Photosynthesis in the Marine Environment (III)

This will be my last post about the book. After having spent a few hours on the post I started to realize the post would become very long if I were to cover all the remaining chapters, and so in the end I decided not to discuss material from chapter 12 (‘How some marine plants modify the environment for other organisms’) here, even though I actually thought some of that stuff was quite interesting. I may decide to talk briefly about some of the stuff in that chapter in another blogpost later on (but most likely I won’t). For a few general remarks about the book, see my second post about it.

Some stuff from the last half of the book below:

“The light reactions of marine plants are similar to those of terrestrial plants […], except that pigments other than chlorophylls a and b and carotenoids may be involved in the capturing of light […] and that special arrangements between the two photosystems may be different […]. Similarly, the CO2-fixation and -reduction reactions are also basically the same in terrestrial and marine plants. Perhaps one should put this the other way around: Terrestrial-plant photosynthesis is similar to marine-plant photosynthesis, which is not surprising since plants have evolved in the oceans for 3.4 billion years and their descendants on land for only 350–400 million years. […] In underwater marine environments, the accessibility to CO2 is low mainly because of the low diffusivity of solutes in liquid media, and for CO2 this is exacerbated by today’s low […] ambient CO2 concentrations. Therefore, there is a need for a CCM also in marine plants […] CCMs in cyanobacteria are highly active and accumulation factors (the internal vs. external CO2 concentrations ratio) can be of the order of 800–900 […] CCMs in eukaryotic microalgae are not as effective at raising internal CO2 concentrations as are those in cyanobacteria, but […] microalgal CCMs result in CO2 accumulation factors as high as 180 […] CCMs are present in almost all marine plants. These CCMs are based mainly on various forms of HCO3 [bicarbonate] utilisation, and may raise the intrachloroplast (or, in cyanobacteria, intracellular or intra-carboxysome) CO2 to several-fold that of seawater. Thus, Rubisco is in effect often saturated by CO2, and photorespiration is therefore often absent or limited in marine plants.”

“we view the main difference in photosynthesis between marine and terrestrial plants as the latter’s ability to acquire Ci [inorganic carbon] (in most cases HCO3) from the external medium and concentrate it intracellularly in order to optimise their photosynthetic rates or, in some cases, to be able to photosynthesise at all. […] CO2 dissolved in seawater is, under air-equilibrated conditions and given today’s seawater pH, in equilibrium with a >100 times higher concentration of HCO3, and it is therefore not surprising that most marine plants utilise the latter Ci form for their photosynthetic needs. […] any plant that utilises bulk HCO3 from seawater must convert it to CO2 somewhere along its path to Rubisco. This can be done in different ways by different plants and under different conditions”

“The conclusion that macroalgae use HCO3 stems largely from results of experiments in which concentrations of CO2 and HCO3 were altered (chiefly by altering the pH of the seawater) while measuring photosynthetic rates, or where the plants themselves withdrew these Ci forms as they photosynthesised in a closed system as manifested by a pH increase (so-called pH-drift experiments) […] The reason that the pH in the surrounding seawater increases as plants photosynthesise is first that CO2 is in equilibrium with carbonic acid (H2CO3), and so the acidity decreases (i.e. pH rises) as CO2 is used up. At higher pH values (above ∼9), when all the CO2 is used up, then a decrease in HCO3 concentrations will also result in increased pH since the alkalinity is maintained by the formation of OH […] some algae can also give off OH to the seawater medium in exchange for HCO3 uptake, bringing the pH up even further (to >10).”

Carbonic anhydrase (CA) is a ubiquitous enzyme, found in all organisms investigated so far (from bacteria, through plants, to mammals such as ourselves). This may be seen as remarkable, since its only function is to catalyse the inter-conversion between CO2 and HCO3 in the reaction CO2 + H2O ↔ H2CO3; we can exchange the latter Ci form to HCO3 since this is spontaneously formed by H2CO3 and is present at a much higher equilibrium concentration than the latter. Without CA, the equilibrium between CO2 and HCO3 is a slow process […], but in the presence of CA the reaction becomes virtually instantaneous. Since CO2 and HCO3 generate different pH values of a solution, one of the roles of CA is to regulate intracellular pH […] another […] function is to convert HCO3 to CO2 somewhere en route towards the latter’s final fixation by Rubisco.”

“with very few […] exceptions, marine macrophytes are not C 4 plants. Also, while a CAM-like [Crassulacean acid metabolism-like, see my previous post about the book for details] feature of nightly uptake of Ci may complement that of the day in some brown algal kelps, this is an exception […] rather than a rule for macroalgae in general. Thus, virtually no marine macroalgae are C 4 or CAM plants, and instead their CCMs are dependent on HCO3 utilization, which brings about high concentrations of CO2 in the vicinity of Rubisco. In Ulva, this type of CCM causes the intra-cellular CO2 concentration to be some 200 μM, i.e. ∼15 times higher than that in seawater.“

“deposition of calcium carbonate (CaCO3) as either calcite or aragonite in marine organisms […] can occur within the cells, but for macroalgae it usually occurs outside of the cell membranes, i.e. in the cell walls or other intercellular spaces. The calcification (i.e. CaCO3 formation) can sometimes continue in darkness, but is normally greatly stimulated in light and follows the rate of photosynthesis. During photosynthesis, the uptake of CO2 will lower the total amount of dissolved inorganic carbon (Ci) and, thus, increase the pH in the seawater surrounding the cells, thereby increasing the saturation state of CaCO3. This, in turn, favours calcification […]. Conversely, it has been suggested that calcification might enhance the photosynthetic rate by increasing the rate of conversion of HCO3 to CO2 by lowering the pH. Respiration will reduce calcification rates when released CO2 increases Ci and/but lowers intercellular pH.”

“photosynthesis is most efficient at very low irradiances and increasingly inefficient as irradiances increase. This is most easily understood if we regard ‘efficiency’ as being dependent on quantum yield: At low ambient irradiances (the light that causes photosynthesis is also called ‘actinic’ light), almost all the photon energy conveyed through the antennae will result in electron flow through (or charge separation at) the reaction centres of photosystem II […]. Another way to put this is that the chances for energy funneled through the antennae to encounter an oxidised (or ‘open’) reaction centre are very high. Consequently, almost all of the photons emitted by the modulated measuring light will be consumed in photosynthesis, and very little of that photon energy will be used for generating fluorescence […] the higher the ambient (or actinic) light, the less efficient is photosynthesis (quantum yields are lower), and the less likely it is for photon energy funnelled through the antennae (including those from the measuring light) to find an open reaction centre, and so the fluorescence generated by the latter light increases […] Alpha (α), which is a measure of the maximal photosynthetic efficiency (or quantum yield, i.e. photosynthetic output per photons received, or absorbed […] by a specific leaf/thallus area, is high in low-light plants because pigment levels (or pigment densities per surface area) are high. In other words, under low-irradiance conditions where few photons are available, the probability that they will all be absorbed is higher in plants with a high density of photosynthetic pigments (or larger ‘antennae’ […]). In yet other words, efficient photon absorption is particularly important at low irradiances, where the higher concentration of pigments potentially optimises photosynthesis in low-light plants. In high-irradiance environments, where photons are plentiful, their efficient absorption becomes less important, and instead it is reactions downstream of the light reactions that become important in the performance of optimal rates of photosynthesis. The CO2-fixing capability of the enzyme Rubisco, which we have indicated as a bottleneck for the entire photosynthetic apparatus at high irradiances, is indeed generally higher in high-light than in low-light plants because of its higher concentration in the former. So, at high irradiances where the photon flux is not limiting to photosynthetic rates, the activity of Rubisco within the CO2-fixation and -reduction part of photosynthesis becomes limiting, but is optimised in high-light plants by up-regulation of its formation. […] photosynthetic responses have often been explained in terms of adaptation to low light being brought about by alterations in either the number of ‘photosynthetic units’ or their size […] There are good examples of both strategies occurring in different species of algae”.

“In general, photoinhibition can be defined as the lowering of photosynthetic rates at high irradiances. This is mainly due to the rapid (sometimes within minutes) degradation of […] the D1 protein. […] there are defense mechanisms [in plants] that divert excess light energy to processes different from photosynthesis; these processes thus cause a downregulation of the entire photosynthetic process while protecting the photosynthetic machinery from excess photons that could cause damage. One such process is the xanthophyll cycle. […] It has […] been suggested that the activity of the CCM in marine plants […] can be a source of energy dissipation. If CO2 levels are raised inside the cells to improve Rubisco activity, some of that CO2 can potentially leak out of the cells, and so raising the net energy cost of CO2 accumulation and, thus, using up large amounts of energy […]. Indirect evidence for this comes from experiments in which CCM activity is down-regulated by elevated CO2

“Photoinhibition is often divided into dynamic and chronic types, i.e. the former is quickly remedied (e.g. during the day[…]) while the latter is more persistent (e.g. over seasons […] the mechanisms for down-regulating photosynthesis by diverting photon energies and the reducing power of electrons away from the photosynthetic systems, including the possibility of detoxifying oxygen radicals, is important in high-light plants (that experience high irradiances during midday) as well as in those plants that do see significant fluctuations in irradiance throughout the day (e.g. intertidal benthic plants). While low-light plants may lack those systems of down-regulation, one must remember that they do not live in environments of high irradiances, and so seldom or never experience high irradiances. […] If plants had a mind, one could say that it was worth it for them to invest in pigments, but unnecessary to invest in high amounts of Rubisco, when growing under low-light conditions, and necessary for high-light growing plants to invest in Rubisco, but not in pigments. Evolution has, of course, shaped these responses”.

“shallow-growing corals […] show two types of photoinhibition: a dynamic type that remedies itself at the end of each day and a more chronic type that persists over longer time periods. […] Bleaching of corals occurs when they expel their zooxanthellae to the surrounding water, after which they either die or acquire new zooxanthellae of other types (or clades) that are better adapted to the changes in the environment that caused the bleaching. […] Active Ci acquisition mechanisms, whether based on localised active H+ extrusion and acidification and enhanced CO2 supply, or on active transport of HCO3, are all energy requiring. As a consequence it is not surprising that the CCM activity is decreased at lower light levels […] a whole spectrum of light-responses can be found in seagrasses, and those are often in co-ordinance with the average daily irradiances where they grow. […] The function of chloroplast clumping in Halophila stipulacea appears to be protection of the chloroplasts from high irradiances. Thus, a few peripheral chloroplasts ‘sacrifice’ themselves for the good of many others within the clump that will be exposed to lower irradiances. […] While water is an effective filter of UV radiation (UVR)2, many marine organisms are sensitive to UVR and have devised ways to protect themselves against this harmful radiation. These ways include the production of UV-filtering compounds called mycosporine-like amino acids (MAAs), which is common also in seagrasses”.

“Many algae and seagrasses grow in the intertidal and are, accordingly, exposed to air during various parts of the day. On the one hand, this makes them amenable to using atmospheric CO2, the diffusion rate of which is some 10 000 times higher in air than in water. […] desiccation is […] the big drawback when growing in the intertidal, and excessive desiccation will lead to death. When some of the green macroalgae left the seas and formed terrestrial plants some 400 million years ago (the latter of which then ‘invaded’ Earth), there was a need for measures to evolve that on the one side ensured a water supply to the above-ground parts of the plants (i.e. roots1) and, on the other, hindered the water entering the plants to evaporate (i.e. a water-impermeable cuticle). Macroalgae lack those barriers against losing intracellular water, and are thus more prone to desiccation, the rate of which depends on external factors such as heat and humidity and internal factors such as thallus thickness. […] the mechanisms of desiccation tolerance in macroalgae is not well understood on the cellular level […] there seems to be a general correlation between the sensitivity of the photosynthetic apparatus (more than the respiratory one) to desiccation and the occurrence of macroalgae along a vertical gradient in the intertidal: the less sensitive (i.e. the more tolerant), the higher up the algae can grow. This is especially true if the sensitivity to desiccation is measured as a function of the ability to regain photosynthetic rates following rehydration during re-submergence. While this correlation exists, the mechanism of protecting the photosynthetic system against desiccation is largely unknown”.

