ʿulamā began to undertake the duties of the Imām in order to overcome this uncertainty and to avoid the possible schism. In the beginning, this delegation of authority was limited to the religious sphere; but, later, its scope gradually became wider. This process of delegation of power, which covers a long process, needs to be examined in its various periods. In this study, this subject will be considered with special reference to the scholars of the fifth century of hijra (hijrī). An effort is made in this article to reveal how the issues of the Imām’s powers are discussed in the context of the problem of expanding or narrowing the authority of the scholars who played significant roles in systemization of Uṣūlī (rationalist) thought in the period after Shaykh al-Mufīd.Summary: In the issues of Imām/Caliphate which led to political division among Muslims after the Prophet Muḥammad, Imāmī Shīʿa opines that the Imāmate theory relies on scriptural evidence and designation. According to this theory, apart from scriptural evidence and designation, personal qualities such as immaculacy, knowledge, bravery, and vantage are found in Ali, Ḥasan, Ḥusayn and nine people from the lineage of Ḥusayn. The Imām as a successor to the Prophet Muḥammad is a person who has both religious and political power which includes implementation of punishments, collecting alms, ensuring justice, declaring holy war. For the Imāmī Shīʿa, there is a need for imām or his deputy who has absolute power to fulfill these duties.Imāmī Shīʿa, who held that the disappeared twelfth Imām would return back to restore justice in the world, had to confront various problems in finding solutions to some issues related to the existence of Imām himself, as well as theological issues during the period of great occultation. Particularly, the period of great occultation (329/941), in which the link with the Imām was severed completely, the Shīʿī community were uncertain on how to fulfill the responsibilities of the Imām probably due to the lack of religious sources. Shaykh al-Mufīd draws attention to the issue of khums (a one-fifth share of the spoils of war and of other specified forms of income). In this period of uncertainty, the Shiite scholars came into prominence in order to fill the gap and to prevent the social disorder. Referring to a tawqī‘ (rescript) from the Twelfth Imām, they claimed that they would take responsibility for the Twelfth Imām on his behalf. In the beginning, the delegation of the power was limited to the religious sphere. It was gradually extended to other spheres by the contribution of some scholars. It reached the largest dimension with the implementation of “wilāyat al-faqīh” theory.From that period until our times, the era when Sharīf al-Murtaḍā and his disciples lived can be considered as the beginning of this period. In the fifth century when Sharīf al-Murtaḍā and his disciples lived the delegation of power was limited to the religious sphere. In this article, how the scholars who played a role in the systematization of Uṣūlī thought dealt with the issue of the limits of the authority of Imām and how they defined the role of the Imāmī jurists (faqīh) will be examined.Sharīf al-Murtaḍā and his disciples were sometimes cautious on the issue of the delegation of the power of Imām. They, however, pointed out the role of the faqīh in the occultation period in order to overcome the uncertainty. As a matter of fact, Shaykh al-Ṭūsī and al-Qādī Ibn al-Barrāj made significant contributions to the issues of collection and distribution of khums. However, Sallār al-Daylamī’s contribution to the subject is more crucial. He considered khums as the grace of God and believed that it can be allocated by taking into account the share of the Imām. They put forward the views that explained in details the role of the faqīh in the collection and distribution of alms. Even Ibn al-Barrāj opined that in the absence of Imām and his deputy alms are to be allocated to the Faqihs on the ground that they know better how to distribute it. Therefore, in the absence of Imām and his deputy, by suggesting that faqīh must be in charge of collecting and distributing alms, they proposed a remedy in an early period.On the issue of leading the Friday prayer (ṣalāt al-jum‘a), which is one of the social duties of Imām, Sharīf al-Murtaḍā and his disciples considered the presence of the Imām or his deputy as a condition for a valid Friday prayer. In addition to this condition, Al-Ḥalabī, also added that a person who meets the necessary conditions can be also considered in leading Friday prayer. This addition by Ḥalabī was an important contribution to the solution of the problems encountered during the period of great occultation on both Friday prayer and delegation of Imām religious and political authorities to faqīh. On the other hand, Sallār, another disciple of Sharīf al-Murtaḍā, opposed the idea of the faqīh leading the Friday prayer in the absence of the Imām even when the necessary conditions are met. It can be said that this approach of Sallār led to the opinion of some Imāmis which considered Friday prayer unlawful in the absence of Imām. In the occultation period, Sharīf al-Murtaḍā and his disciples showed a cautious attitude about the implementation of the punishments. They argued that only Imām could implement the punishments. However, the major step was taken by Shaykh Ṭūsī on the issue of who implements the punishments in the occultation period. He argued that the Imām’s designated the faqihs to implement the punishments. In addition to this subject, Shiite scholars discussed the issue of whether a Shiite officer under the reigning rule in the occultation period implemented the punishments. On this issue, Sharīf al-Murtaḍā compiled a treaty untitled Mas’ala fi’l-‘amal ma‘a’al-sulṭan. For him, the main criteria are whether such person has necessary responsibilities and qualifications. Sharīf al-Murtaḍā and his disciples also continued their master’s conciliatory attitude. In the final analysis, the contribution of Sharīf al-Murtaḍā and his disciples on the issue of who will undertake the duties and responsibilities of the Imām is crucial in the systematization of the idea of transferal of the power of the Imām to faqīh including political one. In fact, Sharīf al-Murtaḍā’s advice to take part in the existing administrations has been considered a way out for the scholars who want to establish relations with the authorities in the later periods. (shrink)

