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Научные публикации

СообщениеДобавлено: 07 авг 2016, 00:52
KKND_4936 (Артём)
Давно была мысль, что подобная тема может быть полезной. Предлагаю тут выкладывать полные библиографические ссылки на различные публикации, описание и, по возможности, их электронный вариант или ссылку на источник, где можно прочесть \ купить \ скачать материал. Примером:

Richardson M., Hanken J., Gooneratne M., Pieau C., Paynaud A., Selwood L., Wright G. There is no highly conserved embryonic state n the vertebrates: implications for current theories of evolution and development. // Anat Embryol. 1997. V. 196. P. 91–106.
Embryos of different species of vertebrate share a common organisation and often look similar. Adult differences among species become more apparent through divergence at later stages. Some authors have suggested that members of most or all vertebrate clades pass through a virtually identical, conserved stage. This idea was promoted by Haeckel, and has recently been revived in the context of claims regarding the universality of developmental mechanisms. Thus embryonic resemblance at the tailbud stage has been linked with a conserved pattern of developmental gene expression – the zootype. Haeckel’s drawings of the external morphology of various vertebrates remain the most comprehensive comparative data purporting to show a conserved stage. However, their accuracy has been questioned and only a narrow range of species was illustrated. In view of the current widespread interest in evolutionary developmental biology, and especially in the conservation of developmental mechanisms, re-examination of the extent of variation in vertebrate embryos is long overdue. We present here the first review of the external morphology of tailbud embryos, illustrated with original specimens from a wide range of vertebrate groups. We find that embryos at the tailbud stage – thought to correspond to a conserved stage – show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel’s drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phyogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype. Our study also highlights the dangers of drawing general conclusions about vertebrate development from studies of gene expression in a small number of laboratory species.

Richardson M.K., Keuck G. Haeckel’s ABC of evolution and development // Biol. Rev. 2002. V. 77. P. 495-528.
One of the central, unresolved controversies in biology concerns the distribution of primitive versus advanced characters at different stages of vertebrate development. This controversy has major implications for evolutionary developmental biology and phylogenetics. Ernst Haeckel addressed the issue with his Biogenetic Law, and his embryo drawings functioned as supporting data. We re-examine Haeckel’s work and its significance for modern efforts to develop a rigorous comparative framework for developmental studies. Haeckel’s comparative embryology was evolutionary but non-quantitative. It was based on developmental sequences, and treated heterochrony as a sequence change. It is not always clear whether he believed in recapitulation of single characters or entire stages. The Biogenetic Law is supported by several recent studies – if applied to single characters only. Haeckel’s important but overlooked alphabetical analogy of evolution and development is an advance on von Baer. Haeckel recognized the evolutionary diversity in early embryonic stages, in line with modern thinking. He did not necessarily advocate the strict form of recapitulation and terminal addition commonly attributed to him. Haeckel’s much-criticized embryo drawings are important as phylogenetic hypotheses, teaching aids, and evidence for evolution. While some criticisms of the drawings are legitimate, others are more tendentious. In opposition to Haeckel and his embryo drawings, Wilhelm His made major advances towards developing a quantitative comparative embryology based on morphometrics. Unfortunately His’s work in this area is largely forgotten. Despite his obvious flaws, Haeckel can be seen as the father of a sequence-based phylogenetic embryology.

Hackett S.J. et al. A phylogenomic study of birds reveals their evolutionary history // Science. 2008. V. 320. № 5884. P. 1763-1768.
Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ~32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

Думаю, что знание некоторых публикаций может быть полезным для каких-нибудь дискуссий, написания докладов и т.д.

Re: Научные публикации

СообщениеДобавлено: 07 авг 2016, 01:01
KKND_4936 (Артём)
Спирин А. С. Где, когда и в каких условиях мог возникнуть и эволюционировать мир РНК? / А. С. Спирин // Палеонтологический журнал. - 2007. - №5. - C. 11-19.
Рассмотрены условия внешней среды, необходимые для существования, амплификации и эволюции мира РНК, трудности абиогенного синтеза РНК и парадоксальные ситуации, возникающие в отношении стабильности РНК, ее функционирования и места мира РНК в геологической истории Земли. Обсуждается, во-первых, несовместимость химической нестабильности ковалентной структуры РНК в водной среде и необходимости воды для формирования ее функционально активных конформаций («водный парадокс»); во-вторых, несовместимость стабильной двуспиральной структуры РНК, требуемой для репликации РНК, и стабильных компактных конформаций одноцепочечных РНК, необходимых для каталитических функций (конформационный парадокс); в третьих, чересчур малый промежуток времени, или его отсутствие, в геологической истории Земли между окончанием массированной метеоритной бомбардировки (3,9 млрд. лет назад) и появлением первых свидетельств клеточной жизни (бактерий) в земных породах (3,8 – 3,85 млрд. лет назад или даже несколько ранее) (геологический парадокс). Сделан вывод о невозможности возникновения, существования и эволюции мира РНК в клеточные формы жизни на Земле. Кратко обсуждается проблема космического происхождения мира РНК и его внеземной эволюции, с последующим распространением в космосе, в основном с помощью комет, клеточной формы жизни как более устойчивой к внешним условиям по сравнению со свободной РНК.

shCherbak V.I., Makukov M.A. The “Wow! signal” of the terrestrial genetic code // Icarus. 2013. V. 224. P. 228-242.
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like “signal” in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns are profound to the extent that the code mapping itself is uniquely deduced from their algebraic representation. The signal displays readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to any natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.

