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Commentary on: Cause of Cambrian explosion – Terrestrial or Cosmic?
... have recently revisited the Panspermia hypothesis of Hoyle, Wickramasinghe and colleagues, that life was seeded on Earth from extraterrestrial sources and that this process continues until the present day. Several lines of evidence are presented and some of these have been criticised by Baverstock (2018) and Moelling (2018). ...
In 2018, Steele and colleagues attempted to revive the Panspermia hypothesis. Some of their more loony ideas have been criticised by others. Here I present some calculations based on their suggestions that (1) all cases of influenza are caused by viruses arriving from space; and (2) bacteria found on the outside of the International Space Station have an extraterrestrial origin. These calculations show, without any doubt, that Steele's suggestions are ridiculous.
... Here we address Duggleby's (2018) other conclusion … " none of the examples mentioned by Steele et al. (2018) is decisive enough to allow no other explanation." Our response here also addresses this direct or implied criticism in the other recent Commentaries (Baverstock, 2018;Moelling, 2018). ...
Based on the chemical properties (isotopic ratios from the fossil sea water sediments and the continents), it is possible to divide the Earth's systems into the basic opposition between the terrigenous and oceanic components. The water/ice environment is considered as a sufficient carrier of panspermia in space due to the characteristic (protecting) properties of water, including UV absorption and superconductivity. Recent observations of L. I. Cleeves show that the oceanic ratio of D/H represents a dilution and heterogeneous origin of the water on Earth, which perhaps comprises the comets, asteroids, and even the dwarf snow‐ball planets or their fragments from the interstellar medium during the formation of the solar protoplanetary disc. Interesting insight was brought by the probe Wild‐2 investigating the composition of the comet Temple‐1, showing a wide spectrum of minerals, among which water ice is dominant and calcium carbonates were detected. This composition shows which kind of the bodies also showered the mantle of Earth during the Late Heavy Bombardment 4.1–3.8 Ga ago. On a molecular base, the Murchison meteorite with 92 amino acids and meteorite Acfer 086 with protein hemolithin represent good examples of this ancient molecular enrichment. The second part of the chapter deals with a possibility of lithopanspermia, i.e., the idea that micro‐organisms can be distributed throughout the planetary system via fragments of rock/ice ejected during a meteoric impact event. Traces of these relationships in case of Earth‐Moon system represent granite and also a specimen of breccia collected on the lunar surface by Apollo 14 and 15 crews. The Chandreyaan‐1 probe confirmed the evidence of the water on both poles of the Moon and the origin of this water is questioned. Similarly, the question of a possible ancient Venus‐Mercury system (Van Flandern's and Harrison's hypothesis), including an alternative explanation for the origin of the water ices in the case of the smaller body.
All diploid sexual organisms have two distinct haploid genomes, one from each parent. There is the male derived haploid genome and the female derived haploid genome. Each genome contains a distinct developmental control network that directs the development of the embryo to an adult. Run separately, independent of the influence of the other network, the each haploid genome produces a morphologically different organism. The interrelationship of the male and female haploid genome networks is governed by an interaction protocol that determines which parental network is in control in any given cell at any given point in development. The protocol consists of two interacting half-protocols, one for each parental hap-loid genome. The full interaction protocol is itself a higher-level, meta-network, or internetwork between the two lower-level, parental developmental control networks. Computer simulations show that if the interaction protocol is random then there is a loss of bilateral symmetry in the generated organism. Therefore, for all bilaterally symmetric organisms, the interaction protocol between the two parental genomes cannot be random. This implies that a nonrandom ur-protocol must have evolved with the first diploid bilaterians in the Precambrian more than 570 million years ago. Nonrandom protocols partition the embryo and adult into dynamic sections that are variably controlled by one or the other parental haploid genome network. Developmental networks and their meta-network protocols provide fundamentally new insights into embryonic and post-embryonic development, developmental pathologies, animal and plant hybrids, heterosis, and evolutionary dynamics.
