Econstudentlog

Marine Biology (I)

This book was ‘okay’.

Some quotes and links related to the first half of the book below.

Quotes:

“The Global Ocean has come to be divided into five regional oceans – the Pacific, Atlantic, Indian, Arctic, and Southern Oceans […] These oceans are large, seawater-filled basins that share characteristic structural features […] The edge of each basin consists of a shallow, gently sloping extension of the adjacent continental land mass and is term the continental shelf or continental margin. Continental shelves typically extend off-shore to depths of a couple of hundred metres and vary from several kilometres to hundreds of kilometres in width. […] At the outer edge of the continental shelf, the seafloor drops off abruptly and steeply to form the continental slope, which extends down to depths of 2–3 kilometres. The continental slope then flattens out and gives way to a vast expanse of flat, soft, ocean bottom — the abyssal plain — which extends over depths of about 3–5 kilometres and accounts for about 76 per cent of the Global Ocean floor. The abyssal plains are transected by extensive mid-ocean ridges—underwater mountain chains […]. Mid-ocean ridges form a continuous chain of mountains that extend linearly for 65,000 kilometres across the floor of the Global Ocean basins […]. In some places along the edges of the abyssal plains the ocean bottom is cut by narrow, oceanic trenches or canyons which plunge to extraordinary depths — 3–4 kilometres below the surrounding seafloor — and are thousands of kilometres long but only tens of kilometres wide. […] Seamounts are another distinctive and dramatic feature of ocean basins. Seamounts are typically extinct volcanoes that rise 1,000 or more metres above the surrounding ocean but do not reach the surface of the ocean. […] Seamounts generally occur in chains or clusters in association with mid-ocean ridges […] The Global Ocean contains an estimated 100,000 or so seamounts that rise more than 1,000 metres above the surrounding deep-ocean floor. […] on a planetary scale, the surface of the Global Ocean is moving in a series of enormous, roughly circular, wind-driven current systems, or gyres […] These gyres transport enormous volumes of water and heat energy from one part of an ocean basin to another

“We now know that the oceans are literally teeming with life. Viruses […] are astoundingly abundant – there are around ten million viruses per millilitre of seawater. Bacteria and other microorganisms occur at concentrations of around 1 million per millilitre”

“The water in the oceans is in the form of seawater, a dilute brew of dissolved ions, or salts […] Chloride and sodium ions are the predominant salts in seawater, along with smaller amounts of other ions such as sulphate, magnesium, calcium, and potassium […] The total amount of dissolved salts in seawater is termed its salinity. Seawater typically has a salinity of roughly 35 – equivalent to about 35 grams of salts in one kilogram of seawater. […] Most marine organisms are exposed to seawater that, compared to the temperature extremes characteristic of terrestrial environments, ranges within a reasonably moderate range. Surface waters in tropical parts of ocean basins are consistently warm throughout the year, ranging from about 20–27°C […]. On the other hand, surface seawater in polar parts of ocean basins can get as cold as −1.9°C. Sea temperatures typically decrease with depth, but not in a uniform fashion. A distinct zone of rapid temperature transition is often present that separates warm seawater at the surface from cooler deeper seawater. This zone is called the thermocline layer […]. In tropical ocean waters the thermocline layer is a strong, well-defined and permanent feature. It may start at around 100 metres and be a hundred or so metres thick. Sea temperatures above the thermocline can be a tropical 25°C or more, but only 6–7°C just below the thermocline. From there the temperature drops very gradually with increasing depth. Thermoclines in temperate ocean regions are a more seasonal phenomenon, becoming well established in the summer as the sun heats up the surface waters, and then breaking down in the autumn and winter. Thermoclines are generally absent in the polar regions of the Global Ocean. […] As a rule of thumb, in the clearest ocean waters some light will penetrate to depths of 150-200 metres, with red light being absorbed within the first few metres and green and blue light penetrating the deepest. At certain times of the year in temperate coastal seas light may penetrate only a few tens of metres […] In the oceans, pressure increases by an additional atmosphere every 10 metres […] Thus, an organism living at a depth of 100 metres on the continental shelf experiences a pressure ten times greater than an organism living at sea level; a creature living at 5 kilometres depth on an abyssal plain experiences pressures some 500 times greater than at the surface”.

“With very few exceptions, dissolved oxygen is reasonably abundant throughout all parts of the Global Ocean. However, the amount of oxygen in seawater is much less than in air — seawater at 20°C contains about 5.4 millilitres of oxygen per litre of seawater, whereas air at this temperature contains about 210 millilitres of oxygen per litre. The colder the seawater, the more oxygen it contains […]. Oxygen is not distributed evenly with depth in the oceans. Oxygen levels are typically high in a thin surface layer 10–20 metres deep. Here oxygen from the atmosphere can freely diffuse into the seawater […] Oxygen concentration then decreases rapidly with depth and reaches very low levels, sometimes close to zero, at depths of around 200–1,000 metres. This region is referred to as the oxygen minimum zone […] This zone is created by the low rates of replenishment of oxygen diffusing down from the surface layer of the ocean, combined with the high rates of depletion of oxygen by decaying particulate organic matter that sinks from the surface and accumulates at these depths. Beneath the oxygen minimum zone, oxygen content increases again with depth such that the deep oceans contain quite high levels of oxygen, though not generally as high as in the surface layer. […] In contrast to oxygen, carbon dioxide (CO2) dissolves readily in seawater. Some of it is then converted into carbonic acid (H2CO3), bicarbonate ion (HCO3-), and carbonate ion (CO32-), with all four compounds existing in equilibrium with one another […] The pH of seawater is inversely proportional to the amount of carbon dioxide dissolved in it. […] the warmer the seawater, the less carbon dioxide it can absorb. […] Seawater is naturally slightly alkaline, with a pH ranging from about 7.5 to 8.5, and marine organisms have become well adapted to life within this stable pH range. […] In the oceans, carbon is never a limiting factor to marine plant photosynthesis and growth, as it is for terrestrial plants.”

“Since the beginning of the industrial revolution, the average pH of the Global Ocean has dropped by about 0.1 pH unit, making it 30 per cent more acidic than in pre-industrial times. […] As a result, more and more parts of the oceans are falling below a pH of 7.5 for longer periods of time. This trend, termed ocean acidification, is having profound impacts on marine organisms and the overall functioning of the marine ecosystem. For example, many types of marine organisms such as corals, clams, oysters, sea urchins, and starfish manufacture external shells or internal skeletons containing calcium carbonate. When the pH of seawater drops below about 7.5, calcium carbonate starts to dissolve, and thus the shells and skeletons of these organisms begin to erode and weaken, with obvious impacts on the health of the animal. Also, these organisms produce their calcium carbonate structures by combining calcium dissolved in seawater with carbonate ion. As the pH decreases, more of the carbonate ions in seawater become bound up with the increasing numbers of hydrogen ions, making fewer carbonate ions available to the organisms for shell-forming purposes. It thus becomes more difficult for these organisms to secrete their calcium carbonate structures and grow.”

“Roughly half of the planet’s primary production — the synthesis of organic compounds by chlorophyll-bearing organisms using energy from the sun—is produced within the Global Ocean. On land the primary producers are large, obvious, and comparatively long-lived — the trees, shrubs, and grasses characteristic of the terrestrial landscape. The situation is quite different in the oceans where, for the most part, the primary producers are minute, short-lived microorganisms suspended in the sunlit surface layer of the oceans. These energy-fixing microorganisms — the oceans’ invisible forest — are responsible for almost all of the primary production in the oceans. […] A large amount, perhaps 30-50 per cent, of marine primary production is produced by bacterioplankton comprising tiny marine photosynthetic bacteria ranging from about 0.5 to 2 μm in size. […] light availability and the strength of vertical mixing are important factors limiting primary production in the oceans. Nutrient availability is the other main factor limiting the growth of primary producers. One important nutrient is nitrogen […] nitrogen is a key component of amino acids, which are the building blocks of proteins. […] Photosynthetic marine organisms also need phosphorus, which is a requirement for many important biological functions, including the synthesis of nucleic acids, a key component of DNA. Phosphorus in the oceans comes naturally from the erosion of rocks and soils on land, and is transported into the oceans by rivers, much of it in the form of dissolved phosphate (PO43−), which can be readily absorbed by marine photosynthetic organisms. […] Inorganic nitrogen and phosphorus compounds are abundant in deep-ocean waters. […] In practice, inorganic nitrogen and phosphorus compounds are not used up at exactly the same rate. Thus one will be depleted before the other and becomes the limiting nutrient at the time, preventing further photosynthesis and growth of marine primary producers until it is replenished. Nitrogen is often considered to be the rate-limiting nutrient in most oceanic environments, particularly in the open ocean. However, in coastal waters phosphorus is often the rate-limiting nutrient.”

“The overall pattern of primary production in the Global Ocean depends greatly on latitude […] In polar oceans primary production is a boom-and-bust affair driven by light availability. Here the oceans are well mixed throughout the year so nutrients are rarely limiting. However, during the polar winter there is no light, and thus no primary production is taking place. […] Although limited to a short seasonal pulse, the total amount of primary production can be quite high, especially in the polar Southern Ocean […] In tropical open oceans, primary production occurs at a low level throughout the year. Here light is never limiting but the permanent tropical thermocline prevents the mixing of deep, nutrient-rich seawater with the surface waters. […] open-ocean tropical waters are often referred to as ‘marine deserts’, with productivity […] comparable to a terrestrial desert. In temperate open-ocean regions, primary productivity is linked closely to seasonal events. […] Although occurring in a number of pulses, primary productivity in temperate oceans [is] similar to [that of] a temperate forest or grassland. […] Some of the most productive marine environments occur in coastal ocean above the continental shelves. This is the result of a phenomenon known as coastal upwelling which brings deep, cold, nutrient-rich seawater to the ocean surface, creating ideal conditions for primary productivity […], comparable to a terrestrial rainforest or cultivated farmland. These hotspots of marine productivity are created by wind acting in concert with the planet’s rotation. […] Coastal upwelling can occur when prevailing winds move in a direction roughly parallel to the edge of a continent so as to create offshore Ekman transport. Coastal upwelling is particularly prevalent along the west coasts of continents. […] Since coastal upwelling is dependent on favourable winds, it tends to be a seasonal or intermittent phenomenon and the strength of upwelling will depend on the strength of the winds. […] Important coastal upwelling zones around the world include the coasts of California, Oregon, northwest Africa, and western India in the northern hemisphere; and the coasts of Chile, Peru, and southwest Africa in the southern hemisphere. These regions are amongst the most productive marine ecosystems on the planet.”

“Considering the Global Ocean as a whole, it is estimated that total marine primary production is about 50 billion tonnes of carbon per year. In comparison, the total production of land plants, which can also be estimated using satellite data, is estimated at around 52 billion tonnes per year. […] Primary production in the oceans is spread out over a much larger surface area and so the average productivity per unit of surface area is much smaller than on land. […] the energy of primary production in the oceans flows to higher trophic levels through several different pathways of various lengths […]. Some energy is lost along each step of the pathway — on average the efficiency of energy transfer from one trophic level to the next is about 10 per cent. Hence, shorter pathways are more efficient. Via these pathways, energy ultimately gets transferred to large marine consumers such as large fish, marine mammals, marine turtles, and seabirds.”

“…it has been estimated that in the 17th century, somewhere between fifty million and a hundred million green turtles inhabited the Caribbean Sea, but numbers are now down to about 300,000. Since their numbers are now so low, their impact on seagrass communities is currently small, but in the past, green turtles would have been extraordinarily abundant grazers of seagrasses. It appears that in the past, green turtles thinned out seagrass beds, thereby reducing direct competition among different species of seagrass and allowing several species of seagrass to coexist. Without green turtles in the system, seagrass beds are generally overgrown monocultures of one dominant species. […] Seagrasses are of considerable importance to human society. […] It is therefore of great concern that seagrass meadows are in serious decline globally. In 2003 it was estimated that 15 per cent of the planet’s existing seagrass beds had disappeared in the preceding ten years. Much of this is the result of increasing levels of coastal development and dredging of the seabed, activities which release excessive amounts of sediment into coastal waters which smother seagrasses. […] The number of marine dead zones in the Global Ocean has roughly doubled every decade since the 1960s”.

“Sea ice is habitable because, unlike solid freshwater ice, it is a very porous substance. As sea ice forms, tiny spaces between the ice crystals become filled with a highly saline brine solution resistant to freezing. Through this process a three-dimensional network of brine channels and spaces, ranging from microscopic to several centimetres in size, is created within the sea ice. These channels are physically connected to the seawater beneath the ice and become colonized by a great variety of marine organisms. A significant amount of the primary production in the Arctic Ocean, perhaps up to 50 per cent in those areas permanently covered by sea ice, takes place in the ice. […] Large numbers of zooplanktonic organisms […] swarm about on the under surface of the ice, grazing on the ice community at the ice-seawater interface, and sheltering in the brine channels. […] These under-ice organisms provide the link to higher trophic levels in the Arctic food web […] They are an important food source for fish such as Arctic cod and glacial cod that graze along the bottom of the ice. These fish are in turn fed on by squid, seals, and whales.”

“[T]he Antarctic marine system consists of a ring of ocean about 10° of latitude wide – roughly 1,000 km. […] The Arctic and Antarctic marine systems can be considered geographic opposites. In contrast to the largely landlocked Arctic Ocean, the Southern Ocean surrounds the Antarctic continental land mass and is in open contact with the Atlantic, Indian, and Pacific Oceans. Whereas the Arctic Ocean is strongly influenced by river inputs, the Antarctic continent has no rivers, and so hard-bottomed seabed is common in the Southern Ocean, and there is no low-saline surface layer, as in the Arctic Ocean. Also, in contrast to the Arctic Ocean with its shallow, broad continental shelves, the Antarctic continental shelf is very narrow and steep. […] Antarctic waters are extremely nutrient rich, fertilized by a permanent upwelling of seawater that has its origins at the other end of the planet. […] This continuous upwelling of cold, nutrient-rich seawater, in combination with the long Antarctic summer day length, creates ideal conditions for phytoplankton growth, which drives the productivity of the Antarctic marine system. As in the Arctic, a well-developed sea-ice community is present. Antarctic ice algae are even more abundant and productive than in the Arctic Ocean because the sea ice is thinner, and there is thus more available light for photosynthesis. […] Antarctica’s most important marine species [is] the Antarctic krill […] Krill are very adept at surviving many months under starvation conditions — in the laboratory they can endure more than 200 days without food. During the winter months they lower their metabolic rate, shrink in body size, and revert back to a juvenile state. When food once again becomes abundant in the spring, they grow rapidly […] As the sea ice breaks up they leave the ice and begin feeding directly on the huge blooms of free-living diatoms […]. With so much food available they grow and reproduce quickly, and start to swarm in large numbers, often at densities in excess of 10,000 individuals per cubic metre — dense enough to colour the seawater a reddish-brown. Krill swarms are patchy and vary greatly in size […] Because the Antarctic marine system covers a large area, krill numbers are enormous, estimated at about 600 billion animals on average, or 500 million tonnes of krill. This makes Antarctic krill one of the most abundant animal species on the planet […] Antarctic krill are the main food source for many of Antarctica’s large marine animals, and a key link in a very short and efficient food chain […]. Krill comprise the staple diet of icefish, squid, baleen whales, leopard seals, fur seals, crabeater seals, penguins, and seabirds, including albatross. Thus, a very simple and efficient three-step food chain is in operation — diatoms eaten by krill in turn eaten by a suite of large consumers — which supports the large numbers of large marine animals living in the Southern Ocean.”

Links:

Ocean gyre. North Atlantic Gyre. Thermohaline circulation. North Atlantic Deep Water. Antarctic bottom water.
Cyanobacteria. Diatom. Dinoflagellate. Coccolithophore.
Trophic level.
Nitrogen fixation.
High-nutrient, low-chlorophyll regions.
Light and dark bottle method of measuring primary productivity. Carbon-14 method for estimating primary productivity.
Ekman spiral.
Peruvian anchoveta.
El Niño. El Niño–Southern Oscillation.
Copepod.
Dissolved organic carbon. Particulate organic matter. Microbial loop.
Kelp forest. Macrocystis. Sea urchin. Urchin barren. Sea otter.
Seagrass.
Green sea turtle.
Manatee.
Demersal fish.
Eutrophication. Harmful algal bloom.
Comb jelly. Asterias amurensis.
Great Pacific garbage patch.
Eelpout. Sculpin.
Polynya.
Crabeater seal.
Adélie penguin.
Anchor ice mortality.

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March 13, 2018 Posted by | Biology, Books, Botany, Chemistry, Ecology, Geology, Zoology | Leave a comment

Lakes (II)

(I have had some computer issues over the last couple of weeks, which was the explanation for my brief blogging hiatus, but they should be resolved by now and as I’m already starting to fall quite a bit behind in terms of my intended coverage of the books I’ve read this year I hope to get rid of some of the backlog in the days to come.)

I have added some more observations from the second half of the book, as well as some related links, below.

“[R]ecycling of old plant material is especially important in lakes, and one way to appreciate its significance is to measure the concentration of CO2, an end product of decomposition, in the surface waters. This value is often above, sometimes well above, the value to be expected from equilibration of this gas with the overlying air, meaning that many lakes are net producers of CO2 and that they emit this greenhouse gas to the atmosphere. How can that be? […] Lakes are not sealed microcosms that function as stand-alone entities; on the contrary, they are embedded in a landscape and are intimately coupled to their terrestrial surroundings. Organic materials are produced within the lake by the phytoplankton, photosynthetic cells that are suspended in the water and that fix CO2, release oxygen (O2), and produce biomass at the base of the aquatic food web. Photosynthesis also takes place by attached algae (the periphyton) and submerged water plants (aquatic macrophytes) that occur at the edge of the lake where enough sunlight reaches the bottom to allow their growth. But additionally, lakes are the downstream recipients of terrestrial runoff from their catchments […]. These continuous inputs include not only water, but also subsidies of plant and soil organic carbon that are washed into the lake via streams, rivers, groundwater, and overland flows. […] The organic carbon entering lakes from the catchment is referred to as ‘allochthonous’, meaning coming from the outside, and it tends to be relatively old […] In contrast, much younger organic carbon is available […] as a result of recent photosynthesis by the phytoplankton and littoral communities; this carbon is called ‘autochthonous’, meaning that it is produced within the lake.”

“It used to be thought that most of the dissolved organic matter (DOM) entering lakes, especially the coloured fraction, was unreactive and that it would transit the lake to ultimately leave unchanged at the outflow. However, many experiments and field observations have shown that this coloured material can be partially broken down by sunlight. These photochemical reactions result in the production of CO2, and also the degradation of some of the organic polymers into smaller organic molecules; these in turn are used by bacteria and decomposed to CO2. […] Most of the bacterial species in lakes are decomposers that convert organic matter into mineral end products […] This sunlight-driven chemistry begins in the rivers, and continues in the surface waters of the lake. Additional chemical and microbial reactions in the soil also break down organic materials and release CO2 into the runoff and ground waters, further contributing to the high concentrations in lake water and its emission to the atmosphere. In algal-rich ‘eutrophic’ lakes there may be sufficient photosynthesis to cause the drawdown of CO2 to concentrations below equilibrium with the air, resulting in the reverse flux of this gas, from the atmosphere into the surface waters.”

“There is a precarious balance in lakes between oxygen gains and losses, despite the seemingly limitless quantities in the overlying atmosphere. This balance can sometimes tip to deficits that send a lake into oxygen bankruptcy, with the O2 mostly or even completely consumed. Waters that have O2 concentrations below 2mg/L are referred to as ‘hypoxic’, and will be avoided by most fish species, while waters in which there is a complete absence of oxygen are called ‘anoxic’ and are mostly the domain for specialized, hardy microbes. […] In many temperate lakes, mixing in spring and again in autumn are the critical periods of re-oxygenation from the overlying atmosphere. In summer, however, the thermocline greatly slows down that oxygen transfer from air to deep water, and in cooler climates, winter ice-cover acts as another barrier to oxygenation. In both of these seasons, the oxygen absorbed into the water during earlier periods of mixing may be rapidly consumed, leading to anoxic conditions. Part of the reason that lakes are continuously on the brink of anoxia is that only limited quantities of oxygen can be stored in water because of its low solubility. The concentration of oxygen in the air is 209 millilitres per litre […], but cold water in equilibrium with the atmosphere contains only 9ml/L […]. This scarcity of oxygen worsens with increasing temperature (from 4°C to 30°C the solubility of oxygen falls by 43 per cent), and it is compounded by faster rates of bacterial decomposition in warmer waters and thus a higher respiratory demand for oxygen.”

