New and Exciting in PLoS ONE

There are 35 brand new papers on PLoS ONE tonight and it is difficult for me to pick the most exciting for the week. So, here is one on the effects of night-shift, one on melanopsin and light perception, one on time perception, one on limb regeneration in the Axolotl, a meta-analysis of the soil ecology literature and, a first for PLoS ONE, an article by a prominent philosopher of science that I expect to be discussed on blogs over the next few days:

Acute Sleep Deprivation and Circadian Misalignment Associated with Transition onto the First Night of Work Impairs Visual Selective Attention:

Overnight operations pose a challenge because our circadian biology promotes sleepiness and dissipates wakefulness at night. Since the circadian effect on cognitive functions magnifies with increasing sleep pressure, cognitive deficits associated with night work are likely to be most acute with extended wakefulness, such as during the transition from a day shift to night shift. To test this hypothesis we measured selective attention (with visual search), vigilance (with Psychomotor Vigilance Task [PVT]) and alertness (with a visual analog scale) in a shift work simulation protocol, which included four day shifts followed by three night shifts. There was a nocturnal decline in cognitive processes, some of which were most pronounced on the first night shift. The nighttime decrease in visual search sensitivity was most pronounced on the first night compared with subsequent nights (p = .04), and this was accompanied by a trend towards selective attention becoming 'fast and sloppy'. The nighttime increase in attentional lapses on the PVT was significantly greater on the first night compared to subsequent nights (p<.05 indicating="" an="" impaired="" ability="" to="" sustain="" focus.="" the="" nighttime="" decrease="" in="" subjective="" alertness="" was="" also="" greatest="" on="" first="" night="" compared="" with="" subsequent="" nights="" these="" nocturnal="" deficits="" attention="" and="" offer="" some="" insight="" into="" why="" occupational="" errors="" accidents="" injuries="" are="" pronounced="" during="" work="" day="" work.="" examination="" of="" vulnerabilities="" underlying="" deployment="" can="" be="" informative="" for="" design="" optimal="" schedules="" implementation="" effective="" countermeasures="" performance="">

Brain Responses to Violet, Blue, and Green Monochromatic Light Exposures in Humans: Prominent Role of Blue Light and the Brainstem:

Melanopsin is a pigment that responds to light and is found in specialised light sensitive cells of the retina. In this paper, Maquet and colleagues investigated the spectral sensitivity of immediate brain responses to light by measuring brain activity in participants exposed to different wavelengths. Their results reveal that short exposures to light induce changes in brain activity and that the melanopsin system provides the most important contribution to these changes.

The Effect of Predictability on Subjective Duration:

Events can sometimes appear longer or shorter in duration than other events of equal length. For example, in a repeated presentation of auditory or visual stimuli, an unexpected object of equivalent duration appears to last longer. Illusions of duration distortion beg an important question of time representation: when durations dilate or contract, does time in general slow down or speed up during that moment? In other words, what entailments do duration distortions have with respect to other timing judgments? We here show that when a sound or visual flicker is presented in conjunction with an unexpected visual stimulus, neither the pitch of the sound nor the frequency of the flicker is affected by the apparent duration dilation. This demonstrates that subjective time in general is not slowed; instead, duration judgments can be manipulated with no concurrent impact on other temporal judgments. Like spatial vision, time perception appears to be underpinned by a collaboration of separate neural mechanisms that usually work in concert but are separable. We further show that the duration dilation of an unexpected stimulus is not enhanced by increasing its saliency, suggesting that the effect is more closely related to prediction violation than enhanced attention. Finally, duration distortions induced by violations of progressive number sequences implicate the involvement of high-level predictability, suggesting the involvement of areas higher than primary visual cortex. We suggest that duration distortions can be understood in terms of repetition suppression, in which neural responses to repeated stimuli are diminished.

Transforming Growth Factor: β Signaling Is Essential for Limb Regeneration in Axolotls:

The axolotl limb has been widely studied in developmental biology because of its unusual ability to regenerate following injury. In this study, the authors investigated the role of the transforming growth factor-beta (TGF-β) family members in axolotl limb regeneration. Their results show that the inhibition of TGF-β stopped the redevelopment process, thus suggesting that TGF-β is essential in limb regeneration.

A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System:

Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate "particularity" (empirical observations) and "generality" (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.

Beyond the Gene by Evelyn Fox Keller and David Harel:

This paper is a response to the increasing difficulty biologists find in agreeing upon a definition of the gene, and indeed, the increasing disarray in which that concept finds itself. After briefly reviewing these problems, we propose an alternative to both the concept and the word gene--an alternative that, like the gene, is intended to capture the essence of inheritance, but which is both richer and more expressive. It is also clearer in its separation of what the organism statically is (what it tangibly inherits) and what it dynamically does (its functionality and behavior). Our proposal of a genetic functor, or genitor, is a sweeping extension of the classical genotype/phenotype paradigm, yet it appears to be faithful to the findings of contemporary biology, encompassing many of the recently emerging--and surprisingly complex--links between structure and functionality.