Design principles for robust biochemical reaction networks: what works, what cannot work, and what might almost work

We bring together recent results that connect the structure of a mass-action reaction network to its capacity for concentration robustness — that is, its capacity to keep the concentration of a critical bio-active species within narrow limits, even against large fluctuations in the overall supply of the network’s constituents.     

Polydomy in ants: what we know, what we think we know, and what remains to be done

The correct identification of colony boundaries is an essential prerequisite for empirical studies of ant behaviour and evolution. Ant colonies function at various organizational levels, and these boundaries may be difficult to assess. Moreover, new complexity can be generated through the presence of spatially discrete subgroups within a more or less genetically homogeneous colony, a situation called polydomy. A colony is polydomous only if individuals (workers and brood) of its constituent nests function as a social and cooperative unit and are regularly interchanged among nests. This condition was previously called polycalic, and the term polydomy was used in a broader sense for a group of daughter nests of the same mother colony (implying limited female dispersal), without regard to whether these different nests continued to exchange individuals. We think that this distinction between ‘polycaly’ and ‘polydomy’ concerns two disparate concepts. We thus prefer the narrower definition of polydomy, which groups individuals that interact socially. Does this new level of organization affect the way in which natural selection acts on social traits? Here, after examining the history of terms, we review all ant species that have been described as expressing polydomous structures. We show that there is no particular syndrome of traits predictably associated with polydomy. We detail the existing theoretical predictions and empirical results on the ecology of polydomy, and the impact of polydomy on social evolution and investment strategies, while carefully distinguishing monogynous from polygynous species. Finally, we propose a methodology for future studies and offer ideas about what remains to be done. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 319–348.     

Correlates of immune protection in HIV-1 infection: what we know, what we don't know, what we should know

The field of vaccinology began in ignorance of how protection was instilled in vaccine recipients. Today, a greater knowledge of immunology allows us to better understand what is being stimulated by various vaccines that leads to their protective effects: that is, their correlates of protection. Here we describe what is known about the correlates of protection for existing vaccines against a range of different viral diseases and discuss the correlates of protection against disease during natural infection with HIV-1. We will also discuss why it is important to design phase 3 clinical trials of HIV vaccines to determine the correlates of protection for each individual vaccine.     

The origin of life: what we know,what we can know and what we will never know

The origin of life (OOL) problem remains one of the more challenging scientific questions of all time. In this essay, we propose that following recent experimental and theoretical advances in systems chemistry, the underlying principle governing the emergence of life on the Earth can in its broadest sense be specified, and may be stated as follows: all stable (persistent) replicating systems will tend to evolve over time towards systems of greater stability. The stability kind referred to, however, is dynamic kinetic stability, and quite distinct from the traditional thermodynamic stability which conventionally dominates physical and chemical thinking. Significantly, that stability kind is generally found to be enhanced by increasing complexification, since added features in the replicating system that improve replication efficiency will be reproduced, thereby offering an explanation for the emergence of life''s extraordinary complexity. On the basis of that simple principle, a fundamental reassessment of the underlying chemistry–biology relationship is possible, one with broad ramifications. In the context of the OOL question, this novel perspective can assist in clarifying central ahistoric aspects of abiogenesis, as opposed to the many historic aspects that have probably been forever lost in the mists of time.     

Neural and behavioral epigenetics; what it is,and what is hype

The ability to examine epigenetic mechanisms in the brain has become readily available over the last 20 years. This has led to an explosion of research and interest in neural and behavioral epigenetics. Of particular interest to researchers, and indeed the lay public, is the possibility that epigenetic processes, such as changes in DNA‐methylation and histone modification, may provide a biochemical record of environmental effects. This has led to some fascinating insights into how molecular changes in the brain can control behavior. However, some of this research has also attracted controversy and, as is dealt with here, some overblown claims. This latter problem is partly linked to the shifting sands of what is defined as ‘epigenetics’. In this review, I provide an overview of what exactly epigenetics is, and what is hype, with the aim of opening up a debate as to how this exciting field moves forward.     

Lipases in lysosomes,what for?

We have all learned in textbooks that “lysosomes contain hydrolases able to degrade all types of intracellular molecules which include proteases, glycosidases, nucleotidases and lipases.” To date, the only logical explanation for the presence of lipases inside of lysosomes was for the degradation of lipoproteins internalized by endocytosis, and for the breakdown of intralysosomal vesicles derived from fusion with autophagosomes or multivesicular bodies. However, in our recent work we found a novel role for ysosomal lipases in the basic cellular process that regulates intracellular lipid stores that we have named “macrolipophagy”.     

Consciousness, the brain and what matters

Grant Gillett argues that it is consciousness which makes a human or other being the 'locus of ethical value'. Since cortical functioning is, in Gillett's view, necessary for conscious activity, an individual whose neocortex is permanently non-functional is no longer a locus of ethical value and cannot be benefited or harmed in a morally relevant sense. This means that there is no obligation to continue treating those who have suffered neocortical death.     

Parsimony, simplicity and what actually happened

The role of a parsimony principle is unclear in most methods which have been claimed to be valid for the reconstruction of tionary kinship. There appear to be two reasons for this: first, the role of parsimony is generally uncertain in scientific method; second, the majority of methods proposed transform data and order them, but are not appropriate to the reconstruction of phyto Commitment to a probabilistic model of tionary processes seems to be the essential component which may enable us justifiably to estimate phylo An example is provided which emphasizes the importance of knowledge about the nature of the process before undertaking estimation of the pattern of kinship.     

The origins of larval forms: what the data indicate,and what they don't

What is a larva, if it is not what survives of an ancestor's adult, compressed into a transient pre‐reproductive phase, as suggested by Haeckel's largely disreputed model of evolution by recapitulation? A recently published article hypothesizes that larva and adult of holometabolous insects are developmental expressions of two different genomes coexisting in the same animal as a result of an ancient hybridization event between an onychophoran and a primitive insect with eventless post‐embryonic development. More likely, however, larvae originated from late embryonic or early post‐embryonic stages of ancestors with direct development. Evolutionary novelties would thus be intercalary rather than terminal, with respect to the ancestor's ontogenetic schedule. This scenario, supported by current research on holometabolous insects and marine invertebrates with complex life cycles, offers a serious alternative to the traditional scenario (‘what is early in ontogeny is also early in phylogeny’) underlying the current perception of the evolution of genetic regulatory networks.