Econstudentlog

Isotopes

A decent book. Below some quotes and links.

“[A]ll mass spectrometers have three essential components — an ion source, a mass filter, and some sort of detector […] Mass spectrometers need to achieve high vacuum to allow the uninterrupted transmission of ions through the instrument. However, even high-vacuum systems contain residual gas molecules which can impede the passage of ions. Even at very high vacuum there will still be residual gas molecules in the vacuum system that present potential obstacles to the ion beam. Ions that collide with residual gas molecules lose energy and will appear at the detector at slightly lower mass than expected. This tailing to lower mass is minimized by improving the vacuum as much as possible, but it cannot be avoided entirely. The ability to resolve a small isotope peak adjacent to a large peak is called ‘abundance sensitivity’. A single magnetic sector TIMS has abundance sensitivity of about 1 ppm per mass unit at uranium masses. So, at mass 234, 1 ion in 1,000,000 will actually be 235U not 234U, and this will limit our ability to quantify the rare 234U isotope. […] AMS [accelerator mass spectrometry] instruments use very high voltages to achieve high abundance sensitivity. […] As I write this chapter, the human population of the world has recently exceeded seven billion. […] one carbon atom in 1012 is mass 14. So, detecting 14C is far more difficult than identifying a single person on Earth, and somewhat comparable to identifying an individual leaf in the Amazon rain forest. Such is the power of isotope ratio mass spectrometry.”

14C is produced in the Earth’s atmosphere by the interaction between nitrogen and cosmic ray neutrons that releases a free proton turning 147N into 146C in a process that we call an ‘n-p’ reaction […] Because the process is driven by cosmic ray bombardment, we call 14C a ‘cosmogenic’ isotope. The half-life of 14C is about 5,000 years, so we know that all the 14C on Earth is either cosmogenic or has been created by mankind through nuclear reactors and bombs — no ‘primordial’ 14C remains because any that originally existed has long since decayed. 14C is not the only cosmogenic isotope; 16O in the atmosphere interacts with cosmic radiation to produce the isotope 10Be (beryllium). […] The process by which a high energy cosmic ray particle removes several nucleons is called ‘spallation’. 10Be production from 16O is not restricted to the atmosphere but also occurs when cosmic rays impact rock surfaces. […] when cosmic rays hit a rock surface they don’t bounce off but penetrate the top 2 or 3 metres (m) — the actual ‘attenuation’ depth will vary for particles of different energy. Most of the Earth’s crust is made of silicate minerals based on bonds between oxygen and silicon. So, the same spallation process that produces 10Be in the atmosphere also occurs in rock surfaces. […] If we know the flux of cosmic rays impacting a surface, the rate of production of the cosmogenic isotopes with depth below the rock surface, and the rate of radioactive decay, it should be possible to convert the number of cosmogenic atoms into an exposure age. […] Rocks on Earth which are shielded from much of the cosmic radiation have much lower levels of isotopes like 10Be than have meteorites which, before they arrive on Earth, are exposed to the full force of cosmic radiation. […] polar scientists have used cores drilled through ice sheets in Antarctica and Greenland to compare 10Be at different depths and thereby reconstruct 10Be production through time. The 14C and 10Be records are closely correlated indicating the common response to changes in the cosmic ray flux.”

“[O]nce we have credible cosmogenic isotope production rates, […] there are two classes of applications, which we can call ‘exposure’ and ‘burial’ methodologies. Exposure studies simply measure the accumulation of the cosmogenic nuclide. Such studies are simplest when the cosmogenic nuclide is a stable isotope like 3He and 21Ne. These will just accumulate continuously as the sample is exposed to cosmic radiation. Slightly more complicated are cosmogenic isotopes that are radioactive […]. These isotopes accumulate through exposure but will also be destroyed by radioactive decay. Eventually, the isotopes achieve the condition known as ‘secular equilibrium’ where production and decay are balanced and no chronological information can be extracted. Secular equilibrium is achieved after three to four half-lives […] Imagine a boulder that has been transported from its place of origin to another place within a glacier — what we call a glacial erratic. While the boulder was deeply covered in ice, it would not have been exposed to cosmic radiation. Its cosmogenic isotopes will only have accumulated since the ice melted. So a cosmogenic isotope exposure age tells us the date at which the glacier retreated, and, by examining multiple erratics from different locations along the course of the glacier, allows us to construct a retreat history for the de-glaciation. […] Burial methodologies using cosmogenic isotopes work in situations where a rock was previously exposed to cosmic rays but is now located in a situation where it is shielded.”

“Cosmogenic isotopes are also being used extensively to recreate the seismic histories of tectonically active areas. Earthquakes occur when geological faults give way and rock masses move. A major earthquake is likely to expose new rock to the Earth’s surface. If the field geologist can identify rocks in a fault zone that (s)he is confident were brought to the surface in an earthquake, then a cosmogenic isotope exposure age would date the fault — providing, of course, that subsequent erosion can be ruled out or quantified. Precarious rocks are rock outcrops that could reasonably be expected to topple if subjected to a significant earthquake. Dating the exposed surface of precarious rocks with cosmogenic isotopes can reveal the amount of time that has elapsed since the last earthquake of a magnitude that would have toppled the rock. Constructing records of seismic history is not merely of academic interest; some of the world’s seismically active areas are also highly populated and developed.”

“One aspect of the natural decay series that acts in favour of the preservation of accurate age information is the fact that most of the intermediate isotopes are short-lived. For example, in both the U series the radon (Rn) isotopes, which might be expected to diffuse readily out of a mineral, have half-lives of only seconds or days, too short to allow significant losses. Some decay series isotopes though do have significantly long half-lives which offer the potential to be geochronometers in their own right. […] These techniques depend on the tendency of natural decay series to evolve towards a state of ‘secular equilibrium’ in which the activity of all species in the decay series is equal. […] at secular equilibrium, isotopes with long half-lives (i.e. small decay constants) will have large numbers of atoms whereas short-lived isotopes (high decay constants) will only constitute a relatively small number of atoms. Since decay constants vary by several orders of magnitude, so will the numbers of atoms of each isotope in the equilibrium decay series. […] Geochronological applications of natural decay series depend upon some process disrupting the natural decay series to introduce either a deficiency or an excess of an isotope in the series. The decay series will then gradually return to secular equilibrium and the geochronometer relies on measuring the extent to which equilibrium has been approached.”

“The ‘ring of fire’ volcanoes around the margin of the Pacific Ocean are a manifestation of subduction in which the oldest parts of the Pacific Ocean crust are being returned to the mantle below. The oldest parts of the Pacific Ocean crust are about 150 million years (Ma) old, with anything older having already disappeared into the mantle via subduction zones. The Atlantic Ocean doesn’t have a ring of fire because it is a relatively young ocean which started to form about 60 Ma ago, and its oldest rocks are not yet ready to form subduction zones. Thus, while continental crust persists for billions of years, oceanic crust is a relatively transient (in terms of geological time) phenomenon at the Earth’s surface.”

“Mantle rocks typically contain minerals such as olivine, pyroxene, spinel, and garnet. Unlike say ice, which melts to form water, mixtures of minerals do not melt in the proportions in which they occur in the rock. Rather, they undergo partial melting in which some minerals […] melt preferentially leaving a solid residue enriched in refractory minerals […]. We know this from experimentally melting mantle-like rocks in the laboratory, but also because the basalts produced by melting of the mantle are closer in composition to Ca-rich (clino-) pyroxene than to the olivine-rich rocks that dominate the solid pieces (or xenoliths) of mantle that are sometimes transferred to the surface by certain types of volcanic eruptions. […] Thirty years ago geologists fiercely debated whether the mantle was homogeneous or heterogeneous; mantle isotope geochemistry hasn’t yet elucidated all the details but it has put to rest the initial conundrum; Earth’s mantle is compositionally heterogeneous.”

