The ribosome-recycling step: consensus or controversy?

Ribosome recycling, the last step in translation, is now accepted as an essential process for prokaryotes. In 2005, three laboratories showed that ribosome-recycling factor (RRF) and elongation factor G (EF-G) cause dissociation of ribosomes into subunits, solving the long-standing problem of how this essential step of translation occurs. However, there remains ongoing controversy regarding the other actions of RRF and EF-G during ribosome recycling. We propose that the available data are consistent with the notion that RRF and EF-G not only split ribosomes into subunits but also participate directly in the release of deacylated tRNA and mRNA for the next round of translation.     

Metabolic theory or metabolic models?

The metabolic theory of ecology (MTE) claims to derive ecological relationships from the structure of resource distribution networks, which is assumed to determine the scaling of metabolism with body mass, and from the effect of temperature on the rate of biological processes. MTE is controversial. I propose that some of the controversy stems from the implicit adoption of different views of science by the proponents and critics of MTE. The perspective of proponents is consistent with the theory-centric view of science called the received view, whereas many of the critics implicitly adopt an alternative view consistent with a model-centric view of science. I propose that adopting the model-centric view can help to settle some of the differences among proponents and critics of MTE.     

Shared or unshared consensus decision in macaques?

Members of a social group have to make collective decisions in order to synchronise their activities. In a shared consensus decision, all group members can take part in the decision whereas in an unshared consensus decision, one individual, usually a dominant member of the group, takes the decision for the rest of the group. It has been suggested that the type of decision-making of a species could be influenced by its social style. To investigate this further, we studied collective movements in two species with opposed social systems, the Tonkean macaque (Macaca tonkeana) and the rhesus macaque (Macaca mulatta). From our results, it appears that the decision to move is the result of the choices and actions of several individuals in both groups. However, this consensus decision involved nearly all group members in Tonkean macaques whereas dominant and old individuals took a prominent role in rhesus macaques. Thus, we suggest that Tonkean macaques display equally shared consensus decisions to move, whereas in the same context rhesus macaque exhibit partially shared consensus decisions. Such a difference in making a collective decision might be linked to the different social systems of the two studied species.     

Junk or functional DNA? ENCODE and the function controversy

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk.     

Brain death: a durable consensus?

Is it even conceivable that this global consensus [on the whole-brain definition of death] could, in time, be regarded as a very temporary and makeshift expedient, a momentary substitute for a resolution of some profoundly difficult issues which for a time, perhaps a brief time, fit with both the technical capacities and the legal needs of those who endorsed it? And that in the long run it could linger as a footnote, or perhaps a chapter heading, in the long history of man's conceptions of life and death? This suggestion is so far from conventional wisdom today that one who espouses it risks being regarded as a crank. Nevertheless, I believe that the argument in its favor, while not conclusive, is much stronger than the argument against it (and in favor of the prevailing consensus). I will state the argument briefly, with particular reference to the landmark report in 1982 in Washington of the President's Commission for the Study of Ethical Problems in Medicine, and will situate the argument in the context of trends in contemporary bioethics. I do not expect to win over, in this one pass, those who have been convinced of the validity of the conventional view. I do hope, however, to re-open the issue; in particular, to provide reasons to regard the issue as far from settled.     

Arrestin-mediated signaling: Is there a controversy?

The activation of the mitogen-activated protein(MAP) kinases extracellular signal-regulated kinase(ERK)1/2 was traditionally used as a readout of signaling of G protein-coupled receptors(GPCRs) via arrestins, as opposed to conventional GPCR signaling via G proteins. Several recent studies using HEK293 cells where all G proteins were genetically ablated or inactivated, or both non-visual arrestins were knocked out, demonstrated that ERK1/2 phosphorylation requires G protein activity, but does not necessarily require the presence of non-visual arrestins. This appears to contradict the prevailing paradigm. Here we discuss these results along with the recent data on gene edited cells and arrestinmediated signaling. We suggest that there is no real controversy. G proteins might be involved in the activation of the upstream-most MAP3Ks, although in vivo most MAP3K activation is independent of heterotrimeric G proteins, being initiated by receptor tyrosine kinases and/or integrins. As far as MAP kinases are concerned, the best-established role of arrestins is scaffolding of the three-tiered cascades(MAP3K-MAP2 K-MAPK). Thus, it seems likely that arrestins, GPCRbound and free, facilitate the propagation of signals in these cascades, whereas signal initiation via MAP3K activation may be independent of arrestins. Different MAP3Ks are activated by various inputs, some of which are mediated by G proteins, particularly in cell culture, where we artificially prevent signaling by receptor tyrosine kinases and integrins, thereby favoring GPCR-induced signaling. Thus, there is no reason to change the paradigm: Arrestins and G proteins play distinct non-overlapping roles in cell signaling.     

