Econstudentlog

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, evolution, genetics, Geology | 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, evolution | Leave a comment

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

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

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

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

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

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

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

February 13, 2015 Posted by | biology, books, evolution, Paleontology, Zoology | Leave a comment

The Voyage of the Beagle (III)

This will be my last post about the book.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

December 14, 2014 Posted by | biology, books, evolution, Geography, history, personal | Leave a comment

Female Infidelity and Paternal Uncertainty – Evolutionary Perspectives on Male Anti-Cuckoldry Tactics

I finished this book yesterday. Below I have posted my goodreads review:

“A couple of chapters were really nice, but the authors repeat themselves *a lot* throughout the book and some chapters are really weak. I was probably at three stars after approximately 100 pages, but the book in my opinion lost steam after that. A couple of chapters are in my opinion really poor – basically they’re just a jumble of data-poor theorizing which is most likely just plain wrong. A main hypothesis presented in one of the chapters is frankly blatantly at odds with a lot of other evidence, some of which is even covered earlier in the same work, but the authors don’t even mention this in the coverage.

I don’t regret reading the book, but it’s not that great.”

Let’s say you have a book where Hrdy’s idea that it’s long been in the interest of human females to confuse paternity by various means, e.g. through extra-pair copulations, because such behaviour reduces the risk of infanticide (I’ve talked about these things before here on the blog, if you’re unfamiliar with this work and haven’t read my posts on the topics see for example this post) is covered, and where various other reasons why females may choose to engage in extra-pair copulations (e.g. ‘genetic benefits’) are also covered. Let’s say that in another, problematic, chapter of said book, a theory is proposed that ‘unfamiliar sperm’ (sperm from an individual the female has not had regular sex with before) leading to pregnancy is more likely to lead to preeclampsia in a female, a pregnancy complication which untreated will often lead to the abortion of the fetus. Let’s say the authors claim in that problematic chapter that the reason why females are more likely to develop preeclampsia in case of a pregnancy involving unfamiliar sperm is that such a pregnancy is likely to be a result of rape, and that the physiological mechanism leading to the pregnancy complication is an evolved strategy on part of the female, aimed at enabling her to exercise (post-copulatory) mate choice and reduce the negative fitness consequences of the rape. Let’s say the authors of the preeclampsia chapter/theory don’t talk at all about e.g. genetic benefits derived from extra-pair copulations which are not caused by rape but are engaged in willingly by the female because it’s in her reproductive interests to engage in them, and that the presumably common evolutionary female strategy of finding a semi-decent provider male as a long-term partner while also occasionally sleeping around with high-quality males (and low quality males – but only when not fertile (e.g. when pregnant…)) and have their children without the provider male knowing about it is not even mentioned. Assume the authors of the chapter seem to assume that getting a child by a male with unfamiliar sperm is always a bad idea.

Yeah, the above is what happened in this book, and it’s part of why it only gets two stars. These people are way too busy theorizing, and that specific theory is really poor – or at least the coverage of it was, as they don’t address the obvious issues which people reading the other chapters wouldn’t even have a hard time spotting. Kappeler et al. is a much better book, and it turns out that there was much less new stuff in this book than I’d thought – a lot of ‘the good stuff’ is also covered there.

It doesn’t help that many of the authors are systematically overestimating the extra-pair paternity rate by relying on samples/studies which are obviously deeply suspect due to selection bias. Not all of them goes overboard and claim the number is 10% or something like that, but many of them do – ‘the number is between 1-30%, with best estimates around 10%’ is a conclusion drawn in at least a couple of chapters. This is wrong. Only one contributor talking about these numbers come to the conclusion that the average number is likely to have been less than 5% in an evolutionary context (“Only very tentative conclusions about typical EPP [extra-pair paternity] rates throughout recent human history (e.g. in the past 50 000 years) can be drawn […] It seems reasonable to suggest that rates have typically been less than 10% and perhaps in most cases less than 5%. It also seems reasonable to suggest that they have probably also been variable across time and place, with some populations characterized by rates of 10% or higher.”). An idea worth mentioning in this context is that human behaviour can easily have been dramatically impacted by things which rarely happen now, because the reason why those things may be rare may well be that a lot of behaviour is aimed towards making sure it is rare and stays rare – this idea should be well known to people familiar with Hrdy’s thesis, and it also to me seems to apply to cuckoldry; cuckoldry may happen relatively infrequently, but perhaps the reason for this is that human males with female partners are really careful not to allow their partners to sleep around quite as much as their genetic code might like them to do. I mentioned in the coverage of Kappeler et al. that female sexual preferences change over the course of her menstrual cycle – they also talk about this in this book, but a related observation also made in the book is that males seem to be more vigilant and seem to intensify their level of mate guarding when their partner is ovulating. There’s probably a lot of stuff which goes on ‘behind the scenes’ which we humans are not aware of. Human behaviour is really complicated.

All these things said, there’s some really nice stuff in the book as well. The basic idea behind much of the coverage is that whereas females always know that their children are their children, males can never know for sure – and in a context where males may derive a fitness benefit from contributing to their offspring and a fitness loss by contributing to another male’s child, this uncertainty is highly relevant for how they might choose to behave in many contexts related to partnership dynamics. Many different aspects of the behaviour of human males is to some extent directed towards minimizing the risk of getting cuckolded and/or the risk of a partner in whom they have invested leaving him. They may choose to hide the female partner from competitors e.g. by monopolizing her time or by using violence to keep her from interacting with male competitors, they may signal to competitors that she is taken and/or perhaps that it may be costly to try to have sex with her (threats to other males, violence directed towards the competitor rather than the partner), they may try to isolate her socially by badmouthing her to potential competitors (e.g. male friends and acquaintances). On a more positive note males may also choose to do ‘nice things’ to keep the partner from leaving him, like ‘giving in to sexual requests’ and ‘performing sexual favors to keep her around’ (in at least one study, “men partnered to women who [were] more likely to be sexually unfaithful [were] also more likely to perform sexual inducements to retain their partners” – but before women reading this conclude that their incentives may look rather different from what they thought they did, it’s probably worth noting that the risk of abuse also goes up when the male thinks the partner might be unfaithful (see below)). If the first anti-cuckold approach, the mate-guarding strategy of trying to keep her from having sex with others, fails, then the male has additional options – one conceptualization in the book splits the strategy choices up into three groups; mate-guarding strategies, intra-vaginal strategies and post-partum strategies (in another chapter they distinguish among “preventative tactics, designed to minimize female infidelity; sperm-competition tactics, designed to minimize conception in the event of female infidelity; and differential paternal investment” – but the overall picture is reasonably similar). Intra-vaginal strategies relate to sperm competition and for example more specifically relate to e.g. the observation that a male may try to minimize the risk of being cuckolded after having been separated from the partner by having sex with the partner soon after they meet up again. A male may also increase the amount of sperm deposited during intercourse in such a context, compared to normal, and ‘sexual mechanics’ may also change as a function of cuckoldry risk (deeper thrusts and longer duration of sex if they’ve been separated for a while). There are five chapters on this stuff in the book, but I’ve limited coverage of this stuff because I don’t think it’s particularly interesting. Post-partum strategies naturally relate to strategies employed after the child has been born. Here the father may observe the child after it’s been born and then try to figure out if it looks like him/his family, and then adjust investment in the child based on how certain he is that he’s actually the father:

“There is growing evidence that human males are […] affected by […] evolutionary pressures to invest in offspring as a function of paternal certainty”, and “Burch and Gallup (2000) have shown that males spend less time with, invest fewer resources in, and are more likely to abuse ostensibly unrelated children than children they assume to be their genetic offspring. They also found that the less a male thinks a child (unrelated or genetic) looks like him, the worse he treats the child and the worse he views the relationship with that child.”

It’s worth mentioning that dividing the strategy set up into three, and exactly three, overall categories seem to me slightly artificial, also because some relevant behaviours may not fit very well into any of them; to take an example, “There is growing evidence that males who question their partner’s fidelity show an increase in spouse abuse during pregnancy, and the abuse is often directed toward the female’s abdomen” – this behavioural pattern relates to none of the three strategy categories mentioned, but also seems ‘relevant’. In general it’s important to observe that employment of a specific type of tactic does not necessarily preclude the employment of other tactics as well – as pointed out in the book:

“A male’s best strategy is to prevent female infidelity and, if he is unsuccessful in preventing female infidelity, he would benefit by attempting to prevent conception by a rival male. If he is unsuccessful in preventing conception by a rival male, he would benefit by adjusting paternal effort according to available paternity cues. The performance of one tactic does not necessitate the neglect of another tactic; indeed, a reproductively wise strategy would be to perform all three categories of anti-cuckoldry tactics”

There’s a lot of food for thought in the book. I’ve included some more detailed observations from the book below – in particular I’ve added some stuff closely related to what I believe people might normally term ‘red flags’ or similar in a relationship context. I’d say that enough research has been done on this kind of stuff for it to make a lot of sense for women to read some of it – in light of the evidence, there are certain types of male behaviours which should most definitely be considered strong warning signs that it may be a bad idea to engage with this individual. (I was annoyed that the book only dealt with male abuse, as there are quite a few female abusers as well, but I can’t really fault the authors for limiting coverage to male behaviours).

