为什么生态学落后于生物学

Dec/ 6/2017
原文链接

Why Ecology Lags Behind Biology ?

Illustration: A. Canamucio The triumph of the mapping of the human genome is eloquent testimony to how fast the life sciences have come from the 1960s when the Nuffield Foundation found it necessary to launch a program of biological scholarships to leaven the “soft” biological sciences with expertise from the “hard”

By Raymond O’connor | October 16, 2000

 

The triumph of the mapping of the human genome is eloquent testimony to how fast the life sciences have come from the 1960s when the Nuffield Foundation found it necessary to launch a program of biological scholarships to leaven the “soft” biological sciences with expertise from the “hard” sciences of physics and chemistry. The program supported academically qualified physicists and chemists seeking careers in the life sciences, or life scientists wishing to obtain a degree in physics or chemistry to aid their career in the biological sciences.

Yet the ecological and environmental sciences have lagged behind the surging advances of most of the life sciences. In no way can one seriously anticipate soon an ecological breakthrough of the magnitude of the human genome project. If the takeover of biological department after biological department by well-funded molecular biologists in the 1970s dismissed ecology as natural history, neither has the subsequent clothing of ecology in a mantle of hypothetico-deductive approaches yielded the expected harvest. As the National Science Foundation’s biocomplexity initiative1 is expected to pour in excess of $50 million of new money into ecological research over the next few years, it is worth asking whether money or mind-set underlies the faltering progress of ecological research.

I believe that ecologists have failed to distinguish form from substance in hypothetico-deductive research. We applaud our students when they learn to recite the mantra “My hypothesis was that …,” but we fail to fault the trivial content of the typical ecological hypothesis. In modern life sciences, as in physics, a hypothesis is typically based on a corpus of theory about how something works. It is operationally expressed as a statement of what will be observed experimentally–or observationally in the case of astronomy–if this theory is correct. Moreover, many of the critical breakthroughs in molecular biology have come from experiments that discriminate between alternate outcomes. Critically, ecology seems to have substituted the statement of what will be observed as the hypothesis. Our typical hypothesis is statistical in nature, establishing only that a pattern departs from some null model (often randomness). It is little wonder that the discussion sections of the resulting papers are so speculative.

Hypothesis statements in ecology range from the absolutely stupid to the truly insightful. The worst, statements such as “I hypothesized that breeding success would not decrease with decrease in forest patch size …,” reveal only the author’s ignorance of Type II errors. Marginally informative hypotheses, such as ” I hypothesized that breeding success would increase with forest patch size,” can hint at process when published for the first time but are barely worth 200 lines in a journal, let alone the 20 pages typically used when reporting the 10th, 11th, 12th,… case study of the phenomenon. Additionally, and in contrast to biomedical research, such hypotheses rarely acknowledge that there may be more than one process that would yield the outcome expected, let alone provide for testing between the alternatives.

Scarce in ecology are hypotheses that quantify anything in advance (“I hypothesized that breeding success would increase linearly with the proportion of forest patch that lay more than 300 meters from an edge, 300 meters being the average distance of penetration by predators into forest”). Truly rare in ecology are hypotheses that start from theory of the particulars of processes and develop unequivocal quantitative predictions. An exceptional example is the model2 of how the fractal geometry and hydrodynamics of branching resource distribution networks predicts universal allometric scaling in life span and fecundity, in energy and resource use and territory size, and in population dynamics.

One cannot read far into articles in the biomedical literature without encountering a specific of a process–the SP1 transcription factor, the U12 spliceosome–whilst in ecology the terms are generalities often imported from everyday life–habitat corridors, sink populations, competition. The Oxford ecologist Charles Elton would be as home with today’s ecological terminology as he was in the 1930s.

The fundamental difference between the successful life sciences and the environmental sciences is, I submit, that life science and biomedical research has developed ideas about how things work whilst ecology has retained a focus on what is. The practitioners of ecology still have a building-bricks-world view of science–the idea that any piece of work in science is like a brick added to a pallet from which a few outstanding architects and builders will construct the walls, and then buildings, edifices of scientific understanding. What is missing with this mind-set is the synergy that has innervated biomedical research. Modern biomedical research is a turmoil of competing ideas, each with a logic that is rapidly followed through to yield predictions inconsistent with those derived from the competitors. Behind this sea of ideas is also a community of expertise providing solutions to the technical problems thrown up in experimental testing between such predictions.