This paper discusses the varieties of capitalism in transitional societies in Latin America and Central / Eastern Europe. The intended purpose of these transitions from semi-closed import-substituting economies in the first case and state socialist ones in the second was to institutionalize open-market economies. Twenty or thirty years later, there is a variety of types of capitalism in these countries, which I classify into three: open-market, neo-mercantilist, and anemic. The question for sociology is whether these quite different variants represent temporary (...) stages or distortions in the same process of transition or whether, on the contrary, they may institutionalize as discrete forms of peripheral capitalism. Neither standard “legacy” argu­ments nor institutionalist theories offer satisfactory answers to this question. The multiple modernities approach, on the other hand, is more appropriate as a theoretical perspective, but it has not produced yet specific propositions applicable to this question. My paper makes two claims. First, the successful transfer of institutions depends on the congruence between these institutions and the broader institutional framework of the recipient economies, a point not developed by institutionalist theories. I offer a hypothesis in this regard: Two critical nodes of congruence are the regulatory and extractive capacity of the state and the strength of civil society. Second, market capitalism (as liberal democracy as well) is a complex institution, and some of its components “travel” more easily across societies and institutional frameworks, and therefore are easier to institutionalize. This is the source of the hybrid variants. (shrink)

Historiography has never been considered as a source of Veblen's thought. This essay draws on previously unknown archival evidence regarding Veblen's experience at Cornell, where he asked to be enrolled as a Ph.D. student in ‘History and Political Science’ in 1891, to shed light on his relationship with both British and American institutional historiography. It is argued that Veblen's studies at this university, under the influence of local historians, is crucial to understanding his later work, particularly his theory of the (...) leisure class, for two fundamental reasons: (1) Cornell was unique for its tendency to combine the study of history with that of politics and society at a time when historiography tended to emancipate itself from the social sciences; (2) Cornell was one of the main epicentres for the diffusion of British historiography in America. Veblen's theory of the leisure class, to which he devoted his first article at Cornell, is thus presented as the fruit of his effort to reassess the historiographical idea of evolution, against its applications by philosophers, by insisting on the importance of path-dependent mentalities and by differentiating the evolutionary pattern followed by political and social institutions, on the one hand, from economic institutions on the other. (shrink)

Horizontal transfer (HT) is the transmission of genetic material between non‐mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective (...) long terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non‐LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution. (shrink)