Background and aims:
Besides biological and chemical impacts, mechanical resistance represents an important obstacle that growing roots face. Graviresponding roots must assess the mechanical resistance of the substrate and take decisions on whether they change growth direction and grow around obstacles or tolerate growth conditions impaired to varying degrees. To test the significance of the root cap, we measured pressure and growth behaviour of single intact, as well as decapped, roots encountering diverse mechanical obstacles. We examined ethylene emission in intact roots as well as roots without a root cap, thereby lacking the capacity to deviate.
Methods:
Roots of fixed seedlings were grown vertically onto diverse mechanical obstacles. Developing pressure profiles of vertically growing roots encountering horizontal mechanical obstacles were measured employing electronic milligram scales, with and without root caps in given local environmental conditions. The evolution of root-borne ethylene was measured in intact roots and roots without the root cap.
Key results:
In contrast to decapped roots, intact roots develop a tentative, short-lasting pressure profile, the resolution of which is characterized by a definite change of growth direction. Similarly, pressure profiles and strengths of roots facing gradually differing surface resistances differ significantly between the two. This correlates in the short term with root cap-dependent ethylene emission which is lacking in roots without caps.
Conclusions:
The way gravistimulated and graviresponding roots cope with exogenous stimuli depends on whether and how they adapt to these impacts. With respect to mechanical hindrances, roots without caps do not seem to be able to evaluate soil strengths in order to respond adequately. On encountering resistance, roots with intact caps emit ethylene, which is not observed in decapped roots. It therefore appears that it is the root cap which specifically orchestrates the resistance needed to overcome mechanical resistance by specifically inducing ethylene.
Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we report putative fossilised microorganisms at least 3770 and possibly 4290 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Canada. These structures occur as micron-scale haematite tubes and filaments with morphologies and mineral assemblages similar to filamentous microbes from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes, magnetite-haematite granules, and associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidised biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3770 million years ago.
Cell fusion is a fundamental phenomenon observed in all eukaryotes. Cells can exchange resources such as molecules or organelles during fusion. In this paper, we ask whether a cell can also transfer an adaptive response to a fusion partner. We addressed this question in the unicellular slime mould Physarum polycephalum, in which celltextendashcell fusion is extremely common. Slime moulds are capable of habituation, a simple form of learning, when repeatedly exposed to an innocuous repellent, despite lacking neurons and comprising only a single cell. In this paper, we present a set of experiments demonstrating that slime moulds habituated to a repellent can transfer this adaptive response by cell fusion to individuals that have never encountered the repellent. In addition, we show that a slime mould resulting from the fusion of a minority of habituated slime moulds and a majority of unhabituated ones still shows an adaptive response to the repellent. Finally, we further reveal that fusion must last a certain time to ensure an effective transfer of the behavioural adaptation between slime moulds. Our results provide strong experimental evidence that slime moulds exhibit transfer of learned behaviour during cell fusion and raise the possibility that similar phenomena may occur in other celltextendashcell fusion systems.
Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire. They have the largest nervous systems among the invertebrates and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole-genome duplications in the octopus lineage. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems.
Tardigrades are known as one of the most radiation tolerant animals on Earth, and several studies on tolerance in adult tardigrades have been published. In contrast, very few studies on radiation tolerance of embryonic stages have been reported. Here we report a study on tolerance to gamma irradiation in eggs of the eutardigrade Richtersius coronifer. Irradiation of eggs collected directly from a natural substrate (moss) showed a clear dose-response, with a steep decline in hatchability at doses up to 0.4 kGy followed by a relatively constant hatchability around 25% up to 2 kGy, and a decline to ca. 5% at 4 kGy above which no eggs hatched. Analysis of the time required for eggs to hatch after irradiation (residual development time) showed that hatching of eggs after exposure to high doses of gamma radiation was associated with short residual development time. Since short residual development time means that the egg was irradiated at a late developmental stage, this suggests that eggs were more tolerant to radiation late in development. This was also confirmed in another experiment in which stage of development at irradiation was controlled. No eggs irradiated at the early developmental stage hatched, and only one egg at middle stage hatched, while eggs irradiated in the late stage hatched at a rate indistinguishable from controls. This suggests that the eggs are more sensitive to radiation in the early stages of development, or that tolerance to radiation is acquired only late in development, shortly before the eggs hatch, hypotheses that are not mutually exclusive. Our study emphasizes the importance of considering specific cell cycle phases and developmental stages in studies of tolerance to radiation in tardigrades, and the potential importance of embryonic studies in revealing the mechanisms behind the radiation tolerance of tardigrades and other cryptobiotic animals.
