Ecological network analysis: forgotten?

A new [preprint article](http://dx.doi.org/10.1016/j.ecolmodel.2009.07.012) pop up in *Ecological Modelling*'s RSS feed today, showing a case study using ecological network analysis in the functional assessment of an estuary ecosystem. I was wondering what is ecological network analysis, and how it assesses a system's function, so I read on.

It turns out that the technical details of ecological network analysis involves food web and information theory. The former I have some understanding, but the latter is too complex for me as a newcomer to dwell in the late night. [Here](http://www.fisheries.ubc.ca/files/ECOPATH%20IISoftwareForEcosystemModels%20_SmallerFileSize.pdf) is the paper describing the ECOPATH II model used by the preprint article. Judging from its number of being cited, many people must have used it successfully in their studies. However, the authors of the model acknowledged that it is based on a steady-state assumption, which arguably hardly exist in any real ecosystem, thus they recommend it used only in snapshot descriptions of ecosystems.

I doubt such a model can be used to describe ecosystem functions, considering that ecosystem functions do not present themselves in full in a "snapshot". The authors of the preprint article seem confident that this method at least identify ecosystem functions based on the goal of management defined by researchers and decision makers. But I think the role of artifacts and stochasticity in this is too significant to let pass.

In preliminary studies, I think this method has its use. If researchers can establish the food web structure and nutrient dynamics in a system, we may use this method to identify some key species or functions of the system. However, its results must be iteratively put back to our picture of the system, to check whether it conforms the dynamics and management goals. The method seems to work only with "pure" ecosystems, while many researchers have moved on to study social-ecological complex systems. I wonder if this is the reason why the method has been silent for all these years.

Christian, R., Brinson, M., Dame, J., Johnson, G., Peterson, C., & Baird, D. (2009). Ecological network analyses and their use for establishing reference domain in functional assessment of an estuary Ecological Modelling DOI: 10.1016/j.ecolmodel.2009.07.012

Christensen, V., & Pauly, D. (1992). ECOPATH II — a software for balancing steady-state ecosystem models and calculating network characteristics Ecological Modelling, 61 (3-4), 169-185 DOI: 10.1016/0304-3800(92)90016-8

Some like it hot ... or variable

I have the impression that someone on researchblogging.org has already used a similar title to describe the link between rising temperature and vectors of contagious diseases. But [this article](http://dx.doi.org/10.1073/pnas.0903423106) has pointed out another layer of complexity existing in the temperature-disease connection. Turns out that malaria does not necessarily need hot weather, a reasonably warm mean temperature with high diurnal temperature range (DTR) will do.

The malaria parasites will need to develop to a certain stage before it can actually infect people. And this takes time. Researchers already know that the length of the period depends on the environmental temperature, and accordingly they predict that the risk of malaria epidemics will increase, as the mean temperatures in many areas rise. It takes less time for the parasite to develop, and the carrier -- mosquitoes -- has more time to bite and infect people before it dies. If the period of development is so long that it almost equals or even exceeds the mosquito's life expectancy, very little harm is done.

The authors of the PNAS paper find that the period of development depends not only on daily mean temperature, but also on the temperature range through the day. In areas with relatively low temperature, given the same mean temperature, malaria parasites in areas with higher temperature variation in a day need significantly shorter time to develop. Similarly, high DTR in areas with high temperature may slow down the development. Thus the authors say the picture of malaria and similar epidemic in a global climate change context may be more complex than we previously think.

The immediate lesson is that we may have overestimated the additional risk in some tropical areas, and underestimated that in some temperate regions. But exactly what are these areas asks for studies at local scale.

Paaijmans, K., Read, A., & Thomas, M. (2009). Understanding the link between malaria risk and climate Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0903423106

北美蝴蝶物种多样性的统计研究

今天在学校听了来自 UC Irvine 的 [Bradford A. Hawkins 教授](http://www.faculty.uci.edu/profile.cfm?faculty_id=4562)的一个讲座。 据说Hawkins 是生物地理学和宏观生态学方面的大牛，可惜听讲前自己没有做足功课，虽然讲座是近期少见的信息量大、富启发意义的题目，却没有听得太明白。 好在回来搜论文找到了 Hawkins 等即将发表的关于同一个研究的[论文](http://dx.doi.org/10.1111/j.1365-2699.2009.02119.x)。

Hawkins 等人使用了墨西哥以北的北美地区夏季和冬季的蝴蝶物种丰度资料，将蝴蝶亚科按照分布范围分成热带和非热带两部分进行讨论。从物种丰度在纬度方向上的梯度看，热带类型的蝴蝶物种明显地表现出夏季向北迁徙或者 recolonize 的趋势；而非热带类型的蝴蝶则很少表现出有长距离的迁移。而以亚科在包括弄蝶总科 Hesperioidea 和凤蝶总科 Papilionoidea 的整个谱系树上的遗传距离（Mean Root Distance, MRD）来看，北美地区靠近热带的南部物种间的距离较短。 如果蝴蝶起源于热带的假设成立，这说明非热带物种多是适应了较寒冷气候的进化支。

