Conversation game: talking bacteria

The story of autonomous unicellular organisms, bacteria with unimaginable computational and evolutionary capabilities along with collective behavior has been running since the first six decades of the twentieth Century. However, do not consider them to be small and simple, because they possess the generic term quorum sensing adopted to describe the cell communication process which co-ordinate gene expression, when the population has reached a high cell density. Bacteria release diffusible signal molecules known as autoinducers or quorum sensing molecules. In recent research, the direction for activating or deactivating nature of a wave of gene expression is predicted experimentally which control bacterial populations subject to a diffusing autoinducer signal. On the other hand, it has been observed that the accumulation of the quorum sensing molecules leads to a negative diffusion coefficient in the solution of governing differential equation.     

Always talking to some purpose

Distinguished molecular biologist, Sydney Brenner, has said he won't write an autobiography. Mark Ptashne reviews the next best thing.     

What we talk about when we talk about access deficits

Semantic impairments have been divided into storage deficits, in which the semantic representations themselves are damaged, and access deficits, in which the representations are intact but access to them is impaired. The behavioural phenomena that have been associated with access deficits include sensitivity to cueing, sensitivity to presentation rate, performance inconsistency, negative serial position effects, sensitivity to number and strength of competitors, semantic blocking effects, disordered selection between strong and weak competitors, correlation between semantic deficits and executive function deficits and reduced word frequency effects. Four general accounts have been proposed for different subsets of these phenomena: abnormal refractoriness, too much activation, impaired competitive selection and deficits of semantic control. A combination of abnormal refractoriness and impaired competitive selection can account for most of the behavioural phenomena, but there remain several open questions. In particular, it remains unclear whether access deficits represent a single syndrome, a syndrome with multiple subtypes or a variable collection of phenomena, whether the underlying deficit is domain-general or domain-specific, whether it is owing to disorders of inhibition, activation or selection, and the nature of the connection (if any) between access phenomena in aphasia and in neurologically intact controls. Computational models offer a promising approach to answering these questions.     

What we talk about when we talk with medical students

In this article, we review how we interact with medical students in our efforts to teach blood pressure regulation and systemic cardiovascular control along with related elements of respiratory and exercise physiology. Rather than provide a detailed lecture with key facts, we attempted to outline our approach to teaching integrative cardiovascular physiology to medical students, which includes five major themes. First, focus on questions versus answers and facts. We believe that this offers both the learner and teacher a number of advantages. Second, avoid teaching dogma in the name of clarity (i.e., heavy focus on teaching "facts" that have not yet been fully investigated). This is especially important because of the way knowledge evolves over time. Third, include laboratory-based experiences in human integrative physiology. Fourth, provide students with intellectual frameworks versus a list of "facts" to serve as a platform for question generation. Finally, focus on the role of integration and regulatory redundancy in physiology and the idea that physiology is a narrative that can help. In this article, we discuss the philosophy behind the themes outlined above and argue that questions, and not answers, are where the action is for both research and education.     

Stop competing,start talking!

According to current belief, the molecular networks orchestrating cell death or exit from mitosis upon extended mitotic arrest do not interact, stubbornly executing two parallel biological programs and competing to define a stochastic decision between death and a chance for survival with uncertain destiny. However, recent findings by Diaz‐Martinez et al ( 2014 ) in this issue of The EMBO Journal now call for a reassessment of the “competing network” hypothesis.     

Time to talk

Debate over the publication of the H5N1 flu virus papers highlights the need for better risk management of dual-use research. Scientists should start this discussion instead of waiting for governments to implement regulation.EMBO reports (2012) 13, 578; doi:10.1038/embor.2012.77Freedom of research is a concept widely respected in democratic societies and is often enshrined in constitutional law. We tout academics′ freedom to pursue their quest for knowledge and understanding as a hallmark of a truly free society.The reality, though, is a little more nuanced. Although academics in democracies are usually free to investigate any idea they like, they are not as free when it comes to the design and conduct of their experiments. In fact, academic research is probably more regulated than most enterprises. Researchers who falsify or misrepresent data might well find themselves joining the queue at the local job centre; when it comes to corporate or financial fraud, only the most egregious cases are ever punished. Experiments conducted on vertebrates must be vetted to ensure they meet the standards of animal welfare; industrial agriculture has no such qualms about how it treats its livestock. Privacy and consent are paramount when conducting research using databases of human genetic and medical data; the business models of Facebook or Google play fast and loose with privacy and consent.Despite the plethora of rules and laws that govern the conduct of science and hold scientists to high standards they do not seem to have slowed the overall pace of research, even if some areas are seen as overregulated. Yet, as Michele Garfinkel pointed out in the context of stem cell research, regulation is a relatively small price to pay in exchange for public trust in—and financial support of—research and researchers[1].New laws and stricter rules should therefore not be seen as an end to academic freedom or an undue hurdle for research. We may well see a new wave of regulations addressing renewed concerns about biosafety and biosecurity, triggered by research into a mutant version of the avian H5N1 influenza virus. Two papers—one published in Nature, one still to come from Science—have attracted considerable attention from the media and politicians, and led to the unprecedented recommendation by the National Science Advisory Board for Biosecurity (NSABB), an advisory board for the US government, to restrict the publication of crucial information. In the meantime, the NSABB has recommended publication of revised versions of these papers, but their original argument—that the information about manipulating the virus could be abused to create a biological weapon—remains valid.Notwithstanding the discussion about murky risks versus vague benefits for public health, there is a broader need to address concerns about research that could endanger human health or the environment. Many biologists feel that this was addressed at the 1975 Asilomar conference on recombinant DNA technology and that nothing bad has happened. Although true, the concerns that inspired the conference have also led to regulations on how to handle recombinant DNA and organisms.What has changed, though, is the ability of molecular biologists to manipulate living matter. At the time of Asilomar, DNA recombinant technology was in its infancy and PCR was not even invented. Modern technologies now allow scientists to analyse whole organisms at different levels of organization, manipulate their genomes and biochemistry, and even create new viruses and bacteria from scratch. Whilst some of these technologies still require a level of instrumentation, know-how and sophistication that few laboratories can muster, it is only a matter of time until these technologies and skills become widely available—including to the mentally unhinged researcher or someone else who may have less then beneficial intents. Misuse need not be criminal in intent: scientists who use cholera toxin for their experiments or work on filoviruses may not even be aware that they are handling a dual-use agent.These risks are ill-defined, but they are not negligible. The lesson from the H5N1 debates is that biological research might require new regulations to manage these risks without unduly hindering research or public health. It would not be in the interests of science, however, if such debates were left to policy-makers and the media. The scientific community should proactively acknowledge the need for better risk management and set discussions in motion.The H5N1 experience has also provided some pointers as to how a system to manage biosafety and biosecurity could look. Two crucial choking points in research are funding and publication. Funding agencies could determine whether any given research project poses dual-use risks, and whether the potential benefits outweigh possible future abuse, and could accordingly demand stricter safety measures. The NSABB has also recommended expanding the role of institutional biosafety review to address dual-use risks and biosecurity. Journals could perform a similar risk–benefit analysis—preferably involving experts in biosafety and biosecurity—to determine whether the information offered for publication poses an undue risk to public or environmental safety. Many journals and funding agencies already require that experiments using human subjects or animals are done in an ethically acceptable manner; biosecurity review would become another measure by which to ensure scientists act responsibly and benefit from public trust in science. It''s time to start talking.     

