Econstudentlog

How Species Interact

There are multiple reasons why I have not covered Arditi and Ginzburg’s book before, but none of them are related to the quality of the book’s coverage. It’s a really nice book. However the coverage is somewhat technical and model-focused, which makes it harder to blog than other kinds of books. Also, the version of the book I read was a hardcover ‘paper book’ version, and ‘paper books’ take a lot more work for me to cover than do e-books.

I should probably get it out of the way here at the start of the post that if you’re interested in ecology, predator-prey dynamics, etc., this book is a book you would be well advised to read; or, if you don’t read the book, you should at least familiarize yourself with the ideas therein e.g. through having a look at some of Arditi & Ginzburg’s articles on these topics. I should however note that I don’t actually think skipping the book and having a look at some articles instead will necessarily be a labour-saving strategy; the book is not particularly long and it’s to the point, so although it’s not a particularly easy read their case for ratio dependence is actually somewhat easy to follow – if you take the effort – in the sense that I believe how different related ideas and observations are linked is quite likely better expounded upon in the book than they might have been in their articles. The presumably wrote the book precisely in order to provide a concise yet coherent overview.

I have had some trouble figuring out how to cover this book, and I’m still not quite sure what might be/have been the best approach; when covering technical books I’ll often skip a lot of detail and math and try to stick to what might be termed ‘the main ideas’ when quoting from such books, but there’s a clear limit as to how many of the technical details included in a book like this it is possible to skip if you still want to actually talk about the stuff covered in the work, and this sometimes make blogging such books awkward. These authors spend a lot of effort talking about how different ecological models work and which sort of conclusions these different models may lead to in different contexts, and this kind of stuff is a very big part of the book. I’m not sure if you strictly need to have read an ecology textbook or two before you read this one in order to be able to follow the coverage, but I know that I personally derived some benefit from having read Gurney & Nisbet’s ecology text in the past and I did look up stuff in that book a few times along the way, e.g. when reminding myself what a Holling type 2 functional response is and how models with such a functional response pattern behave. ‘In theory’ I assume one might argue that you could theoretically look up all the relevant concepts along the way without any background knowledge of ecology – assuming you have a decent understanding of basic calculus/differential equations, linear algebra, equilibrium dynamics, etc. (…systems analysis? It’s hard for me to know and outline exactly which sources I’ve read in the past which helped make this book easier to read than it otherwise would have been, but suffice it to say that if you look at the page count and think that this will be an quick/easy read, it will be that only if you’ve read more than a few books on ‘related topics’, broadly defined, in the past), but I wouldn’t advise reading the book if all you know is high school math – the book will be incomprehensible to you, and you won’t make it. I ended up concluding that it would simply be too much work to try to make this post ‘easy’ to read for people who are unfamiliar with these topics and have not read the book, so although I’ve hardly gone out of my way to make the coverage hard to follow, the blog coverage that is to follow is mainly for my own benefit.

First a few relevant links, then some quotes and comments.

Lotka–Volterra equations.
Ecosystem model.
Arditi–Ginzburg equations. (Yep, these equations are named after the authors of this book).
Nicholson–Bailey model.
Functional response.
Monod equation.
Rosenzweig-MacArthur predator-prey model.
Trophic cascade.
Underestimation of mutual interference of predators.
Coupling in predator-prey dynamics: Ratio Dependence.
Michaelis–Menten kinetics.
Trophic level.
Advection–diffusion equation.
Paradox of enrichment. [Two quotes from the book: “actual systems do not behave as Rosensweig’s model predict” + “When ecologists have looked for evidence of the paradox of enrichment in natural and laboratory systems, they often find none and typically present arguments about why it was not observed”]
Predator interference emerging from trophotaxis in predator–prey systems: An individual-based approach.
Directed movement of predators and the emergence of density dependence in predator-prey models.

“Ratio-dependent predation is now covered in major textbooks as an alternative to the standard prey-dependent view […]. One of this book’s messages is that the two simple extreme theories, prey dependence and ratio dependence, are not the only alternatives: they are the ends of a spectrum. There are ecological domains in which one view works better than the other, with an intermediate view also being a possible case. […] Our years of work spent on the subject have led us to the conclusion that, although prey dependence might conceivably be obtained in laboratory settings, the common case occurring in nature lies close to the ratio-dependent end. We believe that the latter, instead of the prey-dependent end, can be viewed as the “null model of predation.” […] we propose the gradual interference model, a specific form of predator-dependent functional response that is approximately prey dependent (as in the standard theory) at low consumer abundances and approximately ratio dependent at high abundances. […] When density is low, consumers do not interfere and prey dependence works (as in the standard theory). When consumers density is sufficiently high, interference causes ratio dependence to emerge. In the intermediate densities, predator-dependent models describe partial interference.”

“Studies of food chains are on the edge of two domains of ecology: population and community ecology. The properties of food chains are determined by the nature of their basic link, the interaction of two species, a consumer and its resource, a predator and its prey.1 The study of this basic link of the chain is part of population ecology while the more complex food webs belong to community ecology. This is one of the main reasons why understanding the dynamics of predation is important for many ecologists working at different scales.”

“We have named predator-dependent the functional responses of the form g = g(N,P), where the predator density P acts (in addition to N [prey abundance, US]) as an independent variable to determine the per capita kill rate […] predator-dependent functional response models have one more parameter than the prey-dependent or the ratio-dependent models. […] The main interest that we see in these intermediate models is that the additional parameter can provide a way to quantify the position of a specific predator-prey pair of species along a spectrum with prey dependence at one end and ratio dependence at the other end:

g(N) <- g(N,P) -> g(N/P) (1.21)

In the Hassell-Varley and Arditi-Akçakaya models […] the mutual interference parameter m plays the role of a cursor along this spectrum, from m = 0 for prey dependence to m = 1 for ratio dependence. Note that this theory does not exclude that strong interference goes “beyond ratio dependence,” with m > 1.2 This is also called overcompensation. […] In this book, rather than being interested in the interference parameters per se, we use predator-dependent models to determine, either parametrically or nonparametrically, which of the ends of the spectrum (1.21) better describes predator-prey systems in general.”

“[T]he fundamental problem of the Lotka-Volterra and the Rosensweig-MacArthur dynamic models lies in the functional response and in the fact that this mathematical function is assumed not to depend on consumer density. Since this function measures the number of prey captured per consumer per unit time, it is a quantity that should be accessible to observation. This variable could be apprehended either on the fast behavioral time scale or on the slow demographic time scale. These two approaches need not necessarily reveal the same properties: […] a given species could display a prey-dependent response on the fast scale and a predator-dependent response on the slow scale. The reason is that, on a very short scale, each predator individually may “feel” virtually alone in the environment and react only to the prey that it encounters. On the long scale, the predators are more likely to be affected by the presence of conspecifics, even without direct encounters. In the demographic context of this book, it is the long time scale that is relevant. […] if predator dependence is detected on the fast scale, then it can be inferred that it must be present on the slow scale; if predator dependence is not detected on the fast scale, it cannot be inferred that it is absent on the slow scale.”

Some related thoughts. A different way to think about this – which they don’t mention in the book, but which sprang to mind to me as I was reading it – is to think about this stuff in terms of a formal predator territorial overlap model and then asking yourself this question: Assume there’s zero territorial overlap – does this fact mean that the existence of conspecifics does not matter? The answer is of course no. The sizes of the individual patches/territories may be greatly influenced by the predator density even in such a context. Also, the territorial area available to potential offspring (certainly a fitness-relevant parameter) may be greatly influenced by the number of competitors inhabiting the surrounding territories. In relation to the last part of the quote it’s easy to see that in a model with significant territorial overlap you don’t need direct behavioural interaction among predators for the overlap to be relevant; even if two bears never meet, if one of them eats a fawn the other one would have come across two days later, well, such indirect influences may be important for prey availability. Of course as prey tend to be mobile, even if predator territories are static and non-overlapping in a geographic sense, they might not be in a functional sense. Moving on…

“In [chapter 2 we] attempted to assess the presence and the intensity of interference in all functional response data sets that we could gather in the literature. Each set must be trivariate, with estimates of the prey consumed at different values of prey density and different values of predator densities. Such data sets are not very abundant because most functional response experiments present in the literature are simply bivariate, with variations of the prey density only, often with a single predator individual, ignoring the fact that predator density can have an influence. This results from the usual presentation of functional responses in textbooks, which […] focus only on the influence of prey density.
Among the data sets that we analyzed, we did not find a single one in which the predator density did not have a significant effect. This is a powerful empirical argument against prey dependence. Most systems lie somewhere on the continuum between prey dependence (m=0) and ratio dependence (m=1). However, they do not appear to be equally distributed. The empirical evidence provided in this chapter suggests that they tend to accumulate closer to the ratio-dependent end than to the prey-dependent end.”

“Equilibrium properties result from the balanced predator-prey equations and contain elements of the underlying dynamic model. For this reason, the response of equilibria to a change in model parameters can inform us about the structure of the underlying equations. To check the appropriateness of the ratio-dependent versus prey-dependent views, we consider the theoretical equilibrium consequences of the two contrasting assumptions and compare them with the evidence from nature. […] According to the standard prey-dependent theory, in reference to [an] increase in primary production, the responses of the populations strongly depend on their level and on the total number of trophic levels. The last, top level always responds proportionally to F [primary input]. The next to the last level always remains constant: it is insensitive to enrichment at the bottom because it is perfectly controled [sic] by the last level. The first, primary producer level increases if the chain length has an odd number of levels, but declines (or stays constant with a Lotka-Volterra model) in the case of an even number of levels. According to the ratio-dependent theory, all levels increase proportionally, independently of how many levels are present. The present purpose of this chapter is to show that the second alternative is confirmed by natural data and that the strange predictions of the prey-dependent theory are unsupported.”

“If top predators are eliminated or reduced in abundance, models predict that the sequential lower trophic levels must respond by changes of alternating signs. For example, in a three-level system of plants-herbivores-predators, the reduction of predators leads to the increase of herbivores and the consequential reduction in plant abundance. This response is commonly called the trophic cascade. In a four-level system, the bottom level will increase in response to harvesting at the top. These predicted responses are quite intuitive and are, in fact, true for both short-term and long-term responses, irrespective of the theory one employs. […] A number of excellent reviews have summarized and meta-analyzed large amounts of data on trophic cascades in food chains […] In general, the cascading reaction is strongest in lakes, followed by marine systems, and weakest in terrestrial systems. […] Any theory that claims to describe the trophic chain equilibria has to produce such cascading when top predators are reduced or eliminated. It is well known that the standard prey-dependent theory supports this view of top-down cascading. It is not widely appreciated that top-down cascading is likewise a property of ratio-dependent trophic chains. […] It is [only] for equilibrial responses to enrichment at the bottom that predictions are strikingly different according to the two theories”.

As the book does spend a little time on this I should perhaps briefly interject here that the above paragraph should not be taken to indicate that the two types of models provide identical predictions in the top-down cascading context in all cases; both predict cascading, but there are even so some subtle differences between the models here as well. Some of these differences are however quite hard to test.

“[T]he traditional Lotka-Volterra interaction term […] is nothing other than the law of mass action of chemistry. It assumes that predator and prey individuals encounter each other randomly in the same way that molecules interact in a chemical solution. Other prey-dependent models, like Holling’s, derive from the same idea. […] an ecological system can only be described by such a model if conspecifics do not interfere with each other and if the system is sufficiently homogeneous […] we will demonstrate that spatial heterogeneity, be it in the form of a prey refuge or in the form of predator clusters, leads to emergence of gradual interference or of ratio dependence when the functional response is observed at the population level. […] We present two mechanistic individual-based models that illustrate how, with gradually increasing predator density and gradually increasing predator clustering, interference can become gradually stronger. Thus, a given biological system, prey dependent at low predator density, can gradually become ratio dependent at high predator density. […] ratio dependence is a simple way of summarizing the effects induced by spatial heterogeneity, while the prey dependent [models] (e.g., Lotka-Volterra) is more appropriate in homogeneous environments.”

“[W]e consider that a good model of interacting species must be fundamentally invariant to a proportional change of all abundances in the system. […] Allowing interacting populations to expand in balanced exponential growth makes the laws of ecology invariant with respect to multiplying interacting abundances by the same constant, so that only ratios matter. […] scaling invariance is required if we wish to preserve the possibility of joint exponential growth of an interacting pair. […] a ratio-dependent model allows for joint exponential growth. […] Neither the standard prey-dependent models nor the more general predator-dependent models allow for balanced growth. […] In our view, communities must be expected to expand exponentially in the presence of unlimited resources. Of course, limiting factors ultimately stop this expansion just as they do for a single species. With our view, it is the limiting resources that stop the joint expansion of the interacting populations; it is not directly due to the interactions themselves. This partitioning of the causes is a major simplification that traditional theory implies only in the case of a single species.”

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August 1, 2017 Posted by | Biology, Books, Chemistry, Ecology, Mathematics, Studies | Leave a comment

Imported Plant Diseases

I found myself debating whether or not I should read Lewis, Petrovskii, and Potts’ text The Mathematics Behind Biological Invasions a while back, but at the time I in the end decided that it would simply be too much work to justify the potential payoff – so instead of reading the book, I decided to just watch the above lecture and leave it at that. This lecture is definitely a very poor textbook substitute, and I was strongly debating whether or not to blog it because it just isn’t very good; the level of coverage is very low. Which is sad, because some of the diseases discussed in the lecture – like e.g. wheat leaf rust – are really important and worth knowing about. One of the important points made in the lecture is that in the context of potential epidemics, it can be difficult to know when and how to intervene because of the uncertainty involved; early action may be the more efficient choice in terms of resource use, but the earlier you intervene, the less certain will be the intervention payoff and the less you’ll know about stuff like transmission patterns (…would outbreak X ever really have spread very wide if we had not intervened? We don’t observe the counterfactual…). Such aspects of course are not only relevant to plant-diseases, and the lecture also contains other basic insights from epidemiology which apply to other types of disease – but if you’ve ever opened a basic epidemiology text you’ll know all these things already.

May 22, 2017 Posted by | Biology, Botany, Ecology, Epidemiology, Lectures | Leave a comment

Deserts

I recently read Nick Middleton’s short publication on this topic and decided it was worth blogging it here. I gave the publication 3 stars on goodreads; you can read my goodreads review of the book here.

In this post I’ll quote a bit from the book and add some details I thought were interesting.

“None of [the] approaches to desert definition is foolproof. All have their advantages and drawbacks. However, each approach delivers […] global map[s] of deserts and semi-deserts that [are] broadly similar […] Roughly, deserts cover about one-quarter of our planet’s land area, and semi-deserts another quarter.”

“High temperatures and a paucity of rainfall are two aspects of climate that many people routinely associate with deserts […] However, desert climates also embrace other extremes. Many arid zones experience freezing temperatures and snowfall is commonplace, particularly in those situated outside the tropics. […] For much of the time, desert skies are cloud-free, meaning deserts receive larger amounts of sunshine than any other natural environment. […] Most of the water vapour in the world’s atmosphere is supplied by evaporation from the oceans, so the more remote a location is from this source the more likely it is that any moisture in the air will have been lost by precipitation before it reaches continental interiors. The deserts of Central Asia illustrate this principle well: most of the moisture in the air is lost before it reaches the heart of the continent […] A clear distinction can be made between deserts in continental interiors and those on their coastal margins when it comes to the range of temperatures experienced. Oceans tend to exert a moderating influence on temperature, reducing extremes, so the greatest ranges of temperature are found far from the sea while coastal deserts experience a much more limited range. […] Freezing temperatures occur particularly in the mid-latitude deserts, but by no means exclusively so. […] snowfall occurs at the Algerian oasis towns of Ouagla and Ghardaia, in the northern Sahara, as often as once every 10 years on average.”

“[One] characteristic of rainfall in deserts is its variability from year to year which in many respects makes annual average statistics seem like nonsense. A very arid desert area may go for several years with no rain at all […]. It may then receive a whole ‘average’ year’s rainfall in just one storm […] Rainfall in deserts is also typically very variable in space as well as time. Hence, desert rainfall is frequently described as being ‘spotty’. This spottiness occurs because desert storms are often convective, raining in a relatively small area, perhaps just a few kilometres across. […] Climates can vary over a wide range of spatial scales […] Changes in temperature, wind, relative humidity, and other elements of climate can be detected over short distances, and this variability on a small scale creates distinctive climates in small areas. These are microclimates, different in some way from the conditions prevailing over the surrounding area as a whole. At the smallest scale, the shade given by an individual plant can be described as a microclimate. Over larger distances, the surface temperature of the sand in a dune will frequently be significantly different from a nearby dry salt lake because of the different properties of the two types of surface. […] Microclimates are important because they exert a critical control over all sorts of phenomena. These include areas suitable for plant and animal communities to develop, the ways in which rocks are broken down, and the speed at which these processes occur.”

“The level of temperature prevailing when precipitation occurs is important for an area’s water balance and its degree of aridity. A rainy season that occurs during the warm summer months, when evaporation is greatest, makes for a climate that is more arid than if precipitation is distributed more evenly throughout the year.”

“The extremely arid conditions of today[‘s Sahara Desert] have prevailed for only a few thousand years. There is lots of evidence to suggest that the Sahara was lush, nearly completely covered with grasses and shrubs, with many lakes that supported antelope, giraffe, elephant, hippopotamus, crocodile, and human populations in regions that today have almost no measurable precipitation. This ‘African Humid Period’ began around 15,000 years ago and came to an end around 10,000 years later. […] Globally, at the height of the most recent glacial period some 18,000 years ago, almost 50% of the land area between 30°N and 30°S was covered by two vast belts of sand, often called ‘sand seas’. Today, about 10% of this area is covered by sand seas. […] Around one-third of the Arabian subcontinent is covered by sandy deserts”.

“Much of the drainage in deserts is internal, as in Central Asia. Their rivers never reach the sea, but take water to interior basins. […] Salt is a common constituent of desert soils. The generally low levels of rainfall means that salts are seldom washed away through soils and therefore tend to accumulate in certain parts of the landscape. Large amounts of common salt (sodium chloride, or halite), which is very soluble in water, are found in some hyper-arid deserts.”

“Many deserts are very rich in rare and unique species thanks to their evolution in relative geographical isolation. Many of these plants and animals have adapted in remarkable ways to deal with the aridity and extremes of temperature. Indeed, some of these adaptations contribute to the apparent lifelessness of deserts simply because a good way to avoid some of the harsh conditions is to hide. Some small creatures spend hot days burrowed beneath the soil surface. In a similar way, certain desert plants spend most of the year and much of their lives dormant, as seeds waiting for the right conditions, brought on by a burst of rainfall. Given that desert rainstorms can be very variable in time and in space, many activities in the desert ecosystem occur only sporadically, as pulses of activity driven by the occasional cloudburst. […] The general scarcity of water is the most important, though by no means the only, environmental challenge faced by desert organisms. Limited supplies of food and nutrients, friable soils, high levels of solar radiation, high daytime temperatures, and the large diurnal temperature range are other challenges posed by desert conditions. These conditions are not always distributed evenly across a desert landscape, and the existence of more benign microenvironments is particularly important for desert plants and animals. Patches of terrain that are more biologically productive than their surroundings occur in even the most arid desert, geographical patterns caused by many factors, not only the simple availability of water.”

A small side note here: The book includes brief coverage of things like crassulacean acid metabolism and related topics covered in much more detail in Beer et al. I’m not going to go into that stuff here as this stuff was in my opinion much better covered in the latter book (some people might disagree, but people who would do that would at least have to admit that the coverage in Beer et al. is/was much more comprehensive than is Middleton’s coverage in this book). There are quite a few other topics included in the book which I did not include coverage of here in the post but I mention this topic in particular in part because I thought it was actually a good example underscoring how this book is very much just a very brief introduction; you can write book chapters, if not books, about some of the topics Middleton devotes a couple of paragraphs to in his coverage, which is but to be expected given the nature and range of coverage of the publication.

Plants aren’t ‘smart’ given any conventional definition of the word, but as I’ve talked about before here on the blog (e.g. here) when you look closer at the way they grow and ‘behave’ over the very long term, some of the things they do are actually at the very least ‘not really all that stupid’:

“The seeds of annuals germinate only when enough water is available to support the entire life cycle. Germinating after just a brief shower could be fatal, so mechanisms have developed for seeds to respond solely when sufficient water is available. Seeds germinate only when their protective seed coats have been broken down, allowing water to enter the seed and growth to begin. The seed coats of many desert species contain chemicals that repel water. These compounds are washed away by large amounts of water, but a short shower will not generate enough to remove all the water-repelling chemicals. Other species have very thick seed coats that are gradually worn away physically by abrasion as moving water knocks the seeds against stones and pebbles.”

What about animals? One thing I learned from this publication is that it turns out that being a mammal will, all else equal, definitely not give you a competitive edge in a hot desert environment:

“The need to conserve water is important to all creatures that live in hot deserts, but for mammals it is particularly crucial. In all environments mammals typically maintain a core body temperature of around 37–38°C, and those inhabiting most non-desert regions face the challenge of keeping their body temperature above the temperature of their environmental surrounds. In hot deserts, where environmental temperatures substantially exceed the body temperature on a regular basis, mammals face the reverse challenge. The only mechanism that will move heat out of an animal’s body against a temperature gradient is the evaporation of water, so maintenance of the core body temperature requires use of the resource that is by definition scarce in drylands.”

Humans? What about them?

“Certain aspects of a traditional mobile lifestyle have changed significantly for some groups of nomadic peoples. Herders in the Gobi desert in Mongolia pursue a way of life that in many ways has changed little since the times of the greatest of all nomadic leaders, Chinggis Khan, 750 years ago. They herd the same animals, eat the same foods, wear the same clothes, and still live in round felt-covered tents, traditional dwellings known in Mongolian as gers. Yet many gers now have a set of solar panels on the roof that powers a car battery, allowing an electric light to extend the day inside the tent. Some also have a television set.” (these remarks incidentally somehow reminded me of this brilliant Gary Larson cartoon)

“People have constructed dams to manage water resources in arid regions for thousands of years. One of the oldest was the Marib dam in Yemen, built about 3,000 years ago. Although this structure was designed to control water from flash floods, rather than for storage, the diverted flow was used to irrigate cropland. […] Although groundwater has been exploited for desert farmland using hand-dug underground channels for a very long time, the discovery of reserves of groundwater much deeper below some deserts has led to agricultural use on much larger scales in recent times. These deep groundwater reserves tend to be non-renewable, having built up during previous climatic periods of greater rainfall. Use of this fossil water has in many areas resulted in its rapid depletion.”

“Significant human impacts are thought to have a very long history in some deserts. One possible explanation for the paucity of rainfall in the interior of Australia is that early humans severely modified the landscape through their use of fire. Aboriginal people have used fire extensively in Central Australia for more than 20,000 years, particularly as an aid to hunting, but also for many other purposes, from clearing passages to producing smoke signals and promoting the growth of preferred plants. The theory suggests that regular burning converted the semi-arid zone’s mosaic of trees, shrubs, and grassland into the desert scrub seen today. This gradual change in the vegetation could have resulted in less moisture from plants reaching the atmosphere and hence the long-term desertification of the continent.” (I had never heard about this theory before, and so I of course have no idea if it’s correct or not – but it’s an interesting idea).

A few wikipedia links of interest:
Yardang.
Karakum Canal.
Atacama Desert.
Salar de Uyuni.
Taklamakan Desert.
Dust Bowl.
Namib Desert.
Dzud.

August 27, 2016 Posted by | Anthropology, Biology, Books, Botany, Ecology, Engineering, Geography, Zoology | Leave a comment

Photosynthesis in the Marine Environment (II)

Here’s my first post about the book. I gave the book four stars on goodreads – here’s a link to my short goodreads review of the book.

As pointed out in the review, ‘it’s really mostly a biochemistry text.’ At least there’s a lot of that stuff in there (‘it get’s better towards the end’, would be one way to put it – the last chapters deal mostly with other topics, such as measurement and brief notes on some not-particularly-well-explored ecological dynamics of potential interest), and if you don’t want to read a book which deals in some detail with topics and concepts like alkalinity, crassulacean acid metabolism, photophosphorylation, photosynthetic reaction centres, Calvin cycle (also known straightforwardly as the ‘reductive pentose phosphate cycle’…), enzymes with names like Ribulose-1,5-bisphosphate carboxylase/oxygenase (‘RuBisCO’ among friends…) and phosphoenolpyruvate carboxylase (‘PEP-case’ among friends…), mycosporine-like amino acid, 4,4′-Diisothiocyanatostilbene-2,2′-disulfonic acid (‘DIDS’ among friends), phosphoenolpyruvate, photorespiration, carbonic anhydrase, C4 carbon fixation, cytochrome b6f complex, … – well, you should definitely not read this book. If you do feel like reading about these sorts of things, having a look at the book seems to me a better idea than reading the wiki articles.

I’m not a biochemist but I could follow a great deal of what was going on in this book, which is perhaps a good indication of how well written the book is. This stuff’s interesting and complicated, and the authors cover most of it quite well. The book has way too much stuff for it to make sense to cover all of it here, but I do want to cover some more stuff from the book, so I’ve added some quotes below.

“Water velocities are central to marine photosynthetic organisms because they affect the transport of nutrients such as Ci [inorganic carbon] towards the photosynthesising cells, as well as the removal of by-products such as excess O2 during the day. Such bulk transport is especially important in aquatic media since diffusion rates there are typically some 10 000 times lower than in air […] It has been established that increasing current velocities will increase photosynthetic rates and, thus, productivity of macrophytes as long as they do not disrupt the thalli of macroalgae or the leaves of seagrasses”.

Photosynthesis is the process by which the energy of light is used in order to form energy-rich organic compounds from low-energy inorganic compounds. In doing so, electrons from water (H2O) reduce carbon dioxide (CO2) to carbohydrates. […] The process of photosynthesis can conveniently be separated into two parts: the ‘photo’ part in which light energy is converted into chemical energy bound in the molecule ATP and reducing power is formed as NADPH [another friend with a long name], and the ‘synthesis’ part in which that ATP and NADPH are used in order to reduce CO2 to sugars […]. The ‘photo’ part of photosynthesis is, for obvious reasons, also called its light reactions while the ‘synthesis’ part can be termed CO2-fixation and -reduction, or the Calvin cycle after one of its discoverers; this part also used to be called the ‘dark reactions’ [or light-independent reactions] of photosynthesis because it can proceed in vitro (= outside the living cell, e.g. in a test-tube) in darkness provided that ATP and NADPH are added artificially. […] ATP and NADPH are the energy source and reducing power, respectively, formed by the light reactions, that are subsequently used in order to reduce carbon dioxide (CO2) to sugars (synonymous with carbohydrates) in the Calvin cycle. Molecular oxygen (O2) is formed as a by-product of photosynthesis.”

“In photosynthetic bacteria (such as the cyanobacteria), the light reactions are located at the plasma membrane and internal membranes derived as invaginations of the plasma membrane. […] most of the CO2-fixing enzyme ribulose-bisphosphate carboxylase/oxygenase […] is here located in structures termed carboxysomes. […] In all other plants (including algae), however, the entire process of photosynthesis takes place within intracellular compartments called chloroplasts which, as the name suggests, are chlorophyll-containing plastids (plastids are those compartments in cells that are associated with photosynthesis).”

“Photosynthesis can be seen as a process in which part of the radiant energy from sunlight is ‘harvested’ by plants in order to supply chemical energy for growth. The first step in such light harvesting is the absorption of photons by photosynthetic pigments[1]. The photosynthetic pigments are special in that they not only convert the energy of absorbed photons to heat (as do most other pigments), but largely convert photon energy into a flow of electrons; the latter is ultimately used to provide chemical energy to reduce CO2 to carbohydrates. […] Pigments are substances that can absorb different wavelengths selectively and so appear as the colour of those photons that are less well absorbed (and, therefore, are reflected, or transmitted, back to our eyes). (An object is black if all photons are absorbed, and white if none are absorbed.) In plants and animals, the pigment molecules within the cells and their organelles thus give them certain colours. The green colour of many plant parts is due to the selective absorption of chlorophylls […], while other substances give colour to, e.g. flowers or fruits. […] Chlorophyll is a major photosynthetic pigment, and chlorophyll a is present in all plants, including all algae and the cyanobacteria. […] The molecular sub-structure of the chlorophyll’s ‘head’ makes it absorb mainly blue and red light […], while green photons are hardly absorbed but, rather, reflected back to our eyes […] so that chlorophyll-containing plant parts look green. […] In addition to chlorophyll a, all plants contain carotenoids […] All these accessory pigments act to fill in the ‘green window’ generated by the chlorophylls’ non-absorbance in that band […] and, thus, broaden the spectrum of light that can be utilized […] beyond that absorbed by chlorophyll.”