根据对 8 个可能因素的回归分析，热带物种的丰度跟温度正相关，与热带地区的距离成负相关。非热带物种丰度与温度的关系更复杂一些。虽然夏季温度还是与物种丰度正相关，冬季温度较高的地区物种丰度却不一定更高。作者提出的解释是对于适应了较寒冷环境的蝴蝶物种，冬季温度有一个最适范围，高于这个范围的温度可能会扰乱休眠期的蝴蝶的生理活动，导致其数量减少甚至局部灭绝。一些对北半球气候变化造成的物种向北迁移的现象可以作为这个观点的一个注脚。

作者在文末指出形成北美蝴蝶多样性梯度的根本原因在于蝴蝶的热带起源和第三纪中期以来的长期气候变化模式。Hawkins 今天在讲座中进一步指出在欧洲、澳大利亚、智利、南非等地区也都发现了类似的梯度分布，可见他的观点具有相当强的解释力。这一研究不仅能用来解释北美现有的蝴蝶多样性梯度，也有可能被用来进一步研究蝴蝶各亚科和物种的进化和迁徙模式。这种研究方法理论上说也应该可以应用于其它起源于热带的物种，但对于蝶科的生活史、习性和物种分布的完整研究是做出这样研究的前提条件，不知道在无脊椎动物中还有哪些物种有这样完整的研究记录。

这一研究也揭示了气候变化引起的冬季温度变化将会给非热带蝴蝶物种带来的问题。从北美地区来看，热带物种可能不会仅仅因为温度上升就迁往更朝北的地区，但非热带物种聚集的地带可能会向北移动，欧洲也是如此，甚至有可能在热带和非热带物种区之间形成一个空白地带，也许会对这些地区的农业和林业产生影响。

Hawkins, B., & DeVries, P. (2009). Tropical niche conservatism and the species richness gradient of North American butterflies Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02119.x

Crowd-Sourced Science

In [an article](http://dx.doi.org/10.1016/j.tree.2009.03.017) published on TREE, J. Silvertown from the Open University, UK notes a trend that various ecological and evolution studies are engaging non-scientists in a unique way: by letting them collect and analyze data these projects are turning "lay people" into "citizen scientists".

There have been some long-standing projects (starting from early 20th century) that has managed to help scientists collect a huge set of data, most of which related to bird observation. It is pointed out that more data collection projects aided by improved field and software tools are on the horizon to help scientists better understand ecology and evolution of various systems in Europe and North America.

But it is important to note that although collecting data is an important scientific activity, merely doing so hardly qualifies one as a scientist. Arguably, the real meaning of "citizen science" can only be recognized when non-professional people actually take part in proposing hypotheses and analysis of data. The [Evolution MegaLab](http://www.evolutionmegalab.org/) project seems promising enough in this aspect.

The author also mentioned the potential of mobile devices as an instrument for collecting data and as a field guide. The camera and GPS functions of many of today's cellphone, for instance, should be extremely helpful if citizen scientists want to collect species distribution data.

Unfortunately the author did not mention any such project in other parts of the world, nor can I find any in short time. Given the history and experience of some of the citizen science projects, many countries in Asia, to say the least, should now have the capability to establish an environmental/ecological data collecting network. It will both benefit the professional scientists' studies and the science education of thousands of people.

Silvertown, J. (2009). A new dawn for citizen science Trends in Ecology & Evolution DOI: 10.1016/j.tree.2009.03.017

Are mustangs merely horses?

Image via Wikipedia

I just finished this month's issue of National Geographic Magazine and find, among other interesting or informative articles, a [story](http://ngm.nationalgeographic.com/2009/02/wild-horses/fuller-text/1) about mustangs in America's Old West especially thought-provoking. The article mourns about the shrinking habitat for mustangs ("wild horses" or feral horses) and possible loss of a valuable animal (I would reserve in saying it unique) and the spirit behind it.

The preservation of mustangs in my opinion has a larger symbolic purpose rather than a biological or ecological one. As pointed out in the NG article, the mustangs may very likely be the descendant of horses brought by Spanish *conquista* c. 1519. Genetically they may have little or none difference from the original Iberian species or other domestic species produced in the U.S. later. Preserve mustangs therefore is saving meme instead of saving gene, which is rare practice in animal conservation. Considering the huge investment in the conservation of mustangs, I think I have the right to ask as a by-stander: why don't the U.S. put the money to some better conservation use?

The difficulty in conservation lies in mustang's impressive ability to reproduce and extremely limited "wild" habitats nowadays. The authorization did what they can to control the total number of mustangs in the wild so as to make sure they do not graze the grassland into deserts and themselves to death. But this is criticized by people for reducing viability of the wild population. Some other people say that the population should be taken care of by Nature, to live the way they are supposed to be. However, such romantic imagination of Nature may not work in reality, as the habitat is so small and fragmented. All these creates a typical dilemma if you insist that mustangs are indeed a distinctive species that needs protection. Defeatist as it may sound like, I think feral horses should be left by themselves like feral dogs, and [euthanized](http://abcnews.go.com/Technology/AmazingAnimals/wireStory?id=6261967) in a controlled manner if necessary.