Some solutions, such as the development of PCR, are breakthroughs of first order, akin to the discovery of a new phenomenon in physics; others, such as the development of a particular knockout mouse, are specific applications of known principles, akin to engineering achievements. Often straddling multiple streams of such activity are the innovators, scientists with the breadth of knowledge to be able to unite conceptual advances in diverse fields at critical junctions. If science has building bricks, progress lies in identifying the keystones. In contrast, too much of field ecology is what I label as “Me too!” research: Too often, despite there being dozens of previous studies of deer diets in other states and in multiple seasons, a lengthy ecology paper begins, “The fall feeding habits of white-tailed deer in Maine have never been studied, so I ….” Confirmation of previous studies is desirable, and some idea of the breadth of a phenomenon across taxa is informative, so such work perhaps deserves reporting as a short note. The norm in ecology, though, is yet another long paper, typically padded with what is little more than paper on topic X for species Y in region Z to join the dozens already published on the topic and species.

It may be argued that the reproducibility of physiological and molecular processes has allowed the biomedical research community to develop “hard” laws equivalent to the laws of physics. The implication is that ecology at large has to cope with excessive variability in those observations possible, aggravated by restricted ability to conduct experiments. Yet astronomy cannot conduct experiments but still manages to advance the testing of rigorously formulated ideas about the nature of stars and the origins of the universe–ultimate explanations rather than trivial statements about patterns to be observed.

Additionally, in biomedical research, one finds that a clear distinction between measurement error (instrumental error) and variability among the cases in a sample is maintained. Even more telling is the scientific practice universally evident in the rare case histories of outstanding success in ecology. Our understanding of the population dynamics of parasitoids, for example, owes much to the exemplary approach of Michael Hassell in Imperial College in England: His long history of alternating his focus between modeling (to determine which component of then-current ideas about population dynamics generated most uncertainty about outcome) and laboratory experiments (to parameterize the effects of that source) yielded a comprehensive understanding of parasitoid dynamics.3

Contrast that with our abysmal understanding of fishery population dynamics for which contemporary management practices rooted in current ecological understanding has seen every major fishery globally drift down the food chain.4 Lest laboratory experiments seem too close to biomedical work to be a fair representation of ecological research, consider the success of the long-running field experiments of David Tilman at Cedar Creek in bringing order to understanding of plant population dynamics.5 And if even field experiments are too controlled for pure ecology, consider the long-term observational studies of Richard Holmes and Thomas Sherry at Hubbard Brook on the population ecology of black-throated green warblers and America redstarts.6 What each of these studies (and their counterparts in other outposts of quality ecological work) shares with biomedical research is rigorous analysis and logical thinking: Each piece of each of these investigations provided immediate critical feedback to understanding the ecological processes involved.

Each of these researchers has forsaken the building-bricks-of-science approach to substitute “How?” and “Why?” questions for the “What?’ inquiry that dominates contemporary field ecology. It is in this consideration and dissection of how things might work, and of why they should work in that particular way, that effective ecology must converge on the successful practices of biomedical research.

Raymond J. O’Connor, D.Phil., holds degrees in Physics and Zoology. A former Nuffield Foundation Biological Scholar (1969-71), he is a Professor of Wildlife Ecology at the University of Maine.

References

  1. A. Emmett, “Biocomplexity: a new science for survival,” The Scientist, 14[19]:1, Oct. 2, 2000.
  2. G.B. West et al., “A general model for the origin of allometric scaling laws in biology,” Science, 276:122, 1997.
  3. M.P. Hassell et al., “The persistence of host-parasitoid associations in patchy environments,” American Naturalist, 138:568-83, 1991.
  4. D.V. Pauly et al., “Fishing down marine food webs,” Science, 279:860-63. 1998.
  5. D. Tilman, “The ecological consequences of changes in biodiversity: a search for general principles,” The Robert H. MacArthur Award Lecture. Ecology, 80:1455-74, 1999.
  6. T.W. Sherry, R.T. Holmes, “Winter habitat limitation in Neotropical-Nearctic migrant birds: implications for population dynamics and conservation,” Ecology, 77: 36-48. 1996.

