Heterogeneous Single Atom Electrocatalysis,Where “Singles” Are “Married”

There is an intensive search for heterogeneous single atom catalysts (SACs) of high activity, efficiency, durability, and selectivity for a wide variety of electrocatalytic conversion and chemical reactions, such as the hydrogen evolution reaction (HER), oxygen evolution/reduction reaction (OER and ORR), CO₂ reduction reaction (CO₂ RR), and nitrogen reduction reaction (NRR). With the downsizing from nanoparticles and clusters to single atoms, there are steady changes in the bond and coordination environment for each and every atom involved. Indeed, the single atoms in these electrocatalysts are not “singles”; they are “married” to the supporting surfaces, and their performance is controlled by the bonding and coordination with the substrate surfaces. Herein, an overview is presented on the brief history leading to the rapid development of SACs and their current status, by focusing on their synthesis, control of composition, strategies to realize single atoms with the desired bonds and coordination, and targeted performance in selected reactions. Their applications in the selected spectrum of energy conversion and chemical reactions are discussed, in relation to their structures at varying length scales down to the atomic level. A particular emphasis is placed on on‐going research activities, together with the future perspectives and particular challenges for SACs.     

Evolution of Protein Targeting into “Complex” Plastids: The “Secretory Transport Hypothesis”

Abstract: In algae different types of plastids are known, which vary in pigment content and ultrastructure, providing an opportunity to study their evolutionary origin. One interesting feature is the number of envelope membranes surrounding the plastids. Red algae, green algae and glaucophytes have plastids with two membranes. They are thought to originate from a primary endocytobiosis event, a process in which a prokaryotic cyanobacterium was engulfed by a eukaryotic host cell and transformed into a plastid. Several other algal groups, like euglenophytes and heterokont algae (diatoms, brown algae, etc.), have plastids with three or four surrounding membranes, respectively, probably reflecting the evolution of these organisms by so‐called secondary endocytobiosis, which is the uptake of a eukaryotic alga by a eukaryotic host cell. A prerequisite for the successful establishment of primary or secondary endocytobiosis must be the development of suitable protein targeting machineries to allow the transport of nucleus‐encoded plastid proteins across the various plastid envelope membranes. Here, we discuss the possible evolution of such protein transport systems. We propose that the secretory system of the respective host cell might have been the essential tool to establish protein transport into primary as well as into secondary plastids.     

Nachtrag zur “Wurmtheorie” der Vertebraten-Evolution1

This paper presents some new arguments for the metameric-wonn-theory for the evolution of the Vertebrates (Gutmann 1966a). Metameric coelomoducts in Enteropneust larvae (Goodrich 1947) which should be interpreted as metanephridia show that the Enteropneusts can be derived from metameric Chordate-like predecessors. The myomeres of Branchiostoma are no solid organs as there exist sclerocoels. These must be interpreted as vestigial coelomic cavities. They can be cited as a proof for the metameric worm-theory. They function as a canal system, which gathers excretory stuff in the myomeres which these organs could otherwise not get rid of. The coelom-cavities are cleaned by the protonephridia in the gill region. Some additional details of the phylogenetic transformation of metameric coelom cavities into myomeres are reconstructed. It is shown that the problem of coelomic and myomeric metamerism cannot be solved in the way proposed in the literature concerned with this question. The metameric-worm-theory for the evolution of the Vertebrates pretends that metameric metanephridia were fused on the lower level of Vertebrate phylogeny and formed the archinephric ducts. A paper of Goodrich (1947) shows that there are similar cases of fused metanephridia in some Annelids. These are parallels to the postulated formation of the metanephridia in the lowest Vertebrates. The archinephric duct acquired its muscular coat when it was formed by fusion of metanephridia in the bodywall. Muscles of the body wall took over a new function by making peristaltic movements of the newly formed archinephric ducts possible. When the archinephric duct was moved back into the coelom it did not lose the still functioning muscular coat.     

THE EVOLUTION OF PHENOTYPIC CORRELATIONS AND “DEVELOPMENTAL MEMORY”

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent nonlinear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can “store” and “recall” multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and “generalize” (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviors follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well‐understood in the context of neural networks. This helps to explain how development facilitates the evolution of high‐fitness phenotypes and how this ability changes over evolutionary time.     

EXPERIMENTAL EVOLUTION OF SENESCENCE: AN ANALYSIS USING A “HETEROGENEITY” MORTALITY MODEL

A long-term laboratory selection experiment has produced replicated populations of fruit flies that differ in mean life span by more than twofold. An analysis of age-specific mortality rates indicated that differences in mean life span have been achieved principally by evolution of patterns of senescence. These results provide empirical confirmation that senescence can be modified within species by appropriate forms of natural selection, which is a fundamental prediction of theories regarding the genetic basis and evolution of senescence. Mortality data were fit to a model that accounts for the leveling off of cohort mortality rates at older ages, but that does not necessarily imply that very old individuals cease to senesce.     