Links:

Frederick Soddy.
Rutherford–Bohr model.
Isotopes of hydrogen.
Radioactive decay. Types of decay. Alpha decay. Beta decay. Electron capture decay. Branching fraction. Gamma radiation. Spontaneous fission.
Promethium.
Lanthanides.
Radiocarbon dating.
Hessel de Vries.
Dendrochronology.
Suess effect.
Bomb pulse.
Delta notation (non-wiki link).
Isotopic fractionation.
C3 carbon fixation. C4 carbon fixation.
Nitrogen-15 tracing.
Isotopes of strontium. Strontium isotope analysis.
Ötzi.
Mass spectrometry.
Geiger counter.
Townsend avalanche.
Gas proportional counter.
Scintillation detector.
Liquid scintillation spectometry. Photomultiplier tube.
Dynode.
Thallium-doped sodium iodide detectors. Semiconductor-based detectors.
Isotope separation (-enrichment).
Doubly labeled water.
Urea breath test.
Radiation oncology.
Brachytherapy.
Targeted radionuclide therapy.
Iodine-131.
MIBG scan.
Single-photon emission computed tomography.
Positron emission tomography.
Inductively coupled plasma (ICP) mass spectrometry.
Secondary ion mass spectrometry.
Faraday cup (-detector).
δ18O.
Stadials and interstadials. Oxygen isotope ratio cycle.
Insolation.
Gain and phase model.
Milankovitch cycles.
Perihelion and aphelion. Precession.
Equilibrium Clumped-Isotope Effects in Doubly Substituted Isotopologues of Ethane (non-wiki link).
Age of the Earth.
Uranium–lead dating.
Geochronology.
Cretaceous–Paleogene boundary.
Argon-argon dating.
Nuclear chain reaction. Critical mass.
Fukushima Daiichi nuclear disaster.
Natural nuclear fission reactor.
Continental crust. Oceanic crust. Basalt.
Core–mantle boundary.
Chondrite.
Ocean Island Basalt.
Isochron dating.

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November 23, 2017 Posted by | Biology, Books, Botany, Chemistry, Geology, Medicine, Physics | Leave a comment

Organic Chemistry (II)

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

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

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

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

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

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

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

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

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

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

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

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

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

November 11, 2017 Posted by | Biology, Books, Botany, Chemistry, Medicine, Pharmacology, Zoology | Leave a comment

Molecules

This book is almost exclusively devoted to covering biochemistry topics. When the coverage is decent I find biochemistry reasonably interesting – for example I really liked Beer, Björk & Beardall’s photosynthesis book – and the coverage here was okay, but not more than that. I think that Ball was trying to cover a bit too much ground, or perhaps that there was really too much ground to cover for it to even make sense to try to write a book on this particular topic in a series like this. I learned a lot though.

As usual I’ve added some quotes from the coverage below, as well as some additional links to topics/concepts/people/etc. covered in the book.

“Most atoms on their own are highly reactive – they have a predisposition to join up with other atoms. Molecules are collectives of atoms, firmly welded together into assemblies that may contain anything up to many millions of them. […] By molecules, we generally mean assemblies of a discrete, countable number of atoms. […] Some pure elements adopt molecular forms; others do not. As a rough rule of thumb, metals are non-molecular […] whereas non-metals are molecular. […] molecules are the smallest units of meaning in chemistry. It is through molecules, not atoms, that one can tell stories in the sub-microscopic world. They are the words; atoms are just the letters. […] most words are distinct aggregates of several letters arranged in a particular order. We often find that longer words convey subtler and more finely nuanced meanings. And in molecules, as in words, the order in which the component parts are put together matters: ‘save’ and ‘vase’ do not mean the same thing.”

“There are something like 60,000 different varieties of protein molecule in human cells, each conducting a highly specialized task. It would generally be impossible to guess what this task is merely by looking at a protein. They are undistinguished in appearance, mostly globular in shape […] and composed primarily of carbon, hydrogen, nitrogen, oxygen, and a little sulphur. […] There are twenty varieties of amino acids in natural proteins. In the chain, one amino acid is linked to the next via a covalent bond called a peptide bond. Both molecules shed a few extraneous atoms to make this linkage, and the remainder – another link in the chain – is called a residue. The chain itself is termed a polypeptide. Any string of amino acid residues is a polypeptide. […] In a protein the order of amino acids along the chain – the sequence – is not arbitrary. It is selected […] to ensure that the chain will collapse and curl up in water into the precisely determined globular form of the protein, with all parts of the chain in the right place. This shape can be destroyed by warming the protein, a process called denaturation. But many proteins will fold up again spontaneously into the same globular structure when cooled. In other words, the chain has a kind of memory of its folded shape. The details of this folding process are still not fully understood – it is, in fact, one of the central unsolved puzzles of molecular biology. […] proteins are made not in the [cell] nucleus but in a different compartment called the endoplasmic reticulum […]. The gene is transcribed first into a molecule related to DNA, called RNA (ribonucleic acid). The RNA molecules travel from the nucleus to the endoplasmic reticulum, where they are translated to proteins. The proteins are then shipped off to where they are needed.”

[M]icrofibrils aggregate together in various ways. For example, they can gather in a staggered arrangement to form thick strands called banded fibrils. […] Banded fibrils constitute the connective tissues between cells – they are the cables that hold our flesh together. Bone consists of collagen banded fibrils sprinkled with tiny crystals of the mineral hydroxyapatite, which is basically calcium phosphate. Because of the high protein content of bone, it is flexible and resilient as well as hard. […] In contrast to the disorderly tangle of connective tissue, the eye’s cornea contains collagen fibrils packed side by side in an orderly manner. These fibrils are too small to scatter light, and so the material is virtually transparent. The basic design principle – one that recurs often in nature – is that, by tinkering with the chemical composition and, most importantly, the hierarchical arrangement of the same basic molecules, it is possible to extract several different kinds of material properties. […] cross-links determine the strength of the material: hair and fingernail are more highly cross-linked than skin. Curly or frizzy hair can be straightened by breaking some of [the] sulphur cross-links to make the hairs more pliable. […] Many of the body’s structural fabrics are proteins. Unlike enzymes, structural proteins do not have to conduct any delicate chemistry, but must simply be (for instance) tough, or flexible, or waterproof. In principle many other materials besides proteins would suffice; and indeed, plants use cellulose (a sugar-based polymer) to make their tissues.”

“In many ways, it is metabolism and not replication that provides the best working definition of life. Evolutionary biologists would say that we exist in order to reproduce – but we are not, even the most amorous of us, trying to reproduce all the time. Yet, if we stop metabolizing, even for a minute or two, we are done for. […] Whether waking or asleep, our bodies stay close to a healthy temperature of 37 °C. There is only one way of doing this: our cells are constantly pumping out heat, a by-product of metabolism. Heat is not really the point here – it is simply unavoidable, because all conversion of energy from one form to another squanders some of it this way. Our metabolic processes are primarily about making molecules. Cells cannot survive without constantly reinventing themselves: making new amino acids for proteins, new lipids for membranes, new nucleic acids so that they can divide.”

“In the body, combustion takes place in a tightly controlled, graded sequence of steps, and some chemical energy is drawn off and stored at each stage. […] A power station burns coal, oil, or gas […]. Burning is just a means to an end. The heat is used to turn water into steam; the pressure of the steam drives turbines; the turbines spin and send wire coils whirling in the arms of great magnets, which induces an electrical current in the wire. Energy is passed on, from chemical to heat to mechanical to electrical. And every plant has a barrage of regulatory and safety mechanisms. There are manual checks on pressure gauges and on the structural integrity of moving parts. Automatic sensors make the measurements. Failsafe devices avert catastrophic failure. Energy generation in the cell is every bit as complicated. […] The cell seems to have thought of everything, and has protein devices for fine-tuning it all.”