“Photosynthesis is principally a redox process in which carbon dioxide (CO2) is reduced to carbohydrates (or, in a shorter word, sugars) by electrons derived from water. […] since water has an energy level (or redox potential) that is much lower than that of sugar, or, more precisely, than that of the compound that finally reduces CO2 to sugars (i.e. NADPH), it follows that energy must be expended in the process; this energy stems from the photons of light. […] Redox reactions are those reactions in which one compound, B, becomes reduced by receiving electrons from another compound, A, the latter then becomes oxidised by donating the electrons to B. The reduction of B can only occur if the electron-donating compound A has a higher energy level, or […] has a redox potential that is higher, or more negative in terms of electron volts, than that of compound B. The redox potential, or reduction potential, […] can thus be seen as a measure of the ease by which a compound can become reduced […] the greater the difference in redox potential between compounds B and A, the greater the tendency that B will be reduced by A. In photosynthesis, the redox potential of the compound that finally reduces CO2, i.e. NADPH, is more negative than that from which the electrons for this reduction stems, i.e. H2O, and the entire process can therefore not occur spontaneously. Instead, light energy is used in order to boost electrons from H2O through intermediary compounds to such high redox potentials that they can, eventually, be used for CO2 reduction. In essence, then, the light reactions of photosynthesis describe how photon energy is used to boost electrons from H2O to an energy level (or redox potential) high (or negative) enough to reduce CO2 to sugars.”

“Fluorescence in general is the generation of light (emission of photons) from the energy released during de-excitation of matter previously excited by electromagnetic energy. In photosynthesis, fluorescence occurs as electrons of chlorophyll undergo de-excitation, i.e. return to the original orbital from which they were knocked out by photons. […] there is an inverse (or negative) correlation between fluorescence yield (i.e. the amount of fluorescence generated per photons absorbed by chlorophyll) and photosynthetic yield (i.e. the amount of photosynthesis performed per photons similarly absorbed).”

“In some cases, more photon energy is received by a plant than can be used for photosynthesis, and this can lead to photo-inhibition or photo-damage […]. Therefore, many plants exposed to high irradiances possess ways of dissipating such excess light energy, the most well known of which is the xanthophyll cycle. In principle, energy is shuttled between various carotenoids collectively called xanthophylls and is, in the process, dissipated as heat.”

“In order to ‘fix’ CO2 (= incorporate it into organic matter within the cell) and reduce it to sugars, the NADPH and ATP formed in the light reactions are used in a series of chemical reactions that take place in the stroma of the chloroplasts (or, in prokaryotic autotrophs such as cyanobacteria, the cytoplasm of the cells); each reaction is catalysed by its specific enzyme, and the bottleneck for the production of carbohydrates is often considered to be the enzyme involved in its first step, i.e. the fixation of CO2 [this enzyme is RubisCO] […] These CO2-fixation and -reduction reactions are known as the Calvin cycle […] or the C3 cycle […] The latter name stems from the fact that the first stable product of CO2 fixation in the cycle is a 3-carbon compound called phosphoglyceric acid (PGA): Carbon dioxide in the stroma is fixed onto a 5-carbon sugar called ribulose-bisphosphate (RuBP) in order to form 2 molecules of PGA […] It should be noted that this reaction does not produce a reduced, energy-rich, carbon compound, but is only the first, ‘CO2– fixing’, step of the Calvin cycle. In subsequent steps, PGA is energized by the ATP formed through photophosphorylation and is reduced by NADPH […] to form a 3-carbon phosphorylated sugar […] here denoted simply as triose phosphate (TP); these reactions can be called the CO2-reduction step of the Calvin cycle […] 1/6 of the TPs formed leave the cycle while 5/6 are needed in order to re-form RuBP molecules in what we can call the regeneration part of the cycle […]; it is this recycling of most of the final product of the Calvin cycle (i.e. TP) to re-form RuBP that lends it to be called a biochemical ‘cycle’ rather than a pathway.”

“Rubisco […] not only functions as a carboxylase, but […] also acts as an oxygenase […] When Rubisco reacts with oxygen instead of CO2, only 1 molecule of PGA is formed together with 1 molecule of the 2-carbon compound phosphoglycolate […] Not only is there no gain in organic carbon by this reaction, but CO2 is actually lost in the further metabolism of phosphoglycolate, which comprises a series of reactions termed photorespiration […] While photorespiration is a complex process […] it is also an apparently wasteful one […] and it is not known why this process has evolved in plants altogether. […] Photorespiration can reduce the net photosynthetic production by up to 25%.”

“Because of Rubisco’s low affinity to CO2 as compared with the low atmospheric, and even lower intracellular, CO2 concentration […], systems have evolved in some plants by which CO2 can be concentrated at the vicinity of this enzyme; these systems are accordingly termed CO2 concentrating mechanisms (CCM). For terrestrial plants, this need for concentrating CO2 is exacerbated in those that grow in hot and/or arid areas where water needs to be saved by partly or fully closing stomata during the day, thus restricting also the influx of CO2 from an already CO2-limiting atmosphere. Two such CCMs exist in terrestrial plants: the C4 cycle and the Crassulacean acid metabolism (CAM) pathway. […] The C 4 cycle is called so because the first stable product of CO2-fixation is not the 3-carbon compound PGA (as in the Calvin cycle) but, rather, malic acid (often referred to by its anion malate) or aspartic acid (or its anion aspartate), both of which are 4-carbon compounds. […] C4 [terrestrial] plants are […] more common in areas of high temperature, especially when accompanied with scarce rains, than in areas with higher rainfall […] While atmospheric CO2 is fixed […] via the C4 cycle, it should be noted that this biochemical cycle cannot reduce CO2 to high energy containing sugars […] since the Calvin cycle is the only biochemical system that can reduce CO2 to energy-rich carbohydrates in plants, it follows that the CO2 initially fixed by the C4 cycle […] is finally reduced via the Calvin cycle also in C4 plants. In summary, the C 4 cycle can be viewed as being an additional CO2 sequesterer, or a biochemical CO2 ‘pump’, that concentrates CO2 for the rather inefficient enzyme Rubisco in C4 plants that grow under conditions where the CO2 supply is extremely limited because partly closed stomata restrict its influx into the photosynthesising cells.”

“Crassulacean acid metabolism (CAM) is similar to the C 4 cycle in that atmospheric CO2 […] is initially fixed via PEP-case into the 4-carbon compound malate. However, this fixation is carried out during the night […] The ecological advantage behind CAM metabolism is that a CAM plant can grow, or at least survive, under prolonged (sometimes months) conditions of severe water stress. […] CAM plants are typical of the desert flora, and include most cacti. […] The principal difference between C 4 and CAM metabolism is that in C4 plants the initial fixation of atmospheric CO2 and its final fixation and reduction in the Calvin cycle is separated in space (between mesophyll and bundle-sheath cells) while in CAM plants the two processes are separated in time (between the initial fixation of CO2 during the night and its re-fixation and reduction during the day).”

July 20, 2015 Posted by | Biology, Botany, Chemistry, Ecology, Microbiology | Leave a comment

Photosynthesis in the Marine Environment (I)

I’m currently reading this book. Below some observations from part 1.

“The term autotroph is usually associated with the photosynthesising plants (including algae and cyanobacteria) and heterotroph with animals and some other groups of organisms that need to be provided high-energy containing organic foods (e.g. the fungi and many bacteria). However, many exceptions exist: Some plants are parasitic and may be devoid of chlorophyll and, thus, lack photosynthesis altogether6, and some animals contain chloroplasts or photosynthesising algae or
cyanobacteria and may function, in part, autotrophically; some corals rely on the photosynthetic algae within their bodies to the extent that they don’t have to eat at all […] If some plants are heterotrophic and some animals autotrophic, what then differentiates plants from animals? It is usually said that what differs the two groups is the absence (animals) or presence (plants) of a cell wall. The cell wall is deposited outside the cell membrane in plants, and forms a type of exo-skeleton made of polysaccharides (e.g. cellulose or agar in some red algae, or silica in the case of diatoms) that renders rigidity to plant cells and to the whole plant.”

“For the autotrophs, […] there was an advantage if they could live close to the shores where inorganic nutrient concentrations were higher (because of mineral-rich runoffs from land) than in the upper water layer of off-shore locations. However, living closer to shore also meant greater effects of wave action, which would alter, e.g. the light availability […]. Under such conditions, there would be an advantage to be able to stay put in the seawater, and under those conditions it is thought that filamentous photosynthetic organisms were formed from autotrophic cells (ca. 650 million years ago), which eventually resulted in macroalgae (some 450 million years ago) featuring holdfast tissues that could adhere them to rocky substrates. […] Very briefly now, the green macroalgae were the ancestors of terrestrial plants, which started to invade land ca. 400 million years ago (followed by the animals).”

“Marine ‘plants’ (= all photoautotrophic organisms of the seas) can be divided into phytoplankton (‘drifters’, mostly unicellular) and phytobenthos (connected to the bottom, mostly multicellular/macroscopic).
The phytoplankton can be divided into cyanobacteria (prokaryotic) and microalgae (eukaryotic) […]. The phytobenthos can be divided into macroalgae and seagrasses (marine angiosperms, which invaded the shallow seas some 90 million years ago). The micro- and macro-algae are divided into larger groups as based largely on their pigment composition [e.g. ‘red algae‘, ‘brown algae‘, …]

There are some 150 currently recognised species of marine cyanobacteria, ∼20 000 species of eukaryotic microalgae, several thousand species of macroalgae and 50(!) species of seagrasses. Altogether these marine plants are accountable for approximately half of Earth’s photosynthetic (or primary) production.

The abiotic factors that are conducive to photosynthesis and plant growth in the marine environment differ from those of terrestrial environments mainly with regard to light and inorganic carbon (Ci) sources. Light is strongly attenuated in the marine environment by absorption and scatter […] While terrestrial plants rely of atmospheric CO2 for their photosynthesis, marine plants utilise largely the >100 times higher concentration of HCO3 as the main Ci source for their photosynthetic needs. Nutrients other than CO2, that may limit plant growth in the marine environment include nitrogen (N), phosphorus (P), iron (Fe) and, for the diatoms, silica (Si).”

“The conversion of the plentiful atmospheric N2 gas (∼78% in air) into bio-available N-rich cellular constituents is a fundamental process that sustains life on Earth. For unknown reasons this process is restricted to selected representatives among the prokaryotes: archaea and bacteria. N2 fixing organisms, also termed diazotrophs (dia = two; azo = nitrogen), are globally wide-spread in terrestrial and aquatic environments, from polar regions to hot deserts, although their abundance varies widely. [Why is nitrogen important, I hear you ask? Well, when you hear the word ‘nitrogen’ in biology texts, think ‘protein’ – “Because nitrogen is relatively easy to measure and protein is not, protein content is often estimated by assaying organic nitrogen, which comprises from 15 to 18% of plant proteins” (Herrera et al.see this post]. […] . Cyanobacteria dominate marine diazotrophs and occupy large segments of marine open waters […]  sustained N2 fixation […] is a highly energy-demanding process. […] in all diazotrophs, the nitrogenase enzyme complex […] of marine cyanobacteria requires high Fe levels […] Another key nutrient is phosphorus […] which has a great impact on growth and N2 fixation in marine cyanobacteria. […] Recent model-based estimates of N2 fixation suggest that unicellular cyanobacteria contribute significantly to global ocean N budgets.”

“For convenience, we often divide the phytoplankton into different size classes, the pico-phytoplankton (0.2–2 μm effective cell diameter, ECD4); the nanophytoplankton (2–20 μm ECD) and the microphytoplankton (20–200 μm ECD). […] most of the major marine microalgal groups are found in all three size classes […] a 2010 paper estimate that these plants utilise 46 Gt carbon yearly, which can be divided into 15 Gt for the microphytoplankton, 20 Gt for the nanophytoplankton and 11 Gt for the picophytoplankton. Thus, the very small (nano- + pico-forms) of phytoplankton (including cyanobacterial forms) contribute 2/3 of the overall planktonic production (which, again, constitutes about half of the global production”).

“Many primarily non-photosynthetic organisms have developed symbioses with microalgae and cyanobacteria; these photosynthetic intruders are here referred to as photosymbionts. […] Most photosymbionts are endosymbiotic (living within the host) […] In almost all cases, these micro-algae are in symbiosis with invertebrates. Here the alga provides the animal with organic products of photosynthesis, while the invertebrate host can supply CO2 and other inorganic nutrients including nitrogen and phosphorus to the alga […]. In cases where cyanobacteria form the photosymbiont, their ‘caloric’ nutritional value is more questionable, and they may instead produce toxins that deter other animals from eating the host […] Many reef-building […] corals contain symbiotic zooxanthellae within the digestive cavity of their polyps, and in general corals that have symbiotic algae grow much faster than those without them. […] The loss of zooxanthellae from the host is known as coral bleaching […] Certain sea slugs contain functional chloroplasts that were ingested (but not digested) as part of larger algae […]. After digesting the rest of the alga, these chloroplasts are imbedded within the slugs’ digestive tract in a process called kleptoplasty (the ‘stealing’ of plastids). Even though this is not a true symbiosis (the chloroplasts are not organisms and do not gain anything from the association), the photosynthetic activity aids in the nutrition of the slugs for up to several months, thus either complementing their nutrition or carrying them through periods when food is scarce or absent.”

“90–100 million years ago, when there was a rise in seawater levels, some of the grasses that grew close to the seashores found themselves submerged in seawater. One piece of evidence that supports [the] terrestrial origin [of marine angiosperms] can be seen in the fact that residues of stomata can be found at the base of the leaves. In terrestrial plants, the stomata restrict water loss from the leaves, but since seagrasses are principally submerged in a liquid medium, the stomata became absent in the bulk parts of the leaves. These marine angiosperms, or seagrasses, thus evolved from those coastal grasses that successfully managed to adapt to being submerged in saline waters. Another theory has it that the ancestors of seagrasses were freshwater plants that, therefore, only had to adapt to water of a higher salinity. In both cases, the seagrasses exemplify a successful readaptation to marine life […] While there may exist some 20 000 or more species of macroalgae […], there are only some 50 species of seagrasses, most of which are found in tropical seas. […] the ability to extract nutrients from the sediment renders the seagrasses at an advantage over (the root-less) macroalgae in nutrient-poor waters. […] one of the basic differences in habitat utilisation between macroalgae and seagrasses is that the former usually grow on rocky substrates where they are held in place by their holdfasts, while seagrasses inhabit softer sediments where they are held in place by their root systems. Unlike macroalgae, where the whole plant surface is photosynthetically active, large proportions of seagrass plants are comprised of the non-photosynthetic roots and rhizomes. […] This means […] that seagrasses need more light in order to survive than do many algae […] marine plants usually contain less structural tissues than their terrestrial counterparts”.

“if we define ‘visible light’ as the electromagnetic wave upon which those energy-containing particles called quanta ‘ride’ that cause vision in higher animals (those quanta are also called photons) and compare it with light that causes photosynthesis, we find, interestingly, that the two processes use approximately the same wavelengths: While mammals largely use the 380–750 nm (nm = 10-9 m) wavelength band for vision, plants use the 400–700-nm band for photosynthesis; the latter is therefore also termed photosynthetically active radiation (PAR […] If a student
asks “but how come that animals and plants use almost identical wavelengths of radiation for so very different purposes?”, my answer is “sorry, but we don’t have the time to discuss that now”, meaning that while I think it has to do with too high and too low quantum energies below and above those wavelengths, I really don’t know.”

“energy (E) of a photon is inversely proportional to its wavelength […] a blue photon of 400 nm wavelength contains almost double the energy of a red one of 700 nm, while the photons of PAR between those two extremes carry decreasing energies as wavelengths increase. Accordingly, low-energy photons (i.e. of high wavelengths, e.g. those of reddish light) are absorbed to a greater extent by water molecules along a depth gradient than are photons of higher energy (i.e. lower wavelengths, e.g. bluish light), and so the latter penetrate deeper down in clear oceanic waters […] In water, the spectral distribution of PAR reaching a plant is different from that on land. This is because water not only attenuates the light intensity (or, more correctly, the photon flux, or irradiance […]), but, as mentioned above and detailed below, the attenuation with depth is wavelength dependent; therefore, plants living in the oceans will receive different spectra of light dependent on depth […] The two main characteristics of seawater that determine the quantity and quality of the irradiance penetrating to a certain depth are absorption and scatter. […] Light absorption in the oceans is a property of the water molecules, which absorb photons according to their energy […] Thus, red photons of low energy are more readily absorbed than, e.g. blue ones; only <1% of the incident red photons (calculated for 650 nm) penetrate to 20 m depth in clear waters while some 60% of the blue photons (450 nm) remain at that depth. […] Scatter […] is mainly caused by particles suspended in the water column (rather than by the water molecules themselves, although they too scatter light a little). Unlike absorption, scatter affects short-wavelength photons more than long-wavelength ones […] in turbid waters, photons of decreasing wavelengths are increasingly scattered. Since water molecules are naturally also present, they absorb the higher wavelengths, and the colours penetrating deepest in turbid waters are those between the highly scattered blue and highly absorbed red, e.g. green. The greenish colour of many coastal waters is therefore often due not only to the presence of chlorophyll-containing phytoplankton, but because, again, reddish photons are absorbed, bluish photons are scattered, and the midspectrum (i.e. green) fills the bulk part of the water column.”

“the open ocean, several kilometres or miles from the shore, almost always appears as blue. The reason for this is that in unpolluted, particle-free, waters, the preferential absorption of long-wavelength (low-energy) photons is what mainly determines the spectral distribution of light attenuation. Thus, short-wavelength (high-energy) bluish photons penetrate deepest and ‘fill up’ the bulk of the water column with their colour. Since water molecules also scatter a small proportion of those photons […], it follows that these largely water-penetrating photons are eventually also reflected back to our eyes. Or, in other words, out of the very low scattering in clear oceanic waters, the photons available to be scattered and, thus, reflected to our eyes, are mainly the bluish ones, and that is why the clear deep oceans look blue. (It is often said that the oceans are blue because the blue sky is reflected by the water surface. However, sailors will testify to the truism that the oceans are also deep blue in heavily overcast weathers, and so that explanation of the general blueness of the oceans is not valid.)”

“Although marine plants can be found in a wide range of temperature regimes, from the tropics to polar regions, the large bodies of water that are the environment for most marine plants have relatively constant temperatures, at least on a day-to-day basis. […] For marine plants that are found in intertidal regions, however, temperature variation during a single day can be very high as the plants find themselves alternately exposed to air […] Marine plants from tropical and temperate regions tend to have distinct temperature ranges for growth […] and growth optima. […] among most temperate species of microalgae, temperature optima for growth are in the range 18–25 ◦C, while some Antarctic diatoms show optima at 4–6 ◦C with no growth above a critical temperature of 7–12 ◦C. By contrast, some tropical diatoms will not grow below 15–17 ◦C. Similar responses are found in macroalgae and seagrasses. However, although some marine plants have a restricted temperature range for growth (so-called stenothermal species; steno = narrow and thermal relates to temperature), most show some growth over a broad range of temperatures and can be considered eurythermal (eury = wide).”

June 4, 2015 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Microbiology, Physics, Zoology | Leave a comment

Wikipedia articles of interest

i. Lock (water transport). Zumerchik and Danver’s book covered this kind of stuff as well, sort of, and I figured that since I’m not going to blog the book – for reasons provided in my goodreads review here – I might as well add a link or two here instead. The words ‘sort of’ above are in my opinion justified because the book coverage is so horrid you’d never even know what a lock is used for from reading that book; you’d need to look that up elsewhere.

On a related note there’s a lot of stuff in that book about the history of water transport etc. which you probably won’t get from these articles, but having a look here will give you some idea about which sort of topics many of the chapters of the book are dealing with. Also, stuff like this and this. The book coverage of the latter topic is incidentally much, much more detailed than is that wiki article, and the article – as well as many other articles about related topics (economic history, etc.) on the wiki, to the extent that they even exist – could clearly be improved greatly by adding content from books like this one. However I’m not going to be the guy doing that.

ii. Congruence (geometry).

iii. Geography and ecology of the Everglades (featured).

I’d note that this is a topic which seems to be reasonably well covered on wikipedia; there’s for example also a ‘good article’ on the Everglades and a featured article about the Everglades National Park. A few quotes and observations from the article:

“The geography and ecology of the Everglades involve the complex elements affecting the natural environment throughout the southern region of the U.S. state of Florida. Before drainage, the Everglades were an interwoven mesh of marshes and prairies covering 4,000 square miles (10,000 km2). […] Although sawgrass and sloughs are the enduring geographical icons of the Everglades, other ecosystems are just as vital, and the borders marking them are subtle or nonexistent. Pinelands and tropical hardwood hammocks are located throughout the sloughs; the trees, rooted in soil inches above the peat, marl, or water, support a variety of wildlife. The oldest and tallest trees are cypresses, whose roots are specially adapted to grow underwater for months at a time.”

“A vast marshland could only have been formed due to the underlying rock formations in southern Florida.[15] The floor of the Everglades formed between 25 million and 2 million years ago when the Florida peninsula was a shallow sea floor. The peninsula has been covered by sea water at least seven times since the earliest bedrock formation. […] At only 5,000 years of age, the Everglades is a young region in geological terms. Its ecosystems are in constant flux as a result of the interplay of three factors: the type and amount of water present, the geology of the region, and the frequency and severity of fires. […] Water is the dominant element in the Everglades, and it shapes the land, vegetation, and animal life of South Florida. The South Florida climate was once arid and semi-arid, interspersed with wet periods. Between 10,000 and 20,000 years ago, sea levels rose, submerging portions of the Florida peninsula and causing the water table to rise. Fresh water saturated the limestone, eroding some of it and creating springs and sinkholes. The abundance of fresh water allowed new vegetation to take root, and through evaporation formed thunderstorms. Limestone was dissolved by the slightly acidic rainwater. The limestone wore away, and groundwater came into contact with the surface, creating a massive wetland ecosystem. […] Only two seasons exist in the Everglades: wet (May to November) and dry (December to April). […] The Everglades are unique; no other wetland system in the world is nourished primarily from the atmosphere. […] Average annual rainfall in the Everglades is approximately 62 inches (160 cm), though fluctuations of precipitation are normal.”

“Between 1871 and 2003, 40 tropical cyclones struck the Everglades, usually every one to three years.”

“Islands of trees featuring dense temperate or tropical trees are called tropical hardwood hammocks.[38] They may rise between 1 and 3 feet (0.30 and 0.91 m) above water level in freshwater sloughs, sawgrass prairies, or pineland. These islands illustrate the difficulty of characterizing the climate of the Everglades as tropical or subtropical. Hammocks in the northern portion of the Everglades consist of more temperate plant species, but closer to Florida Bay the trees are tropical and smaller shrubs are more prevalent. […] Islands vary in size, but most range between 1 and 10 acres (0.40 and 4.05 ha); the water slowly flowing around them limits their size and gives them a teardrop appearance from above.[42] The height of the trees is limited by factors such as frost, lightning, and wind: the majority of trees in hammocks grow no higher than 55 feet (17 m). […] There are more than 50 varieties of tree snails in the Everglades; the color patterns and designs unique to single islands may be a result of the isolation of certain hammocks.[44] […] An estimated 11,000 species of seed-bearing plants and 400 species of land or water vertebrates live in the Everglades, but slight variations in water levels affect many organisms and reshape land formations.”

“Because much of the coast and inner estuaries are built by mangroves—and there is no border between the coastal marshes and the bay—the ecosystems in Florida Bay are considered part of the Everglades. […] Sea grasses stabilize sea beds and protect shorelines from erosion by absorbing energy from waves. […] Sea floor patterns of Florida Bay are formed by currents and winds. However, since 1932, sea levels have been rising at a rate of 1 foot (0.30 m) per 100 years.[81] Though mangroves serve to build and stabilize the coastline, seas may be rising more rapidly than the trees are able to build.[82]

iv. Chang and Eng Bunker. Not a long article, but interesting:

Chang (Chinese: ; pinyin: Chāng; Thai: จัน, Jan, rtgsChan) and Eng (Chinese: ; pinyin: Ēn; Thai: อิน In) Bunker (May 11, 1811 – January 17, 1874) were Thai-American conjoined twin brothers whose condition and birthplace became the basis for the term “Siamese twins”.[1][2][3]

I loved some of the implicit assumptions in this article: “Determined to live as normal a life they could, Chang and Eng settled on their small plantation and bought slaves to do the work they could not do themselves. […] Chang and Adelaide [his wife] would become the parents of eleven children. Eng and Sarah [‘the other wife’] had ten.”