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ESI生态环境类期刊影响因子

Jul/10/2017

ESI系指基本科学指标数据库(Essential Science Indicators)是世界著名的学术信息出版机构美国科技信息所(ISI)于2001年推出的衡量科学研究绩效、跟踪科学发展趋势的基本分析评价工具,其中生态学的期刊分布在Ecology/Environment这个大类中。我们整理了ESI中Ecology/Environment类杂志的2017年发布的影响因子,供广大读者使用.

Journal title IF
energy & environmental science 29.518
energy & environmental science 29.518
trends in ecology & evolution 15.268
annual review of ecology evolution and systematics 10.182
land degradation & development 9.787
environmental health perspectives 9.776
ecology letters 9.449
systematic biology 8.917
ecological monographs 8.759
global change biology 8.502
renewable & sustainable energy reviews 8.050
frontiers in ecology and the environment 8.039
molecular ecology resources 7.332
environment international 7.088
conservation letters 7.020
water research 6.942
annual review of environment and resources 6.268
environmental science & technology 6.198
molecular ecology 6.086
global ecology and biogeography 6.045
journal of toxicology and environmental health-part b-critical reviews 5.815
journal of ecology 5.813
critical reviews in environmental science and technology 5.790
methods in ecology and evolution 5.708
functional ecology 5.630
journal of environmental informatics 5.562
environmental microbiology 5.395
journal of applied ecology 5.301
environmental pollution 5.099
advances in ecological research 5.056
ecography 4.902
science of the total environment 4.900
conservation biology 4.842
ecology 4.809
bulletin of the american museum of natural history 4.562
environmental research letters 4.404
reviews in environmental science and bio-technology 4.400
water resources research 4.397
diversity and distributions 4.391
ecological applications 4.314
journal of biogeography 4.248
chemosphere 4.208
ecosystems 4.198
american naturalist 4.167
journal of industrial ecology 4.123
agriculture ecosystems & environment 4.099
oikos 4.030
biological conservation 4.022
journal of environmental management 4.010
journal of environmental science and health part c-environmental carcinogenesis & ecotoxicology reviews 4.000
current opinion in environmental sustainability 3.954
reviews of environmental contamination and toxicology 3.930
ecological indicators 3.898
biogeosciences 3.851
environmental research 3.835
environmental health 3.816
environmental science & policy 3.751
ecotoxicology and environmental safety 3.743
ambio 3.687
microbial ecology 3.630
landscape ecology 3.615
environmental chemistry 3.594
journal of water resources planning and management 3.537
geobiology 3.462
sustainability science 3.429
biogeochemistry 3.428
limnology and oceanography 3.383
environmental microbiology reports 3.363
clean technologies and environmental policy 3.331
resources conservation and recycling 3.313
biomass & bioenergy 3.219
environmental reviews 3.196
air quality atmosphere and health 3.184
marine pollution bulletin 3.146
aquatic conservation-marine and freshwater ecosystems 3.130
oecologia 3.130
perspectives in plant ecology evolution and systematics 3.123
journal of flood risk management 3.121
marine environmental research 3.101
hydrological processes 3.014
international biodeterioration & biodegradation 2.962
environmental toxicology and chemistry 2.951
process safety and environmental protection 2.950
environmental toxicology 2.937
journal of environmental sciences-china 2.937
journal of exposure science and environmental epidemiology 2.927
ecological engineering 2.914
bmc ecology 2.896
paleobiology 2.886
ecohydrology 2.852
water resources management 2.848
animal conservation 2.835
environmental science and pollution research 2.741
journal of toxicology and environmental health-part a-current issues 2.731
urban water journal 2.658
environmental geochemistry and health 2.616
aerosol and air quality research 2.606
environmental science-processes & impacts 2.592
ecosphere 2.490
bioenergy research 2.487
biological invasions 2.473
archives of environmental contamination and toxicology 2.467