“Paternal investment in humans and many other species is facultatively expressed: it often benefits offspring but is not always necessary for their survival and thus the quantity and quality of human paternal investment often varies with proximate conditions […] The facultative expression of male parenting reflects the […] cost–benefit trade-offs as these relate to the current social and ecological contexts in which the male is situated. The degree of male investment (1) increases with increases in the likelihood that investment will be provided to his own offspring (i.e. paternity certainty), (2) increases when investment increases the survival and later reproductive prospects of offspring, and (3) decreases when there are opportunities to mate with multiple females. […] the conditional benefits of paternal investment in these species results in simultaneous cost–benefit trade-offs in females. Sometimes it is in the females’ best interest (e.g. when paired with an unhealthy male) to cuckold their partner and mate with higher-quality males […] As a result, women must balance the costs of reduced paternal investment or male retaliation against the benefits of cuckoldry; that is, having their children sired by a more fit man while having their social partner assist in the rearing of these children.”

“In several large but unrepresentative samples, 20–25% of adult women reported having had at least one extra-pair sexual relationship during their marriage […] Using a nationally representative sample in the USA, Wiederman (1997) found that 12% of adult women reported at least one extra-pair sexual relationship during their marriage, and about 2% reported such a relationship during the past 12 months; Treas and Giesen (2000) found similar percentages for another nationally representative sample. These may be underestimates, given that people are reluctant to admit to extra-pair relationships. In any case, the results indicate that some women develop simultaneous and multiple opposite-sex relationships, many of which become sexual and are unknown to their social partner […] The dynamics of these extra-pair relationships are likely to involve a mix of implicit (i.e. unconscious) and explicit (i.e. conscious) psychological processes (e.g. attention to symmetric facial features) and social strategies. […] the finding that attraction to extra-pair partners is influenced by hormonal fluctuations points to the importance of implicit mechanisms. […] The emerging picture is one in which women appear to have an evolved sensitivity to the proximate cues of men’s fitness, a sensitivity that largely operates automatically and implicitly and peaks around the time women ovulate. The implicit operation of these mechanisms enables women to assess the fitness of potential extra-pair partners without a full awareness that they are doing so. In this way, women are psychologically and socially attentive to the relationship with their primary partner and most of the time have no explicit motive to cuckold this partner. If their social partners monitor for indications of attraction to extra-pair men, which they often do […], then these cues are only emitted during a short time frame. Moreover, given that attraction to a potential extra-pair partner is influenced by hormonal mechanisms, often combined with some level of pre-existing and non-sexual emotional intimacy with the extra-pair male […], many of these women may have no intention of an extra-pair sexual relationship before it is initiated. Under these conditions, the dynamics of cuckoldry may involve some level of self deception on women’s part, a mechanism that facilitates their ability to keep the extra-pair relationship hidden from their social partners. […] As with women, men’s anti-cuckoldry biases almost certainly involve a mix of implicit processes and explicit behavioral strategies that can be directed toward their mates, toward potential rivals, and toward the evaluation of the likely paternity of children born to their partners”

“Males have evolved psychological adaptations that produce mate guarding and jealousy […] to reduce or to prevent a mate from being inseminated by another male. Recent evidence suggests that males maximize the utility of their mateguarding strategies by implementing them at ovulation, a key reproductive time in a female’s menstrual cycle […]. Further, jealousy appears to fluctuate with a man’s mate value and, hence, risk of cuckoldry. Brown and Moore (2003), for example, found that males who were less symmetrical were significantly more jealous. These and other data suggest that jealousy has evolved as a means by which males can attempt to deter extra-pair copulations […] When triggered, jealousy often results in a variety of behavioral responses, including male-on-female aggression […], divorce […], the monitoring and attempted control of the social and sexual behavior of their partners […], enhancement of their attractiveness as a mate […], and the monitoring of and aggression toward actual or perceived sexual rivals […]. In total, these behaviors encompass tactics that function to ensure, through coercion or enticement, that their reproductive investment and that of their mate is directed toward the man’s biological children. […] One of the more common behavioral responses to relationship jealousy is mate guarding. For men this involves reducing their partner’s opportunity to mate with other men.”

“Cuckoldry is a reproductive cost inflicted on a man by a woman’s sexual infidelity or temporary defection from her regular long-term relationship. Ancestral men also would have incurred reproductive costs by a long-term partner’s permanent defection from the relationship. These costs include loss of the time, effort, and resources the man has spent attracting his partner, the potential misdirection of his resources to a rival’s offspring, and the loss of his mate’s investment in offspring he may have had with her in the future […] Expressions of male sexual jealousy historically may have been functional in deterring rivals from mate poaching […] and deterring a mate from a sexual infidelity or outright departure from the relationship […] Buss (1988) categorized the behavioral output of jealousy into different ‘‘mate-retention’’ tactics, ranging from vigilance over a partner’s whereabouts to violence against rivals […] Performance of these tactics is assessed by the Mate Retention Inventory (MRI[)] […] Buss’s taxonomy (1988) partitioned the tactics into two general categories: intersexual manipulations and intrasexual manipulations. Intersexual manipulations include behaviors directed toward one’s partner, and intrasexual manipulations include behaviors directed toward same-sex rivals. Intersexual manipulations include direct guarding, negative inducements, and positive inducements. Intrasexual manipulations include public signals of possession. […] Unfortunately, little is known about which specific acts and tactics of men’s mate-retention efforts are linked with violence. The primary exception is the study by Wilson, Johnson, and Daly (1995), which identified several predictors of partner violence – notably, verbal derogation of the mate and attempts at sequestration such as limiting access to family, friends, and income.”

“Tactics within the direct guarding category of the MRI include vigilance, concealment of mate, and monopolization of time. An exemplary act for each tactic is, respectively, ‘‘He dropped by unexpectedly to see what she was doing,’’ ‘‘He refused to introduce her to his same-sex friends,’’ and ‘‘He monopolized her time at the social gathering.’’ Each of these tactics implicates what Wilson and Daly (1992) term ‘‘male sexual proprietariness,’’ which refers to the sense of entitlement men sometimes feel that they have over their partners […] Wilson et al. (1995) demonstrated that violence against women is linked closely to their partners’ autonomy-limiting behaviors. Women who affirmed items such as ‘‘He is jealous and doesn’t want you to talk to other men,’’ were more than twice as likely to have experienced serious violence by their partners.” [What was the base rate? I find myself asking. But it’s still relevant knowledge.] […] Not all mate-retention tactics are expected to predict positively violence toward partners. Some of these tactics include behaviors that are not in conflict with a romantic partner’s interests and, indeed, may be encouraged and welcomed by a partner […] Holding his partner’s hand in public, for example, may signal to a woman her partner’s commitment and devotion to her. […] Tactics within the public signals of possession category include verbal possession signals (e.g. ‘‘He mentioned to other males that she was taken’’), physical possession signals (e.g. ‘‘He held her hand when other guys were around’’), and possessive ornamentation (e.g. ‘‘He hung up a picture of her so others would know she was taken’’).”

“The current studies examined how mate-retention tactics are related to violence in romantic relationships, using the reports of independent samples of several hundred men and women in committed, romantic relationships […], and using the reports of 107 married men and women […] With few exceptions, we found the same pattern of results using three independent samples. Moreover, these samples were not just independent, but provided different perspectives (the male perpetrator’s, the female victim’s, and a combination of the two) on the same behaviors – men’s mate-retention behaviors and men’s violence against their partners. We identified overlap between the best predictors of violence across the studies. For example, men’s use of emotional manipulation, monopolization of time, and punish mate’s infidelity threat are among the best predictors of female-directed violence, according to independent reports provided by men and women, and according to reports provided by husbands and their wives. The three perspectives also converged on which tactics are the weakest predictors of relationship violence. For example, love and care and resource display are among the weakest predictors of female-directed violence. […] The tactic of emotional manipulation was the highest-ranking predictor of violence in romantic relationships in study 1, and the second highest-ranking predictor in studies 2 and 3. The items that comprise the emotional manipulation tactic include, ‘‘He told her he would ‘die’ if she ever left,’’ and ‘‘He pleaded that he could not live without her.’’ Such acts seem far removed from those that might presage violence. […] Monopolization of time also ranked as a strong predictor of violence across the three studies. Example acts included in this tactic are ‘‘He spent all his free time with her so that she could not meet anyone else’’ and ‘‘He would not let her go out without him.’’ […] The acts ‘‘Dropped by unexpectedly to see what my partner was doing’’ and ‘‘Called to make sure my partner was where she said she would be’’ are the third and fifth highest-ranking predictors of violence, respectively. These acts are included in the tactic of vigilance, which is the highest-ranking tactic-level predictor of violence in study 3. Given that (1) two of the top five actlevel predictors of violence are acts of vigilance, (2) the numerically best tactic-level predictor of violence is vigilance, and (3) seven of the nine acts included within the vigilance tactic are correlated significantly with violence […], a man’s vigilance over his partner’s whereabouts is likely to be a key signal of his partner-directed violence. […] Wilson et al. (1995) found that 40% of women who affirmed the statement ‘‘He insists on knowing who you are with and where you are at all times’’ reported experiencing serious violence at the hands of their husbands.”