Image via Wikipedia

All this talk because mustangs are not genetically distinctive to be called as a species. On the other hand, it may sound tyrannical, even unethical, to judge an animal's conservation value merely by their genes. As a population, mustangs do have their culture values that cannot be replaced by purely domestic horses, despite their identical genes. This is just like the value of most human populations is not their genetic uniqueness, but their culture. But to extend the analogy a bit further, we can easily find that the unsuccessful strategy used to conserve mustangs is deemed to be a failure just like such a strategy used to protect a culture. You cannot protect a human population by taking samples from them regularly and put them in a so-called reserved area. The only way for a mustang or human population to be viable is to guarantee them the way of life they are used to and deserve. Different from protecting a human population, it is ethical and necessary to cull existing mustang population and re-introduce their predators into the wildness of the west. As it was mankind who broke the coyote/wolf-horse equilibrium out of balance, now mankind also have the duty to re-introduce the equilibrium, or at least create a human-horse equilibrium, i.e. artificially control mustang population. Failing to do that, all efforts to preserve mustang population and culture would be self-defeating.

To make the equilibrium happen, and to serve other many important ends, it is of paramount importance to conserve a valid wildness. It may not be free from human interference, but should be able to support a viable wild horse population and the ecosystem they are in. Indeed, the need to preserve mustang culture can be itself an emotionally powerful driver for advocating conservation of habitats. But if local stakeholders finds the idea of saving mustangs not so appealing, maybe the authorization can a) find another proxy wildlife to achieve the same goal, or b) persuade local people to accept mustangs as a healthy symbol and a worthy backup gene bank that can be used to strengthen their own livestock. Option (b) seems to be an easier way, and the NG article no doubt does it good.

Now I can't help thinking, if we Chinese linked Chinese sturgeon *Acipenser sinensis* with something more meaningful rather than saying in our dictionaries that it is edible, perhaps Yangtze River as an important habitat would be better protected.

Co-op says No to bee-killing pesticides

Guardian Environment [reports](http://www.guardian.co.uk/environment/2009/jan/28/bees-coop-pesticide): One of the big UK supermarket chains, [Co-op](http://www.co-operative.coop/), has announced in its 10-point [Plan Bee](http://www.co-operative.coop/ethicsinaction/takeaction/planbee/what-The-Co-operative-is-doing-for-bees/) that it will ban the use of 8 neonicotinoid-based pesticides on own-brand fresh products. The pesticides banned are: Acetamiprid (啶虫脒), Clothianidin (噻虫胺或可尼丁), Dinotefuran (呋虫胺或丁诺特呋喃), Fipronil (氟虫腈), Imidacloprid (吡虫啉), Nitenpyram (烯啶虫胺), Thiacloprid (噻虫啉) and Thiamethoxam (噻虫嗪或阿克泰).

It is worthy pointing out that neonicotinoid-based pesticides are considered an ideal replacement of high-toxicity pesticides and are widely used in China and many developing countries, although its harm to beehives have been noticed in China as well. It is not clear now what measures China has taken to prevent or mitigate the impact of these pesticides on its bee populations.

Sustainable energy project cause worries

Image via Wikipedia

A project aiming at utilising tidal power has caused various environmental groups to [express their worries](http://www.guardian.co.uk/environment/2009/jan/26/severn-barrage-tidal) that one of the shortlisted proposal may cause significant environment damage.

The proposal of question involves building a 10-mile barrage at [Severn Estuary](http://en.wikipedia.org/wiki/Severn_Estuary). It is a worry shared by many environmentalists that such a project may ``add to local flooding, reduce fish stocks, damage bird life and destroy the Severn bore, as well as ruin mudflats across an area of more than 77 square miles''. The environmental groups prefers a new technology called tidal lagoon, whose benefit is still not verified, and is believed to be more expensive and generate less energy. Two lagoon proposals made the shortlist.

Despite voices against the barrage proposal, it is believed that the 8 giga-watt project accounting for 5% of UK's electricity need is quite attractive to the decision makers and may well be carried out. The issue is further complicated by accusations that the cost of lagoon solutions was overestimated in the assessment.

Documents about the feasibility studies of the project can be found at the [project's government website](http://severntidalpowerconsultation.decc.gov.uk/). Today also marks the beginning of the first public consultation on the project. You can ``have your say'' after register on the website.