ecology and evolution 2.440
journal of chemical ecology 2.385
ecological modelling 2.363
journal of environmental quality 2.344
journal of environmental radioactivity 2.310
basic and applied ecology 2.292
marine ecology progress series 2.292
river research and applications 2.274
biodiversity and conservation 2.265
ecohealth 2.252
journal of soil and water conservation 2.229
hydrological sciences journal-journal des sciences hydrologiques 2.222
mitigation and adaptation strategies for global change 2.216
biomedical and environmental sciences 2.204
international journal of biometeorology 2.204
aerobiologia 2.202
oryx 2.191
polar research 2.146
systematics and biodiversity 2.127
urban forestry & urban greening 2.113
international journal of environmental research and public health 2.101
international journal of water resources development 2.088
aquatic invasions 2.069
ecological informatics 2.020
journal of paleolimnology 2.017
journal of contaminant hydrology 2.009
pedobiologia 2.000
limnology and oceanography-methods 1.992
inland waters 1.987
urban ecosystems 1.970
ecotoxicology 1.951
polar biology 1.949
rangeland ecology & management 1.940
vadose zone journal 1.932
international journal of environmental science and technology 1.915
environmental management 1.878
population ecology 1.865
international journal of sustainable development and world ecology 1.864
ocean & coastal management 1.861
journal of arid environments 1.835
water 1.832
environmental conservation 1.826
evolutionary ecology 1.818
boreal environment research 1.805
journal of arid land 1.796
sustainability 1.789
ecological complexity 1.784
arctic antarctic and alpine research 1.782
hydrology research 1.754
environmental technology 1.751
biotropica 1.730
restoration ecology 1.724
journal of the american water resources association 1.717
frontiers of environmental science & engineering 1.716
austral ecology 1.708
new zealand journal of ecology 1.704
water air and soil pollution 1.702
environmental monitoring and assessment 1.687
greenhouse gases-science and technology 1.676
carbon management 1.661
journal for nature conservation 1.657
acta oecologica-international journal of ecology 1.652
marine biodiversity 1.646
atmospheric pollution research 1.637
journal of hydroinformatics 1.634
plant ecology 1.615
theoretical population biology 1.613
journal of material cycles and waste management 1.604
canadian water resources journal 1.596
climate research 1.578
wetlands 1.573
environmental earth sciences 1.569
human and ecological risk assessment 1.560
ground water monitoring and remediation 1.550
environmetrics 1.532
conservation genetics 1.515
wetlands ecology and management 1.508
aquatic ecology 1.500
oceanologia 1.500
international journal of sediment research 1.494
geomicrobiology journal 1.485
international journal of environmental health research 1.485
clean-soil air water 1.473
chemistry and ecology 1.463
antarctic science 1.461
journal of limnology 1.451
chemistry & biodiversity 1.440
journal of hydro-environment research 1.429
limnologica 1.427
journal of environmental science and health part a-toxic/hazardous substances & environmental engineering 1.425
bulletin of environmental contamination and toxicology 1.412
isotopes in environmental and health studies 1.386
journal of environmental science and health part b-pesticides food contaminants and agricultural wastes 1.362
fire ecology 1.359
chemoecology 1.298
ecological research 1.283
journal of biological dynamics 1.279
mine water and the environment 1.278
palaeobiodiversity and palaeoenvironments 1.278
lake and reservoir management 1.270
tropical conservation science 1.238
theoretical ecology 1.221
rangeland journal 1.211
international journal of environmental analytical chemistry 1.208
soil & sediment contamination 1.207
natureza & conservacao 1.200
indoor and built environment 1.181
marine ecology-an evolutionary perspective 1.177
arctic 1.165
annales de limnologie-international journal of limnology 1.161
chinese geographical science 1.154