“Relative to women’s reports of their partners’ behavior, men self-reported more frequent use of intersexual negative inducements, positive inducements, and controlling behavior. Although not anticipated, the sex difference in reported frequency of controlling behaviors is not surprising upon examination of the acts included in the CBI [Controlling Behavior Index]. More than half of the acts do not require the woman’s physical presence or knowledge, for example ‘‘Deliberately keep her short of money’’ and ‘‘Check her movements.’’ In addition, such acts might be more effective if the woman is not aware of their occurrence. […] Increased effort devoted to mate retention is predicted to occur when the adaptive problems it was designed to solve are most likely to be encountered – when a mate is particularly desirable, when there exist mate poachers, when there is a mate-value discrepancy, and when the partner displays cues to infidelity or defection”

“Although sometimes referred to as marital rape, spouse rape, or wife rape,we use the term forced in-pair copulation (FIPC) to refer to the forceful act of sexual intercourse by a man against his partner’s will. […] FIPC is not performed randomly […] FIPC reliably occurs immediately after extra-pair copulations, intrusions by rival males, and female absence in many species of waterfowl […] and other avian species […] FIPC in humans often follow[s] accusations of female infidelity”

November 16, 2014 Posted by | anthropology, biology, books, evolution, Psychology | Leave a comment

Sexual Selection in Primates – New and comparative perspectives (II)

You can read my first post about the book here. Let’s talk some more about what we can learn from this publication…

“In a variety of mammals and a few birds, newly immigrated or newly dominant males are known to attack and kill dependent infants […]. Hrdy (1974) was the first to suggest that this bizarre behaviour was the product of sexual selection: by killing infants they did not sire, these males advanced the timing of the mother’s next oestrus and, owing to their new social position, would have a reasonable probability of siring this female’s next infant. […] Although this interpretation, and indeed the phenomenon itself, has been hotly debated for decades […], on balance, this hypothesis provides a far better fit with the observations on primates than any of the alternatives […] several large-scale studies have estimated that the time gained by the infanticidal male amounts to [25-32] per cent of the mean interbirth interval […] Because males rarely, if ever, suffer injuries during infanticidal attacks, and because there is no evidence that committing infanticide leads to reduced tenure length, one can safely conclude that, on average, infanticide is an adaptive male strategy. […] Infanticide often happens when the former dominant male, the most likely sire of most infants even in multi-male groups […], is eliminated or incapacitated. […] dominant males are effective protectors of infants as long as they are not ousted or incapacitated.”

“Conceptually, we can distinguish two kinds of mating by females that may reduce the risk of infanticide. First, by mating polyandrously in potentially fertile periods, females can reduce the concentration of paternity in the dominant male, and spread some of it to other males, so that long-term average paternity probabilities will be somewhat below 1 for the dominant male and somewhat above 0 for the subordinates. Second, by mating during periods of non-fertility […], a female may be able to manipulate the assessment by the various males of their paternity chances, although she obviously cannot change the actual paternity values allocated to the various males. […] The basic prediction is that females that are vulnerable to infanticide by males should be actively polyandrous whenever potentially infanticidal males are present in the mating pool (i.e. the sexually mature males in the social unit or nearby with which the female can mate, in principle). There is ample evidence that primate females in vulnerable species actively pursue polyandrous matings and that they often engage in matings when fertilisation is unlikely or impossible […]. Indeed, females often target low-ranking or peripheral males reluctant to mate in the presence of the dominant males, especially during pregnancy. […] In species vulnerable to infanticide, females often respond to changes in the male cohort of a group with immediate proceptivity, and effectively solicit matings with the new (or newly dominant) male […] It is in the female’s interest to keep individual males guessing as to the extent to which other males have also mated with her […] Hence, females should be likely to mate discreetly, especially with subordinate males. […] We [expect] that matings between females and subordinate males tend to take place out of sight of the dominant male, e.g. at the periphery and away from the group […] it has been noted for several species that matings between females and subordinate males [do] tend to occur rather surreptuously”

“Even though most primates have concealed ovulations, there is evidence that they use various pre-copulatory mechanisms, such as friendships […] or increased proximity […] with favoured males, copulation calls that are likely to attract particular males […], active solicitation of copulations around the likely conception date […], as well as changes in chemical signals […]; unique vocalizations […]; sexual swellings […] and increased frequencies of particular behaviour patterns during the peri-ovulatory phase […] to signal impending ovulation and/or to increase the chances of fertilization by favoured males.” [Recall from the previous post also in this context that which males are actually ‘favoured’ changes significantly during the cycle].

“Thornhill (1983) suggested that females might exhibit what he called ‘cryptic female choice’ – the differential utilisation of sperm from different males. The term ‘cryptic’ referred to the fact that this choice took place out of sight, inside the female reproductive tract. […] Cryptic female choice is difficult to demonstrate [as] one has to control for all male effects, such as sperm numbers or differential fertilising ability […] Cryptic female choice in primates is poorly documented, even though there are theoretical reasons to expect it to be common. […] The strongest indirect evidence for a mechanism of cryptic female choice in primates is provided by the observation that females of several species of anthropoids (mostly macaques, baboons and chimpanzees) exhibit orgasm […] Physiological measures during artificially induced orgasms [have] demonstrated the occurence of the same vaginal and uterine contractions that also characterise human orgasm […] and are thought to accelerate and facilitate sperm transport towards the cervix and ovaries […] female orgasm was observed more often in macaque pairs including high-ranking males (Troisi & Carosi, 1998). A comparable effect of male social status on female orgasm rates has also been reported for humans […]. Orgasm therefore has the potential to be used selectively by females to facilitate fertilisation of their eggs by particular males […] This hypothesis is indirectly supported by the observation that female orgasm apparently does not occur among prosimians […], but rather among Old World primates, where the potential for coercive matings by multiple males is highest […]. Seen this way, female primate orgasm may therefore represent an evolutionary response to male sexual coercion that provided females with an edge in the dynamic competition over the control of fertilisation” [Miller’s account/explanation was quite different. I think both explanations are rather speculative at this point. Speculative, but interesting.]

“It has long been an established fact in ethology that interactions with social partners influence an individual’s motivational state and vice versa, and, through interactions, its physiological development and condition. For example, the suppression of reproductive processes by the presence of a same-sex conspecific has been documented for many species, including primates. […] The existence of a conditional [male mating] strategy with different tactics has been demonstrated in several species of mammals. To mention but one clear example: in savannah baboons, a male may decide what tactic to follow in its relationships with females after assessing what others do. Smuts (1985) has shown that dominant males follow a sexual tactic in which they monopolise access to fertile females by contest competition. A subordinate male may use another tactic. He may persuade a female to choose him for mating by rendering services to the female (e.g. protecting her in between-female competition) and thus forming a ‘friendship’ with the female. Similar variation in tactics has been found in other primates (e.g. in rhesus macaques, Berard et al., 1994).”

And there you probably have at least part of the explanation for why millions of romantically frustrated (…’pathetic’?) human males waste significant parts of their (reproductive) lives catering to the needs of women who already have a sexual partner and are not sexually interested in them – they might not even have been born were it not for the successful application of this type of sit-and-wait strategy on part of some of their ancestors in the past.

The chapter in question has a lot of stuff about male orangutans, and although it’s quite interesting I won’t go much into the details here. I should note however that I think most females will probably prefer the above-mentioned ‘sneaky’ male tactic (I should perhaps note here that in terms of the ‘sneakiness’ of mating strategies, females do pretty well for themselves as well. Indeed in the specific setting it’s not unlikely that it’s actually the females who initiate in a substantial number of cases – see above..) to the mating tactic of unflanged orangutans, which basically amounts to walking around looking for a female unprotected by a flanged male and then raping her when he comes across one. In one sample included in the book of orangutan matings taking place in Tanjung Puting national park (Indonesia), of roughly 20 matings by unflanged males recorded only 1 or 2 (it’s a bar graph) did not involve a female resisting. These guys are great, and apparently really sexy to the opposite gender… The ratio of resisting/not resisting females in the case of the matings involving flanged males was pretty much the reverse; a couple of rapes and ~18-19 unforced mating events. It should be noted that the number of matings achieved by the flanged and unflanged males is roughly similar, so judging from these data approximately half of all matings these female orangutans experience during their lives are forced.

“Especially in long-lived organisms such as primates, a male’s success in competing for mates and protecting his offspring should be affected by the nature of major social decisions, such as whether and when to transfer to other groups or to challenge dominants. Several studies indicate dependence of male decisions about transfer and acquisition of rank on age and local demography […]. Likewise, our work on male long-tailed macaques […] indicated a remarkably tight fit between the behavioural decisions of males and expectations based on known determinants of success […], suggesting that natural selection has endowed males with rules that, on average, produce optimal life-history trajectories (or careers) for a given set of conditions. […] Most non-human primates live in groups with continuous male-female association [“Only a minority of about 10 per cent of primate species live in pairs” – from a previous chapter], in which group membership of reproductively active (usually non-natal) males can last many years. For a male living in such a mixed-sex group, dominance rank reflects his relative power in excluding others from resources. However, the impact of dominance on mating success is variable […] Although rank acquisition is usually considered separately from transfer behaviour and mating success, the hypothesis examined here is that they are interdependent […]. We predict that the degree of paternity concentration in the dominant male, determined by his ability to exclude other males from mating, determines the relative benefits of various modes of acquisition of top rank […], and that these together determine patterns of male transfer”

“the cost of inbreeding may cause females to avoid mating with male relatives […]. This tendency has been invoked to explain an apparent female preference for novel (recently immigrated) males”

“a male can attain top rank in a mixed-sex group in three different ways. First, he can defeat the current dominant male during an aggressive challenge […] Second, he can attain top rank during the formation of a new group[…] A third way to achieve top rank is by default, or through ‘succession’, after the departure or death of the previous top-ranking male, not preceded by challenges from other males”

The chapter which included the above quotes is quite interesting, but in a way also difficult to quote from given the way it is written. They talk about multiple variables which may affect how likely a male is to leave the group in which he was born (for example if there are fewer females in the group, all else equal he’s more likely to leave); which mechanism he’s likely to employ in order to try to achieve top rank in his group, if that’s indeed an option (in small groups they always fight for the top spot and the dominant male will have a very dim view of other mature males trying to encroach upon his territory, whereas in large groups the dominant male is more tolerant of competitors and they’re much less likely to settle things by fighting with each other – the reason why fighting is less common is probably because the male in the latter group is in general unable to monopolize access to the females because of the size of the group, so you to some extent ‘gain less’ by achieving alpha male status), and when he’s likely to act (a young male is stronger than an old male and he can also expect to maintain his tenure as the top male for a longer period of time – so males who try to achieve top rank by fighting for it are likely to be young, whereas males who achieve top rank by other means tend to be older). Whether or not females reproduce in a seasonal pattern also matters. It’s obvious from the data that it’s far from random how and at which point during their lives males make their transfer decisions, and how they settle conflicts about who should get the top spot. The approach in that chapter reminded me a bit of optimal foraging theory stuff, but they didn’t talk about that kind of stuff at all in the chapter. Here’s what they concluded from the data they presented in the chapter:

“We found not only variation between species but also remarkable variation within species, or even populations, in the effect of group size on paternity concentration and thus transfer decisions, as well as mode of rank acquisition and likelihood of natal transfer. This variability suggests that a primate male’s behaviour is guided by a set of conditional rules that allow him to respond to a variety of local situations. […] Primate males appear to have a set of conditional rules that allow them to respond flexibly to variation in the potential for paternity concentration. Before mounting a challenge, they assess the situation in their current group, and before making their transfer decisions they monitor the situation in multiple potential-target groups, where this is possible.”