A ‘normal life’ indeed… The women the twins married were incidentally sisters who ended up disliking each other (I can’t imagine why…).

v. Genie (feral child). This is a very long article, and you should be warned that many parts of it may not be pleasant to read. From the article:

Genie (born 1957) is the pseudonym of a feral child who was the victim of extraordinarily severe abuse, neglect and social isolation. Her circumstances are prominently recorded in the annals of abnormal child psychology.[1][2] When Genie was a baby her father decided that she was severely mentally retarded, causing him to dislike her and withhold as much care and attention as possible. Around the time she reached the age of 20 months Genie’s father decided to keep her as socially isolated as possible, so from that point until she reached 13 years, 7 months, he kept her locked alone in a room. During this time he almost always strapped her to a child’s toilet or bound her in a crib with her arms and legs completely immobilized, forbade anyone from interacting with her, and left her severely malnourished.[3][4][5] The extent of Genie’s isolation prevented her from being exposed to any significant amount of speech, and as a result she did not acquire language during childhood. Her abuse came to the attention of Los Angeles child welfare authorities on November 4, 1970.[1][3][4]

In the first several years after Genie’s early life and circumstances came to light, psychologists, linguists and other scientists focused a great deal of attention on Genie’s case, seeing in her near-total isolation an opportunity to study many aspects of human development. […] In early January 1978 Genie’s mother suddenly decided to forbid all of the scientists except for one from having any contact with Genie, and all testing and scientific observations of her immediately ceased. Most of the scientists who studied and worked with Genie have not seen her since this time. The only post-1977 updates on Genie and her whereabouts are personal observations or secondary accounts of them, and all are spaced several years apart. […]

Genie’s father had an extremely low tolerance for noise, to the point of refusing to have a working television or radio in the house. Due to this, the only sounds Genie ever heard from her parents or brother on a regular basis were noises when they used the bathroom.[8][43] Although Genie’s mother claimed that Genie had been able to hear other people talking in the house, her father almost never allowed his wife or son to speak and viciously beat them if he heard them talking without permission. They were particularly forbidden to speak to or around Genie, so what conversations they had were therefore always very quiet and out of Genie’s earshot, preventing her from being exposed to any meaningful language besides her father’s occasional swearing.[3][13][43] […] Genie’s father fed Genie as little as possible and refused to give her solid food […]

In late October 1970, Genie’s mother and father had a violent argument in which she threatened to leave if she could not call her parents. He eventually relented, and later that day Genie’s mother was able to get herself and Genie away from her husband while he was out of the house […] She and Genie went to live with her parents in Monterey Park.[13][20][56] Around three weeks later, on November 4, after being told to seek disability benefits for the blind, Genie’s mother decided to do so in nearby Temple City, California and brought Genie along with her.[3][56]

On account of her near-blindness, instead of the disabilities benefits office Genie’s mother accidentally entered the general social services office next door.[3][56] The social worker who greeted them instantly sensed something was not right when she first saw Genie and was shocked to learn Genie’s true age was 13, having estimated from her appearance and demeanor that she was around 6 or 7 and possibly autistic. She notified her supervisor, and after questioning Genie’s mother and confirming Genie’s age they immediately contacted the police. […]

Upon admission to Children’s Hospital, Genie was extremely pale and grossly malnourished. She was severely undersized and underweight for her age, standing 4 ft 6 in (1.37 m) and weighing only 59 pounds (27 kg) […] Genie’s gross motor skills were extremely weak; she could not stand up straight nor fully straighten any of her limbs.[83][84] Her movements were very hesitant and unsteady, and her characteristic “bunny walk”, in which she held her hands in front of her like claws, suggested extreme difficulty with sensory processing and an inability to integrate visual and tactile information.[62] She had very little endurance, only able to engage in any physical activity for brief periods of time.[85] […]

Despite tests conducted shortly after her admission which determined Genie had normal vision in both eyes she could not focus them on anything more than 10 feet (3 m) away, which corresponded to the dimensions of the room she was kept in.[86] She was also completely incontinent, and gave no response whatsoever to extreme temperatures.[48][87] As Genie never ate solid food as a child she was completely unable to chew and had very severe dysphagia, completely unable to swallow any solid or even soft food and barely able to swallow liquids.[80][88] Because of this she would hold anything which she could not swallow in her mouth until her saliva broke it down, and if this took too long she would spit it out and mash it with her fingers.[50] She constantly salivated and spat, and continually sniffed and blew her nose on anything that happened to be nearby.[83][84]

Genie’s behavior was typically highly anti-social, and proved extremely difficult for others to control. She had no sense of personal property, frequently pointing to or simply taking something she wanted from someone else, and did not have any situational awareness whatsoever, acting on any of her impulses regardless of the setting. […] Doctors found it extremely difficult to test Genie’s mental age, but on two attempts they found Genie scored at the level of a 13-month-old. […] When upset Genie would wildly spit, blow her nose into her clothing, rub mucus all over her body, frequently urinate, and scratch and strike herself.[102][103] These tantrums were usually the only times Genie was at all demonstrative in her behavior. […] Genie clearly distinguished speaking from other environmental sounds, but she remained almost completely silent and was almost entirely unresponsive to speech. When she did vocalize, it was always extremely soft and devoid of tone. Hospital staff initially thought that the responsiveness she did show to them meant she understood what they were saying, but later determined that she was instead responding to nonverbal signals that accompanied their speaking. […] Linguists later determined that in January 1971, two months after her admission, Genie only showed understanding of a few names and about 15–20 words. Upon hearing any of these, she invariably responded to them as if they had been spoken in isolation. Hospital staff concluded that her active vocabulary at that time consisted of just two short phrases, “stop it” and “no more”.[27][88][99] Beyond negative commands, and possibly intonation indicating a question, she showed no understanding of any grammar whatsoever. […] Genie had a great deal of difficulty learning to count in sequential order. During Genie’s stay with the Riglers, the scientists spent a great deal of time attempting to teach her to count. She did not start to do so at all until late 1972, and when she did her efforts were extremely deliberate and laborious. By 1975 she could only count up to 7, which even then remained very difficult for her.”

“From January 1978 until 1993, Genie moved through a series of at least four additional foster homes and institutions. In some of these locations she was further physically abused and harassed to extreme degrees, and her development continued to regress. […] Genie is a ward of the state of California, and is living in an undisclosed location in the Los Angeles area.[3][20] In May 2008, ABC News reported that someone who spoke under condition of anonymity had hired a private investigator who located Genie in 2000. She was reportedly living a relatively simple lifestyle in a small private facility for mentally underdeveloped adults, and appeared to be happy. Although she only spoke a few words, she could still communicate fairly well in sign language.[3]

April 20, 2015 Posted by | Biology, Books, Botany, Ecology, Geography, History, Mathematics, Psychology, Wikipedia, Zoology | Leave a comment

Mammoths, Sabertooths, and Hominids: 65 Million Years of Mammalian Evolution in Europe (2)

Here’s my first post about the book.

I wasn’t quite sure how to rate the book, but I ended up at four stars on goodreads. The main thing holding me back from giving it a higher rating is that the book is actually quite hard to read and there’s a lot of talk about teeth; one general point I learned from this book is that the teeth animals who lived in the past have left behind for us to find are sometimes really useful, because they can help us to make/support various inferences about other things, from animal behaviours to climatic developments. As for the ‘hard to read’-part, I (mostly) don’t blame the author for this because a book like this would have to be a bit hard to read to provide the level of coverage that is provided; that’s part of why I give it four stars in spite of this. If you have a look at the links in the first post, you’ll notice the many Latin names. You’ll find a lot of those in the text as well. This is perfectly natural as there were a lot of e.g. horse-like and rhino-like species living in the past and you need to be clear about which one of them you’re talking about now because they were all different, lived in different time periods, etc. For obvious reasons the book has a lot of talk about species/genera with no corresponding ‘familiar/popular’ names (like ‘cat’ or ‘dog’), and you need to keep track of the Latin names to make sense of the stuff; as well as keeping track of the various other Latin terms used e.g. in osteometry. So you’ll encounter some passages where there’s some talk about the differences between two groups whose names look pretty similar, and you’re told about how one group had two teeth which were a bit longer than they were in the other group and the teeth also looked slightly different (and you’ll be told exactly which teeth we’re talking about, described in a language you’d probably have to be a dentist to understand without looking up a lot of stuff along the way). Problems keeping track of the animals/groups encountered also stem from the fact that whereas some species encountered in the book do have modern counterparts, others don’t. The coverage helps you to figure out which ecological niche which group may have inhabited, but if you’re completely unfamiliar with the field of ecology I’m not sure how easy it is to get into this mindset. The text does provide some help navigating this weird landscape of the past, and the many fascinating illustrations in the book make it easier to visualize what the animals encountered along the way might have looked like, but reading the book takes some work.

That said, it’s totally worth it because this stuff’s just plain fascinating! The book isn’t quite ‘up there’ with Herrera et al. (it reminded me a bit more of van der Geer et al., not only because of the slight coverage overlap), but some of the stuff in there’s pretty damn awesome – and it’s stuff you ought to know, because it’ll probably change how you think about the world. The really neat thing about reading a book like this is that it exposes a lot of unwarranted assumptions you’ve been making without knowing it, about what the past used to be like. I’m almost certain anyone reading a book like this will encounter ideas which are very surprising to them. We look at the world through the eyes of the present, and it can be difficult to imagine just how many things used to be different. Vague and tentative ideas you might have had about how the world used to look like and how it used to work can through reading books like this one be replaced with a much more clear, and much better supported, picture of the past. Even though there’s still a lot of stuff we don’t know, and will never know. I could mention almost countless examples of things I was very surprised to learn while reading this book, and I’m sure many people reading the book would encounter even more of these, as I actually was somewhat familiar with parts of the related literature already before reading the book.

I’ve added a few sample quotes and observations from the book below.

“Europe, although just an appendage of the Eurasian supercontinent, acted during most of its history as a crossroad where Asian, African, and American faunas passed one another, throughout successive dispersal and extinction events. But these events did not happen in an isolated context, since they were the response to climatic and environmental events of a higher order. Thus this book pays special attention to the abundant literature that for the past few decades has dedicated itself to the climatic evolution of our planet.”

“A common scenario tends to posit the early evolutionary radiation of placental mammals as occurring only after the extinction of the dinosaurs at the end of the Cretaceous period. The same scenario assumes a sudden explosion of forms immediately after the End Cretaceous Mass Extinction, filling the vacancies left by the vanished reptilian faunas. But a close inspection of the first epoch of the Cenozoic provides quite a different picture: the “explosion” began well before the end of the Cretaceous period and was not sudden, but lasted millions of years throughout the first division of the Cenozoic era, the Paleocene epoch. […] our knowledge of this remote time of mammalian evolution is much more obscure and incomplete than our understanding of the other periods of the Cenozoic. […] compared with our present world, and in contrast to the succeeding epochs, the Paleocene appears to us as a strange time, in which the present orders of mammals were absent or can hardly be distinguished: no rodents, no perissodactyls, no artiodactyls, bizarre noncarnivorous carnivorans. […] although the Paleocene was mammalian in character, we do not recognize it as a clear part of our own world; it looks more like an impoverished extension of the late Cretaceous world than the seed of the present Age of Mammals.”

“The diatrymas were human-size — up to 2 m tall — ground-running birds that inhabited the terrestrial ecosystems of Europe and North America in the Paleocene and the early to middle Eocene […] Besides the large diatrymas, a large variety of crocodiles — mainly terrestrial and amphibious eusuchian crocodiles — populated the marshes of the Paleocene rainforests. […] The high diversification of the crocodile fauna throughout the Paleocene and Eocene represents a significant ecological datum, since crocodiles do not tolerate temperatures below 10 to 15°C (exceptionally, they could survive in temperatures of about 5 or 6°C). Their existence in Europe indicates that during the first part of the Cenozoic the average temperature of the coldest month never fell below these values and that these mild conditions persisted at least until the middle Miocene.”

“At the end of the Paleocene, approximately 55.5 million years ago, there was a sudden, short-term warming known as the Latest Paleocene Thermal Maximum. Over a period of tens of thousands of years or less, the temperature of all the oceans increased by around 4°C. This was the highest warming during the entire Cenozoic, reaching global mean temperatures of around 20°C. There is some evidence that the Latest Paleocene Thermal Maximum resulted from a sudden increase in atmospheric CO2. Intense volcanic activity developed at the Paleocene–Eocene boundary, associated with the rifting process in the North Atlantic and the opening of the Norwegian-Greenland Sea. […] According to some analyses, atmospheric CO2 during the early Eocene may have been eight times its present concentration. […] The high temperatures and increasing humidity favored the extension of tropical rainforests over the middle and higher latitudes, as far north as Ellesmere Island, now in the Canadian arctic north. There, an abundant fauna — including crocodiles, monitor lizards, primates, rodents, multituberculates, early perissodactyls, and the pantodont Coryphodon — and a flora composed of tropical elements indicates the extension of the forests as far north as 78 degrees north latitude. […] The global oceanic level at the beginning of the Eocene was high, and extensive areas of Eurasia were still under the sea. In this context, Europe consisted of a number of emerged islands forming a kind of archipelago. A central European island consisted of parts of present-day England, France, and Germany, although it was placed in a much more southerly position, approximately at the present latitude of Naples. […] To the east, the growing Mediterranean opened into a wide sea, since the landmasses of Turkey, Iraq, and Iran were still below sea level. To the east of the Urals, the Turgai Strait still connected the warm waters of the Tethys Sea with the Polar Sea. […] Despite the opening of the Greenland-Norwegian Sea, Europe and North America were still connected during most of the early and middle Eocene across two main land bridges […] the De Geer Corridor [and] the Thule Bridge […] these corridors must have been effective, since the European fossil record shows a massive entry of American elements […] The ischyromyid and ailuravid rodents, as well as the miacid carnivores, were among the oldest representatives of the modern orders of mammals to appear in Europe during the early Eocene. However, they were not the only ones, since the “modernization” of the mammalian communities at this time went even further, and groups such as the first true primates, bats (Chiroptera), flying lemurs (Dermoptera), and oddtoed (Perissodactyla) and even-toed (Artiodactyla) ungulates entered onto the scene, in both Europe and North America.”

“Although it was the first member of the horse lineage, Pliolophus certainly did not look like a horse. As classically stated, it had the dimensions of a medium dog (“a fox-terrier”), bearing four hooves on the front legs and three on the hind legs. […] the first rhino-related forms included Hyrachius, a small rhino about the size of a wolf that during the Eocene inhabited a wide geographic range, from North America to Europe and Asia.” (Yep, in case you didn’t know Europe had rhinos for millions and millions of years…) “The artiodactyls are among the most successful orders of mammals, having diversified in the past 10 million years into a wide array of families, subfamilies, tribes, and genera all around the world, including pigs, peccaries, hippos, chevrotains, camels, giraffes, deer, antelopes, gazelles, goats, and cattle. They are easily distinguished from the perissodactyls because each extremity is supported on the two central toes, instead of on the middle strengthened toe. […] The oldest member of the order is Diacodexis, […] a rabbit-size ungulate”

“Although the number of middle Eocene localities in Europe is quite restricted, we have excellent knowledge of the terrestrial communities of this time thanks to the extraordinary fossiliferous site of Messel, Germany. […] several specimens from Messel retain in their gut their last meal, providing a rare opportunity for testing the teeth-inferred dietary requirements of a number of extinct mammalian groups. […] A dense canopy forest surrounded Messel lake, formed of several tropical and paratropical taxa that today live in Southeast Asia”.

“At the end of the middle Eocene, things began to change in the European archipelago. Several late Paleocene and early Eocene survivors had become extinct […] The last part of the middle Eocene saw a clear change in the structure of the herbivore community as specialized browsing herbivores […] replaced the small to medium-size omnivorous/ frugivorous archaic ungulates of the early Eocene and became the dominant species. […] These changes among the mammalian faunas were most probably a response to the major tectonic transformations occurring at that time and the associated environmental changes. During the middle Eocene, the Indian plate collided with Asia, closing the Tethys Sea north of India. The collision of India and the compression between Africa and Europe formed an active alpine mountain belt along the southern border of Eurasia. In the western Mediterranean, strong compression occurred during the late Eocene, […] leading to the final emergence of the Pyrenees. To the south of the Pyrenees, the sea branch between the Iberian plate and Europe retreated”

“The European terrestrial ecosystems at the end of the Eocene were quite different from those inherited from the Paleocene, which were dominated by archaic, unspecialized groups. In contrast, a diversified fauna of specialized small and large browsing herbivores […] characterized the late Eocene. From our perspective, they looked much more “modern” than those of the early and early-middle Eocene and perfectly adapted to the new late Eocene environmental conditions characterized by the spread of more open habitats.”

“during the Eocene […] Australia and South America were still attached to Antarctica, as the last remnants of the ancient Gondwanan supercontinent. Today’s circumpolar current did not yet exist, and the equatorial South Atlantic and South Pacific waters went closer to the Antarctic coasts, thus transporting heat from the low latitudes to the high southern latitudes. However, this changed during the late Eocene, when a rifting process began to separate Australia from Antarctica. At the beginning of the Oligocene, between 34 and 33 million years ago, the spread between the two continents was large enough to allow a first phase of circumpolar circulation, which restricted the thermal exchange between the low-latitude equatorial waters and the Antarctic waters. A sudden and massive cooling took place, and mean global temperatures fell by about 5°C. […] During a few hundred thousand years (the estimated duration of this early Oligocene glacial episode), the ice sheets expanded and covered extensive areas of Antarctica, particularly in its western regions. […] The onset of Antarctic glaciation and the growing of the ice sheets in western Antarctica provoked an important global sea-level lowering of about 30 m. Several shallow epicontinental seas became continental areas, including those that surrounded the European Archipelago. The Turgai Strait, which during millions of years had isolated the European lands from Asia, vanished and opened a migration pathway for Asian and American mammals to the west. […] The tectonic movements led to the final split of the Tethys Sea into two main seas, the Mediterranean Sea to the south and the Paratethys Sea, the latter covering the formerly open ocean areas of central and eastern Europe. […] After the retreat of the Turgai Strait and the emergence of the Paratethys province, the European Archipelago ceased to exist, and Europe approached its present configuration. The ancient barriers that had prevented Asian faunas from settling in this continental area no longer existed, and a wave of new immigrants entered from the east. This coincided with the trend toward more temperate conditions and the spread of open environments initiated during the late Eocene. Consequently, most of the species that had characterized the middle and late Eocene declined or became completely extinct, replaced by herds of Asian newcomers.”

February 23, 2015 Posted by | Biology, Books, Ecology, Evolutionary biology, Geology, Paleontology, Zoology | Leave a comment

Wikipedia articles of interest

(A minor note: These days when I’m randomly browsing wikipedia and not just looking up concepts or terms found in the books I read, I’m mostly browsing the featured content on wikipedia. There’s a lot of featured stuff, and on average such articles more interesting than random articles. As a result of this approach, all articles covered in the post below are featured articles. A related consequence of this shift may be that I may cover fewer articles in future wikipedia posts than I have in the past; this post only contains five articles, which I believe is slightly less than usual for these posts – a big reason for this being that it sometimes takes a lot of time to read a featured article.)

i. Woolly mammoth.

Ice_age_fauna_of_northern_Spain_-_Mauricio_Antón

“The woolly mammoth (Mammuthus primigenius) was a species of mammoth, the common name for the extinct elephant genus Mammuthus. The woolly mammoth was one of the last in a line of mammoth species, beginning with Mammuthus subplanifrons in the early Pliocene. M. primigenius diverged from the steppe mammoth, M. trogontherii, about 200,000 years ago in eastern Asia. Its closest extant relative is the Asian elephant. […] The earliest known proboscideans, the clade which contains elephants, existed about 55 million years ago around the Tethys Sea. […] The family Elephantidae existed six million years ago in Africa and includes the modern elephants and the mammoths. Among many now extinct clades, the mastodon is only a distant relative of the mammoths, and part of the separate Mammutidae family, which diverged 25 million years before the mammoths evolved.[12] […] The woolly mammoth coexisted with early humans, who used its bones and tusks for making art, tools, and dwellings, and the species was also hunted for food.[1] It disappeared from its mainland range at the end of the Pleistocene 10,000 years ago, most likely through a combination of climate change, consequent disappearance of its habitat, and hunting by humans, though the significance of these factors is disputed. Isolated populations survived on Wrangel Island until 4,000 years ago, and on St. Paul Island until 6,400 years ago.”

“The appearance and behaviour of this species are among the best studied of any prehistoric animal due to the discovery of frozen carcasses in Siberia and Alaska, as well as skeletons, teeth, stomach contents, dung, and depiction from life in prehistoric cave paintings. […] Fully grown males reached shoulder heights between 2.7 and 3.4 m (9 and 11 ft) and weighed up to 6 tonnes (6.6 short tons). This is almost as large as extant male African elephants, which commonly reach 3–3.4 m (9.8–11.2 ft), and is less than the size of the earlier mammoth species M. meridionalis and M. trogontherii, and the contemporary M. columbi. […] Woolly mammoths had several adaptations to the cold, most noticeably the layer of fur covering all parts of the body. Other adaptations to cold weather include ears that are far smaller than those of modern elephants […] The small ears reduced heat loss and frostbite, and the tail was short for the same reason […] They had a layer of fat up to 10 cm (3.9 in) thick under the skin, which helped to keep them warm. […] The coat consisted of an outer layer of long, coarse “guard hair”, which was 30 cm (12 in) on the upper part of the body, up to 90 cm (35 in) in length on the flanks and underside, and 0.5 mm (0.020 in) in diameter, and a denser inner layer of shorter, slightly curly under-wool, up to 8 cm (3.1 in) long and 0.05 mm (0.0020 in) in diameter. The hairs on the upper leg were up to 38 cm (15 in) long, and those of the feet were 15 cm (5.9 in) long, reaching the toes. The hairs on the head were relatively short, but longer on the underside and the sides of the trunk. The tail was extended by coarse hairs up to 60 cm (24 in) long, which were thicker than the guard hairs. It is likely that the woolly mammoth moulted seasonally, and that the heaviest fur was shed during spring.”

“Woolly mammoths had very long tusks, which were more curved than those of modern elephants. The largest known male tusk is 4.2 m (14 ft) long and weighs 91 kg (201 lb), but 2.4–2.7 m (7.9–8.9 ft) and 45 kg (99 lb) was a more typical size. Female tusks averaged at 1.5–1.8 m (4.9–5.9 ft) and weighed 9 kg (20 lb). About a quarter of the length was inside the sockets. The tusks grew spirally in opposite directions from the base and continued in a curve until the tips pointed towards each other. In this way, most of the weight would have been close to the skull, and there would be less torque than with straight tusks. The tusks were usually asymmetrical and showed considerable variation, with some tusks curving down instead of outwards and some being shorter due to breakage.”

“Woolly mammoths needed a varied diet to support their growth, like modern elephants. An adult of six tonnes would need to eat 180 kg (397 lb) daily, and may have foraged as long as twenty hours every day. […] Woolly mammoths continued growing past adulthood, like other elephants. Unfused limb bones show that males grew until they reached the age of 40, and females grew until they were 25. The frozen calf “Dima” was 90 cm (35 in) tall when it died at the age of 6–12 months. At this age, the second set of molars would be in the process of erupting, and the first set would be worn out at 18 months of age. The third set of molars lasted for ten years, and this process was repeated until the final, sixth set emerged when the animal was 30 years old. A woolly mammoth could probably reach the age of 60, like modern elephants of the same size. By then the last set of molars would be worn out, the animal would be unable to chew and feed, and it would die of starvation.[53]

“The habitat of the woolly mammoth is known as “mammoth steppe” or “tundra steppe”. This environment stretched across northern Asia, many parts of Europe, and the northern part of North America during the last ice age. It was similar to the grassy steppes of modern Russia, but the flora was more diverse, abundant, and grew faster. Grasses, sedges, shrubs, and herbaceous plants were present, and scattered trees were mainly found in southern regions. This habitat was not dominated by ice and snow, as is popularly believed, since these regions are thought to have been high-pressure areas at the time. The habitat of the woolly mammoth also supported other grazing herbivores such as the woolly rhinoceros, wild horses and bison. […] A 2008 study estimated that changes in climate shrank suitable mammoth habitat from 7,700,000 km2 (3,000,000 sq mi) 42,000 years ago to 800,000 km2 (310,000 sq mi) 6,000 years ago.[81][82] Woolly mammoths survived an even greater loss of habitat at the end of the Saale glaciation 125,000 years ago, and it is likely that humans hunted the remaining populations to extinction at the end of the last glacial period.[83][84] […] Several woolly mammoth specimens show evidence of being butchered by humans, which is indicated by breaks, cut-marks, and associated stone tools. It is not known how much prehistoric humans relied on woolly mammoth meat, since there were many other large herbivores available. Many mammoth carcasses may have been scavenged by humans rather than hunted. Some cave paintings show woolly mammoths in structures interpreted as pitfall traps. Few specimens show direct, unambiguous evidence of having been hunted by humans.”

“While frozen woolly mammoth carcasses had been excavated by Europeans as early as 1728, the first fully documented specimen was discovered near the delta of the Lena River in 1799 by Ossip Schumachov, a Siberian hunter.[90] Schumachov let it thaw until he could retrieve the tusks for sale to the ivory trade. [Aargh!] […] The 1901 excavation of the “Berezovka mammoth” is the best documented of the early finds. It was discovered by the Berezovka River, and the Russian authorities financed its excavation. Its head was exposed, and the flesh had been scavenged. The animal still had grass between its teeth and on the tongue, showing that it had died suddenly. […] By 1929, the remains of 34 mammoths with frozen soft tissues (skin, flesh, or organs) had been documented. Only four of them were relatively complete. Since then, about that many more have been found.”

ii. Daniel Lambert.

Daniel Lambert (13 March 1770 – 21 June 1809) was a gaol keeper[n 1] and animal breeder from Leicester, England, famous for his unusually large size. After serving four years as an apprentice at an engraving and die casting works in Birmingham, he returned to Leicester around 1788 and succeeded his father as keeper of Leicester’s gaol. […] At the time of Lambert’s return to Leicester, his weight began to increase steadily, even though he was athletically active and, by his own account, abstained from drinking alcohol and did not eat unusual amounts of food. In 1805, Lambert’s gaol closed. By this time, he weighed 50 stone (700 lb; 318 kg), and had become the heaviest authenticated person up to that point in recorded history. Unemployable and sensitive about his bulk, Lambert became a recluse.

In 1806, poverty forced Lambert to put himself on exhibition to raise money. In April 1806, he took up residence in London, charging spectators to enter his apartments to meet him. Visitors were impressed by his intelligence and personality, and visiting him became highly fashionable. After some months on public display, Lambert grew tired of exhibiting himself, and in September 1806, he returned, wealthy, to Leicester, where he bred sporting dogs and regularly attended sporting events. Between 1806 and 1809, he made a further series of short fundraising tours.

In June 1809, he died suddenly in Stamford. At the time of his death, he weighed 52 stone 11 lb (739 lb; 335 kg), and his coffin required 112 square feet (10.4 m2) of wood. Despite the coffin being built with wheels to allow easy transport, and a sloping approach being dug to the grave, it took 20 men almost half an hour to drag his casket into the trench, in a newly opened burial ground to the rear of St Martin’s Church.”

“Sensitive about his weight, Daniel Lambert refused to allow himself to be weighed, but sometime around 1805, some friends persuaded him to come with them to a cock fight in Loughborough. Once he had squeezed his way into their carriage, the rest of the party drove the carriage onto a large scale and jumped out. After deducting the weight of the (previously weighed) empty carriage, they calculated that Lambert’s weight was now 50 stone (700 lb; 318 kg), and that he had thus overtaken Edward Bright, the 616-pound (279 kg) “Fat Man of Maldon”,[23] as the heaviest authenticated person in recorded history.[20][24]

Despite his shyness, Lambert badly needed to earn money, and saw no alternative to putting himself on display, and charging his spectators.[20] On 4 April 1806, he boarded a specially built carriage and travelled from Leicester[26] to his new home at 53 Piccadilly, then near the western edge of London.[20] For five hours each day, he welcomed visitors into his home, charging each a shilling (about £3.5 as of 2014).[18][25] […] Lambert shared his interests and knowledge of sports, dogs and animal husbandry with London’s middle and upper classes,[27] and it soon became highly fashionable to visit him, or become his friend.[27] Many called repeatedly; one banker made 20 visits, paying the admission fee on each occasion.[17] […] His business venture was immediately successful, drawing around 400 paying visitors per day. […] People would travel long distances to see him (on one occasion, a party of 14 travelled to London from Guernsey),[n 5] and many would spend hours speaking with him on animal breeding.”

“After some months in London, Lambert was visited by Józef Boruwłaski, a 3-foot 3-inch (99 cm) dwarf then in his seventies.[44] Born in 1739 to a poor family in rural Pokuttya,[45] Boruwłaski was generally considered to be the last of Europe’s court dwarfs.[46] He was introduced to the Empress Maria Theresa in 1754,[47] and after a short time residing with deposed Polish king Stanisław Leszczyński,[44] he exhibited himself around Europe, thus becoming a wealthy man.[48] At age 60, he retired to Durham,[49] where he became such a popular figure that the City of Durham paid him to live there[50] and he became one of its most prominent citizens […] The meeting of Lambert and Boruwłaski, the largest and smallest men in the country,[51] was the subject of enormous public interest”

“There was no autopsy, and the cause of Lambert’s death is unknown.[65] While many sources say that he died of a fatty degeneration of the heart or of stress on his heart caused by his bulk, his behaviour in the period leading to his death does not match that of someone suffering from cardiac insufficiency; witnesses agree that on the morning of his death he appeared well, before he became short of breath and collapsed.[65] Bondeson (2006) speculates that the most consistent explanation of his death, given his symptoms and medical history, is that he had a sudden pulmonary embolism.[65]

iii. Geology of the Capitol Reef area.

Waterpocket_Fold_-_Looking_south_from_the_Strike_Valley_Overlook

“The exposed geology of the Capitol Reef area presents a record of mostly Mesozoic-aged sedimentation in an area of North America in and around Capitol Reef National Park, on the Colorado Plateau in southeastern Utah.

Nearly 10,000 feet (3,000 m) of sedimentary strata are found in the Capitol Reef area, representing nearly 200 million years of geologic history of the south-central part of the U.S. state of Utah. These rocks range in age from Permian (as old as 270 million years old) to Cretaceous (as young as 80 million years old.)[1] Rock layers in the area reveal ancient climates as varied as rivers and swamps (Chinle Formation), Sahara-like deserts (Navajo Sandstone), and shallow ocean (Mancos Shale).

