Historical retrospects and evolutionary characteristics of paleogenomic science and technology

Paleogenomics is a discipline in which the extraction and analysis of DNA from ancient biological remains are studied to understand the evolutionary history of past organisms.Research on this topic has revealed the evolutionary history of humans and other species,traced human migrations and genetic changes,and investigated ancient diseases and environmental influences due to its uniqueness.This paper reviews the scientific and technological history of the development of paleogenomics,including the molecular cloning era,the polymerase chain reaction(PCR)technique era,the genomics era,and the bio-data analysis era.This field explores the key technological development processes and effects of significant scientific discoveries,ranging from gene cloning technology and sequencing technology to breakthroughs and applications in big data analysis,addressing challenges such as sample contamination and trace collection analysis in paleogenomics research.

Supercontinent tectonics and biogeochemical cycle:A matter of 'life and death'

The formation and disruption of supercontinents have significantly impacted mantle dynamics, solid earth processes, surface environments and the biogeochemical cycle. In the early history of the Earth, the collision of parallel intra-oceanic arcs was an important process in building embryonic continents. Superdownwelling along Y-shaped triple junctions might have been one of the important processes that aided in the rapid assembly of continental fragments into closely packed supercontinents. Various models have been proposed for the fragmentation of supercontinents including thermal blanket and superplume hypotheses. The reassembly of supercontinents after breakup and the ocean closure occurs through ＂introversion＂, ＂extroversion＂ or a combination of both, and is characterized by either Pacific-type or Atlantic-type ocean closure. The breakup of supercontinents and development of hydro- thermal system in rifts with granitic basement create anomalous chemical environments enriched in nutri- ents, which serve as the primary building blocks of the skeleton and bone of early modern life forms. A typical example is the rifting of the Rodinia supercontinent, which opened up an N--S oriented sea way along which nutrient enriched upwelling brought about a habitable geochemical environment. The assembly of supercontinents also had significant impact on life evolution. The role played by the Cambrian Gondwana assembly has been emphasized in many models, including the formation of ＇Trans- gondwana Mountains＇ that might have provided an effective source of rich nutrients to the equatorial waters, thus aiding the rapid increase in biodiversity. The planet has witnessed several mass extinction events during its history, mostly connected with major climatic fluctuations including global cooling and warming events, major glaciations, fluctuations in sea level, global anoxia, volcanic eruptions, asteroid impacts and gamma radiation. Some recent models speculate a relationship between superplumes, supercontinent breakup and mass extinction. Upwelling plumes cause continental rifting and formation of large igneous provinces. Subsequent volcanic emissions and resultant plume-induced ＂winter＂ have catastrophic effect on the atmosphere that lead to mass extinctions and long term oceanic anoxia. The assembly and dispersal of continents appear to have influenced the biogeochemical cycle, but whether the individual stages of organic evolution and extinction on the planet are closely linked to Solid Earth processes remains to be investigated.

A Five-stage Evolution of Earth's Phosphorus Cycle

Phosphorus(P)is a key biological nutrient and probably the ultimate limiter of marine productivity during Earth history.In recent years,a wealth of new knowledge has revolutionized our understanding of the global P cycle,yet its longterm evolution remains incompletely documented.In this paper,we review the effects of three major controlling factors on the long-term evolution of the global P cycle,i.e.,tectonics,marine redox conditions,and bio-evolution,on the basis of which a five-stage model is proposed:StageⅠ(>~2.4 Ga),tectonic-lithogenic-controlled P cycling;StageⅡ(~2.4 Ga to 635Ma),low-efficiency biotic P cycling;StageⅢ(~635 Ma to 380 Ma),transitional biotic P cycling;StageⅣ(~380 Ma to near-modern),high-efficiency biotic P cycling;and Stage V(Anthropocene),human-influenced P cycling.This model implies that the earlier-proposed Ediacaran reorganization of the marine P cycle may represent only the start of a-250-Myr-long transition of the Earth's P cycle(StageⅢ)between the low-efficiency biotic mode of the Proterozoic(StageⅡ)and the high-efficiency biotic mode of the Phanerozoic(StageⅣ).The development of biologically-driven,high-efficiency P cycling may have been a key factor for the increasing frequency and volume of phosphorite deposits since the late Neoproterozoic.