mountain research and development 1.149
water policy 1.144
polar science 1.118
bioremediation journal 1.098
environmental engineering and management journal 1.096
international journal of mining reclamation and environment 1.078
bulletin of the peabody museum of natural history 1.071
water and environment journal 1.063
chemical speciation and bioavailability 1.054
journal of tropical ecology 1.041
journal of water and health 1.041
environmental modeling & assessment 1.023
australasian journal of environmental management 1.019
journal of mountain science 1.016
arid land research and management 1.015
limnetica 0.986
african journal of range & forage science 0.961
journal of coastal conservation 0.959
water sa 0.958
natural areas journal 0.949
journal of freshwater ecology 0.942
international journal of environmental research 0.927
journal of water and climate change 0.917
journal of coastal research 0.915
polar record 0.914
limnology 0.913
water environment research 0.910
ozone-science & engineering 0.892
american museum novitates 0.873
environmental forensics 0.850
evolutionary ecology research 0.837
journal of natural history 0.834
annals of agricultural and environmental medicine 0.829
journal of water supply research and technology-aqua 0.824
toxicological and environmental chemistry 0.795
polish journal of environmental studies 0.793
community ecology 0.782
acta amazonica 0.775
journal of environmental protection and ecology 0.774
proceedings of the academy of natural sciences of philadelphia 0.760
aquatic ecosystem health & management 0.742
biota neotropica 0.734
ecological chemistry and engineering s-chemia i inzynieria ekologiczna s 0.717
archives of environmental protection 0.708
rocznik ochrona srodowiska 0.705
revista chilena de historia natural 0.702
journal of environmental biology 0.697
israel journal of ecology & evolution 0.696
landscape and ecological engineering 0.692
african journal of ecology 0.690
chinese journal of oceanology and limnology 0.688
environmental and ecological statistics 0.688
journal of water sanitation and hygiene for development 0.688
journal of water reuse and desalination 0.686
applied ecology and environmental research 0.681
african journal of aquatic science 0.670
ecoscience 0.668
global nest journal 0.665
international journal of global warming 0.660
journal of elementology 0.641
polish journal of ecology 0.639
american midland naturalist 0.636
polish polar research 0.636
journal of environmental engineering and landscape management 0.635
journal of fish and wildlife management 0.633
revista mexicana de biodiversidad 0.596
water science and technology 0.573
water science and technology-water supply 0.573
northwest science 0.548
animal biodiversity and conservation 0.532
ekoloji 0.516
grundwasser 0.514
hydrologie und wasserbewirtschaftung 0.481
conservation genetics resources 0.470
water quality research journal of canada 0.444
northeastern naturalist 0.431
russian journal of ecology 0.430
natural resource modeling 0.426
fresenius environmental bulletin 0.425
african natural history 0.400
water resources 0.388
southeastern naturalist 0.369
journal of integrative environmental sciences 0.366
revista de biologia marina y oceanografia 0.366
vie et milieu-life and environment 0.343
eco mont-journal on protected mountain areas research 0.333
houille blanche-revue internationale de l eau 0.326
journal of environmental science and management 0.323
international journal of environment and pollution 0.320
western north american naturalist 0.311
contemporary problems of ecology 0.306
biology and environment-proceedings of the royal irish academy 0.302
proceedings of the linnean society of new south wales 0.250
inland water biology 0.241
engenharia sanitaria e ambiental 0.222
interciencia 0.221
southwestern naturalist 0.219
caribbean journal of science 0.200
revista internacional de contaminacion ambiental 0.190
revue d ecologie-la terre et la vie 0.136
wasserwirtschaft 0.135
archives of natural history 0.108
natural history 0.051