“Lake microbiomes play multiple roles in food webs as producers, parasites, and consumers, and as steps into the animal food chain […]. These diverse communities of microbes additionally hold centre stage in the vital recycling of elements within the lake ecosystem […]. These biogeochemical processes are not simply of academic interest; they totally alter the nutritional value, mobility, and even toxicity of elements. For example, sulfate is the most oxidized and also most abundant form of sulfur in natural waters, and it is the ion taken up by phytoplankton and aquatic plants to meet their biochemical needs for this element. These photosynthetic organisms reduce the sulfate to organic sulfur compounds, and once they die and decompose, bacteria convert these compounds to the rotten-egg smelling gas, H2S, which is toxic to most aquatic life. In anoxic waters and sediments, this effect is amplified by bacterial sulfate reducers that directly convert sulfate to H2S. Fortunately another group of bacteria, sulfur oxidizers, can use H2S as a chemical energy source, and in oxygenated waters they convert this reduced sulfur back to its benign, oxidized, sulfate form. […] [The] acid neutralizing capacity (or ‘alkalinity’) varies greatly among lakes. Many lakes in Europe, North America, and Asia have been dangerously shifted towards a low pH because they lacked sufficient carbonate to buffer the continuous input of acid rain that resulted from industrial pollution of the atmosphere. The acid conditions have negative effects on aquatic animals, including by causing a shift in aluminium to its more soluble and toxic form Al3+. Fortunately, these industrial emissions have been regulated and reduced in most of the developed world, although there are still legacy effects of acid rain that have resulted in a long-term depletion of carbonates and associated calcium in certain watersheds.”

“Rotifers, cladocerans, and copepods are all planktonic, that is their distribution is strongly affected by currents and mixing processes in the lake. However, they are also swimmers, and can regulate their depth in the water. For the smallest such as rotifers and copepods, this swimming ability is limited, but the larger zooplankton are able to swim over an impressive depth range during the twenty-four-hour ‘diel’ (i.e. light–dark) cycle. […] the cladocerans in Lake Geneva reside in the thermocline region and deep epilimnion during the day, and swim upwards by about 10m during the night, while cyclopoid copepods swim up by 60m, returning to the deep, dark, cold waters of the profundal zone during the day. Even greater distances up and down the water column are achieved by larger animals. The opossum shrimp, Mysis (up to 25mm in length) lives on the bottom of lakes during the day and in Lake Tahoe it swims hundreds of metres up into the surface waters, although not on moon-lit nights. In Lake Baikal, one of the main zooplankton species is the endemic amphipod, Macrohectopus branickii, which grows up to 38mm in size. It can form dense swarms at 100–200m depth during the day, but the populations then disperse and rise to the upper waters during the night. These nocturnal migrations connect the pelagic surface waters with the profundal zone in lake ecosystems, and are thought to be an adaptation towards avoiding visual predators, especially pelagic fish, during the day, while accessing food in the surface waters under the cover of nightfall. […] Although certain fish species remain within specific zones of the lake, there are others that swim among zones and access multiple habitats. […] This type of fish migration means that the different parts of the lake ecosystem are ecologically connected. For many fish species, moving between habitats extends all the way to the ocean. Anadromous fish migrate out of the lake and swim to the sea each year, and although this movement comes at considerable energetic cost, it has the advantage of access to rich marine food sources, while allowing the young to be raised in the freshwater environment with less exposure to predators. […] With the converse migration pattern, catadromous fish live in freshwater and spawn in the sea.”

“Invasive species that are the most successful and do the most damage once they enter a lake have a number of features in common: fast growth rates, broad tolerances, the capacity to thrive under high population densities, and an ability to disperse and colonize that is enhanced by human activities. Zebra mussels (Dreissena polymorpha) get top marks in each of these categories, and they have proven to be a troublesome invader in many parts of the world. […] A single Zebra mussel can produce up to one million eggs over the course of a spawning season, and these hatch into readily dispersed larvae (‘veligers’), that are free-swimming for up to a month. The adults can achieve densities up to hundreds of thousands per square metre, and their prolific growth within water pipes has been a serious problem for the cooling systems of nuclear and thermal power stations, and for the intake pipes of drinking water plants. A single Zebra mussel can filter a litre a day, and they have the capacity to completely strip the water of bacteria and protists. In Lake Erie, the water clarity doubled and diatoms declined by 80–90 per cent soon after the invasion of Zebra mussels, with a concomitant decline in zooplankton, and potential impacts on planktivorous fish. The invasion of this species can shift a lake from dominance of the pelagic to the benthic food web, but at the expense of native unionid clams on the bottom that can become smothered in Zebra mussels. Their efficient filtering capacity may also cause a regime shift in primary producers, from turbid waters with high concentrations of phytoplankton to a clearer lake ecosystem state in which benthic water plants dominate.”

“One of the many distinguishing features of H2O is its unusually high dielectric constant, meaning that it is a strongly polar solvent with positive and negative charges that can stabilize ions brought into solution. This dielectric property results from the asymmetrical electron cloud over the molecule […] and it gives liquid water the ability to leach minerals from rocks and soils as it passes through the ground, and to maintain these salts in solution, even at high concentrations. Collectively, these dissolved minerals produce the salinity of the water […] Sea water is around 35ppt, and its salinity is mainly due to the positively charged ions sodium (Na+), potassium (K+), magnesium (Mg2+), and calcium (Ca2+), and the negatively charged ions chloride (Cl), sulfate (SO42-), and carbonate CO32-). These solutes, collectively called the ‘major ions’, conduct electrons, and therefore a simple way to track salinity is to measure the electrical conductance of the water between two electrodes set a known distance apart. Lake and ocean scientists now routinely take profiles of salinity and temperature with a CTD: a submersible instrument that records conductance, temperature, and depth many times per second as it is lowered on a rope or wire down the water column. Conductance is measured in Siemens (or microSiemens (µS), given the low salt concentrations in freshwater lakes), and adjusted to a standard temperature of 25°C to give specific conductivity in µS/cm. All freshwater lakes contain dissolved minerals, with specific conductivities in the range 50–500µS/cm, while salt water lakes have values that can exceed sea water (about 50,000µS/cm), and are the habitats for extreme microbes”.

“The World Register of Dams currently lists 58,519 ‘large dams’, defined as those with a dam wall of 15m or higher; these collectively store 16,120km3 of water, equivalent to 213 years of flow of Niagara Falls on the USA–Canada border. […] Around a hundred large dam projects are in advanced planning or construction in Africa […]. More than 300 dams are planned or under construction in the Amazon Basin of South America […]. Reservoirs have a number of distinguishing features relative to natural lakes. First, the shape (‘morphometry’) of their basins is rarely circular or oval, but instead is often dendritic, with a tree-like main stem and branches ramifying out into the submerged river valleys. Second, reservoirs typically have a high catchment area to lake area ratio, again reflecting their riverine origins. For natural lakes, this ratio is relatively low […] These proportionately large catchments mean that reservoirs have short water residence times, and water quality is much better than might be the case in the absence of this rapid flushing. Nonetheless, noxious algal blooms can develop and accumulate in isolated bays and side-arms, and downstream next to the dam itself. Reservoirs typically experience water level fluctuations that are much larger and more rapid than in natural lakes, and this limits the development of littoral plants and animals. Another distinguishing feature of reservoirs is that they often show a longitudinal gradient of conditions. Upstream, the river section contains water that is flowing, turbulent, and well mixed; this then passes through a transition zone into the lake section up to the dam, which is often the deepest part of the lake and may be stratified and clearer due to decantation of land-derived particles. In some reservoirs, the water outflow is situated near the base of the dam within the hypolimnion, and this reduces the extent of oxygen depletion and nutrient build-up, while also providing cool water for fish and other animal communities below the dam. There is increasing attention being given to careful regulation of the timing and magnitude of dam outflows to maintain these downstream ecosystems. […] The downstream effects of dams continue out into the sea, with the retention of sediments and nutrients in the reservoir leaving less available for export to marine food webs. This reduction can also lead to changes in shorelines, with a retreat of the coastal delta and intrusion of seawater because natural erosion processes can no longer be offset by resupply of sediments from upstream.”

“One of the most serious threats facing lakes throughout the world is the proliferation of algae and water plants caused by eutrophication, the overfertilization of waters with nutrients from human activities. […] Nutrient enrichment occurs both from ‘point sources’ of effluent discharged via pipes into the receiving waters, and ‘nonpoint sources’ such the runoff from roads and parking areas, agricultural lands, septic tank drainage fields, and terrain cleared of its nutrient- and water-absorbing vegetation. By the 1970s, even many of the world’s larger lakes had begun to show worrying signs of deterioration from these sources of increasing enrichment. […] A sharp drop in water clarity is often among the first signs of eutrophication, although in forested areas this effect may be masked for many years by the greater absorption of light by the coloured organic materials that are dissolved within the lake water. A drop in oxygen levels in the bottom waters during stratification is another telltale indicator of eutrophication, with the eventual fall to oxygen-free (anoxic) conditions in these lower strata of the lake. However, the most striking impact with greatest effect on ecosystem services is the production of harmful algal blooms (HABs), specifically by cyanobacteria. In eutrophic, temperate latitude waters, four genera of bloom-forming cyanobacteria are the usual offenders […]. These may occur alone or in combination, and although each has its own idiosyncratic size, shape, and lifestyle, they have a number of impressive biological features in common. First and foremost, their cells are typically full of hydrophobic protein cases that exclude water and trap gases. These honeycombs of gas-filled chambers, called ‘gas vesicles’, reduce the density of the cells, allowing them to float up to the surface where there is light available for growth. Put a drop of water from an algal bloom under a microscope and it will be immediately apparent that the individual cells are extremely small, and that the bloom itself is composed of billions of cells per litre of lake water.”

“During the day, the [algal] cells capture sunlight and produce sugars by photosynthesis; this increases their density, eventually to the point where they are heavier than the surrounding water and sink to more nutrient-rich conditions at depth in the water column or at the sediment surface. These sugars are depleted by cellular respiration, and this loss of ballast eventually results in cells becoming less dense than water and floating again towards the surface. This alternation of sinking and floating can result in large fluctuations in surface blooms over the twenty-four-hour cycle. The accumulation of bloom-forming cyanobacteria at the surface gives rise to surface scums that then can be blown into bays and washed up onto beaches. These dense populations of colonies in the water column, and especially at the surface, can shade out bottom-dwelling water plants, as well as greatly reduce the amount of light for other phytoplankton species. The resultant ‘cyanobacterial dominance’ and loss of algal species diversity has negative implications for the aquatic food web […] This negative impact on the food web may be compounded by the final collapse of the bloom and its decomposition, resulting in a major drawdown of oxygen. […] Bloom-forming cyanobacteria are especially troublesome for the management of drinking water supplies. First, there is the overproduction of biomass, which results in a massive load of algal particles that can exceed the filtration capacity of a water treatment plant […]. Second, there is an impact on the taste of the water. […] The third and most serious impact of cyanobacteria is that some of their secondary compounds are highly toxic. […] phosphorus is the key nutrient limiting bloom development, and efforts to preserve and rehabilitate freshwaters should pay specific attention to controlling the input of phosphorus via point and nonpoint discharges to lakes.”

Ultramicrobacteria.
The viral shunt in marine foodwebs.
Proteobacteria. Alphaproteobacteria. Betaproteobacteria. Gammaproteobacteria.
Mixotroph.
Carbon cycle. Nitrogen cycle. AmmonificationAnammox. Comammox.
Methanotroph.
Phosphorus cycle.
Littoral zone. Limnetic zone. Profundal zone. Benthic zone. Benthos.
Phytoplankton. Diatom. Picoeukaryote. Flagellates. Cyanobacteria.
Trophic state (-index).
Amphipoda. Rotifer. Cladocera. Copepod. Daphnia.
Redfield ratio.
δ15N.
Thermistor.
Extremophile. Halophile. Psychrophile. Acidophile.
Caspian Sea. Endorheic basin. Mono Lake.
Alpine lake.
Meromictic lake.
Subglacial lake. Lake Vostock.
Thermus aquaticus. Taq polymerase.
Lake Monoun.
Microcystin. Anatoxin-a.

 

 

February 2, 2018 Posted by | Biology, Books, Botany, Chemistry, Ecology, Engineering, Zoology | Leave a comment

Random stuff

I have almost stopped posting posts like these, which has resulted in the accumulation of a very large number of links and studies which I figured I might like to blog at some point. This post is mainly an attempt to deal with the backlog – I won’t cover the material in too much detail.

i. Do Bullies Have More Sex? The answer seems to be a qualified yes. A few quotes:

“Sexual behavior during adolescence is fairly widespread in Western cultures (Zimmer-Gembeck and Helfland 2008) with nearly two thirds of youth having had sexual intercourse by the age of 19 (Finer and Philbin 2013). […] Bullying behavior may aid in intrasexual competition and intersexual selection as a strategy when competing for mates. In line with this contention, bullying has been linked to having a higher number of dating and sexual partners (Dane et al. 2017; Volk et al. 2015). This may be one reason why adolescence coincides with a peak in antisocial or aggressive behaviors, such as bullying (Volk et al. 2006). However, not all adolescents benefit from bullying. Instead, bullying may only benefit adolescents with certain personality traits who are willing and able to leverage bullying as a strategy for engaging in sexual behavior with opposite-sex peers. Therefore, we used two independent cross-sectional samples of older and younger adolescents to determine which personality traits, if any, are associated with leveraging bullying into opportunities for sexual behavior.”

“…bullying by males signal the ability to provide good genes, material resources, and protect offspring (Buss and Shackelford 1997; Volk et al. 2012) because bullying others is a way of displaying attractive qualities such as strength and dominance (Gallup et al. 2007; Reijntjes et al. 2013). As a result, this makes bullies attractive sexual partners to opposite-sex peers while simultaneously suppressing the sexual success of same-sex rivals (Gallup et al. 2011; Koh and Wong 2015; Zimmer-Gembeck et al. 2001). Females may denigrate other females, targeting their appearance and sexual promiscuity (Leenaars et al. 2008; Vaillancourt 2013), which are two qualities relating to male mate preferences. Consequently, derogating these qualities lowers a rivals’ appeal as a mate and also intimidates or coerces rivals into withdrawing from intrasexual competition (Campbell 2013; Dane et al. 2017; Fisher and Cox 2009; Vaillancourt 2013). Thus, males may use direct forms of bullying (e.g., physical, verbal) to facilitate intersexual selection (i.e., appear attractive to females), while females may use relational bullying to facilitate intrasexual competition, by making rivals appear less attractive to males.”

The study relies on the use of self-report data, which I find very problematic – so I won’t go into the results here. I’m not quite clear on how those studies mentioned in the discussion ‘have found self-report data [to be] valid under conditions of confidentiality’ – and I remain skeptical. You’ll usually want data from independent observers (e.g. teacher or peer observations) when analyzing these kinds of things. Note in the context of the self-report data problem that if there’s a strong stigma associated with being bullied (there often is, or bullying wouldn’t work as well), asking people if they have been bullied is not much better than asking people if they’re bullying others.

ii. Some topical advice that some people might soon regret not having followed, from the wonderful Things I Learn From My Patients thread:

“If you are a teenage boy experimenting with fireworks, do not empty the gunpowder from a dozen fireworks and try to mix it in your mother’s blender. But if you do decide to do that, don’t hold the lid down with your other hand and stand right over it. This will result in the traumatic amputation of several fingers, burned and skinned forearms, glass shrapnel in your face, and a couple of badly scratched corneas as a start. You will spend months in rehab and never be able to use your left hand again.”

iii. I haven’t talked about the AlphaZero-Stockfish match, but I was of course aware of it and did read a bit about that stuff. Here’s a reddit thread where one of the Stockfish programmers answers questions about the match. A few quotes:

“Which of the two is stronger under ideal conditions is, to me, neither particularly interesting (they are so different that it’s kind of like comparing the maximum speeds of a fish and a bird) nor particularly important (since there is only one of them that you and I can download and run anyway). What is super interesting is that we have two such radically different ways to create a computer chess playing entity with superhuman abilities. […] I don’t think there is anything to learn from AlphaZero that is applicable to Stockfish. They are just too different, you can’t transfer ideas from one to the other.”

“Based on the 100 games played, AlphaZero seems to be about 100 Elo points stronger under the conditions they used. The current development version of Stockfish is something like 40 Elo points stronger than the version used in Google’s experiment. There is a version of Stockfish translated to hand-written x86-64 assembly language that’s about 15 Elo points stronger still. This adds up to roughly half the Elo difference between AlphaZero and Stockfish shown in Google’s experiment.”

“It seems that Stockfish was playing with only 1 GB for transposition tables (the area of memory used to store data about the positions previously encountered in the search), which is way too little when running with 64 threads.” [I seem to recall a comp sci guy observing elsewhere that this was less than what was available to his smartphone version of Stockfish, but I didn’t bookmark that comment].

“The time control was a very artificial fixed 1 minute/move. That’s not how chess is traditionally played. Quite a lot of effort has gone into Stockfish’s time management. It’s pretty good at deciding when to move quickly, and when to spend a lot of time on a critical decision. In a fixed time per move game, it will often happen that the engine discovers that there is a problem with the move it wants to play just before the time is out. In a regular time control, it would then spend extra time analysing all alternative moves and trying to find a better one. When you force it to move after exactly one minute, it will play the move it already know is bad. There is no doubt that this will cause it to lose many games it would otherwise have drawn.”

iv. Thrombolytics for Acute Ischemic Stroke – no benefit found.

“Thrombolysis has been rigorously studied in >60,000 patients for acute thrombotic myocardial infarction, and is proven to reduce mortality. It is theorized that thrombolysis may similarly benefit ischemic stroke patients, though a much smaller number (8120) has been studied in relevant, large scale, high quality trials thus far. […] There are 12 such trials 1-12. Despite the temptation to pool these data the studies are clinically heterogeneous. […] Data from multiple trials must be clinically and statistically homogenous to be validly pooled.14 Large thrombolytic studies demonstrate wide variations in anatomic stroke regions, small- versus large-vessel occlusion, clinical severity, age, vital sign parameters, stroke scale scores, and times of administration. […] Examining each study individually is therefore, in our opinion, both more valid and more instructive. […] Two of twelve studies suggest a benefit […] In comparison, twice as many studies showed harm and these were stopped early. This early stoppage means that the number of subjects in studies demonstrating harm would have included over 2400 subjects based on originally intended enrollments. Pooled analyses are therefore missing these phantom data, which would have further eroded any aggregate benefits. In their absence, any pooled analysis is biased toward benefit. Despite this, there remain five times as many trials showing harm or no benefit (n=10) as those concluding benefit (n=2), and 6675 subjects in trials demonstrating no benefit compared to 1445 subjects in trials concluding benefit.”

“Thrombolytics for ischemic stroke may be harmful or beneficial. The answer remains elusive. We struggled therefore, debating between a ‘yellow’ or ‘red’ light for our recommendation. However, over 60,000 subjects in trials of thrombolytics for coronary thrombosis suggest a consistent beneficial effect across groups and subgroups, with no studies suggesting harm. This consistency was found despite a very small mortality benefit (2.5%), and a very narrow therapeutic window (1% major bleeding). In comparison, the variation in trial results of thrombolytics for stroke and the daunting but consistent adverse effect rate caused by ICH suggested to us that thrombolytics are dangerous unless further study exonerates their use.”

“There is a Cochrane review that pooled estimates of effect. 17 We do not endorse this choice because of clinical heterogeneity. However, we present the NNT’s from the pooled analysis for the reader’s benefit. The Cochrane review suggested a 6% reduction in disability […] with thrombolytics. This would mean that 17 were treated for every 1 avoiding an unfavorable outcome. The review also noted a 1% increase in mortality (1 in 100 patients die because of thrombolytics) and a 5% increase in nonfatal intracranial hemorrhage (1 in 20), for a total of 6% harmed (1 in 17 suffers death or brain hemorrhage).”

v. Suicide attempts in Asperger Syndrome. An interesting finding: “Over 35% of individuals with AS reported that they had attempted suicide in the past.”

Related: Suicidal ideation and suicide plans or attempts in adults with Asperger’s syndrome attending a specialist diagnostic clinic: a clinical cohort study.

“374 adults (256 men and 118 women) were diagnosed with Asperger’s syndrome in the study period. 243 (66%) of 367 respondents self-reported suicidal ideation, 127 (35%) of 365 respondents self-reported plans or attempts at suicide, and 116 (31%) of 368 respondents self-reported depression. Adults with Asperger’s syndrome were significantly more likely to report lifetime experience of suicidal ideation than were individuals from a general UK population sample (odds ratio 9·6 [95% CI 7·6–11·9], p<0·0001), people with one, two, or more medical illnesses (p<0·0001), or people with psychotic illness (p=0·019). […] Lifetime experience of depression (p=0·787), suicidal ideation (p=0·164), and suicide plans or attempts (p=0·06) did not differ significantly between men and women […] Individuals who reported suicide plans or attempts had significantly higher Autism Spectrum Quotient scores than those who did not […] Empathy Quotient scores and ages did not differ between individuals who did or did not report suicide plans or attempts (table 4). Patients with self-reported depression or suicidal ideation did not have significantly higher Autism Spectrum Quotient scores, Empathy Quotient scores, or age than did those without depression or suicidal ideation”.