Tardigrades represent one of the most desiccation and radiation tolerant animals on Earth, and several studies have documented their tolerance in the adult stage. Studies on tolerance during embryological stages are rare, but differential effects of desiccation and freezing on different developmental stages have been reported, as well as dose-dependent effect of gamma irradiation on tardigrade embryos. Here, we report a study evaluating the tolerance of eggs from the eutardigrade Milnesium cf. tardigradum to three doses of gamma radiation (50, 200 and 500 Gy) at the early, middle, and late stage of development. We found that embryos of the middle and late developmental stages were tolerant to all doses, while eggs in the early developmental stage were tolerant only to a dose of 50 Gy, and showed a declining survival with higher dose. We also observed a delay in development of irradiated eggs, suggesting that periods of DNA repair might have taken place after irradiation induced damage. The delay was independent of dose for eggs irradiated in the middle and late stage, possibly indicating a fixed developmental schedule for repair after induced damage. These results show that the tolerance to radiation in tardigrade eggs changes in the course of their development. The mechanisms behind this pattern are unknown, but may relate to changes in mitotic activities over the embryogenesis and/or to activation of response mechanisms to damaged DNA in the course of development.
Physicists question whether there are 'universals' in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by Natural Genetic Engineering. Genomes are hierarchically organized as systems assembled from DNA modules. Each genome is formatted and integrated by repetitive DNA sequence elements that do not code for proteins, much as a computer drive is formatted. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, there is a computation-ready Genome System Architecture for each species. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs and their non-random operations help explain how novel genome system architectures can arise in evolution.
Where do new genes come from? For a long time the answer to that question has simply been “from other genes”. The most prolific source of new loci in eukaryotic genomes is gene duplication in all its guises: exon shuffling, tandem duplication, retrocopying, segmental duplication, and genome duplication. However, in recent years there has been a growing appreciation of the oft-dismissed possibility of evolution of new genes from scratch (i.e., de novo) as a rare but consistent feature of eukaryotic genomes [1], [2].
Pioneering work identified several de novo genes in Drosophila [3]–[5], and since then, additional Drosophila cases have been identified [6], as well as cases in yeast [7], [8], Plasmodium [9], rice [10], mouse [11], primates [12], and human [13], [14]. It would appear that whenever anyone makes the effort to search, candidate novel genes are found.
In this issue of PLoS Genetics, Wu et al. [15] report 60 putative de novo human-specific genes. This is a lot higher than a previous, admittedly conservative, estimate of 18 such genes [13], [16]. The genes identified share broad characteristics with other reported de novo genes [13]: they are short, and all but one consist of a single exon. In other words, the genes are simple, and their evolution de novo seems plausible. The potential evolution of complex features such as intron splicing and protein domains within de novo genes remains somewhat puzzling. However, features such as proto-splice sites may pre-date novel genes [9], [17], and the appearance of protein domains by convergent evolution may be more likely than previously thought [2].
The operational definition of a de novo gene used by Wu et al. [15] means that there may be an ORF (and thus potentially a protein-coding gene) in the chimpanzee genome that is up to 80% of the length of the human gene (for about a third of the genes the chimpanzee ORF is at least 50% of the length of the human gene). This is a more lenient criterion than employed by other studies, and this may partly explain the comparatively high number of de novo genes identified. Some of these cases may be human-specific extensions of pre-existing genes, rather than entirely de novo genes—an interesting, but distinct, phenomenon.