大尺度气候指标的适用性

在动植物生态研究中，人们常常用到气候指标来构建生态系统对气候变化响应的模型，并且假设这些气候指标对不同地区的动植物生态具有普遍适用性。但发表在 Global Change Biology 上的[一篇文章](http://dx.doi.org/10.1111/j.1365-2486.2008.01778.x)通过对不同地区的雌鹿体重的比较，发现在一个地区能解释大部分变化的气候指标在另一个地区就成了微不足道的变量。气候因素起什么样的作用，还取决于当地的植被类型和土壤等因素。文章作者们由此推断说，此前的许多研究中，将基于一个地区的观察或实验结果的理论推广到在其它地区的同类型生态系统而得出的结论可能是不可靠的。为了对气候变化在一个地区的影响进行完整的评估，需要弄清气候对生态系统作用的路径，也需要有更完整的当地气候数据。

MARTÍNEZ-JAUREGUI, M., SAN MIGUEL-AYANZ, A., MYSTERUD, A., RODRÍGUEZ-VIGAL, C., CLUTTON-BROCK, T., LANGVATN, R., & COULSON, T. (2009). Are local weather, NDVI and NAO consistent determinants of red deer weight across three contrasting European countries? Global Change Biology, 15 (7), 1727-1738 DOI: 10.1111/j.1365-2486.2008.01778.x

是否应该“为了多样性而多样性”

BBC 在今天的 Green Room 专栏中谈到了[农作物改良导致品种减少](http://news.bbc.co.uk/go/rss/-/1/hi/sci/tech/7753267.stm)的问题。由于不断增长的粮食压力，以及种植改良品种带来的经济利益，许多作物品种正在消失。作者 Jeff Bentley 的主要观点是，面对气候变化，我们需要保留作物的多样性，或许那些耐热、耐旱的作物品种是人类适应这种变化的关键。

在同一个页面上，BBC 也列出了一些读者的评论，其中一条反对意见非常有趣：

> This seems like an overblown issue. For one, if some of these crop varieties, such as O. glaberrima, are superior for a certain climate, would they not naturally outlast their alternatives in such regions anyway? It won't be mankind's cultivation that continues their existence. Furthermore, mankind has been genetically engineering crop species through artificial selection since agriculture has existed? If there is a lack of diversity, it is because mankind has settled on a very productive variety of crop, that makes the others simply not worth cultivating. I was expecting a far more compelling argument for crop diversity, like natural resistance to certain diseases (banana blight, etc.), not just diversity for diversity sake.
> _Chris C, Salt Lake City, USA_

Image via Wikipedia

这里有一个假设，就是对某种气候适应较好的物种必然会全面地淘汰那些并非为这种气候而进化或人工选择的物种。如果这个假设成立的话，物种入侵也就不会是一个如此紧迫的问题了。农业生产中原生的亚种被取代，并不是因为它们对环境的适应性比引进的亚种差（事实可能恰恰相反），而是因为它们带来的经济回报没有引进种高。而对于任何系统，过度的同质化必然带来适应能力的降低。今天大片种植同一品种的田地没有问题，并不代表将来在改变的环境条件下它们仍然没有问题。而如果原生亚种和引进亚种都不能适应变化的环境，我们最好还保留有来自其它地区的物种或亚种，能够起到替代的作用。在这个问题上任由市场做出选择，不是促进竞争和发展的方法，而是会导致农业走向垄断和衰落。从这个意义上说，为了多样性而保护多样性是必要的，我们永远不能预知，也许今天某个被遗忘的亚种，明天就是人类的救星。

幸运的是，商业动机也可以成为保护这些亚种的动力。有些马铃薯亚种已经堂而皇之地在超市里包装上市了。但是更多的作物没有这么幸运，还需要人们在它们彻底消失以前发现它们的价值。

(照片来自 Wikipedia, 由 [Gerry Manacsa](http://en.wikipedia.org/wiki/User:Gmanacsa) 拍摄，按创作共用 [Attribution-Share Alike 2.0](http://creativecommons.org/licenses/by-sa/2.0/) 许可发布。Photo by [Gerry Manacsa](http://en.wikipedia.org/wiki/User:Gmanacsa), under the CC license [by-sa 2.0](http://creativecommons.org/licenses/by-sa/2.0/))

Prioritising conservation objectives

An article in press in a recent issue of TREE proposed that triage approach should be explicitly employed in decision-making about the allocation of limited resources in conservation efforts.

Prioritising conservation objectives, in my opinion, is really not new.  All decision makers have to balance limited funding and other resources among a few (sometimes contradicting) conservation goals.  However, the author of the article argues, triage has been regarded as defeatism thinking and may lead to abandoning conservation efforts that is meaningful and has a high probability of success.  Due to the unpopular image of triage, decision makers often have to avoid mentioning triage in conservation planning explicitly.  Doing so leads to irrational policies and decisions hijacked by evaluations other than those that based on ecological and economical principles.

The author proposes that the triage process should be mentioned explicitly in planning and follow certain rules in consideration so as to achieve rational triage and optimised outcome.  The four principles should be considered are: values, biodiversity benefit, probability of success, and cost.  The latter two are not difficult to understand.  However the evaluation of values and biodiversity benefit may involve some complexities and very lively debate.