The fact that people with Asperger’s are more likely to be depressed and contemplate suicide is consistent with previous observations that they’re also more likely to die from suicide – for example a paper I blogged a while back found that in that particular (large Swedish population-based cohort-) study, people with ASD were more than 7 times as likely to die from suicide than were the comparable controls.

Also related: Suicidal tendencies hard to spot in some people with autism.

This link has some great graphs and tables of suicide data from the US.

Also autism-related: Increased perception of loudness in autism. This is one of the ‘important ones’ for me personally – I am much more sound-sensitive than are most people.

vi. Early versus Delayed Invasive Intervention in Acute Coronary Syndromes.

“Earlier trials have shown that a routine invasive strategy improves outcomes in patients with acute coronary syndromes without ST-segment elevation. However, the optimal timing of such intervention remains uncertain. […] We randomly assigned 3031 patients with acute coronary syndromes to undergo either routine early intervention (coronary angiography ≤24 hours after randomization) or delayed intervention (coronary angiography ≥36 hours after randomization). The primary outcome was a composite of death, myocardial infarction, or stroke at 6 months. A prespecified secondary outcome was death, myocardial infarction, or refractory ischemia at 6 months. […] Early intervention did not differ greatly from delayed intervention in preventing the primary outcome, but it did reduce the rate of the composite secondary outcome of death, myocardial infarction, or refractory ischemia and was superior to delayed intervention in high-risk patients.”

vii. Some wikipedia links:

Behrens–Fisher problem.
Sailing ship tactics (I figured I had to read up on this if I were to get anything out of the Aubrey-Maturin books).
Anatomical terms of muscle.
Phatic expression (“a phatic expression […] is communication which serves a social function such as small talk and social pleasantries that don’t seek or offer any information of value.”)
Three-domain system.
Beringian wolf (featured).
Subdural hygroma.
Cayley graph.
Schur polynomial.
Solar neutrino problem.
Hadamard product (matrices).
True polar wander.
Newton’s cradle.

viii. Determinant versus permanent (mathematics – technical).

ix. Some years ago I wrote a few English-language posts about some of the various statistical/demographic properties of immigrants living in Denmark, based on numbers included in a publication by Statistics Denmark. I did it by translating the observations included in that publication, which was only published in Danish. I was briefly considering doing the same thing again when the 2017 data arrived, but I decided not to do it as I recalled that it took a lot of time to write those posts back then, and it didn’t seem to me to be worth the effort – but Danish readers might be interested to have a look at the data, if they haven’t already – here’s a link to the publication Indvandrere i Danmark 2017.

x. A banter blitz session with grandmaster Peter Svidler, who recently became the first Russian ever to win the Russian Chess Championship 8 times. He’s currently shared-second in the World Rapid Championship after 10 rounds and is now in the top 10 on the live rating list in both classical and rapid – seems like he’s had a very decent year.

xi. I recently discovered Dr. Whitecoat’s blog. The patient encounters are often interesting.

December 28, 2017 Posted by | Astronomy, autism, Biology, Cardiology, Chess, Computer science, History, Mathematics, Medicine, Neurology, Physics, Psychiatry, Psychology, Random stuff, Statistics, Studies, Wikipedia, Zoology | Leave a comment

Organic Chemistry (II)

I have included some observations from the second half of the book below, as well as some links to topics covered.

“[E]nzymes are used routinely to catalyse reactions in the research laboratory, and for a variety of industrial processes involving pharmaceuticals, agrochemicals, and biofuels. In the past, enzymes had to be extracted from natural sources — a process that was both expensive and slow. But nowadays, genetic engineering can incorporate the gene for a key enzyme into the DNA of fast growing microbial cells, allowing the enzyme to be obtained more quickly and in far greater yield. Genetic engineering has also made it possible to modify the amino acids making up an enzyme. Such modified enzymes can prove more effective as catalysts, accept a wider range of substrates, and survive harsher reaction conditions. […] New enzymes are constantly being discovered in the natural world as well as in the laboratory. Fungi and bacteria are particularly rich in enzymes that allow them to degrade organic compounds. It is estimated that a typical bacterial cell contains about 3,000 enzymes, whereas a fungal cell contains 6,000. Considering the variety of bacterial and fungal species in existence, this represents a huge reservoir of new enzymes, and it is estimated that only 3 per cent of them have been investigated so far.”

“One of the most important applications of organic chemistry involves the design and synthesis of pharmaceutical agents — a topic that is defined as medicinal chemistry. […] In the 19th century, chemists isolated chemical components from known herbs and extracts. Their aim was to identify a single chemical that was responsible for the extract’s pharmacological effects — the active principle. […] It was not long before chemists synthesized analogues of active principles. Analogues are structures which have been modified slightly from the original active principle. Such modifications can often improve activity or reduce side effects. This led to the concept of the lead compound — a compound with a useful pharmacological activity that could act as the starting point for further research. […] The first half of the 20th century culminated in the discovery of effective antimicrobial agents. […] The 1960s can be viewed as the birth of rational drug design. During that period there were important advances in the design of effective anti-ulcer agents, anti-asthmatics, and beta-blockers for the treatment of high blood pressure. Much of this was based on trying to understand how drugs work at the molecular level and proposing theories about why some compounds were active and some were not.”

“[R]ational drug design was boosted enormously towards the end of the century by advances in both biology and chemistry. The sequencing of the human genome led to the identification of previously unknown proteins that could serve as potential drug targets. […] Advances in automated, small-scale testing procedures (high-throughput screening) also allowed the rapid testing of potential drugs. In chemistry, advances were made in X-ray crystallography and NMR spectroscopy, allowing scientists to study the structure of drugs and their mechanisms of action. Powerful molecular modelling software packages were developed that allowed researchers to study how a drug binds to a protein binding site. […] the development of automated synthetic methods has vastly increased the number of compounds that can be synthesized in a given time period. Companies can now produce thousands of compounds that can be stored and tested for pharmacological activity. Such stores have been called chemical libraries and are routinely tested to identify compounds capable of binding with a specific protein target. These advances have boosted medicinal chemistry research over the last twenty years in virtually every area of medicine.”

“Drugs interact with molecular targets in the body such as proteins and nucleic acids. However, the vast majority of clinically useful drugs interact with proteins, especially receptors, enzymes, and transport proteins […] Enzymes are […] important drug targets. Drugs that bind to the active site and prevent the enzyme acting as a catalyst are known as enzyme inhibitors. […] Enzymes are located inside cells, and so enzyme inhibitors have to cross cell membranes in order to reach them—an important consideration in drug design. […] Transport proteins are targets for a number of therapeutically important drugs. For example, a group of antidepressants known as selective serotonin reuptake inhibitors prevent serotonin being transported into neurons by transport proteins.”

“The main pharmacokinetic factors are absorption, distribution, metabolism, and excretion. Absorption relates to how much of an orally administered drug survives the digestive enzymes and crosses the gut wall to reach the bloodstream. Once there, the drug is carried to the liver where a certain percentage of it is metabolized by metabolic enzymes. This is known as the first-pass effect. The ‘survivors’ are then distributed round the body by the blood supply, but this is an uneven process. The tissues and organs with the richest supply of blood vessels receive the greatest proportion of the drug. Some drugs may get ‘trapped’ or sidetracked. For example fatty drugs tend to get absorbed in fat tissue and fail to reach their target. The kidneys are chiefly responsible for the excretion of drugs and their metabolites.”

“Having identified a lead compound, it is important to establish which features of the compound are important for activity. This, in turn, can give a better understanding of how the compound binds to its molecular target. Most drugs are significantly smaller than molecular targets such as proteins. This means that the drug binds to quite a small region of the protein — a region known as the binding site […]. Within this binding site, there are binding regions that can form different types of intermolecular interactions such as van der Waals interactions, hydrogen bonds, and ionic interactions. If a drug has functional groups and substituents capable of interacting with those binding regions, then binding can take place. A lead compound may have several groups that are capable of forming intermolecular interactions, but not all of them are necessarily needed. One way of identifying the important binding groups is to crystallize the target protein with the drug bound to the binding site. X-ray crystallography then produces a picture of the complex which allows identification of binding interactions. However, it is not always possible to crystallize target proteins and so a different approach is needed. This involves synthesizing analogues of the lead compound where groups are modified or removed. Comparing the activity of each analogue with the lead compound can then determine whether a particular group is important or not. This is known as an SAR study, where SAR stands for structure–activity relationships.” Once the important binding groups have been identified, the pharmacophore for the lead compound can be defined. This specifies the important binding groups and their relative position in the molecule.”

“One way of identifying the active conformation of a flexible lead compound is to synthesize rigid analogues where the binding groups are locked into defined positions. This is known as rigidification or conformational restriction. The pharmacophore will then be represented by the most active analogue. […] A large number of rotatable bonds is likely to have an adverse effect on drug activity. This is because a flexible molecule can adopt a large number of conformations, and only one of these shapes corresponds to the active conformation. […] In contrast, a totally rigid molecule containing the required pharmacophore will bind the first time it enters the binding site, resulting in greater activity. […] It is also important to optimize a drug’s pharmacokinetic properties such that it can reach its target in the body. Strategies include altering the drug’s hydrophilic/hydrophobic properties to improve absorption, and the addition of substituents that block metabolism at specific parts of the molecule. […] The drug candidate must [in general] have useful activity and selectivity, with minimal side effects. It must have good pharmacokinetic properties, lack toxicity, and preferably have no interactions with other drugs that might be taken by a patient. Finally, it is important that it can be synthesized as cheaply as possible”.

“Most drugs that have reached clinical trials for the treatment of Alzheimer’s disease have failed. Between 2002 and 2012, 244 novel compounds were tested in 414 clinical trials, but only one drug gained approval. This represents a failure rate of 99.6 per cent as against a failure rate of 81 per cent for anti-cancer drugs.”

“It takes about ten years and £160 million to develop a new pesticide […] The volume of global sales increased 47 per cent in the ten-year period between 2002 and 2012, while, in 2012, total sales amounted to £31 billion. […] In many respects, agrochemical research is similar to pharmaceutical research. The aim is to find pesticides that are toxic to ‘pests’, but relatively harmless to humans and beneficial life forms. The strategies used to achieve this goal are also similar. Selectivity can be achieved by designing agents that interact with molecular targets that are present in pests, but not other species. Another approach is to take advantage of any metabolic reactions that are unique to pests. An inactive prodrug could then be designed that is metabolized to a toxic compound in the pest, but remains harmless in other species. Finally, it might be possible to take advantage of pharmacokinetic differences between pests and other species, such that a pesticide reaches its target more easily in the pest. […] Insecticides are being developed that act on a range of different targets as a means of tackling resistance. If resistance should arise to an insecticide acting on one particular target, then one can switch to using an insecticide that acts on a different target. […] Several insecticides act as insect growth regulators (IGRs) and target the moulting process rather than the nervous system. In general, IGRs take longer to kill insects but are thought to cause less detrimental effects to beneficial insects. […] Herbicides control weeds that would otherwise compete with crops for water and soil nutrients. More is spent on herbicides than any other class of pesticide […] The synthetic agent 2,4-D […] was synthesized by ICI in 1940 as part of research carried out on biological weapons […] It was first used commercially in 1946 and proved highly successful in eradicating weeds in cereal grass crops such as wheat, maize, and rice. […] The compound […] is still the most widely used herbicide in the world.”

“The type of conjugated system present in a molecule determines the specific wavelength of light absorbed. In general, the more extended the conjugation, the higher the wavelength absorbed. For example, β-carotene […] is the molecule responsible for the orange colour of carrots. It has a conjugated system involving eleven double bonds, and absorbs light in the blue region of the spectrum. It appears red because the reflected light lacks the blue component. Zeaxanthin is very similar in structure to β-carotene, and is responsible for the yellow colour of corn. […] Lycopene absorbs blue-green light and is responsible for the red colour of tomatoes, rose hips, and berries. Chlorophyll absorbs red light and is coloured green. […] Scented molecules interact with olfactory receptors in the nose. […] there are around 400 different olfactory protein receptors in humans […] The natural aroma of a rose is due mainly to 2-phenylethanol, geraniol, and citronellol.”

“Over the last fifty years, synthetic materials have largely replaced natural materials such as wood, leather, wool, and cotton. Plastics and polymers are perhaps the most visible sign of how organic chemistry has changed society. […] It is estimated that production of global plastics was 288 million tons in 2012 […] Polymerization involves linking molecular strands called polymers […]. By varying the nature of the monomer, a huge range of different polymers can be synthesized with widely differing properties. The idea of linking small molecular building blocks into polymers is not a new one. Nature has been at it for millions of years using amino acid building blocks to make proteins, and nucleotide building blocks to make nucleic acids […] The raw materials for plastics come mainly from oil, which is a finite resource. Therefore, it makes sense to recycle or depolymerize plastics to recover that resource. Virtually all plastics can be recycled, but it is not necessarily economically feasible to do so. Traditional recycling of polyesters, polycarbonates, and polystyrene tends to produce inferior plastics that are suitable only for low-quality goods.”

Adipic acid.
Protease. Lipase. Amylase. Cellulase.
Reflectin.
Agonist.
Antagonist.
Prodrug.
Conformational change.
Process chemistry (chemical development).
Clinical trial.
Phenylbutazone.
Pesticide.
Dichlorodiphenyltrichloroethane.
Aldrin.
N-Methyl carbamate.
Organophosphates.
Pyrethrum.
Neonicotinoid.
Colony collapse disorder.
Ecdysone receptor.
Methoprene.
Tebufenozide.
Fungicide.
Quinone outside inhibitors (QoI).
Allelopathy.
Glyphosate.
11-cis retinal.
Chromophore.
Synthetic dyes.
Methylene blue.
Cryptochrome.
Pheromone.
Artificial sweeteners.
Miraculin.
Addition polymer.
Condensation polymer.
Polyethylene.
Polypropylene.
Polyvinyl chloride.
Bisphenol A.
Vulcanization.
Kevlar.
Polycarbonate.
Polyhydroxyalkanoates.
Bioplastic.
Nanochemistry.
Allotropy.
Allotropes of carbon.
Carbon nanotube.
Rotaxane.
π-interactions.
Molecular switch.

November 11, 2017 Posted by | Biology, Books, Botany, Chemistry, Medicine, Molecular biology, Pharmacology, Zoology | 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

Random Stuff

i. Some new words I’ve encountered (not all of them are from vocabulary.com, but many of them are):

Uxoricide, persnickety, logy, philoprogenitive, impassive, hagiography, gunwale, flounce, vivify, pelage, irredentism, pertinacity,callipygous, valetudinarian, recrudesce, adjuration, epistolary, dandle, picaresque, humdinger, newel, lightsome, lunette, inflect, misoneism, cormorant, immanence, parvenu, sconce, acquisitiveness, lingual, Macaronic, divot, mettlesome, logomachy, raffish, marginalia, omnifarious, tatter, licit.

ii. A lecture:

I got annoyed a few times by the fact that you can’t tell where he’s pointing when he’s talking about the slides, which makes the lecture harder to follow than it ought to be, but it’s still an interesting lecture.

iii. Facts about Dihydrogen Monoxide. Includes coverage of important neglected topics such as ‘What is the link between Dihydrogen Monoxide and school violence?’ After reading the article, I am frankly outraged that this stuff’s still legal!

iv. Some wikipedia links of interest:

Steganography.

Steganography […] is the practice of concealing a file, message, image, or video within another file, message, image, or video. The word steganography combines the Greek words steganos (στεγανός), meaning “covered, concealed, or protected”, and graphein (γράφειν) meaning “writing”. […] Generally, the hidden messages appear to be (or be part of) something else: images, articles, shopping lists, or some other cover text. For example, the hidden message may be in invisible ink between the visible lines of a private letter. Some implementations of steganography that lack a shared secret are forms of security through obscurity, whereas key-dependent steganographic schemes adhere to Kerckhoffs’s principle.[1]

The advantage of steganography over cryptography alone is that the intended secret message does not attract attention to itself as an object of scrutiny. Plainly visible encrypted messages—no matter how unbreakable—arouse interest, and may in themselves be incriminating in countries where encryption is illegal.[2] Thus, whereas cryptography is the practice of protecting the contents of a message alone, steganography is concerned with concealing the fact that a secret message is being sent, as well as concealing the contents of the message.”

H. H. Holmes. A really nice guy.

Herman Webster Mudgett (May 16, 1861 – May 7, 1896), better known under the name of Dr. Henry Howard Holmes or more commonly just H. H. Holmes, was one of the first documented serial killers in the modern sense of the term.[1][2] In Chicago, at the time of the 1893 World’s Columbian Exposition, Holmes opened a hotel which he had designed and built for himself specifically with murder in mind, and which was the location of many of his murders. While he confessed to 27 murders, of which nine were confirmed, his actual body count could be up to 200.[3] He brought an unknown number of his victims to his World’s Fair Hotel, located about 3 miles (4.8 km) west of the fair, which was held in Jackson Park. Besides being a serial killer, H. H. Holmes was also a successful con artist and a bigamist. […]

Holmes purchased an empty lot across from the drugstore where he built his three-story, block-long hotel building. Because of its enormous structure, local people dubbed it “The Castle”. The building was 162 feet long and 50 feet wide. […] The ground floor of the Castle contained Holmes’ own relocated drugstore and various shops, while the upper two floors contained his personal office and a labyrinth of rooms with doorways opening to brick walls, oddly-angled hallways, stairways leading to nowhere, doors that could only be opened from the outside and a host of other strange and deceptive constructions. Holmes was constantly firing and hiring different workers during the construction of the Castle, claiming that “they were doing incompetent work.” His actual reason was to ensure that he was the only one who fully understood the design of the building.[3]

Minnesota Starvation Experiment.

“The Minnesota Starvation Experiment […] was a clinical study performed at the University of Minnesota between November 19, 1944 and December 20, 1945. The investigation was designed to determine the physiological and psychological effects of severe and prolonged dietary restriction and the effectiveness of dietary rehabilitation strategies.

The motivation of the study was twofold: First, to produce a definitive treatise on the subject of human starvation based on a laboratory simulation of severe famine and, second, to use the scientific results produced to guide the Allied relief assistance to famine victims in Europe and Asia at the end of World War II. It was recognized early in 1944 that millions of people were in grave danger of mass famine as a result of the conflict, and information was needed regarding the effects of semi-starvation—and the impact of various rehabilitation strategies—if postwar relief efforts were to be effective.”

“most of the subjects experienced periods of severe emotional distress and depression.[1]:161 There were extreme reactions to the psychological effects during the experiment including self-mutilation (one subject amputated three fingers of his hand with an axe, though the subject was unsure if he had done so intentionally or accidentally).[5] Participants exhibited a preoccupation with food, both during the starvation period and the rehabilitation phase. Sexual interest was drastically reduced, and the volunteers showed signs of social withdrawal and isolation.[1]:123–124 […] One of the crucial observations of the Minnesota Starvation Experiment […] is that the physical effects of the induced semi-starvation during the study closely approximate the conditions experienced by people with a range of eating disorders such as anorexia nervosa and bulimia nervosa.”

Post-vasectomy pain syndrome. Vasectomy reversal is a risk people probably know about, but this one seems to also be worth being aware of if one is considering having a vasectomy.

Transport in the Soviet Union (‘good article’). A few observations from the article:

“By the mid-1970s, only eight percent of the Soviet population owned a car. […]  From 1924 to 1971 the USSR produced 1 million vehicles […] By 1975 only 8 percent of rural households owned a car. […] Growth of motor vehicles had increased by 224 percent in the 1980s, while hardcore surfaced roads only increased by 64 percent. […] By the 1980s Soviet railways had become the most intensively used in the world. Most Soviet citizens did not own private transport, and if they did, it was difficult to drive long distances due to the poor conditions of many roads. […] Road transport played a minor role in the Soviet economy, compared to domestic rail transport or First World road transport. According to historian Martin Crouch, road traffic of goods and passengers combined was only 14 percent of the volume of rail transport. It was only late in its existence that the Soviet authorities put emphasis on road construction and maintenance […] Road transport as a whole lagged far behind that of rail transport; the average distance moved by motor transport in 1982 was 16.4 kilometres (10.2 mi), while the average for railway transport was 930 km per ton and 435 km per ton for water freight. In 1982 there was a threefold increase in investment since 1960 in motor freight transport, and more than a thirtyfold increase since 1940.”