July 28, 2015 Posted by | biology, books, Botany, Chemistry, evolution | Leave a comment

A few lectures

The Institute for Advanced Studies recently released a number of new lectures on youtube and I’ve watched a few of them.

Both this lecture and the one below start abruptly with no introduction, but I don’t think much stuff was covered before the beginning of this recording. The stuff in both lectures is ‘reasonably’ closely related to content covered in the book on pulsars/supernovae/neutron stars by McNamara which I recently finished (goodreads link) (…for some definitions of ‘reasonably’ I should perhaps add – it’s not that closely related, and for example Ramirez’ comment around the 50 minute mark that they’re disregarding magnetic fields seemed weird to me in the context of McNamara’s coverage). The first lecture was definitely much easier for me to follow than was the last one. The fact that you can’t hear the questions being asked I found annoying, but there aren’t that many questions being asked along the way. I was surprised to learn via google that Ramirez seems to be affiliated with the Niels Bohr Institute of Copenhagen (link).

Here’s a third lecture from the IAS:

I really didn’t think much of this lecture, but some of you might like it. It’s very non-technical compared to the first two lectures above, and unlike them the video recording did not start abruptly in the ‘middle’ of the lecture – which in this case on the other hand also means that you can actually easily skip the first 6-7 minutes without missing out on anything. Given the stuff he talks about in roughly the last 10 minutes of the lecture (aside from the concluding remarks) this is probably a reasonable place to remind you that Feynman’s lectures on the character of physical law are available on youtube and uploaded on this blog (see the link). If you have not watched those lectures, I actually think you should probably do that before watching a lecture like the one above – it’s in all likelihood a better use of your time. If you’re curious about things like cosmological scales and haven’t watched any of videos in the Khan Academy cosmology and astronomy lecture series, this is incidentally a good place to go have a look; the first few videos in the lecture series are really nice. Tegmark talks in his lecture about how we’ve underestimated how large the universe is, but I don’t really think the lecture adequately conveys just how mindbogglingly large the universe is, and I think Salman Khan’s lectures are much better if you want to get ‘a proper perspective’ of these things, to the extent that obtaining a ‘proper perspective’ is even possible given the limitations of the human mind.

Lastly, a couple more lectures from khanacademymedicine:

This is a neat little overview, especially if you’re unfamiliar with the topic.

July 24, 2015 Posted by | astronomy, Lectures, medicine, Physics, Psychology | Leave a comment

Photosynthesis in the Marine Environment (II)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

July 20, 2015 Posted by | biology, Botany, Chemistry | Leave a comment


Okay, this blog used to be quite active. At the moment it is not.

Last year I noted in September that I’d posted roughly one post every second day on average that year (“I’ve posted 125 posts in 257 days so far this year”, to be specific – here’s a link to the post in question, which however mainly deals with other stuff). Posting frequency has gone down a lot this year, and now I’m finding it difficult to even post once per week. I feel guilty about this, but I also feel silly about feeling guilty about it because I have many much worse and more significant things to feel guilty about (to quote Emil Cioran, “If I were to be totally sincere, I would say that I do not know why I live and why I do not stop living”. My current state of mind is not conducive to blogging).

I recently got the silly idea to leave a link to the blog elsewhere, which has meant that some people have come by and had a look. I’ve noticed that some of them (‘some of you…’) seem to have come by more than once. If you’re one of these people, you should note that the current posting frequency is very much below what has been usual for this blog, which translates into a) there being potentially a lot of stuff in the archives which might be of interest to you, and b) the observation that the current posting frequency is a noisy signal to use for making long-run blog activity-level estimates.

Aside from the book posts, another resource which might help you navigate older posts I’ve written here more efficiently is the category cloud in the sidebar. If you hover over individual categories you can see how many posts I’ve written about each topic, and if you click the category in question you’ll arrive at a page displaying the posts published on that topic – so for example if you click the ‘anthropology’ link to the right, you’ll get to the 53 posts I’ve written on this topic (other examples: medicine: 163 posts, biology: 159, history: 149, psychology: 137, mathematics: 71 – many of the topics featuring in the cloud have an at least to me reasonably high number of posts). As a side-note I should observe that when going through posts from the archives I’m not sure I would recommend reading posts more than a few years old (but this is again still a substantial number of posts, considering the average length of my posts (/time invested/post) and given the historically relatively high posting frequency). If you’re considering going semi-systematically through the archives – and yes, people sometimes do this – I’d strongly recommend you start out by reading posts published this year and then working your way back in time, rather than you starting out ‘at the beginning’ and working your way forward – the latter approach really cannot be recommended, and if you really want to read posts in the order they were written a much better approach than ‘starting at the beginning’ would be to start out at a random point in time nowhere near the beginning and then working your way forward (that ‘random point in time’ should be January 1st, 2013, or something along those lines – not some date in 2008). I should perhaps also caution that a couple of the categories may cause problems in some contexts; for example if you click the ‘lectures’ category, well, that’s a lot of lectures, and if you’re trying to load, say, 50+ hour-long lectures on one blog page in your browser that may cause problems e.g. with the browser becoming unresponsive (in retrospect this was not a good category to include in the categorization scheme, but I didn’t think of that when I started out). The ‘Khan Academy’ category suffers from the same problem; as I have watched and posted lectures on a wide variety of topics I however think this sort of problem is mostly limited to these two categories. I’m perfectly well aware that the categorization scheme could be improved – e.g. there’s both a ‘health’ category and a ‘medicine’ category, and some reasonably well-covered topics with a substantial number of posts do not feature in the cloud (for example there are 30 posts which deal with archaeology on this blog, despite there being no ‘archaeology’ category in the category cloud) – but the system is better than it used to be and I know from experience that when you have a blog with a very substantial number of posts you can spend a lot of time messing around with tweaking and optimizing this sort of thing, and my time is better spent doing other stuff.

I have no idea how the posting frequency will develop in the future, but in terms of the next weeks/months I’m pessimistic, which is part of why I wrote this post.

July 14, 2015 Posted by | meta | Leave a comment

Random stuff

It’s been a while since I posted anything here so I figured I should at least post something…

i. A few Khan Academy videos I watched a while back:

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(Bookmark remark: (‘Not completely devoid of slight inaccuracies as usual – e.g. in meningitis, neck stiffness is not as much as symptom as it is a clinical sign (see Chamberlain’s symptoms and signs…))’

(Bookmark remark: ‘Very simplified, but not terrible’)

(No comments)

ii. I previously read the wiki on strategic bombing during WW2, but the article did not really satisfy my curiosity and it turns out that the wiki also has a great (featured) article about Air raids on Japan (a topic not covered in a great amount of detail in the aforementioned wiki article). A few random observations from the article:

“Overall, the attacks in May destroyed 94 square miles (240 km2) of buildings, which was equivalent to one seventh of Japan’s total urban area.”

“In Tokyo, Osaka, Nagoya, Yokohama, Kobe, and Kawasaki, “over 126,762 people were killed … and a million and a half dwellings and over 105 square miles (270 km2) of urban space were destroyed.”[136] In Tokyo, Osaka and Nagoya, “the areas leveled (almost 100 square miles (260 km2)) exceeded the areas destroyed in all German cities by both the American and English air forces (approximately 79 square miles (200 km2)).”[136]

“In financial terms, the Allied air campaign and attacks on merchant ships destroyed between one third and a quarter of Japan’s wealth.[289]

“Approximately 40 percent of the urban area of the 66 cities subjected to area attacks were destroyed.[290] This included the loss of about 2.5 million housing units, which rendered 8.5 million people homeless.”

iii. A few longer lectures I’ve watched recently but did not think were particularly good: The Fortress (GM Akobian, Chess), Safety in the Nuclear Industry (Philip Thomas, Gresham College), War, Health and Medicine: The medical lessons of World War I (Mark Harrison, Gresham College – topic had potential, somehow did not like ‘the delivery'; others may find it worth watching).

iv. I play a lot of (too much) chess these days, so I guess it makes sense to post a little on this topic as well. Here’s a list of some of my recent opponents on the ICC: GM Zurab Azmaiparashvili, IM Jerzy Slaby, IM Petar Gojkovic, GM Goran Kosanovic, IM Jeroen Bosch, WGM Alla Grinfeld. I recall encountering a few titled players when I started out on the ICC and my rating was still adjusting and stabilizing, but now I’ve sort of fixed at a level around 1700-1800 in both the 1, 3 and 5 minute pools – sometimes a bit higher, sometimes a bit lower (and I’ve played relatively few 5 minute games so far)). This is a level where at least in bullet some of the semi-regular opponents I’ll meet in the rating pool are guys like these. I was quite dissatisfied with my play when I started out on the ICC because I hadn’t realized how tough it is to maintain a high rating there; having a closer look at which sort of opponents I was actually facing gradually made me realize I was probably doing quite well, all things considered. Lately I’ve been thinking that I have probably even been doing quite a bit better than I’d thought I had. See also this and this link. I’ve gradually concluded that I’m probably never ‘going back’ now that I’ve familiarized myself with the ICC server.

And yes, I do occasionally win against opposition like that, also on position – below an example from a recent game against a player not on the list above (there are quite a few anonymous title-holders as well on the server):

Click to view full size – the list to the lower left is a list of other players online on the server at that point in time, ordered by rating; as should be clear, lots of title-holders have relatively low ratings (I’m not completely sure which rating pool was displayed in the sidebar at that time, but the defaults on display for me are 5- or 3-minutes, so for example the international master ‘softrain’ thus had either a 3 or 5 minute rating of 1799 at that time. Do note that ICC requires proof for titles to display on the server; random non-titled players do not display as titleholders on the ICC (actually the formally approved titled accounts obviously do not account for all accounts held by title-holders as some titled players on the server use accounts which do not give away the fact that they have a title).

Here’s another very nice illustration of how tough the X-minute pools are (/how strong the players playing on the ICC are):

Wang Hao
Again, click to view in full size. This is Chinese Grandmaster Wang Hao‘s ICC account. Wang Hao is currently #39 on the FIDE list of active chess players in the world, with a FIDE rating above 2700. Even his 5-minute rating on the ICC, based on more than a thousand games, is below 2300, and his current 3 minute rating is barely above 2000. With numbers like those, I currently feel quite satisfied with my 1700-1800 ratings (although I know I should be spending less time on chess than I currently do).

v. A few words I’ve recently encountered on Anaphora, usufruct, mimesis, amanuensis, peculate, elide, ataraxia, myrmidon, velleity.

vi. A few other wiki links: Fritz Haber, Great Stink (featured), Edward Low (a really nice guy, it seems – “A story describes Low burning a French cook alive, saying he was a “greasy fellow who would fry well”, and another tells he once killed 53 Spanish captives with his cutlass.[6]“), 1940 Soviet ultimatum to Lithuania (‘good article’).

vii. A really cute paper from the 2013 Christmas edition of the British Medical Journal: Were James Bond’s drinks shaken because of alcohol induced tremor? Here’s the abstract:

Objective To quantify James Bond’s consumption of alcohol as detailed in the series of novels by Ian Fleming.

Design Retrospective literature review.

Setting The study authors’ homes, in a comfy chair.

Participants Commander James Bond, 007; Mr Ian Lancaster Fleming.

Main outcome measures Weekly alcohol consumption by Commander Bond.

Methods All 14 James Bond books were read by two of the authors. Contemporaneous notes were taken detailing every alcoholic drink taken. Predefined alcohol unit levels were used to calculate consumption. Days when Bond was unable to consume alcohol (such as through incarceration) were noted.

Results After exclusion of days when Bond was unable to drink, his weekly alcohol consumption was 92 units a week, over four times the recommended amount. His maximum daily consumption was 49.8 units. He had only 12.5 alcohol free days out of 87.5 days on which he was able to drink.