The area’s first known sediments were laid down as a shallow sea invaded the land in the Permian. At first sandstone was deposited but limestone followed as the sea deepened. After the sea retreated in the Triassic, streams deposited silt before the area was uplifted and underwent erosion. Conglomerate followed by logs, sand, mud and wind-transported volcanic ash were later added. Mid to Late Triassic time saw increasing aridity, during which vast amounts of sandstone were laid down along with some deposits from slow-moving streams. As another sea started to return it periodically flooded the area and left evaporite deposits. Barrier islands, sand bars and later, tidal flats, contributed sand for sandstone, followed by cobbles for conglomerate and mud for shale. The sea retreated, leaving streams, lakes and swampy plains to become the resting place for sediments. Another sea, the Western Interior Seaway, returned in the Cretaceous and left more sandstone and shale only to disappear in the early Cenozoic.”

“The Laramide orogeny compacted the region from about 70 million to 50 million years ago and in the process created the Rocky Mountains. Many monoclines (a type of gentle upward fold in rock strata) were also formed by the deep compressive forces of the Laramide. One of those monoclines, called the Waterpocket Fold, is the major geographic feature of the park. The 100 mile (160 km) long fold has a north-south alignment with a steeply east-dipping side. The rock layers on the west side of the Waterpocket Fold have been lifted more than 7,000 feet (2,100 m) higher than the layers on the east.[23] Thus older rocks are exposed on the western part of the fold and younger rocks on the eastern part. This particular fold may have been created due to movement along a fault in the Precambrian basement rocks hidden well below any exposed formations. Small earthquakes centered below the fold in 1979 may be from such a fault.[24] […] Ten to fifteen million years ago the entire region was uplifted several thousand feet (well over a kilometer) by the creation of the Colorado Plateaus. This time the uplift was more even, leaving the overall orientation of the formations mostly intact. Most of the erosion that carved today’s landscape occurred after the uplift of the Colorado Plateau with much of the major canyon cutting probably occurring between 1 and 6 million years ago.”

iv. Problem of Apollonius.

“In Euclidean plane geometry, Apollonius’s problem is to construct circles that are tangent to three given circles in a plane (Figure 1).

396px-Apollonius_problem_typical_solution.svg

Apollonius of Perga (ca. 262 BC – ca. 190 BC) posed and solved this famous problem in his work Ἐπαφαί (Epaphaí, “Tangencies”); this work has been lost, but a 4th-century report of his results by Pappus of Alexandria has survived. Three given circles generically have eight different circles that are tangent to them […] and each solution circle encloses or excludes the three given circles in a different way […] The general statement of Apollonius’ problem is to construct one or more circles that are tangent to three given objects in a plane, where an object may be a line, a point or a circle of any size.[1][2][3][4] These objects may be arranged in any way and may cross one another; however, they are usually taken to be distinct, meaning that they do not coincide. Solutions to Apollonius’ problem are sometimes called Apollonius circles, although the term is also used for other types of circles associated with Apollonius. […] A rich repertoire of geometrical and algebraic methods have been developed to solve Apollonius’ problem,[9][10] which has been called “the most famous of all” geometry problems.[3]

v. Globular cluster.

“A globular cluster is a spherical collection of stars that orbits a galactic core as a satellite. Globular clusters are very tightly bound by gravity, which gives them their spherical shapes and relatively high stellar densities toward their centers. The name of this category of star cluster is derived from the Latin globulus—a small sphere. A globular cluster is sometimes known more simply as a globular.

Globular clusters, which are found in the halo of a galaxy, contain considerably more stars and are much older than the less dense galactic, or open clusters, which are found in the disk. Globular clusters are fairly common; there are about 150[2] to 158[3] currently known globular clusters in the Milky Way, with perhaps 10 to 20 more still undiscovered.[4] Large galaxies can have more: Andromeda, for instance, may have as many as 500. […]

Every galaxy of sufficient mass in the Local Group has an associated group of globular clusters, and almost every large galaxy surveyed has been found to possess a system of globular clusters.[8] The Sagittarius Dwarf galaxy and the disputed Canis Major Dwarf galaxy appear to be in the process of donating their associated globular clusters (such as Palomar 12) to the Milky Way.[9] This demonstrates how many of this galaxy’s globular clusters might have been acquired in the past.

Although it appears that globular clusters contain some of the first stars to be produced in the galaxy, their origins and their role in galactic evolution are still unclear.”

October 23, 2014 Posted by | Astronomy, Biology, Ecology, Geography, Geology, History, Mathematics, Paleontology, Wikipedia, Zoology | Leave a comment

Ecological Dynamics (I?)

“Mathematical models underpin much ecological theory, […] [y]et most students of ecology and environmental science receive much less formal training in mathematics than their counterparts in other scientific disciplines. Motivating both graduate and undergraduate students to study ecological dynamics thus requires an introduction which is initially accessible with limited mathematical and computational skill, and yet offers glimpses of the state of the art in at least some areas. This volume represents our attempt to reconcile these conflicting demands […] Ecology is the branch of biology that deals with the interaction of living organisms with their environment. […] The primary aim of this book is to develop general theory for describing ecological dynamics. Given this aspiration, it is useful to identify questions that will be relevant to a wide range of organisms and/or habitats. We shall distinguish questions relating to individuals, populations, communities, and ecosystems. A population is all the organisms of a particular species in a given region. A community is all the populations in a given region. An ecosystem is a community related to its physical and chemical environment. […] Just as the physical and chemical properties of materials are the result of interactions involving individual atoms and molecules, so the dynamics of populations and communities can be interpreted as the combined effects of properties of many individuals […] All models are (at best) approximations to the truth so, given data of sufficient quality and diversity, all models will turn out to be false. The key to understanding the role of models in most ecological applications is to recognise that models exist to answer questions. A model may provide a good description of nature in one context but be woefully inadequate in another. […] Ecology is no different from other disciplines in its reliance on simple models to underpin understanding of complex phenomena. […] the real world, with all its complexity, is initially interpreted through comparison with the simplistic situations described by the models. The inevitable deviations from the model predictions [then] become the starting point for the development of more specific theory.”

I haven’t blogged this book yet even if it’s been a while since I finished it, and I figured I ought to talk a little bit about it now. As pointed out on goodreads, I really liked the book. It’s basically a math textbook for biologists which deals with how to set up models in a specific context, that dealing with questions pertaining to ecological dynamics; having read the above quote you should at this point at least have some idea which kind of stuff this field deals with. Here are a few links to examples of applications mentioned/covered in the book which may give you a better idea of the kinds of things covered.

There are 9 chapters in the book, and only the introductory chapter has fewer than 50 ‘named’ equations – most have around 70-80 equations, and 3 of them have more than 100. I have tried to avoid equations in this post in part because it’s hell to deal with them in wordpress, so I’ll be leaving out a lot of stuff in my coverage. Large chunks of the coverage was to some extent review but there was also some new stuff in there. The book covers material both intended for undergraduates and graduates, and even if the book is presumably intended for biology majors many of the ideas also can be ‘transferred’ to other contexts where the same types of specific modelling frameworks might be applied; for example there are some differences between discrete-time models and continuous-time models, and those differences apply regardless of whether you’re modelling animal behaviour or, say, human behaviour. A local stability analysis looks quite similar in the contexts of an economic model and an ecological model. Etc. I’ve tried to mostly talk about rather ‘general stuff’ in this coverage, i.e. model concepts and key ideas covered in the book which might also be applicable in other fields of research as well. I’ve tried to keep things reasonably simple in this post, and I’ve only talked about stuff from the first three chapters.

“The simplest ecological models, called deterministic models, make the assumption that if we know the present condition of a system, we can predict its future. Before we can begin to formulate such a model, we must decide what quantities, known as state variables, we shall use to describe the current condition of the system. This choice always involves a subtle balance of biological realism (or at least plausibility) against mathematical complexity. […] The first requirement  in formulating a usable model is […] to decide which characteristics are dynamically important in the context of the questions the model seeks to answer. […] The diversity of individual characteristics and behaviours implies that without considerable effort at simplification, a change of focus towards communities will be accompanied by an explosive increase in model complexity. […] A dynamical model is a mathematical statement of the rules governing change. The majority of models express these rules either as an update rule, specifying the relationship between the current and future state of the system, or as a differential equation, specifying the rate of change of the state variables. […] A system with [the] property [that the update rule does not depend on time] is said to be autonomous. […] [If the update rule depends on time, the models are called non-autonomous].”

“Formulation of a dynamic model always starts by identifying the fundamental processes in the system under investigation and then setting out, in mathematical language, the statement that changes in system state can only result from the operation of these processes. The “bookkeeping” framework which expresses this insight is often called a conservation equation or a balance equation. […] Writing down balance equations is just the first step in formulating an ecological model, since only in the most restrictive circumstances do balance equations on their own contain enough information to allow prediction of future values of state variables. In general, [deterministic] model formulation involves three distinct steps: *choose state variables, *derive balance equations, *make model-specific assumptions.
Selection of state variables involves biological or ecological judgment […] Deriving balance equations involves both ecological choices (what processes to include) and mathematical reasoning. The final step, the selection of assumptions particular to any one model, is left to last in order to facilitate model refinement. For example, if a model makes predictions that are at variance with observation, we may wish to change one of the model assumptions, while still retaining the same state variables and processes in the balance equations. […] a remarkably good approximation to […] stochastic dynamics is often obtained by regarding the dynamics as ‘perturbations’ of a non-autonomous, deterministic system. […] although randomness is ubiquitous, deterministic models are an appropriate starting point for much ecological modelling. […] even where deterministic models are inadequate, an essential prerequisite to the formulation and analysis of many complex, stochastic models is a good understanding of a deterministic representation of the system under investigation.”

“Faced with an update rule or a balance equation describing an ecological system, what do we do? The most obvious line of attack is to attempt to find an analytical solution […] However, except for the simplest models, analytical solutions tend to be impossible to derive or to involve formulae so complex as to be completely unhelpful. In other situations, an explicit solution can be calculated numerically. A numerical solution of a difference equation is a table of values of the state variable (or variables) at successive time steps, obtained by repeated application of the update rule […] Numerical solutions of differential equations are more tricky [but sophisticated methods for finding them do exist] […] for simple systems it is possible to obtain considerable insight by ‘numerical experiments’ involving solutions for a number of parameter values and/or initial conditions. For more complex models, numerical analysis is typically the only approach available. But the unpleasant reality is that in the vast majority of investigations it proves impossible to obtain complete or near-complete information about a dynamical system, either by deriving analytical solutions or by numerical experimentation. It is therefore reassuring that over the past century or so, mathematicians have developed methods of determining the qualitative properties of the solutions of dynamic equations, and thus answering many questions […] without explicitly solving the equations concerned.”

“[If] the long-term behaviour of the state variable is independent of the initial condition […] the ‘end state’ […] is known as an attractor. […] Equilibrium states need not be attractors; they can be repellers [as well] […] if a dynamical system has an equilibrium state, any initial condition other than the exact equilibrium value may lead to the state variable converging towards the equilibrium or diverging away from it. We characterize such equilibria as stable and unstable respectively. In some models all initial conditions result in the state variable eventually converging towards a single equilibrium value. We characterize such equilibria as globally stable. An equilibrium that is approached only from a subset of all possible initial conditions (often those close to the equilibrium itself) is said to be locally stable. […] The combination of non-periodic solutions and sensitive dependence on initial conditions is the signature of the pattern of behaviour known to mathematicians as chaos.

“Most variables and parameters in models have units. […] However, the behaviour of a natural system cannot be affected by the units in which we chose to measure the quantities we use to describe it. This implies that it should be possible to write down the defining equations of a model in a form independent of the units we use. For any dynamical equation to be valid, the quantities being equated must be measured in the same units. How then do we restate such an equation in a form which is unaffected by our choice of units? The answer lies in identifying a natural scale or base unit for each quantity in the equations and then using the ratio of each variable to its natural scale in our dynamic description. Since such ratios are pure numbers, we say that they are dimensionless. If a dynamic equation couched in terms of dimensionless variables is to be valid, then both sides of any equality must likewise be dimensionless. […] the process of non-dimensionalisation, which we call dimensional analysis, can […] yield information on system dynamics. […] Since there is no unique dimensionless form for any set of dynamical equations, it is tempting to cut short the scaling process by ‘setting some parameter(s) equal to one’. Even experienced modellers make embarrasing blunders doing this, and we strongly recommend a systematic […] approach […] The key element in the scaling process is the selection of appropriate base units – the optimal choice being dependent on the questions motivating our study.”

“The starting point for selecting the appropriate formalism [in the context of the time dimension] must […] be recognition that real ecological processes operate in continuous time. Discrete-time models make some approximation to the outcome of these processes over a finite time interval, and should thus be interpreted with care. This caution is particularly important as difference equations are intuitively appealing and computationally simple. […] incautious empirical modelling with difference equations can have surprising (adverse) consequences. […] where the time increment of a discrete-time model is an arbitrary modelling choice, model predictions should be shown to be robust against changes in the value chosen.”

“Of the almost limitless range of relations between population flux and local density, we shall discuss only two extreme possibilities. Advection occurs when an external physical flow (such as an ocean current) transports all the members of the population past the point, x [in a spatially one-dimensional model], with essentially the same velocity, v. […] Diffusion occurs when the members of the population move at random. […] This leads to a net flow rate which is proportional to the spatial gradient of population density, with a constant of proportionality D, which we call the diffusion constant. […] the net flow [in this case] takes individuals from regions of high density to regions of low density” […] […some remarks about reaction-diffusion models, which I’d initially thought I’d cover here but which turned out to be too much work to deal with (the coverage is highly context-dependent)].

October 19, 2014 Posted by | Biology, Books, Ecology, Mathematics | Leave a comment

An Introduction to Tropical Rain Forests (III)

This will be my last post about the book. I’ve included some observations from the second half of the book below.

“In the present chapter we look at […] time scales of a few years to a few centuries, up to the life spans of one or a few generations of trees. Change is examined in the context of development and disintegration of the forest canopy, the forest growth cycle […] There seems to be a general model of forest dynamics which holds in many different biomes, albeit with local variants. […] Two spatial scales of canopy dynamics can be distinguished: patch disturbance, which involves one or a few trees, and community-wide disturbance. Patch disturbance is sometimes called ‘forest gap-phase dynamics’ and since about the mid-1970s has been one of the main interests of forest scientists in many parts of the world.”

“Species differ in the microclimate in which they successfully regenerate. […] the microclimates within a rain forest […] are mainly determined by size of the canopy gap. The microclimate above the forest canopy, which is similar to that in a large clearing, is substantially different from that near the floor below mature phase forest. […] Outside, wind speeds during the day are higher, as is air temperature, while relative humidity is lower. […] The light climate within a forest is complex. There are four components, skylight coming through canopy holes, direct sunlight, seen as sunflecks on the forest floor, light transmitted through leaves, and light reflected from leaves, trunks and other surfaces. […] Both the quantity and quality of light reaching the plant is known to be of profound importance in the mechanisms of gap-phase dynamics […] The waveband 400 to 700 nm (which is approximately the visual spectrum) is utilized for photosynthesis and is known as photosynthetically active radiation or PAR. The forest floor only receives up to c. 2 per cent of the PAR incident on the forest canopy […] In addition to reduction in quantity of PAR within the forest canopy, PAR also changes in quality with a shift in the ratio of red to far-red wavelenghts […] the temporal pattern of sunfleck distribution through the day […] is of importance, not just the daily total PAR. […] The role of irradiance in seedling growth and release is easy to observe and has been much investigated. By contrast, little attention has been given to the potential role of plant mineral nutrients. […] So far, nutrients seem unimportant compared to radiation. […] Overall the shade/nutrient interaction story remains unresolved. One part of the picture is likely to be that there is no response to nutrients in dark conditions where irradiance is limiting, but a response at higher irradiances.”

“Canopy gaps have an aerial microclimate like that above the forest but the smaller the gap the less different it is from the forest interior […] Gaps were at first regarded as having a microclimate varying with their size, to be contrasted with closed-forest microclimate. But this is a simplification. […] gaps are neither homogenous holes nor are they sharply bounded. Within a gap the microclimate is most extreme towards the centre and changes outwards to the physical gap edge and beyond […] The larger the gap the more extreme the microclimate of its centre. […] there is much more variability between small gaps than large ones in microclimate [and] gap size is a poor surrogate measure of microclimate, most markedly over short periods.”

“tree species differ in the amount of solar radiation required for their regeneration. […] Ecologists and foresters continue to engage in vigorous debate as to whether species along [the] spectrum of light climates can be divided into clear, separate groups. […] some strong light-demanders require full light for both seed germination and seedling establishment. These are the pioneer species, set apart from all others by these two features.[168] By contrast, all other species have the capacity to germinate and establish below canopy shade. These may be called climax species. They are able to perpetuate in the same place, but are an extremely diverse group. […] Pioneer species germinate and establish in a gap after its creation […] They grow fast […] Below the canopy seedlings of climax species establish and, as the pioneer canopy breaks up after the death of individual trees, these climax species are ‘released’ […] and grow up as a second growth cycle. Succession has occurred as a group of climax species replaces the group of pioneer species.[…] Climax species as a group […] perpetuate themselves in situ, there is no directional change in species composition. This is called cyclic regeneration or replacement. In a small gap, pre-existing climax seedlings are released. In a large gap pioneers, which appear after gap creation, form the next forest growth cycle. One of the puzzles which remains unsolved is what determines gap-switch size. […] In all tropical rain forest floras there are fewer pioneer than climax species, and they mostly belong to a few families […] The most species-rich forested landscape will be one that includes both patches of secondary forest recovering from a big disturbance and consisting of pioneers, and also patches of primary forest composed of climax species.”

“Rain forest silviculture is the manipulation of the forest to favour species and thereby to enhance its value to humans. […] Timber properties, whether heavy or light, dark or pale, durable or not, are strongly correlated with growth rate and thus to the extent to which the species is light-demanding […]. Thus, the ecological basis of natural forest silviculture is the manipulation of the forest canopy. The biological principle of silviculture is that by controlling canopy gap size it is possible to influence species composition of the next growth cycle. The bigger the gaps the more fast-growing light-demanders will be favoured. This concept has been known in continental Europe since at least the twelth century. […] The silvicultural systems that have been applied to tropical rain forests belong to one of two kinds: the polycyclic and monocyclic systems, respectively […]. As the name implies, polycyclic systems are based on the repeated removal of selected trees in a continuing series of felling cycles, whose length is less than the time it takes the tree to mature [rotation age]. The aim is to remove trees before they begin to deteriorate from old age […] extraction on a polycyclic system tends to result in the formation of scattered small gaps in the forest canopy. By contrast, monocyclic systems remove all saleable trees at a single operation, and the length of the cycle more or less equals the rotation age of the trees. Except in those cases where there are few saleable trees, damage to the forest is more drastic than under a polycyclic system, the canopy is more extensively destroed, and bigger gaps are formed. […] the two kinds of system will tend to favour shade-bearing and light-demanding species, respectively, but the extent of the difference will depend on how many trees are felled at each cycle in a polycyclic system. […] Low intensity selective logging on a polycyclic system closely mimics the natural processes of forest dynamics and scarcely alters the composition. Monocyclic silvicultural systems, and polycyclic systems with many stems felled per hectare, shift species composition […] The amount of damage to the forest depends more on how many trees are felled than on timber volume extracted. It is commonly the case that for every tree removed for timber (logged) a second tree is totally smashed and a third tree receives damage from which it will recover”

“The essense of shifting agriculture (sometimes called swidden agriculture) is to fell a patch of forest, allow it to dry to the point where it will burn well, and then to set it on fire. The plant mineral nutrients are thereby mobilized and become available to plants in the ash. One or two fast-maturing crops of staple food species are grown […]. Yields then fall and the patch is abandoned to allow secondary forest to grow. Longer-lived species, such as chilli […] and fruit trees, and some root crops such as cassava […] are planted with the staples and continue to yield in the first years of the fallow period. Besides fruit and root crops the bush fallow, as it is often called, provides firewood, medicines, and building materials. After a minimum of 7 to 10 years the cycle can be repeated. There are many variants. Shifting agriculture was invented independently in all parts of the tropical world[253] and has proved sustainable over many centuries. […] It is now realized that shifting agriculture, as traditionally practised, is a sustainable low-input form of cultivation which can continue indefinitely on the infertile soils underlying most tropical rain forest […], provided the carrying capacity of the land is not exceeded. […] Shifting agriculture has the limitation that it can usually only support 10-20 persons km-2 […] because at any one time only c. 10 per cent of the area is under cultivation. It breaks down if either the bush fallow period is excessively shortened or if the period of cultivation is extended for too long, either of which is likely to occur if population increases and a land shortage develops. There is, however, another mode of shifting agriculture which is totally destructive […]. Farmers fell and burn the forest and grow crops on the released nutrients for several years in succession, continuing until coppicing potential and the soil seed bank are exhausted, pernicious weeds invade, and soil nutrients are seriously depleted. They then move on to a new patch of virgin forest. This is happening, for example, in parts of western Amazonia […] Replacement of forests by agriculture totally destroys them. If farmland is abandoned it is likely to take several centuries before all signs of forest succession have disappeared, and species-rich, structurally complex primary forest restored […] Agriculture is the main purpose for which rain forests are cleared. There are several major kinds of agriculture and their impact varies from place to place. Important detail is lost by pan-tropical generalization.”

“The mixed cultivation of trees and crops, agroforestry […], makes use of nutrient cycling by trees, as does shifting agriculture. Trees act as pumps, bringing nutrients into the superficial layers of the soil where shallow-rooted herbacious crops can utilize them. […] Early research led to the belief that nearly all the mineral nutrients in tropical rain forests are in the above-ground biomass and, despite much evidence to the contrary, this view is still sometimes expressed. [However] the popular belief that most of the nutrients of a tropical rain forest are in the biomass is seldom true.”

“Given a rich regional flora, forests are particularly favourable for the co-existence of many species in the same community, because they provide many different niches. […] The forest provides a whole array of different internal microclimates, both horizontally and vertically [recall this related observation from McMenamin & McMenamin: “One aspect of the environment that controls the number and types of organisms living in the environment is called its dimensionality […]. Two-dimensional (or Dimension 2) environments tend to be flat, whereas three-dimensional environments (Dimension 3) have, to a greater or lesser degree, a third dimension. This third dimension can be either in an upward or a downward direction, or a combination of both directions.” Additional dimensions add additional opportunities for specialization.] […] The same processes operate in all forests but forests have different degrees of complexity in canopy structure and differ in the number of species that occupy the many facets of what may be termed the ‘regeneration niche’. […] one-to-one specialization between a single plant and animal species as a factor of species richness exists only in a few cases […] Guilds of insects specialized to feed on (and where necessary detoxify) particular families or similar families of plants […] is a looser and commoner form of co-evolution and plays a more substantial role in the packing together of numerous sympatric species […] Browsing pressure (‘pest pressure’) of herbivores […] may be one factor that sometimes prevents any single species from attaining dominance, and acts to maintain species richness. In a similar manner dense seedling populations below a parent tree are often thinned out by disease or herbivory […] and this also therefore contributes to the prevention of single species dominance.”

“An important difference of tropical rain forests from others is the occurence of locally endemic species […]. This is one component of their species richness on the extensive scale. It means that in different places a particular niche may be occupied by different species which never compete because they never meet. It has the consequence that species are likely to become extinct when a rain forest is reduced in extent, more so than in other forest biomes. […] the main reasons why some tropical rain forests are extremely rich in species results from firstly, a long stable climatic history without episodes of extinction, in an equable environment, and in which there is no ‘climatic sieve’ to eliminate some species. Secondly, a forest canopy provides large numbers of spatial and temporal niches […] Thirdly, richness results from interactions with animals, mainly as pollinators, dispersers, or pests. Some of these factors underly species richness in other biomes also. […] The overall effeect of all of humankind’s many different impacts on tropical rain forests is to diminish the numerous dimensions of species richness. Not only does man destroy species, he also simplifies the ecosystems the remaining species inhabit.”

“the claim sometimes made that rain forests contain enormous numbers of drugs just awaiting exploitation does not survive critical examination.[319] Reality is more complex, and there are serious difficulties in developing an economic case for biodiversity conservation based on undiscovered pharmaceuticals. […] The cessation of logging is [likewise] not a realistic option, as too much money is at stake for both the nations and individuals involved.”

“Animal geneticists have given considerable thought to the question of how many individuals are necessary to maintain the full genetic integrity of a species in perpetuity.[425] Much has been learned from zoos. A simple but extremely crude rule-of-thumb is that a minimum population of 50 breeding adults maintains fitness in the short term, thus preserving a species ‘frozen’ at one instant of time. To prevent continual loss of genetic diversity (‘genetic erosion’) over the long term […] requires a big population, and a minimum of 500 breeding adults has been suggested to be necessary. This 50/500 rule is only a very rough approximation and can differ widely between species. […] Most difficult to conserve are animals (or indeed plants too) that live at very low population density (e.g. hornbills, tapir, and top carnivores, such as jaguar and tiger), or that have large territories (e.g. gaur, elephant) […] Increasingly in the future, tropical rain forest will only remain as fragments. […] There is a problem that such fragments may break the 50/500 rule […] and contain too few individuals of a species for its long-term genetic integrity. Species that occur at low density are especially vulnerable to genetic erosion, to chance extinction when numbers fall […], or to inbreeding depression. In particular, many trees live several centuries and may be persisting today but unable to breed, so the species is ‘living but dead’, doomed to extinction. […] small forest remnants may be too small to support certain species and this may have repercussions on other components of the ecosystem. […] Besides reduction in area, forest fragmentation also increases the proportion of edge relative to interior […] and if the fragments are surrounded by open land this will result in a change of microclimate.”

 

September 23, 2014 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Genetics, Geography | Leave a comment

An Introduction to Tropical Rain Forests (II)

First an update on the issues I mentioned earlier this week: I had a guy come by and ‘fix the internet problem’ yesterday. Approximately an hour after he left I lost my connection, and it was gone for the rest of the day. I have internet now. If the problem is not solved by a second visit on Monday (they’ll send another guy over), the ISP just lost a customer – I’ll give them no more chances, I can’t live like this. The uncertainty is both incredibly stressful and frankly infuriating. I actually lost internet while writing this post. Down periods seem completely random and may last from 5 minutes to 12 hours. I’m much more dependent on the internet than are most people in part because most of my social interaction with others takes place online.

I’ve read four Christie novels within the last week and I finished The Gambler by Dostoyevsky earlier today – in case you were wondering why I’ve suddenly started reading a lot of fiction, the answer is simple: I’m awake for 16+ hours each day, and if I can’t go online to relax during my off hours I have to find some other way to distract-/enjoy-/whatever myself. Novels are one of the tools I’ve employed.

The internet issue is more important than the computer issue also in terms of the blogging context; the computer I’m using at the moment is unreliable, but seems to cause a limited amount of trouble when I’m doing simple stuff like blogging.

Okay, on to the book. I was rather harsh in my first post, but I did also mention that it had a lot of good stuff. I’ve included some of that stuff in this post below.

“Forests, because of their stature, have internal microclimates that differ from the general climate outside the canopy. […] In general terms, it is cool, humid, and dark near the floor of a mature patch of forest, progressively altering upwards to the canopy top. Different plants and animal species have specialized to the various forest interior microclimates […] Night is the winter of the tropics, because the diurnal range of mean daily temperature exceeds the annual range and is greater in drier months. […] Rain forests develop where every month is wet (with 100 mm rainfal or more), or there are only short dry periods which occur mainly as unpredictable spells lasting only a few days or weeks. Where there are several dry months (60 mm rainfal or less) of regular occurence, monsoon forests exist. Outside Asia these are usually called tropical seasonal forests. […] To the biologist […] there are major differences, and this book is about tropical rain forests, those which occur in the everwet (perhumid) climates, with only passing mention of monsoon forests.”

“Tropical rain forests occur in all three tropical land areas […]. Most extensive are the American or neotropical rain forests, about half the global total, 4 x 106 km2 in area, and one-sixth of the total broad-leaf forest of the world. […] The second largest block of tropical rain forest occurs in the Eastern tropics, and is estimated to cover 2.5 x 106 km2. It is centred on the Malay archipelago, the region known to botanists as Malesia. Indonesia[25] occupies most of the archipelago and is second to Brazil in the amount of rain forest it possesses. […] Africa has the smallest block of tropical rain forest, 1.8 x 106 km2. This is centred on the Congo basin, reaching from the high mountains at its eastern limit westwards to the Atlantic Ocean, with outliers in East Africa. […] Outside the Congo core the African rain forests have been extensively destroyed.”