October 14, 2014 Posted by | biology, books, evolution, Zoology | 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, evolution, genetics, Geography | Leave a comment

Evolution and the Levels of Selection

After I’d read the book I googled the author and I came across this lecture, which is actually a really nice lecture about many of the ideas also included in the book:

The stuff covered during the last five minutes or so of the talk is not in the book – there’s no political theory or similar in there – but most of the other stuff is. The book is somewhat more theoretical than the lecture; there’s no stuff about vampire bats in there. It probably also goes without saying that the coverage in the book provides a lot more detail than does the lecture, which only really scratches the surface; the analytical level is quite a bit higher in the book.

The book is in my opinion an example of really good philosophy of science. I liked the book a lot, it’s really nicely written and the author seems to be a very precise and careful writer and thinker. There are pretty much no superfluous pages in the book, which also means that I’ve actually been a bit conflicted about how to blog it, because it seemed impossible to go over all those ideas in just a blog post or two. I suggest you watch the lecture; if you like the lecture and/or want to know more about the ideas presented there, you’ll want to read this book.

The book includes some equations here and there, but nothing you shouldn’t be able to handle. Some really important ideas in the book are not mentioned in the lecture, but this is natural given the format – there’s only so much stuff you can pack into one lecture. For example in any two-level setting including ‘particles’ and ‘collectives’, the question arises of how to even define collective (/’group’) fitness. One might define it as “the average or total fitness of its constituent particles; so the fittest collective is the one that contributes most offspring particles to future generations of particles.” Or one might define it as “the number of offspring collectives it leaves; so the fittest collective is the one that contributes the most offspring collectives to future generations of collectives.” The distinction between these two conceptualizations of collective fitness actually is really important in some analytical contexts, and this is definitely a distinction worth keeping in mind.

I may cover the book in more detail later, but for now I’ll limit coverage to the comments above and to the lecture. In my opinion it’s a really nice book, I gave it five stars on goodreads.

August 9, 2014 Posted by | biology, books, evolution, genetics, Lectures | 12 Comments

Sexually Transmitted Diseases (4th edition) (IV)

Here’s a link to a previous post about the book, which includes links to the first two posts I wrote about it.

I was not super impressed with the coverage in part 3, although there was a lot of interesting stuff as well. However the level of coverage and amount of detail included is high in part four and five. There were a lot of details which evaded me in some of the recent chapters, but I also learned a great deal. There’s quite a lot of coverage of various ‘related topics’ (microbiology, biochemistry, immunology, oncology) in the parts of the book I’ve read recently, and like many other medical texts this book will help you realize that many things you in your mind had thought of as unrelated actually are connected in various interesting ways. It’s worth noting that given how many aspects of these things the book covers (again, 2000+ pages…) you actually get to know a lot of stuff about a lot of other things besides just ‘classic STDs’. It turns out that in Jamaica and Trinidad, over 70% of all lymphoid malignancies are attributable to exposure to a specific herpes virus most people probably haven’t heard about, HTLV-1 (prevalence is also high in other parts of the world, e.g. southern Japan). I didn’t expect to learn this from a book about sexually transmitted diseases, but there we are.

I hope that I’ve picked out stuff from this part of the coverage which is also intelligible to people who didn’t read the 95+% of those chapters I didn’t quote (I always like feedback on such aspects).

“At the simplest level, infection of a cell by a virus or bacterium may lead to cell death. In the case of viruses, specific disease syndromes may be caused by destruction of certain subsets of cells that express essential differentiated functions. A classic example of this is the development of the AIDS following HIV-1 mediated depletion of the CD4 lymphocyte population. Virus-induced cell death may result from one or more specific mechanisms. Many viruses express specific proteins that have as their major function the induction of a blockade in normal host cell metabolism (cellular translation and transcription) such that the metabolic machinery of the cell is subverted preferentially to viral replication. For obvious reasons, the expression of such proteins is usually highly toxic to the cell. Cellular destruction or “direct cytopathic effect” is considered responsible for the disease manifestations of many lytic viruses, including, for example, HSV and poliovirus. On the other hand, many cells may respond to the presence of an invading virus by the induction of apoptosis and the initiation of programmed cell death. Some viruses appear to have evolved mechanisms to prevent or delay apoptosis, thus potentially prolonging productive infection and maximizing replication. For example, HSV-1 infection induces apoptosis at multiple metabolic checkpoints but has also evolved mechanisms to block apoptosis at each point.28 Importantly, the inhibition of apoptosis by HSV-1 also prevents apoptosis induced by virus-specific cytotoxic T lymphocytes, thereby conferring on the infected cell a certain measure of resistance to the host’s cell-mediated immune responses.29

However, many viruses are not intrinsically cytopathic. HBV is a prime example, as many infected HBsAg carriers are asymptomatic and without overt evidence of active liver disease. Despite this, such carriers may be very infectious […] The presence or absence of liver disease is largely determined by the T-cell response to the virus.30 Thus, chronic hepatitis B results from a relatively vigorous but unsuccessful attempt on the part of the host to eliminate the infection. […] chronic liver inflammation and the occurrence of hepatocellular carcinoma reflect the immune response to the virus, rather than specific virus effects. Similar indirect mechanisms may contribute to the progressive immune destruction of infected CD4-positive lymphocytes in patients with HIV-1 infection.

Some bacterial disease processes may also be caused largely to immunopathologic responses. For instance, there is substantial evidence that complications of genital chlamydia infections (salpingitis, Reiter’s syndrome) are correlated with and may be owing to stimulation of antibodies against a heatshock protein (hsp60).33,34 […] In contrast, gonococcal tissue damage appears to be caused by the direct toxic effects of lipid A and peptidoglycan fragments”

“Some viruses are capable of altering differentiated cellular functions, resulting in the production of disease by mechanisms that do not exist among bacteria. A prime example is the altered cellular growth that follows infections by molluscum contagiosum virus (MCV) […]. A more extreme example is the proliferation of epithelial cells that is induced by infection with HPVs. HPV-related epithelial malignancies and cellular transformation are related to the expression of two specific HPV proteins, the E6 and E7 oncoproteins, by high-risk HPV subtypes.22 These proteins interact with p53 and pRb, both promoting cellular proliferation and cell survival. Oncogenic transformation is usually associated with high-level expression of E7 from integrated HPV DNA. The Kaposi’s sarcoma-associated herpes virus (KSHV) also expresses a number of proteins that mimic important host regulators of cellular proliferation and survival […] Expression of these proteins may result in deregulation of cell growth, with changes in the cellular morphology and/or acquisition of the ability of the cells to form colonies in soft agar, changes that are indicative of transformation.

On the other hand, hepatocellular cancers occurring in the context of chronic viral hepatitis are likely to have an alternative explanation. Although it is possible that integration of HBV DNA may be responsible for altered cellular growth control in some hepatitis B-associated cases, liver cancer in this setting may be primarily immunopathogenic.30,32 Chronic inflammation accompanied by oxidative stress and cellular DNA damage are likely to pla[y] important roles.”

“The human immunodeficiency viruses (HIV-1 and HIV-2) and the simian immunodeficiency viruses (SIV) (with a subscript indicating the species of origin) are members of the lentivirus genus of the Retroviridae family, commonly called retroviruses. […] Retroviruses are divided into two subfamilies: Orthoretrovirinae and Spumaretrovirinae […] The spumaretroviruses have distinctive features of their replication cycle that require this more distant classification. They have been isolated from primates, but not humans, and are not associated with any known disease. The orthoretroviruses are divided into six genera and represent viruses that infect snakes, fish, birds, and mammals. […] Human infections occur with viruses from two of these genera. The Deltaretrovirus genus includes human T-cell leukemia virus type I (HTLV-I), the causative agent of adult T-cell leukemia,5, 6, 7 and human T-cell leukemia virus type II (HTLV-II), which is not known to be associated with any disease syndrome. HTLV-I is also associated with another syndrome called HTLV-associated myelopathy (HAM). HTLV-I and HTLV-II are related to viruses found in primates and more distantly related to bovine leukemia virus. The lentivirus genus includes HIV-18 and HIV-29 as well as viruses found in a variety of mammals ranging from primates to sheep. Viruses within these different genera vary widely in the diseases they cause and the mechanisms of disease induction, in contrast to the many common features of their replication cycle. […] In its DNA form the viral genome is inserted into the host genome […]. This step in the virus life cycle has important implications for several features of virus-host interactions. For example, viral DNA that integrates into the genome of a cell but is not expressed becomes silently carried in the descendents of that cell. When this happens in a germline cell, or in the cell of an early embryo that becomes a germline cell, this copy of viral DNA becomes a linked physical part of the host genome, is present in every cell in the body, and is passed on to subsequent generations. Such a genetic element is called an endogenous retrovirus. Most of the elements that become fixed are defective, as there is probably a strong selective pressure against elements that can activate to produce infectious virus. Thus, they represent an archive within the host genome of previous waves of retroviral infections. In fact, the human genome carries a record of retroviral infections over the last 40 million years of primate evolution. These are viruses that we do not recognize as active in the human population at present but are represented by 110,000 genomic inserts of gammaretroviruses, 10,000 inserts of betaretroviruses, and 80,000 inserts of a genus that may be distantly related to spumaretroviruses or may represent an uncharacterized lineage.10 Most of these elements contain large deletions; however, if these deletions had been retained, our genomes would be 40% endogenous retroviruses by mass and outnumber our normal genes 7 to 1.”