Conclusions James Bond’s level of alcohol intake puts him at high risk of multiple alcohol related diseases and an early death. The level of functioning as displayed in the books is inconsistent with the physical, mental, and indeed sexual functioning expected from someone drinking this much alcohol. We advise an immediate referral for further assessment and treatment, a reduction in alcohol consumption to safe levels, and suspect that the famous catchphrase “shaken, not stirred” could be because of alcohol induced tremor affecting his hands.”

viii. A couple of other non-serious links which I found hilarious:
1) The Prof(essor) or Hobo quiz (via SSC).
2) Today’s SMBC. I’ll try to remember the words in the votey in the highly unlikely case I’ll ever have use for them – in my opinion it would be a real tragedy if one were to miss an opportunity to make a statement like that, given that it was at all suitable to the situation at hand..

July 6, 2015 Posted by | Chess, diabetes, history, Khan Academy, Lectures, medicine, personal | Leave a comment


i. “The curse which lies upon marriage is that too often the individuals are joined in their weakness rather than in their strength, each asking from the other instead of finding pleasure in giving.” (Simone de Beauvoir)

ii. “Revolt against a tyrant is legitimate; it can succeed. Revolt against human nature is doomed to failure.” (André Maurois)

iii. “It is easy to be admired when one remains inaccessible.” (-ll-)

iv. “The life of a couple is lived on the mental level of the more mediocre of the two beings who compose it.” (-ll-)

v. “Marriage is not something that can be accomplished all at once; it has to be constantly reaccomplished. A couple must never indulge in idle tranquility with the remark: “The game is won; let’s relax.” The game is never won. […] A successful marriage is an edifice that must be rebuilt every day.” (-ll-)

vi. “Almost all men improve on acquaintance.” (-ll-)

vii. “There is no absurdity or contradiction to which passion may not lead a man. When love or hate takes control, reason must submit and then discover justifications for their folly.” (-ll-)

viii. “When I hear somebody sigh that “Life is hard,” I am always tempted to ask, “Compared to what?”” (Sydney J. Harris)

ix. “The most worthwhile form of education is the kind that puts the educator inside you, as it were, so that the appetite for learning persists long after the external pressure for grades and degrees has vanished. Otherwise you are not educated; you are merely trained.” (-ll-)

x. “As we grow older, we should learn that these are two quite different things. Character is something you forge for yourself; temperament is something you are born with and can only slightly modify. Some people have easy temperaments and weak characters; others have difficult temperaments and strong characters. We are all prone to confuse the two in assessing people we associate with. Those with easy temperaments and weak characters are more likable than admirable; those with difficult temperaments and strong characters are more admirable than likable.” (-ll-)

xi. “There seems to be a kind of order in the universe, in the movement of the stars and the turning of the earth and the changing of the seasons, and even in the cycle of human life. But human life itself is almost pure chaos. Everyone takes his stance, asserts his own rights and feelings, mistaking the motives of others, and his own.” (Katherine Anne Porter)

xii. “The historian’s one task is to tell the thing as it happened.” (Lucian of Samosata)

xiii. “Innocence most often is a good fortune and not a virtue.” (Anatole France) (L’innocence, le plus souvent, est un bonheur et non pas une vertu.)

xiv. “It is almost impossible systematically to constitute a natural moral law. Nature has no principles. She furnishes us with no reason to believe that human life is to be respected. Nature, in her indifference, makes no distinction between good and evil.” (-ll-) (Il est à peu près impossible de constituer systématiquement une morale naturelle. La nature n’a pas de principes. Elle ne nous fournit aucune raison de croire que la vie humaine est respectable. La nature, indifférente, ne fait nulle distinction du bien et du mal.)

xv. “When a thing has been said and well said, have no scruple: take it and copy it.” (-ll-) (Quand une chose a été dite et bien dite, n’ayez aucun scrupule, prenez-la, copiez.)

xvi. “The whole art of teaching is only the art of awakening the natural curiosity of young minds for the purpose of satisfying it afterwards.” (-ll-) (L’art d’enseigner n’est que l’art d’éveiller la curiosité des jeunes âmes pour la satisfaire ensuite.) (Two related links)

xvii. “All changes, even the most longed for, have their melancholy; for what we leave behind us is a part of ourselves; we must die to one life before we can enter another.” (-ll-) (Tous les changements, même les plus souhaités ont leur mélancolie, car ce que nous quittons, c’est une partie de nous-mêmes; il faut mourir à une vie pour entrer dans une autre.)

xviii. “We need some imaginative stimulus, some not impossible ideal such as may shape vague hope, and transform it into effective desire, to carry us year after year, without disgust, through the routine-work which is so large a part of life.” (Walter Pater)

xix. “When we lose one we love, our bitterest tears are called forth by the memory of hours when we loved not enough.” (Maurice Maeterlinck) (Quand nous perdons un être aimé, ce qui nous fait pleurer les larmes qui ne soulagent point, c’est le souvenir des moments où nous ne l’avons pas assez aimé.)

xx. “All our knowledge merely helps us to die a more painful death than the animals that know nothing.” (-ll-)

June 30, 2015 Posted by | quotes | Leave a comment

Promoting the unknown, a continuing series

June 26, 2015 Posted by | music | Leave a comment

Chronic depression (II)

This will be my last post about the book. Below I have added some more observations from some of the remaining chapters of the book – I noticed after I’d published this post that a few similar observations were also included in the first post, but in the end I decided against removing those arguably superfluous observations from this post (‘if the authors are allowed to repeat themselves, so am I…’).

“General avoidance often weaves its way through the fabric of depressed persons’ lives. One of my (Pettit’s) first clinical supervisors proposed that avoidance captures the true essence of depression. He argued that depression, at its root, is simply the opposite of participation. Although this is surely an overly broad and simplistic conceptualization of depression, it highlights the idea that depressed people are often passive recipients of life, rather than active participants in life. […] depressed persons often have less developed social networks […] depressed persons often exhibit generalized problems with social avoidance. What’s more, evidence suggests that depression is frequently preceded by anxiety of some form […]. Anxiety, of course, is characterized by avoidance of some feared object, cognition, or event. Although anxiety and general social avoidance certainly play a role in depression, a more specific form of social avoidance appears more pertinent to the propagation of depression: Avoidance of interpersonal conflict. We argue that depression is characterized, and even propagated, by a pattern of interpersonal conflict avoidance.”

“It is well-known that depression is associated with a number of factors related to interpersonal avoidance. Four such factors (i.e., low assertiveness, social withdrawal, general avoidance, and shyness) have specifically been identified as interpersonal characteristics of a large number of depressed individuals. […] Two characteristics of assertive behaviors may be of great difficulty to depressed persons. First, asserting oneself requires active engagement with others, which forces the depressed person to overcome feelings of general social anxiety, in addition to overcoming the lethargy and indifference that retard activity in general among such individuals. Second, and more important, assertive behaviors entail making explicit requests of others. Social conventions dictate that requests naturally merit a response, be it positive or negative, and it is at this point that the interpersonal stage for potential disharmony is set. To reach this point, one must conquer general social anxiety and place himself or herself in a position that allows for the possibility of negative, rejecting responses from others. This latter possibility appears to be the sticking point for many depressed persons. That is, depressed persons overcome social inhibition and inertia but are often unwilling to knowingly make themselves vulnerable to interpersonal rejection (although they often engage in behaviors that unknowingly place themselves at greater risk of rejection, such as excessive reassurance-seeking). […] assertiveness is often quite difficult for depressed people. Assertiveness is a necessary component of successful conflict negotiation. […] Avoiding assertive behaviors […] allows the individual to escape the discomfort of receiving negative reactions from others. It also, however, lessens the individual’s chances of obtaining desired outcomes”.

“Price, Sloman, Gardner, Gilbert, and Rohde (1994) argued that depression-related states and behaviors represent evolved forms of a primordial “involuntary subordinate strategy.” Price et al. contended that the involuntary subordinate strategy arose primarily as a means to cope with social competition and conflict, particularly losses therein. Out of this framework, the primary function of depression is to resolve interpersonal conflicts by presenting a “no threat” signal to others. Recent animal research has provided a degree of support for this proposition. In work with cynomolgus monkeys, Shively, Laber-Laird, and Anton (1997) manipulated the social status of a group of females, such that previously dominant monkeys became subordinate to formerly subordinate monkeys. This reduction in social status produced behavioral and hormonal reactions corresponding to depressive reactions among humans. Behaviorally, these monkeys exhibited fearful scanning of the environment, and more important, decreased social affiliation. These behavioral changes suggest that the newly subordinate monkeys were engaging in interpersonal avoidance. Similarly, the monkeys’ hormonal activity transformed, and they began hypersecreting cortisol. Research has demonstrated that hypersecretion of cortisol occurs more frequently among depressed humans […]. Other studies of animal social hierarchies and avoidance provide results consistent with those of Shively et al.”

“It is interesting to note that [a] pattern of being overly reserved or acquiescing with strangers, but extremely negative and antagonistic toward close relatives or romantic partners, is quite common among people who are depressed.”

“[R]esearch on a phenomenon called self-handicapping indicates that depressed people may gain self-protective and other rewards for depressive cognition and behavior. These rewards serve to maintain depressive cognition and behavior, and thereby perpetuate depression. Self-handicapping, a concept with origins in the field of social psychology, refers to placing obstacles in the way of one’s performance on tasks so as to furnish oneself with an external attribution when future outcomes are uncertain […]. That is, in the anticipation of a possible failure or a poor performance of some sort, people may either claim to have some limitation or actuallyproduce a limitation that provides an explanation in the event that they perform poorly. Self-handicapping is a frequently occurring phenomenon and is not limited to depressed people. […] A series of studies by Baumgardner (1991) found self-handicapping, in general, appears to occur in one of two situations. First, it may occur when people have experienced a failure privately and hold concerns about that failure becoming public. […] People may also self-handicap when they have experienced a success publicly yet doubt their ability to maintain that success.”

“[T]wo forms of self-handicapping exist: claimed and acquired (these have also been referred to as self-reported and behavioral, respectively). Claimed handicaps are likely more common than acquired handicaps. […] claimed handicaps occur when people believe that the handicap will explain their poor performance. Acquired handicaps, however, occur when people (a) believe the handicap will explain their poor performance and (b) believe that the handicap will lower others’ future expectations. Both forms of self-handicapping are likely relevant to depression […] evidence suggests that self-handicapping, at least behavioral self-handicapping, occurs more frequently among men than women […]. Self-reported, or claimed, handicaps occur at similar rates among men and women. […] empirical evidence confirms that depressed people are more likely to self-handicap than others.”

“[S]elf-handicapping operates on both intrapsychic and interpersonal levels. That is, the handicap provides the individual a cognitive explanation of the failed performance and also provides an explanation to others who may be privy to the failure. […] In addition to providing an external attribution for failure, barriers to performance increase the likelihood of internal credit for success (i.e., self-enhancement). Consequently, individuals who self-handicap apparently benefit regardless of whether they succeed or fail. […] people self-handicap in the social arena with the goal of promoting a more positive image. Ironically, self-handicapping tends to have the reverse effect [“the perception that people [are] making excuses for their performance” can be damaging, regardless of actual performance] […] lower social expectations presage lower social opportunities, which by itself is a bad prognostic sign for depression. […] Although further empirical research on the interpersonal sequelae of these behaviors is needed before firm conclusions are drawn, they likely reduce opportunities for positive social engagement, increase antagonistic behaviors from others, and reconfirm depressed persons’ views that they are socially inept. The end result, tragically, is continued and exacerbated depression. […] When taken to an extreme, chronic behavioral self-handicapping may significantly hinder interpersonal relations and lead to the development of maladaptive behaviors such as alcoholism and substance dependence.”