The objective function that the author proposed is the product of the first three factors divided by cost.  The resources are allocated to project that yields highest outcome in this equation.  Such an approach is straightforward.  Nevertheless, the questions that how to estimate the value of a particular species or ecosystem and how they affect local and global biodiversity have no definitive answers.  Theories such as the driver-passenger analogy may help but cannot address all the complexities in ecosystems.  Species-by-species conservation may overlook species and ecological functions that deemed not important or economically worthy of conserving.  Even the loss of a few seeming unimportant species with overlapping ecological functions in the long run may cause sudden collapse of the system by decreasing system resilience.

Thus it is necessary to examine the value of species and their biodiversity benefits from multiple perspectives.  The real benefit of making triage decision-making explicit, in my opinion, is to allow multiple stakeholder groups as well as researchers with different conservation goals to evaluate the conservation options and achieve more informed decisions.  The positive role triage approach plays therefore depends on how open and constructive the decision-making process is.

生态/环境研究的新挑战

Holling (1973)[1. Holling, C. S. Resilience and stability of ecological systems. Annual Review of Ecology and Systematics, 4:1–23, 1973.] 这样定义生态系统的 resilience：系统在发生重构和功能变化之前能够接受的最大扰动。而 Pimm (1984)[2. Pimm, S. L. The complexity and stability of ecosystems. Nature, 307:321–326, 1984. ] 在十年之后才提出 resilience 的另一个定义：系统受到扰动后回到初始状态所需的时间。虽然 Pimm 的定义提出较晚，但却得到了广泛得多的应用。而对于 Holling 的定义，虽然研究者往往会提及，却很少有人将其应用到实际研究中，以致到现在这个概念的研究者和实践者似乎已经成了一个不为人注意的学派。为什么 Holling 的想法应者如此寥寥？

Resilience and the Behavior of Large-Scale Systems（以下 RBLSS）这本书可以看作是这个久被忽视的学派争取学界注意的又一次努力，书中文章的主要作者包括 L. H. Gunderson，C. S. Holling，G. D. Peterson，B. H. Walker，S. R. Carpenter 和 D. Ludwig 等人，事实上他们就是仅有的几位我们通过一般的期刊搜索能比较容易地找到的，主张利用 Holling 的 resilience 定义研究社会-生态复合系统的学者。在书中他们重申了自己的想法，即 Pimm 的 resilience 的前提是不成立的，复杂系统并没有一个唯一、恒定、稳固的均衡（equilibrium）状态，相反系统可能有多个均衡状态，外力可以导致系统在这些状态间转换。在一个均衡状态附近（称为均衡域或吸引域），系统的变化是连续而接近线性的，可以用方程描述，但一旦变化超过了一定范围，系统的转变就是突然、非线性的。定义或者评价一个系统的 resilience，就是要找出均衡域的范围和其它可能的均衡状态。

这样的说法比较抽象，所以 Holling 的追随者们使用盆中的小球这个概念来说明：小球相当于系统，放在一个盆（均衡域）当中，盆的宽度就是 resilience 的强弱程度，而小球一旦越出盆沿，就会落入另一个盆，即一个性质、结构、功能都可能完全不同的系统状态。在数学上，他们则利用二分点这个概念来说明系统是如何离开均衡域的：类似我们熟悉的量变引起质变的思想，系统某些变量的取值会使类似下面方程的性质在这个取值附近发生巨大的改变：

$$\frac{dx}{dt} = -x(x^{2} - \alpha)$$

这类变量称为系统中的“慢变量”，变化往往较慢，却对系统的性质和功能有根本性的影响。到这里我们已经可以看到 Holling 的定义固然比 Pimm 的定义更能把握生态系统的非均衡本质，同时也避免了过度的还原论思想，但其实践比起 Pimm 的仅仅通过经验性的观察就可以测量的方法要困难许多，要求研究者对于系统的全面性质和各种内外影响因素都有较全面的了解，这在大的生态和社会经济系统中是难以做到的，难怪许多人望而却步。

也许正是因为这一点，RBLSS 这本脱胎于 workshop 的书将重点放在对大型系统的具体案例研究上。其研究的系统包括了主要的陆地生态系统如森林、湿地和草原，以及水生生态系统如湖泊和珊瑚礁群，研究方法也是多种多样，包括情境分析，数学建模，实地观测和地理信息科学等等。这些案例确实体现了 resilience 这个概念的普适性，但也暴露了它的一个重大不足，就是对于不同的生态系统缺乏一个一致的方法体系。即使在同类的生态系统中，由于物种和扰动因素的不同，研究者也往往不能套用书中给出的分析结果，而要自己从概念模型开始分析。在整个体系中缺乏“可重用”的部分，无疑也限制了这一概念像环境影响评价那样成为工业和学界中通行的做法。

