Acquisition and loss of modules: the construction set of transposable elements

Phylogenetic analysis of transposable elements (TEs) allows us to define the relationships between the domains or gene(s) that compose them. Moreover, modules of a few amino-acids can be detected within gag, pol, env genes or within the integrase domain of retrotransposons and transposase of DNA elements. The combination of these observations clearly shows that the evolutionary history of TEs is the outcome of the acquisition and loss of modules with differing origins and histories. This raises the question of the origin of TEs: are they derived from viruses? Are they where viruses come from? Do the basic building bricks come from the prokaryotes, and can they be assembled in the eukaryotes? Are the TEs found in prokaryotes the result of the disintegration of complex elements such as retroelements? Do they evolve from the simplest to the more complex, or are they opportunistic sequences evolving by acquiring and/or losing modules which may be either important or superfluous to their fitness (i.e., their ability to transpose). These are some of the questions that are addressed and discussed in the light of the comparative structures of TEs.     

Wild justice and fair play: cooperation,forgiveness, and morality in animals

In this paper I argue that we can learn much about ‘wild justice’ and the evolutionary origins of social morality – behaving fairly – by studying social play behavior in group-living animals, and that interdisciplinary cooperation will help immensely. In our efforts to learn more about the evolution of morality we need to broaden our comparative research to include animals other than non-human primates. If one is a good Darwinian, it is premature to claim that only humans can be empathic and moral beings. By asking the question ‘What is it like to be another animal?’ we can discover rules of engagement that guide animals in their social encounters. When I study dogs, for example, I try to be a ‘dogocentrist’ and practice ‘dogomorphism.’ My major arguments center on the following ‘big’ questions: Can animals be moral beings or do they merely act as if they are? What are the evolutionary roots of cooperation, fairness, trust, forgiveness, and morality? What do animals do when they engage in social play? How do animals negotiate agreements to cooperate, to forgive, to behave fairly, to develop trust? Can animals forgive? Why cooperate and play fairly? Why did play evolve as it has? Does ‘being fair’ mean being more fit – do individual variations in play influence an individual's reproductive fitness, are more virtuous individuals more fit than less virtuous individuals? What is the taxonomic distribution of cognitive skills and emotional capacities necessary for individuals to be able to behave fairly, to empathize, to behave morally? Can we use information about moral behavior in animals to help us understand ourselves? I conclude that there is strong selection for cooperative fair play in which individuals establish and maintain a social contract to play because there are mutual benefits when individuals adopt this strategy and group stability may be also be fostered. Numerous mechanisms have evolved to facilitate the initiation and maintenance of social play to keep others engaged, so that agreeing to play fairly and the resulting benefits of doing so can be readily achieved. I also claim that the ability to make accurate predictions about what an individual is likely to do in a given social situation is a useful litmus test for explaining what might be happening in an individual's brain during social encounters, and that intentional or representational explanations are often important for making these predictions.     

On the functional and structural characterization of hubs in protein–protein interaction networks

A number of interesting issues have been addressed on biological networks about their global and local properties. The connection between the topological properties of proteins in Protein–Protein Interaction (PPI) networks and their biological relevance has been investigated focusing on hubs, i.e. proteins with a large number of interacting partners. We will survey the literature trying to answer the following questions: Do hub proteins have special biological properties? Do they tend to be more essential than non-hub proteins? Are they more evolutionarily conserved? Do they play a central role in modular organization of the protein interaction network? Are there structural properties that characterize hub proteins?     

Infanticide by Male Lions Hypothesis: A Fallacy Influencing Research into Human Behavior

Recently, familial abuse and killing of children have been correlated with infanticidal behavior by nonhuman male animals which is postulated to be genetic. However, infanticide by males as an evolutionary mechanism is unlikely to occur in primates, and is equally unlikely in lions. To investigate the sexual selection hypothesis of infanticide for lions, four questions should be considered: (1) because they all mate freely with lionesses, are male pride lions closely related? (often they are not), (2) do males kill the young cubs when they join a pride? (few such cases have been observed), (3) do the females then mate with the new males to produce offspring? (yes), and (4) do the males remain with the pride for over two years to protect this new generation? (often not). Field data indicate that in NO instance do we know that male lions killed cubs in a new pride, mated with their mother, and then remained with the pride to protect their own young. Rather, female lions may kill more cubs than males and certainly cause many more cub deaths by allowing them to starve, [ infanticide by male lions, infanticide hypothesis, faulty science]     

The case for studying tadpole autecology,with comments on strategies to study other small,fast-moving animals in nature