“It is now believed that about half the world’s species occur in tropical rain forests although they only occupy about seven per cent of the land area. […] Just how many species the world’s rain forests contain is still […] only a matter of rough conjecture. For mammals, birds, and other larger animals there are roughly twice as many species in tropical regions as temperate ones […]. These groups are fairly well studied, insects and other invertebrates much less so […] The humid tropics are extremely rich in plant species. Of the total of approximately 250 000 species of flowering plants in the world, about two-thirds (170 000) occur in the tropics. Half of these are in the New World south of the Mexico/US frontier, 21 000 in tropical Africa (plus 10 000 in Madagascar) and 50 000 in tropical and subtropical Asia, with 36 000 in Malesia. […] There are similarities, especially at family level, between all three blocks of tropical rain forest, but there are fewer genera in common and not many species. […] In flora Africa has been called ‘the odd man out’;[52] there are fewer families, fewer genera, and fewer species in her rain forests than in either America or Asia. For example, there are 18 genera and 51 species of native palms on Singapore island,[53] as many as on the whole of mainland Africa (15 genera, 50 species) […] There are also differences within each rain forest region. […] meaningful discussions of species richness must specify scale.[60] For example, we may usefully compare richness within rain forests by counting tree species on plots of c. 1 ha. This within-community diversity has been called alpha diversity. At the other extreme we can record species richness of a whole landscape made up of several communities, and this has been called gamma diversity. The fynbos is very rich with 8500 species on 89 000 km2. It is made up of a mosaic of different floristic communities, each of which has rather few species. That is to say fynbos has low alpha and high gamma diversity. Within a single floristic community species replace each other from place to place. This gives a third component to richness, known as beta diversity. For example, within lowland rain forest there are differences in species within a single community between ridges, hillsides, and valleys.”

“Most rain forest trees […] exhibit intermittent shoot growth […] The intermittent growth of the shoot tips is seldom reflected by growth rings in the wood, and where it is these are not annual and often not annular either. Rain forest trees, unlike those of seasonal climates, cannot be aged by counting wood rings […] tree age cannot be measured directly. It has [also] been found that the fastest growing juvenile trees in a forest are the ones most likely to succeed, so growth rates averaged from a number of stems are misleading. […] we have very little reliable information on how long trees can live. […] Most of the root biomass is in the top 0.3 m or so of the soil and there is sometimes a concentration or root mat at the surface. […] Roots up to 2 mm in diameter form 20-50 per cent of the total root biomass[79] and their believed rapid turnover is probably a significant part of ecosystem nutrient cycles”

“Besides differences between the three tropical regions there are other differences within them. One major pattern is that within the African and American rain forests there are areas of especially high species richness, set like islands in a sea of relative poverty. […] No such patchiness has been detected in Asia, where the major pattern is set by Wallace’s Line, one of the sharpest zoogeographical boundaries in the world and which delimits the continental Asian faunas from the Australasian […]. These patterns are now realized to have explanations based on Earth[‘s] history […] Gondwanaland and Laurasia were [originally] separated by the great Tethys Ocean. Tethys was closed by the northwards movement of parts of Gondwanaland […]. First Africa and then India drifted north and collided with the southern margin of Laurasia. Further east the continental plate which comprised Antarctica/Australia/southern New Guinea moved northwards, broke in two leaving Antarctica behind, and, as a simplification, collided with the southeast extremity of Laurasia, at about 15 million years ago, the mid-Miocene; this created the Malay archipelago (Malesia) as it exists today. Both super-continents had their own sets of plants and animals. […] Western and eastern Malesia have very different animals, demarcated by a very sharp boundary, Wallace’s line. […] the evolution of the Malay archipelago was in fact more complex than a single collision.[145] Various shards progressively broke off Gondwana from the Jurassic onwards, drifted northwards, and became embedded in what is now continental Asia […]  The climate of the tropics has been continually changing. The old idea of fixity is quite wrong; climatic changes have had profound influences on species ranges.”

“Most knowledge about past climates is for the last 2 million years, the Quaternary period, during which there has been repeated alternation at high latitudes near the poles between Ice Ages or Glacial periods and Interglacials. During Glacial periods tropical climates were slightly cooler and drier, with lower and more seasonal rainfall. During these times rain forests became less extensive and seasonal forests expanded. Most of the Quaternary was like that; present-day climates are extreme and not typical of the period as a whole. Today we live at the height of an Interglacial. […] At the Glacial maxima sea levels were lower by as much as 180 m […] Sea surface temperature was cooler than today, by 5 ° C or more[147] at 18 000 BP in the tropics. […] Rain forests were more extensive than at any time in the Quaternary during the early Pliocene, parts of the Miocene, and especially the early Eocene; so these were all warm periods. Then, in the late Tertiary, fluctuations similar to those of the Quaternary occurred. […] Africa [as mentioned] has a much poorer flora than the other two rain forest regions.[152] This is believed to be because it was much more strongly dessicated during the Tertiary. […] Australia too suffered strong Tertiary dessication. At that time its mesic vegetation became mainly confined to the eastern seaboard. The strip of tropical rain forests found today in north Queensland is only 2-30 km wide and is of particular interest because it contains the relicts of the old mesic flora. This includes the ancestors from which many modern Australian species adapted to hot dry climates are believed to have evolved […] New Caledonia is a shard of Gondwanaland which drifted away eastwards from northeast Australia starting in the Upper Cretaceous 82 million BP. Because it is an island its vegetation has suffered less from the drier Glacial climates so more of the old flora has survived. The lands bordering the western Pacific have the greatest concentration of primitive flowering plants found anywhere […] It is most likely that they survived here as relicts.”

“rain forests have waxed and waned in extent during the Quaternary, and probably in the Tertiary too, and are not the ancient and immutable bastions where life originated which populist writings still sometimes suggest. In the present Interglacial they are as extensive as they have ever been, or nearly so. At glacial maxima lowland rain forests are believed to have contracted and only to have persisted in places where conditions remained favourable for them, as patches surrounded by tropical seasonal forests, like islands set in a sea. In subsequent Interglacials, as perhumid conditions returned, the rain forests expanded out of these patches, which have come to be called Pleistocene refugia. In the late 1960s it was shown that within Amazonia birds have areas of high species endemism and richness which are surrounded by relatively poorer areas. The same was soon demonstrated for lizards.[153] Subsequently many groups of animals have been shown to exhibit such patchiness […] The centres of concentration more or less coincide with each other […] These loci overlap with areas that geoscientific evidence suggests retained rain forest during Pleistocene glaciations […] In the African rain forests four groups of loci of species richness and endemism are now recognized […] Most parts of Malesia today are about as equally rich in species, including endemics, as the Pleistocene refugia of Africa and America. At the Glacial maxima the Sunda and Sahul continental shelves were exposed by falling sealevel. Rain forests were likely to have become confined to the more mountaineous places where there was more, orographic, rain. The main development of seasonal forests in this region is likely to have been on the newly exposed lowlands, and when sea-level rose again at the next Interglacial these and the physical signs of seasonal climates […] were drowned. The parts of Malesia that are above sea-level today probably remained, largely perhumid and covered by rain forest, which explains their extreme species richness and their lack of geoscientific evidence of seasonal past climates. […] Present-day lowland rain forest communities consist of plant and animal species that have survived past climatic vicissitudes or have immigrated since the climate ameliorated. Thus many species co-exist today as a result of historical chance, not because they co-evolved together. Their communities are neither immutable nor finely tuned. This point is of great importance to the ideas scientists have expressed concerning plant-animal interactions […] Those parts of the world’s tropical rain forests that are most rich in species are those that the evidence shows have been the most stable, where species have evolved and continued to accumulate with the passage of time without episodes of extinction caused by unfavourable climatic periods. This is similar to the pattern observed in other forest biomes”

September 20, 2014 Posted by | Biology, Books, Botany, climate, Ecology, Evolutionary biology, Geography, Geology | Leave a comment

An Introduction to Tropical Rain Forests (I)

This will just be a brief introductory post to the book, which I gave two stars on goodreads – I have internet and the computer seems to not give me too much trouble right now, so I thought I should post something while I have the chance. The book was hard to rate, in a way. Some parts were highly informative and really quite nice. In other parts the author was ‘out of line’, and he goes completely overboard towards the end – the last couple of chapters contain a lot of political stuff. I have included below a couple of examples of some passages the inclusion of which I had issues with:

“It is also fair comment that human-induced extinction today is as great as any of the five previous extinction spasms life on earth has experienced.”

I have read about the human impact on species diversity before, e.g. in Wilson or van der Geer et al.. I have also read about those other extinction events he talks about. I mention this because if you have not read about both, it may be natural to not feel perfectly confident judging on the matter – but I have, and I do. My conclusion is that saying that the human-induced extinction occuring today is “as great as” the Permian extinction event in my mind makes you look really stupid. Either the author doesn’t know what he’s talking about, or he had stopped thinking when he wrote that, which is something that often happens when people get emotional and start going into tribal defence mode and making political points. Which is why I try to avoid political books. Here’s a funny combination of quotes:

i. “The failure of silviculture follows from working beyond the limits of the inherent dynamic capabilities of the forest ecosystem. This is commonly because rules drawn up by silviculturalists are not enforced, often because of political intervention. It may also be because economists, eager to enrich a nation, enforce their dismal pseudoscience to override basic logical principles and dictate the removal of a larger harvest than the forest can sustain without degradation.”

ii. “There have been attempts by campaigning groups in recent years to turn the clock back, sometimes claiming forests have a greater cash value for minor forest products than for timber.[324] A review of 24 studies found that the median annual value per hectare of sustainably produced, marketable non-timber forest products was $50 year−1.[325] As a natural rain forest grows commercial timber at 1-2 m3 year−1 ha−1 or more, and this is worth over $100 m−3, sustainable production of timber is of greater value by a factor of at least two to four.”

The word ‘hypocrite’ sprang to mind when I read the second quote. Who does he think conducts such review studies – soil scientists? If economics is pseudo-science, as he himself indicated that he thought earlier in the book, then why should we trust those estimates? On a related note, should evolutionary biologists stop using game theory as well – where does he think core concepts in evolutionary biology like ESS come from? Good luck analyzing equilibrium dynamics of any kind without using tools also used in economics and/or developed by economists.

It actually seems to me to be a general problem in some fields of biology that lots of researchers have a problem separating politics and science – the social sciences really aren’t the only parts of academia where this kind of stuff is a problem. I have a strong preference for not encountering emotional/political arguments in academic publications, and so I tend to notice them when they’re there, whether or not I agree with them. There’s a lot of good stuff in this book and I’ll talk about this later here on the blog, but there’s a lot of problematic stuff as well, and I punish that kind of stuff hard regardless of where I find it. The quotes above are not unique but to me seem to illustrate the mindset reasonably well.

The book covers stuff also covered in Herrera et al., Wilson, and van der Geer et al., and concepts I knew about from McMenamin & McMenamin also popped up along the way. Herrera et al. of course contains entire chapters about stuff only covered in a paragraph or two in this book. The book deals with aspects of ecological dynamics as well through the coverage of the forest growth cycle and gap-phase dynamics as well as related stuff like nutrient cycles, but the coverage in here is much less technical than is Gurney and Nisbet’s coverage – this book is easy to read compared to their text. I mention these things because although I think the book was quite readable I have seen a lot of coverage of related stuff already at this point, so I may not be the best person to ask. My overall impression is however that people reading along here should not have great difficulties reading and understanding this book.

September 18, 2014 Posted by | Biology, Books, Botany, Ecology, Paleontology | Leave a comment

Wikipedia articles of interest

i. Dodo (featured article).

“The dodo (Raphus cucullatus) is an extinct flightless bird that was endemic to the island of Mauritius, east of Madagascar in the Indian Ocean. Its closest genetic relative was the also extinct Rodrigues solitaire, the two forming the subfamily Raphinae of the family of pigeons and doves. […] Subfossil remains show the dodo was about 1 metre (3.3 feet) tall and may have weighed 10–18 kg (22–40 lb) in the wild. The dodo’s appearance in life is evidenced only by drawings, paintings and written accounts from the 17th century. Because these vary considerably, and because only some illustrations are known to have been drawn from live specimens, its exact appearance in life remains unresolved. Similarly, little is known with certainty about its habitat and behaviour.”

“The first recorded mention of the dodo was by Dutch sailors in 1598. In the following years, the bird was hunted by sailors, their domesticated animals, and invasive species introduced during that time. The last widely accepted sighting of a dodo was in 1662. Its extinction was not immediately noticed, and some considered it to be a mythical creature. In the 19th century, research was conducted on a small quantity of remains of four specimens that had been brought to Europe in the early 17th century. Among these is a dried head, the only soft tissue of the dodo that remains today. Since then, a large amount of subfossil material has been collected from Mauritius […] The dodo was anatomically similar to pigeons in many features. […] The dodo differed from other pigeons mainly in the small size of the wings and the large size of the beak in proportion to the rest of the cranium. […] Many of the skeletal features that distinguish the dodo and the Rodrigues solitaire, its closest relative, from pigeons have been attributed to their flightlessness. […] The lack of mammalian herbivores competing for resources on these islands allowed the solitaire and the dodo to attain very large sizes.[19]” [If the last sentence sparked your interest and/or might be something about which you’d like to know more, I have previously covered a great book on related topics here on the blog]

“The etymology of the word dodo is unclear. Some ascribe it to the Dutch word dodoor for “sluggard”, but it is more probably related to Dodaars, which means either “fat-arse” or “knot-arse”, referring to the knot of feathers on the hind end. […] The traditional image of the dodo is of a very fat and clumsy bird, but this view may be exaggerated. The general opinion of scientists today is that many old European depictions were based on overfed captive birds or crudely stuffed specimens.[44]

“Like many animals that evolved in isolation from significant predators, the dodo was entirely fearless of humans. This fearlessness and its inability to fly made the dodo easy prey for sailors.[79] Although some scattered reports describe mass killings of dodos for ships’ provisions, archaeological investigations have found scant evidence of human predation. […] The human population on Mauritius (an area of 1,860 km2 or 720 sq mi) never exceeded 50 people in the 17th century, but they introduced other animals, including dogs, pigs, cats, rats, and crab-eating macaques, which plundered dodo nests and competed for the limited food resources.[37] At the same time, humans destroyed the dodo’s forest habitat. The impact of these introduced animals, especially the pigs and macaques, on the dodo population is currently considered more severe than that of hunting. […] Even though the rareness of the dodo was reported already in the 17th century, its extinction was not recognised until the 19th century. This was partly because, for religious reasons, extinction was not believed possible until later proved so by Georges Cuvier, and partly because many scientists doubted that the dodo had ever existed. It seemed altogether too strange a creature, and many believed it a myth.”

Some of the contemporary accounts and illustrations included in the article, from which behavioural patterns etc. have been inferred, I found quite depressing. Two illustrative quotes and a contemporary engraving are included below:

“Blue parrots are very numerous there, as well as other birds; among which are a kind, conspicuous for their size, larger than our swans, with huge heads only half covered with skin as if clothed with a hood. […] These we used to call ‘Walghvogel’, for the reason that the longer and oftener they were cooked, the less soft and more insipid eating they became. Nevertheless their belly and breast were of a pleasant flavour and easily masticated.[40]

“I have seen in Mauritius birds bigger than a Swan, without feathers on the body, which is covered with a black down; the hinder part is round, the rump adorned with curled feathers as many in number as the bird is years old. […] We call them Oiseaux de Nazaret. The fat is excellent to give ease to the muscles and nerves.[7]

640px-Jacht_op_dodo's_door_Willem_van_West-Zanen_uit_1602

ii. Armero tragedy (featured).

“The Armero tragedy […] was one of the major consequences of the eruption of the Nevado del Ruiz stratovolcano in Tolima, Colombia, on November 13, 1985. After 69 years of dormancy, the volcano’s eruption caught nearby towns unaware, even though the government had received warnings from multiple volcanological organizations to evacuate the area when volcanic activity had been detected in September 1985.[1]

As pyroclastic flows erupted from the volcano’s crater, they melted the mountain’s glaciers, sending four enormous lahars (volcanically induced mudslides, landslides, and debris flows) down its slopes at 50 kilometers per hour (30 miles per hour). The lahars picked up speed in gullies and coursed into the six major rivers at the base of the volcano; they engulfed the town of Armero, killing more than 20,000 of its almost 29,000 inhabitants.[2] Casualties in other towns, particularly Chinchiná, brought the overall death toll to 23,000. […] The relief efforts were hindered by the composition of the mud, which made it nearly impossible to move through without becoming stuck. By the time relief workers reached Armero twelve hours after the eruption, many of the victims with serious injuries were dead. The relief workers were horrified by the landscape of fallen trees, disfigured human bodies, and piles of debris from entire houses. […] The event was a foreseeable catastrophe exacerbated by the populace’s unawareness of the volcano’s destructive history; geologists and other experts had warned authorities and media outlets about the danger over the weeks and days leading up to the eruption.”

“The day of the eruption, black ash columns erupted from the volcano at approximately 3:00 pm local time. The local Civil Defense director was promptly alerted to the situation. He contacted INGEOMINAS, which ruled that the area should be evacuated; he was then told to contact the Civil Defense directors in Bogotá and Tolima. Between 5:00 and 7:00 pm, the ash stopped falling, and local officials instructed people to “stay calm” and go inside. Around 5:00 pm an emergency committee meeting was called, and when it ended at 7:00 pm, several members contacted the regional Red Cross over the intended evacuation efforts at Armero, Mariquita, and Honda. The Ibagué Red Cross contacted Armero’s officials and ordered an evacuation, which was not carried out because of electrical problems caused by a storm. The storm’s heavy rain and constant thunder may have overpowered the noise of the volcano, and with no systematic warning efforts, the residents of Armero were completely unaware of the continuing activity at Ruiz. At 9:45 pm, after the volcano had erupted, Civil Defense officials from Ibagué and Murillo tried to warn Armero’s officials, but could not make contact. Later they overheard conversations between individual officials of Armero and others; famously, a few heard the Mayor of Armero speaking on a ham radio, saying “that he did not think there was much danger”, when he was overtaken by the lahar.[20]

“The lahars, formed of water, ice, pumice, and other rocks,[25] incorporated clay from eroding soil as they traveled down the volcano’s flanks.[26] They ran down the volcano’s sides at an average speed of 60 kilometers (40 mi) per hour, dislodging rock and destroying vegetation. After descending thousands of meters down the side of the volcano, the lahars followed the six river valleys leading from the volcano, where they grew to almost four times their original volume. In the Gualí River, a lahar reached a maximum width of 50 meters (160 ft).[25]

Survivors in Armero described the night as “quiet”. Volcanic ash had been falling throughout the day, but residents were informed it was nothing to worry about. Later in the afternoon, ash began falling again after a long period of quiet. Local radio stations reported that residents should remain calm and ignore the material. One survivor reported going to the fire department to be informed that the ash was “nothing”.[27] […] At 11:30 pm, the first lahar hit, followed shortly by the others.[28] One of the lahars virtually erased Armero; three-quarters of its 28,700 inhabitants were killed.[25] Proceeding in three major waves, this lahar was 30 meters (100 ft) deep, moved at 12 meters per second (39 ft/s), and lasted ten to twenty minutes. Traveling at about 6 meters (20 ft) per second, the second lahar lasted thirty minutes and was followed by smaller pulses. A third major pulse brought the lahar’s duration to roughly two hours; by that point, 85 percent of Armero was enveloped in mud. Survivors described people holding on to debris from their homes in attempts to stay above the mud. Buildings collapsed, crushing people and raining down debris. The front of the lahar contained boulders and cobbles which would have crushed anyone in their path, while the slower parts were dotted by fine, sharp stones which caused lacerations. Mud moved into open wounds and other open body parts – the eyes, ears, and mouth – and placed pressure capable of inducing traumatic asphyxia in one or two minutes upon people buried in it.”

“The volcano continues to pose a serious threat to nearby towns and villages. Of the threats, the one with the most potential for danger is that of small-volume eruptions, which can destabilize glaciers and trigger lahars.[51] Although much of the volcano’s glacier mass has retreated, a significant volume of ice still sits atop Nevado del Ruiz and other volcanoes in the Ruiz–Tolima massif. Melting just 10 percent of the ice would produce lahars with a volume of up to 200 million cubic meters – similar to the lahar that destroyed Armero in 1985. In just hours, these lahars can travel up to 100 km along river valleys.[33] Estimates show that up to 500,000 people living in the Combeima, Chinchina, Coello-Toche, and Guali valleys are at risk, with 100,000 individuals being considered to be at high risk.”

iii. Asteroid belt (featured).

“The asteroid belt is the region of the Solar System located roughly between the orbits of the planets Mars and Jupiter. It is occupied by numerous irregularly shaped bodies called asteroids or minor planets. The asteroid belt is also termed the main asteroid belt or main belt to distinguish its members from other asteroids in the Solar System such as near-Earth asteroids and trojan asteroids. About half the mass of the belt is contained in the four largest asteroids, Ceres, Vesta, Pallas, and Hygiea. Vesta, Pallas, and Hygiea have mean diameters of more than 400 km, whereas Ceres, the asteroid belt’s only dwarf planet, is about 950 km in diameter.[1][2][3][4] The remaining bodies range down to the size of a dust particle.”

“The asteroid belt formed from the primordial solar nebula as a group of planetesimals, the smaller precursors of the planets, which in turn formed protoplanets. Between Mars and Jupiter, however, gravitational perturbations from Jupiter imbued the protoplanets with too much orbital energy for them to accrete into a planet. Collisions became too violent, and instead of fusing together, the planetesimals and most of the protoplanets shattered. As a result, 99.9% of the asteroid belt’s original mass was lost in the first 100 million years of the Solar System’s history.[5]

“In an anonymous footnote to his 1766 translation of Charles Bonnet‘s Contemplation de la Nature,[8] the astronomer Johann Daniel Titius of Wittenberg[9][10] noted an apparent pattern in the layout of the planets. If one began a numerical sequence at 0, then included 3, 6, 12, 24, 48, etc., doubling each time, and added four to each number and divided by 10, this produced a remarkably close approximation to the radii of the orbits of the known planets as measured in astronomical units. This pattern, now known as the Titius–Bode law, predicted the semi-major axes of the six planets of the time (Mercury, Venus, Earth, Mars, Jupiter and Saturn) provided one allowed for a “gap” between the orbits of Mars and Jupiter. […] On January 1, 1801, Giuseppe Piazzi, Chair of Astronomy at the University of Palermo, Sicily, found a tiny moving object in an orbit with exactly the radius predicted by the Titius–Bode law. He dubbed it Ceres, after the Roman goddess of the harvest and patron of Sicily. Piazzi initially believed it a comet, but its lack of a coma suggested it was a planet.[12] Fifteen months later, Heinrich Wilhelm Olbers discovered a second object in the same region, Pallas. Unlike the other known planets, the objects remained points of light even under the highest telescope magnifications instead of resolving into discs. Apart from their rapid movement, they appeared indistinguishable from stars. Accordingly, in 1802 William Herschel suggested they be placed into a separate category, named asteroids, after the Greek asteroeides, meaning “star-like”. […] The discovery of Neptune in 1846 led to the discrediting of the Titius–Bode law in the eyes of scientists, because its orbit was nowhere near the predicted position. […] One hundred asteroids had been located by mid-1868, and in 1891 the introduction of astrophotography by Max Wolf accelerated the rate of discovery still further.[22] A total of 1,000 asteroids had been found by 1921,[23] 10,000 by 1981,[24] and 100,000 by 2000.[25] Modern asteroid survey systems now use automated means to locate new minor planets in ever-increasing quantities.”

“In 1802, shortly after discovering Pallas, Heinrich Olbers suggested to William Herschel that Ceres and Pallas were fragments of a much larger planet that once occupied the Mars–Jupiter region, this planet having suffered an internal explosion or a cometary impact many million years before.[26] Over time, however, this hypothesis has fallen from favor. […] Today, most scientists accept that, rather than fragmenting from a progenitor planet, the asteroids never formed a planet at all. […] The asteroids are not samples of the primordial Solar System. They have undergone considerable evolution since their formation, including internal heating (in the first few tens of millions of years), surface melting from impacts, space weathering from radiation, and bombardment by micrometeorites.[34] […] collisions between asteroids occur frequently (on astronomical time scales). Collisions between main-belt bodies with a mean radius of 10 km are expected to occur about once every 10 million years.[63] A collision may fragment an asteroid into numerous smaller pieces (leading to the formation of a new asteroid family). Conversely, collisions that occur at low relative speeds may also join two asteroids. After more than 4 billion years of such processes, the members of the asteroid belt now bear little resemblance to the original population. […] The current asteroid belt is believed to contain only a small fraction of the mass of the primordial belt. Computer simulations suggest that the original asteroid belt may have contained mass equivalent to the Earth.[37] Primarily because of gravitational perturbations, most of the material was ejected from the belt within about a million years of formation, leaving behind less than 0.1% of the original mass.[29] Since their formation, the size distribution of the asteroid belt has remained relatively stable: there has been no significant increase or decrease in the typical dimensions of the main-belt asteroids.[38]

“Contrary to popular imagery, the asteroid belt is mostly empty. The asteroids are spread over such a large volume that it would be improbable to reach an asteroid without aiming carefully. Nonetheless, hundreds of thousands of asteroids are currently known, and the total number ranges in the millions or more, depending on the lower size cutoff. Over 200 asteroids are known to be larger than 100 km,[44] and a survey in the infrared wavelengths has shown that the asteroid belt has 0.7–1.7 million asteroids with a diameter of 1 km or more. […] The total mass of the asteroid belt is estimated to be 2.8×1021 to 3.2×1021 kilograms, which is just 4% of the mass of the Moon.[2] […] Several otherwise unremarkable bodies in the outer belt show cometary activity. Because their orbits cannot be explained through capture of classical comets, it is thought that many of the outer asteroids may be icy, with the ice occasionally exposed to sublimation through small impacts. Main-belt comets may have been a major source of the Earth’s oceans, because the deuterium–hydrogen ratio is too low for classical comets to have been the principal source.[56] […] Of the 50,000 meteorites found on Earth to date, 99.8 percent are believed to have originated in the asteroid belt.[67]

iv. Series (mathematics). This article has a lot of stuff, including lots of links to other stuff.

v. Occupation of Japan. Interesting article, I haven’t really read very much about this before. Some quotes:

“At the head of the Occupation administration was General MacArthur who was technically supposed to defer to an advisory council set up by the Allied powers, but in practice did everything himself. As a result, this period was one of significant American influence […] MacArthur’s first priority was to set up a food distribution network; following the collapse of the ruling government and the wholesale destruction of most major cities, virtually everyone was starving. Even with these measures, millions of people were still on the brink of starvation for several years after the surrender.”

“By the end of 1945, more than 350,000 U.S. personnel were stationed throughout Japan. By the beginning of 1946, replacement troops began to arrive in the country in large numbers and were assigned to MacArthur’s Eighth Army, headquartered in Tokyo’s Dai-Ichi building. Of the main Japanese islands, Kyūshū was occupied by the 24th Infantry Division, with some responsibility for Shikoku. Honshū was occupied by the First Cavalry Division. Hokkaido was occupied by the 11th Airborne Division.

By June 1950, all these army units had suffered extensive troop reductions and their combat effectiveness was seriously weakened. When North Korea invaded South Korea (see Korean War), elements of the 24th Division were flown into South Korea to try to stem the massive invasion force there, but the green occupation troops, while acquitting themselves well when suddenly thrown into combat almost overnight, suffered heavy casualties and were forced into retreat until other Japan occupation troops could be sent to assist.”