“Sacco [argued in a publication] that depressed people’s relationship partners develop mental representations of them that become relatively autonomous and that bias subsequent perceptions of their depressed partners. […] students [in the study] were more likely to attribute the depressed person’s failures to internal, controllable causes, whereas the nondepressed person’s failures were judged to result more from external, uncontrollable factors. Students also considered the causes for failures to be more stable and have a wider impact on the depressed person’s life, as compared with the nondepressed person. The reverse pattern was seen for successful events. That is, successes were judged to result from external, uncontrollable factors among the depressed person but internal, controllable factors for the nondepressed person. Both of these processes are important — depressed persons not only are blamed more for negative events but also are given less credit when positive events occur […] [That] [f]ailures [are] attributed to enduring traits of depressed persons [by others] [and are] viewed as under the control of depressed persons (i.e., the depressed person could have avoided the failure if they had really tried) […] is strikingly similar to depressed persons’ characteristic self-blaming attitude. They attribute their own failures to internal, stable, and global factors […] [In short,] most depressed persons’, attributions are clearly saturated with self-directed blame [and] others tend to adopt the same negative, blaming attributions and behaviors toward depressed persons. […] Once formed, the mental representations [of others] remain stable, regardless of whether the depression has remitted. […] representations of negative behaviors, once solidified, are more difficult to alter than representations of positive behaviors”.

“Others not only fail to recognize positive attributes but also alter their interaction styles with the depressed person. There is evidence that others’ negative views subserve the communications they emit to the negatively represented person. For example, the literature on attributions and relationship functioning has documented a connection between negative attributions and blaming communications […] In short, negative attributions lead to blaming communications and decreased relationship satisfaction. […] Blaming communications, in turn, represent a specific instance of the array of interpersonal indicators shown to predict depression chronicity. […] blame maintenance essentially assures that others will continue to hold negative views of depressed persons, regardless of the depressed persons’ presentations. […] In the context of specifically targeting blame maintenance (or any of the other processes), simultaneous attention to the other processes is warranted, lest resolution of one exacerbate another […]. As an example, blame may serve as a source of selfverification for depressed people. If blame is reduced, negative self-verification strivings may be thwarted, which, in turn, may lead to attempts to restore blame or to meet self-verification needs in other ways (e.g., by reducing performance in a previously adaptive domain) or in other relationships (e.g., with friends).”

“The tendency to avoid potentially uncomfortable social interactions is a stable trait, with shyness demonstrating remarkable consistency from early childhood until late adulthood. […] Shyness has been implicated as a risk factor for depression. […] Social skills represent another potential stable vulnerability to depression. […] people who display poor social skills are less likely to obtain positive outcomes and avoid negative outcomes in interpersonal relationships. As a result, they are more likely to become and stay depressed […] an impressive amount of evidence suggests that people who are depressed also display poor social skills. […] When maladaptive interpersonal behaviors compromise relationships, shy people are more likely to experience loneliness [and] less likely to have good social support […], and are therefore more likely to become even more depressed.”

June 25, 2015 Posted by | books, Psychology | Leave a comment


i. “Habit is habit and not to be flung out of the window by any man, but coaxed downstairs a step at a time.” (Mark Twain)

ii. “We can do without any article of luxury we have never had; but when once obtained, it is not in human natur’ to surrender it voluntarily.” (Thomas Chandler Haliburton)

iii. “An aphorism can contain only as much wisdom as overstatement will permit.” (Clifton Fadiman)

iv. “When you re-read a classic you do not see in the book more than you did before. You see more in you than there was before.” (-ll-)

v. “Statistician: A man who believes figures don’t lie, but admits that under analysis some of them won’t stand up either.” (Esar’s Comic Dictionary, by Evan Esar)

vi. “Many a man who falls in love with a dimple make the mistake of marrying the whole girl.” (-ll-)

vii. “The wise man will live as long as he ought, not as long as he can.” (Seneca the Younger)

viii. “No one is bound to be clever, but every one is under an obligation to be good.” (Jean-Louis Guez de Balzac) (Il n’y a personne qui soit tenu d’être habile; mais il n’y en a point qui ne soit obligé d’être bon.)

ix. “Solitude is certainly a fine thing; but there is pleasure in having someone who can answer, from time to time, that it is a fine thing.” (-ll-) (La solitude est certainement une belle chose, mais il y a plaisir d’avoir quelqu’un qui sache répondre, à qui on puisse dire de temps en temps, que c’est un belle chose.)

x. “Zealous men are ever displaying to you the strength of their belief, while judicious men are shewing you the grounds of it.” (William Shenstone)

xi. “A man has generally the good or ill qualities which he attributes to mankind.” (-ll-)

xii. “Any knowledge that doesn’t lead to new questions quickly dies out: it fails to maintain the temperature required for sustaining life.” (Wisława Szymborska)

xiii. “We are not indeed obliged always to speak what we think, but we must always think what we speak.” (Anne-Thérèse de Marguenat de Courcelles, marquise de Lambert)

xiv. “The most necessary disposition to relish pleasures is to know how to be without them.” (-ll-)

xv. “The pleasures of the world are deceitful; they promise more than they give. They trouble us in seeking them, they do not satisfy us when possessing them and they make us despair in losing them.” (-ll-)

xvi. “Would you be esteemed? live with persons that are estimable.” (-ll-)

xvii. “Nothing is more dangerous than an idea, when it’s the only one we have.” (Émile Chartier)

xviii. “Politeness is for people toward whom we feel indifferent, and moods, both good and bad, are for those we love.” (-ll-)

xix. “Happiness is a reward that comes to those that have not looked for it.” (-ll-)

xx. “It is very true that we ought to think of the happiness of others; but it is not often enough said that the best thing we can do for those who love us is to be happy ourselves.” (-ll-)

June 21, 2015 Posted by | quotes | Leave a comment

Chronic depression (I)

“This book develops a new explanatory framework for chronic depression […]. The framework rests on the premise that depression appears to include self-sustaining processes, that these processes may be, at least in part, interpersonal, and that understanding of these processes from an interpersonal standpoint may be useful in applied settings.”

I read this book a couple of days ago – here’s my short goodreads review. As mentioned in the review, the book includes quite a bit of rather old research and a lot of theorizing, which would probably be my two main points of criticism. I gave the book two stars on goodreads, but I should emphasize that this two star rating doesn’t really mean I think it’s a bad book; sometimes two star books are ‘borderline’, but this one isn’t and I found some of the coverage quite interesting. Given that the book explores how depression relates to interpersonal factors, I’ve of course read at least some stuff about many of the topics touched upon in the book before, e.g. here, here, here, here, and here. There was quite a bit of new stuff as well, though – in particular previous works dealing with depression which I’ve read have not had that much to say about how depression impacts people’s behaviours towards others and others’ behaviours towards the person who is depressed; the ‘interpersonal factors’ part of the coverage of previous works I’ve read on these topics has usually been limited to observations to the effect that lonely people are more likely to be depressed and similar, though the effects of social anxiety, often observed in depressed individuals (“the co-occurrence of depression and anxiety is very common. As many as 50% of people with major depression also experience an anxiety disorder” – a quote from the book), have admittedly also been pointed out to me before. This book however goes into more detail about these things and cover effects I do not recall having seen mentioned before.

Below I have added some observations from the book.

“There is good reason to emphasize the chronic nature of depression. First, some forms of depression, such as dysthymia, are chronic by definition (at least 2 years’ persistence in the case of dysthymia). Second, depression appears to be persistent within an episode, and, once it finally lets up, it tends to come back. Depression is both persistent within episodes and recurrent across episodes. […] Recurrence is defined as the reestablishment of clinical depression following a diagnosis-free period. […] Relapse is the resumption of symptoms in the vulnerable timeframe just following remission of a depressive episode. […] Several theorists have argued that depressive symptoms have a way of sustaining themselves. In this view, it is as if depression “feeds off itself,” “maintains its own momentum,” and “self-amplifies.” A key argument of this book is that these self-sustaining processes in depression may be interpersonal in nature. […] interpersonal factors are among the strongest predictors of depression chronicity. […] People with more interpersonal problems experience longer duration of depressive episodes”.

“Dysregulations of serotonin neurotransmitter systems, as well as of the hypothalamic-pituitary-adrenal axis (which regulates cortisol levels), have […] been proposed as a stable depression risk. There is little question that serotonin and cortisol levels are altered during depressive episodes (and related phenomena such as suicide). It is interesting to note that animals defeated in social skirmishes display behavioral and neurochemical similarities to depressed people […]. However, there is little persuasive evidence that dysregulation of these systems provides a full account of depression’s causes. [You can find some recent discussion of these topics, which also touches upon the observations included below, here] […] Regarding psychological explanations […], these theories can be grouped into those emphasizing cognitive vulnerability factors (e.g., pessimism), those emphasizing interpersonal vulnerability factors (e.g., excessive dependency), and those emphasizing personality-based vulnerability factors (e.g., high neuroticism, low extroversion). As with genetic—neurobiological explanations, psychological approaches have made some progress but cannot claim to provide a complete account of depression’s causes. […] shyness represents a stable vulnerability for depression. […] Although the notion that stable vulnerabilities like shyness only lead to depression in the context of some stressor is a reasonable view, it does not account for the finding that some shy (or otherwise vulnerable) people experience depression independent of negative life events. Partly in response to this quandary, a main purpose of this book is to explore interpersonal mechanisms whereby depression prolongs itself, even in the absence of external causes like negative life events.”

“there is some reason to suspect that depression’s properties may differ in certain subsets of people. Regarding late-life populations — for example, depressions that first occur in later life, as compared with those that first occur in early adulthood — occurrences may be about equally common in men and women (whereas “early” depressions are more common in women […]). In addition, late-life first occurrences are less associated with first-degree relatives’ depression risk […]; more related to neurological or medical disease […]; less severe […]; less associated with suicidal and anxious symptoms […]; and less related to personality problems, such as excessive dependency and avoidance […] Definitional problems plague depression research.”

“The incidence of clinical depression and depressive symptoms is two to three times higher among women than men. […] Although the gender differential in depression is consistent and well documented, little is known about the processes that underlie these differences.”

“In studies with follow-ups of 10 years or more, Coryell and Winokur (1992) found that 70% of people with one depressive episode subsequently experienced at least one more.”

“The link between life stress and depression is well-known — in general, the occurrence of life stressors appears to contribute to the development of depression […] Haramen (1991) theorized that depressed people are particularly stress-prone, in the sense that they actively generate negative life events. (It is important to distinguish active from intentional here — we do not believe that depressed people intentionally create problems for themselves, but that some of their behaviors have the unintended consequence of making life more stressful). If so, a self-sustaining process would be implicated in which formerly depressed people actively generate future life events that, in turn, sow the seeds of future depression. This would explain, at least in part, why depression persists and recurs. In a series of empirical studies, Hammen, Davila, Brown, Ellicott, and Gitlin, (1992) have documented the phenomenon of “stress generation.” […] In a 1-year study of women with depression, bipolar disorder, medical illness, or no disorder, Hammen (1991) showed that depressed women experienced more interpersonal stress to which the women themselves contributed (e.g., disputes with teachers or bosses; conflicts with children or partners), even compared with the women with bipolar disorder and medical illness. The finding was specific to interpersonal events — depressed women did not differ from others with regard to “fateful” events (i.e., those that really are randomly foisted on people). This result highlights the importance of interpersonal events, as well as the idea that nonrandom, self-produced negative events are characteristic of depressed people. Notably, the depressed women in Hammen’s (1991) study all experienced chronic forms of depression. This finding has been replicated in samples of men and women […] marital couples […] adolescent women […] children […] as well as by other research groups […] This line of research implicates the important possibility that, although depression may occur in the wake of stress, so may stress occur in depression’s wake.”

“Evidence suggests that people who are depressed demonstrate average problem-solving skills in impersonal settings (e.g., solving a puzzle), yet display specific problem-solving deficits in interpersonal settings […]. Examples of lapses in interpersonal problem solving may include the misperception of an offhand, trivial comment as an insulting attack; persistently avoiding someone who represents a key source of social support because of a minor misunderstanding; and angry, accusing confrontation of someone who was sincerely trying to help.”