“Most histories of retroviruses start with the dramatic discovery by Peyton Rous in 1911 that a virus, Rous sarcoma virus (RSV), could cause cancer. […] The isolation of other tumor-causing retroviruses followed and in time it became apparent that there were two broad classes of agents: one class of viruses caused cancer after a long latency period […], while the other class caused tumors that appeared rapidly […]. We now know that the acutely transforming retroviruses carry a cell-derived oncogene that is responsible for the transforming activity,14 while the slowly transforming retroviruses act by the chance integration of viral DNA near these cellular oncogenes in the host genome to induce their expression and promote tumor formation.15,16 Importantly, many of these same genes can be mutated or overexpressed in human cancers, and the proteins they encode are now the targets of new generations of specific antitumor therapies […] One can confidently surmise that the remnants of the beta- and gammaretroviruses littered in our genomes had such oncogenic effects when they were active. Ironically, for the active human retroviruses, HTLV-I causes tumors by a different but still poorly understood mechanism, and HIV is involved in tumor formation only indirectly through immune suppression. […] There are two fundamental differences between lentiviruses and most other retroviruses: Lentiviruses do not cause cancer [directly…] and they establish chronic infections that result in a long incubation period followed by a chronic symptomatic disease. The “slow” (lenti is Latin for slow), chronic nature of these viral infections was first appreciated for a disease of sheep called maedi-visna (maedi = labored breathing, visna = paralysis and wasting).”

“Using the current sequence diversity in the HIV-1 population, the 1959 sequence, and estimates of the rate of sequence change per year, it has been possible to suggest that the cross-species transmission event that gave rise to the M group of HIV-1 occurred early in the twentieth century.38 If we accept that SIVcpz [HIV in chimps…] has entered the human population three times in the last century (the three groups N,O, and M), then it follows that this virus likely has been transmitted to humans any number of times over the last 10,000 years. Only in the last century the human institutions of large cities and efficient transportation corridors have given these transmission events access to a human environment that could support an epidemic.”

“Over 100 herpesviruses have been identified, with at least eight infecting humans [I had no idea there were that many of them, and I had no clue some of the ones mentioned were actually herpes viruses…]. All human herpesviruses are well adapted to their natural host, being endemic in all human populations studied and carried by a significant fraction of persons in each population. The human herpesviruses include herpes simplex viruses types 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpesvirus 6 (HHV-6), human herpesvirus 7 (HHV-7), and human herpesvirus 8 (HHV-8) or Kaposi’s sarcoma (KS)-associated herpesvirus. Disease caused by human herpesviruses tends to be relatively mild and self-limited in immunocompetent persons, although severe and quite unusual disease can be seen with immunosuppression. […] all herpesviruses share biologic traits. These include expression of a large number of viral enzymes, assembly of the nucleocapsid in the cell nucleus, cytopathic effects on the cell during productive infection, and ability to establish latent infections in an infected host.”

“Vaccine development poses great challenges in the case of herpesviruses because recovery from natural disease is not associated with elimination of virus and does not always protect against another episode of disease.
Live-attenuated, killed, and recombinant subunit herpesvirus vaccines have all been studied. Whole-virus vaccines have the advantage of exposing the immune system to all viral antigens. Live-attenuated vaccines have tended to produce longer-lasting immunity than killed preparations. However, live-attenuated herpesvirus vaccines may be capable of establishing latent infections. The risks are not clear and there is concern that vaccine recipients who subsequently become immunosuppressed may develop disease caused by reactivated virus. Two avirulent HSV strains have been shown to generate lethal recombinants in mice.127 Thus, recombination between an attenuated vaccine strain and a superinfecting wild-type strain could occur. Because several herpesviruses have been associated with malignancies in humans, the long-term safety of any live-attenuated vaccine needs careful study.”

“In the most recent data from NHANES, the prevalence of HSV-1 appears to have fallen slightly from 62% in the years 1988-1994 to 57.7% in the years 1999-2004 in the general population.30 In Western Europe, the prevalence of HSV-1 infection in young adults remains 10-20% higher than that in the United States.31 In STD clinics in the United States, about 60% of attendees have HSV-1 antibodies. In Asia and Africa, HSV-1 infection remains almost universal […] The cumulative lifetime incidence of HSV-2 reaches 25% in white women, 20% in white men, 80% in African American women and 60% in African American men […] Transmission of HSV between sexual partners has been addressed most often in prospective studies of serologically discordant couples, i.e., in couples in whom one partner has and the other does not have HSV-2. Longitudinal studies of such couples have shown that the transmission rate varies from 3% to 12% per year. […] Unlike other STDs, persons usually acquire genital HSV-1 and genital HSV-2 in the context of a steady rather than casual relationship.91 Women have higher rates of acquisition than men; in one study the attack rate among seronegative women approached 30% per year.88 […] Subclinical or asymptomatic viral shedding is an important aspect of the clinical and epidemiologic understanding of genital herpes, as most episodes of sexual and vertical transmission appear to occur during such shedding. […] the risk of HSV transmission is likely similar regardless of the presence of lesions, supporting the epidemiologic observation that most HSV is acquired from asymptomatic partners. […] Subclinical HSV reactivation is highest in the first year after acquisition of infection. During this time period, HSV can be detected from genital sites by PCR on a mean of 25-30% of days […]. This is about 1.5 times higher than patients sampled later in their disease course.”

“The major morbidity of recurrent genital herpes is its frequent reactivation rate. Most likely, all HSV-2 seropositive persons reactivate HSV-2 in the genital region. Moreover, because of the extensive area enervated by the sacral nerve root ganglia, reactivation of HSV-2 is widespread over a large anatomic area.

A prospective study of 457 patients with documented first-episode genital herpes infection has shown that 90% of patients with genital HSV-2 developed recurrences in the first 12 months of infection.93 The median recurrence rate was 0.33 recurrences/month. Most patients experienced multiple clinical reactivations. After primary HSV-2 infection, 38% of patients had at least 6 recurrences and 20% had more than 10 recurrences in the first year of infection. Men had slightly more frequent recurrences than women, median 5 per year compared with 4 recurrences per year [it’s important to note that the recurrence rate is substantial even in patients on suppressive therapy: “About 25% of persons on suppressive therapy will develop a breakthrough recurrence each 3-month period”] […] Recently, long-term cohort studies indicate that the frequency of symptomatic recurrences gradually decreases over time. In the initial years of infection, reported recurrence rate decreases by a median of 1 recurrence per year. […] subclinical shedding episodes account for one-third to one-half of the total episodes of HSV reactivation as measured by viral isolation and for 50-75% of reactivations as measured by PCR. […] Rather than regarding HSV-2 as a predominantly silent infection with occasional clinical outbreaks with marked viral shedding, HSV is a dynamic infection, with very frequent reactivation, mostly subclinical, and active effort on the part of the immune system of the host is required to control mucosal viral replication. […] Immunocompromised patients have frequent and prolonged mucocutaneous HSV infections.226, 227, 228 Over 70% of renal and bone marrow transplant recipients who have serologic evidence of HSV infection reactivate HSV infection clinically within the first month after transplantation […] Recurrent genital herpes in immunosuppressed patients often results in the development of large numbers of vesicles which coalesce into extensive deep, often necrotic, ulcerative lesions.228 […] about 70% of HIV-infected persons in the developed world and 95% in the developing world have HSV-2 antibody. […] The epidemiologic interactions between HIV and HSV-2 have led to calculation of potential population-level impact of these intersecting epidemics. […] The population attributable risk will depend on the prevalence of HSV-2 in the population at risk; at 50% HSV-2 prevalence, common among MSM [Males who have Sex with Males, US], or African Americans in the United States, or general population in sub-Saharan Africa, 35% of HIV infections will be attributable to HSV-2. […] the risk of transmitting HSV [from the mother] to the neonate is 30-50% in women with newly acquired HSV [during the last part of the pregnancy] versus <1% in women with established infection.” [This is relevant not only because herpes sucks, but also because it sucks even more when a newborn child gets it].