 

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热带森林生态系统光合作用的最适温度

Jun/20/2017

关注并发现温度(Temperature, T)对于植物生长发育的三基点特性(Cardinal temperature),距今已逾百年。生物物种多样,其基点温度上的差异很大,甚至同种的不同个体也迥然相异,所以基点温度的普适性认知还没有形成。

植物的光合作用(Photosynthesis, A)有明显的基点温度特征。光合作用仅在温度高于某一水平下方才进行,并且随着温度的升高,光合作用不断增强,直到某个特定温度水平,光合作用达到最大值,其后温度的进一步上升将导致光合作用下降。也就是说,∂A/∂T是一个单峰函数,∂A/∂T=0时对应的温度即为最适温度(Optimal temperature, Topt)。

热带森林的基点温度,特别是Topt,目前了解的还很少,却又非常重要。结构复杂、物种丰富、生物量巨大的热带森林,其Topt是否已经超过了环境温度?一旦超过,任何的进一步温暖化将减缓光合作用,降低碳素的蓄积,不利于缓解气候变化。

利用实测数据量化了7个热带森林生态系统的Topt,探讨了Topt和环境温度之间的关系。一般地,环境温度越高的生态系统,Topt也较高,呈现出空间上的温度驯化(Temperature acclimation)。为了深入探究生化因子(Vcmax、Jmax)、呼吸作用以及气孔过程在Topt温度驯化形成过程中的作用和贡献,使用模型参数反演的方法,追本溯源,发现气孔过程是其中最主要的控制因素。当环境CO2浓度的上升,叶片同化单位量碳素所需求的气孔导度降低,这种效应可以缓解温暖化对热带森林光合作用的影响。来看,全球变化(包含温暖化和CO2浓度上升)对热带森林的影响,并没有预想的那么严酷。这个观点,不论在模型模拟(Lloyd and Farquhar 2008)还是叶片尺度的实测数据(Slot et al. 2017)方面都获得了支持。

详细内容见:Optimum air temperature for tropical forest photosynthesis: mechanisms involved and implications for climate warming

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一种计算森林净初级生产力的新方法探讨

Jun/20/2017

生态系统净初级生产力(Net primary production, NPP)的测定难度很大,高大复杂的森林生态系统尤为明显。国际生物圈计划(International Biosphere Program, IBP)期间所提出的一种自下而上(Bottom-Up)的方法,是目前NPP计测的一种主要方法。该方法原理如下,

NPP = Mi+1 – Mi + N0

其中,Mi和Mi+1分别指i和i+1时刻的生物量,N0指i至i+1期间损失的生物量,比如物质凋落分解损失、虫食损失等。该方法可以进一步细化如下,

NPP = NPPwoody + NPPcanopy + NPPfineroot + NPPh + ε

其中NPPwoody、NPPcanopy、NPPfineroot、NPPh 分别指木质、冠层、细根和虫食净初级生产力,ε为残差项。

在具体的应用中,使用上式来计算森林的NPP存在明显的局限性(Clark et al. 2001),可归纳为:

(1)NPPwoody常用两次测定间隔之间的生物量差来计算,这部分差值很小,体现在林木的生长变化上非常微弱。并且,这个微弱的变化还容易受到其他因素的干扰,比如树干储水的变化。

(2)难以具体测定每一个项目,比如根系分泌物、凋落物在到达收集框之前的损失,叶虫食量等。

(3)几乎无法得到高时间分辨率的NPP变化,比如每天的变化。

(4)难以实现自动监测,人力资源耗费高。

为了克服传统方法的局限,同时作为一种互补的、独立的方法,遂提出了一种自顶而下(Top-Down)的NPP测算方法。根据定义,NPP还可表示为,

NPP = GPP – Ra

其中,GPP为总初级生产力,Ra为森林自养呼吸量。使用定义来计算NPP,在过去的很长一段时间内,不具备可行性。GPP和Ra这两个量都不容易获得,基于这二者而得到NPP自然难以实现。随着科技的进步,GPP可以通过基于涡度相关法的NEE拆分而得,并且成功的用于全球尺度的GPP估算(Beer et al. 2010)。相反,Ra的测定始终是一个难点,特别是如何将局部器官的呼吸量,尺度扩展到整个森林生态系统。

代谢生态学(Metabolic theory ecology)是近年来尺度扩展领域的一个热点。该理论认为特定温度下的生物代谢的速率只依赖于生物的大小(Size),并且二者呈幂函数关系(Brown et al. 2004)。而呼吸作用本身就是生物的一种代谢形式,是否意味着只要知道生物大小的参数,便可以进行生物自养呼吸代谢的预测呢?Mori et al. (2010)做了一个非常了不起的尝试,他们南到东南亚赤道,北至西伯利亚,选取了不同生境和森林类型中自然生长的林木合计271株,在野外进行原位整株林木的呼吸作用测定,发现林木的生物量与呼吸代谢速率之间有非常强的相关性(r=0.99),并且符合代谢理论中关于幂函数的预测。这个工作,为我们求算Ra提供了一个极好的选择。

在此基础上,我们提出了一种新的估算NPP的方法。这种方法的工作原理基本流程图如下。将这种新方法应用到了六个不同的森林中,发现新方法和传统的IBP方法之间的结果吻合度很高,没有统计学上的差异,并且新方法可以提供高时间分辨率的NPP数据。此外,我们还进行了敏感性分析,深入探讨了方法的不确定性。这种方法,经过进一步的完善和补充,将会是森林生态系统NPP测算的一个有力补充。

工作原理基本流程图

原文链接:Quantifying forest net primary production: combining eddy flux, inventory and metabolic theory

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