“Many stress generation studies examine the links between self-reported depression and self-reported negative life stress. Because self-report is the source for assessment of both depression and stress, it is possible that increases in reported negative life events may merely reflect an increasingly hopeless outlook, rather than actual stress increases. A depressed person may thus perceive and report stress, even when stress is not actually present. […] the possible influence of increasing hopelessness in stress generation deserves attention […], especially insofar as hopelessness is a hallmark of major descriptive and etiological accounts of depression […] hopelessness, because of its embittering and stultifying effects on other people, may be particularly likely to disaffect others (i.e., to generate the stress of interpersonal rejection).”

“depression chronicity itself may be involved in stress generation. As depression persists, those who experience it may become more and more hopeless, and their significant others may become more and more burdened and disaffected. […] A second possibility is that hopelessness, because it has embittering and stultifying effects, may lead to cognitive representations of depressed people in the minds of significant others that are negative and change resistant. Sacco (1999) argued that once these representations are developed, they selectively guide attention and expectancies to confirm the representation. These social-cognitive processes may occur spontaneously and outside of awareness […] Once crystallized, cognitive representations of negative behaviors are more change resistant than representations of positive behaviors […]. Moreover, such representations gain momentum with use, in that they come to disproportionately influence social cognition relative to actual subsequent behaviors of the represented person […] With regard to others’ perceptions, the hopeless and potentially depressed person may face a very difficult problem: Continued hopelessness may only serve to maintain others’ negative views and thus generate stress in the form of criticism; positive changes, because they do not match others’ schemata, may be unnoticed or misattributed, leaving others’ negative representations unchanged.”

“there is accumulating evidence that depressed people actively generate their own stress, especially interpersonal stress […] For example, negative feedback-seeking (defined as the tendency to directly or indirectly invite criticism from other people and viewed as motivated by self-verification strivings […] represents a specific mechanism by which depression-prone people contribute to such stressors as relationship dissatisfaction and dissolution. Similarly, excessive reassurance-seeking (defined as the tendency to repeatedly and persistently demand assurance from others as to one’s lovability and worth, even after such is provided; […] also directly contributes to interpersonal stress. Interpersonal conflict avoidance ([…] defined as the anxious avoidance of self-assertion situations), also sows the seeds of stress generation. […] Research on self-handicapping and inoculation indicates that depressed people may gain self-protective and other rewards for depressive cognition and behavior. These rewards serve to maintain depressive cognition and behavior, and thereby [also] increase depression chronicity”.

[S]elf-verification theory […] proposes that people strive to attain and preserve predictable, certain, and familiar self-concepts. Further, the theory indicates that people accomplish this by actively seeking self-confirming interpersonal responses from those in their social environment. A key and perhaps counterintuitive implication of the theory is that there is no difference in the self-verification needs between people with positive self-concepts and people with negative self-concepts. […] In Study 1 [of Katz and Joiner (2002)], people in stable dating relationships were most intimate with and somewhat more committed to partners when they perceived that partners evaluated them as they evaluated themselves (even if negative). In Study 2, men reported the greatest esteem for same-sex roommates who evaluated them in a self-verifying manner (even if negative). Results from Study 2 were replicated and extended to both male and female roommate dyads in Study 3. […] In related research, it has been demonstrated that feedback that matches one’s self-concept is more “attention-grabbing,” more memorable, more rewarding, and more believable […]. In addition, a growing body of research suggests that people are more satisfied with and intimate in self-verifying relationships”.

“neither we nor self-verification theory imply that people enjoy the pain of abusive relationships and therefore seek them out. That is, self-verification theory is not talking about masochism. Rather, the theory points out the intractable dilemma of people with low self-esteem. If they choose (by whatever means, conscious or not) affirming relationships, relationship dysfunction, including abuse, may be in the cards. If they choose healthier relationships, they may have to grapple with the feeling that these relationships, despite their healthy qualities, do not provide them with self-confirmation. This represents a very difficult problem that has obvious effects on people’s well-being. […] there is growing evidence that people with depressive symptoms actively seek self-verification (i.e., negative feedback), often receive it, and may become depressed as a result. […] Depression may [also] perpetuate itself as a function of encouraging negative feedback-seeking. That is, people with depressive symptoms may solicit negative appraisals (and get them), and the receipt of negative feedback may serve to maintain or amplify their depression.”

“Coyne’s interpersonal theory of depression (1976b) proposed that in response to doubts as to their own worth or as to whether others truly care about them, initially nondepressed individuals may seek reassurance from others. Others may provide reassurance, but with little effect, because potentially depressed people doubt the reassurance, attributing it instead to others’ sense of pity or obligation. Potentially depressed people thus face a very difficult problem: They both need and doubt others’ reassurance. The need is emotionally powerful and thus may win out (at least temporarily), compelling the potentially depressed individuals to again “go back to the well” for reassurance from others; even if received, however, the reassurance is again doubted, and the pattern is repeated. Because the pattern is repetitive and resistant to change, the increasingly depressed persons’ significant others become confused, frustrated, and irritated and thus increasingly likely to reject the depressed persons and to become depressed themselves. […] We suggest that there is a considerable difference between the routine and adaptive solicitation of social support across distinct situations, and the repeated and persistent seeking of reassurance within the same situation, even when reassurance has already been provided.”

“Joiner and Katz (1999) reviewed the literature on contagious depression, and concluded that 40 findings from 36 separate studies provided substantial overall support for the proposition that depressed mood, and particularly, depressive symptoms, are contagious. […] excessive reassurance-seeking may explain, in part, when depression will be interpersonally transmitted. Taken together with research on interpersonal rejection, the work on contagious depression suggests that the joint operation of depressive symptoms and excessive reassurance-seeking disaffects significant others, by distancing them actually (e.g., ending the relationship) or functionally (e.g., emotional unavailability due to frustration or to contagious depression). […]  In the interpersonal arena, excessive reassurance-seeking and negative feedback-seeking compound one another by creating a particularly confusing and frustrating experience for relationship partners of depressed people. […] It is interesting to note that this process has been confirmed empirically: Joiner and Metalsky (1995) found that relationship partners of depressed people are particularly likely to evaluate them negatively if they engaged in both excessive reassurance-seeking and negative feedback-seeking.”

June 19, 2015 Posted by | books, Psychology | 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.

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, Geology, history, Physics, wikipedia, Zoology | Leave a comment

A few lectures

This one is not quite new, but I have never seen it or blogged it before. The sound is not completely optimal and as is so often the case for lectures like these it’s at times slightly annoying that you can’t tell what she’s pointing at when she’s talking about the slides, but these issues are relatively minor and should not keep you from watching the lecture.

This is a really nice introduction to some main ideas in the Nimzo Indian defence.

June 10, 2015 Posted by | astronomy, Chess, Lectures | 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, Zoology | Leave a comment

(10.000) Words…

“The language denotes the man. A coarse or refined character finds its expression naturally in a coarse or refined phraseology.” (Christian Nestell Bovee)


(Click to view details/full size)

Doff, pabulum, astringent, enervate, mountebank, argot, sluice, sequin, indite, vitiate, simper, tarry, casuistry, saturnine, sidle, meretricious, fugacious, esurient, scabrous, disquisition, winsome, sedulous, badinage, abeyance, effrontery, minatory, synecdoche, lubricious, adjure, asperse, encumbrance, careen, desuetude, syllepsis, limn, bathetic, surcease, taut, tribulation, chrysalis, farrier, vane, virago, rictus, gewgaw, vituperate, curdleichthyology, abrogate, stultify, approbatory, intrepid, nugatory, contumacious, append, vociferate, tenebrous, arrogate, vermilion, descry, sententious, repine, procrustean, undulate, abstemious, palter, iniquitous, endue, lugubrious, obloquy, obdurate, importunate, apotheosis, obviateperegrinate, sacrum, …

In a way it makes absolutely no sense for someone like me to spend as much time on this stuff as I have over the last year or two; I almost never engage in conversations with other people as I rarely interact with other people at all (and also tend to avoid conversations when I do because conversations are usually unpleasant), and when I do both interact and converse with other people I only rarely engage in conversations in English as my first language, and the first language of most of the people with whom I interact regularly, is Danish. If the aim were to improve my vocabulary in order to hide my stupidity (‘make me look smarter’), I’d do a lot better by learning some more fancy-sounding Danish words. As it is, I can’t even remember the last time I last looked up a word in a Danish dictionary, but it’s been at least a few years (if not much more than that). Of course on the other hand I do read a lot of books, and I only read books in English. So it’s probably not a complete waste of time. But I’ve been thinking lately that I might derive a lot more benefit from these sorts of activities, in the sense that more words would ‘stick’, if I actually had to interact with other people in English on a daily basis. It seems to me likely that in a sense my language production capabilities might not be improved as much by these activities as are my language consumption capabilities. What I mean by this is that I frequently encounter new words I’ve worked on in the books I read, but at the same time I’m very rarely forced to ever actually use any of them in conversations with other people, so I don’t. I don’t know enough about linguistics to tell if this distinction between production and consumption matters, but it seems to me that it might. On a related note I’ve recently had the idea that my activities in these areas might implicitly be lowering my opportunity costs of book-reading, compared to personal interactions with others, because these activities make it easier for me to read books but does not at the same time much improve upon my social skills (e.g. conversational skills; though I’m on a related note open to the suggestion that conversational skills and vocabulary size are in some contexts relevant to this discussion in fact perhaps best conceived of as orthogonal variables (which doesn’t help at all…)) – which is hardly what I would conceive of as a desirable outcome. Oh well.

As you should have been able to infer from the screencap above and/or the post title, I’ve by now reached another major milestone (here’s the first one) on the site as I have now ‘mastered’ more than 10.000 words on the site – I figured it made sense to make a post about this and related matters, and this is the post in question. In the time that has passed since I wrote the post to which I link above the site has undergone a few minor changes, but actually most of it works pretty much the same way it did last year; if you’re curious about how the site works and you have not heard about it before, go have a look at that post before reading on. As I have noted before I don’t fully trust the dictionary; or at least I like Webster’s online dictionary better, which is why the links above are all to Webster entries. I’ll often ‘check out’ particular words which I’m curious about after having encountered them on, because sometimes specific interpretations of the words in question are simply wrong, or at least so I would argue; if the site is trying to tell me that a specific word means X, but I ‘know’ that it doesn’t and the Webster entry also provides zero support for this specific usage/interpretation – or actively ‘disagrees’ – then I go with Webster and I’ll get annoyed at the people behind (again). One thing to note when making comparisons here is that in general I believe that the dictionary has a greater ‘range’ of meanings covered, which also means that if you look up the entries to which I link above you might fail to appreciate how many different types of questions that might be required for someone to ‘master’ the words on; if the word has some rare meaning in a very specific context, you can expect to ask you about that before you master the word (and you can expect a subset of those questions to be poorly worded, making you angry at the programmers behind the site). This also means that even if you think you know a word, the site may still cause you some challenges along the way.

I’ve used the site pretty much every week during the last year, though in some periods I used the site very little; the relative inactivity meant that I dropped out of the top 100 list for a while, but over the last weeks I’ve done some more work on the site, and I’m now back in the top 100. So I seem to focus more on improving my vocabulary than do most users on the site, which I actually find somewhat curious given that this tool has apparently been introduced to thousands of children throughout the US. On the other hand I’ve put in a lot of hours when you add them all together (the site actually logging the hours you put in is incidentally a new feature which was not present when I posted my first couple of posts about the site a year ago; I actually didn’t like this feature to start with, in part because I realized how much time I’d spent on this stuff).