The core theme of the special issue in which this article appears is the inherent impossibility of confining the knowledge required to build and sustain the instruments of travel to a single space or institution. This is certainly true for the ships that built empires – the large sailing and later steam ships produced by navies and companies in the process of European expansion. Ships traveled between polities and required repairs overseas, taking the construction knowledge and practices with them. Skilled (...) laborers – experienced shipwrights and increasingly also trained engineers – helped to transfer shipbuilding practices across oceans, and to adapt these practices to local conditions based on forms of “blended know-how.” This article explores how the circulation of shipbuilding knowledge and practices within and between maritime empires changed with the increasing pace of industrialization. It does so on the basis of three moments: the Dutch East India Company’s shipbuilding activities in Asia in the seventeenth and eighteenth centuries; the interaction between private industry and the Dutch state in advancing machine-manufacturing in both the Netherlands and on Java in the 1830s and 1840s; and the aid provided by Dutch engineers in laying the groundwork for Japanese industrial warship-construction in the second half of the nineteenth century. Such transfers put high demands on the capacities of states and naval administrators in controlling the flows of necessary resources and skilled labor, requiring complex arrangements between states and private capital. Industrialization did not change this basic fact, but it did change the nature of these arrangements. Although shipbuilding knowledge always remained practice-driven, highly mobile and susceptible to local adaptation, the increasing technological demands created by the transition from sail to steam and wood to iron, combined with the extension of the power of states and transnationally operating manufacturing companies, considerably changed the institutional embeddings and societal consequences of its circulation. (shrink)

Hegel, in his work _Philosophy of Right_, defines ownership through three elements: acquisition by occupation, use, and transfer. To own something involves mere acquisition and encompasses its appropriate use and potential transfer to others. Subsequently, the final aspect mentioned was the concept of infinite judgement. The acts of owning and transferring to others are diametrically opposed, and Hegel’s unique logic forcibly connects these opposing concepts. This form of infinite judgement was advocated by the young Hegel during the era (...) of _Phenomenology of Spirit_. There, he stated, “Spirit is a bone”. However, when he later wrote _Science of Logic_ or _Encyclopedia_, the formulation of infinite judgement changed to “Spirit is not something that is bone”. This shift was influenced by Kant. In _Logic_, the discourse advances into syllogism, inferential theory, leading to “Spirit is a bone for such-and-such reasons”. In essence, Hegel binarily connected spirit and bone in his youth and introduced a mediating term in this connection later in his life, establishing inferential links. However, the notion of forcibly connecting opposing concepts remains. Therefore, the statement “Ownership is transfer” represents an infinite judgement while simultaneously signifying syllogism that “I truly own this object if I can transfer it to others”. This contributes to the reasoning that “I and objects can be connected through the intermediary of others”, progressing to the inference that “I and others can be connected through objects”, thereby laying the foundation for society. (shrink)

The most common form of the CO2‐fixing enzyme rubisco is a form I enzyme, heretofore found universally in oxygenic phototrophs (cyanobacteria and plastids) and widely in proteobacteria. Two groups(1–4), however, now report that in dinoflagellate plastids the usual form I rubisco has been replaced by the distantly related form II enzyme, known previously only from anaerobic proteobacteria. This raises the important question of how such an oxygensensitive rubisco could function in an aerobic organism. Moreover, the dinoflagellate rubisco has unusual molecular (...) properties: it is encoded as a polyprotein, by nuclear (rather than plastid) genes, and these genes contain noncanonical spliceosomal introns. The nuclear location and alphaproteobacterial affinity of dinoflagellate rubisco genes hint at a possible mitochondrial origin and highlight the extraordinary richness of lateral gene transfers, both between and within organisms, that have occurred during rubisco evolution. (shrink)

‘Transversality’ is a key term in the work of Félix Guattari. As a conceptual and pragmatic motor for the generation of heterogeneity, it extends throughout all of his work, including the writing he undertook with Deleuze. It promotes the rupture and redistribution of hierarchical structures, the mobilisation of operations of deterritorialisation across the social and cultural field, and it gains a ‘chaosmic’ dimension in the later writings. Its ‘origins’, however, are to be found in Guattari's early work at the Clinique (...) de la Borde and in militant Marxist movements in the 1950s and early 1960s. This is an initial and necessarily provisional effort to embed the concept in a social and therapeutic pragmatics and thus counter a debateable tendency towards a dilution or diffusion of transversality in theoretical abstraction, where it risks becoming a synonym for a generalised sense of creative differentiation. (shrink)