“More than 50% of individuals in most populations throughout the world demonstrate serological evidence of prior CMV infection.6 The coevolution with and adaptation to its human host over millions of years may account for the observation that in most cases, CMV infection causes few if any symptoms.5 However, in immunocompromised individuals, primary infection or reactivation of latent virus can be life-threatening. As well, congenital infections are common and can result in serious lifelong sequelae. […] Although CMV does not typically come to medical attention as a result of genital tract lesions or disease, it can be transmitted sexually and has important consequences for the sexually active, child-bearing population. […] As with many viruses that cause chronic infection, CMV seems to have coevolved with humans to a balanced state in which the virus persists but generally causes little clinical illness. The host’s innate and adaptive immune responses are usually successful at limiting CMV infection as is evident by the clear association of immune system dysfunction with CMV disease. In the absence of prophylactic antiviral treatment, CMV often reactivates in seropositive individuals who undergo hematopoietic stem cell transplantation (HSCT).41 Immunosuppression resulting from drugs used to treat cancer and autoimmune disorders, and from impaired T-cell function that occurs with advanced AIDS, is also associated with reactivation of CMV. […] The development of primary CMV infection has been noted in up to 79% of liver transplants and 58% of kidney or heart transplants in which the donor is seropositive and the recipient is seronegative.134,135 In the setting of HSCT, several studies have documented that CMV seropositivity of the recipient results in significantly increased overall posttransplant mortality compared to CMV seronegative recipients with a seronegative donor.136 When the recipient is CMV seronegative, overall mortality is increased when the donor is seropositive compared to the situation where the donor is seronegative.137 […] the transplant recipient is at particularly high risk of CMV reactivation during periods of potent immunosuppression that accompany graft rejection or graft-versus-host disease.”

 

July 7, 2014 Posted by | books, evolution, genetics, medicine | Leave a comment

Natural Conflict Resolution (3)

This will be my last post about the book, which I gave four stars on goodreads. You can read my previous posts about the book here and here.

The last part had some interesting stuff, but I think I liked some of the chapters in the middle best. There are obvious parallels to be drawn between the coverage in a few of the last chapters and some of the work of Boyd and Richerson, though these guys’ approach and methodology is quite different.

I’ve included some stuff from the last part of the book below. Although I haven’t exactly read the works of a lot of moral philosophers (except perhaps random quotes of theirs – I’ve probably read quite a few of those over the years), I do think that some of the ideas and observations included in this part of the book are ideas and observations which many of them might benefit (/have benefited) from knowing (/more) about.

“The social interactions between two animals depend not only on their individual characteristics (e.g., age, sex, dominance rank, temperament) but also on the history of interactions between them, provided that they possess the capacity for individual recognition, have sufficient memory to remember the outcome of social interactions, and repeatedly meet each other. The two animals can thus be said to have developed a social relationship. This relationship is not directly visible. Observers decide it exists because the history of previous interactions allows them to predict the outcome of subsequent interactions between the same animals […]. Of course, it also allows the animals to predict the actions and responses of the partner with reasonable accuracy. This makes social intercourse much more efficient, obviating the need for thorough reassessment of the partner’s strength and possible other qualities every time they come close, which is why the establishment of relationships is adaptive for the participants. […] Social behavior is about conflict and cooperation, and relationships characterized by only one of these two probably do not exist. Even the most collaborative relationships tend to contain an element of competition — for instance, because collaborators need to decide on how to divide the benefits of their cooperative effort […] social relationships always contain elements of both cooperation and competition.”

“The partners in an established relationship need to communicate about their relative balance of power (i.e., physical strength and social influence) and about the exchange rate of services. The need for some form of communication is clear in even the simplest relationship. For example, individuals can alternate grooming each other and thus provide benefits in terms of hygiene […], tension reduction […], and endorphin release […] By varying the duration and frequency of their own grooming bouts, the partners can express their perceived relative power in the relationship and, through refusals of grooming invitations or variations in length, negotiate the actual power balance. Communication about the relationship is all the more important because the partners’ values change all the time. Individual qualities, such as strength or experience, change over time, as do their needs for services. External factors—for instance, group composition—may change the value of a partner because they affect the number of other group members who can offer the same service [these effects are termed ‘market effects’ in the literature] […] Changing assessments can be communicated by ceasing to support or share, by taking larger shares than before, or even by punishing partners after they failed to reciprocate […] Communication before engaging in the interaction […] is critical when interactions involve high risks, especially when the partners do not have reliable relationships. Agonistic support between males is a prime example because it involves high risks and because male alliances are fickle.”

“Given the dynamic nature of relationships, it is critical for one or both partners to establish whether the conflict signifies a growing mismatch in the assessments of each other’s value or whether it is a mere hiccup in an otherwise unchanged relationship. We believe this is why reconciliation evolved […] Reconciliation can be viewed as communication about the value of the relationship: it shows how much each partner is interested in the relationship and thereby is willing to repair it after the disturbance due to the conflict. According to this view, reconciliation is not only an effective way to end the conflict but is also a primary tool for relationship management […] The most important generalization to emerge from two decades of work on reconciliation (i.e., post-conflict friendly reunion between opponents) in primates is that individuals that reconcile are likely to have a strong social bond (de Waal, Chapter 2; Cords & Aureli, Chapter 9).”

“In primates, the benefits [of relationships] include selective tolerance around resources […], cooperative hunting […], food sharing […], services for mating privileges […], agonistic support, and protection against harassment. The last two are probably the most widespread and critical benefits related to relationship-dependent cooperation in primates. […] A coalition takes place when individuals support one another in an agonistic conflict […] An alliance is a type of relationship in which the two partners repeatedly form coalitions. Thus, coalitions are interactions that can be formed on a case-by-case basis, whereas alliances are enduring cooperative relationships […] The basic rule for coalitions and alliances is simple: they should be formed when they improve access to limiting resources for both partners […] The limiting resources are usually different for the two sexes because the fitness of males and females is limited by very different factors […] Male mammals […] usually contribute little to the development of the young. […] females usually compete for food or shelter, whereas males compete for mating opportunities (Emlen & Oring 1977).”

“Some of the most significant threats faced by female primates are social ones, in particular, sexual harassment and infanticide by males. Protective bonds between females, and especially those between males and females, may serve to reduce these social threats […] Species with lactational amenorrhea are vulnerable to infanticide by males unlikely to have fathered the infant, because this will speed up the female’s next conception. Many primates have lactational amenorrhea; male infanticide is reported for a remarkably high proportion of primate species […]. Yet male infanticide is rare in most of the species in which it occurs. Perhaps this is because of effective social counterstrategies […] Associations and social relationships can often be seen as strategies to reduce the negative impact of some challenge. Paradoxically, the selective forces that produced particular social behavior are often hard to discern because the behavior it has produced is effective in eliminating the fitness impact of these ultimate causes. Hence, their action is rarely apparent.”

“Among primate males, strong bonds to maintain alliances are expected to serve to improve mating access to females, and indeed they do. However, they are less common and shorter-lived than those among females […]. In various primate species, only a single male stays in a group of females, preventing the establishment of male bonds. But even in the all-male bands commonly found in these species […] or in many species with multimale groups, male bonds are not pervasive. The reasons for this are largely speculative at this stage. […] Most examples of male-female alliances are from species with limited sexual dimorphism, in which males and females can potentially provide mutual agonistic support.”

“When a group is faced with external threats, relationships within the group and with allies increase in importance. Group pressure is exerted on disputants to reconcile conflicts that threaten valued defensive alliances or solidarity. […] in-group/out-group distinctions are also a very salient dimension of nonhuman primate interactions.”

“we make two fundamental assertions regarding the evolution of morality: (1) there are specific types of behavior demonstrated by both human and nonhuman primates that hint at a shared evolutionary background to morality; and (2) there are theoretical and actual connections between morality and conflict resolution in both nonhuman primates and human development. […] the transition from nonmoral or premoral to moral is more gradual than commonly assumed. No magic point appears in either evolutionary history or human development at which morality suddenly comes into existence. In both early childhood and in animals closely related to us, we can recognize behaviors (and, in the case of children, judgments) that are essential building blocks of the morality of the human adult. […] The obvious common ground between current evolutionary and developmental approaches is that, instead of looking at human morality as coming from the outside — imposed by adults on the passive child, or imposed by culture on a fundamentally nasty human nature — it is generated from the inside. What we mean by “inside” is not that things happen in isolation from outside influences: evolution operates on the basis of ecological pressures, which come from the outside, and development takes place in constant interplay with the outside world. What we mean instead is that the decision making and emotions underlying moral judgments are generated within the individual rather than being simply imposed by society. They are a product of evolution, an integrated part of the human genetic makeup, that makes the child construct a moral perspective through interactions with other members of its species. […] Much research has shown that children acquire morality through a social-cognitive process; children make connections between acts and consequences. Through a gradual process, children develop concepts of justice, fairness, and equality, and they apply these concepts to concrete everyday situations (Killen & Hart 1995).”

“From our perspective, we assert that emotions such as empathy and sympathy provide an experiential basis by which children construct moral judgments. Emotional reactions from others, such as distress or crying, provide experiential information that children use to judge whether an act is right or wrong […] when a child hits another child, a crying response provides emotional information about the nature of the act, and this information enables the child, in part, to determine whether and why the transgression is wrong. Therefore, recognizing signs of distress in another person may be a basic requirement of the moral judgment process. The fact that responses to distress in another have been documented both in infancy and in the nonhuman primate literature provides initial support for the idea that these types of moral-like experiences are common to children and nonhuman primates. As an illustration, de Waal (1996) documents reactions to distressed individuals and the tendency to share food with others. Generally, it seems that our closest relatives, the great apes, go further in this regard than more distantly related primates, such as the monkeys. For example, “consolation” has thus far been demonstrated only in chimpanzees despite systematic attempts to find it in monkeys. Consolation is defined as friendly or reassuring contact provided by a bystander to a recipient of aggression […]. In the chimpanzee, this kind of interaction typically consists of putting an arm around the victim or patting him or her gently on the back or shoulder. Because of the contrast between monkeys and apes in this regard, de Waal & Aureli (1996) have recently speculated that consolation may require empathy. Since higher forms of empathy and sympathy require the ability to take someone else’s perspective, the difference may result from Hominoids (i.e., humans and apes) possessing this ability but not monkeys.”