ATP is the key to the maintenance of cellular integrity and organization, and so the cell puts a great deal of effort into making as much of it as possible from each molecule of glucose that it burns. About 40 per cent of the energy released by the combustion of food is conserved in ATP molecules. ATP is rich in energy because it is like a coiled spring. It contains three phosphate groups, linked like so many train carriages. Each of these phosphate groups has a negative charge; this means that they repel one another. But because they are joined by chemical bonds, they cannot escape one another […]. Straining to get away, the phosphates pull an energetically powerful punch. […] The links between phosphates can be snipped in a reaction that involves water […] called hydrolysis (‘splitting with water’). Each time a bond is hydrolysed, energy is released. Setting free the outermost phosphate converts ATP to adenosine diphosphate (ADP); cleave the second phosphate and it becomes adenosine monophosphate (AMP). Both severances release comparable amounts of energy.”

“Burning sugar is a two-stage process, beginning with its transformation to a molecule called pyruvate in a process known as glycolysis […]. This involves a sequence of ten enzyme-catalysed steps. The first five of these split glucose in half […], powered by the consumption of ATP molecules: two of them are ‘decharged’ to ADP for every glucose molecule split. But the conversion of the fragments to pyruvate […] permits ATP to be recouped from ADP. Four ATP molecules are made this way, so that there is an overall gain of two ATP molecules per glucose molecule consumed. Thus glycolysis charges the cell’s batteries. Pyruvate then normally enters the second stage of the combustion process: the citric acid cycle, which requires oxygen. But if oxygen is scarce – that is, under anaerobic conditions – a contingency plan is enacted whereby pyruvate is instead converted to the molecule lactate. […] The first thing a mitochondrion does is convert pyruvate enzymatically to a molecule called acetyl coenzyme A (CoA). The breakdown of fatty acids and glycerides from fats also eventually generates acetyl CoA. The [citric acid] cycle is a sequence of eight enzyme-catalysed reactions that transform acetyl CoA first to citric acid and then to various other molecules, ending with […] oxaloacetate. This end is a new beginning, for oxaloacetate reacts with acetyl CoA to make citric acid. In some of the steps of the cycle, carbon dioxide is generated as a by-product. It dissolves in the bloodstream and is carried off to the lungs to be exhaled. Thus in effect the carbon in the original glucose molecules is syphoned off into the end product carbon dioxide, completing the combustion process. […] Also syphoned off from the cycle are electrons – crudely speaking, the citric acid cycle sends an electrical current to a different part of the mitochondrion. These electrons are used to convert oxygen molecules and positively charged hydrogen ions to water – an energy-releasing process. The energy is captured and used to make ATP in abundance.”

“While mammalian cells have fuel-burning factories in the form of mitochondria, the solar-power centres in the cells of plant leaves are compartments called chloroplasts […] chloroplast takes carbon dioxide and water, and from them constructs […] sugar. […] In the first part of photosynthesis, light is used to convert NADP to an electron carrier (NADPH) and to transform ADP to ATP. This is effectively a charging-up process that primes the chloroplast for glucose synthesis. In the second part, ATP and NADPH are used to turn carbon dioxide into sugar, in a cyclic sequence of steps called the Calvin–Benson cycle […] There are several similarities between the processes of aerobic metabolism and photosynthesis. Both consist of two distinct sub-processes with separate evolutionary origins: a linear sequence of reactions coupled to a cyclic sequence that regenerates the molecules they both need. The bridge between glycolysis and the citric acid cycle is the electron-ferrying NAD molecule; the two sub-processes of photosynthesis are bridged by the cycling of an almost identical molecule, NAD phosphate (NADP).”

“Despite the variety of messages that hormones convey, the mechanism by which the signal is passed from a receptor protein at the cell surface to the cell’s interior is the same in almost all cases. It involves a sequence of molecular interactions in which molecules transform one another down a relay chain. In cell biology this is called signal transduction. At the same time as relaying the message, these interactions amplify the signal so that the docking of a single hormone molecule to a receptor creates a big response inside the cell. […] The receptor proteins span the entire width of the membrane; the hormone-binding site protrudes on the outer surface, while the base of the receptor emerges from the inner surface […]. When the receptor binds its target hormone, a shape change is transmitted to the lower face of the protein, which enables it to act as an enzyme. […] The participants of all these processes [G protein, guanosine diphosphate and -triphosphate, adenylate cyclase… – figured it didn’t matter if I left out a few details – US…] are stuck to the cell wall. But cAMP floats freely in the cell’s cytoplasm, and is able to carry the signal into the cell interior. It is called a ‘second messenger’, since it is the agent that relays the signal of the ‘first messenger’ (the hormone) into the community of the cell. Cyclic AMP becomes attached to protein molecules called protein kinases, whereupon they in turn become activated as enzymes. Most protein kinases switch other enzymes on and off by attaching phosphate groups to them – a reaction called phosphorylation. […] The process might sound rather complicated, but it is really nothing more than a molecular relay. The signal is passed from the hormone to its receptor, then to the G protein, on to an enzyme and thence to the second messenger, and further on to a protein kinase, and so forth. The G-protein mechanism of signal transduction was discovered in the 1970s by Alfred Gilman and Martin Rodbell, for which they received the 1994 Nobel Prize for medicine. It represents one of the most widespread means of getting a message across a cell membrane. […] it is not just hormonal signalling that makes use of the G-protein mechanism. Our senses of vision and smell, which also involve the transmission of signals, employ the same switching process.”

“Although axon signals are electrical, they differ from those in the metal wires of electronic circuitry. The axon is basically a tubular cell membrane decorated along its length with channels that let sodium and potassium ions in and out. Some of these ion channels are permanently open; others are ‘gated’, opening or closing in response to electrical signals. And some are not really channels at all but pumps, which actively transport sodium ions out of the cell and potassium ions in. These sodium-potassium pumps can move ions […] powered by ATP. […] Drugs that relieve pain typically engage with inhibitory receptors. Morphine, the main active ingredient of opium, binds to so-called opioid receptors in the spinal cord, which inhibit the transmission of pain signals to the brain. There are also opioid receptors in the brain itself, which is why morphine and related opiate drugs have a mental as well as a somatic effect. These receptors in the brain are the binding sites of peptide molecules called endorphins, which the brain produces in response to pain. Some of these are themselves extremely powerful painkillers. […] Not all pain-relieving drugs (analgesics) work by blocking the pain signal. Some prevent the signal from ever being sent. Pain signals are initiated by peptides called prostaglandins, which are manufactured and released by distressed cells. Aspirin (acetylsalicylic acid) latches onto and inhibits one of the enzymes responsible for prostaglandin synthesis, cutting off the cry of pain at its source. Unfortunately, prostaglandins are also responsible for making the mucus that protects the stomach lining […], so one of the side effects of aspirin is the risk of ulcer formation.”

“Shape changes […] are common when a receptor binds its target. If binding alone is the objective, a big shape change is not terribly desirable, since the internal rearrangements of the receptor make heavy weather of the binding event and may make it harder to achieve. This is why many supramolecular hosts are designed so that they are ‘pre-organized’ to receive their guests, minimizing the shape change caused by binding.”

“The way that a protein chain folds up is determined by its amino-acid sequence […] so the ‘information’ for making a protein is uniquely specified by this sequence. DNA encodes this information using […] groups of three bases [to] represent each amino acid. This is the genetic code.* How a particular protein sequence determines the way its chain folds is not yet fully understood. […] Nevertheless, the principle of information flow in the cell is clear. DNA is a manual of information about proteins. We can think of each chromosome as a separate chapter, each gene as a word in that chapter (they are very long words!), and each sequential group of three bases in the gene as a character in the word. Proteins are translations of the words into another language, whose characters are amino acids. In general, only when the genetic language is translated can we understand what it means.”