While cochlear implantation has benefitted many patients with single-sided deafness (SSD), there is great variability in cochlear implant (CI) outcomes and binaural performance remains poorer than that of normal-hearing (NH) listeners. Differences in sound quality across ears – temporal fine structure (TFS) information with acoustic hearing versus coarse spectro-temporal envelope information with electric hearing – may limit integration of acoustic and electric patterns. Binaural performance may also be limited by inter-aural mismatch between the acoustic input frequency and the place of (...) stimulation in the cochlea. SSD CI patients must learn to accommodate these differences between acoustic and electric stimulation to maximize binaural performance. It is possible that training may increase and/or accelerate accommodation and further improve binaural performance. In this study, we evaluated lateralization training in NH subjects listening to broad simulations of SSD CI signal processing. A 16-channel vocoder was used to simulate the coarse spectro-temporal cues available with electric hearing; the degree of inter-aural mismatch was varied by adjusting the simulated insertion depth (SID) to be 25 mm (SID25), 22 mm (SID22), and 19 mm (SID19) from the base of the cochlea. Lateralization was measured using headphones and head-related transfer functions (HRTFs). Baseline lateralization was measured for unprocessed speech (UN) delivered to the left ear to simulate SSD and for binaural performance with the acoustic ear combined with the 16-channel vocoders (UN+SID25, UN+SID22, and UN+SID19). After completing baseline measurements, subjects completed 6 lateralization training exercises with the UN+SID22 condition, after which performance was re-measured for all baseline conditions. Post-training performance was significantly better than baseline for all conditions (p<0.05 in all cases), with no significant difference in training benefits among conditions. Given that there was no significant difference between the SSD and the SSD CI conditions before or after training, the results suggest that NH listeners were unable to integrate TFS and coarse spectro-temporal cues across ears for lateralization, and that inter-aural mismatch played a secondary role at best. While lateralization training may benefit SSD CI patients, the training may largely improve spectral analysis with the acoustic ear alone, rather than improve integration of acoustic and electric hearing. (shrink)

DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction‐modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co‐opted into epigenetic regulatory systems, primarily via establishing connections (...) with the chromatin environment. While C5‐methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4‐methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co‐option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems. (shrink)

Dawkins in his The Selfish Gene(1) quite aptly applies the term “selfish” to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously (...) by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional “tree of life”.(5–10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT. BioEssays 27:741–747, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

De Smet et al. (2018) propose that when functionally similar constructions come to overlap, analogical attraction may occur. So may differentiation, but this process involves attraction to other subnetworks and is both “accidental” and “exceptional”. I argue that differentiation plays a considerably more significant role than De Smet et al. allow. My case study is the development of the dative and benefactive alternations. The rise of the dative alternation (e.g., “gave the Saxons land” ∼ “gave land to the Saxons”) has (...) been shown to occur in later Middle English between 1400 and 1500 (Zehentner 2018). Building on Zehentner and Traugott (2020), the rise of the benefactive alternation (e.g., “build her a house” ∼ “build a house for her”) in Early Modern English c1650 is analyzed from a historical constructionalist perspective and compared with the rise of the dative alternation. The histories of the alternations exemplify the rise of functionally similar constructions that overlap, and show that differentiation from each other plays as large a role as attraction. Both attraction and differentiation occur at several levels of abstraction: verb-specific constructions, schemas and larger systemic changes. (shrink)

A collection of thoughtul presentations on transference and countertransference highlights _The Realities of Transference_, Volume 6 in the Progress in Self Psychology series. The selfobject transferences receive special attention. Elsewhere in this volme, selfobject phenomena are examined in relation to the process of working through, the origins of ambition, the psychology of addiction, the psychodynamic consequences of AIDS, and creativity. An exploration of the selfobjects of the second half of life offers new insight into later development.