当然，仅从框架来说，这本书也提供了一个可供套用的模式，包括概念模型的建立，跨比例过程和慢变量的识别等等，可供有意利用这个概念进行研究的人参考。但我认为这本书更大的意义在于指出了一条有可能让生态学研究从目前的还原主义研究方法飞跃到真正综合性的，把“人”这一因素纳入研究范围的研究的途径，向传统的研究方法提出了挑战。同时，相对于基于 Pimm 概念的，以某一特定状态为目标、要求保持和固守的环境管理，Holling 的 resilience 概念使得他能够提出新的生态/环境管理思想，即适应性的管理，承认生态和社会系统的变化和非均衡性，这比 resilience 这个概念本身有更大的实践意义，已经在一些具体的环境管理方案中得到应用。在 resilience 的评估当中，又要求研究者对现有的生态模型进行检验，并研究和归纳具体生态系统当中的各种主体和相互作用，这在一定程度上也促进了传统生态学理论和方法论的发展。从这个意义上说，这本书和 resilience 概念本身，对于生态和环境科学的研究者来说具有超越直接价值的意义。

Emergence, or merely a mistake?

When I conduct DFA on my NDVI data, I found some interesting behaviour of the result.  Apparently the system behaves differently in different spatial scales, which is reflected in the fluctuation-temporal scale correlation and the slope of $$\text{log}F(L)/\text{log}L$$ (i.e. $$\alpha$$).

The DFA result for the whole map is like the picture below, $$\alpha$$ is between 0.5 and 1, indicating a correlation between fluctuation and time.  But the pixel results are seemingly random (this is expected), and all have $$\alpha << 0.5$$ (this is quite unexpected), indicating anti-correlations.

After examined the scripts and data in question I believe the design of the experiment has no fault that I could find.  I have also considered the possibility that nonstationarity and trend may have effects on the result, but the NDVI data I used have already had seasonal trend eliminated, while nonstationarity is not likely to cause such dramatic change in $$\alpha$$.  The result, if not a technical failure, will suggest that the system's behaviour at 8km (single pixel) and regional scales are different.  At the fine-grained scale, the fluctuation reduces as temporal scale increases, i.e. a fluctuation is likely to cause smaller and smaller fluctuations in the distant future.  But at coarser scale the behaviour is inversed, a fluctuation may cause larger and larger fluctuations at long intervals.

It is possible that the system's behaviour at coarser scales is the result of relatively simpler interactions at finer scales, creating a phenomenon known as emergence.  But the question is, if it is really emergence, what is the critical scale that such behaviour shift takes place.  Besides, what I have now is at best correlation, are there any intrinsic mechanism that determine such emergence?  In ecology, has there been similar emergence taking place in the shift from community to biome scale?

The system I'm studying is a pastoral socio-ecosystem.  If there is really emergence like this, does it suggest that the system at the farm scale is resilient but as a whole is not [1. There are some resilience researchers noted the problem of emergence, such as

Allen, C.R., Gunderson, L. & Johnson, A.R., 2005. The Use of Discontinuities and Functional Groups to Assess Relative Resilience in Complex Systems. Ecosystems, 8(8), 958-966. and

Folke, C., 2006. Resilience: The emergence of a perspective for social-ecological systems analyses. Global Environmental Change, 16(3), 253-267.]?  This is a really intriguing question.  I just hope it is not raised from a false observation.

Find underlying fluctuation using DFA

We often have to deal with NDVI time series like this.  What does it tell on earth?  Very little information can be identified from this figure and its subsets.  However, techniques like DFA allow us to dig some information on the fluctuation and its cause.

Detrended Fluctuation Analysis (DFA) was first used in DNA analysis to identify whether the purine and pyrimidine base's distubution is scalable, or fractal.  Later it has been used by many to examine whether a bounded time series has fractal characteristics and is self-similar.  First of all the time series has to be converted to a random walk series using equation:

$$X_{t} = \sum_{i=1}^{t}(x_{i}-\langle x_{i} \rangle)$$

Where $$\langle x_{i} \rangle$$ is a value within the range of the time series, or a variable that changes with the element in the time series according to certain rule.  This is the "detrending" step.  Once the series has been converted, one can split the whole series into a number of non-overlapping "windows", each with a equal number of samples or length $$n$$.

Least Square fit is done to each of the windows to get the local trend.  The root-mean-squared deviation from the trend is called fluctuation:

$$F(L) = \[\frac{1}{L}\sum_{i=1}^{L}(X_{i} - ai -b)^{2}\]^{\frac{1}{2}}$$

For different window size $$L$$ we can obtain different $$F(L)$$.  On a log$$F(L)$$ vs. log$$L$$ plot, we have a straight line whose slope is $$\alpha$$ if the random walk has self-affinity.  The values of $$\alpha$$ have different meanings.  $$\frac{1}{2} < \alpha < 1$$ indicates that the fluctuation is correlated with time; while $$\alpha$$ close to 0.5 indicates white noise [1. Detrended fluctuation analysis. (2007, October 31). In Wikipedia, The Free Encyclopedia. Retrieved 13:15, August 1, 2008, from http://en.wikipedia.org/w/index.php?title=Detrended_fluctuation_analysis&oldid=168313780].