Re: Научные публикации

СообщениеДобавлено: 02 сен 2016, 23:43
KKND_4936 (Артём)
Abraham Loeb, Rafael Batista, and David Sloan, “Relative Likelihood for Life as a Function of Cosmic Time,” Journal of Cosmology and Astroparticle Physics (August 2016): doi:10.1088/1475-7516/2016/08/040.
Is life most likely to emerge at the present cosmic time near a star like the Sun? We address this question by calculating the relative formation probability per unit time of habitable Earth-like planets within a fixed comoving volume of the Universe, dP(t)/dt, starting from the first stars and continuing to the distant cosmic future. We conservatively restrict our attention to the context of “life as we know it” and the standard cosmological model, ΛCDM. We find that unless habitability around low mass stars is suppressed, life is most likely to exist near ∼ 0.1M stars ten trillion years from now. Spectroscopic searches for biosignatures in the atmospheres of transiting Earth-mass planets around low mass stars will de ermine whether present-day lif is indeed premature or typical from a cosmic perspective.

Wells J (2014). Membrane patterns carry ontogenetic information that is specified independently of DNA. BIO-Complexity 2014 (2):1–28.

Embryo development (ontogeny) depends on developmental gene regulatory networks (dGRNs), but dGRNs depend on preexisting spatial anisotropies that are defined by early embryonic axes, and those axes are established long before the embryo’s dGRNs are put in place. For example, the anterior-posterior axis in Drosophila and the animal-vegetal axis in Xenopus and echinoderms are initially derived from the architecture of the ovary through processes mediated by cytoskeletal and membrane patterns rather than dGRNs. This review focuses on plasma membrane patterns, which serve essential ontogenetic functions by providing targets and sources for intracellular signaling and transport, by regulating cell-cell interactions, and by generating endogenous electric fields that provide three-dimensional coordinate systems for embryo development. Membrane patterns are not specified by DNA sequences. Because of processes such as RNA splicing, RNA editing, protein splicing, alternative protein folding, and glycosylation, DNA sequences do not specify the final functional forms of most membrane components. Still less does DNA specify the spatial arrangements of those components. Yet their spatial arrangements carry essential ontogenetic information. The fact that membrane patterns carry ontogenetic information that is not specified by DNA poses a problem for any theory of evolution (such as Neo-Darwinism) that attributes the origin of evolutionary novelties to changes in a genetic program—whether at the level of DNA sequences or dGRNs. This review concludes by suggesting that relational biology and category theory might be a promising new approach to understanding how the ontogenetic information in membrane patterns could be specified and undergo the orchestrated changes needed for embryo development.

Re: Научные публикации

СообщениеДобавлено: 06 сен 2016, 16:37
KKND_4936 (Артём)
Алтухов Ю. П. Вид и видообразование // Соросовский Образовательный Журнал. — 1997. — № 4. — С. 2—10.
Статья представляет собой сжатый обзор основных типологических популяционных представлений о виде и видообразовании. Делается вывод, что современная биология всё ещё не располагает завершённой концепцией вида, за последние 15-20 лет получено много новых фактов, противоречащих общепринятым представлениям о видообразовании как вероятностном процессе.

Алтухов Ю.П., Рычков Ю.Г. Генетический мономорфизм видов и его возможное биологическое значение // Журнал общей биологии. 1972. Т. 33. №. 3. С. 281-300.
Рассматривается внутри- и межвидовая изменчивость полиморфных и мономорфных белков - генетических маркеров. Обсуждается значение генетического мономорфизма в связи с аспектами эволюционной трансформации и адаптивной стабилизации видов.

Re: Научные публикации

СообщениеДобавлено: 12 фев 2017, 13:28
KKND_4936 (Артём)
Lee, Y.-C. et al. Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy. Nat. Commun. 8, 14220 doi: 10.1038/ncomms14220 (2017).
Fossilized organic remains are important sources of information because they provide a unique form of biological and evolutionary information, and have the long-term potential for genomic explorations. Here we report evidence of protein preservation in a terrestrial vertebrate found inside the vascular canals of a rib of a 195-million-year-old sauropodomorph dinosaur, where blood vessels and nerves would normally have been present in the living organism. The in situ synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectra exhibit the characteristic infrared absorption bands for amide A and B, amide I, II and III of collagen. Aggregated haematite particles (α-Fe2O3) about 6∼8 μm in diameter are also identified inside the vascular canals using confocal Raman microscopy, where the organic remains were preserved. We propose that these particles likely had a crucial role in the preservation of the proteins, and may be remnants partially contributed from haemoglobin and other iron-rich proteins from the original blood.