This article examines tafsir (interpretation of the Qurʾān) - translation relationship in the example of the translation of verse 184 of the Surat al-Baqara into Turkish. Undoubtedly, when the verses are translated into another language, it is necessary to reflect to translate what the first interlocutors understood from them. The fact that the rules (hukm) in some verses were repealed (naskh) or allocated (takhsis) later does not change this requirement. In verse 184 of surat al-Baqara, those who can afford to (...) fast but choose not to fast are ordered to pay ransom (fidya) for every day, that is, to pay the daily amount to feed a poor person. According to the detailed information and rumors in the tafsir literature; this rule was applied when the fast was made obligatory (fard) for the first time, and then it was abrogated. However, this practice, which was canceled for healthy and unexcused people, remained as a permission (rukhṣa) for those who were too old and sick to fast. Both the narrations conveyed from the companions (sahaba) and the general opinions of the mufassirs confirm the abrogation of this rule and that it remains a rukhṣa. The fact that the situation is described as naskh or takhsis does not make a difference in terms of transferring the verse to Turkish or another language. The verses on the subject were examined in the light of the most basic tafsir sources. To give an example that reflects the general opinion; It is stated in the thirty-five narrations reported by Tabari from the companions and tābiʿūn that the 184th verse expresses the option (takhyir) of not fasting in return for fidya for those who can fast. This option has been canceled in the next verse but it has remained for, -some people with special conditions-, as the elderly who cannot afford to fast, pregnant women and breastfeeding women who worry about harm to themselves or their childrens. According to the qirāʾa that is "وعلى الذين يُطوَّقونه", it is said that the verse is not abrogated, it is meant for old men and women. But as emphasized by Abū Ḥayyān, it is understood that this qirāʾa is not actually a qirāʾa but a kind of interpretation of the expression "وَعَلَى الَّذِينَ يُطِيقُونَهُ" in terms of rukhṣa. Therefore, the claim that it has not been repealed is probably due to the continued practice of fiqh. On the other hand, also rational evidence shows that the right to choose (takhyir), which was given initially, was later repealed. For example, in verse 184, it is stated that those who are sick and travelers should perform fasting on other days with the expression "فَمَنْ كَانَ مِنْكُمْ مَرِيضًا أَوْ عَلَى سَفَرٍ فَعِدَّةٌ مِنْ أَيَّامٍ أُخَرَ"; The same issue is stated in verse 185 with the expression "وَمَنْ كَانَ مَرِيضًا أَوْ عَلَى سَفَرٍ فَعِدَّةٌ مِنْ أَيَّامٍ أُخَرَ". The repetition in question shows that the two verses were sent not together but at different times. This state of affairs confirms that the second verse has repealed the right of choosing (takhyir) in first one. In addition, as Imam Māturīdi's determined by hit, if those who cannot endure fasting were meant in verse 184, it would be unwise to call these people at the end of the verse as "However, that you fast is better for you, if you only knew!" In the overwhelming majority of Turkish translations of the Qurʾān, it is seen that there is no emphasis on the meaning of the verse when it was first sent. Even the expression “Upon those who are able to fast...” in the verse is translated as “Upon those who aren’t able to fast...”. Whereas it is more consistent and appropriate to reflect the literal meaning of the verse in the translation and explain the situation with additional notes. In this way, it will be understood that two verses that contain the same words and come one after another are sent different times and about different things, hence the reader will be given accurate information. In the nearly thirty examples of translations in the article, it is seen that the translations belonging to Mehmet Akif and Süleyman Tevfik and the translation of the delegation chaired by Hüseyin Kazım are in full harmony with the data in tafsir literature and the general opinion of mufassirs. Rifat Börekçi, the first president of Religious Affairs of the Republic of Turkey, has criticized the translation committee headed by Hüseyin Kazım extremely harshly. Then, with the choice made by Elmalılı Hamdi, almost the direction of the wind changed and the translators could not surpass it. Although there have been some translations in line with the text of the verse, the relevant explanations of these authors reveal that they did not understand the issue in detail and did not make a conscious translation. Meantime the analysis made in the aforementioned verse example shows that reliable translations cannot be made without referring to detailed tafsir information and therefore a correct Qurʾān translation is often not possible without tafsir. (shrink)