The site is in my opinion very bad at explaining how to properly use the site to learn new words in the semi-long run, so I should probably explain why I recently came to ‘rediscover’ my joy of using the site. The main factor rekindling my interest was that I discovered how to use ‘lists’ to focus on new words. If you play the challenge without any bells and whistles and never add lists or anything, you’ll at some point get to a situation where you may well be given 500 questions without ‘mastering’ more than one or two new words; the site will recycle and recycle, asking you hundreds of questions about words you’ve already mastered and occasionally ask you about a new word which you’ll never get enough questions about to actually ever master – this is incredibly frustrating, to the point where I last year decided to send the staff an email suggesting they make changes to the algorithms, because this just seemed insane and probably killed the motivation for a lot of users. You’d put in 20 hours almost without being allowed to actually achieve mastery of any of the new words, then suddenly you’d ‘master’ more than a thousand words one after the other because now suddenly the site could be bothered to finally allow you to show that you’ve mastered those words the site last asked you about last April – or whenever. Or not – I have a suspicion that a lot of users have given up before this point was reached and just said ‘screw this’ before getting to the mastery questions at the end of the line, and that stuff like this may be part of the reason why I’m in the top 100 list now. If this is true it’s sort of sad, because it seems like such a big missed opportunity; what you’d ideally want is not just a site useful for learning a few thousand words after which the way the site is coded will contribute strongly to making many people sick of it, but rather a site which mixes new words and old in an optimal manner which might encourage users to keep using the site in the long run. People may argue about what’s an optimal mix, but I don’t think you can argue with a straight face that the current configuration is anywhere near this point – and if the perceived optimal mix is different for different people, why not allow users to have an influence on this variable in the first place? In a way the site implicitly does, in an admittedly roundabout manner, give people some influence on these sorts of variables via the lists, but I remained unaware of this for a very long time so a lot of users presumably don’t know this. Either way I certainly think I’m justified in assuming that far more care has been taken to optimize the user experience early on than has been taken to making sure the site remains useful even to people who’ve already mastered a lot of words; I’d argue that the site has an excessive focus on review questions, compared to questions about new words, and from personal experience it has seemed to me that this problem seems to get bigger and bigger the more words you learn.

Adding to the problems mentioned above it also does not help that some of the review questions – not many of them, but some – are so poorly thought out that you can’t really tell what the right answer is supposed to be despite knowing very well what the word means, so you risk getting stuck in loops where a substantial proportion of the questions you’re asked are about words you already know at least in part because the questions are bad (if you answer a tricky review question like that incorrectly, you’ll be given quite a few more other questions in the future about this word you don’t care about and don’t want to answer questions about anymore, because an incorrect answer to a review question is always taken by the site as an indication that you don’t understand the word as well as you should, and never as an indication that someone should seriously have a closer look at some of those shitty questions (again, there aren’t that many of them, but they’re very annoying to someone like me)).

So in short, if you’re contemplating using the site or already does, don’t do what I did – instead of just playing the basic challenge, at some point it becomes necessary to instead start exploring the lists. If you add a list to learn, the site will mostly (though not exclusively) focus on the words on the list you’re currently learning, avoiding the outcome outlined above. You can add more than one list simultaneously. I’ll put it bluntly – if you don’t use lists, this site will eventually kill pretty much all desire to use it, because you’ll eventually get to a point where you’ll feel you’re not making any progress and you’ll also at the same time have the distinct impression that the site actively refuses to give you any opportunities to making progress. I can’t be the only person who until recently did not use lists, and frankly without lists this site is a disaster waiting to happen. If you use lists well, it is however a very useful tool.

The site does not help you with grammar – if you know about a site that does, I’d be curious to know about it in the comments below. On a related note I thought I should end this post with this quite amusing quote from Jerome Jerome’s book Three Men on the Bummel, published in 1900:

“In the course of the century, I am inclined to think that Germany will solve her difficulty in this respect by speaking English. Every boy and girl in Germany, above the peasant class, speaks English. Were English pronunciation less arbitrary, there is not the slightest doubt but that in the course of a very few years, comparatively speaking, it would become the language of the world. All foreigners agree that, grammatically, it is the easiest language of any to learn. A German, comparing it with his own language, where every word in every sentence is governed by at least four distinct and separate rules, tells you that English has no grammar. A good many English people would seem to have come to the same conclusion; but they are wrong. As a matter of fact, there is an English grammar, and one of these days our schools will recognise the fact, and it will be taught to our children, penetrating maybe even into literary and journalistic circles. But at present we appear to agree with the foreigner that it is a quantity neglectable. English pronunciation is the stumbling-block to our progress. English spelling would seem to have been designed chiefly as a disguise to pronunciation. It is a clever idea, calculated to check presumption on the part of the foreigner; but for that he would learn it in a year.”

June 1, 2015 Posted by | language, personal, quotes | Leave a comment


i. “Without feeling abashed by my ignorance, I confess that I am absolutely unable to say. In the absence of an appearance of learning, my answer has at least one merit, that of perfect sincerity.” (Jean Henri Fabre)

ii. “It is right to be content with what we have, but never with what we are.” (James Mackintosh)

iii. “God is a hypothesis constructed by man to help him understand what existence is all about.” (Julian Huxley)

iv. “Sooner or later, false thinking brings wrong conduct.” (-ll-)

v. “A man has no reason to be ashamed of having an ape for his grandfather.” (Thomas Henry Huxley)

vi. “The improver of natural knowledge absolutely refuses to acknowledge authority, as such. For him, scepticism is the highest of duties; blind faith the one unpardonable sin.” (-ll-)

vii. “Perhaps the most valuable result of all education is the ability to make yourself do the thing you have to do, when it ought to be done, whether you like it or not; it is the first lesson that ought to be learned; and, however early a man’s training begins, it is probably the last lesson that he learns thoroughly.” (-ll-)

viii. “The doctrine that all men are, in any sense, or have been, at any time, free and equal, is an utterly baseless fiction.” (-ll-)

ix. “Try to learn something about everything and everything about something.” (-ll-)

x. “The known is finite, the unknown infinite; intellectually we stand on an islet in the midst of an illimitable ocean of inexplicability. Our business in every generation is to reclaim a little more land, to add something to the extent and the solidity of our possessions.” (-ll-)

xi. “There will always be people who are ahead of the curve, and people who are behind the curve. But knowledge moves the curve.” (Bill James)

xii. “No field of knowledge is so transparently simple as another’s.” (Michael Flynn)

xiii. “If we would have new knowledge, we must get us a whole world of new questions.” (Susanne Langer)

xiv. “Any ethics that needs religion is bad ethics […]  If you view religion as necessary for ethics, you’ve reduced us to the ethical level of 4 year olds. “If you follow these commandments you’ll go to heaven, if you don’t’ you’ll burn in hell” is just a spectacular version of the carrots and sticks with which you raise your children.” (Susan Neiman)

xv. “Truths are not relative. What is relative are opinions about truth.” (Nicolás Gómes Dávila)

xvi. “To tolerate does not mean to forget that what we tolerate does not deserve anything more.” (-ll-)

xvii. “At all times pseudoprofound aphorisms have been more popular than rigorous arguments.” (Mario Bunge)

xviii. “Instead […] of saying that Man is the creature of Circumstance, it would be nearer the mark to say that Man is the architect of Circumstance. It is Character which builds an existence out of Circumstance.” (George Lewes)

xix. “A man must be himself convinced if he is to convince others. The prophet must be his own disciple, or he will make none. Enthusiasm is contagious: belief creates belief.” (-ll-)

xx. “No deeply-rooted tendency was ever extirpated by adverse argument. Not having originally been founded on argument, it cannot be destroyed by logic.” (-ll-)

May 28, 2015 Posted by | quotes | Leave a comment


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.


“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, history, Khan Academy, Lectures, medicine, wikipedia | Leave a comment

Providing practical support for people with autism spectrum disorder – supported living in the community

I actually wasn’t planning on blogging this book because of how disappointing it was. Here’s what I wrote in my goodreads review:

“The last few chapters managed to almost push me all the way towards giving the book one star. You can’t just claim in a book like this that very expensive and comprehensive support systems which you’re dreaming about are cost-effective without citing a single study, especially not in a context where you’ve just claimed that activities which usually end up costing a lot of money will end up saving money. If you envision a much more comprehensive support system, you can’t not address obvious cost drivers.

Some interesting stuff and important observations are included in the book, but the level of coverage is not high and you should not take my two star (‘ok’) rating to indicate that I am in agreement with the author. The main reason why I ended up finishing it was that it was easy to read, not that it was a good book.”

There are no inline citations, and examples of things people with ASD might need help with and ways to help them with these problems seem to be derived from anecdotes, not systematic research. The author repeatedly emphasizes that aid should be individualized and focused on the specific needs of the person with ASD, and although this makes a lot of sense it also makes recommendations very difficult to evaluate (it’s a bit like figuring out what’s going on in the context of other areas of psychological research, where therapists will often ‘mix methods’ when dealing with specific individuals, making it impossible to figure out which components of the treatment regime are actually helpful and which are not because even if people were to try to figure this out, power issues would make it impossible to estimate the relevant interaction effects even in theory); though it should be made clear that the author makes no attempt to do this.

I however found some of the observations included and specific points raised in the book to be interesting, and I’ll mention some of these in the coverage below.

“Professional support needs to be developed and executed in partnership with people and families. For support to be successful, all concerned need to be aware of its objectives and agree with the plan and strategies involved.”

I decided to start out the coverage with this quote because the book is full of postulates like these. Often specific cases will be used to illustrate points like these, but don’t expect any references to actual research on such topics – it’s not that kind of book. The approach employed makes the book incredibly hard for me to evaluate; some of the ideas are presumably sound, but it’s difficult to tell which because they didn’t do the research. In theory it’s sometimes easy to see how a given approach mentioned might lead to, or solve, specific problems, but you’ll often get the idea that perhaps there are tradeoffs at play here which the advice included does not take into account, meaning that in specific cases an alternative solution/piece of advice to the one proposed might lead to better outcomes by trading off the problems associated with the approach mentioned and the problems associated with an alternative approach. In some cases you perhaps would ideally prefer the parents of an adult child living outside the home of the parents to not have too much influence on support strategies employed even though they might traditionally have had a significant role to play in the context of support provision, because the family’s approach to problem solving might be counterproductive, in which case a support plan not supported by the parents might still in some cases be preferable to one which would be supported by them. The emphasis on individualized care throughout the book is, it must be said, on the other hand helpful in terms of thinking about such potential problems, but you still have this impression that a lot of the suggestions in the book are really not based on anywhere near a sufficient amount of data or research, and although they’re often ‘common sense suggestions’ it’s quite clear from a lot of different areas of psychological research by now that common sense can sometimes deceive us.

A general problem I have with the book is, I think, that I think the author is too confident about which support approaches/strategies/etc. might, or might not, work – and perhaps a key reason why she seems overconfident is that she’s not provided the research results in the book which one would in my opinion need in order to draw conclusions like the ones she draws, regardless of whether such research actually exists. A related problem is that quite a few of the concluding statements in the book are at least partly normative statements (which I generally dislike to encounter in non-fiction), not descriptive statements (which I do like to encounter). In the book she repeatedly makes claims about what people with ASD are like without referring to research on these topics, so you’re wondering how she knows these things, and whether or not those claims are actually true, or just true for a small subset of people with ASD which she’s encountered or read about. Many of the observations seemed familiar to me (having encountered them either in other textbooks, or having personal experience with the issues mentioned) so I’d be likely to grant that many of the observations are valid, but you are sometimes wondering how she knows the things she claims to know. A big problem is actually the way she covers the material; she covers various topics in various chapters, but the way she does is makes it relatively hard for a reader to know which parts of a given chapter might actually be useful for a specific individual curious about these things; another way to do things might have been to split the coverage up into chapters about support provision for people with low support requirements, and other chapters about support provision for people with high support requirements. It’s made clear in the book that needs are different for different individuals, but you’re often sort of wondering which passages are most relevant to which groups of people with ASD. One might argue that ‘people ought to be able to tell this on their own’, but then we get to the problems that people with ASD tend to be bad at asking for support, perhaps not realizing that they need it, and the problem that people without ASD who do not know much about ASD perhaps have a difficult time figuring out which types of help might be useful in a specific setting. This stuff is difficult as it is, but I don’t think the way the coverage is structured in this book is helping at all with solving these sorts of issues.