150 Jahre “Biogenetisches Grundgesetz”

150 years “Biogenetic Law” The zoologist Ernst Haeckel is one of the most well‐known, but also one of the most controversial scientists of the late 19th and early 20th centuries. He was one of the earliest Darwinists and a forceful advocate of evolutionary theory. Together with “Darwin's Bulldog” Thomas Henry Huxley, Haeckel was a central figure in the early history and popularization of Darwinism. But his name is not only a symbol for the disputes about the theory of evolution and its popularization, but also for a campaign for monism, a world‐view or philosophy created by Haeckel himself. Together with Fritz Müller, Ernst Haeckel was one of the first to formulate a “Biogenetic Law”. He also created several concepts and terms still in use in biology today, such as “ontogeny”, “phylogeny”, “ecology”, “cholorogy” and “phylum” in his first, and maybe most important book “General Morphology of Organism”, which was published in 1866, 150 years ago.     

The role of “the aquatic” in human evolution: Constraining the aquatic ape hypothesis

Few things show the distinctiveness of human evolution research better than the Aquatic Ape Hypothesis (AAH). On one hand, we have “orthodox” research into human evolution, firmly based on land; on the other, we have the aquatic ape community, convinced not only that our ancestors went through an aquatic phase, but that the professional scientific community ignores their work and keeps it out of the mainstream. How many fields of science have two entirely parallel communities that essentially are hermetically sealed from each other?     

Light matters: testing the “Light Environment Hypothesis” under intra‐ and interspecific contexts

The “Light Environment Hypothesis” (LEH) proposes that evolution of interspecific variation in plumage color is driven by variation in light environments across habitats. If ambient light has the potential to drive interspecific variation, a similar influence should be expected for intraspecific recognition, as color signals are an adaptive response to the change in ambient light levels in different habitats. Using spectrometry, avian‐appropriate models of vision, and phylogenetic comparative methods, I quantified dichromatism and tested the LEH in both intra‐ and interspecific contexts in 33 Amazonian species from the infraorder Furnariides living in environments with different light levels. Although these birds are sexually monochromatic to humans, 81.8% of the species had at least one dichromatic patch in their plumage, mostly from dorsal areas, which provides evidence for a role for dichromatism in sex recognition. Furthermore, birds from habitats with high levels of ambient light had higher dichromatism levels, as well as brighter, more saturated, and more diverse plumages, suggesting that visual communication is less constrained in these habitats. Overall, my results provide support for the LEH and suggest that ambient light plays a major role in the evolution of color signals in this group of birds in both intra‐ and interspecific contexts. Additionally, plumage variation across light environments for these drab birds highlights the importance of considering ambient light and avian‐appropriate models of vision when studying the evolution of color signals in birds.     

“Menstrual induction” with sulproston

The PGE₂-analogue Sulproton (16-phenoxy·ω-17,18,19,20-tetranor-PGE₂-mythylsulfonylamide) was administered to 200 medically and gynecologically normal women who were 17±0.4 days beyond their expected menstrual period and who had a positive pregnancy test. The intramuscular impact dose (500 μg repeated after 4 hours) caused an immediate tonic uterine contraction which compromised the estradiol 17β, progesterone and chorionic gonadotropin production within the fetoplacental unit, and thereby allowed the evolution of cyclic uterine activity, cervical dilatation and tissue expulsion.Pregnancy termination was complete in 92% of women, 5.5% required surgical curettage and 2.5% were given a second Sulproston treatment 2–3 weeks after the first to remove retained tissue from the uterus. The medical induction of menstruation was preferred by 83% of the women who had previously experienced surgical termination of pregnancy. Normal menstruation resumed in all women after 36±0.9 days. The majority of 42 women questioned found Sulproston a satisfactory, safe, simple and effective drug regimen for “menstrual induction”.     

A striking example of developmental bias in an evolutionary process: The “domestication syndrome”

The question of whether “developmental bias” can influence evolution is still controversial, despite much circumstantial evidence and a good theoretical argument. Here, I will argue that the domestication of mammalian species, which took place independently more than two dozen times, provides a particularly convincing example of developmental bias in evolution. The singular finding that underlies this claim is the repeated occurrence in domesticated mammals of a set of distinctive traits, none of which were deliberately selected. This phenomenon has been termed “the domestication syndrome”. In this article, I will: (a) describe the properties of the domestication syndrome; (b) show how it can be explained in terms of the operation of a specific genetic regulatory network, that which governs neural crest cell development; and (c) discuss Dmitry Belyaev's idea of “destabilizing selection,” which holds that selecting for a new behavior often entails neuroendocrine alterations that alter many aspects of development. Finally, I will argue for the potential general significance of such destabilizing selection, in combination with developmental bias, in animal evolution.     