March 3, 2016 Posted by | Biology, Cryptography, Engineering, History, Language, Lectures, Ophthalmology, Random stuff, Wikipedia, Zoology | Leave a comment

The Origin of Species

I figured I ought to blog this book at some point, and today I decided to take out the time to do it. This is the second book by Darwin I’ve read – for blog content dealing with Darwin’s book The Voyage of the Beagle, see these posts. The two books are somewhat different; Beagle is sort of a travel book written by a scientist who decided to write down his observations during his travels, whereas Origin is a sort of popular-science research treatise – for more details on Beagle, see the posts linked above. If you plan on reading both the way I did I think you should aim to read them in the order they are written.

I did not rate the book on goodreads because I could not think of a fair way to rate the book; it’s a unique and very important contribution to the history of science, but how do you weigh the other dimensions? I decided not to try. Some of the people reviewing the book on goodreads call the book ‘dry’ or ‘dense’, but I’d say that I found the book quite easy to read compared to quite a few of the other books I’ve been reading this year and it doesn’t actually take that long to read; thus I read a quite substantial proportion of the book during a one day trip to Copenhagen and back. The book can be read by most literate people living in the 21st century – you do not need to know any evolutionary biology to read this book – but that said, how you read the book will to some extent depend upon how much you know about the topics about which Darwin theorizes in his book. I had a conversation with my brother about the book a short while after I’d read it, and I recall noting during that conversation that in my opinion one would probably get more out of reading this book if one has at least some knowledge of geology (for example some knowledge about the history of the theory of continental drift – this book was written long before the theory of plate tectonics was developed), paleontology, Mendel’s laws/genetics/the modern synthesis and modern evolutionary thought, ecology and ethology, etc. Whether or not you actually do ‘get more out of the book’ if you already know some stuff about the topics about which Darwin speaks is perhaps an open question, but I think a case can certainly be made that someone who already knows a bit about evolution and related topics will read this book in a different manner than will someone who knows very little about these topics. I should perhaps in this context point out to people new to this blog that even though I hardly consider myself an expert on these sorts of topics, I have nevertheless read quite a bit of stuff about those things in the past – books like this, this, this, this, this, this, this, this, this, this, this, this, this, this, and this one – so I was reading the book perhaps mainly from the vantage point of someone at least somewhat familiar both with many of the basic ideas and with a lot of the refinements of these ideas that people have added to the science of biology since Darwin’s time. One of the things my knowledge of modern biology and related topics had not prepared me for was how moronic some of the ideas of Darwin’s critics were at the time and how stupid some of the implicit alternatives were, and this is actually part of the fun of reading this book; there was a lot of stuff back then which even many of the people presumably held in high regard really had no clue about, and even outrageously idiotic ideas were seemingly taken quite seriously by people involved in the debate. I assume that biologists still to this day have to spend quite a bit of time and effort dealing with ignorant idiots (see also this), but back in Darwin’s day these people were presumably to a much greater extent taken seriously even among people in the scientific community, if indeed they were not themselves part of the scientific community.

Darwin was not right about everything and there’s a lot of stuff that modern biologists know which he had no idea about, so naturally some mistaken ideas made their way into Origin as well; for example the idea of the inheritance of acquired characteristics (Lamarckian inheritance) occasionally pops up and is implicitly defended in the book as a credible complement to natural selection, as also noted in Oliver Francis’ afterword to the book. On a general note it seems that Darwin did a better job convincing people about the importance of the concept of evolution than he did convincing people that the relevant mechanism behind evolution was natural selection; at least that’s what’s argued in wiki’s featured article on the history of evolutionary thought (to which I have linked before here on the blog).

Darwin emphasizes more than once in the book that evolution is a very slow process which takes a lot of time (for example: “I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time”, p.123), and arguably this is also something about which he is part right/part wrong because the speed with which natural selection ‘makes itself felt’ depends upon a variety of factors, and it can be really quite fast in some contexts (see e.g. this and some of the topics covered in books like this one); though you can appreciate why he held the views he did on that topic.

A big problem confronted by Darwin was that he didn’t know how genes work, so in a sense the whole topic of the ‘mechanics of the whole thing’ – the ‘nuts and bolts’ – was more or less a black box to him (I have included a few quotes which indirectly relate to this problem in my coverage of the book below; as can be inferred from those quotes Darwin wasn’t completely clueless, but he might have benefited greatly from a chat with Gregor Mendel…) – in a way a really interesting thing about the book is how plausible the theory of natural selection is made out to be despite this blatantly obvious (at least to the modern reader) problem. Darwin was incidentally well aware there was a problem; just 6 pages into the first chapter of the book he observes frankly that: “The laws governing inheritance are quite unknown”. Some of the quotes below, e.g. on reciprocal crosses, illustrate that he was sort of scratching the surface, but in the book he never does more than that.

Below I have added some quotes from the book.

“Certainly no clear line of demarcation has as yet been drawn between species and sub-species […]; or, again, between sub-species and well-marked varieties, or between lesser varieties and individual differences. These differences blend into each other in an insensible series; and a series impresses the mind with the idea of an actual passage. […] I look at individual differences, though of small interest to the systematist, as of high importance […], as being the first step towards such slight varieties as are barely thought worth recording in works on natural history. And I look at varieties which are in any degree more distinct and permanent, as steps leading to more strongly marked and more permanent varieties; and at these latter, as leading to sub-species, and to species. […] I attribute the passage of a variety, from a state in which it differs very slightly from its parent to one in which it differs more, to the action of natural selection in accumulating […] differences of structure in certain definite directions. Hence I believe a well-marked variety may be justly called an incipient species […] I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for mere convenience’ sake. […] the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species have once existed as varieties, and have thus originated: whereas, these analogies are utterly inexplicable if each species has been independently created.”

“Owing to [the] struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man’s power of selection. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art. […] In looking at Nature, it is most necessary to keep the foregoing considerations always in mind – never to forget that every single organic being around us may be said to be striving to the utmost to increase in numbers; that each lives by a struggle at some period of its life; that heavy destruction inevitably falls either on the young or old, during each generation or at recurrent intervals. Lighten any check, mitigate the destruction ever so little, and the number of the species will almost instantaneously increase to any amount. The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force. […] A corollary of the highest importance may be deduced from the foregoing remarks, namely, that the structure of every organic being is related, in the most essential yet often hidden manner, to that of all other organic beings, with which it comes into competition for food or residence, or from which it has to escape, or on which it preys.”

“Under nature, the slightest difference of structure or constitution may well turn the nicely-balanced scale in the struggle for life, and so be preserved. How fleeting are the wishes and efforts of man! how short his time! And consequently how poor will his products be, compared with those accumulated by nature during whole geological periods. […] It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the long lapses of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were.”

“I have collected so large a body of facts, showing, in accordance with the almost universal belief of breeders, that with animals and plants a cross between different varieties, or between individuals of the same variety but of another strain, gives vigour and fertility to the offspring; and on the other hand, that close interbreeding diminishes vigour and fertility; that these facts alone incline me to believe that it is a general law of nature (utterly ignorant though we be of the meaning of the law) that no organic being self-fertilises itself for an eternity of generations; but that a cross with another individual is occasionally perhaps at very long intervals — indispensable. […] in many organic beings, a cross between two individuals is an obvious necessity for each birth; in many others it occurs perhaps only at long intervals; but in none, as I suspect, can self-fertilisation go on for perpetuity.”

“as new species in the course of time are formed through natural selection, others will become rarer and rarer, and finally extinct. The forms which stand in closest competition with those undergoing modification and improvement, will naturally suffer most. […] Whatever the cause may be of each slight difference in the offspring from their parents – and a cause for each must exist – it is the steady accumulation, through natural selection, of such differences, when beneficial to the individual, which gives rise to all the more important modifications of structure, by which the innumerable beings on the face of this earth are enabled to struggle with each other, and the best adapted to survive.”

“Natural selection, as has just been remarked, leads to divergence of character and to much extinction of the less improved and intermediate forms of life. On these principles, I believe, the nature of the affinities of all organic beings may be explained. It is a truly wonderful fact – the wonder of which we are apt to overlook from familiarity – that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold – namely, varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. The several subordinate groups in any class cannot be ranked in a single file, but seem rather to be clustered round points, and these round other points, and so on in almost endless cycles. On the view that each species has been independently created, I can see no explanation of this great fact in the classification of all organic beings; but, to the best of my judgment, it is explained through inheritance and the complex action of natural selection, entailing extinction and divergence of character […] The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

“No one has been able to point out what kind, or what amount, of difference in any recognisable character is sufficient to prevent two species crossing. It can be shown that plants most widely different in habit and general appearance, and having strongly marked differences in every part of the flower, even in the pollen, in the fruit, and in the cotyledons, can be crossed. […] By a reciprocal cross between two species, I mean the case, for instance, of a stallion-horse being first crossed with a female-ass, and then a male-ass with a mare: these two species may then be said to have been reciprocally crossed. There is often the widest possible difference in the facility of making reciprocal crosses. Such cases are highly important, for they prove that the capacity in any two species to cross is often completely independent of their systematic affinity, or of any recognisable difference in their whole organisation. On the other hand, these cases clearly show that the capacity for crossing is connected with constitutional differences imperceptible by us, and confined to the reproductive system. […] fertility in the hybrid is independent of its external resemblance to either pure parent. […] The foregoing rules and facts […] appear to me clearly to indicate that the sterility both of first crosses and of hybrids is simply incidental or dependent on unknown differences, chiefly in the reproductive systems, of the species which are crossed. […] Laying aside the question of fertility and sterility, in all other respects there seems to be a general and close similarity in the offspring of crossed species, and of crossed varieties. If we look at species as having been specially created, and at varieties as having been produced by secondary laws, this similarity would be an astonishing fact. But it harmonizes perfectly with the view that there is no essential distinction between species and varieties. […] the facts briefly given in this chapter do not seem to me opposed to, but even rather to support the view, that there is no fundamental distinction between species and varieties.”

“Believing, from reasons before alluded to, that our continents have long remained in nearly the same relative position, though subjected to large, but partial oscillations of level, I am strongly inclined to…” (…’probably get some things wrong…’, US)

“In considering the distribution of organic beings over the face of the globe, the first great fact which strikes us is, that neither the similarity nor the dissimilarity of the inhabitants of various regions can be accounted for by their climatal and other physical conditions. Of late, almost every author who has studied the subject has come to this conclusion. […] A second great fact which strikes us in our general review is, that barriers of any kind, or obstacles to free migration, are related in a close and important manner to the differences between the productions of various regions. […] A third great fact, partly included in the foregoing statements, is the affinity of the productions of the same continent or sea, though the species themselves are distinct at different points and stations. It is a law of the widest generality, and every continent offers innumerable instances. Nevertheless the naturalist in travelling, for instance, from north to south never fails to be struck by the manner in which successive groups of beings, specifically distinct, yet clearly related, replace each other. […] We see in these facts some deep organic bond, prevailing throughout space and time, over the same areas of land and water, and independent of their physical conditions. The naturalist must feel little curiosity, who is not led to inquire what this bond is.  This bond, on my theory, is simply inheritance […] The dissimilarity of the inhabitants of different regions may be attributed to modification through natural selection, and in a quite subordinate degree to the direct influence of different physical conditions. The degree of dissimilarity will depend on the migration of the more dominant forms of life from one region into another having been effected with more or less ease, at periods more or less remote; on the nature and number of the former immigrants; and on their action and reaction, in their mutual struggles for life; the relation of organism to organism being, as I have already often remarked, the most important of all relations. Thus the high importance of barriers comes into play by checking migration; as does time for the slow process of modification through natural selection. […] On this principle of inheritance with modification, we can understand how it is that sections of genera, whole genera, and even families are confined to the same areas, as is so commonly and notoriously the case.”

“the natural system is founded on descent with modification […] and […] all true classification is genealogical; […] community of descent is the hidden bond which naturalists have been unconsciously seeking, […] not some unknown plan or creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike.”

September 27, 2015 Posted by | Biology, Books, Botany, Evolutionary biology, Genetics, Geology, Zoology | Leave a comment

Loneliness (II)

Here’s my first post about the book. I’d probably have liked the book better if I hadn’t read the Cognitive Psychology text before this one, as knowledge from that book has made me think a few times in specific contexts that ‘that’s a bit more complicated than you’re making it out to be’ – as I also mentioned in the first post, the book is a bit too popular science-y for my taste. I have been reading other books in the last few days – for example I started reading Darwin a couple of days ago – and so I haven’t really spent much time on this one since my first post; however I have read the first 10 chapters (out of 14) by now, and below I’ve added a few observations from the chapters in the middle.

“In 1958, in a now-legendary, perhaps infamous experiment, the psychologist Harry Harlow of the University of Wisconsin removed newborn rhesus monkeys from their mothers. He presented these newborns instead with two surrogates, one made of wire and one made of cloth […]. Either stand-in could be rigged with a milk bottle, but regardless of which “mother” provided food, infant monkeys spent most of their time clinging to the one made of cloth, running to it immediately when startled or upset. They visited the wire mother only when that surrogate provided food, and then, only for as long as it took to feed.2

Harlow found that monkeys deprived of tactile comfort showed significant delays in their progress, both mentally and emotionally. Those deprived of tactile comfort and also raised in isolation from other monkeys developed additional behavioral aberrations, often severe, from which they never recovered. Even after they had rejoined the troop, these deprived monkeys would sit alone and rock back and forth. They were overly aggressive with their playmates, and later in life they remained unable to form normal attachments. They were, in fact, socially inept — a deficiency that extended down into the most basic biological behaviors. If a socially deprived female was approached by a normal male during the time when hormones made her sexually receptive, she would squat on the floor rather than present her hindquarters. When a previously isolated male approached a receptive female, he would clasp her head instead of her hindquarters, then engage in pelvic thrusts. […] Females raised in isolation became either incompetent or abusive mothers. Even monkeys raised in cages where they could see, smell, and hear — but not touch — other monkeys developed what the neuroscientist Mary Carlson has called an “autistic-like syndrome,” with excessive grooming, self-clasping, social withdrawal, and rocking. As Carlson told a reporter, “You were not really a monkey unless you were raised in an interactive monkey environment.””

In the authors’ coverage of oxytocin’s various roles in human- and animal social interaction they’re laying it on a bit thick in my opinion, and the less than skeptical coverage there leads me to also be somewhat skeptical of their coverage of the topic of mirror neurons, also on account of stuff like this. However I decided to add a little of the coverage of this topic anyway:

“In the 1980s the neurophysiologist Giacomo Rizzolatti began experimenting with macaque monkeys, running electrodes directly into their brains and giving them various objects to handle. The wiring was so precise that it allowed Rizzolatti and his colleagues to identify the specific monkey neurons that were activated at any moment.

When the monkeys carried out an action, such as reaching for a peanut, an area in the premotor cortex called F5 would fire […]. But then the scientists noticed something quite unexpected. When one of the researchers picked up a peanut to hand it to the monkey, those same motor neurons in the monkey’s brain fired. It was as if the animal itself had picked up the peanut. Likewise, the same neurons that fired when the monkey put a peanut in its mouth would fire when the monkey watched a researcher put a peanut in his mouth. […] Rizzolatti gave these structures the name “mirror neurons.” They fire even when the critical point of the action—the person’s hand grasping the peanut, for instance — is hidden from view behind some object, provided that the monkey knows there is a peanut back there. Even simply hearing the action — a peanut shell being cracked — can trigger the response. In all these instances, it is the goal rather than the observed action itself that is being mirrored in the monkey’s neural response. […] Rizzolatti and his colleagues confirmed the role of goals […] by performing brain scans while people watched humans, monkeys, and dogs opening and closing their jaws as if biting. Then they repeated the scans while the study subjects watched humans speak, monkeys smack their lips, and dogs bark.9 When the participants watched any of the three species carrying out the biting motion, the same areas of their brains were activated that activate when humans themselves bite. That is, observing actions that could reasonably be performed by humans, even when the performers were monkeys or dogs, activated the appropriate portion of the mirror neuron system in the human brain. […] the mirror neuron system isn’t simply “monkey see, monkey do,” or even “human see, human do.” It functions to give the observing individual knowledge of the observed action from a “personal” perspective. This “personal” understanding of others’ actions, it appears, promotes our understanding of and resonance with others.”

“In a study of how people monitor social cues, when researchers gave participants facts related to interpersonal or collective social ties presented in a diary format, those who were lonely remembered a greater proportion of this information than did those who were not lonely. Feeling lonely increases a person’s attentiveness to social cues just as being hungry increases a person’s attentiveness to food cues.28 […] They [later] presented images of twenty-four male and female faces depicting four emotions — anger, fear, happiness, and sadness — in two modes, high intensity and low intensity. The faces appeared individually for only one second, during which participants had to judge the emotional timbre. The higher the participants’ level of loneliness, the less accurate their interpretation of the facial expressions.”

“As we try to determine the meaning of events around us, we humans are not particularly good at knowing the causes of our own feelings or behavior. We overestimate our own strengths and underestimate our faults. We overestimate the importance of our contribution to group activities, the pervasiveness of our beliefs within the wider population, and the likelihood that an event we desire will occur.3 A At the same time we underestimate the contribution of others, as well as the likelihood that risks in the world apply to us. Events that unfold unexpectedly are not reasoned about as much as they are rationalized, and the act of remembering itself […] is far more of a biased reconstruction than an accurate recollection of events. […] Amid all the standard distortions we engage in, […] loneliness also sets us apart by making us more fragile, negative, and self-critical. […] One of the distinguishing characteristics of people who have become chronically lonely is the perception that they are doomed to social failure, with little if any control over external circumstances. Awash in pessimism, and feeling the need to protect themselves at every turn, they tend to withdraw, or to rely on the passive forms of coping under stress […] The social strategy that loneliness induces — high in social avoidance, low in social approach — also predicts future loneliness. The cynical worldview induced by loneliness, which consists of alienation and little faith in others, in turn, has been shown to contribute to actual social rejection. This is how feeling lonely creates self-fulfilling prophesies. If you maintain a subjective sense of rejection long enough, over time you are far more likely to confront the actual social rejection that you dread.8 […] In an effort to protect themselves against disappointment and the pain of rejection, the lonely can come up with endless numbers of reasons why a particular effort to reach out will be pointless, or why a particular relationship will never work. This may help explain why, when we’re feeling lonely, we undermine ourselves by assuming that we lack social skills that in fact, we do have available.”

“Because the emotional system that governs human self-preservation was built for a primitive environment and simple, direct dangers, it can be extremely naïve. It is impressionable and prefers shallow, social, and anecdotal information to abstract data. […] A sense of isolation can make [humans] feel unsafe. When we feel unsafe, we do the same thing a hunter-gatherer on the plains of Africa would do — we scan the horizon for threats. And just like a hunter-gatherer hearing an ominous sound in the brush, the lonely person too often assumes the worst, tightens up, and goes into the psychological equivalent of a protective crouch.”

“One might expect that a lonely person, hungry to fulfill unmet social needs, would be very accepting of a new acquaintance, just as a famished person might take pleasure in food that was not perfectly prepared or her favorite item on the menu. However, when people feel lonely they are actually far less accepting of potential new friends than when they feel socially contented.17 Studies show that lonely undergraduates hold more negative perceptions of their roommates than do their nonlonely peers.”

August 30, 2015 Posted by | Biology, Books, Psychology, Zoology | Leave a comment

Wikipedia articles of interest

i. Motte-and-bailey castle (‘good article’).