It has largely been assumed that when an intentional community loses its charismatic leader for one reason or another, the group will most likely disband unless that individual’s charisma has become routinized. The Kashi Ashram in Sebastian, Florida, is a spiritual community that was established, thanks to the vision of their Guru, Ma Jaya Sati Bhagavati. Her students were so devoted to her that her physical death in 2012 could have initiated a crisis in the community. Although bureaucratic offices had (...) been established to carry out some of the necessary functions of the Ashram, no one came close to filling her role as a spiritual teacher. And yet, more than 6 years later, new members are still joining the community and the way they describe Ma’s presence in their lives is little different from how older members that knew Ma in this lifetime talk about her. While I do not disagree that the routinization of charisma is an important step in ensuring the longevity of new religious movements, in this paper, I argue that an individual’s charisma may be transferred to a geographic place such that the Ashram becomes an active agent in the attraction and retention of new members. (shrink)

The scope and significance of lateral gene transfer (LGT) has been discussed periodically since the early twentieth century. In sketching this history here we see that the pendulum of opinion has swung from one extreme that LGT is a rare phenomenon to the other that it is fundamental to evolution. That phages are sources of bacterial evolutionary innovation has been discussed since the 1920s in association with evidence that symbiosis is a major source of evolutionary innovation. Concepts of (...) infectious heredity re-emerged with the rise of bacterial genetics after the Second World War, but LGT was generally discounted as a significant evolutionary force. LGT received increased attention in the 1960s and 1970s because of its role in antibiotic resistance outbreaks. Some speculated that the new molecular approaches to bacterial phylogenetics were ill-conceived because of LGT. With the rise of genomics in the 1990s, it became clear to phylogeneticists that LGT is the principal mode of generating evolutionary novelty in the prokaryotic world. All microbiologists agree today that the Darwinian concept of a bifurcating tree is an inadequate, if not misleading, representation of the evolutionary process in the microbial world. Phages are also reconceived not only as agents of bacterial gene exchange, but also as organisms in their own right, and fundamental in the evolution of new genes. (shrink)

Efforts to bring science into early 19th century breeding practices in Central Europe, organised from Brno, the Hapsburg city in which Mendel would later turn breeding experiments into a body of timeless theory, are here considered as a significant prelude to the great discovery. During those years prior to Mendel's arrival in Brno, enlightened breeders were seeking ways to regulate the process of heredity, which they viewed as a force to be controlled. Many were specialising in sheep breeding for the (...) benefit of the local wool industry while others were showing an interest in commercial plants, especially fruit trees and vines, and later cereals. Breeders explained their problems in regulating heredity in terms of climatic influences disruption due to crossing sports or saltations. Practical experience led them to the concepts of 'inheritance capacity' and the 'mutual elective affinity' of parents. The former was seen to differ among individuals and also among traits; the latter was proposed as a means of adding strength to heredity. The breeders came to recognise that traits might be hidden and yet transmitted as a 'potential' to future generations. They also grew to understand that heredity would be strengthened when a quality was 'fixed' within a lineage by 'pure blood relations.' Continued selection of the desired quality might then lead to 'a higher perfection.' But the ultimate 'physiological' question about breeding, 'what is inherited and how?,' found no answer. Major figures in this development included Abbot Napp, the one who asked this question and who was due to receive Mendel into the monastery in 1843, and Professor Diebl whose lectures on agriculture and natural science at the Brno Philosophical Institute Mendel would attend in 1846. Here we analyse their progress in theorizing about breeding up until about 1840. In discussing this development, we refer to certain international contacts, especially with respect to information transfer and scientific education, within the wider context of the late Enlightenment. (shrink)

According to scientific realists, the predictive success of mature theories provides a strong epistemic basis for thinking that such theories are approximately true. However, we know that many theories once regarded as well-confirmed and predictively successful were eventually replaced with successor theories, and some claim this undermines the epistemic confidence we should have in the approximate truth of current science. Selective scientific realists in turn argue that if one can show that the predictive success of some rejected theory T is (...) a function of theoretical claims consistent with current science, then T’s failure doesn’t undermine the claim that current successful theories are approximately true. As such, Selective Scientific Realism (SSR) can be tested through historical examples. Showing that the predictive success of a failed theory is the result of theoretical features later rejected provides a counterexample to SSR. Conversely, SSR is supported if its explanation of the predictive success of failed theories--namely, that the factors which lead to predictive success in the failed theory survive in the successor theory--is able to handle a wide array of historical cases. (shrink)