Two of the most fundamental questions in tadpole biology, also applicable to most small, under-studied organisms are: (1) ‘Why are they built the way they are?’ and (2) ‘Why do they live where they do?’ Regrettably, despite significant progress in most aspects of tadpole biology, the answers to these questions are not much better now than they were in the last century. We propose that an autecological approach, that is the careful observation of individuals and how they interact with the environment, is a potential path towards a fuller understanding of tadpole ecomorphology and evolution. We also discuss why more attention should be given to studying atypical tadpoles from atypical environments, such as torrential streams, water-filled cavities of terrestrial plants and wet rock surfaces neighbouring streams. Granted, tadpoles are rare in these settings, but in those unusual habitats the physical environments can be well described and characterized. In contrast, the more common ponds where tadpoles are found are typically too structurally complex to be easily delineated. This makes it difficult to know exactly what individual tadpoles are doing and what environmental parameters they are responding to. Our overall thesis is that to understand tadpoles we must see exactly what they are doing, where they are doing it, and how they are doing it. This takes work, but we suggest it is feasible and could greatly advance our understanding of how anuran larvae have evolved. The same strategies for studying tadpoles that we encourage here can be applied to the study of many other small and fast-moving animals.     

Acquisition/Loss of Modules: the Construction Set of Transposable Elements

Phylogenetic analysis of transposable elements (TEs) allows us to define the relationships between the domains or gene(s) that compose them. Moreover, modules of a few amino-acids can be detected within gag, pol, envgenes or within the integrase domain of retrotransposons and transposase of DNA elements. The combination of these observations clearly shows that the evolutionary history of TEs is the outcome of the acquisition and loss of modules with differing origins and histories. This raises the question of the origin of TEs: are they derived from viruses? Do the basic building bricks come from the prokaryotes, and can they be assembled in the eukaryotes? Are the TEs found in prokaryotes the result of the disintegration of complex elements such as retroelements? Do they evolve from the simplest to the more complex, or are they opportunistic sequences evolving by acquiring and/or losing modules which may be either important or superfluous to their fitness (i.e., their ability to transpose). These are some of the questions that are addressed and discussed in the light of the comparative structures of TEs.     

Abundance and generalisation in mutualistic networks: solving the chicken‐and‐egg dilemma

A frequent observation in plant–animal mutualistic networks is that abundant species tend to be more generalised, interacting with a broader range of interaction partners than rare species. Uncovering the causal relationship between abundance and generalisation has been hindered by a chicken‐and‐egg dilemma: is generalisation a by‐product of being abundant, or does high abundance result from generalisation? Here, we analyse a database of plant–pollinator and plant–seed disperser networks, and provide strong evidence that the causal link between abundance and generalisation is uni‐directional. Specifically, species appear to be generalists because they are more abundant, but the converse, that is that species become more abundant because they are generalists, is not supported by our analysis. Furthermore, null model analyses suggest that abundant species interact with many other species simply because they are more likely to encounter potential interaction partners.     

Artophagy: The art of autophagy—Macroautophagy

Many of us have sketched (by hand or on the computer) depictions of macroautophagy; however, how often have we considered which elements in the drawing are key to illustrating the process? These types of illustrations are easily modified and/or discarded. On the other hand, if you plan to depict the process of macroautophagy in a more permanent medium you need to be more thoughtful about the composition. What items must be included? How should they be situated? What should be the size of each component? Here, we consider one example of an artist’s approach to depicting macroautophagy in a mixed-medium sculpture.     

Toward a dynamic model of deposition and utilization of yolk steroids

The discovery by Schwabl that maternal steroid hormones aretransferred to the egg yolk and have effects on the phenotypeof offspring revealed a new pathway for non-genetic maternaleffects. The initial model relied on passive transfer. The thinkingwas that steroids passively entered the lipophillic yolk duringyolk deposition and then were deposited in the yolk until theywere passively delivered to the embryo as the yolk was used.Subsequent studies revealed that the system is much more dynamicthan that. Here, we explore questions about how dynamic thesystem really is and look at questions like: Is transfer ofmaternal steroids to the yolk passive or is it actively regulated?At what stages of the maternal reproductive cycle are steroidstransferred? During reproduction, how dynamic are the levelsof yolk steroids? Especially in the case of potentially deleterioussteroids (e.g., androgens in female offspring; glucocorticoids),once deposited can they come out of the yolk over time? Canthey be metabolized by the yolk or by the embryo? During incubation,how much do steroid levels in the yolk change? Can steroidsdiffuse from the yolk to the embryo prior to yolk utilization?Does the embryo contribute to yolk steroid levels as it develops?We believe that comprehensive answers to questions like thesewill eventually allow us to generate a much more accurate andcomplete model of the transfer and utilization of yolk steroidsand that this model will be much more dynamic and active thanthe one initially proposed.     