Germline genome editing: Moratorium,hard law,or an informed adaptive consensus?

With the development of practical means of human germline genome editing (HGGE) in recent years, there have been calls for stricter regulation and oversight over HGGE interventions with potential for heritable changes in the germline. An international moratorium has been advocated. We examine the practicality of such a proposal, as well as of a regulation through the “traditional” mechanisms of international and municipal laws. We argue that these mechanisms are unlikely to achieve their intended objectives and that the better approach is to engage the international community of stakeholders, researchers, scientists, clinicians, and other workers directly involved in the field in working toward the development of an “informed adaptive consensus”. We offer suggestions as to how this may be achieved and how existing indirect levers of regulation may be harnessed toward this end.     

Metabolic pathway compartmentalization: an underappreciated opportunity?

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Radwaste at sea: A new era of polarization or a new basis for consensus?

Abstract

A coalition of third world nations, led by the Pacific island countries and those European nations who have developed land‐based disposal programs for their radioactive wastes, seek to amend the London Convention on Dumping (the international treaty controlling ocean disposal of radioactive and other wastes) in order to ban ocean disposal of low‐level radioactive wastes. Pro‐dumping nations maintain that the treaty may only be amended based on science and that current scientific research indicates that low‐level waste represents neither a threat to the integrity of the marine environment nor human health. Anti‐dumping nations, on the other hand, argue that the same science, particularly the models used to predict the fate and the effects of these wastes, exhibits sufficient uncertainty to preclude judgments about the absence of harm from future disposal activities. These differing conclusions mirror differing assessments of risk. These assessments build on the differing social, political, and economic values placed on use of the ocean and on conflicting conceptions of the fundamental rights and obligations of nations whose use of the ocean may impinge on the resources of others. Each side's continued intransigence may result in unilateral ocean disposal activities with serious consequences for the London Convention on Dumping (LDC) and its control over other wastes transported to sea for disposal. Initiatives of anti‐dumping nations to expand the LDC's decision‐making framework to examine the social, economic, and political issues underlying each side's interpretation of scientific evidence offer hope to address the underlying non‐scientific issues and perhaps to strengthen decision‐making within the LDC.     

Prion hypothesis: the end of the controversy?

Forty-three years have passed since it was first proposed that a protein could be the sole component of the infectious agent responsible for the enigmatic prion diseases. Many discoveries have strongly supported the prion hypothesis, but only recently has this once heretical hypothesis been widely accepted by the scientific community. In the past 3 years, researchers have achieved the 'Holy Grail' demonstration that infectious material can be generated in vitro using completely defined components. These breakthroughs have proven that a misfolded protein is the active component of the infectious agent, and that propagation of the disease and its unique features depend on the self-replication of the infectious folding of the prion protein. In spite of these important discoveries, it remains unclear whether another molecule besides the misfolded prion protein might be an essential element of the infectious agent. Future research promises to reveal many more intriguing features about the rogue prions.     

Nuclear targeting sequences--a consensus?

Nuclear targeting sequences are essential for the transport of proteins into the nucleus. The seven-amino-acid nuclear targeting sequence of the SV40 large T antigen has been regarded as the model; however, many nuclear targeting sequences appear to be more complex. We suggest in this review that, despite this diversity, a consensus bipartite motif can be identified.     

A. A. Ukhtomskiĭ and I. P. Pavlov: a controversy or a dialogue?

Pavlov's concept of conditioned reflexes and Ukhtomskii theory of dominanta fall within the biological line in physiology. They unravel the integral adaptive and active nature of the organism behavior in the environment. It is impossible to develop modern concepts about the determinants of goal-directed behavior of animals and voluntary activity of humans without in-depth study of the achievements of these Russian physiological schools which not only formed the methodological basis for the current studies but also directed the way for their further development.     

Trophic levels and trophic dynamics: A consensus emerging?

There are three clearly different views on trophic levels. The systems-ecological tradition sees trophic levels as relatively discrete and well-defined units whose interactions cannot be derived from interactions between constituent populations. The reductionist population-ecological tradition sees trophic levels as inappropriate abstractions that cannot be used in formulating predictive theories. The tradition of trophic dynamics sees the first three trophic levels of autotroph-based ecosystems as reasonable abstractions, useful in formulating predictive theories, but devoid of properties that could not be directly extrapolated from those of constituent populations. Recent literature suggests that the first two schools are converging towards the viewpoints of the third, though the latter has also been modified by the interaction.