“During the Occupation, GHQ/SCAP mostly abolished many of the financial coalitions known as the Zaibatsu, which had previously monopolized industry.[20] […] A major land reform was also conducted […] Between 1947 and 1949, approximately 5,800,000 acres (23,000 km2) of land (approximately 38% of Japan’s cultivated land) were purchased from the landlords under the government’s reform program and resold at extremely low prices (after inflation) to the farmers who worked them. By 1950, three million peasants had acquired land, dismantling a power structure that the landlords had long dominated.[22]

“There are allegations that during the three months in 1945 when Okinawa was gradually occupied there were rapes committed by U.S. troops. According to some accounts, US troops committed thousands of rapes during the campaign.[36][37]

Many Japanese civilians in the Japanese mainland feared that the Allied occupation troops were likely to rape Japanese women. The Japanese authorities set up a large system of prostitution facilities (RAA) in order to protect the population. […] However, there was a resulting large rise in venereal disease among the soldiers, which led MacArthur to close down the prostitution in early 1946.[39] The incidence of rape increased after the closure of the brothels, possibly eight-fold; […] “According to one calculation the number of rapes and assaults on Japanese women amounted to around 40 daily while the RAA was in operation, and then rose to an average of 330 a day after it was terminated in early 1946.”[40] Michael S. Molasky states that while rape and other violent crime was widespread in naval ports like Yokosuka and Yokohama during the first few weeks of occupation, according to Japanese police reports and journalistic studies, the number of incidents declined shortly after and were not common on mainland Japan throughout the rest of occupation.[41] Two weeks into the occupation, the Occupation administration began censoring all media. This included any mention of rape or other sensitive social issues.”

“Post-war Japan was chaotic. The air raids on Japan’s urban centers left millions displaced and food shortages, created by bad harvests and the demands of the war, worsened when the seizure of food from Korea, Taiwan, and China ceased.[58] Repatriation of Japanese living in other parts of Asia only aggravated the problems in Japan as these displaced people put more strain on already scarce resources. Over 5.1 million Japanese returned to Japan in the fifteen months following October 1, 1945.[59] Alcohol and drug abuse became major problems. Deep exhaustion, declining morale and despair were so widespread that it was termed the “kyodatsu condition” (虚脱状態 kyodatsujoutai?, lit. “state of lethargy”).[60] Inflation was rampant and many people turned to the black market for even the most basic goods. These black markets in turn were often places of turf wars between rival gangs, like the Shibuya incident in 1946.”

August 16, 2014 Posted by | Astronomy, Biology, Ecology, Evolutionary biology, Geology, History, Mathematics, Wikipedia, Zoology | Leave a comment

The Emergence of Animals: The Cambrian Breakthrough (II)

I decided to write one more post (this one) about the book and leave it at that. Go here for my first post about the book, which has some general remarks about the book, as well as a lot of relevant links to articles from wikipedia which cover topics also covered in the book. Below I have added some observations from the second half of the book.

“Use of bedrock geology to reconstruct ancient continental positions relies on the idea that if two separated continents were once joined to form a single, larger continent, then there ought to be distinctive geological terranes (such as mineral belts, mountain chains, bodies of igneous rock of similar age, and other roughly linear to irregularly-shaped large-scale geologic features) that were once contiguous but are now separated. Matching of these features can provide clues to the positions of continents that were once together. […] The main problem with using bedrock geology features to match continental puzzle pieces together is that many of the potentially most useful linear geologic features on the continents (such as volcanic arcs or chains of volcanoes, and continental margin fold belts or parallel mountain chains formed by compression of strata) are parallel to the edge of the continent. Therefore, these features generally run parallel to rift fractures, and are less likely to continue and be recognizable on any continent that was once connected to the continent in question.

Paleomagnetic evidence is an important tool for the determination of ancient continent positions and for the reconstruction of supercontinents. Nearly all rock types, be they sedimentary or igneous, contain minerals that contain the elements iron or titanium. Many of these iron- and titanium-bearing minerals are magnetic. […] The magnetization of a crystal of a magnetic mineral (such as magnetite) is established immediately after the mineral crystallizes from a volcanic melt (lava) but before it cools below the Curie point temperature. Each magnetic mineral has its own specific Curie point. […] As the mineral grain passes through the Curie point, the ambient magnetic field is “frozen” into the crystal and will remain unchanged until the crystal is destroyed by weathering or once again heated above the Curie point. This “locking in” of the magnetic signal in igneous rock crystals is the crucial event for paleomagnetism, for it indicates the direction of magnetic north at the time the crystal cooled (sometime in the distant geologic past for most igneous rocks). The ancient latitudinal position of the rock (and the continent of which it is a part) can be determined by measuring the direction of the crystal’s magnetization. For ancient rocks, this direction can be quite different from the direction of present day magnetic north. […] Paleomagnetic reconstruction is a form of geological analysis that is, unfortunately, fraught with uncertainties. The original magnetization is easily altered by weathering and metamorphism, and can confuse or obliterate the original magnetic signal. An inherent limitation of paleomagnetic reconstruction of ancient continental positions is that the magnetic remanence only gives information concerning the rocks’ latitudinal position, and gives no clue as to the original longitudinal position of the rocks in question. For example, southern Mexico and central India, although nearly half a world apart, are both at about 20 degrees North latitude, and, therefore, lavas cooling in either country would have essentially the same primary magnetic remanence. One of the few ways to get information about the ancient longitudinal positions of continents is to use comparison of life forms on different continents. The study of ancient distributions of organisms is called paleobiogeography.”

“Photosynthesis is generally considered to be a characteristic of plants in the traditional usage of the term “plant.” Nonbiologists are sometimes surprised to learn that [some] animals are photosynthetic […] One might argue that marine animals with zooxanthellae (symbiotic protists) are not truly photosynthetic because it is the protists that do the photosynthesis, not the animal. The protists just happen to be inside the animal. We would argue that this is not an important consideration, since photosynthesis in all eukaryotic (nucleated) cells is accomplished by chloroplasts, tiny organelles that are the cell’s photosynthesis factories. Chloroplasts are now thought by many biologists to have arisen by a symbiosis event in which a small, photosynthetic moneran took up symbiotic residence within a larger microbe […]. The symbiotic relationship eventually became so well established that it became an obligatory relationship for both the host microbe and the smaller symbiont moneran. Reproductive provisions were made to pass the genetic material of the symbiont, as well as the host, on to succeeding generations. It would sound strange to describe an oak as a “multicellular alga invaded by photosynthetic moneran symbionts,” but that is — in essence — what a tree is. Animals with photosynthetic protists in their bodies are able to create food internally, in the same way that an oak tree can, so we feel that these animals can be correctly called photosynthetic. […] Many of the most primitive types of living metazoa contain photosymbiotic
microbes or chloroplasts derived from microbes.”

“The most obvious reason for any organism, regardless of what kingdom it belongs to, to evolve a leaf-shaped body is to maximize its surface area. Leaf shape evolves in response to factors in addition to surface area requirement, but the surface area requirement, in all cases we are aware of, is the most important factor. […] Leaves of modern plants and Ediacaran animals probably evolved similar shapes for the same reason, namely, maximization of surface area. […] Photosymbiosis is not the only possible departure from heterotrophic feeding, the usual method of food acquisition for modern animals. Seilacher (1984) notes that flat bodies are good for absorption of simple compounds such as hydrogen sulfide, needed for one type of chemosymbiosis. In chemosymbiosis as in photosymbiosis, microbes (in this case bacteria) are held within an animal’s tissues as paying guests. The bacteria are able to use the energy stored in hydrogen sulphide molecules that diffuse into the host animal’s tissues. The bacteria use the hydrogen sulfide to create food, using biochemical reactions that would be impossible for animals to do by themselves. The bacteria use some of the food for themselves, but great excesses are produced and passed on to the host animal’s tissues. […] There may be important similarities between the ecologies of
[…] flattened Ediacaran creatures and the modern deep sea vent faunas. […] A form of chemotrophy (feeding on chemicals) that does not involve symbiosis is simple absorption of nutrients dissolved in sea water. Although this might not seem a particularly efficient way of obtaining food, there are tremendous amounts of “unclaimed” organic material dissolved in sea water. Monerans allow these nutrients to diffuse into their cells, a fact well known to microbiologists. Less well known is the fact that larger organisms can feed in this way also. Benthic foraminifera up to 38 millimeters long from McMurdo Sound, Antarctica, take up dissolved organic matter largely as a function of the surface area of their branched bodies”

“Although there is as of yet no unequivocal proof, it seems reasonable to infer from their shapes that members of the Ediacaran fauna used photosymbiosis, chemosymbiosis, and direct nutrient absorption to satisfy their food needs. Since these methods do not involve killing, eating, and digesting other living things, we will refer to them as “soft path” feeding strategies. Heterotrophic organisms use “hard path” feeding strategies because they need to use up the bodies of other organisms for energy. The higher in the food pyramid, the “harder” the feeding strategy, on up to the keystone predator (top carnivore) at the top of any particular ecosystem’s trophic pyramid. It is important to note that the term “hard,” as used here, does not necessarily imply that autotrophic organisms have any easier a time obtaining their food than do heterotrophic organisms. Green plants are not very efficient at converting sunlight to food; sunlight can be thought of as an elusive prey because it is not a concentrated energy source […]. Low food concentrations are a major difficulty encountered by organisms employing soft path feeding strategies. Deposit feeding is intermediate between hard and soft paths. […] Filter feeding, or capturing food suspended in the water, also has components of both hard and soft paths because suspension feeders can take both living and nonliving food from the water.”

“Probing deposit feeders […] began to excavate sediments to depths of several centimeters at the beginning of the Cambrian. Dwelling burrows several centimeters in length, such as Skolithos, first appeared in the Cambrian, and provided protection for filter-feeding animals. If a skeleton is broadly defined as a rigid body support, a burrow is in essence a skeleton formed of sediment […] Movement of metazoans into the substrate had profound implications for sea floor marine ecology. One aspect of the environment that controls the number and types of organisms living in the environment is called its dimensionality […]. Two-dimensional (or Dimension 2) environments tend to be flat, whereas three-dimensional environments (Dimension 3) have, to a greater or lesser degree, a third dimension. This third dimension can be either in an upward or a downward direction, or a combination of both directions. The Vendian sea floor was essentially a two-dimensional environment. […] With the probable exception of some of the stalked frond fossils, most Vendian soft-bodied forms hugged the sea floor. Deep burrowers added a third dimension to the benthos (sea floor communities), creating a three-dimensional environment where a two-dimensional situation had prevailed. The greater the dimensionality in any given environment, the longer the food chain and the taller the trophic pyramid can be […]. If the appearance of abundant predators is any indication, lengthening of the food chain seems to be an important aspect of the Cambrian explosion. Changes in animal anatomy and intelligence can be linked to this lengthening of the food chain. Most Cambrian animals are three-dimensional creatures, not flattened like many of their Vendian predecessors. Animals like mollusks and worms, even if they lack mineralized skeletons, are able to rigidify their bodies with the use of a water-filled internal skeleton called a coelom […] This fluid-filled cavity gives an animal’s body stiffness, and acts much like a turgid, internal, water balloon. A coelom allows animals to burrow in sediment in ways that a flattened animal (such as, for instance, a flatworm) cannot. It is most likely that a coelom first evolved in those Vendian shallow scribble-trail makers that were contemporaries of the large soft-bodied fossils. Some of these Ediacaran burrows show evidence of peristaltic burrowing. Inefficient peristaltic burrowing can be done without a coelom, but with a coelom it becomes dramatically more effective.”

Bilateral symmetry is important when considering the behavior of […] early coelomate animals. The most likely animal to evolve a brain is one with bilateral symmetry. Concomitant with the emergence of animals during the Vendian was the origin of brains. The Cambrian explosion was the first cerebralization or encephalization event. As part of the increase in the length of the food chain discussed above, higher-level consumers such as top or keystone predators established a mode of life that requires the seeking out and attacking of prey. These activities are greatly aided by having a brain able to organize and control complex behavior. […] Specialized light receptors seem to be a characteristic of all animals and many other types of organisms; […] photoreceptors have originated independently in at least forty and perhaps as many as sixty groups. Most animal phyla have at a minimum several pigmented eye spots. But advanced vision (i. e., compound or image-forming eyes) tied directly into a centralized brain is not common or well developed until the Cambrian. The tendency to have eyes is more pronounced for bilateral than for radial animals. […] some of the earliest trilobites had large compound eyes. Trilobites were probably not particularly smart by modern standards, but chances are that their behavioral capabilities far outstripped any that had existed during the early Vendian. […] Actively moving or vagile predators are, as a rule, smarter than their prey, because of the more rigorous requirements of information processing in a predatory life mode. Anomalocaris as a seek-and-destroy top predator may have been the brainiest Early Cambrian animal.”

“why didn’t brains and advanced predation develop much earlier that they did? A simple, thought experiment may help address this problem. Consider a jellyfish 1 mm in length and a cylindrical worm 1 mm in length. Increase the size (linear dimension) of each (by growth of the individual or by evolutionary change over thousands of generations) one hundred times. […] The worm will need internal plumbing because of its cylindrical body. The jellyfish won’t be as dependent on plumbing because its body has a higher surface area. […] Our enlarged, 10 cm long worm will possess a brain which has a volume one million times greater than the brain of its 1 mm predecessor (assuming that the shape of the brain remains constant). The jellyfish will also get more nerve tissue as it enlarges. But its nervous system is spread out in a netlike fashion; at most, its nerve tissue will be concentrated at a few radially symmetric points. The potential for complex and easily reprogrammed behavior, as well as sophisticated processing of sensory input data, is much greater in the animal with the million times larger brain (containing at least a million times as many brain cells as its tiny predecessor). Complex neural pathways are more likely to form in the larger brain. This implies no mysterious tendency for animals to grow larger brains; perfectly successful, advanced animals (echinoderms) and even slow-moving predators (sea spiders) get along fine without much brain. But centralized nerve tissue can process information better than a nerve net and control more complex responses to stimuli. Once brains were used to locate food, the world would never again be the same. This can be thought of as a “brain revolution” that permanently changed the world a half billion years ago.”

“There is little doubt that organisms produced oxygen before 2 billion years ago, but this oxygen was unable to accumulate as a gas because iron dissolved in seawater combined with the oxygen to form rust (iron oxide), a precipitate that sank, chemically inactive, to accumulate on the sea floor. Just as salt has accumulated in the oceans over billions of years, unoxidized (or reduced) iron was abundant in the seas before 2 billion years ago, and was available to “neutralize” the waste oxygen. Thus, dissolved iron performed an important oxygen disposal service; oxygen is a deadly toxin to organisms that do not have special enzymes to limit its reactivity. Once the reduced iron was removed from sea water (and precipitated on the sea floor as Precambrian iron formations; much of the iron mined for our automobiles is derived from these formations), oxygen began to accumulate in water and air. Life in the seas was either restricted to environments where oxygen remained rare, or was forced to develop enzymes […] capable of detoxifying oxygen. Oxygen could also be used by heterotrophic organisms to “burn” the biologic fuel captured in the form of the bodies of their prey. […] Much research has focused on lowered levels of atmospheric oxygen during the Precambrian. The other alternative, that oxygen levels were higher at times during the Precambrian than at present has not been much discussed. Once the “sinks” for free oxygen, such as dissolved iron, were saturated, there is little that would have prevented oxygen levels in the Precambrian from getting much higher than they are today. This is particularly so since there is no evidence for the presence of Precambrian land plants which could have acted as a negative feedback for continued increases in oxygen levels” [Here’s a recent-ish paper on the topicdo note that there’s an important distinction to be made between atmospheric oxygen levels and the oxygen levels of the oceans].

August 4, 2014 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Geology, Microbiology, Paleontology, Zoology | Leave a comment

The Emergence of Animals: The Cambrian Breakthrough (I)

Here’s what I wrote about the book on goodreads:

This book is almost 25 years old, and this is one of the main reasons why I did not give it five stars. Parts of this book is just amazing, but the fact that I felt that it was necessary to continually look up terms and ideas covered in the book made it slightly less fun to read than it could have been. Some parts of the scientific vocabulary applied throughout the book are frankly outdated, and this aspect reflects not only a change in which words are used but also, more importantly, a change in how people think about these things. That progress has been made since the book was written is a good thing, but it did subtract a little from the overall reading experience that I very often felt that I had to be quite careful about which specific conclusions to accept and which to question. It does not help that some of the main conclusions towards the end of the book seem to have been proven, for lack of a better word, wrong.

But all in all it’s really a very nice book – there’s a lot of fascinating stuff in there.”

A few sample quotes from the book:

“a distinction needs to be made between the two major types of animal fossils — body fossils and trace fossils. Body fossils are either actual parts of the organism’s body (such as a shell or a bone), or impressions of body parts (even if the parts themselves have been dissolved away or otherwise destroyed). The imprint of a feather or leaf or the external surface of a shell are examples of body fossils. […] Trace fossils are markings in the sediment (usually made while the sediment was still soft) left by the feeding, traveling, or burrowing activities of animals. Familiar examples of trace fossils include tracks and trails made by worms as they plow through sediment looking for food and ingesting sediment. […] Completely unrelated organisms can make trace fossils which are indistinguishable to paleontologists. Trace fossils are part of the fabric of the sediment, and therefore can be very resistant to destruction by metamorphism of the surrounding rock. Body fossils, on the other hand, are often destroyed by chemical reactions with the surrounding sediment. But body fossils are the only fossil type that can consistently give reliable information about the identity of the organism which left the remains. […] The worst problem in the search for the oldest animal fossils is mistaken identity. Sedimentary rocks are replete with irregular structures and small scale disturbances or interruptions of the horizontal bedding or layering. Some of these disturbances are caused by organisms, but many are not. […] Usually a well-preserved and well-formed trace fossil is unquestionably biologic in origin, and all paleontologists would agree that the trace was formed by an animal. Yet it can be difficult to define precisely what it is about a trace fossil that makes it convincingly biogenic (formed by life). […] A sedimentary structure that resembles, but is in fact not, a trace fossil (or a body fossil, for that matter) is called a pseudofossil. Pseudofossils have plagued the study of Precambrian paleontology because many inorganic sediment disturbances look deceptively like fossils.”

“Convincing trace fossils are known from the late Precambrian, sometimes in association with the soft bodied Ediacaran fossils (Glaessner 1969). These trace fossils are generally simpler, less common, and less diverse than Cambrian trace fossils. There is a significant difference in the complexity and depth of burrowing between Cambrian and Precambrian trace fossils, and it has been argued that the changeover from simple trace fossils to more complex types of traces occurred at more or less the same time as the Cambrian explosion, the first appearance of abundant Cambrian shelly fossils. […] Even shallow, sediment surface burrows in the Cambrian show a marked change in character over their Precambrian predecessors. […] something outstanding happened to the abilities of trace-fossil makers across the Precambrian-Cambrian boundary. Animals discovered a large number of ways to effectively use the sediment as a food resource, and also began to move deeper into the substrate for deposit feeding and homebuilding.”

“Seilacher (1984, 1985) recognizes that flattened body shapes maximize surface area for the takeup of oxygen and food dissolved in seawater, and perhaps also for the absorption of light. “Normal” metazoan animals generally have plump, more or less cylindrical, bodies. For very small, thin skinned animals, cells near the body surface can get oxygen and expel waste by simple diffusion across the cell surface membranes. Waste products such as carbon dioxide will be supersaturated inside of the animal’s body, and will tend to migrate out of its cells and into the open environment. The reverse is true for oxygen; it will tend to migrate into the cells because its concentration is greater on the outside than on the inside of an oxygen-respiring animal. Animals such as frogs and salamanders are able to respire (at least in part) in this way. But for most large, cylindrical animals, diffusion respiration will not work because diffusion is ineffective for cells buried deep within the animal’s body. This is a consequence of the fact that as an animal increases its size, its total volume outstrips its surface area by a large margin. […] metazoans have developed intricate systems of pipework and tubing to deliver nutrient and waste removal services to interior cells. Circulatory systems, digestive tracts, gills, and lungs are all solutions to the problems associated with volume increase.”

Monoplacophorans […] are cap-shaped shells distinguished by two rows of muscle scars on the interior of the shell. They were thought extinct until living specimens were dredged from the deep sea and described in the late 1950s. Monoplacophorans have had an unusual history of discovery. They are the only group of animals that has been: (a) described hypothetically before being discovered; (b) found as fossils before being found alive,- and (c) dredged from the depths of the oceans before being collected from shallower marine waters (Pojeta et al. 1987). […] Rostroconchs are a major, extinct, order of mollusks that first appeared in the earliest Cambrian. Rostroconchs have a shell that is shaped like a clam shell, except that instead of having an organic ligament connecting the two valves, the two halves of a rostroconch shell are fused together to form a single valve. Despite this fusion, larger rostroconchs look very much like clam fossils with valves still articulated, which partly explains why rostroconchs were not recognized as a major, distinct, group until the 1970s. […] Slightly after the first appearance of rostroconchs, the first true clams or bivalves appear. Clams probably had the same ancestor as the rostroconchs […]. Instead of keeping the two valves fused as in rostroconchs, clams hinged the valves with articulating teeth and a tough, organic ligament. This evidently proved to be the more successful approach, since bivalve shells now litter the beaches all over the earth, whereas rostroconchs dwindled to extinction in the Permian.”

“Of the earliest Cambrian shelly fossils, many groups are truly problematic in the sense that not only do we have no idea what kind of animal made them, but also we have no clear conception of the function or functions of the skeletal remains. […] there is an anomalously high proportion of small shelly fossils that do not belong to later phyla. “Living fossils” are creatures alive today that have undergone very little morphologic change for long stretches (sometimes 100 million years or more) of geologic time. Few living fossils remain from the earliest Paleozoic fauna. […] Many of the groups that were most important in the Cambrian are unimportant or extinct today, for example, the trilobites, the inarticulate brachiopods, hyoliths, monoplacophorans, eocrinoids, the sclerite-bearers, and phosphatic tube-formers. True metazoans were undoubtedly present before the Cambrian, but they were all, with [few] exception[s] […], soft-bodied. New types of soft-bodied animals appear in the Cambrian as well, but our understanding of these forms is restricted to rare finds of Cambrian soft-bodied fossils, which are even rarer than finds of the Ediacaran fauna.”

I’ll just quote that last part again: “our understanding of these forms is restricted to rare finds of Cambrian soft-bodied fossils”.

They’re talking about the findings of soft-bodied organisms who did not make shells or anything like that which lived more than 500 million years ago. To get a sense of perspective in terms of how long ago this is, have a look at this picture – that’s one guess at what we think the Earth might have looked like back then. In my mind, the fact that we know anything at all about soft-bodied animals living back then is pretty amazing to think about.

I could easily write perhaps four posts about this book, but I’m not going to do that. Instead I have decided for now to limit my coverage here to the stuff above and some links to relevant stuff I looked up while reading the book, which I have posted below – I was surprised how much relevant stuff wikipedia has on related matters, and if you’re curious you should really go have a look at some of those links. I should note that I will probably add another post about the book later on with some more observations from the book – it seems wrong to me to limit coverage of this great book to one post, but there’s no way I can cover all the good stuff in there anyway.

Here are as mentioned some relevant wiki links to the kinds of stuff they talk about in this book – most of the links are in my opinion links to articles of what I’d consider to be a ‘reasonable’ length/quality, and although I have not read all of them I’d note that some of them are quite good:

Cambrian explosion.
Ediacara biota (featured).
Kleptoplasty.
Trace fossil.
Cloudinid (‘good article’).
Sclerite.
Archaeocyatha.
Trilobite.
Echinoderm.
Brachiopod (‘good article’).
Bivalvia (featured).
Chiton.
Bryozoa (‘good article’).
Adam Sedgwick.
Roderick Murchison.
Global Boundary Stratotype Section and Point (noteworthy in this context is that the Precambrian/Cambrian boundary GSSP at Fortune Head had not been decided upon when this book was written – they have a whole chapter about these and related things).
Manorian glaciation (this is not what it’s called in the book, but that is what they’re talking about anyway).
Snowball Earth.
Timeline of glaciation.
Cryogenian.
Rodinia.
Mirovia.
Curie temperature.
Autotroph.
Heterotroph.
Microbial mat.
Anomalocaris.
Stromatolite.
Acritarch.
Great Oxygenation Event.
Methane clathrate.

July 29, 2014 Posted by | Biology, Books, Ecology, Evolutionary biology, Geology, Paleontology, Zoology | Leave a comment

Plant-Animal Interactions: An Evolutionary Approach (3)

This will be my last post about the book. You can read my previous posts about the book here and here.

As I have already mentioned, I really liked this book. Below I have covered some of the parts of the book which I have not yet talked about here on the blog, and in particular I’ve included stuff about how plants and animals cooperate with each other. I have of course had to leave a lot of stuff out.

“The lack of mobility in plants creates a physical obstacle in the dispersal of their genes. In a majority of all plants, this obstacle has been alleviated through the formation of mutualisms with animals that transport pollen grains between stigmas and also disperse seeds. In the case of pollination, the goal for the plant is to receive pollen on its stigma and to have pollen picked up and deposited on conspecific stigmas of other plants. The animal most commonly seeks a food reward. It is important to appreciate that mutualisms such as these represent reciprocal exploitation with an underlying evolutionary conflict. Selection in mutualisms favours selfish behaviour […] One manifestation of such selection […] is the widespread phenomenon of plant species that no longer reward pollinators but instead attract visitors by deception. […] Non-rewarding plants species constitute a substantial portion of all angiosperms, especially among orchids, but they are mostly minor components of the plant community in which they grow. […] Likewise, many flower-visitors (if not most) do not contribute to pollination but do remove floral resources such as nectar and pollen. […] A fair number of plants mimic not flowers but rather pollinator mates or oviposition sites. Flowers of the well-studied European fly orchids (Ophrys) and caladeniine Australian hammer orchids provide visual, olfactory and tactile cues mistaken by naïve wasp males for conspecific females (Stowe 1988), and pollination happens as males attempt copulation with the flowers.” [This sentence made me laugh!]

“pollination mutualisms evolve amid simultaneous antagonistic interactions; the plant is under selection to maximize the net fitness of attracting potentil mutualists at the lowest net cost while minimizing the detrimental effects of non-mutualists or low-quality mutualists. This tradeoff does not exist in antagonistic interactions […] Floral traits are likely to be as much the result of selection for avoidance of some animals as for attraction of others. […] The vast majority of all extant pollination mutualisms […] involve flowering plants, which dominate most biota on earth today.”

“Given that the benefit to plants of animals as pollen vectors is transport across longer distances, it is not surprising that the three extant groups of animals that have evolved flight – insects, birds and bats – contain a very large proportion of all pollinators. Among the insects, flower-visiting species are particularly frequent within the large orders Hymenoptera (bees and wasps), Lepidoptera (moths and butterflies), Diptera (flies) and Coleoptera (bettles). […] The Lepidoptera alone, whose coiling tongues make them flower specialists and effective consumers of nectar, constitute 11% of all described species on Earth […] Among birds, six phylogenetically independent groups have diversified as flower-visitors and often as pollinators […] Together these groups constitute over 10% of all recognized bird species. […] Flowers offer an extraordinary range of shapes, colours and scents, reflecting high rates of evolutionary change in these traits. […] Almost any flower part or even adjacent leaves are modified for the purpose of attracting pollinators. There is arguably more plasticity in these secondary reproductive traits in plants than in any other organismal groups, with the possible exception of birds.”