“A motte-and-bailey castle is a fortification with a wooden or stone keep situated on a raised earthwork called a motte, accompanied by an enclosed courtyard, or bailey, surrounded by a protective ditch and palisade. Relatively easy to build with unskilled, often forced labour, but still militarily formidable, these castles were built across northern Europe from the 10th century onwards, spreading from Normandy and Anjou in France, into the Holy Roman Empire in the 11th century. The Normans introduced the design into England and Wales following their invasion in 1066. Motte-and-bailey castles were adopted in Scotland, Ireland, the Low Countries and Denmark in the 12th and 13th centuries. By the end of the 13th century, the design was largely superseded by alternative forms of fortification, but the earthworks remain a prominent feature in many countries. […]

Various methods were used to build mottes. Where a natural hill could be used, scarping could produce a motte without the need to create an artificial mound, but more commonly much of the motte would have to be constructed by hand.[19] Four methods existed for building a mound and a tower: the mound could either be built first, and a tower placed on top of it; the tower could alternatively be built on the original ground surface and then buried within the mound; the tower could potentially be built on the original ground surface and then partially buried within the mound, the buried part forming a cellar beneath; or the tower could be built first, and the mound added later.[25]

Regardless of the sequencing, artificial mottes had to be built by piling up earth; this work was undertaken by hand, using wooden shovels and hand-barrows, possibly with picks as well in the later periods.[26] Larger mottes took disproportionately more effort to build than their smaller equivalents, because of the volumes of earth involved.[26] The largest mottes in England, such as Thetford, are estimated to have required up to 24,000 man-days of work; smaller ones required perhaps as little as 1,000.[27] […] Taking into account estimates of the likely available manpower during the period, historians estimate that the larger mottes might have taken between four and nine months to build.[29] This contrasted favourably with stone keeps of the period, which typically took up to ten years to build.[30] Very little skilled labour was required to build motte and bailey castles, which made them very attractive propositions if forced peasant labour was available, as was the case after the Norman invasion of England.[19] […]

The type of soil would make a difference to the design of the motte, as clay soils could support a steeper motte, whilst sandier soils meant that a motte would need a more gentle incline.[14] Where available, layers of different sorts of earth, such as clay, gravel and chalk, would be used alternatively to build in strength to the design.[32] Layers of turf could also be added to stabilise the motte as it was built up, or a core of stones placed as the heart of the structure to provide strength.[33] Similar issues applied to the defensive ditches, where designers found that the wider the ditch was dug, the deeper and steeper the sides of the scarp could be, making it more defensive. […]

Although motte-and-bailey castles are the best known castle design, they were not always the most numerous in any given area.[36] A popular alternative was the ringwork castle, involving a palisade being built on top of a raised earth rampart, protected by a ditch. The choice of motte and bailey or ringwork was partially driven by terrain, as mottes were typically built on low ground, and on deeper clay and alluvial soils.[37] Another factor may have been speed, as ringworks were faster to build than mottes.[38] Some ringwork castles were later converted into motte-and-bailey designs, by filling in the centre of the ringwork to produce a flat-topped motte. […]

In England, William invaded from Normandy in 1066, resulting in three phases of castle building in England, around 80% of which were in the motte-and-bailey pattern. […] around 741 motte-and-bailey castles [were built] in England and Wales alone. […] Many motte-and-bailey castles were occupied relatively briefly and in England many were being abandoned by the 12th century, and others neglected and allowed to lapse into disrepair.[96] In the Low Countries and Germany, a similar transition occurred in the 13th and 14th centuries. […] One factor was the introduction of stone into castle building. The earliest stone castles had emerged in the 10th century […] Although wood was a more powerful defensive material than was once thought, stone became increasingly popular for military and symbolic reasons.”

ii. Battle of Midway (featured). Lots of good stuff in there. One aspect I had not been aware of beforehand was that Allied codebreakers also here (I was quite familiar with the works of Turing and others in Bletchley Park) played a key role:

“Admiral Nimitz had one priceless advantage: cryptanalysts had partially broken the Japanese Navy’s JN-25b code.[45] Since the early spring of 1942, the US had been decoding messages stating that there would soon be an operation at objective “AF”. It was not known where “AF” was, but Commander Joseph J. Rochefort and his team at Station HYPO were able to confirm that it was Midway; Captain Wilfred Holmes devised a ruse of telling the base at Midway (by secure undersea cable) to broadcast an uncoded radio message stating that Midway’s water purification system had broken down.[46] Within 24 hours, the code breakers picked up a Japanese message that “AF was short on water.”[47] HYPO was also able to determine the date of the attack as either 4 or 5 June, and to provide Nimitz with a complete IJN order of battle.[48] Japan had a new codebook, but its introduction had been delayed, enabling HYPO to read messages for several crucial days; the new code, which had not yet been cracked, came into use shortly before the attack began, but the important breaks had already been made.[49][nb 8]

As a result, the Americans entered the battle with a very good picture of where, when, and in what strength the Japanese would appear. Nimitz knew that the Japanese had negated their numerical advantage by dividing their ships into four separate task groups, all too widely separated to be able to support each other.[50][nb 9] […] The Japanese, by contrast, remained almost totally unaware of their opponent’s true strength and dispositions even after the battle began.[27] […] Four Japanese aircraft carriers — Akagi, Kaga, Soryu and Hiryu, all part of the six-carrier force that had attacked Pearl Harbor six months earlier — and a heavy cruiser were sunk at a cost of the carrier Yorktown and a destroyer. After Midway and the exhausting attrition of the Solomon Islands campaign, Japan’s capacity to replace its losses in materiel (particularly aircraft carriers) and men (especially well-trained pilots) rapidly became insufficient to cope with mounting casualties, while the United States’ massive industrial capabilities made American losses far easier to bear. […] The Battle of Midway has often been called “the turning point of the Pacific”.[140] However, the Japanese continued to try to secure more strategic territory in the South Pacific, and the U.S. did not move from a state of naval parity to one of increasing supremacy until after several more months of hard combat.[141] Thus, although Midway was the Allies’ first major victory against the Japanese, it did not radically change the course of the war. Rather, it was the cumulative effects of the battles of Coral Sea and Midway that reduced Japan’s ability to undertake major offensives.[9]

One thing which really strikes you (well, struck me) when reading this stuff is how incredibly capital-intensive the war at sea really was; this was one of the most important sea battles of the Second World War, yet the total Japanese death toll at Midway was just 3,057. To put that number into perspective, it is significantly smaller than the average number of people killed each day in Stalingrad (according to one estimate, the Soviets alone suffered 478,741 killed or missing during those roughly 5 months (~150 days), which comes out at roughly 3000/day).

iii. History of time-keeping devices (featured). ‘Exactly what it says on the tin’, as they’d say on TV Tropes.

Clepsydra-Diagram-Fancy
It took a long time to get from where we were to where we are today; the horologists of the past faced a lot of problems you’ve most likely never even thought about. What do you do for example do if your ingenious water clock has trouble keeping time because variation in water temperature causes issues? Well, you use mercury instead of water, of course! (“Since Yi Xing’s clock was a water clock, it was affected by temperature variations. That problem was solved in 976 by Zhang Sixun by replacing the water with mercury, which remains liquid down to −39 °C (−38 °F).”).

iv. Microbial metabolism.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe’s ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles. […]

All microbial metabolisms can be arranged according to three principles:

1. How the organism obtains carbon for synthesising cell mass:

2. How the organism obtains reducing equivalents used either in energy conservation or in biosynthetic reactions:

3. How the organism obtains energy for living and growing:

In practice, these terms are almost freely combined. […] Most microbes are heterotrophic (more precisely chemoorganoheterotrophic), using organic compounds as both carbon and energy sources. […] Heterotrophic microbes are extremely abundant in nature and are responsible for the breakdown of large organic polymers such as cellulose, chitin or lignin which are generally indigestible to larger animals. Generally, the breakdown of large polymers to carbon dioxide (mineralization) requires several different organisms, with one breaking down the polymer into its constituent monomers, one able to use the monomers and excreting simpler waste compounds as by-products, and one able to use the excreted wastes. There are many variations on this theme, as different organisms are able to degrade different polymers and secrete different waste products. […]

Biochemically, prokaryotic heterotrophic metabolism is much more versatile than that of eukaryotic organisms, although many prokaryotes share the most basic metabolic models with eukaryotes, e. g. using glycolysis (also called EMP pathway) for sugar metabolism and the citric acid cycle to degrade acetate, producing energy in the form of ATP and reducing power in the form of NADH or quinols. These basic pathways are well conserved because they are also involved in biosynthesis of many conserved building blocks needed for cell growth (sometimes in reverse direction). However, many bacteria and archaea utilize alternative metabolic pathways other than glycolysis and the citric acid cycle. […] The metabolic diversity and ability of prokaryotes to use a large variety of organic compounds arises from the much deeper evolutionary history and diversity of prokaryotes, as compared to eukaryotes. […]

Many microbes (phototrophs) are capable of using light as a source of energy to produce ATP and organic compounds such as carbohydrates, lipids, and proteins. Of these, algae are particularly significant because they are oxygenic, using water as an electron donor for electron transfer during photosynthesis.[11] Phototrophic bacteria are found in the phyla Cyanobacteria, Chlorobi, Proteobacteria, Chloroflexi, and Firmicutes.[12] Along with plants these microbes are responsible for all biological generation of oxygen gas on Earth. […] As befits the large diversity of photosynthetic bacteria, there are many different mechanisms by which light is converted into energy for metabolism. All photosynthetic organisms locate their photosynthetic reaction centers within a membrane, which may be invaginations of the cytoplasmic membrane (Proteobacteria), thylakoid membranes (Cyanobacteria), specialized antenna structures called chlorosomes (Green sulfur and non-sulfur bacteria), or the cytoplasmic membrane itself (heliobacteria). Different photosynthetic bacteria also contain different photosynthetic pigments, such as chlorophylls and carotenoids, allowing them to take advantage of different portions of the electromagnetic spectrum and thereby inhabit different niches. Some groups of organisms contain more specialized light-harvesting structures (e.g. phycobilisomes in Cyanobacteria and chlorosomes in Green sulfur and non-sulfur bacteria), allowing for increased efficiency in light utilization. […]

Most photosynthetic microbes are autotrophic, fixing carbon dioxide via the Calvin cycle. Some photosynthetic bacteria (e.g. Chloroflexus) are photoheterotrophs, meaning that they use organic carbon compounds as a carbon source for growth. Some photosynthetic organisms also fix nitrogen […] Nitrogen is an element required for growth by all biological systems. While extremely common (80% by volume) in the atmosphere, dinitrogen gas (N2) is generally biologically inaccessible due to its high activation energy. Throughout all of nature, only specialized bacteria and Archaea are capable of nitrogen fixation, converting dinitrogen gas into ammonia (NH3), which is easily assimilated by all organisms.[14] These prokaryotes, therefore, are very important ecologically and are often essential for the survival of entire ecosystems. This is especially true in the ocean, where nitrogen-fixing cyanobacteria are often the only sources of fixed nitrogen, and in soils, where specialized symbioses exist between legumes and their nitrogen-fixing partners to provide the nitrogen needed by these plants for growth.

Nitrogen fixation can be found distributed throughout nearly all bacterial lineages and physiological classes but is not a universal property. Because the enzyme nitrogenase, responsible for nitrogen fixation, is very sensitive to oxygen which will inhibit it irreversibly, all nitrogen-fixing organisms must possess some mechanism to keep the concentration of oxygen low. […] The production and activity of nitrogenases is very highly regulated, both because nitrogen fixation is an extremely energetically expensive process (16–24 ATP are used per N2 fixed) and due to the extreme sensitivity of the nitrogenase to oxygen.” (A lot of the stuff above was of course for me either review or closely related to stuff I’ve already read in the coverage provided in Beer et al., a book I’ve talked about before here on the blog).

v. Uranium (featured). It’s hard to know what to include here as the article has a lot of stuff, but I found this part in particular, well, interesting:

“During the Cold War between the Soviet Union and the United States, huge stockpiles of uranium were amassed and tens of thousands of nuclear weapons were created using enriched uranium and plutonium made from uranium. Since the break-up of the Soviet Union in 1991, an estimated 600 short tons (540 metric tons) of highly enriched weapons grade uranium (enough to make 40,000 nuclear warheads) have been stored in often inadequately guarded facilities in the Russian Federation and several other former Soviet states.[12] Police in Asia, Europe, and South America on at least 16 occasions from 1993 to 2005 have intercepted shipments of smuggled bomb-grade uranium or plutonium, most of which was from ex-Soviet sources.[12] From 1993 to 2005 the Material Protection, Control, and Accounting Program, operated by the federal government of the United States, spent approximately US $550 million to help safeguard uranium and plutonium stockpiles in Russia.[12] This money was used for improvements and security enhancements at research and storage facilities. Scientific American reported in February 2006 that in some of the facilities security consisted of chain link fences which were in severe states of disrepair. According to an interview from the article, one facility had been storing samples of enriched (weapons grade) uranium in a broom closet before the improvement project; another had been keeping track of its stock of nuclear warheads using index cards kept in a shoe box.[45]

Some other observations from the article below:

“Uranium is a naturally occurring element that can be found in low levels within all rock, soil, and water. Uranium is the 51st element in order of abundance in the Earth’s crust. Uranium is also the highest-numbered element to be found naturally in significant quantities on Earth and is almost always found combined with other elements.[10] Along with all elements having atomic weights higher than that of iron, it is only naturally formed in supernovae.[46] The decay of uranium, thorium, and potassium-40 in the Earth’s mantle is thought to be the main source of heat[47][48] that keeps the outer core liquid and drives mantle convection, which in turn drives plate tectonics. […]

Natural uranium consists of three major isotopes: uranium-238 (99.28% natural abundance), uranium-235 (0.71%), and uranium-234 (0.0054%). […] Uranium-238 is the most stable isotope of uranium, with a half-life of about 4.468×109 years, roughly the age of the Earth. Uranium-235 has a half-life of about 7.13×108 years, and uranium-234 has a half-life of about 2.48×105 years.[82] For natural uranium, about 49% of its alpha rays are emitted by each of 238U atom, and also 49% by 234U (since the latter is formed from the former) and about 2.0% of them by the 235U. When the Earth was young, probably about one-fifth of its uranium was uranium-235, but the percentage of 234U was probably much lower than this. […]

Worldwide production of U3O8 (yellowcake) in 2013 amounted to 70,015 tonnes, of which 22,451 t (32%) was mined in Kazakhstan. Other important uranium mining countries are Canada (9,331 t), Australia (6,350 t), Niger (4,518 t), Namibia (4,323 t) and Russia (3,135 t).[55] […] Australia has 31% of the world’s known uranium ore reserves[61] and the world’s largest single uranium deposit, located at the Olympic Dam Mine in South Australia.[62] There is a significant reserve of uranium in Bakouma a sub-prefecture in the prefecture of Mbomou in Central African Republic. […] Uranium deposits seem to be log-normal distributed. There is a 300-fold increase in the amount of uranium recoverable for each tenfold decrease in ore grade.[75] In other words, there is little high grade ore and proportionately much more low grade ore available.”

vi. Radiocarbon dating (featured).

Radiocarbon dating (also referred to as carbon dating or carbon-14 dating) is a method of determining the age of an object containing organic material by using the properties of radiocarbon (14C), a radioactive isotope of carbon. The method was invented by Willard Libby in the late 1940s and soon became a standard tool for archaeologists. Libby received the Nobel Prize for his work in 1960. The radiocarbon dating method is based on the fact that radiocarbon is constantly being created in the atmosphere by the interaction of cosmic rays with atmospheric nitrogen. The resulting radiocarbon combines with atmospheric oxygen to form radioactive carbon dioxide, which is incorporated into plants by photosynthesis; animals then acquire 14C by eating the plants. When the animal or plant dies, it stops exchanging carbon with its environment, and from that point onwards the amount of 14C it contains begins to reduce as the 14C undergoes radioactive decay. Measuring the amount of 14C in a sample from a dead plant or animal such as piece of wood or a fragment of bone provides information that can be used to calculate when the animal or plant died. The older a sample is, the less 14C there is to be detected, and because the half-life of 14C (the period of time after which half of a given sample will have decayed) is about 5,730 years, the oldest dates that can be reliably measured by radiocarbon dating are around 50,000 years ago, although special preparation methods occasionally permit dating of older samples.

The idea behind radiocarbon dating is straightforward, but years of work were required to develop the technique to the point where accurate dates could be obtained. […]

The development of radiocarbon dating has had a profound impact on archaeology. In addition to permitting more accurate dating within archaeological sites than did previous methods, it allows comparison of dates of events across great distances. Histories of archaeology often refer to its impact as the “radiocarbon revolution”.”

I’ve read about these topics before in a textbook setting (e.g. here), but/and I should note that the article provides quite detailed coverage and I think most people will encounter some new information by having a look at it even if they’re superficially familiar with this topic. The article has a lot of stuff about e.g. ‘what you need to correct for’, which some of you might find interesting.

vii. Raccoon (featured). One interesting observation from the article:

“One aspect of raccoon behavior is so well known that it gives the animal part of its scientific name, Procyon lotor; “lotor” is neo-Latin for “washer”. In the wild, raccoons often dabble for underwater food near the shore-line. They then often pick up the food item with their front paws to examine it and rub the item, sometimes to remove unwanted parts. This gives the appearance of the raccoon “washing” the food. The tactile sensitivity of raccoons’ paws is increased if this rubbing action is performed underwater, since the water softens the hard layer covering the paws.[126] However, the behavior observed in captive raccoons in which they carry their food to water to “wash” or douse it before eating has not been observed in the wild.[127] Naturalist Georges-Louis Leclerc, Comte de Buffon, believed that raccoons do not have adequate saliva production to moisten food thereby necessitating dousing, but this hypothesis is now considered to be incorrect.[128] Captive raccoons douse their food more frequently when a watering hole with a layout similar to a stream is not farther away than 3 m (10 ft).[129] The widely accepted theory is that dousing in captive raccoons is a fixed action pattern from the dabbling behavior performed when foraging at shores for aquatic foods.[130] This is supported by the observation that aquatic foods are doused more frequently. Cleaning dirty food does not seem to be a reason for “washing”.[129] Experts have cast doubt on the veracity of observations of wild raccoons dousing food.[131]

And here’s another interesting set of observations:

“In Germany—where the racoon is called the Waschbär (literally, “wash-bear” or “washing bear”) due to its habit of “dousing” food in water—two pairs of pet raccoons were released into the German countryside at the Edersee reservoir in the north of Hesse in April 1934 by a forester upon request of their owner, a poultry farmer.[186] He released them two weeks before receiving permission from the Prussian hunting office to “enrich the fauna.” [187] Several prior attempts to introduce raccoons in Germany were not successful.[188] A second population was established in eastern Germany in 1945 when 25 raccoons escaped from a fur farm at Wolfshagen, east of Berlin, after an air strike. The two populations are parasitologically distinguishable: 70% of the raccoons of the Hessian population are infected with the roundworm Baylisascaris procyonis, but none of the Brandenburgian population has the parasite.[189] The estimated number of raccoons was 285 animals in the Hessian region in 1956, over 20,000 animals in the Hessian region in 1970 and between 200,000 and 400,000 animals in the whole of Germany in 2008.[158][190] By 2012 it was estimated that Germany now had more than a million raccoons.[191]

June 14, 2015 Posted by | Archaeology, Biology, Botany, Engineering, Geology, History, Microbiology, Physics, Wikipedia, Zoology | 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

Stuff

Sorry for the infrequent updates. I realized blogging Wodehouse books takes more time than I’d imagined, so posting this sort of stuff is probably a better idea.

i. Dunkirk evacuation (wikipedia ‘good article’). Fascinating article, as are a few of the related ones which I’ve also been reading (e.g. Operation Ariel).

“On the first day of the evacuation, only 7,669 men were evacuated, but by the end of the eighth day, a total of 338,226 soldiers had been rescued by a hastily assembled fleet of over 800 boats. Many of the troops were able to embark from the harbour’s protective mole onto 39 British destroyers and other large ships, while others had to wade out from the beaches, waiting for hours in the shoulder-deep water. Some were ferried from the beaches to the larger ships by the famous little ships of Dunkirk, a flotilla of hundreds of merchant marine boats, fishing boats, pleasure craft, and lifeboats called into service for the emergency. The BEF lost 68,000 soldiers during the French campaign and had to abandon nearly all of their tanks, vehicles, and other equipment.”

One way to make sense of the scale of the operations here is to compare them with the naval activities on D-day four years later. The British evacuated more people from France during three consecutive days in 1940 (30th and 31st of May, and 1st of June) than the Allies (Americans and British combined) landed on D-day four years later, and the British evacuated roughly as many people on the 31st of May (68,014) as they landed by sea on D-day (75,215). Here’s a part of the story I did not know:

“Three British divisions and a host of logistic and labour troops were cut off to the south of the Somme by the German “race to the sea”. At the end of May, a further two divisions began moving to France with the hope of establishing a Second BEF. The majority of the 51st (Highland) Division was forced to surrender on 12 June, but almost 192,000 Allied personnel, 144,000 of them British, were evacuated through various French ports from 15–25 June under the codename Operation Ariel.[104] […] More than 100,000 evacuated French troops were quickly and efficiently shuttled to camps in various parts of southwestern England, where they were temporarily lodged before being repatriated.[106] British ships ferried French troops to Brest, Cherbourg, and other ports in Normandy and Brittany, although only about half of the repatriated troops were deployed against the Germans before the surrender of France. For many French soldiers, the Dunkirk evacuation represented only a few weeks’ delay before being killed or captured by the German army after their return to France.[107]

ii. A pretty awesome display by the current world chess champion:

If you feel the same way I do about Maurice Ashley, you’ll probably want to skip the first few minutes of this video. Don’t miss the games, though – this is great stuff. Do keep in mind when watching this video that the clock is a really important part of this event; other players in the past have played a lot more people at the same time while blindfolded than Carlsen does here – “Although not a full-time chess professional [Najdorf] was one of the world’s leading chess players in the 1950s and 1960s and he excelled in playing blindfold chess: he broke the world record twice, by playing blindfold 40 games in Rosario, 1943,[8] and 45 in São Paulo, 1947, becoming the world blindfold chess champion” (link) – but a game clock changes things a lot. A few comments and discussion here.
In very slightly related news, I recently got in my first win against a grandmaster in a bullet game on the ICC.

iii. Gastric-brooding frog.

