Epistemological issues in the study of microbial life: alternative terran biospheres?

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.     

The self-organization of speech sounds

The speech code is a vehicle of language: it defines a set of forms used by a community to carry information. Such a code is necessary to support the linguistic interactions that allow humans to communicate. How then may a speech code be formed prior to the existence of linguistic interactions? Moreover, the human speech code is discrete and compositional, shared by all the individuals of a community but different across communities, and phoneme inventories are characterized by statistical regularities. How can a speech code with these properties form? We try to approach these questions in the paper, using the "methodology of the artificial". We build a society of artificial agents, and detail a mechanism that shows the formation of a discrete speech code without pre-supposing the existence of linguistic capacities or of coordinated interactions. The mechanism is based on a low-level model of sensory-motor interactions. We show that the integration of certain very simple and non-language-specific neural devices leads to the formation of a speech code that has properties similar to the human speech code. This result relies on the self-organizing properties of a generic coupling between perception and production within agents, and on the interactions between agents. The artificial system helps us to develop better intuitions on how speech might have appeared, by showing how self-organization might have helped natural selection to find speech.     

In Vitro Selection of a Deoxyribozyme That Can Utilize Multiple Substrates

Deoxyribozymes that could catalyze the formation of an internucleotide phosphorothioester linkage were selected from a random sequence pool. During the course of the selection, the pool was successively challenged with five oligonucleotide substrates, each of which terminated in the same hexanucleotide sequence. Selected deoxyribozyme ligases could use all five substrates, albeit to different degrees, and appeared to form secondary structures that allow differential pairing between the deoxyribozyme and each substrate. These results suggest that early replicases may have been able to bind a variety of oligonucleotide substrates while catalyzing ligation via a common junction. Received: 12 December 2000 / Accepted: 28 June 2001     

室性早搏患者射频消融术预后与起源部位的相关性

目的:探讨室性早搏(PVCs)患者射频消融术(RFCA)预后与起源部位的相关性。方法:回顾性分析2016年12月～2017年12月第二军医大学第一附属医院长海医院心血管内科收治并接受RFCA治疗的PVCs患者的临床资料,根据起源部位分为右心室组(n=58),左心室组(n=24)。记录两组RFCA手术时间、X线曝光时间及手术成功率等指标,术后随访6个月,比较两组术后心功能指标的改善情况,记录24h PVCs总数及复发情况。结果:与左心室组比较,右心室组手术时间、X线曝光时间明显延长,手术成功率明显下降(P0.05)。术后3个月,右心室组LVESD、LVEDD均明显减小,LVEF明显升高(P0.05);术后6个月,两组24h PVCs数均较术前显著降低,且右心室组下降幅度更为显著(P0.05)。术后6个月,两组各心功能指标均较术前明显改善,右心室组较术后3个月进一步改善,且明显优于左心室组(P0.05)。结论:射频消融术治疗PVCs的预后与起源部位存在一定相关性,右心室起源相对左心室起源的PVCs手术成功率更高,更有利于抑制心室重构、改善心功能。     

Evolution in biological and nonbiological systems under different mechanisms of generation and inheritance

The majority of definitions of life and evolution include the notion that part of an organism has to be copied to its offspring and that this includes some form of coded information. This article presents the thesis that this conception is too restrictive and that evolution can occur in systems in which there is no copy of information between generations. For that purpose, this article introduces a new set of concepts and a theoretical framework that is designed to be equally applicable to the study of the evolution of biological and nonbiological systems. In contrast to some theoretical approaches in evolution, like neo-Darwinism, the approach presented here is not focused on the transmission and change of hereditary information that can be copied (like in the case of DNA). Instead, multiple mechanisms by which a system can generate offspring (with and without copying) and by which information in it affects the structure and evolution of its offspring are considered. The first part of this article describes in detail these new concepts. The second part of this article discusses how these concepts are directly applicable to the diversity of systems that can evolve. The third part introduces hypotheses concerning (1) how different mechanisms of generation and inheritance can arise from each other during evolution, and (2) how the existence of several inheritance mechanisms in an organism can affect its evolution.     

A late divergence hypothesis

The possibility of a Middle-Late Miocene separation of the human lineage from the lineages leading to the extant great apes, based on paleontological and phenetic evidence, is presented. Middle Miocene Sivapithecus, rather then Early Miocene Dryopithecus, is supported as a last common ancestor of Pongo, Pan, Gorilla, and Homo. Estimates for the branching of the lineages are a maximum of 15 m.y.a. for the Pongo lineage and a range from 14-6 m.y.a. for the Pan, Gorilla, and Ausralopithecus/Homo lineages. Weaknesses of the late divergence hypothesis are discussed.     

Viruses and asthma

Background

Viral respiratory infection has long been known to influence the occurrence of asthma exacerbations. Over the last 20 years much effort has been put into clarifying the role that viral respiratory infections play in the eventual development of asthma.

Scope of review

In this review we give a general background of the role of viruses in the processes of asthma exacerbation and asthma induction. We review recent additions to the literature in the last 3 years with particular focus on clinical and epidemiologic investigations of influenza, rhinovirus, bocavirus, respiratory syncytial virus, and metapneumovirus.

Major conclusions

The development of asthma emerges from a complex interaction of genetic predisposition and environmental factors with viral infection likely playing a significant role in the effect of environment on asthma inception. This article is part of a Special Issue entitled: Biochemistry of Asthma.

General significance

Further understanding of the role that viruses play in asthma exacerbation and inception will contribute to decreased asthma morbidity in the future. This article is part of a Special Issue entitled: Biochemistry of Asthma.