Phylogeny mandalas for illustrating the Tree of Life

"Chance and Necessity" on the Molecular Evolution of REV3 (a Catalytic Subunit of DNA Polymerase ζ)-The Dual Roles of Translesion and Neuronal Extension

Catalytic subunit of DNA polymerase ζ (REV3), involved in translesion-replication is evolutionarily conserved from yeast and plants to higher eukaryotes. However, a large intermediate domain is inserted in REV3 of humans and mice. The domain has "DUF4683" region, which is significantly similar to human neurite extension and migration factor (NEXMIF). This region was also found in REV3 of invertebrates such as Ciona intestinalis (sea squirt) … and Lingula anatina (Brachiopoda). We hypothesize foreign sequences were introduced into the Rev3 genes in the ancestral species of L. anatina, which would have gradually evolved into the DUF4683 region through overly complicated processes. Besides DUF4683, various exogenous sequences would have been inserted during the REV3 evolution. Therefore, insertion events of foreign sequences are all products of "necessity". tBLASTn analysis of the Callorhinchus milii (elephant shark) genome with the C. milii REV3 sequence identified three neural factors (NEXMIF, NEXMIF-like and AHDC1) in distinct positions of the genome. These factors may have differentiated from the Rev3 gene in Chondrichthyes, which had experienced two rounds of whole-genome duplication, and may have evolved into neurite-forming proteins in vertebrates. L. anatina has the DUF4683 C-terminal proximal consensus (SPPRA/CWSP) in REV3. However, the consensus was not necessarily maintained in Mollusca, the closely related animal phylum of L. anatina. Just as written by Jacques Monod, we assume "chance" (mutation in DNA) and "necessity" (selection at the "organism" population level) were frequently repeated on the Rev3 in Cambrian ancestors. As a result, certain species developed the DUF4683 consensus of a neurite extension activity.

Phylogeny and evolutionary history of the amniote egg

We review morphological features of the amniote egg and embryos in a comparative phylogenetic framework, including all major clades of extant vertebrates. We discuss 40 characters that are relevant for an analysis of the evolutionary history of the vertebrate egg. Special attention is given to the morphology of the cellular yolk sac, the eggshell, and extraembryonic membranes. Many features that are typically assigned to amniotes, such as a large yolk sac, delayed egg deposition, and terrestrial reproduction have evolved independently and convergently in numerous clades of vertebrates. We use phylogenetic character mapping and ancestral character state reconstruction as tools to recognize sequence, order, and patterns of morphological evolution and deduce a hypothesis of the evolutionary history of the amniote egg. Besides amnion and chorioallantois, amniotes ancestrally possess copulatory organs (secondarily reduced in most birds), internal fertilization, and delayed deposition of eggs that contain an embryo in the primitive streak or early somite stage. Except for the amnion, chorioallantois, and amniote type of eggshell, these features evolved convergently in almost all major clades of aquatic vertebrates possibly in response to selective factors such as egg predation, hostile environmental conditions for egg development, or to adjust hatching of young to favorable season. A functionally important feature of the amnion membrane is its myogenic contractility that moves the (early) embryo and prevents adhering of the growing embryo to extraembryonic materials. This function of the amnion membrane and the liquid-filled amnion cavity may have evolved under the requirements of delayed deposition of eggs that contain developing embryos. The chorioallantois is a temporary embryonic exchange organ that supports embryonic development. A possible evolutionary scenario is that the amniote egg presents an exaptation that paved the evolutionary pathway for reproduction on land. As shown by numerous examples from anamniotes, reproduction on land has occurred multiple times among vertebrates-the amniote egg presenting one "solution" that enabled the conquest of land for reproduction.

Scientific iconoclasm and active imagination: synthetic cells as techno-scientific mandalas

Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is "iconoclastic", as Gaston Bachelard phrases it (i.e. bent on replacing living entities by symbolic data: e.g. biochemical and mathematical symbols and codes), scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the "Morse code" of life, the "barcode" of life and the "book" of life. This paper focuses on a different type of metaphor, however, namely on the archetypal metaphor of the mandala as a symbol of restored unity and wholeness. Notably, mandala images emerge in textual materials (papers, posters, PowerPoints, etc.) related to one of the new "frontiers" of contemporary technoscience, namely the building of a synthetic cell: a laboratory artefact that functions like a cell and is even able to replicate itself. The mandala symbol suggests that, after living systems have been successfully reduced to the elementary building blocks and barcodes of life, the time has now come to put these fragments together again. We can only claim to understand life, synthetic cell experts argue, if we are able to technically reproduce a fully functioning cell. This holistic turn towards the cell as a meaningful whole (a total work of techno-art) also requires convergence at the "subject pole": the building of a synthetic cell as a practice of the self, representing a turn towards integration, of multiple perspectives and various forms of expertise.