Efforts to bring science into early 19th century breeding practices in Central Europe, organised from Brno, the Hapsburg city in which Mendel would later turn breeding experiments into a body of timeless theory, are here considered as a significant prelude to the great discovery. During those years prior to Mendel's arrival in Brno, enlightened breeders were seeking ways to regulate the process of heredity, which they viewed as a force to be controlled. Many were specialising in sheep breeding for the (...) benefit of the local wool industry while others were showing an interest in commercial plants, especially fruit trees and vines, and later cereals. Breeders explained their problems in regulating heredity in terms of (1) climatic influences (2) disruption due to crossing (3) sports or saltations. Practical experience led them to the concepts of 'inheritance capacity' and the 'mutual elective affinity' of parents. The former was seen to differ among individuals and also among traits; the latter was proposed as a means of adding strength to heredity. The breeders came to recognise that traits might be hidden and yet transmitted as a 'potential' to future generations. They also grew to understand that heredity would be strengthened when a quality was 'fixed' within a lineage by 'pure blood relations.' Continued selection of the desired quality might then lead to 'a higher perfection.' But the ultimate 'physiological' question about breeding, 'what is inherited and how?,' found no answer. Major figures in this development included Abbot Napp, the one who asked this question and who was due to receive Mendel into the monastery in 1843, and Professor Diebl whose lectures on agriculture and natural science at the Brno Philosophical Institute Mendel would attend in 1846. Here we analyse their progress in theorizing about breeding up until about 1840. In discussing this development, we refer to certain international contacts, especially with respect to information transfer and scientific education, within the wider context of the late Enlightenment. (shrink)

ABSTRACTJean-François Lyotard famously described the task of philosophy as “bearing witness to the differend”, a differend being a conflict that cannot be equitably solved due to the lack of a rule...

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of (...) the changes are caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

Since the beginning of time, the pre-biological and the biological world have seen a steady increase in complexity of form and function based on a process of combination and re-combination. The current modern synthesis of evolution known as the neo-Darwinian theory emphasises population genetics and does not explain satisfactorily all other occurrences of evolutionary novelty. The authors suggest that symbiosis and hybridisation and the more obscure processes such as polyploidy, chimerism and lateral transfer are mostly overlooked and not (...) featured sufficiently within evolutionary theory. They suggest, therefore, a revision of the existing theory including its language, to accommodate the scientific findings of recent decades. (shrink)

The study of vegetables represents one of the main topics in Bacon’s Sylva sylvarum. Not only in quantitative terms, because plants occupy about a third of the entire book, but the centuries on plants are among the most structured, and this reveals Bacon’s particular interest for the topic. The key to understanding Bacon’s interest can be found in both his Sylva sylvarum and the Historia vitae et mortis, where Bacon explains how the results of studying certain processes in plants can (...) be later transferred and applied to animals and humans. In the context of his discussion of nourishing foods and drinks, Bacon addresses the question of how nourishment gets assimilated in the body. One of the ways in which the... (shrink)

Our understanding of what microbes are and how they evolve has undergone many radical shifts since the late nineteenth century, when many still believed that bacteria could be spontaneously generated and most thought microbial “species” (if any) to be unstable and interchangeable in form and function (pleomorphic). By the late twentieth century, an ontology based on single cells and definable species with predictable properties, evolving like species of animals or plants, was widely accepted. Now, however, genomic and metagenomic data show (...) that lateral gene transfer compromises this picture of stability and predictability, and refocuses our attention on multilineage communities. Treating such communities as unstable but identifiable evolving “individuals” makes us again pleomorphists, of a sort. (shrink)