Oh well, let’s move on…:

“The ultimate aim of support should be to improve skills and develop strategies to enable the person with ASD to feel in control and better able to cope independently.”

“The fact is that extremely able people with ASD frequently struggle with day-to-day life skills. Very intelligent students cannot organize themselves to launder their clothes, and may get up to find they are all dirty or still wet in the machine from several days ago. This is one of those superficially trivial things that can be a major problem to the person it repeatedly happens to. On a practical domestic front, what may be a massive difficulty for a person with ASD, may be an easily solved problem for someone without it. […] People with ASD like to have regular routines. The ability to adhere to routine is an advantage in many situations, and this skill can be used productively. Structure and organization can be brought to running the household. As a plan is constructed, problems can be considered and systems put in place to deal with them. A planning session when the individual collaborates with support to work out a weekly menu and the necessary shopping plan, gives the person more autonomy, than having someone turn up to go shopping or cook with them. Having someone alongside is sometimes necessary, but has the disadvantage of creating dependence. The individual is empowered instead by being facilitated to complete tasks independently. […] The best support methods promote independence. […] The aspects of forward planning can be incredibly challenging for a person with ASD, regardless of their intellectual level. […] As people with ASD have great difficulty seeing consequences or planning ahead, they may find it hard to become motivated if the gratification is not instant. Things have to be broken down and explained in a practical way.”

“Most people instigate minor changes easily. It may be more convenient to vary a normal routine on a particular day, even pleasurable. I might decide that as it is a sunny day I will go out, and do the housework in the evening. As a supporter for someone with ASD it is vital to remember, that he will not have the flexibility of thought that people generally have and so may need routines to be more stringently adhered to. Such a simple adjustment may not be easy, and it may be preferable to stay with the usual unless there is a strong argument for change. The world becomes easier to interpret if as much as possible is held constant. […] Change is easier to manage if we know it is coming. The better prepared someone is for a change, generally the easier it is to cope. For people with ASD, it helps if the preparation can be as concrete as possible.”

“The paradoxical nature of ASD is demonstrated again in attention span. The person will be absolutely absorbed, blocking out the rest of the world, when he is engrossed in something of particular interest; but at other times his attention span can be low. Most people will recognize the experience of being called away to answer a phone call, or speaking to a visitor and completely forgetting that they were in the middle of doing something. This distractibility is a common experience for those with ASD. […] I often think that ASD is the source of the stereotype of the ‘absent-minded professor’.”

A personal remark on these topics is perhaps in order here, and I add it because it is my impression that mass media portrails of individuals with these sorts of traits are generally if anything favourably inclined; in the sense that distractibility, forgetfulness and these sorts of traits are in those contexts in general traits you smile about and which are mildly funny. My impression is that the first word that springs to mind in these contexts is ‘amusing’, or something along those lines, not ‘annoying’. The downsides are usually to some extent neglected. However I know from Real Life experience that things like forgetfulness and distractability can be really annoying. Forgetting the key to your flat and locking yourself out of your flat (multiple times); forgetting to bring home your laptop from the university and having to go back and get it while worrying about whether or not it’s been stolen in the meantime (it fortunately wasn’t); getting caught up in an interesting exchange on the internet causing you to you forget that you turned on the stove an hour ago (or was it two hours ago? Time flies when you’re engaged in stuff that interests you…), so now you’ll have to spend another hour trying to clean the pot and separate the charred chunks of vegetables and the metal; getting a burn while taking something out of the oven because you were thinking about something else and didn’t pay sufficient attention to the task at hand – these things border from annoying to dangerous, as also noted in the book: “Depending on what we were doing, finding that we have left something in the middle of it can be anything from mildly annoying (left the kitchen half cleaned) to very distressing (left the pan on the hob and burnt the house down).” Similar observations might be made in the context of ‘clumsiness’ (not a diagnostic trait, but apparently often observed) and combinations of these traits. The sorts of things people often find amusing when they happen to, say, cartoon characters are a lot less funny when they happen to you personally, especially if you are having difficulties finding ways to address the issues and other people are impacted by them as well. Problems like these may cause amusement among others, but I know from both personal experience and the experiences of a good friend of mine that they may also cause profound exasperation among the people around you.

“Difficulty with communication is a core problem for those with autism spectrum disorder (ASD). Some people have little or no speech, some have an extensive vocabulary, some make grammatical mistakes, some have a wide use of language – but all people with ASD have problems with communication. These problems are extremely complex, leading to much misunderstanding, confusion and stress. The more sophisticated the person’s language is the greater the problem may be. Ros Blackburn, a highly intelligent British woman with ASD who gives many talks on the subject, highlights that a person’s ability can also be their greatest disability. As a verbal, intellectually able woman, she finds that people do not appreciate the support that she needs in everyday and social situations. The power to have a seemingly normal conversation can cause many troubles for a person with ASD by giving a false impression of their comprehension. […] Care should be taken not to give too much information at one time. People with ASD generally process language slowly and have difficulty handling a lot of verbal input. […] People with ASD work through matters slowly, and speed of discussion is problematic. […] So time needs to be offered to assimilate information before a response is expected. […] For most people with ASD, it is easier to talk if there are fewer people in the group. In a large meeting there is too much to take in, and few silences in which to process what has been said. […] They almost always prefer one to one conversation to group discussion, and small intimate gatherings to parties.”

“We all make blunders in relationships. We misjudge what is acceptable in a situation, mistake another person’s intention or misinterpret someone’s meaning. We then feel upset, isolated and embarrassed. People with ASD are more prone to doing this sort of thing than most – and they do experience the same unpleasant aftermath. […] Coping well is a double-edged sword; the better a person manages, the more likely he is to be judged harshly when he does make a mistake. […]  Some people with ASD are able to think their way through social situations. They teach themselves or have been taught to interpret non-verbal signals. They can use cognition to remember that the other person may feel differently to them, and to compute what their perception and emotions may be. This is a slow, cumbersome method compared to the automatic, rapid assimilation that those without ASD make. Even those who compensate well appear slow, stilted, awkward, and are liable to make significant mistakes.”

“Neurotypical people (NTs) are as lacking in empathy towards people with ASD as vice versa.” This is in my opinion a bold claim and I’m not sure it’s true, but I think she does have a point here. I think it’s likely that NTs often judge people with ASD based on the standards of NTs; standards which may well be impossible for the person with ASD to ever meet, regardless of the amount of effort the individual puts into meeting those standards. She however argues later on in the coverage that: “Most people are not unkind, but are unthinking or, because of lack of knowledge about disability, make incorrect assumptions.” This seems plausible.

“The rigidity of AS thinking and the tendency to obsess means that a worry can escalate and dominate a person’s life. […] As a basic rule of thumb, regular, familiar routines are better stress busters than a novel idea. A holiday, for example, is more likely to add to stress than relieve it.” (This sounds very familiar, and I’ll keep this quote in mind…)

“Many people with ASD remain more susceptible to parental influence than the majority of their peers. […] All people with ASD, including the highly intelligent, are susceptible to being led by others and it is very easy for the person offering support, either knowingly or unwittingly, to lead the person down a route, which is not the course he wants to follow.”

“Social inabilities create problems for people with autism spectrum disorder (ASD) in establishing peer relationships and so naturally accessing the support that evolves between members of groups, such as work colleagues, fellow students or regulars in the pub. Asking for assistance appropriately will be challenging for people with ASD. […] adults often only appear on the services ‘radar’ when they reach crisis point. Forty-nine per cent of adults with ASD are still living with their parents. […] Only 6 per cent of adults with ASD are in full-time employment [no sources provided, US]”

“It is not always possible to tell from meeting a person or even from having regular contact with him that he has autism spectrum disorder (ASD). Individuals therefore face the decision as to whether or not to disclose that they have the disorder. […] Generally disclosure is on a sliding scale. Most people tell close family; whilst it would probably be inappropriate to tell a casual stranger. Some will disclose to professionals, but prefer to keep the information from social contacts. […] There are no easy answers as to who and when to tell. Disclosure to professionals in formal situations appears advisable so that all are aware of the condition and any differences are accepted and planned for. Informal social situations are more fluid and difficult to read.”

“NAS statistics show that only six per cent of people with autism spectrum disorder (ASD) (12% of those with Asperger Syndrome (AS)) in the UK are in full-time employment. This compares with 49 per cent of people with general disabilities who are employed. […] Given the talents which many with ASD have, this is a great loss to the workforce. […] Traits common to ASD, such as conscientiousness, attention to detail, perseverance and loyalty, are great assets to an employer. […] People with ASD tend to be loyal, to stick to routines and dislike change. […] The characteristics of the disorder mean that the individual may not make a good impression at interview. Social skills will not be a forté. […] The employer needs to be aware of any ASD traits the person displays, such as lack of eye contact. Questions may be prepared with support so that they elicit the information needed, but are specific, factual and clear. Broad questions, such as, ‘Tell me about yourself ’, will leave the interviewee floundering. […] Interviews are not always the most appropriate way of assessing candidates, especially not those with ASD.”

The author does not address in the book the specific problems and tradeoffs related to the question of whether or not it’s optimal to disclose an autism spectrum disorder to a potential employer, but rather seems to take it for granted that the interviewee should always disclose, preferably beforehand. I’ve given this a lot of thought, and I’m really not convinced this is always the right approach.

May 17, 2015 Posted by | books, medicine, personal, Psychology | Leave a comment

Random stuff/Open Thread

i. A lecture on mathematical proofs:

ii. “In the fall of 1944, only seven percent of all bombs dropped by the Eighth Air Force hit within 1,000 feet of their aim point.”

From wikipedia’s article on Strategic bombing during WW2. The article has a lot of stuff. The ‘RAF estimates of destruction of “built up areas” of major German cities’ numbers in the article made my head spin – they didn’t bomb the Germans back to the stone age, but they sure tried. Here’s another observation from the article:

“After the war, the U.S. Strategic Bombing Survey reviewed the available casualty records in Germany, and concluded that official German statistics of casualties from air attack had been too low. The survey estimated that at a minimum 305,000 were killed in German cities due to bombing and estimated a minimum of 780,000 wounded. Roughly 7,500,000 German civilians were also rendered homeless.” (The German population at the time was roughly 70 million).

iii. Also war-related: Eddie Slovik:

Edward Donald “Eddie” Slovik (February 18, 1920 – January 31, 1945) was a United States Army soldier during World War II and the only American soldier to be court-martialled and executed for desertion since the American Civil War.[1][2]

Although over 21,000 American soldiers were given varying sentences for desertion during World War II, including 49 death sentences, Slovik’s was the only death sentence that was actually carried out.[1][3][4]

During World War II, 1.7 million courts-martial were held, representing one third of all criminal cases tried in the United States during the same period. Most of the cases were minor, as were the sentences.[2] Nevertheless, a clemency board, appointed by the Secretary of War in the summer of 1945, reviewed all general courts-martial where the accused was still in confinement.[2][5] That Board remitted or reduced the sentence in 85 percent of the 27,000 serious cases reviewed.[2] The death penalty was rarely imposed, and those cases typically were for rapes or murders. […] In France during World War I from 1917 to 1918, the United States Army executed 35 of its own soldiers, but all were convicted of rape and/or unprovoked murder of civilians and not for military offenses.[13] During World War II in all theaters of the war, the United States military executed 102 of its own soldiers for rape and/or unprovoked murder of civilians, but only Slovik was executed for the military offense of desertion.[2][14] […] of the 2,864 army personnel tried for desertion for the period January 1942 through June 1948, 49 were convicted and sentenced to death, and 48 of those sentences were voided by higher authority.”