Rheobatrachus_silus

“The genus was unique because it contained the only two known frog species that incubated the prejuvenile stages of their offspring in the stomach of the mother.[3] […] What makes these frogs unique among all frog species is their form of parental care. Following external fertilization by the male, the female would take the eggs or embryos into her mouth and swallow them.[19] […] Eggs found in females measured up to 5.1 mm in diameter and had large yolk supplies. These large supplies are common among species that live entirely off yolk during their development. Most female frogs had around 40 ripe eggs, almost double that of the number of juveniles ever found in the stomach (21–26). This means one of two things, that the female fails to swallow all the eggs or the first few eggs to be swallowed are digested. […] During the period that the offspring were present in the stomach the frog would not eat. […] The birth process was widely spaced and may have occurred over a period of as long as a week. However, if disturbed the female may regurgitate all the young frogs in a single act of propulsive vomiting.”

Fascinating creatures.. Unfortunately they’re no longer around (they’re classified as extinct).

iv. I’m sort of conflicted about what to think about this:

“Epidemiological studies show that patients with type-2-diabetes (T2DM) and individuals with a diabetes-independent elevation in blood glucose have an increased risk for developing dementia, specifically dementia due to Alzheimer’s disease (AD). These observations suggest that abnormal glucose metabolism likely plays a role in some aspects of AD pathogenesis, leading us to investigate the link between aberrant glucose metabolism, T2DM, and AD in murine models. […] Recent epidemiological studies demonstrate that individuals with type-2 diabetes (T2DM) are 2–4 times more likely to develop AD (35), individuals with elevated blood glucose levels are at an increased risk to develop dementia (5), and those with elevated blood glucose levels have a more rapid conversion from mild cognitive impairment (MCI) to AD (6), suggesting that disrupted glucose homeostasis could play a […] causal role in AD pathogenesis. Although several prominent features of T2DM, including increased insulin resistance and decreased insulin production, are at the forefront of AD research (710), questions regarding the effects of elevated blood glucose independent of insulin resistance on AD pathology remain largely unexplored. In order to investigate the potential role of glucose metabolism in AD, we combined glucose clamps and in vivo microdialysis as a method to measure changes in brain metabolites in awake, freely moving mice during a hyperglycemic challenge. Our findings suggest that acute hyperglycemia raises interstitial fluid (ISF) Aβ levels by altering neuronal activity, which increases Aβ production. […] Since extracellular Aβ, and subsequently tau, aggregate in a concentration-dependent manner during the preclinical period of AD while individuals are cognitively normal (27), our findings suggest that repeated episodes of transient hyperglycemia, such as those found in T2DM, could both initiate and accelerate plaque accumulation. Thus, the correlation between hyperglycemia and increased ISF Aβ provides one potential explanation for the increased risk of AD and dementia in T2DM patients or individuals with elevated blood glucose levels. In addition, our work suggests that KATP channels within the hippocampus act as metabolic sensors and couple alterations in glucose concentrations with changes in electrical activity and extracellular Aβ levels. Not only does this offer one mechanistic explanation for the epidemiological link between T2DM and AD, but it also provides a potential therapeutic target for AD. Given that FDA-approved drugs already exist for the modulation of KATP channels and previous work demonstrates the benefits of sulfonylureas for treating animal models of AD (26), the identification of these channels as a link between hyperglycemia and AD pathology creates an avenue for translational research in AD.”

Why am I conflicted? Well, on the one hand it’s nice to know that they’re making progress in terms of figuring out why people get Alzheimer’s and potential therapeutic targets are being identified. On the other hand this – “our findings suggest that repeated episodes of transient hyperglycemia […] could both initiate and accelerate plaque accumulation” – is bad news if you’re a type 1 diabetic (I’d much rather have them identify risk factors to which I’m not exposed).

v. I recently noticed that Khan Academy has put up some videos about diabetes. From the few ones I’ve had a look at they don’t seem to contain much stuff I don’t already know so I’m not sure I’ll explore this playlist in any more detail, but I figured I might as well share a few of the videos here; the first one is about the pathophysiology of type 1 diabetes and the second one’s about diabetic nephropathy (kidney disease):

vi. On Being the Right Size, by J. B. S. Haldane. A neat little text. A few quotes:

“To the mouse and any smaller animal [gravity] presents practically no dangers. You can drop a mouse down a thousand-yard mine shaft; and, on arriving at the bottom, it gets a slight shock and walks away, provided that the ground is fairly soft. A rat is killed, a man is broken, a horse splashes. For the resistance presented to movement by the air is proportional to the surface of the moving object. Divide an animal’s length, breadth, and height each by ten; its weight is reduced to a thousandth, but its surface only to a hundredth. So the resistance to falling in the case of the small animal is relatively ten times greater than the driving force.

An insect, therefore, is not afraid of gravity; it can fall without danger, and can cling to the ceiling with remarkably little trouble. It can go in for elegant and fantastic forms of support like that of the daddy-longlegs. But there is a force which is as formidable to an insect as gravitation to a mammal. This is surface tension. A man coming out of a bath carries with him a film of water of about one-fiftieth of an inch in thickness. This weighs roughly a pound. A wet mouse has to carry about its own weight of water. A wet fly has to lift many times its own weight and, as everyone knows, a fly once wetted by water or any other liquid is in a very serious position indeed. An insect going for a drink is in as great danger as a man leaning out over a precipice in search of food. If it once falls into the grip of the surface tension of the water—that is to say, gets wet—it is likely to remain so until it drowns. A few insects, such as water-beetles, contrive to be unwettable; the majority keep well away from their drink by means of a long proboscis. […]

It is an elementary principle of aeronautics that the minimum speed needed to keep an aeroplane of a given shape in the air varies as the square root of its length. If its linear dimensions are increased four times, it must fly twice as fast. Now the power needed for the minimum speed increases more rapidly than the weight of the machine. So the larger aeroplane, which weighs sixty-four times as much as the smaller, needs one hundred and twenty-eight times its horsepower to keep up. Applying the same principle to the birds, we find that the limit to their size is soon reached. An angel whose muscles developed no more power weight for weight than those of an eagle or a pigeon would require a breast projecting for about four feet to house the muscles engaged in working its wings, while to economize in weight, its legs would have to be reduced to mere stilts. Actually a large bird such as an eagle or kite does not keep in the air mainly by moving its wings. It is generally to be seen soaring, that is to say balanced on a rising column of air. And even soaring becomes more and more difficult with increasing size. Were this not the case eagles might be as large as tigers and as formidable to man as hostile aeroplanes.

But it is time that we pass to some of the advantages of size. One of the most obvious is that it enables one to keep warm. All warmblooded animals at rest lose the same amount of heat from a unit area of skin, for which purpose they need a food-supply proportional to their surface and not to their weight. Five thousand mice weigh as much as a man. Their combined surface and food or oxygen consumption are about seventeen times a man’s. In fact a mouse eats about one quarter its own weight of food every day, which is mainly used in keeping it warm. For the same reason small animals cannot live in cold countries. In the arctic regions there are no reptiles or amphibians, and no small mammals. The smallest mammal in Spitzbergen is the fox. The small birds fly away in winter, while the insects die, though their eggs can survive six months or more of frost. The most successful mammals are bears, seals, and walruses.” [I think he’s a bit too categorical in his statements here and this topic is more contested today than it probably was when he wrote his text – see wikipedia’s coverage of Bergmann’s rule].

May 26, 2015 Posted by | Biology, Chess, Diabetes, Engineering, Epidemiology, History, Khan Academy, Lectures, Medicine, Nephrology, Neurology, Wikipedia, 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, Engineering, Geography, History, Mathematics, Psychology, Wikipedia, Zoology | Leave a comment

Mammoths, Sabertooths, and Hominids: 65 Million Years of Mammalian Evolution in Europe (3)

Here’s a previous post in the series. In this post I’ll pick up roughly where I left off in my last post, around the time of the ‘Grande Coupure‘ roughly 34 million years ago.

“The extinction of the arboreal primates and the reduction or extinction of several browsing groups […] are strong evidence for the retreat of the forests during the early Oligocene and their replacement by open woodlands or even drier biotopes. […] Among the most distinctive species to enter Europe after the “Grande Coupure” were the first true rhinoceroses [which] achieved a high diversity and were going to characterize the mammalian faunas of Europe for millions of years, until the extinction of the last woolly rhinos during the late Pleistocene. […] the evolution of this group produced the largest terrestrial mammals of any time. The giant Paraceratherium […] was 6 m tall at the shoulders and had a 1.5-m-long skull […]. The males of this animal weighed around 15 tons, while the females were somewhat smaller, about 10 tons.” [Wikipedia has a featured article about these things here].

“One of the most significant features of the early Oligocene small-mammal communities was the first entry of lagomorphs into Europe. The lagomorphs — that is, the order of mammals that includes today’s hares and rabbits — originated very early on the Asian continent and from there colonized North America. The presence of the Turgai Strait prevented this group from entering Europe during the Eocene. […] the most characteristic immigrants during the early Oligocene were the cricetids of the genus Atavocricetodon. The cricetids are today represented in Europe by hamsters, reduced to three or four species […] These cricetids are typical inhabitants of the cold steppes of eastern Europe and Central Asia, and their limited representation in today’s European ecosystems does not reflect their importance in the history of the Cenozoic mammalian faunas of Eurasia. After its first entry following the “Grande Coupure,” this group experienced extraordinary success, diversifying into several genera and species. Even more significantly, the cricetids gave rise to the rodent groups that were going to be dominant during the Pliocene and Pleistocene — that is, the murids (the family of mice and rats) and arvicolids (the family of voles). […] In addition, new carnivore families, like the nimravids, appeared […]. The nimravids were once regarded as true felids (the family that includes today’s big and small cats) because of their similar dental and cranial adaptations. […] one of the more distinctive attributes of the nimravids was their long, laterally flattened upper canines, which were similar to those of the Miocene and Pliocene saber-toothed cats […]. However, most of these features have proved to be the result of a similar adaptation to hypercarnivorism, and the nimravids are now placed in a separate family of early carnivores whose evolution paralleled that of the large saber-toothed felids.” [Actually some of the nimravids were in some sense ‘even more sabertoothed’ than the (‘true’) saber-toothed cats which came later: “Although [the nimravid] Eusmilus bidentatus was no larger than a modern lynx, the adaptations for gape seen on its skull and mandible are more advanced than in any of the felid sabertooths of the European Pliocene and Pleistocene.”]

“About 30 million years ago, a new glacial phase began, and for 4 million years Antarctica was subjected to multiple glaciation episodes. The global sea level experienced the largest lowering in the whole Cenozoic, dropping by about 150 m […]. A possible explanation for this new glacial event lies in the final opening of the Drake Passage between Antarctica and South America, which led to the completion of a fully circumpolar circulation and impeded any heat exchange between Antarctic waters and the warmer equatorial waters. A second, perhaps complementary cause for this glacial pulse is probably related to the final opening of the seaway between Greenland and Norway. The cold Arctic waters, largely isolated since the Mesozoic, spread at this time into the North Atlantic. The main effect of this cooling was a new extension of the dry landscapes on the European and western Asian lands. For instance, we know from pollen evidence that a desert vegetation was dominant in the Levant during the late Oligocene and earliest Miocene […] This glacial event led to the extinction of several forms that had persisted from the Eocene”.

“Among the carnivores, the late Oligocene saw the decline and local extinction of the large nimravids [Key word: local. They came back to Europe later during the early Miocene, and “the nimravids maintained a remarkable stability throughout the Miocene, probably in relation to a low speciation rate”]. In contrast, the group of archaic feloids that had arisen during the early Oligocene […] continued its evolution into the late Oligocene and diversified into a number of genera […] The other group of large carnivores that spread during the late Oligocene were the “bear-dog” amphicyonids, which from that time on became quite diverse, with many different ecological adaptations. […] The late Oligocene saw, in addition to the bearlike amphicyonids, the spread of the first true ursids […]. The members of this genus did not have the massive body dimensions of today’s bears but were medium-size omnivores […] Another group of carnivores that spread successfully during the late Oligocene were the mustelids, the family that includes today’s martens, badgers, skunks, and otters. […] In contrast to these successes, the creodonts of the genus Hyaenodon, which had survived all periods of crisis since the Eocene, declined during the late Oligocene. The last Hyaenodon in Europe was recorded at the end of the Oligocene […], and did not survive into the Miocene. This was the end in Europe of a long-lived group of successful carnivorans that had filled the large-predator guild for millions of years. However, as with other Oligocene groups, […] the hyaenodonts persisted in Africa and, from there, made a short incursion into Europe during the early Miocene”.

“After a gradual warming during the late Oligocene, global temperatures reached a climatic optimum during the early Miocene […] Shallow seas covered several nearshore areas in Europe […] as a consequence of a general sea-level rise. A broad connection was established between the Indian Ocean and both the Mediterranean and Paratethys Seas […] Widespread warm-water faunas including tropical fishes and nautiloids have been found, indicating conditions similar to those of the present-day Guinea Gulf, with mean surface-water temperatures around 25 to 27°C. Important reef formations bounded most of the shallow-water Mediterranean basins. […] Reef-building corals that today inhabit the Great Barrier Reef within a temperature range of 19 to 28°C became well established on North Island, New Zealand […] The early Miocene climate was warm and humid, indicating tropical conditions […]. Rich, extensive woodlands with varied kinds of plants developed in different parts of southern Europe […] The climatic optimum of the early Miocene also led to a maximum development of mangroves. These subtropical floras extended as far north as eastern Siberia and Kamchatka”.

“Despite the climatic stability of the early Miocene, an important tectonic event disrupted the evolution of the Eurasian faunas during this epoch. About 19 million years ago, the graben system along the Red Sea Fault, active in the south since the late Oligocene, opened further […] Consequently, the Arabian plate rotated counterclockwise and collided with the Anatolian plate. The marine gateway from the Mediterranean toward the Indo-Pacific closed, and a continental migration bridge (known as the Gomphothere Bridge) between Eurasia and Africa came into existence. This event had enormous consequences for the further evolution of the terrestrial faunas of Eurasia and Africa. Since the late Eocene, Africa had evolved in isolation, developing its own autochthonous fauna. Part of this fauna consisted of a number of endemic Oligocene survivors, such as anthracotheres, hyaenodonts, and primates, for which Africa had acted as a refuge […] The first evidence of an African–Eurasian exchange was the presence of the anthracothere Brachyodus in a number of early Miocene sites in Europe […] a second dispersal event from Africa, that of the gomphothere and deinothere proboscideans, had much more lasting effects. […] Today we can easily identify any proboscidean by its long proboscis and tusks. However, the primitive proboscideans from the African Eocene had a completely different appearance and are hardly recognizable as the ancestors of today’s elephants. Instead, they were hippolike semiamphibious ungulates with massive, elongated bodies supported by rather short legs. […] The first proboscideans entering Europe were the so-called gomphotheres […] which dispersed worldwide during the early Miocene from Africa to Europe, Asia, and North America […]. Gomphotherium was the size of an Indian elephant, about 2.5 m high at the withers. Its skull and dentition, however, were different from those of modern elephants. Gomphotherium’s skull was long […] and displayed not two but four tusks, one pair in the upper jaw and the other pair at the end of the lower jaw. […] Shortly after the entry of Gomphotherium and Zygolophodon [a second group of mastodons], a third proboscidean group, the deinotheres, successfully settled in Eurasia. Unlike the previous genera, the deinotheres were not elephantoids but represented a different, now totally extinct kind of proboscidean.”

“The dispersal of not only the African proboscideans but also many eastern immigrants contributed to a significant increase in the diversity of the impoverished early Miocene terrestrial biotas. The entry of this set of immigrants probably led to the extinction of a number of late Oligocene and early Miocene survivors, such as tapirids, anthracotherids, and primitive suids [pigs] and moschoids. In addition to the events that affected the Middle East area, sea-level fluctuations enabled short-lived mammal exchanges across the Bering Strait between Eurasia and North America, permitting the arrival of the browsing horse Anchitherium in Eurasia […] Widely used for biostragraphic purposes, the dispersal of Anchitherium was the first of a number of similar isolated events undergone by North American equids that entered Eurasia and rapidly spread on this continental area.”

“A new marine transgression, known as the Langhian Transgression, characterized the beginning of the middle Miocene, affecting the circum-Mediterranean area. Consequently, the seaway to the Indo-Pacific reopened for a short time, restoring the circum-equatorial warm-water circulation. […] tropical conditions became established as far north as Poland in marine coastal and open-sea waters. After the optimal conditions of the early Miocene, the middle Miocene was a period of global oceanic reorganization, representing a major change in the climatic evolution of the Cenozoic. Before this process began, high-latitude paleoclimatic conditions were generally warm although oscillating, but they rapidly cooled thereafter, leading to an abrupt high-latitude cooling event at about 14.5 million years ago […] Increased production of cold, deep Antarctic waters caused the extinction of several oceanic benthic foraminifers that had persisted from the late Oligocene–early Miocene and promoted a significant evolutionary turnover of the oceanic assemblages from about 16 to 14 million years ago […] This middle Miocene cooling was associated with a major growth of the Eastern Antarctic Ice Sheets (EAIS) […] Middle Miocene polar cooling and east Antarctic ice growth had severe effects on middle- to low-latitude terrestrial environments. There was a climatic trend to cooler winters and decreased summer rainfall. Seasonal, summer-drought-adapted schlerophyllous vegetation progressively evolved and spread geographically during the Miocene, replacing the laurophyllous evergreen forests that were adapted to moist, subtropical and tropical conditions with temperate winters and abundant summer rainfalls […] These effects were clearly seen in a wide area to the south of the Paratethys Sea, extending from eastern Europe to western Asia. According to the ideas of the American paleontologist Ray Bernor, this region, known as the Greek-Iranian (or sub-Paratethyan) Province, acted as a woodland environmental “hub” for a corridor of open habitats that extended from northwestern Africa eastward across Arabia into Afghanistan, north into the eastern Mediterranean area, and northeast into northern China. The Greek-Iranian Province records the first evidence of open woodlands in which a number of large, progressive open-country mammals—such as hyaenids, thick-enameled hominoids, bovids, and giraffids — diversified and dispersed into eastern Africa and southwestern Asia […] the peculiar biotope developed in the Greek-Iranian Province acted as the background from which the African savannas evolved during the Pliocene and Pleistocene.”

“The most outstanding effect of the Middle Miocene Event is seen among the herbivorous community, which showed a trend toward developing larger body sizes, more-hypsodont teeth, and more-elongated distal limb segments […]. Increasing body size in herbivores is related to a higher ingestion of fibrous and low-quality vegetation. Browsers and grazers have to be large because they need long stomachs and intestines to process a large quantity of low-energy food (this is why they have to eat almost continuously). Because of the mechanism of rumination, ruminants are the only herbivores that can escape this rule and subsist at small sizes. Increasing hypsodonty and high-crowned teeth are directly related to the ingestion of more-abrasive vegetation […] Finally, the elongation of the distal limb segments is related to increasing cursoriality. The origin of cursoriality can be linked to the expansion of the home range in open, low-productive habitats. […] At the taxonomic level, this habitat change in the low latitudes involved the rapid adaptive radiation of woodland ruminants (bovids and giraffids). […] Gazelles dispersed into Europe at this time from their possible Afro-Arabian origins […] Not only gazelles but also the giraffids experienced a wide adaptive radiation into Africa after their dispersal from Asia. […] Among the suids [pigs], the listriodontines evolved in a peculiar way in northern Africa, leading to giant forms such as Kubanochoerus, with a weight of about 500 kg, which in some species may have reached 800 kg.”

March 8, 2015 Posted by | Biology, Books, climate, Evolutionary biology, Geology, Paleontology, Zoology | Leave a comment

Wikipedia articles of interest

i. Invasion of Poland. I recently realized I had no idea e.g. how long it took for the Germans and Soviets to defeat Poland during WW2 (the answer is 1 month and five days). The Germans attacked more than two weeks before the Soviets did. The article has lots of links, like most articles about such topics on wikipedia. Incidentally the question of why France and Britain applied a double standard and only declared war on Germany, and not the Soviet Union, is discussed in much detail in the links provided by u/OldWorldGlory here.

ii. Huaynaputina. From the article:

“A few days before the eruption, someone reported booming noise from the volcano and fog-like gas being emitted from its crater. The locals scrambled to appease the volcano, preparing girls, pets, and flowers for sacrifice.”