“Specificity among visitors is a necessity for effective pollination; if animals visit flowers of different species indiscriminately, heterospecific pollen transfer will result, which reduces the probability of pollen reaching a conspecific stigma […] The number of plant species visited varies greatly among flower-visiting species. […] Individual visitors often tend to specialize on a subset of potential flowers during any one foraging bout; in bees perhaps 90% of all visits may be made to a given species, with occasional visits to other species. This short-term specialization is referred to as floral constancy. The dominant flower may vary among simultaneously foraging conspecifics, and within individual visitors on successive foraging bouts. Reasons for such short-term selectivity have been explored in insects, and focus on the effects of foraging rate as a result of memory constraints. Insects must learn by trial and error how to effectively access a reward such as nectar in more complex flowers, as the rewards are concealed and most quickly accessed using a particular approach. Minimum handling time may be approached only after as many as 100 visits to a given zygomorphic flower […] visitors may be unable to keep more than one sensorimotor protocol in active memory, thus making it a superior strategy to focus on one food source at a time […] Specialization is often not in the evolutionary interest of a flower-visiting animal, as its ultimate interest is to optimize the reward harvesting rate over time. A foraging pattern that maximizes the harvesting rate of commodities such as nectar and pollen can include two or more coexisting plant species, especially if their floral structure is fairly similar so that the visitor can use a single visit behaviour protocol. […] The vast majority of all plants are pollinated by two or more species”

“With the […] exception of ants […], invertebrates play only an anecdotal role as seed-dispersers […] All major lineages of vertebrates take part in fruit consumption and seed dispersal, but their importance as dispersal agents is very unequal. Birds and mammals are the only or main dispersers of the vast majority of vertebrate-dispersed plants […] About 36% of 135 extant families of terrestrial birds, and 20% of 107 families of non-marine mammals, are partly or predominately frugivorous […] Fruit consumption by vertebrate dispersers […] has selected for fruit traits that enhance detectability by frugivores […] Although exceptions abound, fruits that are green or otherwise dull-coloured when ripe tends to be associated with seed dispersal by mammals, whereas fruits dispersed by birds tend to be brightly pigmented. The partial dichotomy between ‘bright’ and ‘dull’ ripe fruits has probably been selected for by the contrasting sensory capacities of birds and mammals […] Size is an important attribute of fruits, because it sets limits to ingestion by relatively small-sized dispersers that swallow them whole, like birds. […] Fruits eaten by mammals tend to be larger than those eaten by birds […] Fruit pulp is the reward offered by plants to dispersers, and its nutritional value is a critical element in the plant-disperser interaction. Compared to other biological materials, fruit pulp is characterized, on average, by high water and carbohydrate content, and low protein and lipid content. […] the occurence of secondary metabolites within ripe pulp presumably represents a tradeoff with respect to defence from damaging agents and palatability for dispersers […] A number of studies provide unequivocal support for the ‘palatability-defence tradeoff hypothesis’. […] increased frugivory is quite often associated with increased intestinal length, as an adaptive response for increasing intestinal absorption of the water-diluted nutrients in fruit juice. […] Most fruits are very deficient in nitrogen, which perhaps represents the most important nutritional constraint that frugivorous animals must cope with. Regular ingestion of small amounts of animal food seems to be the commonest way of complementing the poor protein intake associated with frugivory.”

“Abundance of fruit varies markedly among years and seasons, and within as well as between habitats, which generally leads to patchy and unpredictable distributions in time and space […] A distinct suite of behavioural and physiological traits allow frugivores to withstand or escape from temporary situations of fruit scarcity and efficiently locate unpredictable fruit sources. Seasonal migration and habitat shifts are the two most common generalized responses of frugivores to fluctuations in fruit availability. […] Plant-vertebrate dispersal systems are characterized not only by the absence of obligate partnershipts, but also by weak mutual dependence between species of plants and animals, and by the prevalence of unspecific relationships. […] the general picture is one of loose interdependence between species of plants and species of dispersers. […] pollen and seed dispersal by animals are fundamentally dissimilar […], and their differences have manifold evolutionary implications. The two most important distinctions are (i) that a definite target exists for dispersing pollen grains (the conspecific stigma) but not for dispersing seeds; and (ii) that the plant can control pollinators movements by providing incentives at the target site (nectar, pollen), but there are no similar incentives for seed dispersers to drop seeds in appropriate places. These differences are best framed in terms of the departure-related versus arrival-related advantages of dispersal [You can say that seed-dispersal systems work on the basis of ‘advance payment’ alone, whereas pollen dispersal mechanisms also include ‘payment upon delivery’ aspects].”

Finally, ants! Ants are awesome…

“Ants are one of the most abundant, diverse and ecologically dominant animal groups in the world. They make up from 10 to 15% of the entire animal biomass in many habitats, and in the Amazonian rainforest, for example, one hectare of soil may contain 8 million individuals. The impact of ants on the terrestrial environment is correspondingly great. In most habitats they are among the leading predators of other insects and small invertebrates, and in some environments they are the principal herbivores and seed predators. Ants can alter their physical environment profoundly, moving more soil than earthworms, and being major channellers of energy and cyclers of nutrients. […] It is probably fair to say that no other animal group interacts with plants in such diverse ways. Indeed, the fact that ants are the only specific taxa mentioned in the chapter headings of this book reflects their ecological importance in the lives of most plant species. Ants can protect plants directly from herbivores or from competition with other plants. They can also affect plant-community composition and dynamics by selective weeding or ‘gardening’, altering nutrient availability, pollinating flowers, or dispersing and harvesting seeds. Plants provide ants with food and shelter […]. Some relationships between ants and plants appear to be highly coevolved mutualisms and it is these interactions that have received the most study. But the majority of ant and plant species interact in more generalized ways, often through the influence of ants on the chemical and physical properties of soil. […] The oldest ant species, Sphecomyrma freyi, has been dated from amber to be about 80 million years old. [….] there is evidence that ants have been both remarkably diverse and ecologically successful for at least 50 million years”

“Cultivation of fungus by attine ants originated about 50 million years ago. The relationship between the higher attine ants and the symbiotic fungus they cultivate is obligate. Foundress queens propagate the fungus clonally by carrying a pellet of fungus in their mouths during their nuptial flight to establish new colonies. […] The relationship between the attines and their fungus has been termed an ‘unholy alliance’ because it combines the ants’ ability to circumvent plants’ anti-fungal defences with the ability of the fungus to subvert plants’ anti-insect defences. The ants benefit because the fungus breaks down plant tissue such as cellulose, starch and xylan, and possibly detoxifies insecticidal plant compounds. The fungus thus enable them to make use of plant material that would otherwise be unavailable and allows the ants to be truly polyphagous in the midst of diverse flora. […] the relationship between the ants and the fungus has recently been found to be a triumvirate, with evidence that an antibiotic-producing bacterium is an important component of the symbiosis. […] fungus gardens are particularly prone to infection by a group of closely related, highly specialized parasites in the fungal genus Escovopsis. […] Escovopsis is found in gardens of virtually all species of fungus-growing ants, but not elsewhere. The parasite is usually found at low levels, but if the health of the garden is compromised it can quickly take over and destroy the fungal crop. In healthy gardens, Currie et al. (1999) have shown that the fungus is kept in check by specific antibiotics produced by Streptomyces bacteria living on the bodies of the ants […] The bacterium can also promote the growth of the cultivated fungi. The position of the bacterium on the ant integument is genus-specific, indicating that the association with the ants is both highly evolved and of ancient origin […] Attine symbiosis appears to be a coevolutionary arms race between the garden parasite Escovopsis on the one hand, and the tripartite association of the actinomycete, the ant hosts and the fungus on the other. The relationship raises the interesting question of how the attine antibiotics have remained effective against the fungus-garden pathogens for such a long time, given that resistance to antibiotics is a well known problem in human and other populations.”

“The coevolution of ants and plants involving systems of rewards and services has resulted in a variety of elaborate and complex mutualistic interactions collectively known as ant-guard systems. Here the rewards are extra-floral nectar, specialized food bodies and nest sites, while the service is the protection of the plants from herbivory. […] Plant structures known as domatia are developmentally determined and appear to be specific adaptions for ant occupation. They are often formed by the hypertrophy of internal tissue at particular locations in the plant, creating internal cavities attractive to ants […] the plant species that bear them are known as myrmecophytes. […] Some myrmecophytes are actually ‘fed’ by the ants they house. Experiments have shown that two genera in the family Rubiaceae […] absorb nutrients from the wastes of the Iridomyrmex colonies they house in tunnels inside large tubers […] A variety of field studies have shown there is strong competition among ants for dormatia […] Ant-guard systems involving extra-floral nectaries are often complicated by the presence of Homoptera or lepidopteran larvae that secrete nectar-like fluids collectively known as honeydew. In such situations, the ants have a choice of food and the outcome of these three-way interactions between plants, ants and herbivores appears to be extremely variable. The Homoptera include herbivores such as aphids, leafhoppers, scale insects and coccids. Each animal is armed with a proboscis that penetrates plant vascular tissue, tapping into the nutrient supply. With little apparent effort, the sap enters the front end of the homopteran gut, later appearing at the back end as droplets, somewhat depleted in quality but still containing many nutrients, where it is ejected as honeydew. Many ant species harvest the honeydew and, in return, protect the homopterans from predators and parasites […] As a result, ant activity can increase levels of herbivory as well as other forms of damage […] Ant interactions with plant species that produce extra-floral nectaries, food bodies and domatia have evolved both in the presence of homopterans and lepidopteran larvae and the ant behaviour that protects them. For example, homopterans of various kinds are routinely maintained within domatia and they frequently feed on plants that bear extra-floral nectaries. This leads to the situation where plants are providing rewards for ant-guards that attack some of the plant’s enemies but protect others. A solution to this apparent conflict of interest was first proposed by Janzen (1979) who suggested that the presence of homopterans was part of the cost of the ant-guard system […] The evoluation of extra-floral nectaries has itself been viewed as a defence against homopteran attack, weaning ants away from the herbivores […] Homopterans are common herbivores and have been around for a very long time; thus, given their ubiquity, selection for extra-floral nectaries may have resulted in the plants exerting greater control over the ant-guards, provided ants preferred nectar to honeydew.”

June 24, 2014 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Zoology | Leave a comment

Plant-Animal Interactions: An Evolutionary Approach (2)

This is my second post about the book – you can read my first post about the book here; that post includes some more general comments and observations. In this post I’ll cover plant-insect interactions and mammalian herbivory.

“Herbivory, which is the consumption of plants by animals, encompasses many different types of interactions that differ in their duration and deadliness to the plant. Insect herbivores, like mammals, feed on plants in numerous ways. Seed and seedling herbivory are predatory interactions because herbivores immediately kill individuals in the plant population. Insect herbivores that feed on leaves and other parts of mature plants typically do not cause plant mortality. In the rare cases when they do, it usually requires much time to kill the host plant. Such relationships are closer to parasite-host than predator-prey relationships. […] Insect herbivores differ from mammalian herbivores in their size, numbers, and the kinds of damage they inflict. Because of their small size, insects often have an intimate, lifelong association with the host plant. Moreover, while their associations are lifelong, often their lives are rather short, predisposing them to rapid rates of evolution. On average, insect herbivores are much more specialized than their mammalian counterparts. […] There has long been debate over why specialist feeding habits are widespread in herbivorous insects. […] There are clearly a number of hypotheses, each with some empirical support […] Because specialization is a complex trait, we don’t necessarily expect a single hypothesis to explain the phenomenon.”

“Insect populations frequently fluctuate in size, and this fact has prompted a good deal of speculation as to what factors limit the size of herbivore populations. Hairston, Smith and Slobodkin (1960) reasoned that, since herbivores rarely consume all of their plant resources (the world is green), herbivore populations are likely to be limited by parasites and predators, but not by resource abundance […] However, whether herbivorous insect populations are limited by food (bottom-up forces in a food web) or by predators (top-down forces) remains a hotly debated topic […], and it is unlikely that either force dominates all insect populations”

“The first obstacle that an insect faces is the fact that, on average, only about 10% of the energy available to one trophic level makes it to the next trophic level. Sources of energy loss include the fact that not everything ingested can be assimilated (e.g. lignin, cellulose). […] the chemistry of plant and animal tissues is very dissimilar. Liebig’s law of the minimum states that growth is possible to the extent determined by the nutrient that is in shortest supply. For herbivores, one such nutrient is protein. Because nitrogen is relatively easy to measure and protein is not, protein content is often estimated by assaying organic nitrogen, which comprises from 15 to 18% of plant proteins […] sap-feeding insects, like cicadas and other homopterans, often eat 100 to 1000 times their body weight per day because amino acids make up only a tiny proportion of the sap […] In general, both micro- and macronutrients can limit the growth rate of insect herbivores.”

I want to interpose an observation here – I find it quite interesting how seemingly unrelated fields can so often become related in ways you do not expect them to. I’m currently reading Mary Barasi’s Nutrition at a glance (which despite its low page count is actually quite a bit of work, as I’ve found out..). It makes sense in retrospect that some things overlap here, but when I started reading Barasi I did not expect stuff covered in this book to be relevant to the coverage in that book (she only deals with humans). It turns out that the stuff above – and some other stuff covered elsewhere in the book as well – is quite relevant to Barasi’s coverage; I’d probably have been somewhat confused by the focus on nitrogen in the protein chapters of Barasi if I had not read the stuff covered in chapter three of this book. When you’re about to learn some new stuff you never really know how that new stuff you’re about to learn may relate to stuff you already know, or for that matter how it may relate to stuff you’ll learn later on. I always love making new connections like these and connect dots I didn’t even know could be connected.

Okay, moving on…

“Aside from nutritional hurdles and the limited availability of some plant parts, herbivores may also be prevented from feeding as a result of plant defences. […] Adaptions include physical barriers, toxins, anti-feedants, decoys and even other organisms [ants!]. Some defences are always present on the plant; we call these constitutive defences. Many others, including thorns and spikes, are inducible, that is, they are augmented only after the plant is attacked […] The list of chemicals that owe their defensive value to their ability to interfere with insect physiology or behaviour is a very long one. While the elaboration of thorns, spines and hairs is restricted largely to their size and shape, the number of possible combinations, principally of carbon, oxygen, hydrogen, nitrogen and sulfur, is enormous. […] These plant constituents are commonly referred to as ‘secondary’ compounds. […] When the role of a secondary compound is defensive, it is commonly referred to as an ‘allelochemical’. […] Synergists are chemicals that enhance the toxicity of chemicals with which they are mixed. […] Our current understanding is that the presence of secondary compounds can deter many herbivores from using plants, but that almost every plant species has a suite of specialized herbivores that are adapted to use these compounds as attractants, as feeding stimulants or as a source of toxins for use in defence against their enemies. […] As many means as plants have to deter insects, insects have ways of circumventing them. […] The overall responses of plants subjected to herbivory may be viewed as a tradeoff between growth and defence.” [my bold, US]

“As a group, insect herbivores tend to have larger effects than mammalian herbivores on plant growth and reproduction […] when a plant is attacked by one herbivore it may become more or less vulnerable to attack by others. […] the degree to which plants can evolve to become better defended, might be constrained by the preferences of beneficial pollinators. […] While it is clear that herbivores can affect plant community composition and species distribution, the reciprocal effect also exists: plant community composition affects insect herbivore loads. […] The ‘resource concentration hypothesis [states that] herbivores are more likely to find hosts that are concentrated, and herbivores remain longer on hosts growing in dense or pure stands. […] The ‘enemies hypothesis’ [states that] increased diversity of predators and parasitoids in diverse stands may limit population densities of herbivores in these stands. The idea that diverse plant community composition may result in reduced attack by herbivores has been called ‘associational resistance’. […] both community composition and the dispersal abilities of herbivores in relation to the scale of community diversity will affect the degree to which plants receive damage from herbivores.”

“In summary, insect herbivores respond to selection by plant defences and nutritional status. Plants strongly affect insect fitness so that, in general, insect herbivores are relatively specialized with respect to their diet breadth (in comparison with mammalian herbivores). […] Plants affect insect abundance through their defences, which often entail the actions of other species, such as predacious and parasitic enemies of herbivores.
Insects in turn affect plant fitness, and may exert selection on plant defences, both physical and chemical. There is a growing body of evidence suggesting that these defences come at some cost to the plant. On a larger ecological scale, insects affect plant distribution and abundance, as well as the species diversity of plant communities. Frass, honeydew and greenfall from insect outbreaks also alter nutrient cycling regimes in the soil and the availability of nutrients to plants.
Finally, many of the adaptions and counter-adaptions of plants and their insect herbivores support the idea that much of the biodiversity of the earth is a result of the arms race between insect herbivores and their host plants.” [my bold, US]

“The amount of food differs between biomes. The tundra has a primary production of only about 140 g m−2 yr–1, while swamps and marshes reach about 3000 g m−2 yr–1, i.e. a 20-fold difference between the extremes […] The plant biomass, or standing crop, shows an even greater range between the least and most productive biomes, i.e. a 75 fold difference from about 600 g m−2 in the tundra to 45 000 in tropical rainforests. Estimates of food resources are vital for understanding the relations between plants and herbivores […] and [there is a] need for estimates that capture both the static and dynamic situations of the food resources. […] Given the large spatial and temporal variation in food abundance and quality, mobility is a valuable trait and the migratory habits of many ungulates represents an adaptive response. There are no strictly sedentary herbivores […] Herbivores have the advantage of feeding on objects that cannot escape, but on the other hand plant food has low nutritive value (it is low in nitrogen and must be digested slowly). […] Diet composition is commonly used to classify animals into functional groups, e.g. predators, omnivores and herbivores. Mammals, like all other living organisms, have a perverse tendency to defy exact classification […] Sixteen different categories of dietary specialization have been proposed, and seven of them refer to herbivores […] a large majority of the [mammalian] herbivores have quite a mixed diet and also feed on animal matter. [my bold, US] […] It is increasingly clear that mammalian herbivory on a given plant species can result in a continuum of responses, depending on the characteristics of the plant, the type of herbivory and the environment. […] there is no simple typical response for a given plant species.”

“The metabolic requirements of mammals increase with (body mass)0.75 (Kleiber 1932), but the capacity of the gastrointestinal tract with (body mass)1.0 […] Smaller animals thus have higher mass-specific food requirements without any accompanying proportional increase in the gut capacity, which limits the volume of digesta retained and its passage […] There is a tradeoff between the rate of intake and the time allowed for chewing. […] The theory of optimal foraging is based on the assumption that an animal would forage in such a way that it optimizes its fitness […] Food, in terms of quantity or quality, is usually highly variable and is sometimes distributed in more or less discrete patches. Therefore, one crucial point in the optimal foraging concept will be the criteria for when to leave a feeding patch and move to another. The ‘marginal value theorem’ states that a herbivore should stay as long as the extraction rate is above the average for the environment as a whole. […] Understanding the decision rules used by a herbivore requires an understanding of its behavioural responses on various time-scales. It is less probable that an animal optimizes its diet at each bite, but rather that it bases future decisions on an integration over longer periods.” [I found these observations rather funny in a way – some of this stuff is a lot like microeconomic theory, it’s just that in this case the hypotheses made relate to the behaviours of non-human organisms, rather than humans..]

June 18, 2014 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Zoology | Leave a comment

Plant-Animal Interactions: An Evolutionary Approach (1)

This book, aimed at upper-division undergraduate students and those starting graduate studies, attempts to provide a manageable synthesis of recent developments in the field of terrestrial plant-animal interactions”, they write in the introduction. One of the amazon reviewers claimed that “This is a VERY easy read” – which was actually, in combination with the high ratings it’s got, a large factor leading me to give this book a try; I figured that I shouldn’t be too worried about the fact that this book is written for advanced undergraduates/graduate students in a field I’m not super familiar with.

The book is actually not terribly difficult to read – in the sense that most concepts/terms applied throughout the book are defined along the way, meaning that you’re unlikely to have major issues understanding what’s going on even if you’re not an evolutionary biologist (I’m not, so I should know). It also helps that many of the terms which are not defined along the way will be sort of obvious to you from the context (they never really tell you what coprolite is, but I should think a picture of a dinosaur turd would help… I incidentally read about those things last year, so that particular word did not cause me problems). Although not all ‘potentially problematic terms’ are defined in the book most of them are, and there are a lot of definitions in this book. It’s quite dense; it’s a book where my average reading speed will be around 10 pages per hour, when measured over multiple hours and including necessary reading breaks and so on – perhaps 13-15 when things are going really well. I recently started reading Christie’s Peril at End House, and I’m reasonably sure it’ll take me less time to read that entire book than it took me reading chapter 2 of this book (chapter 2 was, I should perhaps add, significantly longer than the average chapter). I’m well aware that some textbooks are worse than 10-15 pages/hour and I have my eyes on another text dealing with related stuff which I’m reasonably sure will be a bit more work than this one was, and I’m also aware that some books catering to a more advanced audience will presumably take familiarity with many of the terms defined in this book for granted; but even so, calling this ‘a very easy read’ is perhaps a bit much. I should note that although I don’t want to delude anyone into thinking this book is easier to read than it is, I also really don’t want to give people reading along here more excuses not to read this book than is strictly necessary, because I think it’s just a great book.

I have decided to give the book a couple of posts here on the blog, perhaps 3, but I don’t know when I’ll post the others – I have finished the book, and I’ve started reading Kuhn. I’m somewhat behind on the book blogging at the moment, which tends to happen when I’m reading stuff offline; in part because blogging books I’ve read offline is in general a lot more work, among other things because I can’t copy/paste relevant segments when quoting from the books.

I’ve given the book five stars on goodreads simply because as mentioned it’s a really great book – it’s the sort of book which does all those things I’ve been consistently annoyed about popular science books dealing with topics related to the ones covered in this book not doing, and it’s on the other hand also the sort of book which does none of those annoying things the other type of books tend to do. The book doesn’t spend a page talking about how butterflies look nice, ‘you could see the sun setting in the distance…’, or some anecdote about the uncle of the author or crap like that; you have definitions, functional relationships and dynamics explored in detail – a thoroughly analytical approach, without all the infuriating crud. Occasional appreciation, yes, but mainly just the data, the dynamics, the science.

In biology you have two major fields called zoology (dealing with animals) and botany (dealing with plants), but “the knowledge of these two groups of organisms has traditionally progressed along separate lanes, under the leadership of different researchers and independently of each other” (a quote from the introduction). What this means is that there haven’t been a lot of people who’ve done work on ‘the stuff in the middle’ – which is a shame, as “we will never fully understand the evolution of the morphology, behaviour and life history of plants and animals unless we understand in sufficient detail their reciprocal influences in ecological and evolutionary time” (another quote from the introduction). So they’ve written down some of the things they know about these things. The book has nine chapters written by 13 different contributors. The first two chapters are sort of ‘general’ chapters; the first one is about: ‘Species interactions and the evolution of biodiversity’, and the second (much longer) one is about: ‘The history of associations between plants and animals’. In part 2 of the book, dealing with ‘mostly antagonisms’, they talk about plant-insect interactions (chapter 3), mammalian herbivory (chapter 4) and granivory (chapter 5 – “Granivory describes the interaction between plants and the animals (termed granivores or seed-predators) that feed mainly or exclusively on seeds.”). In part 3, dealing with ‘mostly mutualisms’, they talk about pollination by animals (chapter 6) and seed dispersal by vertebrates (chapter 7). In the last part, ‘synthesis’, they talk about ant-plant interactions (chapter 8) and a little bit about ‘future directions’ in research on these matters (chapter 9). In my opinion there were no bad chapters in this book – this is a ‘pure’ five star rating, without any kind of ‘compensatory stuff’ going on. Other people may disagree, but my opinion is that the book is well written, deals with super interesting stuff, and that this stuff is just plain fascinating!

It would be easy to write one post dealing with each of the chapters but I’m not going to do that, and so my posts about this book are going to be another set of those posts where you’ll spend perhaps 10-15 minutes on perhaps 10 hours of material. The book has a lot of stuff I simply cannot cover here, and I highly recommend that you read it if you find the stuff I cover here interesting. It’s been hard to blog this book because it’s in general really difficult to know what to exclude, and very easy to find new things to add. The stuff below covers some of the material from the first two chapters, corresponding to roughly 75 pages.

“The majority of terrestrial organisms fly. […] The evolution of propelled and passive flight, and their consequences, may well be regarded as the most creative force in the development of biodiversity. Most plants fly at one stage of their life cycle or another, as pollen or as seeds or both. Spores of ferns and fungi fly. Pollen, spores and seeds are carried on the wind by a multitude of winged animals: insects, birds, bats and perhaps pterosaurs in their day. […] the vast majority of terrestrial organisms exist in trophic systems based on plants, be they the plant themselves, herbivores, carnivores, pollinators, frugivores or granivores […] as we climb the trophic ladder, species richness increases by orders of magnitude. A plant species, such as an oak, birch or willow, may be host to 200-300 insect herbivore species. Each herbivorous insect may be utilized by 10-20 carnivores, either predators or parasites. The plant provides both food and habitat for the associated fauna and many microhabitats are available for colonization […] Including undescribed species, there may be 10-100 million species of all kinds living today, over half of them insects, of which 99,5% can fly in the adult stage. […] Add to the insects about 9000 species of birds and 1000 bat species, together making up 80% of the warm-blooded vertebrates, and we see that conquest of the air has been an evolutionary ‘success’ of extreme proportions.”

“The basis for the spectacular radiations of animals on earth today is clearly the resources provided by the plants. They are the major primary producers, autotrophically energizing planet Earth. […] Well over 90% of energy in terrestrial systems is fixed by autotrophic plants (the remainder by algae and bacteria), and almost all terrestrial animals depend on autotrophic production, either directly as herbivores or saprophages, or for shelter and microhabitats, or indirectly as predators and parasites utilizing the second trophic level of herbivores. […] plant-animal interactions are both direct and indirect and ramify throughout the trophic system. […] multitrophic-level interactions are ubiquitous and important both for the understanding of natural interactions and for effective management of landscapes dominated by humans […] while plant hosts and their varied insect herbivores evolve and are constantly replaced in time and space, their associations nonetheless remain constant. A Paleozoic palaeodictyopterid insect imbibing vascular tissue sap from a marattialean tree fern is functionally playing the same role as an aphic today feeding on the same tissues in an angiosperm […] Given the taxonomic turnover of vascular plants and herbivorous insects and yet the survival of persistent ecological associations, the phenomenon of ecological convergence is an important long-term pattern […] multidisciplinary evidence from various geological disciplines, particularly those applied to the earlier part of the fossil record, indicate that the more ancient the ecosystem, the less it resembles the present.”

“Three hypotheses have been proposed for assessing how ecological units, such as functional feeding groups, dietary guilds and mouthpart classes, expand in macroevolutionary time […] The first hypothesis, the ecological saturation hypothesis (ESH), advocated by palaeobiologists, maintains that the total number of ecological positions, or roles, has remained approximately constant through time after an initial exponential rise […] Thus taxa enter and exit the ecological arena of the biological community […], but their associations or roles remain virtually level. By contrast, the expanding resource hypothesis (ERH) is favoured by biologists and states that there is a gradual increase in food resources and availability of niches through time […] the intrinsic trend of diversification hypothesis (ITDH) […] holds that the long-term patterns of ESH and ERH vary among groups of organisms […] This view would imply that the proportion of occupied ecological roles has a globally disjunct pattern according to group, time and space. Of these, the current data favors ESH, if one assumes that the ecological clock was set during the Pennsylvanian and the previous fossil record is too poor for analysis.”