Russian comparative embryology takes form: a conceptual metamorphosis toward “evo‐devo”

This essay recapitulates major paths followed by the Russian tradition of what we refer to today as evolutionary developmental biology (“evo‐devo”). The article addresses several questions regarding the conceptual history of evolutionary embryological thought in its particularly Russian perspective: (1) the assertion by the St. Petersburg academician Wolff regarding the possible connections between environmental modifications during morphogenesis and the “transformation” of species, (2) the discovery of shared “principles” underlying animal development by von Baer, (3) the experimental expression of Baer's principles by Kowalevsky and Mechnikoff, (4) Severtsov's theory of phylembryogenesis, (5) Filatov's approach to the study of evolution using comparative “developmental mechanics”, and (6) Shmalgausen's concept of “stabilizing” selection as an attempt to elucidate the evolution of developmental mechanisms. The focus on comparative evolutionary embryology, which was established by Kowalevsky and Mechnikoff, still continues to be popular in present‐day “evo‐devo” research in Russia.     

Isotope chirality in long‐armed multifunctional organosilicon (“Cephalopod”) molecules

Long‐armed multifunctional organosilicon molecules display self‐replicating and self‐perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry.     

Genomic insights into the adaptation and evolution of the nautilus,an ancient but evolving “living fossil”

The nautilus, commonly known as a “living fossil,” is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.     

Phylum Tardigrada: an “individual” approach

Phylum Tardigrada consists of ～1000 tiny, hardy metazoan species distributed throughout terrestrial, limno‐terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super‐families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re‐working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled. © The Willi Hennig Society 2008.     

Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with “Common Design”1

ABSTRACT. Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co‐occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree‐like representations of life's diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated‐tree model, ring of life, symbiogenesis whole‐organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron‐ and NAD⁺ as cofactors, and the substrates acetyl‐CoA for ALDH and acetaldehyde for ADH. Alternative views invoking “common design” (i.e. the non‐naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.     

Evaluating the “dual selection” hypothesis of canine reduction

A recently proposed model for canine reduction in hominid evolution (the “dual selection” model) suggests that canine reduction occurs as a result for incorporation of the canines into a functional incisal field. Among the evidence used to support this model are patterns of wear and occlusion of the canine teeth, particularly in female anthropoid primates. We examined wear and occlusal patterns of the canine teeth of 311 male and female anthropoid primates. We find no evidence that the canines are typically occluded tip-to-tip, or that they show wear patterns indicating a “gripping and pulling” function during food ingestion and processing. Furthermore, we do not find compelling evidence that the development of the mesial cristid is associated with canine reduction. While we agree that the mechanisms of selective pressures underlying canine reduction need to be investigated, the “dual selection” hypothesis is unsupported by comparative data. © 1996 Wiley-Liss, Inc.     

THE EVOLUTION OF COSTLY MATE PREFERENCES II. THE “HANDICAP” PRINCIPLE

We use a general additive quantitative genetic model to study the evolution of costly female mate choice by the “handicap” principle. Two necessary conditions must be satisfied for costly preference to evolve. The conditions are (i) biased mutation pressure on viability and (ii) a direct relationship between the degree of expression of the male mating character and viability. These two conditions explain the success and failure of previous models of the “handicap” principle. Our model also applies to other sources of fitness variation like migration and host-parasite coevolution, which cause effects equivalent to biased mutation.     

A simulation test of Smith's “degrees of freedom” correction for comparative studies

Computer simulation was used to test Smith's (1994) correction for phylogenetic nonindependence in comparative studies. Smith's method finds effective N, which is computed using nested analysis of variance, and uses this value in place of observed N as the baseline degrees of freedom (df) for calculating statistical significance levels. If Smith's formula finds the correct df, distributions of computer-generated statistics from simulations with observed N nonindependent species should match theoretical distributions (from statistical tables) with the df based on effective N. The computer program developed to test Smith's method simulates character evolution down user-specified phylogenies. Parameters were systematically varied to discover their effects on Smith's method. In simulations in which the phylogeny and taxonomy were identical (tests of narrow-sense validity), Smith's method always gave conservative statistical results when the taxonomy had fewer than five levels. This conservative departure gave way to a liberal deviation in type I error rates in simulations using more than five taxonomic levels, except when species values were nearly independent. Reducing the number of taxonomic levels used in the analysis, and thereby eliminating available information regarding evolutionary relationships, also increased type I error rates (broad-sense validity), indicating that this may be inappropriate under conditions shown to have high type I error rates. However, the use of taxonomic categories over more accurate phylogenies did not create a liberal bias in all cases in the analysis performed here. The effect of correlated trait evolution was ambiguous but, relative to other parameters, negligible. © 1995 Wiley-Liss, Inc.     

Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations

The existence of complex (multiple‐step) genetic adaptations that are “irreducible” (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce “irreducibly complex” adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley‐crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.