This makes sense – what else would one do in a situation like that? Finding a few virgins, dogs and flowers seems like the sensible approach – yes, you have to love humans and how they always react in sensible ways to such crises.

I’m not really sure the rest of the article is really all that interesting, but I found the above sentence both amusing and depressing enough to link to it here.

iii. Albert Pierrepoint. This guy killed hundreds of people.

On the other hand people were fine with it – it was his job. Well, sort of, this is actually slightly complicated. (“Pierrepoint was often dubbed the Official Executioner, despite there being no such job or title”).

Anyway this article is clearly the story of a guy who achieved his childhood dream – though unlike other children, he did not dream of becoming a fireman or a pilot, but rather of becoming the Official Executioner of the country. I’m currently thinking of using Pierrepoint as the main character in the motivational story I plan to tell my nephew when he’s a bit older.

iv. Second Crusade (featured). Considering how many different ‘states’ and ‘kingdoms’ were involved, a surprisingly small amount of people were actually fighting; the article notes that “[t]here were perhaps 50,000 troops in total” on the Christian side when the attack on Damascus was initiated. It wasn’t enough, as the outcome of the crusade was a decisive Muslim victory in the ‘Holy Land’ (Middle East).

v. 0.999… (featured). This thing is equal to one, but it can sometimes be really hard to get even very smart people to accept this fact. Lots of details and some proofs presented in the article.

vi. Shapley–Folkman lemma (‘good article’ – but also a somewhat technical article).

vii. Multituberculata. This article is not that special, but I add it here also because I think it ought to be and I’m actually sort of angry that it’s not; sometimes the coverage provided on wikipedia simply strikes me as grossly unfair, even if this is perhaps a slightly odd way to think about stuff. As pointed out in the article (Agustí points this out in his book as well), “The multituberculates existed for about 120 million years, and are often considered the most successful, diversified, and long-lasting mammals in natural history.” Yet notice how much (/little) coverage the article provides. Now compare the article with this article, or this.

February 25, 2015 Posted by | Biology, Economics, Evolutionary biology, History, Mathematics, Paleontology, Wikipedia, Zoology | 2 Comments

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

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

I’m currently reading this book. It’s quite nice so far, though the title is slightly misleading (I’ve read 82 pages so far and I’ve yet to come across any mammoths, sabertooths or hominids…). I mentioned yesterday that I wanted to cover the systems analysis text in more detail today, but that turned out to be really difficult to do without actually rewriting the book (or at the very least quoting very extensively), something I really don’t want to do. I decided to cover this book instead, though it’s admittedly slightly ‘lazy coverage’. Below I have added some links to stuff he talks about in the book. It’s the sort of book which is reasonably easy to blog, so I’m quite sure I’ll add more detail and context later, especially considering how most people presumably know far more (…okay, well, more) about the lives of the dinosaurs than they do about the lives of their much more recent ancestors, which lived during the Cenozoic.

The book frequently has more information about a given species/genus than does wikipedia’s corresponding article (and there’s stuff in here which wikipedia does not have articles about at all…), and/but I’ve tried to avoid linking to stubs below. Some articles below have decent coverage, but these are in general topics not well covered on wikipedia – I don’t think there’s a single featured article among the articles included. Even so, it’s probably worth having a look at some of the articles below if you’re curious to know which kind of stuff’s covered in this book. Aside from the links, I decided to also include a few pictures from the articles.

Paleocene.
Eocene.
Late Paleocene Thermal Maximum.
Turgai Strait.
Multituberculata.
Leptictidium.
Messel site.
Hyaenodon.

Hyaenodon_Heinrich_Harder
Pantolestidae.
Mixodectidae.
Condylarth.
Arctocyonidae.
Purgatorius.
Dyrosauridae.
Hypsodont.
Gastornis.

Gastornis,_a_large_flightless_bird_from_the_Eocene_of_Wyoming
Plesiadapis.
Pristichampsus.
Pantodonta.
Barylambda_BWMiacids.
Carnassial.
Coryphodon.
Alpine orogeny.
Phenacondus.
Perissodactyla.
Icaronycteris.
Palaeochiropteryx.

800px-Palaeochiropteryx_Paleoart
Adapidae.
Omomyidae.
Artiodactyla.
Palaeotherium.
Chalicotheres.
Eurotamandua.
Strigogyps.

February 13, 2015 Posted by | Biology, Books, Evolutionary biology, Geology, Paleontology, Zoology | Leave a comment

Wikipedia articles of interest

i. Pendle witches.

“The trials of the Pendle witches in 1612 are among the most famous witch trials in English history, and some of the best recorded of the 17th century. The twelve accused lived in the area around Pendle Hill in Lancashire, and were charged with the murders of ten people by the use of witchcraft. All but two were tried at Lancaster Assizes on 18–19 August 1612, along with the Samlesbury witches and others, in a series of trials that have become known as the Lancashire witch trials. One was tried at York Assizes on 27 July 1612, and another died in prison. Of the eleven who went to trial – nine women and two men – ten were found guilty and executed by hanging; one was found not guilty.

The official publication of the proceedings by the clerk to the court, Thomas Potts, in his The Wonderfull Discoverie of Witches in the Countie of Lancaster, and the number of witches hanged together – nine at Lancaster and one at York – make the trials unusual for England at that time. It has been estimated that all the English witch trials between the early 15th and early 18th centuries resulted in fewer than 500 executions; this series of trials accounts for more than two per cent of that total.”

“One of the accused, Demdike, had been regarded in the area as a witch for fifty years, and some of the deaths the witches were accused of had happened many years before Roger Nowell started to take an interest in 1612.[13] The event that seems to have triggered Nowell’s investigation, culminating in the Pendle witch trials, occurred on 21 March 1612.[14]

On her way to Trawden Forest, Demdike’s granddaughter, Alizon Device, encountered John Law, a pedlar from Halifax, and asked him for some pins.[15] Seventeenth-century metal pins were handmade and relatively expensive, but they were frequently needed for magical purposes, such as in healing – particularly for treating warts – divination, and for love magic, which may have been why Alizon was so keen to get hold of them and why Law was so reluctant to sell them to her.[16] Whether she meant to buy them, as she claimed, and Law refused to undo his pack for such a small transaction, or whether she had no money and was begging for them, as Law’s son Abraham claimed, is unclear.[17] A few minutes after their encounter Alizon saw Law stumble and fall, perhaps because he suffered a stroke; he managed to regain his feet and reach a nearby inn.[18] Initially Law made no accusations against Alizon,[19] but she appears to have been convinced of her own powers; when Abraham Law took her to visit his father a few days after the incident, she reportedly confessed and asked for his forgiveness.[20]

Alizon Device, her mother Elizabeth, and her brother James were summoned to appear before Nowell on 30 March 1612. Alizon confessed that she had sold her soul to the Devil, and that she had told him to lame John Law after he had called her a thief. Her brother, James, stated that his sister had also confessed to bewitching a local child. Elizabeth was more reticent, admitting only that her mother, Demdike, had a mark on her body, something that many, including Nowell, would have regarded as having been left by the Devil after he had sucked her blood.”

“The Pendle witches were tried in a group that also included the Samlesbury witches, Jane Southworth, Jennet Brierley, and Ellen Brierley, the charges against whom included child murder and cannibalism; Margaret Pearson, the so-called Padiham witch, who was facing her third trial for witchcraft, this time for killing a horse; and Isobel Robey from Windle, accused of using witchcraft to cause sickness.[33]

Some of the accused Pendle witches, such as Alizon Device, seem to have genuinely believed in their guilt, but others protested their innocence to the end.”

“Nine-year-old Jennet Device was a key witness for the prosecution, something that would not have been permitted in many other 17th-century criminal trials. However, King James had made a case for suspending the normal rules of evidence for witchcraft trials in his Daemonologie.[42] As well as identifying those who had attended the Malkin Tower meeting, Jennet also gave evidence against her mother, brother, and sister. […] When Jennet was asked to stand up and give evidence against her mother, Elizabeth began to scream and curse her daughter, forcing the judges to have her removed from the courtroom before the evidence could be heard.[48] Jennet was placed on a table and stated that she believed her mother had been a witch for three or four years. She also said her mother had a familiar called Ball, who appeared in the shape of a brown dog. Jennet claimed to have witnessed conversations between Ball and her mother, in which Ball had been asked to help with various murders. James Device also gave evidence against his mother, saying he had seen her making a clay figure of one of her victims, John Robinson.[49] Elizabeth Device was found guilty.[47]

James Device pleaded not guilty to the murders by witchcraft of Anne Townley and John Duckworth. However he, like Chattox, had earlier made a confession to Nowell, which was read out in court. That, and the evidence presented against him by his sister Jennet, who said that she had seen her brother asking a black dog he had conjured up to help him kill Townley, was sufficient to persuade the jury to find him guilty.[50][51]

“Many of the allegations made in the Pendle witch trials resulted from members of the Demdike and Chattox families making accusations against each other. Historian John Swain has said that the outbreaks of witchcraft in and around Pendle demonstrate the extent to which people could make a living either by posing as a witch, or by accusing or threatening to accuse others of being a witch.[17] Although it is implicit in much of the literature on witchcraft that the accused were victims, often mentally or physically abnormal, for some at least, it may have been a trade like any other, albeit one with significant risks.[74] There may have been bad blood between the Demdike and Chattox families because they were in competition with each other, trying to make a living from healing, begging, and extortion.”

ii. Kullback–Leibler divergence.

This article is the only one of the five ‘main articles’ in this post which is not a featured article. I looked this one up because the Burnham & Anderson book I’m currently reading talks about this stuff quite a bit. The book will probably be one of the most technical books I’ll read this year, and I’m not sure how much of it I’ll end up covering here. Basically most of the book deals with the stuff ‘covered’ in the (very short) ‘Relationship between models and reality’ section of the wiki article. There are a lot of details the article left out… The same could be said about the related wiki article about AIC (both articles incidentally include the book in their references).

iii Atmosphere of Jupiter.

The first thing that would spring to mind if someone asked me what I knew about it would probably be something along the lines of: “…well, it’s huge…”

Jupiter-Earth-Spot_comparison

…and it is. But we know a lot more than that – some observations from the article:

“The atmosphere of Jupiter is the largest planetary atmosphere in the Solar System. It is mostly made of molecular hydrogen and helium in roughly solar proportions; other chemical compounds are present only in small amounts […] The atmosphere of Jupiter lacks a clear lower boundary and gradually transitions into the liquid interior of the planet. […] The Jovian atmosphere shows a wide range of active phenomena, including band instabilities, vortices (cyclones and anticyclones), storms and lightning. […] Jupiter has powerful storms, always accompanied by lightning strikes. The storms are a result of moist convection in the atmosphere connected to the evaporation and condensation of water. They are sites of strong upward motion of the air, which leads to the formation of bright and dense clouds. The storms form mainly in belt regions. The lightning strikes on Jupiter are hundreds of times more powerful than those seen on Earth.” [However do note that later on in the article it is stated that: “On Jupiter lighting strikes are on average a few times more powerful than those on Earth.”]

“The composition of Jupiter’s atmosphere is similar to that of the planet as a whole.[1] Jupiter’s atmosphere is the most comprehensively understood of those of all the gas giants because it was observed directly by the Galileo atmospheric probe when it entered the Jovian atmosphere on December 7, 1995.[26] Other sources of information about Jupiter’s atmospheric composition include the Infrared Space Observatory (ISO),[27] the Galileo and Cassini orbiters,[28] and Earth-based observations.”

“The visible surface of Jupiter is divided into several bands parallel to the equator. There are two types of bands: lightly colored zones and relatively dark belts. […] The alternating pattern of belts and zones continues until the polar regions at approximately 50 degrees latitude, where their visible appearance becomes somewhat muted.[30] The basic belt-zone structure probably extends well towards the poles, reaching at least to 80° North or South.[5]

The difference in the appearance between zones and belts is caused by differences in the opacity of the clouds. Ammonia concentration is higher in zones, which leads to the appearance of denser clouds of ammonia ice at higher altitudes, which in turn leads to their lighter color.[15] On the other hand, in belts clouds are thinner and are located at lower altitudes.[15] The upper troposphere is colder in zones and warmer in belts.[5] […] The Jovian bands are bounded by zonal atmospheric flows (winds), called jets. […] The location and width of bands, speed and location of jets on Jupiter are remarkably stable, having changed only slightly between 1980 and 2000. […] However bands vary in coloration and intensity over time […] These variations were first observed in the early seventeenth century.”

“Jupiter radiates much more heat than it receives from the Sun. It is estimated that the ratio between the power emitted by the planet and that absorbed from the Sun is 1.67 ± 0.09.”

iv. Wife selling (English custom).

Wife selling in England was a way of ending an unsatisfactory marriage by mutual agreement that probably began in the late 17th century, when divorce was a practical impossibility for all but the very wealthiest. After parading his wife with a halter around her neck, arm, or waist, a husband would publicly auction her to the highest bidder. […] Although the custom had no basis in law and frequently resulted in prosecution, particularly from the mid-19th century onwards, the attitude of the authorities was equivocal. At least one early 19th-century magistrate is on record as stating that he did not believe he had the right to prevent wife sales, and there were cases of local Poor Law Commissioners forcing husbands to sell their wives, rather than having to maintain the family in workhouses.”

“Until the passing of the Marriage Act of 1753, a formal ceremony of marriage before a clergyman was not a legal requirement in England, and marriages were unregistered. All that was required was for both parties to agree to the union, so long as each had reached the legal age of consent,[8] which was 12 for girls and 14 for boys.[9] Women were completely subordinated to their husbands after marriage, the husband and wife becoming one legal entity, a legal status known as coverture. […] Married women could not own property in their own right, and were indeed themselves the property of their husbands. […] Five distinct methods of breaking up a marriage existed in the early modern period of English history. One was to sue in the ecclesiastical courts for separation from bed and board (a mensa et thoro), on the grounds of adultery or life-threatening cruelty, but it did not allow a remarriage.[11] From the 1550s, until the Matrimonial Causes Act became law in 1857, divorce in England was only possible, if at all, by the complex and costly procedure of a private Act of Parliament.[12] Although the divorce courts set up in the wake of the 1857 Act made the procedure considerably cheaper, divorce remained prohibitively expensive for the poorer members of society.[13][nb 1] An alternative was to obtain a “private separation”, an agreement negotiated between both spouses, embodied in a deed of separation drawn up by a conveyancer. Desertion or elopement was also possible, whereby the wife was forced out of the family home, or the husband simply set up a new home with his mistress.[11] Finally, the less popular notion of wife selling was an alternative but illegitimate method of ending a marriage.”

“Although some 19th-century wives objected, records of 18th-century women resisting their sales are non-existent. With no financial resources, and no skills on which to trade, for many women a sale was the only way out of an unhappy marriage.[17] Indeed the wife is sometimes reported as having insisted on the sale. […] Although the initiative was usually the husband’s, the wife had to agree to the sale. An 1824 report from Manchester says that “after several biddings she [the wife] was knocked down for 5s; but not liking the purchaser, she was put up again for 3s and a quart of ale”.[27] Frequently the wife was already living with her new partner.[28] In one case in 1804 a London shopkeeper found his wife in bed with a stranger to him, who, following an altercation, offered to purchase the wife. The shopkeeper agreed, and in this instance the sale may have been an acceptable method of resolving the situation. However, the sale was sometimes spontaneous, and the wife could find herself the subject of bids from total strangers.[29] In March 1766, a carpenter from Southwark sold his wife “in a fit of conjugal indifference at the alehouse”. Once sober, the man asked his wife to return, and after she refused he hanged himself. A domestic fight might sometimes precede the sale of a wife, but in most recorded cases the intent was to end a marriage in a way that gave it the legitimacy of a divorce.”

“Prices paid for wives varied considerably, from a high of £100 plus £25 each for her two children in a sale of 1865 (equivalent to about £12,500 in 2015)[34] to a low of a glass of ale, or even free. […] According to authors Wade Mansell and Belinda Meteyard, money seems usually to have been a secondary consideration;[4] the more important factor was that the sale was seen by many as legally binding, despite it having no basis in law. […] In Sussex, inns and public houses were a regular venue for wife-selling, and alcohol often formed part of the payment. […] in Ninfield in 1790, a man who swapped his wife at the village inn for half a pint of gin changed his mind and bought her back later.[42] […] Estimates of the frequency of the ritual usually number about 300 between 1780 and 1850, relatively insignificant compared to the instances of desertion, which in the Victorian era numbered in the tens of thousands.[43]

“In 1825 a man named Johnson was charged with “having sung a song in the streets describing the merits of his wife, for the purpose of selling her to the highest bidder at Smithfield.” Such songs were not unique; in about 1842 John Ashton wrote “Sale of a Wife”.[nb 6][58] The arresting officer claimed that the man had gathered a “crowd of all sorts of vagabonds together, who appeared to listen to his ditty, but were in fact, collected to pick pockets.” The defendant, however, replied that he had “not the most distant idea of selling his wife, who was, poor creature, at home with her hungry children, while he was endeavouring to earn a bit of bread for them by the strength of his lungs.” He had also printed copies of the song, and the story of a wife sale, to earn money. Before releasing him, the Lord Mayor, judging the case, cautioned Johnson that the practice could not be allowed, and must not be repeated.[59] In 1833 the sale of a woman was reported at Epping. She was sold for 2s. 6d., with a duty of 6d. Once sober, and placed before the Justices of the Peace, the husband claimed that he had been forced into marriage by the parish authorities, and had “never since lived with her, and that she had lived in open adultery with the man Bradley, by whom she had been purchased”. He was imprisoned for “having deserted his wife”.[60]

v. Bog turtle.

Baby_bog_turtle_in_palm_(cropped)

“The bog turtle (Glyptemys muhlenbergii) is a semiaquatic turtle endemic to the eastern United States. […] It is the smallest North American turtle, measuring about 10 centimeters (4 in) long when fully grown. […] The bog turtle can be found from Vermont in the north, south to Georgia, and west to Ohio. Diurnal and secretive, it spends most of its time buried in mud and – during the winter months – in hibernation. The bog turtle is omnivorous, feeding mainly on small invertebrates.”

“The bog turtle is native only to the eastern United States,[nb 1] congregating in colonies that often consist of fewer than 20 individuals.[23] […] densities can range from 5 to 125 individuals per 0.81 hectares (2.0 acres). […] The bog turtle spends its life almost exclusively in the wetland where it hatched. In its natural environment, it has a maximum lifespan of perhaps 50 years or more,[47] and the average lifespan is 20–30 years.”

“The bog turtle is primarily diurnal, active during the day and sleeping at night. It wakes in the early morning, basks until fully warm, then begins its search for food.[31] It is a seclusive species, making it challenging to observe in its natural habitat.[11] During colder days, the bog turtle will spend much of its time in dense underbrush, underwater, or buried in mud. […] Day-to-day, the bog turtle moves very little, typically basking in the sun and waiting for prey. […] Various studies have found different rates of daily movement in bog turtles, varying from 2.1 to 23 meters (6.9 to 75.5 ft) in males and 1.1 to 18 meters (3.6 to 59.1 ft) in females.”

“Changes to the bog turtle’s habitat have resulted in the disappearance of 80 percent of the colonies that existed 30 years ago.[7] Because of the turtle’s rarity, it is also in danger of illegal collection, often for the worldwide pet trade. […] The bog turtle was listed as critically endangered in the 2011 IUCN Red List.[53]

January 3, 2015 Posted by | Astronomy, Biology, History, Statistics, Wikipedia, Zoology | Leave a comment

The Voyage of the Beagle (III)

This will be my last post about the book.

I have for some time, probably roughly since the internet problems I had earlier this year were resolved, structured my reading in a way so that I’ll more or less never read fiction/’pure enjoyment’ books while at home. I now only read fiction when I’m out taking walks, and then I limit my book reading to non-fiction while I’m at home. I take long(ish) walks most days so I guess I still finish a fiction book every week or so at the current rate. This change in my reading habits is relevant to my reading of this book because back when I implemented this change, I’d mentally classified the Darwin book as a fiction book/’pure enjoyment’ book – the kind of book I should only be reading while taking walks. It isn’t really fiction, but it is a very enjoyable book to read and in many ways it’s conceptually really much closer to normal fiction stories than it is to a Springer publication about heart disease or mathematics. As it’s often raining in Denmark, it’s often not convenient to take walks while reading ‘paper books’, and my edition of Darwin is a ‘paper book’; I sometimes bring paper books on my walks, but if there’s a risk of rain I’ll usually much prefer to bring my e-reader, which can deal quite well with a few drops of water. A different problem is that I always highlight and write notes in my books, which means that the more interesting and well-written a paper book is, the more inconvenient it is to bring it on walks; I can’t highlight or take notes while walking (I’ve tried, but it doesn’t work), so I have to stop walking every time I come across an interesting sequence which I’d like to highlight or comment upon, of which there are many more in good books than in bad books, and taking a lot of breaks like that can be bothersome in the long run. Some paper books are also too big/heavy to conveniently bring on my walks; however this particular book is not one of those.