What motivated me to read the article was mostly curiosity about how many people were actually executed for deserting during the war, a question I’d never encountered any answers to previously. The US number turned out to be, well, let’s just say it’s lower than I’d expected it would be. American soldiers who chose to desert during the war seem to have had much, much better chances of surviving the war than had soldiers who did not. Slovik was not a lucky man. On a related note, given numbers like these I’m really surprised desertion rates were not much higher than they were; presumably community norms (”desertion = disgrace’, which would probably rub off on other family members…’) played a key role here.

iv. Chess and infinity. I haven’t posted this link before even though the thread is a few months old, and I figured that given that I just had a conversation on related matters in the comment section of SCC (here’s a link) I might as well repost some of this stuff here. Some key points from the thread (I had to make slight formatting changes to the quotes because wordpress had trouble displaying some of the numbers, but the content is unchanged):

“Shannon has estimated the number of possible legal positions to be about 1043. The number of legal games is quite a bit higher, estimated by Littlewood and Hardy to be around 1010^5 (commonly cited as 1010^50 perhaps due to a misprint). This number is so large that it can’t really be compared with anything that is not combinatorial in nature. It is far larger than the number of subatomic particles in the observable universe, let alone stars in the Milky Way galaxy.

As for your bonus question, a typical chess game today lasts about 40­ to 60 moves (let’s say 50). Let us say that there are 4 reasonable candidate moves in any given position. I suspect this is probably an underestimate if anything, but let’s roll with it. That gives us about 42×50 ≈ 1060 games that might reasonably be played by good human players. If there are 6 candidate moves, we get around 1077, which is in the neighbourhood of the number of particles in the observable universe.”

“To put 1010^5 into perspective:

There are 1080 protons in the Universe. Now imagine inside each proton, we had a whole entire Universe. Now imagine again that inside each proton inside each Universe inside each proton, you had another Universe. If you count up all the protons, you get (1080 )3 = 10240, which is nowhere near the number we’re looking for.

You have to have Universes inside protons all the way down to 1250 steps to get the number of legal chess games that are estimated to exist. […]

Imagine that every single subatomic particle in the entire observable universe was a supercomputer that analysed a possible game in a single Planck unit of time (10-43 seconds, the time it takes light in a vacuum to travel 10-20 times the width of a proton), and that every single subatomic particle computer was running from the beginning of time up until the heat death of the Universe, 101000 years ≈ 1011 × 101000 seconds from now.

Even in these ridiculously favorable conditions, we’d only be able to calculate

1080 × 1043 × 1011 × 101000 = 101134

possible games. Again, this doesn’t even come close to 1010^5 = 10100000 .

Basically, if we ever solve the game of chess, it definitely won’t be through brute force.”

v. An interesting resource which a friend of mine recently shared with me and which I thought I should share here as well: Nature Reviews – Disease Primers.

vi. Here are some words I’ve recently encountered on augury, spangle, imprimatur, apperception, contrition, ensconce, impuissance, acquisitive, emendation, tintinnabulation, abalone, dissemble, pellucid, traduce, objurgation, lummox, exegesis, probity, recondite, impugn, viscid, truculence, appurtenance, declivity, adumbrate, euphony, educe, titivate, cerulean, ardour, vulpine.

May 16, 2015 Posted by | Chess, Computer science, history, Lectures, mathematics | Leave a comment


i. “Calumny can injure you only if you reflect yourself in others and not in your conscience.” (Fausto Cercignani).

ii. “Emulation can be positive, if you succeed in avoiding imitation.” (-ll-).

iii. “Your identity is like your shadow: not always visible and yet always present.” (-ll-).

iv. “Sometimes moderation is a bad counselor.” (-ll-).

v. “It is error only, and not truth, that shrinks from inquiry.” (Thomas Paine)

vi. “A long habit of not thinking a thing wrong, gives it a superficial appearance of being right, and raises at first a formidable outcry in defense of custom.” (-ll-)

vii. “A body of men, holding themselves accountable to nobody, ought not to be trusted by any body.” (-ll-)

viii. “All national institutions of churches, whether Jewish, Christian, or Turkish, appear to me no other than human inventions set up to terrify and enslave mankind, and monopolize power and profit.” (-ll-)

ix. “Example has more followers than reason.” (Christian Nestell Bovee)

xii. “Education is an ornament for the prosperous, a refuge for the unfortunate.” (Democritus)

xiii. “There is no such thing as a Scientific Mind. Scientists are people of very dissimilar temperaments doing different things in very different ways. Among scientists are collectors, classifiers and compulsive tidiers-up; many are detectives by temperament and many are explorers; some are artists and others artisans. There are poet-scientists and philosopher-scientists and even a few mystics. What sort of mind or temperament can all these people be supposed to have in common? Obligative scientists must be very rare, and most people who are in fact scientists could easily have been something else instead.” (Peter Medawar)

xiv. “The purpose of scientific enquiry is not to compile an inventory of factual information, nor to build up a totalitarian world picture of natural Laws in which every event that is not compulsory is forbidden. We should think of it rather as a logically articulated structure of justifiable beliefs about nature.” (-ll-)

xv.  “the spread of secondary and latterly tertiary education has created a large population of people, often with well-developed literary and scholarly tastes, who have been educated far beyond their capacity to undertake analytical thought.” (-ll-)

xvi. “If a person a) is poorly, b) receives treatment intended to make him better, and c) gets better, no power of reasoning known to medical science can convince him that it may not have been the treatment that restored his health.” (-ll-)

xvii. “I once spoke to a human geneticist who declared that the notion of intelligence was quite meaningless, so I tried calling him unintelligent. He was annoyed, and it did not appease him when I went on to ask how he came to attach such a clear meaning to the notion of lack of intelligence. We never spoke again.” (-ll-)

xviii. “There is no feeling so simple that it is not immediately complicated and distorted by introspection.” (André Gide)

xix. “Men need history; it helps them to have an idea of who they are.” (V. S. Naipaul)

xx. “There is a great deal of difference between the eager man who wants to read a book, and the tired man who wants a book to read.” (G. K. Chesterton)

May 15, 2015 Posted by | quotes | Leave a comment

Wodehouse (II)

Here’s a link to the first post in this series. The quotes below are from the book Full Moon, which is one of the books in Wodehouse’ Blandings Castle series. I have not read a book in that series which I did not enjoy reading.

“I really am feeling astoundingly well. It’s what I’ve always said – alcohol’s a tonic. Where most fellows go wrong is that they don’t take enough of it. […] He never drank tea, having always had a prejudice against the stuff since his friend Buffy Struggles back in the nineties had taken to it as a substitute for alcohol and had perished miserably as a result. (Actually what had led to the late Mr Struggles’s turning in his dinner pail had been a collision in Piccadilly with a hansom cab, but Gally had always felt that this could have been avoided if the poor dear old chap had not undermined his constitution by swilling a beverage whose dangers are recognized by every competent medical authority.)”

“Some little while later Veronica, starting the conversational ball rolling once more, said that she had been bitten on the nose that afternoon by a gnat. Tipton, shuddering at this, said that he had never liked gnats. Veronica said that she too, did not like gnats, but that they were better than bats. Yes, assented Tipton, oh, sure, yes a good deal better than bats. Of cats Veronica said she was fond, and Tipton agreed that cats as a class were swell. On the subject of rats they were also as one, both holding strong views regarding their lack of charm.
The ice thus broken, the talk flowed pretty easily until Veronica said that perhaps they had better be going in now. Tipton said, “Oh, shoot!” and Veronica said, “I think we’d better,” and Tipton said, “Well, okay, if we must.” His heart was racing and bounding as he accompanied her to the drawing-room. If there had ever been any doubt in his mind that this girl and he were twin souls, it no longer existed. It seemed to him absolutely amazing that two people should think so alike on everything – on gnats, bats, cats, rats, in fact absolutely everything.”

“Tipton removed his gaze from the cow. As a matter of fact, he had seen about as much of it as he wanted to see. A fine animal, but, as is so often the case with cows, not much happening.”

“‘Look here, Guv’nor, will you do something for me?’
‘What?’ asked Lord Emsworth, cautiously.
‘What were you thinking of buying Vee?’
‘I had in mind some little inexpensive trinket, such as girls like to wear. A wrist watch was your aunt’s suggestion.’
‘Good. That fits my plans like the paper on the wall. Go to Aspinall’s in Bond Street. They have wrist watches of all descriptions. And when you get there, tell them that you are empowered to act for F. Threepwood. I left Aggie’s necklace with them to be cleaned, and at the same time ordered a pendant for Vee. Tell them to send the necklace to … Are you following me, Guv’nor?’
‘No,’ said Lord Emsworth.
‘It’s quite simple. On the one hand, the necklace; on the other, the pendant. Tell them to send the necklace to Aggie at the Ritz Hotel, Paris—‘
‘Who’, asked Lord Emsworth, mildly interested, ‘is Aggie?’
‘Come, come, Guv’nor. This is not the old form. My wife.’
‘I thought your wife’s name was Frances.’
‘Well, it isn’t. It’s Niagara.’
‘What a peculiar name.’
‘Her parents spent their honeymoon at the Niagara Falls hotel.’
‘Niagara is a town in America, is it not?’
‘Not so much a town as a rather heavy downpour.’
‘A town, I always understood.’
‘You were misled by your advisers, Guv’nor. But do you mind if we get back to the res. Time presses. Tell these Aspinall birds to mail the necklace to Aggie at the Ritz Hotel, Paris, and bring back the pendant with you. Have no fear that you will be left holding the baby—‘
Again Lord Emsworth was interested. This was the first he’d heard of this.
‘Have you a baby? Is it a boy? How old is he? What do you call him? Is he at all like you?’ he asked, with a sudden pang of pity for the unfortunate suckling.
‘I was speaking figuratively, Guv’nor,’ said Freddie patiently. ‘When I said, “Have no fear that you will be left holding the baby,” I meant, “Entertain no alarm lest they may shove the bill off on you.” The score is all paid up. Have you got it straight?’
‘Let me hear the story in your own words.’
‘There is a necklace and a pendant—‘
‘Don’t go getting them mixed.’
‘I never get anything mixed. You wish me to have the pendant sent to your wife and to bring back—‘
‘No, no, the other way round.’
‘Or, rather, as I was just about to say, the other way round. It is all perfectly clear. Tell me,’ said Lord Emsworth, returning to the subject which really interested him, ‘why is Frances nicknamed Niagara?’
‘Her name isn’t Frances, and she isn’t.’
‘Isn’t what?’
‘Nicknamed Niagara.’
‘You told me she was. Has she taken the baby to Paris with her?’
Freddie produced a light blue handkerchief from his sleeve and passed it over his forehead.
‘Look here, Guv’nor, do you mind if we call the whole thing off? Not the necklace and pendant sequence, but all this stuff about Frances and babies—‘
‘I like the name Frances.’
‘Me, too. Music to the ears. But shall we just let it go, just forget all about it? We shall both feel easier and happier.’
Lord Emsworth uttered a pleased exlamation.
‘Not Niaraga. Chicago. This is the town I was thinking of. There is a town in America called Chicaco.'”

“‘I’ve got it,’ he said, returning. ‘The solution came to me in a flash. We will put the pig in Veronica’s room.’
A rather anxious expression stole across Freddie’s face. Of the broad general principle of putting pigs in girls’ rooms he of course approved, but he did not like that word ‘we’. […]
‘What’s the good of putting pigs in Vee’s room?’
‘My dear fellow, have you no imagination? What happens when a girl finds a pig in her room?’
‘I should think she’d yell her head off.’
‘Precisely. I confidently expect Veronica to raise the roof. Whereupon, up dashes young Plimsoll to her rescue. If you can think of a better way to bring two young people together, I should be interested to hear it.'”

“‘Is he wanted by the police?’
‘No, he is not wanted by the police.’
‘How I sympathize with the police,’ said Lady Hermione. ‘I know just how they feel.'”

May 12, 2015 Posted by | books | Leave a comment


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