This technique is further used to identify whether there is identifiable trend in the variation of NDVI throughout years.  Telesca et al. (2005)[2. Luciano Telesca, Rosa Lasaponara, Antonio Lanorte, 1/f* fluctuations in the time dynamics of Mediterranean forest ecosystems by using normalized difference vegetation index satellite data, Physica A: Statistical Mechanics and its Applications, Volume 361, Issue 2, 1 March 2006, Pages 699-706.] has utilised the technique and identified positive feedbacks and reduced adaptability in Italian forest ecosystem.  Note that NDVI has natural periodic fluctuation due to seasonality, before DFA is applied, one should first reduce this fluctuation from the data.

This technique may also be applied in my study as I am also looking at NDVI trends.  Some spatial analysis may be added by using the technique on single pixels and/or "windows".

Evil Genius, Mad Scientist 和 Iron Man 的科学解释

唔，我不是要讨论为什么钢铁侠可以做6个G的战术机动而没有把腰椎折断或者完全无视动量定律从数千米高空硬着陆还没有把眼珠子摔出来这种无解的问题，而是：为什么 Tony Stark 在被绑架，被囚禁，坠“机”若干次以后仍然是个天才没有变傻。对这个问题的解释相信也会对理解为什么电影里充满了邪恶天才和疯狂科学家这两种典型人物有所帮助。

根据 Wired 杂志和 Smith et al. (2008) [1. Smith, P.K., Jostmann, N.B., Galinsky, A.D., van Dijk, W.W. (2008). Lacking Power Impairs Executive Functions. Psychological Science, 19(5), 441-447. DOI:10.1111/j.1467-9280.2008.02107.x] 的理论，原因有二：其一，TS 很少体验害怕和压力；其二，他没有什么人好怕。

这个月 Wired 杂志的封面故事是“Get Smarter”，其中提到人的杏仁体（Amygdala）作为情绪中枢在压力和恐惧状态下不仅影响我们的行动，控制肾上腺素等激素的分泌，而且作为恐惧反应的一部分在紧急情况下其作用强于主管记忆和认知功能的前额皮质（prefrontal cortex），导致有关的功能——IQ，创造力和记忆力都有所下降，而且这种状况在抑郁或其他原因引起的压力状态下也会发生。作为逃生本能，杏仁体的这种作用是有用的，但是对于生活中充满压力的现代人，杏仁体的这种行为也可能起到了不时把我们的智商拉回到穴居人水平的作用。

另一方面，有 blog 引用 Smith et al. 的研究，指出在群体中权力（Power）和权威的分布影响了群体成员的思维能力，感到缺乏权力的成员的认知功能遭到抑制，相反，拥有较多权力的成员这样的能力得到加强。同时，缺乏决定行动方向的权力的成员倾向于将更多的精力用于观察决策者的行动和猜测其目的并按决策者的指示行动，从而造成了思维能力的浪费（blog 作者还提了一句 Monkeys show similar behaviour.）。这构成一个正反馈的循环，使得群体中的权力结构趋向稳定。这也许可以解释为什么许多没有明显层级关系的群体里——不管是紧密结合的像业主委员会或者松散结合的像群体 blog 这样的——总有主导性的声音提出很有见地的意见。喂你们也别太得意，说不定你们只是抑制了别人的天才而已啦！

这两个导致认知和思维能力下降的原因结合起来看，在我这个门外汉看来还是很有心理学和社会学意义的。我们早已知道 focus group 这样的团体中如果控制不当会出现个别人主宰整个发言的情形，现在看来这并不只是他们能说会道占据了其他人的发言时间而已，可能只是某种先发优势（不一定是智力上的，可能只是对话题或者对其他成员的熟悉程度这样的原因）被他们掌握。这种情况下讨论组的协调员为了获得其他人的见解，光是提“XX，你对这个问题怎么看？”这样的问题是不够的，或者说仅仅给人发言的时间是不够的，还要通过适当的引导把类似的优势暂时赋予被压制的成员才行。这个理论如果被政策制定者接受，对于社会层级和教育公平的政策应该也会有影响。

开始说疯话的分割线~

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而对于我个人的心理，这两个发现也很有意义（所以你们才能在我 blog 上看到这篇 entry，哈哈哈哈）。作为一个杏仁体可能有点过度发达的人，在一到两个月之前我曾经被某个在我的群体里很有威慑力的猪头（不是贬义，大家就是这么叫ta的）莫名其妙发火骂傻过，而且一直傻到几天前（认知能力开始恢复正常以对阅读和写 blog 的兴趣开始恢复为标志）。我现在明白了为什么守序善良的 paladin 往往都是废柴，性格中有些 chaotic 的成分比较能促进思考。而 Sith 之所以单挑时往往强过 Jedi 也是因为他们不用考虑政治正确（Dark Side 的诱惑很强大啊，桀桀桀），不过 Jedi 的训诫也有可取的地方：

There is no emotion; there is peace.

There is no ignorance; there is knowledge.

There is no passion; there is serenity.

There is no death; there is the Force.