It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary 'recent' specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes.
When investigating the biological effects of ionizing radiation on the haemopoietic system, a confounding problem lies in possible differences between the biological effects of sparsely ionizing, low linear energy transfer radiation such as X-, beta- or gamma-rays, and densely ionizing, high linear energy transfer radiation such as alpha-particles. To address this problem we have developed novel techniques for studying haemopoietic cells irradiated with environmentally relevant doses of alpha-particles from a plutonium-238 source. Using a clonogenic culture system, cytogenetic aberrations in individual colonies of haemopoietic cells derived from irradiated stem cells have been studied. Exposure to alpha-particles (but not X-rays) produced a high frequency of non-clonal aberrations in the clonal descendants, compatible with alpha-emitters inducing lesions in stem cells that result in the transmission of chromosomal instability to their progeny. Such unexpected instability may have important implications for radiation leukaemogenesis.
Although it is not known when or where life on Earth began, some of the earliest habitable environments may have been submarine-hydrothermal vents. Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,280 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Quebec, Canada. These structures occur as micrometre-scale haematite tubes and filaments with morphologies and mineral assemblages similar to those of filamentous microorganisms from modern hydrothermal vent precipitates and analogous microfossils in younger rocks. The Nuvvuagittuq rocks contain isotopically light carbon in carbonate and carbonaceous material, which occurs as graphitic inclusions in diagenetic carbonate rosettes, apatite blades intergrown among carbonate rosettes and magnetite-haematite granules, and is associated with carbonate in direct contact with the putative microfossils. Collectively, these observations are consistent with an oxidized biomass and provide evidence for biological activity in submarine-hydrothermal environments more than 3,770 million years ago. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). Most species, during their geological history, either do not change in any appreciable way, or else they fluctuate mildly in morphology, with no apparent direction. Phyletic gradualism is very rare and too slow, in any case, to produce the major events of evolution. Evolutionary trends are not the product of slow, directional transformation within lineages; they represent the differential success of certain species within a clade—speciation may be random with respect to the direction of a trend (Wright's rule).
As an a priori bias, phyletic gradualism has precluded any fair assessment of evolutionary tempos and modes. It could not be refuted by empirical catalogues constructed in its light because it excluded contrary information as the artificial result of an imperfect fossil record. With the model of punctuated equilibria, an unbiased distribution of evolutionary tempos can be established by treating stasis as data and by recording the pattern of change for all species in an assemblage. This distribution of tempos can lead to strong inferences about modes. If, as we predict, the punctuational tempo is prevalent, then speciation—not phyletic evolution—must be the dominant mode of evolution.
We argue that virtually none of the examples brought forward to refute our model can stand as support for phyletic gradualism; many are so weak and ambiguous that they only reflect the persistent bias for gradualism still deeply embedded in paleontological thought. Of the few stronger cases, we concentrate on Gingerich's data for
Hyopsodus
and argue that it provides an excellent example of species selection under our model. We then review the data of several studies that have supported our model since we published it five years ago. The record of human evolution seems to provide a particularly good example: no gradualism has been detected within any hominid taxon, and many are long-ranging; the trend to larger brains arises from differential success of essentially static taxa. The data of molecular genetics support our assumption that large genetic changes often accompany the process of speciation.
Phyletic gradualism was an a priori assertion from the start—it was never “seen” in the rocks; it expressed the cultural and political biases of 19th century liberalism. Huxley advised Darwin to eschew it as an “unnecessary difficulty.” We think that it has now become an empirical fallacy. A punctuational view of change may have wide validity at all levels of evolutionary processes. At the very least, it deserves consideration as an alternate way of interpreting the history of life.
