Phylogenetic thinking in the modern biology

Any research activity is conducted within the framework of a cognitive situation which is defined by certain basic assumptions about ontology of the portion of the objective world under investigation. From the standpoint of the non-classical scientific epistemology, a part of that situation is constituted by personal knowledge which is formed by a set of thinking (cognitive) styles. The scholastic thinking existing in taxonomy and phylogenetics is considered as an example showing unavoidability of such styles in the natural history knowledge. It is initially rooted in the antic, mythological by its essence, persuasion of isomorphism between movements of the objective reality and of the mind. The instrumentalism entailed by scholastic thinking is based on the mythologeme according to which the "right method" par excellence can lead to the "right knowledge". That is why any disputes between different numerical methods of phylogenetic reconstructions are vain: their validity could be assessed not formally but within particular cognitive situations formed by particular basic models of the phylogenesis. Phylogenetic thinking is of the key importance in evolutionary biology and has great impact on various fields of biology based on it. It is pretty mythological because of non-observability of the phylogenesis: the latter is rather "thinked-in" in the objective world then is induced from the observed facts. It constitutes a part of the evolutionary thinking considering mainly macroevolutionary trends and stressing the initial causes in the structure of causal relations in the analyses of the diversity of organisms. The "tree thinking" of O'Hara is its rough operational equivalent. Relation between phylogenetic thinking and some other styles are considered, which are population, phenetic, typological, and epigenetic ("developmental" of O'Hara). Phylogenetic thinking makes it obliged inclusion of the initial causes in the explanatory models which underlie adaptive and functional peculiarities of organisms, as well as of the entire structure of the biodiversity. It manifests itself in such kind of models through uncovering the phylogenetic signal. This thinking style has great effect on understanding of the ontology of taxa and acknowledges the objective status of the phylogenetic pattern. It is intrinsically included in the argumentation schemes of constructional morphology, comparative phylogenetics. The central metaphor of the phylogenetics is the Tree of Life. Emagination of its unity and uniquiness is of naturphilosophical nature. From the contemporary epistemological standpoint, it should be considered as a generalization upon partial hypotheses of evolution of particular structures each corresponding to certain consideration aspect of the global phylogenesis. Acknowledging of multi-aspectness of the phylogenesis constitutes one of the important points of modern phylogenetic thinking. As different semogeneses are incompletely congruent, the Tree of Life is less certain than each of the initial hypotheses. Any attempt to make it more resolved would lead to its reduction to any of the particular semogenetic scheme (i.e. to a "gene tree") or to its "decay" into several trees each corresponding to a particular consideration aspect of the global Tree.     

Theoretical biology in the third millennium

During the 20th century our understanding of genetics and the processes of gene expression have undergone revolutionary change. Improved technology has identified the components of the living cell, and knowledge of the genetic code allows us to visualize the pathway from genotype to phenotype. We can now sequence entire genes, and improved cloning techniques enable us to transfer genes between organisms, giving a better understanding of their function. Due to the improved power of analytical tools databases of sequence information are growing at an exponential rate. Soon complete sequences of genomes and the three-dimensional structure of all proteins may be known. The question we face in the new millennium is how to apply this data in a meaningful way. Since the genes carry the specification of an organism, and because they also record evolutionary changes, we need to design a theoretical framework that can take account of the flow of information through biological systems.     

结合分子生物学课程对大学生创新能力进行培养的尝试

大学教育应以建设创新型国家为己任,为培养创新型人才服务。根据分子生物学课程的特点,从课堂教学和实验教学两方面同时入手,结合教师的科研情况、学科的前沿动态以及引导学生进行课外阅读等几方面对学生的创新能力的培养进行尝试,取得良好效果。     

pGLO mutagenesis: a laboratory procedure in molecular biology for biology students

A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with mutagenized pGLO plasmid. EZ-Tn5 carries the kanamycin resistance (Kan(R)) gene, and the pGLO plasmid carries the β-lactamase gene for ampicillin resistance (Amp(R)), the gene encoding green fluorescent protein (GFP) and the arabinose operon repressor (araC). Insertion of the Tn5 transposon into pGLO occurs randomly, and any gene into which it inserts is knocked out. By screening cells transformed with mutagenized pGLO with kanamycin, ampicillin, arabinose and/or for GFP expression in different combinations, pGLO plasmids with mutations in different genes are identified. The locations of these insertions are then mapped approximately by restriction fragment analysis and precisely by sequence analysis of the pGLO plasmid.     