“No biologist and few social scientists would deny that our species has natural aggressive potentials, but we possess many other natural tendencies as well, some of which serve to keep aggression in check. Thus, to call us naturally peaceful (which is, after all, a state observed far more often than war and strife) would be at least as justified as calling us naturally aggressive.”

“the “ought” question, which has occupied moral philosophers over the ages, may reach all the way back to rather mundane mechanisms of how to get along and when to repair relationships.”

June 27, 2014 Posted by | anthropology, biology, books, ethics, evolution, 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, evolution, 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, evolution, Zoology | Leave a comment

Plant-Animal Interactions: An Evolutionary Approach (1)

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

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

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

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

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

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

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

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

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

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

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

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

June 12, 2014 Posted by | biology, books, Botany, evolution, Paleontology, Zoology | 4 Comments

The Origin and Evolution of Cultures (V)

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

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

Here’s the stuff from the introduction:

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

And below I’ve posted the chapter coverage:

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

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

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

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

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

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

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

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

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

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

June 6, 2014 Posted by | anthropology, biology, books, culture, economics, evolution, mathematics, science | Leave a comment

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

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

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

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

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

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

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

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

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

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

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

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

January 27, 2014 Posted by | biology, books, evolution, Geography | Leave a comment

The Red Queen

I read the book yesterday.

It’s an easy book to read and most people who’ve read it seem to like it – it has a rating average of 4.04 on goodreads. I decided in the end to give it two stars. It’ll be the last popular science book of this type I’ll read in a while, and you should note that if I didn’t happen to feel sick and tired of popular science books at this point I might have given it a higher rating – I don’t really think it’s any worse than Miller’s The Mating Mind which I gave three stars, but the question remains if I ought to subtract a star from that one rather than give this one another star. The main problem with these books is that I at this point feel that I just don’t learn enough new stuff from them to justify reading them, and they often make me annoyed due to the authors’ relatively lax standards of evidence and imprecise language (compared to, say, the language of academic textbooks), both of which are more or less direct consequences of the format.

I think there’s generally in these types of books too much speculation and too little worry on part of the author about saying things which are not supported by the data. Funny enough, thinking back to the discussion I had with Miao when covering Miller I should note that Ridley also seemed to have trouble figuring out how large vocabularies people tend to have. But unlike Miller, Ridley didn’t even feel any need to source his hilariously wrong estimate (see below) and that’s not a point in his favour even though the estimate isn’t in any way critical to the coverage. There are interesting observations in the book, quite a few of them, but often it’s harder to trust the author than it ought to be because he also says things which are plain wrong in his book and occasionally it’s very hard to pinpoint the source of an interesting observation, or even figure out if a source exists, because whole paragraphs may be supported by one source which doesn’t necessarily cover all the material in the paragraph in question – there are no (authors X and Y, 20XX) references like in academic papers, only an occasional number and a source in the back of the book; and once you realize that he says unsourced things which are not true in the text, you start worrying about the existence of unsourced observations within the sourced paragraphs as well. Or at least I did. Of course the fact that a statement is sourced doesn’t necessarily mean it’s right, but it’s a better starting point than is the alternative. Another major problem is that there are a lot of sentences which would be improved greatly by probability indicators like ‘perhaps’, ‘it’s likely that’, and similar – this relates to the ‘imprecise language’ part above. There’s too little doubt, and he’s sometimes way too categorical in his statements and/or give a too simplified view of the problem at hand.

Stuff I’ve read which covers some of the same stuff as is covered in this book includes Miller, Bobbi Low, the first couple of chapters in Scarre, a few chapters from Majerus, and some of Dawkins’ work. I already knew about the sex-parasites thing because that idea has been covered elsewhere, though of course the book has more details on this stuff. Anyway I think it’s safe to say that if you’re reasonably well-informed there’ll be a lot of pages in this book covering stuff you already know.

I’ve focused mainly on the good stuff in the book below, but I didn’t think it was right to only include good stuff, so there are a few ‘bad quotes’ and related critical remarks here and there as well.

“Selection within the species is always going to be more important than selection between the species.[13]” [The source given to this claim is ‘Humphrey 1983’. This is a good example of the ‘he’s too categorical’ – Always??? I wonder what the hundreds of species which went extinct in Lake Victoria following the introduction of the Nile Perch have to say about that? Or what about the Dodo? Important in what way and for whom?]

“If a population is small […] or the number of genes in the creature is very large, [Muller’s] ratchet has a severe effect on an asexual lineage. […] being sexual was a prerequisite for being big (and therefore few), or, conversely, sex is unnecessary if you stay small.[38]”

“among mammals, the amount of recombinations bears no relation to the number of young, little relation to body size, and close relation to age at maturity. In other words long-lived, late-maturing animals do more genetic mixing regardless of their size or fecundity than short-lived, early-maturing animals.”

“the probability that a family of animals will become extinct does not depend on how long that family has already existed. In other words, species do not get better at surviving […] Their chances of extinction are random. […] The struggle for existence never gets easier. However well a species may adapt to its environment, it can never relax, because its competitors and its enemies are also adapting to their niches. Survival is a zero-sum game.”

“Sex, according to the Red Queen theory, has nothing to do with adapting to the inanimate world […] but is all about combating the enemy that fights back. Biologists have persistently overestimated the importance of physical causes of premature death rather than biological ones. […] The things that kill animals or prevent them from reproducing are only rarely physical factors. Far more often they are other creatures – parasites, predators and competitors. […] Parasites have a deadlier effect than predators for two reasons. One is that there are more of them. […] The second reason, which is the cause of the first, is that parasites are usually smaller than their hosts while predators are usually larger. This means that the parasites live shorter lives and pass through more generations in a given time than their hosts.” […] Parasites and their hosts are locked in a close evolutionary embrace. The more successful the parasite’s attack […] the more the host’s chances of survival will depend on whether it can invent a defence. The better the host defends, the more natural selection will promote the parasites that can overcome the defence. So the advantage will always be swinging from one to the other: the more dire the emergency for one, the better it will fight. […] the notion of a host-parasite arms race is one of the most basic and unavoidable consequences of evolution.”

“The advantage of sex [to fight parasites] can appear in a single generation. This is because whatever lock is common in one generation will produce among the parasites the key that fits it. So you can be sure that it is the very lock not to have a few generations later. For by then the key that fits it will be common. Rarity is at a premium. […] many of the most notoriously polymorphic genes, such as the blood groups, the histocompatibility antigens and the like, are the very genes that affect resistance to disease – the genes for locks. Moreover, some of these polymorphisms are astonishingly ancient. […] Some very powerful force is at work ensuring that most versions of each gene survive, and that no version changes very much. That force is almost certainly disease. […] most asexual plants are short-lived annuals. Long-lived trees face a particular problem, because their parasites have time to evolve to their genetic defences – to evolve. […] Disease might almost put a sort of limit on longevity: there is little point in living much longer than it takes your parasites to adapt to you.” […this last sentence sort of conveys an old idea which I’ve had before, but the framing is different and the framing is important. When thinking about this aspect in the past I’ve usually tended to think only about the selective pressures imposed by predators, rather than e.g. those of diseases, but of course the latter are likely to play a major role as well.]

“larger, more intelligent and more social animals are generally more flexible in their mating systems than smaller, stupid or more solitary ones.”

“A female human being does not have to share her sexual favours with many males to prevent infanticide, but she may have a good reason to share them with one well-chosen male apart from her husband. This is because her husband is, almost by definition, usually not the best male there is – else how would he have ended up married to her? His value is that he is monogamous and will therefore not divide his child-rearing efforts among several families. But why accept his genes? Why not have his parental care and some other male’s genes? […] the principle – marry a nice guy but have an affair with your boss, or marry a rich but ugly man and take a handsome lover – is not unknown among female human beings.” […] [According to findings by Robin Baker and Mark Bellis] the typical woman’s pattern of infidelity […] is exactly what you would expect to find if she were unconsciously trying to get pregnant by a lover, while not leaving a husband.” [I don’t really know to which extent one should trust these findings, however, as other findings by them described by Ridley simply can’t be true and to me indicate questionable methodology at best:] “In a block of flats in Liverpool, they found by genetic tests that less than four in every five people were the sons of their ostensible fathers. The rest were apparently fathered by somebody else. In case this was something to do with Liverpool, they did the same tests in southern England and got the same result.” [As I put it in the margin, ‘these numbers are way too high.’ See e.g. this post by Razib Khan.]

“Cuckoldry paranoia is deep-seated in men. […] Cuckoldry is an asymmetrical fate. A woman loses no genetic investment if her husband is unfaithful, but a man risks unwittingly raising a bastard. […] It is not that a woman need not mind about her husband’s infidelity: it might lead to him leaving her, or wasting his time and money on his mistress, or picking up a nasty disease. But it does imply that men are likely to mind even more about their wives’ infidelity than vice versa. History, and law, have long reflected just that.”

“There has been no genetic change since we were hunter-gatherers, but deep in the mind of modern man is a simple hunter-gatherer rule: strive to acquire power and use it to lure women who will bear heirs; strive to acquire wealth and use it to buy affairs with other men’s wives who will bear bastards.” [“There has been no genetic change since we were hunter-gatherers – did he actually just say that? You just can’t write stuff like that. Again, this is way too categorical – it’s just plain wrong. There are plenty of recent genetic changes to be found (see e.g. this), if you care to look for it. Also, on a different matter the ‘strive to acquire wealth’ part of human behaviour today may well somehow be related to things which took place in hunter-gatherer times, but a male decision rule to strive for wealth in order to have more babies sure as hell isn’t derived from hunter-gatherer times; as he himself points out in his book, “accumulation of wealth was not possible in hunter-gatherer societies” (this is a direct quote from the book). It’s as if he’s unable to connect the chunks of knowledge he has obtained, and although that may well occasionally be hard this is just borderline weird.]