What all of above stuff means is of course that for quite a while I didn’t really read very much in this book because I’d settled on not reading it while I was at home, but I also usually had a different book on my e-reader which it was easier and more convenient to bring on my walks. At the end I decided that I should really read the rest of this book because it’s quite good (before I started rereading the book it was on my list of favourites on goodreads, and it still is), and so I decided to read it at home.

The book is really nice. If you liked the quotes I included either in my previous posts about the book and/or in this post, it’s worth considering taking the time to read the book. I may be wrong, but I could easily imagine this being the sort of book that many people might think to themselves that they’ll read when they get old, but then when they reach the pension age they’ll never get around to actually doing it; if this impression is correct, that’s just a damn shame. Reading books like this one or perhaps something like Mark Twain’s The Innocents Abroad (available for free here) will, aside from giving you some enjoyable experiences in the company of good writers, probably make it easier for you to think about the world in a slightly different manner than the one you’re used to.

The book is full of good stuff and so I had to leave out a lot of good stuff in my posts. Below I have added a few more illustrative quotes from the book.

“I heard also of an old lady who, at a dinner at Coquimbo, remarked how wonderfully strange it was that she should have lived to dine in the same room with an Englishman; for she remembered as a girl, that twice, at the mere cry of “Los Ingleses,” every soul, carrying what valuables they could, had taken to the mountains.”

“The connection between earthquakes and the weather has been often disputed: it appears to me to be a point of great interest, which is little understood.”

“My geological examination of the country generally created a good deal of surprise amongst the Chilenos: it was long before they could be convinced that I was not hunting for mines. This was sometimes troublesome: I found the most ready way of explaining my employment, was to ask them how it was that they themselves were not curious concerning earthquakes and volcanos? – why some springs were hot and others cold? – why there were mountains in Chile, and not a hill in La Plata? These bare questions at once satisfied and silenced the greater number; some, however (like a few in England who are a century behind hand), thought that all such inquiries were useless and impious; and that it was quite sufficient that God had thus made the mountains.”

“Our arrival in the offing caused some little apprehension. Peru was in a state of anarchy; and each party having demanded a contribution, the poor town of Iquique was in tribulation, thinking the evil hour was come. The people had also their domestic troubles; a short time before, three French carpenters had broken open, during the same night, the two churches, and stolen all the plate: one of the robbers, however, subsequently confessed, and the plate was recovered. The convicts were sent to Arequipa, which though the capital of this province, is two hundred leagues distant, the government there thought it a pity to punish such useful workmen, who could make all sorts of furniture; and accordingly liberated them. Things being in this state, the churches were again broken open, but this time the plate was not recovered. The inhabitants became dreadfully enraged, and declaring that none but heretics would thus “eat God Almighty,” proceeded to torture some Englishmen, with the intention of afterwards shooting them. At last the authorities interfered, and peace was established.”

“We did not reach the saltpetre-works till after sunset, having ridden all day across an undulating country, a complete and utter desert. The road was strewed with the bones and dried skins of many beasts of burden which had perished on it from fatigue. Excepting the Vultur aura, which preys on the carcasses, I saw neither bird, quadruped, reptile, nor insect. […] I cannot say I liked the very little I saw of Peru: in summer, however, it is said that the climate is much pleasanter. In all seasons, both inhabitants and foreigners suffer from severe attacks of ague. This disease is common on the whole coast of Peru, but is unknown in the interior. The attacks of illness which arise from miasma never fail to appear most mysterious. […] Callao is a filthy, ill-built, small seaport. The inhabitants, both here and at Lima, present every imaginable shade of mixture, between European, Negro, and Indian blood. They appear a depraved, drunken set of people.”

“Of land-birds I obtained twenty-six kinds, all peculiar to the group and found nowhere else, with the exception of one lark-like finch from North America […] The remaining land-birds form a most singular group of finches, related to each other in the structure of their beaks, short tails, form of body and plumage […] The most curious fact is the perfect gradation in the size of the beaks in the different species […] Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends. […] With the exception of a wren with a fine yellow breast, and of a tyrant-flycatcher with a scarlet tuft and breast, none of the birds are brilliantly coloured, as might have been expected in an equatorial district. Hence it would appear probable, that the same causes which here make the immigrants of some peculiar species smaller, make most of the peculiar Galapageian species also smaller, as well as very generally more dusky coloured.” [For more on related topics, see incidentally this previous post of mine].

“As I at first observed, these islands are not so remarkable for the number of the species of reptiles, as for that of the [number of] individuals […] we must admit that there is no other quarter of the world where this Order replaces the herbivorous mammalia in so extraordinary a manner. […] by far the most remarkable feature in the natural history of this archipelago [is] that the different islands to a considerable extent are inhabited by a different set of beings. […] The inhabitants […] state that they can distinguish the tortoises from the different islands; and that they differ not only in size, but in other characters. […] I have strong reasons to suspect that some of the [finch] species of the sub-group Geospiza are confined to separate islands. If the different islands have their representatives of Geospiza, it may help to explain the singularly large number of the species of this sub-group in this one small archipelago, and as a probable consequence of their numbers, the perfectly graduated series in the size of their beaks. […] The distribution of the tenants of this archipelago would not be nearly so wonderful, if, for instance, one island had a mocking-thrush, and a second island some other quite distinct genus,- if one island had its genus of lizard, and a second island another distinct genus, or none whatever; -or if the different islands were inhabited, not by representative species of the same genera of plants, but by totally different genera […]. But it is the circumstance, that several of the islands possess their own species of the tortoise, mocking-thrush, finches, and numerous plants, these species having the same general habits, occupying analogous situations, and obviously filling the same place in the natural economy of this archipelago, that strikes me with wonder. It may be suspected that some of these representative species, at least in the case of the tortoise and of some of the birds, may hereafter prove to be only well-marked races; but this would be of equally great interest to the philosophical naturalist.”

“I was much disappointed in the personal appearance of the [Tahiti] women; they are far inferior in every respect to the men.” [Good luck writing anything like that today and getting it published…] […] After the main discussion was ended, several of the chiefs took the opportunity of asking Captain Fitz Roy many intelligent questions on international customs and laws, relating to the treatment of ships and foreigners. […] This Tahitian parliament lasted for several hours; and when it was over Captain Fitz Roy invited Queen Pomarre to pay the Beagle a visit. […] In the evening four boats were sent for her majesty; the ship was dressed with flags, and the yards manned on her coming on board. She was accompanied by most of the chiefs. The behaviour of all was very proper: they begged for nothing, and seemed much pleased with Captain Fitz Roy’s presents.”

“When I showed the chief a very small bundle, which I wanted carried, it became absolutely necessary for him to take a slave. These feelings of pride are beginning to wear away; but formerly a leading man would sooner have died, than undergone the indignity of carrying the smallest burden.”

“Some time ago, Mr. Bushby suffered a […] serious attack. A chief and a party of men tried to break into his house in the middle of the night, and not finding this so easy, commenced a brisk firing with their muskets. Mr. Bushby was slightly wounded, but the party was at length driven away. Shortly afterwards it was discovered who was the aggressor; and a general meeting of the chiefs was convened to consider the case. It was considered by the New Zealanders as very atrocious, inasmuch as it was a night attack, and that Mrs. Bushby was lying ill in the house: this latter circumstance, much to their honour, being considered in all cases as a protection. The chiefs agreed to confiscate the land of the aggressor to the King of England. The whole proceeding, however, in thus trying and punishing a chief was entirely without precedent. The aggressor, moreover, lost caste in the estimation of his equals and this was considered by the British as of more consequence than the confiscation of his land. […] a chief and a party of men volunteered to walk with us to Waiomio, a distance of four miles. The chief was at this time rather notorious from having lately hung one of his wives and a slave for adultery. When one of the missionaries remonstrated with him he seemed surprised, and said he thought he was exactly following the English method.”

“It is impossible to behold these waves without feeling a conviction that an island, though built of the hardest rock, let it be porphyry, granite, or quartz, would ultimately yield and be demolished by such an irresistible power. Yet these low, insignificant coral-islets stand and are victorious: for here another power, as an antagonist, takes part in the contest. The organic forces separate the atoms of carbonate of lime, one by one, from the foaming breakers, and unite them into a symmetrical structure. Let the hurricane tear up its thousand huge fragments; yet what will that tell against the accumulated labour of myriads of architects at work night and day, month after month? […] We feel surprise when travellers tell us of the vast dimensions of the Pyramids and other great ruins, but how utterly insignificant are the greatest of these, when compared to these mountains of stone accumulated by the agency of various minute and tender animals! This is a wonder which does not at first strike the eye of the body, but, after reflection, the eye of reason.”

“Those who look tenderly at the slave owner, and with a cold heart at the slave, never seem to put themselves into the position of the latter”

December 14, 2014 Posted by | Biology, Books, Evolutionary biology, Geography, Geology, History, Personal, Zoology | Leave a comment

The Voyage of the Beagle (I)

“”You care for nothing but shooting, dogs, and rat-catching,” Dr. Darwin had said, “and you will be a disgrace to yourself and all your family.””

The above quote is included in the introduction to the book, by David Quammen. I somehow really like that quote.

I generally don’t blog fiction and ‘fiction-like’ books (by which I mean memoirs and such) like this one unless I have a good excuse, but I didn’t seem to have many problems coming up with excuses for covering this particular book here on the blog. When I first read the book some years ago I read a version of it I did not personally own, in Danish – later on I bought a(n English-language) copy for myself. Lately I have been rereading it. It’s a nice book. The world was a very different place 180 years ago, and a book like this gives you a lot of details which help you understand just how different. The book is interesting not only for the many glimpses it gives you into the lives of different people living in the 19th century, but of course also from a history of science point of view; this relates not only to how the trip helped Darwin develop his ideas about natural selection but also relates to many other aspects, some more related to his ‘big idea’ than others. Darwin’s geological observations more than a century before the idea of plate tectonics was accepted by the geological community are for example fascinating, but he also shares some of his ideas about e.g. local weather pattern and meteorological phenomena encountered along the way, and stuff like animal breeding. It should be emphasized that this is a travel book and not a scientific treatise. I’m reasonably certain that if Darwin had never come up with the idea for which he is now known and had not included any biology-related observations in the book, there would still be many parts of this book which would be very much worth reading for other reasons; Darwin experienced a lot of interesting stuff during this trip, and the trip would have made for a very good story even if they’d skipped the trip to the Galapagos Islands and had returned home to Britain after the visit to Chile. Though it’s a good thing for biology that they didn’t.

Many of his observations are interesting not because they tell you what a young man like Darwin might have thought about, say, weather patterns in 1835, but because they give you some wonderful insights into stuff like prevailing social mores and dynamics in South American societies around the 1830s; as mentioned, the world was a very different place back then. Just how different should be clear from some of the quotes below, and part of what I sometimes found really interesting about the account was how Darwin would not comment on or question specific things he observed – things someone born in the late 20th century might well have thought about in a very different manner. Darwin took a lot of stuff for granted, just like someone born in the late 20th century does, but the things he took for granted were sometimes very different from the things we might take for granted. It’s however noteworthy in this context that although there’s a big gap, both in terms of knowledge and presumably also in terms of values, between Darwin and the modern reader, there often seems to be if anything a bigger gap between him and some of the people he encounters along the way; sometimes you sort of think it would be easier for you, the modern reader, to understand ‘where Darwin was coming from’ than it must have been for some of the people whom he met during his travels. There’s more than one good reason to read this book.

I’ve added some quotes from the book below. I should point out that Darwin writes in a manner some might well find boring in part because he tends to go into a lot of detail when talking about some specific thing he considers to be interesting (you may find that boring if you don’t find that topic interesting), but there’s some really nice stuff hidden in there and it’s very much worth reading the book even if you don’t enjoy all of it equally well.

“As it was growing dark we passed under one of the massive, bare, and steep hills of granite which are so common in this country. This spot is notorious from having been, for a long time, the residence of some runaway slaves, who, by cultivating a little ground near the top, contrived to eke out a subsistence. At length they were discovered, and a party of soldiers being sent, the whole were seized with the exception of one old woman, who, sooner than again be led into slavery, dashed herself to pieces from the summit of the mountain. In a Roman matron this would have been called the noble love of freedom: in a poor negress it is mere brutal obstinacy. We continued riding for some hours. [No more comments about this event – three sentences later he talks about fireflies…]”

“On such fazêndas as these, I have no doubt the slaves pass happy and contented lives. On Saturday and Sunday they work for themselves, and in this fertile climate the labour of two days is sufficient to support a man and his family for the whole week.”

“While staying at this estate, I was very nearly being an eyewitness to one of those atrocious acts which can only take place in a slave country. Owing to a quarrel and a lawsuit, the owner was on the point of taking all the women and children from the male slaves, and selling them separately at the public auction at Rio. Interest, and not any feeling of compassion, prevented this act. Indeed, I do not believe the inhumanity of separating thirty families, who had lived together for many years, even occurred to the owner.”

“I first visited the forest in which these Plenariae [some worms] were found, in company with an old Portuguese priest who took me out to hunt with him. The sport consisted in turning into the cover a few dogs, and then patiently waiting to fire at any animal which might appear.”

“I may mention, as a proof of how cheap everything is in this country, that I paid only two dollars a day, or eight shillings, for two men, together with a troop of about a dozen riding-horses. My companions were well armed with pistols and sabres; a precaution which I thought rather unnecessary: but the first piece of news we heard was, that, the day before, a traveller from Monte Video had been found dead on the road, with his throat cut. This happened close to a cross, the record of a former murder.
On the first night we slept at a retired little country-house; and there I soon found out that I possessed two or three articles, especially a pocket compass, which created unbounded astonishment. In every house I was asked to show the compass, and by its aid, together with a map, to point out the direction of various places. It excited the liveliest admiration that I, a perfect stranger, should know the road (for direction and road are synonymous in this open country) to places where I had never been. […] this retired part of the country is seldom visited by foreigners. I was asked whether the earth or sun moved; whether it was hotter or colder to the north; where Spain was, and many other such questions. The greater number of inhabitants had an indistinct idea that England, London, and North America, were different names for the same place; but the better informed well knew that London and North America were separate countries close together, and that England was a large town in London!”

“On approaching the house of a stranger, it is usual to follow several little points of etiquette: riding up slowly to the door, the salutation of Ave Maria is given, and until somebody comes out and asks you to alight, it is not customary even to get off your horse […] Having entered the house, some general conversation is kept up for a few minutes, till permission is asked to pass the night there. This is granted as a matter of course. The stranger then takes his meals with the family, and a room is assigned him, where with the horsecloths belonging to his recado (or saddle of the Pampas) he makes his bed. It is curious how similar circumstances produce such similar results in manners. At the Cape of Good Hope the same hospitality, and very nearly the same points of etiquette, are universally observed.”

“To the northward of the Rio Negro, between it and the inhabited country near Buenos Ayres, the Spaniards have only one small settlement, recently established at Bahia Blanca. The distance in a straight line to Buenos Ayres is very nearly five hundred British miles. The wandering tribes of horse Indians, which have always occupied the greater part of this country, having of late much harassed the outlying estancias, the government at Buenos Ayres equipped some time since an army under the command of General Rosas for the purpose of exterminating them. The troops were now encamped on the banks of the Colorado; a river lying about eighty miles northward of the Rio Negro. […] It was supposed that General Rosas had about six hundred Indian allies. […] The duty of the women is to load and unload the horses; to make the tents for the night; in short to be, like the wives of all savages, useful slaves. The man fight, hunt, take care of the horses, and make the riding gear. […] While changing horses at the Guardia several people questioned us much about the army, – I never saw anything like the enthusiasm for Rosas, and for the success of “the most just of all wars, because against barbarians.””

“A few days afterwards I saw another troop of these banditti-like soldiers start on an expedition against a tribe of Indians at the small Salinas, who had been betrayed by a prisoner cacique. The Spaniard who brought the orders of this expedition was a very intelligent man. He gave me an account of the last engagement at which he was present. Some Indians, who had been taken prisoners, gave information of a tribe living north of the Colorado. Two hundred soldiers were sent; and they first discovered the Indians by a cloud of dust from their horses’ feet, as they chanced to be travelling. The country was mountainous and wild, and it must have been far in the interior, for the Cordillera was in sight. The Indians, men, women, and children, were about one hundred and ten in number, and they were nearly all taken or killed, for the soldiers sabre every man. The Indians are now so terrified that they offer no resistance in a body, but each neglecting even his wife and children; but when overtaken, like wild animals, they fight against any number to the last moment. […] This is a dark picture; but how much more shocking is the unquestionable fact, that all the women who appear above twenty years old are massacred in cold blood! When I exclaimed that this appeared rather inhuman, he answered, “Why, what can be done? They breed so!”
Every one here is fully convinced that this is the most just war, because it is against barbarians. Who would believe in this age that such atrocities could be committed in a Christian civilized country? The children of the Indians are saved, to be sold or given away as servants, or rather slaves for as long time as the owners can make them believe themselves slaves; but I believe in their treatment there is little to complain of.”

“We passed a train of waggons and a troop of beasts on their road to Mendoza. The distance is about 580 geographical miles, and the journey is generally performed in fifty days.”

“a niata bull and cow invariably produce niata calves. A niata bull with a common cow, or the reverse cross, produces offspring having an intermediate character, but with the niata characters strongly displayed: according to Señor Muniz, there is the clearest evidence, contrary to the common belief of agriculturalists in analogous cases, that the niata cow when crossed with a common bull transmits her peculiarities more strongly than the niata bull when crossed with a common cow. When the pasture is tolerably long, the niata cattle feed with the tongue and palate as well as common cattle, but during the great droughts, when so many animals perish, the niata breed is under a great disadvantage, and would be exterminated if not attended to; for the common cattle, like horses, are able just to keep alive, by browsing with their lips on twigs of trees and reeds; this the niata cannot so well do, as their lips do not join, and hence they are found to perish before the common cattle. This strikes me as a good illustration of how little we are able to judge from the ordinary habits of life, on what circumstances, occurring only at long intervals, the rarity of extinction of a species may be determined.”

“Police and justice are quite inefficient. If a man who is poor commits murder and is taken, he will be imprisoned, and perhaps even shot; but if he is rich and has friends, he may rely on it no very severe consequences will ensue. […] A traveller has no protection besides his fire-arms; and the constant habit of carrying them is the main check to more frequent robberies. […] Nearly every public officer can be bribed. The head man in the post-office sold forged government franks.”

“The results of all the attempts to colonize this side of America south of 41°, has been miserable. Port Famine expresses by its name the lingering and extreme sufferings of several hundred wretched people, of whom one alone survived to relate their misfortunes. At St. Joseph’s Bay, on the coast of Patagonia, a small settlement was made; but during one Sunday the Indians made an attack and massacred the whole party, excepting two men, who remained captives during many years. At the Rio Negro I conversed with one of these men, now in extreme old age.”

“Every animal in a state of nature regularly breeds; yet in a species long established, any great increase in numbers is obviously impossible, and must be checked by some means. We are, nevertheless, seldom able with certainty to tell in any given species, at what period of life, or at what period of the year, or whether only at long intervals, the check falls; or, again, what is the precise nature of the check. Hence probably it is, that we feel so little surprise at one, of two species closely allied in habits, being rare and the other abundant in the same district; or, again, that one should be abundant in one district, and another, filling the same place in the economy of nature, should be abundant in a neighbouring district, differing very little in its conditions. If asked how this is, one immediately replies that it is determined by some slight difference, in climate, food, or the number of enemies: yet how rarely, if ever, we can point out the precise cause and manner of action of the check! We are, therefore, driven to the conclusion, that causes generally quite inappreciable by us, determine whether a given species shall be abundant or scanty in numbers. […] To admit that species generally become rare before they become extinct – to feel no surprise at the comparative rarity of one species with another, and yet to call in some extraordinary agent and to marvel greatly when a species ceases to exist, appears to me much the same as to admit that sickness in the individual is the prelude to death – but when the sick man dies to wonder, and to believe that he died through violence.”

November 26, 2014 Posted by | Biology, Books, History, 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