“It is thought that only about 2–3 per cent of the entire human genome codes for proteins. […] Some people object to genetic engineering on the grounds that it is ethically wrong to tamper with the fundamental material of life – DNA – whether it is in bacteria, humans, tomatoes, or sheep. One can understand such objections, and it would be arrogant to dismiss them as unscientific. Nevertheless, they do sit uneasily with what we now know about the molecular basis of life. The idea that our genetic make-up is sacrosanct looks hard to sustain once we appreciate how contingent, not to say arbitrary, that make-up is. Our genomes are mostly parasite-riddled junk, full of the detritus of over three billion years of evolution.”

Links:

Roald Hoffmann.
Molecular solid.
Covalent bond.
Visible spectrum.
X-ray crystallography.
Electron microscope.
Valence (chemistry).
John Dalton.
Isomer.
Lysozyme.
Organic chemistry.
Synthetic dye industry/Alizarin.
Paul Ehrlich (staining).
Retrosynthetic analysis. [I would have added a link to ‘rational synthesis as well here if there’d been a good article on that topic, but I wasn’t able to find one. Anyway: “Organic chemists call [the] kind of procedure […] in which a starting molecule is converted systematically, bit by bit, to the desired product […] a rational synthesis.”]
Paclitaxel synthesis.
Protein.
Enzyme.
Tryptophan synthase.
Ubiquitin.
Amino acid.
Protein folding.
Peptide bond.
Hydrogen bond.
Nucleotide.
Chromosome.
Structural gene. Regulatory gene.
Operon.
Gregor Mendel.
Mitochondrial DNA.
RNA world.
Ribozyme.
Artificial gene synthesis.
Keratin.
Silk.
Vulcanization.
Aramid.
Microtubule.
Tubulin.
Carbon nanotube.
Amylase/pepsin/glycogen/insulin.
Cytochrome c oxidase.
ATP synthase.
Haemoglobin.
Thylakoid membrane.
Chlorophyll.
Liposome.
TNT.
Motor protein. Dynein. Kinesin.
Sarcomere.
Sliding filament theory of muscle action.
Photoisomerization.
Supramolecular chemistry.
Hormone. Endocrine system.
Neurotransmitter.
Ionophore.
DNA.
Mutation.
Intron. Exon.
Transposon.
Molecular electronics.

October 30, 2017 Posted by | Biology, Books, Botany, Chemistry, Genetics, Neurology, Pharmacology | Leave a comment

Earth System Science

I decided not to rate this book. Some parts are great, some parts I didn’t think were very good.

I’ve added some quotes and links below. First a few links (I’ve tried not to add links here which I’ve also included in the quotes below):

Carbon cycle.
Origin of water on Earth.
Gaia hypothesis.
Albedo (climate and weather).
Snowball Earth.
Carbonate–silicate cycle.
Carbonate compensation depth.
Isotope fractionation.
CLAW hypothesis.
Mass-independent fractionation.
δ13C.
Great Oxygenation Event.
Acritarch.
Grypania.
Neoproterozoic.
Rodinia.
Sturtian glaciation.
Marinoan glaciation.
Ediacaran biota.
Cambrian explosion.
Quarternary.
Medieval Warm Period.
Little Ice Age.
Eutrophication.
Methane emissions.
Keeling curve.
CO2 fertilization effect.
Acid rain.
Ocean acidification.
Earth systems models.
Clausius–Clapeyron relation.
Thermohaline circulation.
Cryosphere.
The limits to growth.
Exoplanet Biosignature Gases.
Transiting Exoplanet Survey Satellite (TESS).
James Webb Space Telescope.
Habitable zone.
Kepler-186f.

A few quotes from the book:

“The scope of Earth system science is broad. It spans 4.5 billion years of Earth history, how the system functions now, projections of its future state, and ultimate fate. […] Earth system science is […] a deeply interdisciplinary field, which synthesizes elements of geology, biology, chemistry, physics, and mathematics. It is a young, integrative science that is part of a wider 21st-century intellectual trend towards trying to understand complex systems, and predict their behaviour. […] A key part of Earth system science is identifying the feedback loops in the Earth system and understanding the behaviour they can create. […] In systems thinking, the first step is usually to identify your system and its boundaries. […] what is part of the Earth system depends on the timescale being considered. […] The longer the timescale we look over, the more we need to include in the Earth system. […] for many Earth system scientists, the planet Earth is really comprised of two systems — the surface Earth system that supports life, and the great bulk of the inner Earth underneath. It is the thin layer of a system at the surface of the Earth […] that is the subject of this book.”

“Energy is in plentiful supply from the Sun, which drives the water cycle and also fuels the biosphere, via photosynthesis. However, the surface Earth system is nearly closed to materials, with only small inputs to the surface from the inner Earth. Thus, to support a flourishing biosphere, all the elements needed by life must be efficiently recycled within the Earth system. This in turn requires energy, to transform materials chemically and to move them physically around the planet. The resulting cycles of matter between the biosphere, atmosphere, ocean, land, and crust are called global biogeochemical cycles — because they involve biological, geological, and chemical processes. […] The global biogeochemical cycling of materials, fuelled by solar energy, has transformed the Earth system. […] It has made the Earth fundamentally different from its state before life and from its planetary neighbours, Mars and Venus. Through cycling the materials it needs, the Earth’s biosphere has bootstrapped itself into a much more productive state.”

“Each major element important for life has its own global biogeochemical cycle. However, every biogeochemical cycle can be conceptualized as a series of reservoirs (or ‘boxes’) of material connected by fluxes (or flows) of material between them. […] When a biogeochemical cycle is in steady state, the fluxes in and out of each reservoir must be in balance. This allows us to define additional useful quantities. Notably, the amount of material in a reservoir divided by the exchange flux with another reservoir gives the average ‘residence time’ of material in that reservoir with respect to the chosen process of exchange. For example, there are around 7 × 1016 moles of carbon dioxide (CO2) in today’s atmosphere, and photosynthesis removes around 9 × 1015 moles of CO2 per year, giving each molecule of CO2 a residence time of roughly eight years in the atmosphere before it is taken up, somewhere in the world, by photosynthesis. […] There are 3.8 × 1019 moles of molecular oxygen (O2) in today’s atmosphere, and oxidative weathering removes around 1 × 1013 moles of O2 per year, giving oxygen a residence time of around four million years with respect to removal by oxidative weathering. This makes the oxygen cycle […] a geological timescale cycle.”

“The water cycle is the physical circulation of water around the planet, between the ocean (where 97 per cent is stored), atmosphere, ice sheets, glaciers, sea-ice, freshwaters, and groundwater. […] To change the phase of water from solid to liquid or liquid to gas requires energy, which in the climate system comes from the Sun. Equally, when water condenses from gas to liquid or freezes from liquid to solid, energy is released. Solar heating drives evaporation from the ocean. This is responsible for supplying about 90 per cent of the water vapour to the atmosphere, with the other 10 per cent coming from evaporation on the land and freshwater surfaces (and sublimation of ice and snow directly to vapour). […] The water cycle is intimately connected to other biogeochemical cycles […]. Many compounds are soluble in water, and some react with water. This makes the ocean a key reservoir for several essential elements. It also means that rainwater can scavenge soluble gases and aerosols out of the atmosphere. When rainwater hits the land, the resulting solution can chemically weather rocks. Silicate weathering in turn helps keep the climate in a state where water is liquid.”