Nuclear geyser model of the origin of life:Driving force to promote the synthesis of building blocks of life

We propose the nuclear geyser model to elucidate an optimal site to bear the first life.Our model overcomes the difficulties that previously proposed models have encountered.Nuclear geyser is a geyser driven by a natural nuclear reactor,which was likely common in the Hadean Earth,because of a much higher abundance of 235U as nuclear fuel.The nuclear geyser supplies the following：（1）high-density ionizing radiation to promote chemical chain reactions that even tar can be used for intermediate material to restart chemical reactions,（2）a system to maintain the circulation of material and energy,which includes cyclic environmental conditions（warm/cool,dry/wet,etc.）to enable to produce complex organic compounds,（3）a lower temperature than 100℃ as not to break down macromolecular organic compounds,（4）a locally reductive environment depending on rock types exposed along the geyser wall,and（5）a container to confine and accumulate volatile chemicals.These five factors are the necessary conditions that the birth place of life must satisfy.Only the nuclear geyser can meet all five,in contrast to the previously proposed birth sites,such as tidal flat,submarine hydrothermal vent,and outer space.The nuclear reactor and associated geyser,which maintain the circulations of material and energy with its surrounding environment,are regarded as the nuclear geyser system that enables numerous kinds of chemical reactions to synthesize complex organic compounds,and where the most primitive metabolism could be generated.

Bi-variable damage model for fatigue life prediction of metal components

Based on the theory of continuum damage mechanics,a bi-variable damage mechanics model is developed,which,according to thermodynamics,is accessible to derivation of damage driving force,damage evolution equation and damage evolution criteria. Furthermore,damage evolution equations of time rate are established by the generalized Drucker＇s postulate. The damage evolution equation of cycle rate is obtained by integrating the time damage evolution equations,and the fatigue life prediction method for smooth specimens under repeated loading with constant strain amplitude is constructed. Likewise,for notched specimens under the repeated loading with constant strain amplitude,the fatigue life prediction method is obtained on the ground of the theory of conservative integral in damage mechanics. Thus,the material parameters in the damage evolution equation can be obtained by reference to the fatigue test results of standard specimens with stress concentration factor equal to 1,2 and 3.

Three-step modernization of the ocean:Modeling of carbon cycles and the revolution of ecological systems in the Ediacaran/Cambrian periods

Important ecological changes of the Earth （oxidization of the atmosphere and the ocean） increase in nutrient supply due to the break-up of the super continent （Rodinia） and the appearance of multi-cellular organisms （macroscopic algae and metazoan） took place in the Ediacaran period, priming the Cambrian explosion. The strong perturbations in carbon cycles in the ocean are recorded as excursions in carbonate and organic carbon isotope ratio （δ13Ccarb and δ13Corg） from the Ediacaran through early Cambrian periods. The Ediacaran-early Cambrian sediment records of δ13Ccarb and δ13Corg, obtained from the drill-core samples in Three Gorges in South China, are compared with the results of numerical simulation of a sim- ple one-zone model of the carbon cycle of the ocean, which has two reservoirs （i.e., dissolved organic carbon （DOC） and dissolved inorganic carbon （DIC）. The fluxes from the reservoirs are assumed to be proportional to the mass of the carbon reservoirs. We constructed a model, referred to here as the Best Fit Model （BFM）, which reproduce δ13Ccarb and δ13Corg records in the Ediacaran-early Cambrian period noted above. BFM reveals that the Shuram excursion is related to three major changes in the carbon cycle or the global ecological system of the Earth： （1） an increase in the coefficient of remineralization by a factor of ca. 100, possibly corresponding to a change in the dominant metabolism from anaerobic respiration to aerobic respiration, （2） an increase of carbon fractionation index from 25‰, to 33‰, possibly corresponding to the change in the primary producer from rock-living cyanobacteria to free-living macro algae, and （3） an in- crease in the coefficient of the organic carbon burial by a factor of ca. 100, possibly corresponding to the onset of a biological pump driven by the flourishing metazoan and zooplankton. The former two changes took place at the start of the Shuram excursion, while the third occurred at the end of the Shuram excursion. The other two excursions are explained by the tentative decrease in primary production due to cold periods, which correspond to the Gaskiers （ca. 580 Ma） and Bikonor （ca. 542 Ma） glaciations.