To clone humans is deliberately to generate two or more individuals who share the same nuclear deoxyribonucleic acid. Using animals, researchers have performed two basic types of cloning that will eventually yield commercial benefits. Embryo twinning involves separating the individual cells of an embryo and allowing each to cleave for later transfer to a uterus. Cloning by nuclear transfer involves removing the nuclei from embryonic cells or fetal or adult somatic cells and fusing those nuclei with enucleated donor (...) egg cells. Although for the purposes of commercial biotechnology these techniques do not raise undue concern when attempted with animals, embryo twinning, embryo nuclear transfer, fetal somatic cell nuclear transfer, and adult somatic cell nuclear transfer all provoke intense ethical discussions when considered for human use. (shrink)

To clone humans is deliberately to generate two or more individuals who share the same nuclear deoxyribonucleic acid. Using animals, researchers have performed two basic types of cloning that will eventually yield commercial benefits. Embryo twinning involves separating the individual cells of an embryo and allowing each to cleave for later transfer to a uterus. Cloning by nuclear transfer involves removing the nuclei from embryonic cells or fetal or adult somatic cells and fusing those nuclei with enucleated donor (...) egg cells. Although for the purposes of commercial biotechnology these techniques do not raise undue concern when attempted with animals, embryo twinning, embryo nuclear transfer, fetal somatic cell nuclear transfer, and adult somatic cell nuclear transfer all provoke intense ethical discussions when considered for human use. (shrink)

The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to (...) a quantitatively similar degree. An important illustration of the difference is that eukaryotes do not exhibit pangenomes, though prokaryotes do. Eukaryotes reveal no detectable cumulative effects of LGT, though prokaryotes do. A critical analysis suggests that something is deeply amiss with eukaryote LGT theories. In prokaryotes, genes from the environment can enter the genome via lateral gene transfer. In eukaryote genetics, natural variation comes from within the genome, not from the environment. Yet many reports claim that eukaryotes undergo LGT just like prokaryotes. Such claims do not withstand scrutiny and are probably untrue. (shrink)

Since intelligent design (ID) advocates claimed the ubiquitous mouse trap as an example of systems that cannot have evolved, mouse trap history is doubly relevant to studying material culture. On the one hand, debunking ID claims about mouse traps and, by implication, also about other irreducibly complex systems has a high educational value. On the other hand, a case study of mouse trap history may contribute insights to the academic discussion about material culture evolution. Michael Behe argued that mouse traps (...) cannot trap mice with any part missing; therefore, they cannot have a precursor with one part less, therefore, cannot have a continuous history, and therefore, cannot have evolved. The patented and seminal precursor of current flat snap traps, however, had one part less, because spring and striker were formed of one wire. Secondly, historical records that reach back into the Bronze Age suggest that its history continued for a very long time. Thirdly, all prerequisites for evolution (variation, transmission, and selection) abound in mouse trap populations. Hence, Behe’s triple-jump conclusion about mouse traps is false each step. There is no, in principle, impossibility for mouse traps to evolve. An evolutionary account of mouse trap history also has academic merits beyond its educational value. Three important conclusions can be drawn: (1) reticulate phylogenies of artifact systems may be resolvable as overlapping, but branching, phylogenies of parts; (2) homologous ideas may be realized by analogous material, that is, phylogenies of information do not necessarily coincide with those of material parts; (3) recombination of parts between different artifact systems increases the cumulative nature of cultural evolution. (shrink)

The soil bacteria rhizobia have the capacity to establish nitrogen‐fixing symbiosis with their leguminous host plants. In most Rhizobium species the genes for nodule development and nitrogen fixation have been localized on large indigenous plasmids that are transmissible, allowing lateral transfer of symbiotic functions. A recent paper reports on the complete sequencing of the symbiotic plasmid pNGR234a from Rhizobium species NGR234(1), revealing not only putative new symbiotic genes but also possible mechanisms for evolution and lateral dispersal of (...) symbiotic nitrogen‐fixing abilities among rhizobia. (shrink)

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. (...) At the same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (shrink)

Lateral gene transfer, the exchange of genetic information between lineages, not only makes construction of a universal Tree of Life difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. (...) We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit. (shrink)

In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of (...) horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic‐metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice‐binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism.Editor's suggested further reading in BioEssays Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution Abstract. (shrink)

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and (...) hybridization. Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (shrink)