“In modern terms, plants acquire their carbon from carbon dioxide in the atmosphere, add electrons derived from water molecules to the carbon, and emit oxygen to the atmosphere as a waste product. […] In energy terms, global photosynthesis today captures about 130 terrawatts (1 TW = 1012 W) of solar energy in chemical form — about half of it in the ocean and about half on land. […] All the breakdown pathways for organic carbon together produce a flux of carbon dioxide back to the atmosphere that nearly balances photosynthetic uptake […] The surface recycling system is almost perfect, but a tiny fraction (about 0.1 per cent) of the organic carbon manufactured in photosynthesis escapes recycling and is buried in new sedimentary rocks. This organic carbon burial flux leaves an equivalent amount of oxygen gas behind in the atmosphere. Hence the burial of organic carbon represents the long-term source of oxygen to the atmosphere. […] the Earth’s crust has much more oxygen trapped in rocks in the form of oxidized iron and sulphur, than it has organic carbon. This tells us that there has been a net source of oxygen to the crust over Earth history, which must have come from the loss of hydrogen to space.”

“The oxygen cycle is relatively simple, because the reservoir of oxygen in the atmosphere is so massive that it dwarfs the reservoirs of organic carbon in vegetation, soils, and the ocean. Hence oxygen cannot get used up by the respiration or combustion of organic matter. Even the combustion of all known fossil fuel reserves can only put a small dent in the much larger reservoir of atmospheric oxygen (there are roughly 4 × 1017 moles of fossil fuel carbon, which is only about 1 per cent of the O2 reservoir). […] Unlike oxygen, the atmosphere is not the major surface reservoir of carbon. The amount of carbon in global vegetation is comparable to that in the atmosphere and the amount of carbon in soils (including permafrost) is roughly four times that in the atmosphere. Even these reservoirs are dwarfed by the ocean, which stores forty-five times as much carbon as the atmosphere, thanks to the fact that CO2 reacts with seawater. […] The exchange of carbon between the atmosphere and the land is largely biological, involving photosynthetic uptake and release by aerobic respiration (and, to a lesser extent, fires). […] Remarkably, when we look over Earth history there are fluctuations in the isotopic composition of carbonates, but no net drift up or down. This suggests that there has always been roughly one-fifth of carbon being buried in organic form and the other four-fifths as carbonate rocks. Thus, even on the early Earth, the biosphere was productive enough to support a healthy organic carbon burial flux.”

“The two most important nutrients for life are phosphorus and nitrogen, and they have very different biogeochemical cycles […] The largest reservoir of nitrogen is in the atmosphere, whereas the heavier phosphorus has no significant gaseous form. Phosphorus thus presents a greater recycling challenge for the biosphere. All phosphorus enters the surface Earth system from the chemical weathering of rocks on land […]. Phosphorus is concentrated in rocks in grains or veins of the mineral apatite. Natural selection has made plants on land and their fungal partners […] very effective at acquiring phosphorus from rocks, by manufacturing and secreting a range of organic acids that dissolve apatite. […] The average terrestrial ecosystem recycles phosphorus roughly fifty times before it is lost into freshwaters. […] The loss of phosphorus from the land is the ocean’s gain, providing the key input of this essential nutrient. Phosphorus is stored in the ocean as phosphate dissolved in the water. […] removal of phosphorus into the rock cycle balances the weathering of phosphorus from rocks on land. […] Although there is a large reservoir of nitrogen in the atmosphere, the molecules of nitrogen gas (N2) are extremely strongly bonded together, making nitrogen unavailable to most organisms. To split N2 and make nitrogen biologically available requires a remarkable biochemical feat — nitrogen fixation — which uses a lot of energy. In the ocean the dominant nitrogen fixers are cyanobacteria with a direct source of energy from sunlight. On land, various plants form a symbiotic partnership with nitrogen fixing bacteria, making a home for them in root nodules and supplying them with food in return for nitrogen. […] Nitrogen fixation and denitrification form the major input and output fluxes of nitrogen to both the land and the ocean, but there is also recycling of nitrogen within ecosystems. […] There is an intimate link between nutrient regulation and atmospheric oxygen regulation, because nutrient levels and marine productivity determine the source of oxygen via organic carbon burial. However, ocean nutrients are regulated on a much shorter timescale than atmospheric oxygen because their residence times are much shorter—about 2,000 years for nitrogen and 20,000 years for phosphorus.”

“[F]orests […] are vulnerable to increases in oxygen that increase the frequency and ferocity of fires. […] Combustion experiments show that fires only become self-sustaining in natural fuels when oxygen reaches around 17 per cent of the atmosphere. Yet for the last 370 million years there is a nearly continuous record of fossil charcoal, indicating that oxygen has never dropped below this level. At the same time, oxygen has never risen too high for fires to have prevented the slow regeneration of forests. The ease of combustion increases non-linearly with oxygen concentration, such that above 25–30 per cent oxygen (depending on the wetness of fuel) it is hard to see how forests could have survived. Thus oxygen has remained within 17–30 per cent of the atmosphere for at least the last 370 million years.”

“[T]he rate of silicate weathering increases with increasing CO2 and temperature. Thus, if something tends to increase CO2 or temperature it is counteracted by increased CO2 removal by silicate weathering. […] Plants are sensitive to variations in CO2 and temperature, and together with their fungal partners they greatly amplify weathering rates […] the most pronounced change in atmospheric CO2 over Phanerozoic time was due to plants colonizing the land. This started around 470 million years ago and escalated with the first forests 370 million years ago. The resulting acceleration of silicate weathering is estimated to have lowered the concentration of atmospheric CO2 by an order of magnitude […], and cooled the planet into a series of ice ages in the Carboniferous and Permian Periods.”

“The first photosynthesis was not the kind we are familiar with, which splits water and spits out oxygen as a waste product. Instead, early photosynthesis was ‘anoxygenic’ — meaning it didn’t produce oxygen. […] It could have used a range of compounds, in place of water, as a source of electrons with which to fix carbon from carbon dioxide and reduce it to sugars. Potential electron donors include hydrogen (H2) and hydrogen sulphide (H2S) in the atmosphere, or ferrous iron (Fe2+) dissolved in the ancient oceans. All of these are easier to extract electrons from than water. Hence they require fewer photons of sunlight and simpler photosynthetic machinery. The phylogenetic tree of life confirms that several forms of anoxygenic photosynthesis evolved very early on, long before oxygenic photosynthesis. […] If the early biosphere was fuelled by anoxygenic photosynthesis, plausibly based on hydrogen gas, then a key recycling process would have been the biological regeneration of this gas. Calculations suggest that once such recycling had evolved, the early biosphere might have achieved a global productivity up to 1 per cent of the modern marine biosphere. If early anoxygenic photosynthesis used the supply of reduced iron upwelling in the ocean, then its productivity would have been controlled by ocean circulation and might have reached 10 per cent of the modern marine biosphere. […] The innovation that supercharged the early biosphere was the origin of oxygenic photosynthesis using abundant water as an electron donor. This was not an easy process to evolve. To split water requires more energy — i.e. more high-energy photons of sunlight — than any of the earlier anoxygenic forms of photosynthesis. Evolution’s solution was to wire together two existing ‘photosystems’ in one cell and bolt on the front of them a remarkable piece of biochemical machinery that can rip apart water molecules. The result was the first cyanobacterial cell — the ancestor of all organisms performing oxygenic photosynthesis on the planet today. […] Once oxygenic photosynthesis had evolved, the productivity of the biosphere would no longer have been restricted by the supply of substrates for photosynthesis, as water and carbon dioxide were abundant. Instead, the availability of nutrients, notably nitrogen and phosphorus, would have become the major limiting factors on the productivity of the biosphere — as they still are today.” [If you’re curious to know more about how that fascinating ‘biochemical machinery’ works, this is a great book on these and related topics – US].

“On Earth, anoxygenic photosynthesis requires one photon per electron, whereas oxygenic photosynthesis requires two photons per electron. On Earth it took up to a billion years to evolve oxygenic photosynthesis, based on two photosystems that had already evolved independently in different types of anoxygenic photosynthesis. Around a fainter K- or M-type star […] oxygenic photosynthesis is estimated to require three or more photons per electron — and a corresponding number of photosystems — making it harder to evolve. […] However, fainter stars spend longer on the main sequence, giving more time for evolution to occur.”