Link: http://www.nature.com/articles/ncomms14220
На всякий случай скопипастил статью в вордовский документ:

Re: Научные публикации

СообщениеДобавлено: 12 фев 2017, 13:41
KKND_4936 (Артём)
Ю. Н. Ефремов, А. Д. Чернин, “Крупномасштабное звездообразование в галактиках”, УФН, 173:1 (2003), 3–25
Кратко описана история возникновения современных представлений о продолжающемся и в нашу эпоху формировании звезд в газовых дисках галактик. Работы последних лет показывают, что в процессе звездообразования решающая роль принадлежит взаимодействию собственной гравитации газа и его турбулентных движений. Крупномасштабные сверхзвуковые движения газа создают в нем первоначальные уплотнения, которые затем дают начало гравитационной конденсации газа в звезды. Рассмотрены вопросы образования звездных скоплений, ассоциаций и комплексов, а также возможность возникновения изолированных звезд. Особое внимание уделено проблеме возникновения звезд под действием динамического давления.

Re: Научные публикации

СообщениеДобавлено: 05 сен 2017, 15:21
KKND_4936 (Артём)
Don N. Page. «Return of the Boltzmann Brains,» Phys.Rev.D78:063536,2008, [arXiv:hep-th/0611158v1 [hep-th]]
Linde in hep-th/0611043 shows that some (though not all) versions of the global (volume-weighted) description avoid the "Boltzmann brain" problem raised in hep-th/0610079 if the universe does not have a decay time less than 20 Gyr. Here I give an apparently natural version of the volume-weighted description in which the problem persists, highlighting the ambiguity of taking the ratios of infinite volumes that appear to arise from eternal inflation.

Don N. Page, «Bayes Keeps Boltzmann Brains at Bay,» Alberta-Thy-6-17, [arXiv:1708.00449v1 [hep-th]]
Sean Carroll has recently argued that theories predicting that observations are dominated by Boltzmann Brains should be rejected because they are cognitively unstable: "they cannot simultaneously be true and justifiably believed." While such Boltzmann Brain theories are indeed cognitively unstable, one does not need to appeal to this argumentation to reject them. Instead, they may be ruled out by conventional Bayesian reasoning, which is sufficient to keep Boltzmann Brains at bay.

Re: Научные публикации

СообщениеДобавлено: 29 июн 2018, 13:28
KKND_4936 (Артём)
Luke A. Barnes, Pascal J. Elahi, Jaime Salcido, Richard G. Bower, Geraint F. Lewis, Tom Theuns, Matthieu Schaller, Robert A. Crain, Joop Schaye. «Galaxy Formation Efficiency and the Multiverse Explanation of the Cosmological Constant with EAGLE Simulations,» 10.1093/mnras/sty846, [arXiv:1801.08781v2 [astro-ph.CO]]
Models of the very early universe, including inflationary models, are argued to produce varying universe domains with different values of fundamental constants and cosmic parameters. Using the cosmological hydrodynamical simulation code from the eagle collaboration, we investigate the effect of the cosmological constant on the formation of galaxies and stars. We simulate universes with values of the cosmological constant ranging from Lambda = 0 to Lambda_0 = 300, where Lambda_0 is the value of the cosmological constant in our Universe. Because the global star formation rate in our Universe peaks at t = 3.5 Gyr, before the onset of accelerating expansion, increases in Lambda of even an order of magnitude have only a small effect on the star formation history and efficiency of the universe. We use our simulations to predict the observed value of the cosmological constant, given a measure of the multiverse. Whether the cosmological constant is successfully predicted depends crucially on the measure. The impact of the cosmological constant on the formation of structure in the universe does not seem to be a sharp enough function of Lambda to explain its observed value alone.

Jaime Salcido, Richard G. Bower, Luke A. Barnes, Geraint F. Lewis, Pascal J. Elahi, Tom Theuns, Matthieu Schaller, Robert A. Crain, Joop Schaye. «The impact of dark energy on galaxy formation. What does the future of our Universe hold?,» 10.1093/mnras/sty879, [arXiv:1710.06861v3 [astro-ph.CO]]
We investigate the effect of the accelerated expansion of the Universe due to a cosmological constant, Λ, on the cosmic star formation rate. We utilise hydrodynamical simulations from the EAGLE suite, comparing a ΛCDM Universe to an Einstein-de Sitter model with Λ=0. Despite the differences in the rate of growth of structure, we find that dark energy, at its observed value, has negligible impact on star formation in the Universe. We study these effects beyond the present day by allowing the simulations to run forward into the future (t>13.8 Gyr). We show that the impact of Λ becomes significant only when the Universe has already produced most of its stellar mass, only decreasing the total co-moving density of stars ever formed by ≈15%. We develop a simple analytic model for the cosmic star formation rate that captures the suppression due to a cosmological constant. The main reason for the similarity between the models is that feedback from accreting black holes dramatically reduces the cosmic star formation at late times. Interestingly, simulations without feedback from accreting black holes predict an upturn in the cosmic star formation rate for t>15 Gyr due to the rejuvenation of massive (>1011M⊙) galaxies. We briefly discuss the implication of the weak dependence of the cosmic star formation on Λ in the context of the anthropic principle.