“Taphonomy is the study of the physical, chemical and biotic events that affect organisms after death, including pre-burial processes that transform the original living community into an entombed death assemblage that may be encountered by paleobiologists many aeons later. The fidelity to which the preserved assemblage actually resembles the source community is an issue in dicussions of the quality of the fossil record […] A full appreciation of the fossil associational record [between insects and plants] requires an evaluation of the five major types of qualitative evidence: plant reproductive biology, plant damage, dispersed coprolites, gut contents, and insect mouthparts. […] Collectively, these five types of evidence range from the direct, ‘smoking gun’ of gut contents, where the consumer and consumed are typically identifiable, to the more remote and circumstantial evidence of floral reproductive biology and mouthparts, where inferences are based on functional understanding, usually from modern analogues. […] Of all types of evidence for plant-arthropod associations, plant damage has the most extensive fossil record […] gut contents are the rarest type of evidence for plant-animal associations”

“Functional feeding groups can be sorted into 14 basic ways that insects access food” [I had no idea! And yes, they talk about all of these in the book. Note that you can easily split up those ‘basic ways’ into more subcategories if you like:] “In well-preserved Cretaceous and Caenozoic angiosperm-dominated floras, there are approximately 30 distinct types of external foliage-feeding, ranging from generalized bite-marks on margins to highly stereotyped and often intricate patterns of slot-hole feeding: earlier floras have fewer recognizable types of damage. […] The history of arthropod feeding on plants began during the Late Silurian to early Devonian […] by the close of the Pennsylvanian, the expansion of arthropod herbivory had invaded all plant organisms and virtually all plant tissues […] This expansion of dietary breadth provided a modern cast to the spectrum of insect diets. […] while the overwhelming bulk of the 14 plant-associated diet types was in place during the late Pennsylvanian, it was followed by the addition of 4 novel diet types during the Mesozoic in conjunction with the establishment of freshwater ecosystems and the diversification of advanced seed plants. […] When expressed as a diversity curve spanning the past 400 million years, there is a linear but stepped rise in mouthpart class diversity from the Early Devonian to the Early Jurassic, where it reached a plateau, followed by only a few subsequent additions […] Thus virtually all basic mouthpart innovation, including plant-associated mouthpart classes, was established prior to the angiosperm ecological expansion during the Middle Cretaceous [this was when flowering plants really took off, US], suggesting that mouthpart classes are attributable to basic associations with seed plants, or vascular plants of the more remote past, rather than the relatively late-appearing angiosperms […] Arthropods have used plants extensively for shelter probably since the Early Devonian”

“The amount of live plant tissue assimilated by arthropods is significantly greater than that of vertebrates in virtually all biomes except grasslands […] The fossil evidence indicates that this arthropod dominance has probably been the case since the establishment of the earliest terrestrial ecosystems. In fact, it was not until the latest Devonian that vertebrates emerged on land […], for which evidence indicates obligate carnivory. […] Direct evidence for vertebrate herbivory does not occur until the latest Pennsylvanian to earliest Permian […], about 100 million years after it appeared among mid-Paleozoic arthropods. […] A consequence of large vertebrate size is that consumption of plant organs is frequently complete and not partial as it is among arthropods, leaving minimal evidence from leaves, seeds and other wholly-consumed items. Also, the rarity of vertebrates when compared to arthropods may result in an underestimate of vertebrate importance in their interactions with plants. […] An interesting aspect of Paleozoic tetrapod herbivores is that they were uniformly short-necked and short-limbed browsers that cropped plant material within a metre to perhaps two metres of the ground surface. This trend continued […] into the Late Triassic, at which time basal dinosaur lineages began their diversification into virtually all major terrestrial feeding niches […] While Paleocene to middle Eocene mammalian herbivores were dominated by small to medium-sized forms consuming fruit, seeds and leaves, later herbivores were much larger, and invaded the browsing and eventually grazing adaptive zones […] This shift is related to the mid-Caenozoic origin of savanna and grassland biomes concomitant with the ecological spread of grasses. The oldest grasses reliably documented in the fossil record occur at the Palaeocene/Eocene boundary [~56 mya, US] […], although the earliest evidence for a grassland-adapted mammalian fauna is from the middle Oligocene [~28 mya, US] of Mongolia […] During the Pleistocene (2.65 Ma to 10 000 yr BP), much of the Planet underwent severe climactic pertubations from five major episodes of continental and associated alpine glaciation. Continental faunas were considerably reorganized during and after this interval in terms of dominance and composition of species […] Much evidence now supports a view that continental species did not respond as cohesive assemblages to these major environmental shifts, but rather individualistically […] An important exception to this trend are insects with high host specificity, which responded differently, retaining ancestral plant associations to the present […] or becoming extinct. Herbivorous mammals have less obligate dependence on plant species […] and thus exhibit greater dietary flexibility during times of major environmental stress.”

June 12, 2014 Posted by | Biology, Books, Botany, Ecology, Evolutionary biology, Paleontology, Zoology | 4 Comments

The Origin and Evolution of Cultures (V)

This will be my last post about the book. Go here for a background post and my overall impression of the book – I’ll limit this post to coverage of the ‘Simple Models of Complex Phenomena’-chapter which I mentioned in that post, as well as a few observations from the introduction to part 5 of the book, which talks a little bit about what the chapter is about in general terms. The stuff they write in the chapter is in a way a sort of overview over the kind of approach to things which you may well end up adopting unconsciously if you’re working in a field like economics or ecology and a defence of such an approach; I’ve as mentioned in the previous post about the book talked about these sorts of things before, but there’s some new stuff in here as well. The chapter is written in the context of Boyd and Richerson’s coverage of their ‘Darwinian approach to evolution’, but many of the observations here are of a much more general nature and relate to the application of statistical and mathematical modelling in a much broader context; and some of those observations that do not directly relate to broader contexts still do as far as I can see have what might be termed ‘generalized analogues’. The chapter coverage was actually interesting enough for me to seriously consider reading a book or two on these topics (books such as this one), despite the amount of work I know may well be required to deal with a book like this.

I exclude a lot of stuff from the chapter in this post, and there are a lot of other good chapters in the book. Again, you should read this book.

Here’s the stuff from the introduction:

“Chapter 19 is directed at those in the social sciences unfamiliar with a style of deploying mathematical models that is second nature to economists, evolutionary biologists, engineers, and others. Much science in many disciplines consists of a toolkit of very simple mathematical models. To many not familiar with the subtle art of the simple model, such formal exercises have two seemingly deadly flaws. First, they are not easy to follow. […] Second, motivation to follow the math is often wanting because the model is so cartoonishly simple relative to the real world being analyzed. Critics often level the charge ‘‘reductionism’’ with what they take to be devastating effect. The modeler’s reply is that these two criticisms actually point in opposite directions and sum to nothing. True, the model is quite simple relative to reality, but even so, the analysis is difficult. The real lesson is that complex phenomena like culture require a humble approach. We have to bite off tiny bits of reality to analyze and build up a more global knowledge step by patient step. […] Simple models, simple experiments, and simple observational programs are the best the human mind can do in the face of the awesome complexity of nature. The alternatives to simple models are either complex models or verbal descriptions and analysis. Complex models are sometimes useful for their predictive power, but they have the vice of being difficult or impossible to understand. The heuristic value of simple models in schooling our intuition about natural processes is exceedingly important, even when their predictive power is limited. […] Unaided verbal reasoning can be unreliable […] The lesson, we think, is that all serious students of human behavior need to know enough math to at least appreciate the contributions simple mathematical models make to the understanding of complex phenomena. The idea that social scientists need less math than biologists or other natural scientists is completely mistaken.”

And below I’ve posted the chapter coverage:

“A great deal of the progress in evolutionary biology has resulted from the deployment of relatively simple theoretical models. Staddon’s, Smith’s, and Maynard Smith’s contributions illustrate this point. Despite their success, simple models have been subjected to a steady stream of criticism. The complexity of real social and biological phenomena is compared to the toylike quality of the simple models used to analyze them and their users charged with unwarranted reductionism or plain simplemindedness.
This critique is intuitively appealing—complex phenomena would seem to require complex theories to understand them—but misleading. In this chapter we argue that the study of complex, diverse phenomena like organic evolution requires complex, multilevel theories but that such theories are best built from toolkits made up of a diverse collection of simple models. Because individual models in the toolkit are designed to provide insight into only selected aspects of the more complex whole, they are necessarily incomplete. Nevertheless, students of complex phenomena aim for a reasonably complete theory by studying many related simple models. The neo-Darwinian theory of evolution provides a good example: fitness-optimizing models, one and multiple locus genetic models, and quantitative genetic models all emphasize certain details of the evolutionary process at the expense of others. While any given model is simple, the theory as a whole is much more comprehensive than any one of them.”

“In the last few years, a number of scholars have attempted to understand the processes of cultural evolution in Darwinian terms […] The idea that unifies all this work is that social learning or cultural transmission can be modeled as a system of inheritance; to understand the macroscopic patterns of cultural change we must understand the microscopic processes that increase the frequency of some culturally transmitted variants and reduce the frequency of others. Put another way, to understand cultural evolution we must account for all of the processes by which cultural variation is transmitted and modified. This is the essence of the Darwinian approach to evolution.”

“In the face of the complexity of evolutionary processes, the appropriate strategy may seem obvious: to be useful, models must be realistic; they should incorporate all factors that scientists studying the phenomena know to be important. This reasoning is certainly plausible, and many scientists, particularly in economics […] and ecology […], have constructed such models, despite their complexity. On this view, simple models are primitive, things to be replaced as our sophistication about evolution grows. Nevertheless, theorists in such disciplines as evolutionary biology and economics stubbornly continue to use simple models even though improvements in empirical knowledge, analytical mathematics, and computing now enable them to create extremely elaborate models if they care to do so. Theorists of this persuasion eschew more detailed models because (1) they are hard to understand, (2) they are difficult to analyze, and (3) they are often no more useful for prediction than simple models. […] Detailed models usually require very large amounts of data to determine the various parameter values in the model. Such data are rarely available. Moreover, small inaccuracies or errors in the formulation of the model can produce quite erroneous predictions. The temptation is to ‘‘tune’’ the model, making small changes, perhaps well within the error of available data, so that the model produces reasonable answers. When this is done, any predictive power that the model might have is due more to statistical fitting than to the fact that it accurately represents actual causal processes. It is easy to make large sacrifices of understanding for small gains in predictive power.”

“In the face of these difficulties, the most useful strategy will usually be to build a variety of simple models that can be completely understood but that still capture the important properties of the processes of interest. Liebenstein (1976: ch. 2) calls such simple models ‘‘sample theories.’’ Students of complex and diverse subject matters develop a large body of models from which ‘‘samples’’ can be drawn for the purpose at hand. Useful sample theories result from attempts to satisfy two competing desiderata: they should be simple enough to be clearly and completely grasped, and at the same time they should reflect how real processes actually do work, at least to some approximation. A systematically constructed population of sample theories and combinations of them constitutes the theory of how the whole complex process works. […] If they are well designed, they are like good caricatures, capturing a few essential features of the problem in a recognizable but stylized manner and with no attempt to represent features not of immediate interest. […] The user attempts to discover ‘‘robust’’ results, conclusions that are at least qualitatively correct, at least for some range of situations, despite the complexity and diversity of the phenomena they attempt to describe. […] Note that simple models can often be tested for their scientific content via their predictions even when the situation is too complicated to make practical predictions. Experimental or statistical controls often make it possible to expose the variation due to the processes modeled, against the background of ‘‘noise’’ due to other ones, thus allowing a ceteris paribus prediction for purposes of empirical testing.”

“Generalized sample theories are an important subset of the simple sample theories used to understand complex, diverse problems. They are designed to capture the qualitative properties of the whole class of processes that they are used to represent, while more specialized ones are used for closer approximations to narrower classes of cases. […] One might agree with the case for a diverse toolkit of simple models but still doubt the utility of generalized sample theories. Fitness-maximizing calculations are often used as a simple caricature of how selection ought to work most of the time in most organisms to produce adaptations. Does such a generalized sample theory have any serious scientific purpose? Some might argue that their qualitative kind of understanding is, at best, useful for giving nonspecialists a simplified overview of complicated topics and that real scientific progress still occurs entirely in the construction of specialized sample theories that actually predict. A sterner critic might characterize the attempt to construct generalized models as loose speculation that actually inhibits the real work of discovering predictable relationships in particular systems. These kinds of objections implicitly assume that it is possible to do science without any kind of general model. All scientists have mental models of the world. The part of the model that deals with their disciplinary specialty is more detailed than the parts that represent related areas of science. Many aspects of a scientist’s mental model are likely to be vague and never expressed. The real choice is between an intuitive, perhaps covert, general theory and an explicit, often mathematical, one. […] To insist upon empirical science in the style of physics is to insist upon the impossible. However, to give up on empirical tests and prediction would be to abandon science and retreat to speculative philosophy. Generalized sample theories normally make only limited qualitative predictions. The logistic model of population growth is a good elementary example. At best, it is an accurate model only of microbial growth in the laboratory. However, it captures something of the biology of population growth in more complex cases. Moreover, its simplicity makes it a handy general model to incorporate into models that must also represent other processes such as selection, and intra- and interspecific competition. If some sample theory is consistently at variance with the data, then it must be modified. The accumulation of these kinds of modifications can eventually alter general theory […] A generalized model is useful so long as its predictions are qualitatively correct, roughly conforming to the majority of cases. It is helpful if the inevitable limits of the model are understood. It is not necessarily an embarrassment if more than one alternative formulation of a general theory, built from different sample models, is more or less equally correct. In this case, the comparison of theories that are empirically equivalent makes clearer what is at stake in scientific controversies and may suggest empirical and theoretical steps toward a resolution.”

“The thorough study of simple models includes pressing them to their extreme limits. This is especially useful at the second step of development, where simple models of basic processes are combined into a candidate generalized model of an interesting question. There are two related purposes in this exercise. First, it is helpful to have all the implications of a given simple model exposed for comparative purposes, if nothing else. A well-understood simple sample theory serves as a useful point of comparison for the results of more complex alternatives, even when some conclusions are utterly ridiculous. Second, models do not usually just fail; they fail for particular reasons that are often very informative. Just what kinds of modifications are required to make the initially ridiculous results more nearly reasonable? […]  The exhaustive analysis of many sample models in various combinations is also the main means of seeking robust results (Wimsatt, 1981). One way to gain confidence in simple models is to build several models embodying different characterizations of the problem of interest and different simplifying assumptions. If the results of a model are robust, the same qualitative results ought to obtain for a whole family of related models in which the supposedly extraneous details differ. […] Similarly, as more complex considerations are introduced into the family of models, simple model results can be considered robust only if it seems that the qualitative conclusion holds for some reasonable range of plausible conditions.”

“A plausibility argument is a hypothetical explanation having three features in common with a traditional hypothesis: (1) a claim of deductive soundness, of in-principle logical sufficiency to explain a body of data; (2) sufficient support from the existing body of empirical data to suggest that it might actually be able to explain a body of data as well as or better than competing plausibility arguments; and (3) a program of research that might distinguish between the claims of competing plausibility arguments. The differences are that competing plausibility arguments (1) are seldom mutually exclusive, (2) can seldom be rejected by a single sharp experimental test (or small set of them), and (3) often end up being revised, limited in their generality or domain of applicability, or combined with competing arguments rather than being rejected. In other words, competing plausibility arguments are based on the claims that a different set of submodels is needed to achieve a given degree of realism and generality, that different parameter values of common submodels are required, or that a given model is correct as far as it goes, but applies with less generality, realism, or predictive power than its proponents claim. […] Human sociobiology provides a good example of a plausibility argument. The basic premise of human sociobiology is that fitness-optimizing models drawn from evolutionary biology can be used to understand human behavior. […] We think that the clearest way to address the controversial questions raised by competing plausibility arguments is to try to formulate models with parameters such that for some values of the critical parameters the results approximate one of the polar positions in such debates, while for others the model approximates the other position.”

“A well-developed plausibility argument differs sharply from another common type of argument that we call a programmatic claim. Most generally, a programmatic claim advocates a plan of research for addressing some outstanding problem without, however, attempting to construct a full plausibility argument. […] An attack on an existing, often widely accepted, plausibility argument on the grounds that the plausibility argument is incomplete is a kind of programmatic claim. Critiques of human sociobiology are commonly of this type. […] The criticism of human sociobiology has far too frequently depended on mere programmatic claims (often invalid ones at that, as when sociobiologists are said to ignore the importance of culture and to depend on genetic variation to explain human differences). These claims are generally accompanied by dubious burden-of-proof arguments. […] We have argued that theory about complex-diverse phenomena is necessarily made up of simple models that omit many details of the phenomena under study. It is very easy to criticize theory of this kind on the grounds that it is incomplete (or defend it on the grounds that it one day will be much more complete). Such criticism and defense is not really very useful because all such models are incomplete in many ways and may be flawed because of it. What is required is a plausibility argument that shows that some factor that is omitted could be sufficiently important to require inclusion in the theory of the phenomenon under consideration, or a plausible case that it really can be neglected for most purposes. […] It seems to us that until very recently, ‘‘nature-nurture’’ debates have been badly confused because plausibility arguments have often been taken to have been successfully countered by programmatic claims. It has proved relatively easy to construct reasonable and increasingly sophisticated Darwinian plausibility arguments about human behavior from the prevailing general theory. It is also relatively easy to spot the programmatic flaws in such arguments […] The problem is that programmatic objections have not been taken to imply a promise to deliver a full plausibility claim. Rather, they have been taken as a kind of declaration of independence of the social sciences from biology. Having shown that the biological theory is in principle incomplete, the conclusion is drawn that it can safely be ignored.”

“Scientists should be encouraged to take a sophisticated attitude toward empirical testing of plausibility arguments […] Folk Popperism among scientists has had the very desirable result of reducing the amount of theory-free descriptive empiricism in many complex-diverse disciplines, but it has had the undesirable effect of encouraging a search for simple mutually exclusive hypotheses that can be accepted or rejected by single experiments. By our argument, very few important problems in evolutionary biology or the social sciences can be resolved in this way. Rather, individual empirical investigations should be viewed as weighing marginally for or against plausibility arguments. Often, empirical studies may themselves discover or suggest new plausibility arguments or reconcile old ones.”

“We suspect that most evolutionary biologists and philosophers of biology on both sides of the dispute would pretty much agree with the defense of the simple models strategy presented here. To reject the strategy of building evolutionary theory from collections of simple models is to embrace a kind of scientific nihilism in which there is no hope of achieving an understanding of how evolution works. On the other hand, there is reason to treat any given model skeptically. […] It may be possible to defend the proposition that the complexity and diversity of evolutionary phenomena make any scientific understanding of evolutionary processes impossible. Or, even if we can obtain a satisfactory understanding of particular cases of evolution, any attempt at a general, unified theory may be impossible. Some critics of adaptationism seem to invoke these arguments against adaptationism without fully embracing them. The problem is that alternatives to adaptationism must face the same problem of diversity and complexity that Darwinians use the simple model strategy to finesse. The critics, when they come to construct plausibility arguments, will also have to use relatively simple models that are vulnerable to the same attack. If there is a vulgar sociobiology, there is also a vulgar criticism of sociobiology.”

June 6, 2014 Posted by | Anthropology, Biology, Books, culture, Ecology, Economics, Evolutionary biology, Mathematics, Science | Leave a comment

Evolution of Island Mammals: Adaption and Extinction of Placental Mammals on Islands

I was spending time with family this weekend, and as the environment was somewhat noisier than usual I had difficulties reading the Handbook. So I decided to engage in some lighter reading, which is where this Wiley-Blackwell publication enters the picture. Along the way I realized it wasn’t actually much lighter reading, but I enjoyed it and so decided to keep going…

I was very uncertain if I should give the book three stars or four on goodreads, and when I finished it yesterday I gave it three stars. I have now changed that rating to four stars. It is a fascinating book, but it is a bit dry at times. It probably deserves two posts, but I couldn’t be bothered to write more than one. I watched this Gresham College lecture a while back, and that lecture provided part of the motivation for reading the book. Wilson touched upon some of the themes covered in the book as well – his name does come up, naturally. Still, it should be emphasized that there was a lot of stuff covered in this book which I’d never really thought about and about which I knew nothing, and reading books which deal with such things is always nice.

Say you have an island formed in the middle of the ocean. There’s water all around it, perhaps lots of water, and it’s always been far away from continents and other islands. Which kinds of animals turn up there, how many different kinds, and how do they get there? Does the size of the island matter, and how does it matter? What usually happens after a new visitor has become established on an island?

Animals don’t just pop up and start hanging around – we are used to there being so many species around us that it would be easy to forget that it’s not necessarily the natural state of affairs that there are hundreds of species of animals all around you. On an isolated island which literally rose from the ocean animals have to somehow establish themselves before they can start a life there, and until they get there and find mates and enough food to survive, the island will be rather boring from the biased perspective of living organisms such as ourselves. Some animals are better colonizers than others, and that goes for some species/genera/families of mammals as well. Not all islands incidentally rise from the ocean; some get separated from the continent from which they originated, perhaps due to a combination of plate tectonics and/or eustatic sea level rise. In biology islands in a more general sense, understood as habitats where some types of organisms are isolated from their conspecifics, play an important role in speciation processes, so there are many reasons why one might be interested to learn more about such things – though it should be pointed out here that this book only deals with ‘proper’ islands, i.e. the kinds with water around them and so on.

Some islands display a great deal of species diversity, whereas a lot of others have a very unbalanced and impoverished fauna. By impoverished, I mean really impoverished – it’s amazing how few types of mammals sometimes made it to a specific island and got themselves established before humans started messing around with stuff. Or perhaps the amazing thing is rather that any of them did at all? I don’t know. To take an example of an impoverished island fauna, Cyprus is a good illustrative example. The only mammals on Cyprus (that we know about) during the Pleistocene were pygmy hippopotami, dwarf elephants, and perhaps bats. No cats, no dogs, no mice or rats, no goats, no pigs, no bovids, no deer, no nothing. When I set out reading this book I had in my mind some not-particularly-well-thought-out ideas about which sorts of animals normally hang around in the environment, and sometimes reading books can really mess with such ‘ideas you were not even aware that you had’; the fact of the matter is that in the case of some specific islands every single mammal species you’ll encounter on that isolated island (which incidentally today may not actually seem particularly isolated on account of technology, human transport methods etc.) will have some unique and probably quite fascinating story, explaining how it got there – and members of species which don’t have such a story to tell simply aren’t/weren’t around at all. Of course many of the island species mentioned can’t tell their story either anymore because they’ve gone extinct – again Cyprus provides an example. We talked about Pleistocene – well, at the onset of the Holocene a few more species were added (a genet, a mouse, and some fruitbats). They did okay and nothing much changed. But then later on the island stasis was interrupted, presumably because of human agency, and all the mammals that had established themselves before that time went extinct. A wonderful story that makes you proud to be a human.

As mentioned rather than being isolated species-poor places, some island groups have large species diversity; the West Indies is an example of that type. The book deals with a lot of different islands, and although there are some common patterns and trends there is also a lot of variation – and the variation seems to be reasonably well understood in most cases, although lack of evidence sometimes make things a bit harder to figure out than one would like them to be. A thing I feel compelled to note and emphasize is that an impoverished fauna does not an uninteresting fauna make: Some awesome animals have inhabited various islands around the world, and I’ve occasionally been saddened to read a chapter because of the realization of what has been lost (after having been first greatly fascinated by what was actually there). I’ve probably have had in the past a tendency to think of mammals as the bad guys in the story of islands because of how anthropogenically introduced invasive species such as rats and rabbits have wreaked havoc around the world, but birds aren’t the only types of animals that colonize islands and lots of mammal species around the world have been natural elements of island ecosystems for millions of years. To get back to the awesome animals and our example of Cyprus from above, the pygmy hippopotamus which used to live there is estimated to have been about 125 cm long, with a shoulder height of about 70 cm. The dwarf elephant that lived there was a bit larger; it’s estimated to have had a shoulder height of 1.40 metres. These animals were actually much larger than the pygmy elephants which inhabited nearby Sicily roughly 450.000 years ago, which had female shoulder heights of about 0.9 metres and male shoulder heights of about 1,3 metres, and an estimated body weight of around 100 kg. Yep. You’re probably used to think of mammoths as huge creatures (I was), and in that case you may be interested to know that an estimate of the size of the Cretan pygmy mammoth (…yes, there were mammoths living on Crete! I know! I had no idea either!) is 1.5 meters. Proboscideans were incidentally quite successful island colonizers, showing up all over the world:

“Endemic proboscideans have been reported from islands all over the world. Apparently, proboscideans were the most successful lineage of large-sized island colonizers, ranging from stegodons and mastodons to mammoths and elephants. Everywhere they developed a smaller size, eventually reaching dwarf or even pygmy proportions compared with their mainland ancestors. It is hard to think of an island with a rich fossil record lacking any proboscidean remains. Exceptions are the Balearics, Gargano, the central Ryukyu Islands, and the West Indies.”

Again, I had no clue! Mammoths used to live as far apart as Crete and Japan… Lions and hyenas used to live on Sicily, and tigers used to inhabit Japan. Incidentally proboscideans got smaller on islands, but many small mammals have tended to grow in size instead once they established themselves on isolated islands. On Minorca there used to live giant hares weighing 14 kg, and giant rats still inhabit the island of Flores; these guys are up to 45 centimeters long, with tails up to 70 centimeters. Body size is not the only thing that tends to change on islands; a stockier build (shorter limbs, stiffer joints), and changes in dentition also often happens, but body size changes are certainly noteworthy. Note that size changes don’t just mean that animals will get smaller or larger; greater size variation on islands is common due to adaptive radiation. You’ll have both small and large animals of a similar species, at least to start with – if the process is allowed to continue for millions of years you may easily end up with multiple different species derived from the same ancestor. Lemurs are a good example of where you may end up. Life is different on islands. Generally intraspecific competition tend to increase and interspecific competition tend to decrease (as a general rule carnivores are much less likely to become established on islands than are herbivores), but interspecific competition is still very important; the existence or absence of competing taxa can have major effects on the course of evolution. For example the Sicilian pygmy elephants developed during a time period where there were no deer present on the island; during the time where there were deer on Sicily, proboscideans reached dwarf proportions but never went smaller than that (in the book they apply the pygmy label to species half the ancestral size or less, and the term dwarf for forms which are 80–60% of the ancestral body size).

The book has three parts. The first part is called ‘Beyond the mainland’, and aside from a few introductory remarks it briefly talks about the history of island studies and then moves on to talk about ‘how islands are different’ from the mainland and how this affects the fauna. Part two is the main part of the book, and it deals with how mammal species have lived, died, evolved etc. on many different islands around the world; each island is to some extent unique, so each chapter deals with one island. The islands included in the coverage are: Cyprus, Crete, Gargano, Sicily, Malta, Sardinia and Corsica, The Balearic Islands, Madagascar, Java, Flores, Sulawesi, The Philippines, Japan, the Southern and Central Ryukyu Islands (the northern islands are included in the coverage of Japan), the Californian Channel Islands, and the West Indies. So the book does give a reasonably global view of island mammal life, although there are many chapters dealing with the Mediterranean. The book deals with evolutionary biology, but in order to tackle this topic you also need to deal with other areas such as geology. For example the Mediterranean looked very different 5-6 million years ago, and such changes have had huge consequences for how species adapted and evolved to their local environments. Some of the most fascinating stuff in this book in my mind related to how different the world used to look like, even if you don’t go back all that far. Japan used to be part of the mainland, Crete was a submerged mountain chain at the bottom of the ocean a while back, and the island of Flores emerged above the sea during the Early Miocene. Roughly 2 million years ago much of the current island of Java was at the bottom of the ocean, but on the other hand 800.000 years ago the island, as well as Sumatra and Borneo, may well have been connected with the mainland due to changes in global sea levels. Madagascar and India stuck together when they left Africa a long time ago, but they picked different routes and ended up different places, with different fauna. The chapters in this part of the book also provides some history of how we came to know what we know, who were some of the key people involved in figuring these things out, and so on, which is often rather interesting. In a way you sort of have to deal with such matters to some extent e.g. because the taxonomy is sometimes a bit messy when analyzing island data. Lumpers and splitters will disagree violently about the number of species, and understanding how the people who first looked at the bones arrived at the conclusions they did is often interesting.

Part three of the book deals with ‘Species and Processes’. After dealing with all the various islands an attempt is made here to sum up what we’ve learned from the coverage; first by taking a closer look at the species we’ve encountered along the way, then towards the end of the book by adding some general remarks and observations. The species covered in this section are naturally the species which have engaged in most island colonization activities. I was a little frustrated along the way while reading the book that few general principles were formulated, and that the coverage focused a great deal on ‘the specifics’ of the island in question, but this part sort of partly makes up for it and some people would surely argue that the method applied is perfectly justified. The species covered in the chapters in this part of the book are: ‘Elephants, Mammoths, Stegodons and Mastodons’, ‘Rabbits, Hares and Pikas’, ‘Rats, Dormice, Hamsters, Caviomorphs and other Rodents’, ‘Insectivores and Bats’, ‘Cervids and Bovids’, ‘Hippopotamuses and Pigs’, and ‘Carnivores’. The last two chapters of the book deal with some general ‘Patterns and Trends’ as well as ‘Evolutionary Processes in Island Environments’; I’ve covered some of that stuff above already.

Overall I really liked the book. Aside from the small problems such as ‘too specific, a few too many remarks about Cuvier‘, the only problem I had with the book was that there was very little focus on mammalian interactions with non-mammals on the islands. But given the focus of the book this was perhaps only to be expected. It’s a nice book and I enjoyed reading it.

January 27, 2014 Posted by | Biology, Books, Ecology, Evolutionary biology, Geography, Geology, Zoology | Leave a comment