“There was a lot more energy to go around in the post-oxidation world, because respiration of organic matter with oxygen yields an order of magnitude more energy than breaking food down anaerobically. […] The revolution in biological complexity culminated in the ‘Cambrian Explosion’ of animal diversity 540 to 515 million years ago, in which modern food webs were established in the ocean. […] Since then the most fundamental change in the Earth system has been the rise of plants on land […], beginning around 470 million years ago and culminating in the first global forests by 370 million years ago. This doubled global photosynthesis, increasing flows of materials. Accelerated chemical weathering of the land surface lowered atmospheric carbon dioxide levels and increased atmospheric oxygen levels, fully oxygenating the deep ocean. […] Although grasslands now cover about a third of the Earth’s productive land surface they are a geologically recent arrival. Grasses evolved amidst a trend of declining atmospheric carbon dioxide, and climate cooling and drying, over the past forty million years, and they only became widespread in two phases during the Miocene Epoch around seventeen and six million years ago. […] Since the rise of complex life, there have been several mass extinction events. […] whilst these rolls of the extinction dice marked profound changes in evolutionary winners and losers, they did not fundamentally alter the operation of the Earth system.” [If you’re interested in this kind of stuff, the evolution of food webs and so on, Herrera et al.’s wonderful book is a great place to start – US]

“The Industrial Revolution marks the transition from societies fuelled largely by recent solar energy (via biomass, water, and wind) to ones fuelled by concentrated ‘ancient sunlight’. Although coal had been used in small amounts for millennia, for example for iron making in ancient China, fossil fuel use only took off with the invention and refinement of the steam engine. […] With the Industrial Revolution, food and biomass have ceased to be the main source of energy for human societies. Instead the energy contained in annual food production, which supports today’s population, is at fifty exajoules (1 EJ = 1018 joules), only about a tenth of the total energy input to human societies of 500 EJ/yr. This in turn is equivalent to about a tenth of the energy captured globally by photosynthesis. […] solar energy is not very efficiently converted by photosynthesis, which is 1–2 per cent efficient at best. […] The amount of sunlight reaching the Earth’s land surface (2.5 × 1016 W) dwarfs current total human power consumption (1.5 × 1013 W) by more than a factor of a thousand.”

“The Earth system’s primary energy source is sunlight, which the biosphere converts and stores as chemical energy. The energy-capture devices — photosynthesizing organisms — construct themselves out of carbon dioxide, nutrients, and a host of trace elements taken up from their surroundings. Inputs of these elements and compounds from the solid Earth system to the surface Earth system are modest. Some photosynthesizers have evolved to increase the inputs of the materials they need — for example, by fixing nitrogen from the atmosphere and selectively weathering phosphorus out of rocks. Even more importantly, other heterotrophic organisms have evolved that recycle the materials that the photosynthesizers need (often as a by-product of consuming some of the chemical energy originally captured in photosynthesis). This extraordinary recycling system is the primary mechanism by which the biosphere maintains a high level of energy capture (productivity).”

“[L]ike all stars on the ‘main sequence’ (which generate energy through the nuclear fusion of hydrogen into helium), the Sun is burning inexorably brighter with time — roughly 1 per cent brighter every 100 million years — and eventually this will overheat the planet. […] Over Earth history, the silicate weathering negative feedback mechanism has counteracted the steady brightening of the Sun by removing carbon dioxide from the atmosphere. However, this cooling mechanism is near the limits of its operation, because CO2 has fallen to limiting levels for the majority of plants, which are key amplifiers of silicate weathering. Although a subset of plants have evolved which can photosynthesize down to lower CO2 levels [the author does not go further into this topic, but here’s a relevant link – US], they cannot draw CO2 down lower than about 10 ppm. This means there is a second possible fate for life — running out of CO2. Early models projected either CO2 starvation or overheating […] occurring about a billion years in the future. […] Whilst this sounds comfortingly distant, it represents a much shorter future lifespan for the Earth’s biosphere than its past history. Earth’s biosphere is entering its old age.”

September 28, 2017 Posted by | Astronomy, Biology, Books, Botany, Chemistry, Geology, Paleontology, Physics | Leave a comment

Quotes

(The Pestallozzi quotes below are from The Education of Man, a short and poor aphorism collection I can not possibly recommend despite the inclusion of quotes from it in this post.)

i. “Only a good conscience always gives man the courage to handle his affairs straightforwardly, openly and without evasion.” (Johann Heinrich Pestalozzi)

ii. “An intimate relationship in its full power is always a source of human wisdom and strength in relationships less intimate.” (-ll-)

iii. “Whoever is unwilling to help himself can be helped by no one.” (-ll-)

iv. “He who has filled his pockets in the service of injustice will have little good to say on behalf of justice.” (-ll-)

v. “It is Man’s fate that no one knows the truth alone; we all possess it, but it is divided up among us. He who learns from one man only, will never learn what the others know.” (-ll-)

vi. “No scoundrel is so wicked that he cannot at some point truthfully reprove some honest man” (-ll-)

vii. “The man too keenly aware of his good reputation is likely to have a bad one.” (-ll-)

viii. “Many words make an excuse anything but convincing.” (-ll-)

ix. “Fashions are usually seen in their true perspective only when they have gone out of fashion.” (-ll-)

x. “A thing that nobody looks for is seldom found.” (-ll-)

xi. “Many discoveries must have been stillborn or smothered at birth. We know only those which survived.” (William Ian Beardmore Beveridge)

xii. “Time is the most valuable thing a man can spend.” (Theophrastus)

xiii. “The only man who makes no mistakes is the man who never does anything.” (Theodore Roosevelt)

xiv. “It is hard to fail, but it is worse never to have tried to succeed.” (-ll-)

xv. “From their appearance in the Triassic until the end of the Creta­ceous, a span of 140 million years, mam­mals remained small and inconspicuous while all the ecological roles of large ter­restrial herbivores and carnivores were monopolized by dinosaurs; mammals did not begin to radiate and produce large species until after the dinosaurs had al­ready become extinct at the end of the Cretaceous. One is forced to conclude that dinosaurs were competitively su­perior to mammals as large land vertebrates.” (Robert T. Bakker)

xvi. “Plants and plant-eaters co-evolved. And plants aren’t the passive partners in the chain of terrestrial life. […] A birch tree doesn’t feel cosmic fulfillment when a moose munches its leaves; the tree species, in fact, evolves to fight the moose, to keep the animal’s munching lips away from vulnerable young leaves and twigs. In the final analysis, the merciless hand of natural selection will favor the birch genes that make the tree less and less palatable to the moose in generation after generation. No plant species could survive for long by offering itself as unprotected fodder.” (-ll-)

xvii. “… if you look at crocodiles today, they aren’t really representative of what the lineage of crocodiles look like. Crocodiles are represented by about 23 species, plus or minus a couple. Along that lineage the more primitive members weren’t aquatic. A lot of them were bipedal, a lot of them looked like little dinosaurs. Some were armored, others had no teeth. They were all fully terrestrial. So this is just the last vestige of that radiation that we’re seeing. And the ancestor of both dinosaurs and crocodiles would have, to the untrained eye, looked much more like a dinosaur.” (Mark Norell)

xviii. “If we are to understand the interactions of a large number of agents, we must first be able to describe the capabilities of individual agents.” (John Henry Holland)

xix. “Evolution continually innovates, but at each level it conserves the elements that are recombined to yield the innovations.” (-ll-)

xx. “Model building is the art of selecting those aspects of a process that are relevant to the question being asked. […] High science depends on this art.” (-ll-)

June 19, 2017 Posted by | Biology, Books, Botany, Evolutionary biology, Paleontology, Quotes/aphorisms | Leave a comment

Imported Plant Diseases

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

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

Deserts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Humans? What about them?