国内外生命文化学:一个研究综述

生命是世界上最为复杂的现象之一,生命文化学以现实的、个体的生命为研究对象,是一门跨学科性、综合性较强的学科。它对于进一步理解与认识生命的意义,提升生命价值,促进与生命相关的交叉学科发展均具有重要意义,在近年来备受关注。国外最早是为了解决人类学的界定问题而产生了社会科学中的进化学派,之后又发展了基因―文化协同进化模型,其研究实质是基于生物学视角的一种拓展。近年来,国内关于生命文化学的学科界定、元理论体系的构建和研究方法的选择进行了初步探索。将国内外生命文化学的相关研究进行梳理,进而从其发展脉络提出学科未来发展的一些建议。

夯筑生命美学的第一块基石——潘知常《没有美万万不能——美学导论》的进化论启示

潘知常教授的新著《没有美万万不能——美学导论》在生命美学的学科意义上有着生命进化论的启示:因为身体的站立,让视野更加开阔而促使思维的活跃;因为快感的突破,让感受更加舒适而导致美感的诞生;因为需求的无限,让人性更加丰富而促成信仰的降临;因为死亡的超越,让现实更加充实而带来生命的永恒。

Atmospheric and Oceanic Oxygenation and Evolution of Early Life on Earth: New Contributions from China

The buildup of oxygen in the Earth＇s atmosphere and oceans has fundamentally reshaped the dynamics of nearly all major biogeochemical cycles and ultimately paved the way for the diversification of complex life on Earth. Over the past decades there have been sustained efforts to develop a more comprehensive understanding of ocean-atmosphere redox evolution and its relationship to the evolution of early life （Fig. 1）. It is generally accepted that the development of oxygenic photosynthesis at ~2.7 Ga may have been responsible for the Great Oxidation Event （GOE） at the beginning of the Proterozoic Eon, whereas a second big O2 rise at the end of the Proterozoic Eon （the so-called Neoproterozoic Oxidation Event or NOE） was responsible for the diversification of metazoans （Lyons et al., 2014）.

动机进化论:关于自然界从生命起源进化到人类的学术思考

生命起源与进化是地球历史发展过程中的一个自然现象。即便是能够通过考古学和历史学研究等知晓人类是从动物进化而来的,然而通常也很难理解自然界进化出复杂生命现象的目的、动机和意义。虽然有"存在即合理"的说法,但如果进化是随机的,那么,自然界又怎么会进化出号称"万物之灵"的人类这一特殊的高级物种呢?从原始社会发展到现代社会,人类经历了数不胜数的自然灾害、疾病和战争等痛苦与磨难,其成长和发展过程实属不易。当前虽已进入21世纪,人类在物质文明与精神文明获得大发展的同时,却依然面临病毒疫情、慢病顽疾、焦虑抑郁、恐怖袭击、难民危机、战争阴云等压力,这就不得不令人深思,人类的出现与发展是否必须面对这些痛苦。在此前提出"菌心进化论"的基础上,进一步从"动机进化论"的角度进行学术探讨,旨在为人类存在与发展的意义和价值提供一种新解释,有利于对人类社会未来健康美好的生活图景进行科学展望。

简论生命科学发展的三个阶段

本文回顾、剖析了生物学科从诞生到目前这一长久的历史发展过程,依据其哲学指导思想、带头的学科、研究工作方式和最大的科学贡献等四个方面划分为三个阶段,即博物学阶段、生物学阶段和生命科学阶段,并就每个阶段的哲学指导思想、带头的学科、研究工作方式和解决的最根本科学问题等方面进行分析梳理,旨在抛砖引玉,为生命科学的研究发展提供哲学指导。