适当抑制我们的杏仁体可以促进认知能力（当然适当的紧张也是有好处的）。作为一个先天这方面不足（过剩？）的人，我决心向所有的疯狂科学家学习，不再为了诸如我尊敬的某猪头的评价或者女朋友的反应而担心害怕生气忧伤饮食难安彻夜不眠，以 mind 之强大弥补 heart 之不足，并在适当的时候向 evil genius 的方向迈进。当然，如果不小心成了个邪恶的蠢货，还是被一箭射死算了。

Effects directly attributed to climate change

Attributing physical and biological impacts to anthropogenic climate change

This is the first time observed changes in physical and biological characters of natural systems are explicitly linked to anthropogenic climate change.  The method used seems to be data mining and statistics.

An evolution paradox

Fittest Males Don't Always Get the Girl

Here's an article from ScienceDaily discussing about a (seems simple) question: if males who are more aggressive and can win more fights and have more offspring, why human and many animals are not selected extremely aggressive nowadays?

The answer given in the article is that aggressiveness is not always the best strategy under all circumstances. Or rather, there is no "best" strategy. Yet the author noted that the female may not always choose the strongest male. Is the need for diversity "hard-wired"? Or is the female choice simply based on the availability and scarcity of males? In other words, does the diversity of environment drives species to diversify their possible strategies, or females mate with not-so-competent males just because they have no chance to get better ones?

Another explanation that I can offer to the lack of extremely aggressive behaviour in today's gene pool is that more aggressive individuals tend to have more fights and higher mortality in their most productive age. This of course is compatible with the two hypotheses above. This is an interesting question anyway.

Loss of water system resilience

ScienceDaily has a story on possible "ecosystem flipping" in water systems. Traditionally water management focused on "blue water", which includes water bodies that are easy to perceive, such as rivers and lakes. It is argued that water managers have long ignored "green water", whose cycles are not readily observable yet are essential for the function of ecosystems. It is pointed out that

Modern agriculture and land-use practices may lead to major disruptions of the world's water flows, with potentially sudden and dire consequences for regions least able to cope with them[...]

Soil nutrient as a slow variable is being changed due to agriculture practices, and that may cause a sudden ecosystem flip when it reaches a threshold. Yet it is difficult to tell where the threshold is. The original article claims that the most vulnerable area may be poor dryland areas. Using the "ball in the bowl" analogy, one can say that the domain of attraction for the current system is small and shallow. Modern agriculture may have contributed to the situation. But would it be better if the old way of planting crops remains? Would it jeopardise other aspects of the system? The adoption of modern agriculture can be seen as a necessary step to take when the system transits from r to K phase in the adaptive cycle. The task now is to prevent the system from collapsing in the next phase.

To build the resilience, or to build the capacity of adaptation is probably the key. Both call for more flexible mechanisms. This would be difficult for a system in K phase. Some local measures are feasible, but the change of the whole system may depend on external aid. There are other systems yet at the dawn of r phase. Is it possible to focus the accumulation of capital on resilience in order to facilitate the transition and reconstruction in the Ω phase?

By the way, it seems there are too few influential people in the resilience study circle. Buzz Holling, Garry Peterson mentioned in the article, and Brian Walker, they are about all and share almost the same opinion. Perhaps we can say the resilience researchers as a community is not resilient due to lack of diversity.

NewScientist: China's boom sparks mass species invasion

http://environment.newscientist.com/channel/earth/...-invasion.html

This problem is hardly new, I think. Although the author did mention that the rapidly increasing foreign trade ports and airports in China makes the control of imported horticulture products more difficult. Apparently, species emigration and immigration happens at the same time on both borders. This is a new challenge to biodiversity conservation, and perhaps a result of globalisation. The problem is as old as trade itself, but nowadays at a completely different scale. Impact can be limited, though, if both sides take actions.

A quick one: temperature as a slow variable

This week's Nature has a news article on Antarctic species threatened by increasing sea water temperature and invasive species utilising the new niche created by this high temperature.  In this instance sea water temperature as a slow variable is indirectly controlled by the fast variable: the carbon emission.  The system may flip to another state in which the previous ecosystem will be essentially eliminated.  In this sense the change is irreversible.

A similar effect will be observed in other systems, perhaps in a more subtle way.  The resilience theory suggests that such changes in slow variables may generate sudden changes in fast variables.  In most natural systems this will manifest itself as loss of niches, habitats and species.  As reverting a slow variable is also difficult, this can be considered as loss of these system's resilience.  To preserve current state, measures maintaining the fast variables or reverting their changes are possible, yet to preserve resilience, the slow variable must be restored.

Be fair to ugly guys/gals

This is half a month old but seems not many in the blogsphere take notice in this yet. It is common phenomenon that conservation efforts (and budgets) are mostly given to cute animals. But let's face this, the most ecologically important species are not necessarily appealing to us human.

On 31st January the Independent composed a (not complete) list of species which are at the brink of distinction and needs more attention.

Below are some illustrated descriptions of these ugly-but-need-care species. Without other specification, the photos are from Wikimedia Commons.