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

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

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

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

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

The Origin of Species

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

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

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

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

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

Below I have added some quotes from the book.

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

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

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

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

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

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

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

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

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

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

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

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, Evolutionary biology, Microbiology | Leave a comment

Photosynthesis in the Marine Environment (II)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Wikipedia articles of interest

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

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

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

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

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

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

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

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

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

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

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

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

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

iv. Microbial metabolism.

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

All microbial metabolisms can be arranged according to three principles:

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

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

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

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

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

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

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

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

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

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

Some other observations from the article below:

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

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

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

vi. Radiocarbon dating (featured).

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

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

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

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

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

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

And here’s another interesting set of observations:

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

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

Photosynthesis in the Marine Environment (I)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Wikipedia articles of interest

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

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

ii. Congruence (geometry).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Wikipedia articles of interest

i. Trade and use of saffron.

Saffron has been a key seasoning, fragrance, dye, and medicine for over three millennia.[1] One of the world’s most expensive spices by weight,[2] saffron consists of stigmas plucked from the vegetatively propagated and sterile Crocus sativus, known popularly as the saffron crocus. The resulting dried “threads”[N 1] are distinguished by their bitter taste, hay-like fragrance, and slight metallic notes. The saffron crocus is unknown in the wild; its most likely precursor, Crocus cartwrightianus, originated in Crete or Central Asia;[3] The saffron crocus is native to Southwest Asia and was first cultivated in what is now Greece.[4][5][6]

From antiquity to modern times the history of saffron is full of applications in food, drink, and traditional herbal medicine: from Africa and Asia to Europe and the Americas the brilliant red threads were—and are—prized in baking, curries, and liquor. It coloured textiles and other items and often helped confer the social standing of political elites and religious adepts. Ancient peoples believed saffron could be used to treat stomach upsets, bubonic plague, and smallpox.

Saffron crocus cultivation has long centred on a broad belt of Eurasia bounded by the Mediterranean Sea in the southwest to India and China in the northeast. The major producers of antiquity—Iran, Spain, India, and Greece—continue to dominate the world trade. […] Iran has accounted for around 90–93 percent of recent annual world production and thereby dominates the export market on a by-quantity basis. […]

The high cost of saffron is due to the difficulty of manually extracting large numbers of minute stigmas, which are the only part of the crocus with the desired aroma and flavour. An exorbitant number of flowers need to be processed in order to yield marketable amounts of saffron. Obtaining 1 lb (0.45 kg) of dry saffron requires the harvesting of some 50,000 flowers, the equivalent of an association football pitch’s area of cultivation, or roughly 7,140 m2 (0.714 ha).[14] By another estimate some 75,000 flowers are needed to produce one pound of dry saffron. […] Another complication arises in the flowers’ simultaneous and transient blooming. […] Bulk quantities of lower-grade saffron can reach upwards of US$500 per pound; retail costs for small amounts may exceed ten times that rate. In Western countries the average retail price is approximately US$1,000 per pound.[5] Prices vary widely elsewhere, but on average tend to be lower. The high price is somewhat offset by the small quantities needed in kitchens: a few grams at most in medicinal use and a few strands, at most, in culinary applications; there are between 70,000 and 200,000 strands in a pound.”

ii. Scramble for Africa.

“The “Scramble for Africa” (also the Partition of Africa and the Conquest of Africa) was the invasion and occupation, colonization and annexation of African territory by European powers during the period of New Imperialism, between 1881 and 1914. In 1870, 10 percent of Africa was under European control; by 1914 it was 90 percent of the continent, with only Abyssinia (Ethiopia) and Liberia still independent.”

Here’s a really neat illustration from the article:

Scramble-for-Africa-1880-1913

“Germany became the third largest colonial power in Africa. Nearly all of its overall empire of 2.6 million square kilometres and 14 million colonial subjects in 1914 was found in its African possessions of Southwest Africa, Togoland, the Cameroons, and Tanganyika. Following the 1904 Entente cordiale between France and the British Empire, Germany tried to isolate France in 1905 with the First Moroccan Crisis. This led to the 1905 Algeciras Conference, in which France’s influence on Morocco was compensated by the exchange of other territories, and then to the Agadir Crisis in 1911. Along with the 1898 Fashoda Incident between France and Britain, this succession of international crises reveals the bitterness of the struggle between the various imperialist nations, which ultimately led to World War I. […]

David Livingstone‘s explorations, carried on by Henry Morton Stanley, excited imaginations. But at first, Stanley’s grandiose ideas for colonisation found little support owing to the problems and scale of action required, except from Léopold II of Belgium, who in 1876 had organised the International African Association (the Congo Society). From 1869 to 1874, Stanley was secretly sent by Léopold II to the Congo region, where he made treaties with several African chiefs along the Congo River and by 1882 had sufficient territory to form the basis of the Congo Free State. Léopold II personally owned the colony from 1885 and used it as a source of ivory and rubber.

While Stanley was exploring Congo on behalf of Léopold II of Belgium, the Franco-Italian marine officer Pierre de Brazza travelled into the western Congo basin and raised the French flag over the newly founded Brazzaville in 1881, thus occupying today’s Republic of the Congo. Portugal, which also claimed the area due to old treaties with the native Kongo Empire, made a treaty with Britain on 26 February 1884 to block off the Congo Society’s access to the Atlantic.

By 1890 the Congo Free State had consolidated its control of its territory between Leopoldville and Stanleyville, and was looking to push south down the Lualaba River from Stanleyville. At the same time, the British South Africa Company of Cecil Rhodes was expanding north from the Limpopo River, sending the Pioneer Column (guided by Frederick Selous) through Matabeleland, and starting a colony in Mashonaland.

To the West, in the land where their expansions would meet, was Katanga, site of the Yeke Kingdom of Msiri. Msiri was the most militarily powerful ruler in the area, and traded large quantities of copper, ivory and slaves — and rumours of gold reached European ears. The scramble for Katanga was a prime example of the period. Rhodes and the BSAC sent two expeditions to Msiri in 1890 led by Alfred Sharpe, who was rebuffed, and Joseph Thomson, who failed to reach Katanga. Leopold sent four CFS expeditions. First, the Le Marinel Expedition could only extract a vaguely worded letter. The Delcommune Expedition was rebuffed. The well-armed Stairs Expedition was given orders to take Katanga with or without Msiri’s consent. Msiri refused, was shot, and the expedition cut off his head and stuck it on a pole as a “barbaric lesson” to the people. The Bia Expedition finished the job of establishing an administration of sorts and a “police presence” in Katanga.

Thus, the half million square kilometres of Katanga came into Leopold’s possession and brought his African realm up to 2,300,000 square kilometres (890,000 sq mi), about 75 times larger than Belgium. The Congo Free State imposed such a terror regime on the colonised people, including mass killings and forced labour, that Belgium, under pressure from the Congo Reform Association, ended Leopold II’s rule and annexed it in 1908 as a colony of Belgium, known as the Belgian Congo. […]

“Britain’s administration of Egypt and the Cape Colony contributed to a preoccupation over securing the source of the Nile River. Egypt was overrun by British forces in 1882 (although not formally declared a protectorate until 1914, and never an actual colony); Sudan, Nigeria, Kenya and Uganda were subjugated in the 1890s and early 20th century; and in the south, the Cape Colony (first acquired in 1795) provided a base for the subjugation of neighbouring African states and the Dutch Afrikaner settlers who had left the Cape to avoid the British and then founded their own republics. In 1877, Theophilus Shepstone annexed the South African Republic (or Transvaal – independent from 1857 to 1877) for the British Empire. In 1879, after the Anglo-Zulu War, Britain consolidated its control of most of the territories of South Africa. The Boers protested, and in December 1880 they revolted, leading to the First Boer War (1880–81). British Prime Minister William Gladstone signed a peace treaty on 23 March 1881, giving self-government to the Boers in the Transvaal. […] The Second Boer War, fought between 1899 and 1902, was about control of the gold and diamond industries; the independent Boer republics of the Orange Free State and the South African Republic (or Transvaal) were this time defeated and absorbed into the British Empire.”