How does a single-cell creature, such as an amoeba, lead such a sophisticated life? How does it hunt living prey, respond to lights, sounds, and smells, and display complex sequences of movements without the benefit of a nervous system? This book offers a startling and original answer. In clear, jargon-free language, Dennis Bray taps the findings of the new discipline of systems biology to show that the internal chemistry of living cells is a form of computation. Cells are built out of molecular circuits that perform logical operations, as electronic devices do, but with unique properties. Bray argues that the computational juice of cells provides the basis of all the distinctive properties of living systems: it allows organisms to embody in their internal structure an image of the world, and this accounts for their adaptability, responsiveness, and intelligence. In Wetware, Bray offers imaginative, wide-ranging and perceptive critiques of robotics and complexity theory, as well as many entertaining and telling anecdotes. For the general reader, the practicing scientist, and all others with an interest in the nature of life, the book is an exciting portal to some of biology's latest discoveries and ideas.
In describing the flawless regularity of developmental processes and the correlation between changes at certain genetic loci and changes in morphology, biologists frequently employ two metaphors: that genes ‘control’ development, and that genomes embody ‘programs’ for development. Although these metaphors have an admirable sharpness and punch, they lead, when taken literally, to highly distorted pictures of developmental processes. A more balanced, and useful, view of the role of genes in development is that they act as suppliers of the material needs of development and, in some instances, as context-dependent catalysts of cellular changes, rather than as ‘controllers’ of developmental progress and direction. The consequences of adopting this alternative view of development are discussed.
The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin's proportional numbers are influencing their ecosystems. Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype. In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.
Cellular life can be viewed as one of many physical natural systems that extract free energy from their environments in the most efficient way, according to fundamental physical laws, and grow until limited by inherent physical constraints. Thus, it can be inferred that it is the efficiency of this process that natural selection acts upon. The consequent emphasis on metabolism, rather than replication, points to a metabolism-first origin of life with the adoption of DNA template replication as a second stage development. This order of events implies a cellular regulatory system that pre-dates the involvement of DNA and might, therefore, be based on the information acquired as peptides fold into proteins, rather than on genetic regulatory networks. Such an epigenetic cell regulatory model, the independent attractor model, has already been proposed to explain the phenomenon of radiation induced genomic instability. Here it is extended to provide an epigenetic basis for the morphological and functional diversity that evolution has yielded, based on natural selection of the most efficient free energy transduction. Empirical evidence which challenges the current genetic basis of cell and molecular biology and which supports the above proposal is discussed.
Two models for mammalian cell regulation that invoke the concept of cellular phenotype represented by high dimensional dynamic attractor states are compared. In one model the attractors are derived from an experimentally determined genetic regulatory network (GRN) for the cell type. As the state space architecture within which the attractors are embedded is determined by the binding sites on proteins and the recognition sites on DNA the attractors can be described as "hard-wired" in the genome through the genomic DNA sequence. In the second model attractors arising from the interactions between active gene products (mainly proteins) and independent of the genomic sequence, are descended from a pre-cellular state from which life originated. As this model is based on the cell as an open system the attractor acts as the interface between the cell and its environment. Environmental sources of stress can serve to trigger attractor and therefore phenotypic, transitions without entailing genotypic sequence changes. It is asserted that the evidence from cell and molecular biological research and logic, favours the second model. If correct there are important implications for understanding how environmental factors impact on evolution and may be implicated in hereditary and somatic disease.
This addresswas presented by Freeman J. Dyson as the NishinaMemorial
Lecture at the University of Tokyo, on October 17, 1984, and at Yukawa
Institute for Theoretical Physics, on October 23, 1984.
A simple statistical model is constructed, describing the transition from disorder to order in a population of mutually catalytic molecules undergoing random mutations. The consequences of the model are calculated, and its possible relevance to the problem of the origin of life is discussed. The main conclusion of the analysis is that the model allows populations of several thousand molecular units to make the transition from disorder to order with reasonable probability.