How to break recombinant bacteria: does it matter?

Recombinant proteins and other materials of industrial interest produced in?Escherichia coli are usually retained within the bacterial cell, in the cytoplasmic?space, where they have been produced. Different protocols for cell disruption?have been implemented as an initial downstream step, which keeps the?biological and mechanical properties of the process products. Being necessarily?mild, these approaches often result in 95-99% cell disruption, what is more than?acceptable from the yield point of view. However, when the bacterial product?are nano or microparticulate entities that tend to co-sediment with entire?bacterial cells, the remaining undisrupted bacteria appear as abounding?contaminants, making the product not suitable for a spectrum of biomedical?applications. Since bacterial inclusion bodies are now seen as bacterial?materials valuable in different fields, we have developed an alternative cell?disruption protocol that permits obtaining fully bacterial free protein particles,?keeping the conformational status of the embedded proteins and the?mechanical properties of the full aggregates.     

Olfactory ensheathing cells - another miracle cure for spinal cord injury?

Several recent publications describe remarkably promising effects of transplanting olfactory ensheathing cells as a potential future method to repair human spinal cord injuries. But why were cells from the nose transplanted into the spinal cord? What are olfactory ensheathing cells, and how might they produce these beneficial effects? And more generally, what do we mean by spinal cord injury? To what extent can we compare repair in an animal to repair in a human?     

Race,ethnicity and disciplinary divides: what is the path forward?

We pose several questions that emerged for us from Valdez and Golash-Boza’s “U.S. Racial and Ethnic Relations in the twenty-first Century.” First, we raise questions about their framing of the problem with current scholarship – are immigration/ethnicity and race scholars talking past each other or are they having more fundamental disagreements? Second, we raise questions about their critique of the “the race literature” – do too many of us ignore questions of agency and inclusion? Finally, we raise questions about the stability and utility of the concepts they deploy (“race” and “ethnicity”) and draw on recent scholarship that has argued that we need new language or frameworks to adequately describe the reality on the ground.     

What Are Imprinted Genes Doing in the Brain?

As evidence for the existence of brain?expressed imprinted genes accumulates, we need to address exactly what they are doing in this tissue, especially in terms of organizational themes and the major challenges posed by reconciling imprinted gene action in brain with current evolutionary theories attempting to explain the origin and maintenance of genomic imprinting. We are at the beginning of this endeavor and much work remains to be done but already it is clear that imprinted genes have the potential to influence diverse behavioral processes via multiple brain mechanisms. There are also grounds to believe that imprinting may contribute to risk of mental and neurological disease. As well as being a source of basic information about imprinted genes in the brain (e.g., via the newly established website, www.bgg.cardiff.ac.uk/imprinted_tables/index.html), we have used this chapter to identify and focus on a number of key questions. How are brain?expressed imprinted genes organized at the molecular and cellular levels? To what extent does imprinted action depend on neurodevelopmental mechanisms? Do imprinted gene effects interact with other epigenetic influences, especially early on in life? Are imprinted effects on adult behaviors adaptive or just epiphenomena? If they are adaptive, what areas of brain function and behavior might be sensitive to imprinted effects? These are big questions and, as shall become apparent, we need much more data, arising from interactions between behavioral neuroscientists, molecular biologists and evolutionary theorists, if we are to begin to answer them.     

贵州穿洞遗址1979年发现的磨制骨器的初步研究

贵州省普定县穿洞出土的骨器是穿洞文化的重要标志。1979年首次试掘出土的骨器基本为磨制者, 类型主要有骨锥、骨铲、骨叉、骨棒及骨针等,多采用较厚的动物骨骼的碎片为原料加工而成。一次性出土数量如此多骨器的遗址在我国非常少见, 为研究中国旧石器时代晚期文化的多样性提供了一个重要地点和一批有意义的文化遗物, 并对研究我国旧石器时代骨器提供了丰富的材料, 增加了我们对骨器工具的制造工艺及用途的了解。     

The relative importance for plant invasiveness of trait means, and their plasticity and integration in a multivariate framework