There are a lot of unsourced claims in the article and some parts of it actually aren’t very good, but this is a topic about which I did not know much (I had no idea most of colonial Africa was acquired by the European powers as late as was actually the case). This is another good map from the article to have a look at if you just want the big picture.

iii. Cursed soldiers.

“The cursed soldiers (that is, “accursed soldiers” or “damned soldiers”; Polish: Żołnierze wyklęci) is a name applied to a variety of Polish resistance movements formed in the later stages of World War II and afterwards. Created by some members of the Polish Secret State, these clandestine organizations continued their armed struggle against the Stalinist government of Poland well into the 1950s. The guerrilla warfare included an array of military attacks launched against the new communist prisons as well as MBP state security offices, detention facilities for political prisoners, and concentration camps set up across the country. Most of the Polish anti-communist groups ceased to exist in the late 1940s or 1950s, hunted down by MBP security services and NKVD assassination squads.[1] However, the last known ‘cursed soldier’, Józef Franczak, was killed in an ambush as late as 1963, almost 20 years after the Soviet take-over of Poland.[2][3] […] Similar eastern European anti-communists fought on in other countries. […]

Armia Krajowa (or simply AK)-the main Polish resistance movement in World War II-had officially disbanded on 19 January 1945 to prevent a slide into armed conflict with the Red Army, including an increasing threat of civil war over Poland’s sovereignty. However, many units decided to continue on with their struggle under new circumstances, seeing the Soviet forces as new occupiers. Meanwhile, Soviet partisans in Poland had already been ordered by Moscow on June 22, 1943 to engage Polish Leśni partisans in combat.[6] They commonly fought Poles more often than they did the Germans.[4] The main forces of the Red Army (Northern Group of Forces) and the NKVD had begun conducting operations against AK partisans already during and directly after the Polish Operation Tempest, designed by the Poles as a preventive action to assure Polish rather than Soviet control of the cities after the German withdrawal.[5] Soviet premier Joseph Stalin aimed to ensure that an independent Poland would never reemerge in the postwar period.[7] […]

The first Polish communist government, the Polish Committee of National Liberation, was formed in July 1944, but declined jurisdiction over AK soldiers. Consequently, for more than a year, it was Soviet agencies like the NKVD that dealt with the AK. By the end of the war, approximately 60,000 soldiers of the AK had been arrested, and 50,000 of them were deported to the Soviet Union’s gulags and prisons. Most of those soldiers had been captured by the Soviets during or in the aftermath of Operation Tempest, when many AK units tried to cooperate with the Soviets in a nationwide uprising against the Germans. Other veterans were arrested when they decided to approach the government after being promised amnesty. In 1947, an amnesty was passed for most of the partisans; the Communist authorities expected around 12,000 people to give up their arms, but the actual number of people to come out of the forests eventually reached 53,000. Many of them were arrested despite promises of freedom; after repeated broken promises during the first few years of communist control, AK soldiers stopped trusting the government.[5] […]

The persecution of the AK members was only a part of the reign of Stalinist terror in postwar Poland. In the period of 1944–56, approximately 300,000 Polish people had been arrested,[21] or up to two million, by different accounts.[5] There were 6,000 death sentences issued, the majority of them carried out.[21] Possibly, over 20,000 people died in communist prisons including those executed “in the majesty of the law” such as Witold Pilecki, a hero of Auschwitz.[5] A further six million Polish citizens (i.e., one out of every three adult Poles) were classified as suspected members of a ‘reactionary or criminal element’ and subjected to investigation by state agencies.”

iv. Affective neuroscience.

Affective neuroscience is the study of the neural mechanisms of emotion. This interdisciplinary field combines neuroscience with the psychological study of personality, emotion, and mood.[1]

This article is actually related to the Delusion and self-deception book, which covered some of the stuff included in this article, but I decided I might as well include the link in this post. I think some parts of the article are written in a somewhat different manner than most wiki articles – there are specific paragraphs briefly covering the results of specific meta-analyses conducted in this field. I can’t really tell from this article if I actually like this way of writing a wiki article or not.

v. Hamming distance. Not a long article, but this is a useful concept to be familiar with:

“In information theory, the Hamming distance between two strings of equal length is the number of positions at which the corresponding symbols are different. In another way, it measures the minimum number of substitutions required to change one string into the other, or the minimum number of errors that could have transformed one string into the other. […]

The Hamming distance is named after Richard Hamming, who introduced it in his fundamental paper on Hamming codes Error detecting and error correcting codes in 1950.[1] It is used in telecommunication to count the number of flipped bits in a fixed-length binary word as an estimate of error, and therefore is sometimes called the signal distance. Hamming weight analysis of bits is used in several disciplines including information theory, coding theory, and cryptography. However, for comparing strings of different lengths, or strings where not just substitutions but also insertions or deletions have to be expected, a more sophisticated metric like the Levenshtein distance is more appropriate.”

vi. Menstrual synchrony. I came across that one recently in a book, and when I did it was obvious that the author had not read this article, and lacked some knowledge included in this article (the phenomenon was assumed to be real in the coverage, and theory was developed assuming it was real which would not make sense if it was not). I figured if that person didn’t know this stuff, a lot of other people – including people reading along here – probably also do not, so I should cover this topic somewhere. This is an obvious place to do so. Okay, on to the article coverage:

Menstrual synchrony, also called the McClintock effect,[2] is the alleged process whereby women who begin living together in close proximity experience their menstrual cycle onsets (i.e., the onset of menstruation or menses) becoming closer together in time than previously. “For example, the distribution of onsets of seven female lifeguards was scattered at the beginning of the summer, but after 3 months spent together, the onset of all seven cycles fell within a 4-day period.”[3]

Martha McClintock’s 1971 paper, published in Nature, says that menstrual cycle synchronization happens when the menstrual cycle onsets of two women or more women become closer together in time than they were several months earlier.[3] Several mechanisms have been hypothesized to cause synchronization.[4]

After the initial studies, several papers were published reporting methodological flaws in studies reporting menstrual synchrony including McClintock’s study. In addition, other studies were published that failed to find synchrony. The proposed mechanisms have also received scientific criticism. A 2013 review of menstrual synchrony concluded that menstrual synchrony is doubtful.[4] […] in a recent systematic review of menstrual synchrony, Harris and Vitzthum concluded that “In light of the lack of empirical evidence for MS [menstrual synchrony] sensu stricto, it seems there should be more widespread doubt than acceptance of this hypothesis.” […]

The experience of synchrony may be the result of the mathematical fact that menstrual cycles of different frequencies repeatedly converge and diverge over time and not due to a process of synchronization.[12] It may also be due to the high probability of menstruation overlap that occurs by chance.[6]

 

December 4, 2014 Posted by | Biology, Botany, Computer science, Geography, History, Medicine, Neurology, Psychology, Wikipedia | Leave a comment

An Introduction to Tropical Rain Forests (III)

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

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

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

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

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

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

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

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

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

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

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

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

 

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

An Introduction to Tropical Rain Forests (II)

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

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

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

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

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

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

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

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

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

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

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

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

An Introduction to Tropical Rain Forests (I)

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

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

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

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

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

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

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

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

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

The Emergence of Animals: The Cambrian Breakthrough (II)

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

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

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

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

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

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

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

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

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

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

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

Plant-Animal Interactions: An Evolutionary Approach (3)

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

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

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

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

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

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

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

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

Finally, ants! Ants are awesome…

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

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

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

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

Plant-Animal Interactions: An Evolutionary Approach (2)

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

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

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

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

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

Okay, moving on…

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

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

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

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

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

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