What we talk about when we talk about capacitance measured with the voltage-clamp step method

Capacitance is a fundamental neuronal property. One common way to measure capacitance is to deliver a small voltage-clamp step that is long enough for the clamp current to come to steady state, and then to divide the integrated transient charge by the voltage-clamp step size. In an isopotential neuron, this method is known to measure the total cell capacitance. However, in a cell that is not isopotential, this measures only a fraction of the total capacitance. This has generally been thought of as measuring the capacitance of the ??well-clamped?? part of the membrane, but the exact meaning of this has been unclear. Here, we show that the capacitance measured in this way is a weighted sum of the total capacitance, where the weight for a given small patch of membrane is determined by the voltage deflection at that patch, as a fraction of the voltage-clamp step size. This quantifies precisely what it means to measure the capacitance of the ??well-clamped?? part of the neuron. Furthermore, it reveals that the voltage-clamp step method measures a well-defined quantity, one that may be more useful than the total cell capacitance for normalizing conductances measured in voltage-clamp in nonisopotential cells.     

Gould talking past Dawkins on the unit of selection issue

My general aim is to clarify the foundational difference between Stephen Jay Gould and Richard Dawkins concerning what biological entities are the units of selection in the process of evolution by natural selection. First, I recapitulate Gould’s central objection to Dawkins’s view that genes are the exclusive units of selection. According to Gould, it is absurd for Dawkins to think that genes are the exclusive units of selection when, after all, genes are not the exclusive interactors: those agents directly engaged with, directly impacted by, environmental pressures. Second, I argue that Gould’s objection still goes through even when we take into consideration Sterelny and Kitcher’s defense of gene selectionism in their admirable paper “The Return of the Gene.” Third, I propose a strategy for defending Dawkins that I believe obviates Gould’s objection. Drawing upon Elisabeth Lloyd’s careful taxonomy of the various understandings of the unit of selection at play in the philosophy of biology literature, my proposal involves realizing that Dawkins endorses a different understanding of the unit of selection than Gould holds him to, an understanding that does not require genes to be the exclusive interactors.     

If walls could talk

The plant cell wall is very complex, both in structure and function. The wall components and the mechanical properties of the wall have been implicated in conveying information that is important for morphogenesis. Proteoglycans, fragments of polysaccharides and the structural integrity of the wall may relay signals that influence cellular differentiation and growth control. Furthering our knowledge of cell wall structure and function is likely to have a profound impact on our understanding of how plant cells communicate with the extracellular environment.     

From behind the curtain: talking about values in LCA

Purpose

Practitioners of life cycle assessment (LCA) acknowledge that more input from social scientists can help advance the cause of life cycle management (LCM). This commentary offers a social science perspective on a long-running question within LCA, namely, how the field should manage not only stakeholders’ values but also those of practitioners themselves.

Methods

More than 60 interviews were conducted with LCA practitioners and their industry clients. Qualitative data were also collected through participant observation at several LCA and LCM conferences, a study of the field’s history, and extensive content and discourse analysis of LCA publications and online forums.

Results and discussion

Results show that LCA practitioners’ values are informed partly by the knowledge acquired through their LCA work. At the same time, LCA standards and professional norms implicitly advise practitioners to keep those values out of their work as much as possible, so as not to compromise its apparent objectivity. By contrast, many social scientists contend openly that value-based judgments, based on “situated knowledge,” can actually enhance the rigor, accountability, and credibility of scientific assessments.

Conclusions

LCA practitioners’ own situated knowledge justifies not only the value choices required by LCA but also their evaluative judgments of contemporary life cycle-based sustainability initiatives. This more critical voice could advance the goals of LCM while also boosting the credibility of LCA more generally.