? Functional traits, their plasticity and their integration in a phenotype have profound impacts on plant performance. We developed structural equation models (SEMs) to evaluate their relative contribution to promote invasiveness in plants along resource gradients. ? We compared 20 invasive-native phylogenetically and ecologically related pairs. SEMs included one morphological (root-to-shoot ratio (R/S)) and one physiological (photosynthesis nitrogen-use efficiency (PNUE)) trait, their plasticities in response to nutrient and light variation, and phenotypic integration among 31 traits. Additionally, these components were related to two fitness estimators, biomass and survival. ? The relative contributions of traits, plasticity and integration were similar in invasive and native species. Trait means were more important than plasticity and integration for fitness. Invasive species showed higher fitness than natives because: they had lower R/S and higher PNUE values across gradients; their higher PNUE plasticity positively influenced biomass and thus survival; and they offset more the cases where plasticity and integration had a negative direct effect on fitness. ? Our results suggest that invasiveness is promoted by higher values in the fitness hierarchy -- trait means are more important than trait plasticity, and plasticity is similar to integration -- rather than by a specific combination of the three components of the functional strategy.     

Waiting periods, instructive signals and positional information

Two former biologists play at dice. In the center of the table there are several banknotes from a prize they had won a few years before they dropped out of science. The rule of the game is that each player gets a banknote whenever he correctly predicts how many throws it will take after throwing a 6 to throw the next 6. One of the two players, a former theoretical biologist, remembers that the frequency of throwing a 6 is one in six, so he always foretells that the waiting period will be 6. The other player's cause for failing in science was opposite: he believed in superstitions. As his lucky number is three, he guesses after each 6 that the next 6 will occur three throws later. Which of the two fellows will recover more from the prize money? And is there a waiting period that could be predicted that would make more money?     

EvoS: A Prescription for What Ails Pre-Medical Education?

Pre-medical students are certainly a widely varied group, with different motivations and experiences, different skills sets and interests. However, they often tend to approach their undergraduate education as a necessary evil that they must endure in order to achieve their ultimate goals. This article summarizes recent literature addressing some of the questions that have been raised regarding pre-medical education programs. Are students prepared for the intellectual, emotional, and even physical challenges of medical training? What deficiencies are commonly seen in entering medical students? What are students’ perceptions of how well their pre-medical studies helped them? Many of these studies have resulted in a call for more science training, while some have advocated for less, but with an enhanced focus on humanistic studies. We supply a brief outline of our Evolutionary Studies (EvoS) program and reflect upon how participation in this program can enhance pre-medical students’ education. Importantly, we argue that EvoS can expand students’ depth of understanding of science, as well as nurture their ability to think about the needs of their patients and the context of their medical practice.     

The theoretical and political framing of the population factor in development

The silence about population growth in recent decades has hindered the ability of those concerned with ecological change, resource scarcity, health and educational systems, national security, and other global challenges to look with maximum objectivity at the problems they confront. Two central questions about population—(i) is population growth a problem? and (2) what causes fertility decline?—are often intertwined; if people think the second question implies possible coercion, or fear of upsetting cultures, they can be reluctant to talk about the first. The classic and economic theories explaining the demographic transition assume that couples want many children and they make decisions to have a smaller family when some socio-economic change occurs. However, there are numerous anomalies to this explanation. This paper suggests that the societal changes are neither necessary nor sufficient for family size to fall. Many barriers of non-evidence-based restrictive medical rules, cost, misinformation and social traditions exist between women and the fertility regulation methods and correct information they need to manage their family size. When these barriers are reduced, birth rates tend to decline. Many of the barriers reflect a patriarchal desire to control women, which can be largely explained by evolutionary biology. The theoretical explanations of fertility should (i) attach more weight to the many barriers to voluntary fertility regulation, (ii) recognize that a latent desire to control fertility may be far more prevalent among women than previously understood, and (iii) appreciate that women implicitly and rationally make benefit–cost analyses based on the information they have, wanting modern family planning only after they understand it is a safe option. Once it is understood that fertility can be lowered by purely voluntary means, comfort with talking about the population factor in development will rise.     

Bias in the estimation of horizontal resistance to airborne fungi in plant breeding

Summary

The question is posed: do mixed plots of plant breeding materials selected for horizontal resistance to airborne fungal pathogens provide unbiased estimates? Alternatively, is the common belief that resistance is often under-estimated in mixed plantings justified? A review of the literature and some simple calculations suggest that systematic bias is indeed to be expected, provided that the components of resistance are positively correlated. If they are not, resistance is likely to be unpredictably mis-estimated. There is room for much more critical experimentation and better theory on what is, after all, an important matter.