Evolutionary dynamics and population biology of a polymorphic insect

Conspicuous heritable polymorphisms are useful to address the question if morph frequencies are stable or whether they fluctuate between generations. Ecological geneticists have studied colour polymorphisms in the past, but there are few long-term studies of genetic dynamics across multiple generations. We studied morph-frequency dynamics and female fecundity in the trimorphic blue-tailed damselfly (Ischnura elegans). The morphs include a male-coloured (androchrome) type of female, which is thought to be maintained by frequency-dependent sexual conflict. Morph frequencies changed significantly between years across all populations. There was evidence for directional frequency change since androchrome females increased in 9 of 10 populations across a 4-year period. There was heterogeneity between populations in their evolutionary trajectories, partly caused by population age: androchrome frequencies were initially high in young populations but gradually decreased and approached the level of old populations. We discuss the possible causes of morph-frequency fluctuations, and the role of morph-specific fecundity, dispersal and other forces influencing evolutionary dynamics in this system.     

Evolutionary crossroads in developmental biology: amphioxus

The phylogenetic position of amphioxus, together with its relatively simple and evolutionarily conserved morphology and genome structure, has led to its use as a model for studies of vertebrate evolution. In particular, the recent development of technical approaches, as well as access to the complete amphioxus genome sequence, has provided the community with tools with which to study the invertebrate-chordate to vertebrate transition. Here, we present this animal model, discussing its life cycle, the model species studied and the experimental techniques that it is amenable to. We also summarize the major findings made using amphioxus that have informed us about the evolution of vertebrate traits.     

Evolutionary crossroads in developmental biology: annelids

Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology. With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen. As one of the major phyla within Lophotrochozoa, Annelida are playing an important role in deducing the developmental biology of the last common ancestor of the protostomes and deuterostomes, an animal from which >98% of all described animal species evolved.     

Evolutionary crossroads in developmental biology: hemichordates

Hemichordates are a deuterostome phylum, the sister group to echinoderms, and closely related to chordates. They have thus been used to gain insights into the origins of deuterostome and chordate body plans. Developmental studies of this group have a long and distinguished history. Recent improvements in animal husbandry, functional tool development and genomic resources have resulted in novel developmental data from several species in this group. In this Primer, we introduce representative hemichordate species with contrasting modes of development and summarize recent findings that are beginning to yield important insights into deuterostome developmental mechanisms.     

Evolutionary crossroads in developmental biology: Cnidaria

There is growing interest in the use of cnidarians (corals, sea anemones, jellyfish and hydroids) to investigate the evolution of key aspects of animal development, such as the formation of the third germ layer (mesoderm), the nervous system and the generation of bilaterality. The recent sequencing of the Nematostella and Hydra genomes, and the establishment of methods for manipulating gene expression, have inspired new research efforts using cnidarians. Here, we present the main features of cnidarian models and their advantages for research, and summarize key recent findings using these models that have informed our understanding of the evolution of the developmental processes underlying metazoan body plan formation.     

The associations between social-media use and academic performance among undergraduate students in biology

Recent studies have been conducted in regards to the use of social- media by students and how it can impact his/her academic performance. However, much of this research has been focused on how to use social-media websites in the classroom to facilitate student learning. Therefore, we aimed to address how the use of social-media can be either beneficial or detrimental to undergraduate students, with respect to their academic performance. We distributed a survey to 234 participants, all attending the same four-year university. Throughout the survey, the students self-reported their grade point average (GPA), study habits, and social-media use. We established that female students use social-media websites more often than their male peers, and using a Pearson’s correlation, we found that GPA negatively correlated with the number of social-media websites to which students subscribe (p < 0.05). Furthermore, we found that using more social-media websites correlated positively with the amount of time students spend using social-media platforms on a daily basis. Although previous studies indicate that social-media websites should be incorporated into the classroom, our results suggest that this addition may have negative effects on the study habits and academic performance of undergraduate students, particularly those within the field of biological sciences.