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


i. “Everyone realizes that one can believe little of what people say about each other. But it is not so widely realized that even less can one trust what people say about themselves.” (Rebecca West)

ii. “There is no means of proving it is preferable to be than not to be.” (Emil Cioran)

iii. “The obsession with suicide is characteristic of the man who can neither live nor die, and whose attention never swerves from this double impossibility.” (-ll-)

iv. “Once upon a time leftists and radicals talked of liberation or the abolition of work. Now the talk is about full employment.” (Russell Jacoby)

v. “Among artists without talent Marxism will always be popular, since it enables them to blame society for the fact that nobody wants to hear what they have to say.” (Clive James)

vi. “the moment when a historian says that something had to happen is the moment when he stops writing history and starts predicting the past.” (-ll-)

vii. “The answer to the nagging conundrum of how a civilized country like Germany could produce the Holocaust is that Germany ceased to be civilized from the moment Hitler came to power.” (-ll-)

viii. “One of the most obvious facts about grown-ups to a child is that they have forgotten what it is like to be a child.” (Randall Jarrell)

ix. “…in this world, often, there is nothing to praise but no one to blame…” (-ll-)

x. “The people who live in a Golden Age usually go around complaining how yellow everything looks.” (-ll-)

xi. “Even to-day, […] there are few men who doubt that motorcars will in five years’ time be more comfortable and cheaper than to-day. They believe in this as they believe that the sun will rise in the morning. The metaphor is an exact one. For, in fact, the common man, finding himself in a world so excellent, technically and socially, believes that it has been produced by nature, and never thinks of the personal efforts of highly-endowed individuals which the creation of this new world presupposed. Still less will he admit the notion that all these facilities still require the support of certain difficult human virtues, the least failure of which would cause the rapid disappearance of the whole magnificent edifice.” (José Ortega y Gasset)

xii. “Even in the most insignificant details of our daily life, none of us can be said to constitute a material whole, which is identical for everyone, and need only be turned up like a page in an account-book or the record of a will; our social personality is created by the thoughts of other people.” (Marcel Proust)

xiii. “We are not provided with wisdom, we must discover it for ourselves, after a journey through the wilderness which no one else can take for us, an effort which no one can spare us.” (-ll-)

xiv. “Central to the paradigm that the mind is modulated by hormones is the recognition that the stuff of thought is not caged in the brain but is scattered all over the body; regulatory hormones are ubiquitous. (Richard Bergland)

xv. “There is a relation between persons and role. But the relationship answers to the interactive system—to the frame—in which the role is performed and the self of the performer is glimpsed. Self, then, is not an entity half-concealed behind events, but a changeable formula for managing oneself during them. Just as the current situation prescribes the official guise behind which we will conceal ourselves, so it provides where and how we will show through, the culture itself prescribing what sort of entity we must believe ourselves to be in order to have something to show through in this manner.” (Erving Goffman)

xvi. “The happiness of most people we know is not ruined by great catastrophes or fatal errors, but by the repetition of slowly destructive little things.” (Ernest Dimnet)

xvii. “The admonitions of those who seldom remonstrate are more effective than the commands of naggers.” (Ruth Rendell, A judgement in stone)

xviii. “Like all true eccentrics, he thought other people very odd.” (-ll-)

xix. “selfishness is not living as one wishes to live, it is asking others to live as one wishes to live.” (-ll-)

xx. “It takes many good deeds to build a good reputation, and only one bad one to lose it.” (Benjamin Franklin)


July 14, 2015 Posted by | quotes | 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:

(No comments)

(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’)

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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