“the evidence for the average male brain differing in certain ways from the average female brain is now all but undeniable. […] There is no a priori reason for assuming that men and women have identical minds and no amount of wishing it were so will make it so if it is not so. […] to assume the sexes are mentally identical in the face of evidence that they are not is just as unfair as to assume sexual difference in the face of evidence that they are the same. […] mankind may be the mammal with the greatest division of sexual labour, and the greatest of mental differences between the sexes.” [He starts out well in that chapter. But then the politically correct crap shows its ugly face anyway…] “I think it is easy and, given the evidence, rational to believe that the [mental] differences between the natures of men of different races are trivial, while the differences between the natures of men and women of the same race are considerable.” [Yeah, well… IQ data shows a similar pattern to the one in the link: Good luck finding gender differences as large as the racial differences. I remember a finding from a paper from a course I took last year on the economics of education; they found that the average SAT score of black college-educated in their (US) sample was about the same as the average SAT score of a white high school graduate. I can’t be bothered to find the link, but the link above tells a similar story; the differences are huge. Switch ‘sexes’ with ‘races’, ‘males’ an ‘females’/’men’ and ‘women’ with ‘blacks’ and whites’ in the sentences quoted above and see where you end up. We didn’t have as much data on that kind of stuff when Ridley wrote his book as we do now, but we did have data back then as well and given the observed differences Ridley cannot have had good reasons for holding the view that he does. I won’t go so far as to call him a hypocrite, but he should at the very least consider reading Clifford.]

“True, we learn a lot more than bats and cuckoos do. We learn mathematics and a vocabulary of ten thousand words, and what people’s characters are like.” [No source in the book. Of course there isn’t – this number is bullshit, it’s not even close. See also this discussion. On the one hand the fact that he didn’t even feel the need to source the estimate makes him look worse than Miller, but on the other hand this isn’t an estimate which is as critical to the book or the chapter as it was to Miller. In Ridley’s case it’s likely just a number he drew out of a hat, not caring enough about whether it was right or not to actually try to find out. Intellectual laziness is the problem, not the fact that the number is wrong.]

“As Horace Barlow of Cambridge University has pointed out, the things of which we are conscious are mostly the mental events that concern social actions: we remain unconscious of how we see, walk, hit a tennis ball or write a word. Like a military hierarchy, consciousness operates on a ‘need to know’ policy.”

December 1, 2013 Posted by | anthropology, biology, books, evolution | Leave a comment

The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature (2)

Given the title of the post and some of the material covered, this post may by some be considered NSFW. I don’t know. Now you’re warned anyway.

I finished the book. My goodreads review reads as follows:

“Torn between two stars and three, I may still decide to give it two stars. First half was interesting (3,5 stars), second half was in my opinion very weak (1,5 stars). I was close to not finishing it. Very speculative, especially towards the end – it devolves into more or less pure storytelling.”

I’m quite disappointed. There’s good stuff in the second half, especially in the first part of the second half, but there’s a lot of crap too – chapter 9 was weak, and chapter 10 was bad too. Some of the stuff looked to me to be pretty much nothing but wild speculation supported by very little evidence, and bad evidence at that. Even worse, I get the distinct impression at least a few places that he seems to deliberately pick evidence that supports his views even though different evidence (and more relevant evidence) might very well lead to different conclusions – why would you use the vocabulary size of modern English speakers (60.000 words) to infer stuff about the language abilities and behaviours of our far ancestors, when it would presumably be much more informative to look at the vocabulary sizes of e.g. today’s Bushmen or Australian Aboriginals? And to which extent does it even make sense to make such inferences in the first place? On a different if related note he at one point spends a couple of pages to motivate why the reciprocity theory of courtship is obviously wrong, but what he’s actually arguing against is a straw-man that is very hard to take seriously and seems completely irrelevant to the validity of the model. He employs manipulative argumental strategies along the way more than once and when he does this it makes it hard for me not to jump to the conclusion that his arguments stink even though they may not actually do so – I don’t like it when I get the impression that someone is trying to manipulate me, and Miller comes off as occasionally quite manipulative to me in this book.

Anyway, some quotes from the last half as well as a few comments. I’ve mostly (but not only) quoted from the good stuff because I don’t want to spend a lot of time on the other stuff:

“When we see a human perceptual or cognitive ability that looks curiously sensitive to stimulation yet resistant to satisfaction, we should not assume that it is a poorly designed information processing system. It may be part of a system for sexual or social discrimination. […] Female orgasm seems poorly designed as a pair-bonding mechanism, but it is perfectly designed as a discriminatory system that separates the men from the boys.”

“It seems likely that male choice shaped breasts not to distinguish girls from young women, but to distinguish young women from older women. Here, the informative thing about breasts is the way they droop with the effects of age and gravity. There is a relatively narrow age window in which large breasts can appear pert before repeated cycles of pregnancy and breast-feeding causes them to sag. There were no bras or breast-lift operations in the Pleistocene. […] hominid males probably favoured younger women for their higher fertility. Any indicator of youth, such as large, pert breasts, would tend to be favoured by males. […] an attractiveness benefit in youth can often outweigh an unattractiveness cost in older age. This is why it can be in the interest of females to evolve youth indicators such as large breasts that tend to droop, fine skin that tends to wrinkle, and buttocks that tend to develop stretch marks. […] women with more symmetric breasts tend to be more fertile. […] The larger the breasts, the easier it is to notice asymmetries. […] The role of breasts as fitness indicators may help to explain why there is so much variation in breast size between women. […] fitness indicators do not tend to converge on a single size in a population. They maintain their variation indefinitely, due to the effects of genetic mutation and variation in condition.”

“Most evolutionary psychologists have viewed human morality as a question of altruism, and have tried to explain altruism as a side-effect of instincts for nepotism (kindness to those who may reciprocate). I think human morality is much more likely to be a direct result of sexual judgments today because our ancestors favored sexual partners who were kind, generous, helpful, and fair. We still have the same preferences. David Buss’s study of global sexual preferences found that ‘kindness’ was the single most important feature desired in a sexual partner by both men and women in every one of the 37 cultures he studied. It ranked above intelligence, above beauty, and above status.” (If not for the fact that he actually thinks this stuff is true, it’d be hilarious. Here’s a link. I’m pretty sure Buss’s study belongs in the “completely useless” category. This is just stupid.)

“Ecologists have long understood that the typical interaction between any two individuals or species is neither competition nor cooperation, but neutralism. Neutralism means apathy: the animals just ignore each other. If their paths threaten to cross, they get out of each other’s way. Anything else usually takes too much energy. Being nasty has costs, and being nice has costs, and animals evolve to avoid costs whenever possible. […] most of the violent competition happens within a species, because animals of the same species are competing for the same resources and the same mates. […] If we were typical animals, our attitudes to others would be dominated not by hate, exploitation, spite, competitiveness, or treachery, but by indifference. And so they are.”

“Verbal courtship can be viewed narrowly as face-to-face flirtation, or broadly as anything we say in public that might increase our social status or personal attractiveness in the eyes of potential mates. […] Verbal courtship in the broader sense explains why we compete to say interesting, relevant things in groups. Sexual choice permeates human social life, because anything that raises social status tends to improve mating prospects.” […] In cooperative communication, the receiver may be mildly skeptical about the information conveyed. In courtship, the receiver is extremely judgmental not only about the information, but about the signaller. When listening, we automatically evaluate whether what is being said makes sense, whether it is congruent with what we know and believe, whether it is novel and interesting, and whether we can draw intriguing inferences from it. But we also use all of these judgments to form an impression of the speaker’s intelligence, creativity, knowledge, status, and personality. We assess the information content of utterances not just to make inferences about the world, but to make attributions about the speaker.”

“People tend to socialize with friends and sexual partners who show roughly their own verbal ability level – their verbal compatibility has already determined which social relationships were formed. The majority of human conversation occurs between sexual partners and long-term friends. They have already chosen each other as mates or friends precisely because their first few conversations were mutually interesting, evoking mutual respect and attraction.”

“we present our lives in the best possible light. We mention our successes rather than our failures, impressive relatives rather than wastrels, dramatic trips more than solitary depressions, and palatable beliefs more than secret bigotries. Our life stories presents us as the heroes of the grand adventures that are our lives, rather than the Rosenkrantz and Guildenstern to someone else’s Hamlet. Nevertheless, because most people distort their life stories to more or less the same degree, they remain a valid basis for mate choice. Initially at least, our life stories will be compared not to the truth, but to the equally distorted life stories of our sexual competitors.” (No, honest signalling in this framework simply doesn’t make any sense. Lying isn’t optional.)

“How should we interpret the female superiority on language comprehension tests [“women comprehend more words on average, and this sex difference accounts for almost 5 percent of the individual variation in vocabulary size.”], given the greater male motivation to produce public verbal displays? The latter has not been so well quantified yet, but it is still obvious. Men write more books. Men give more lectures. Men ask more questions after lectures. Men dominate mixed-sex committee discussions. […] men can’t be quiet because that would give other men a chance to show off verbally. Men often bully women into silence, but this is usually to make room for their own display. ”

“Human courtship, like courtship in other animals, has a typical time-course. Courtship effort is low when first assessing a sexual prospect, increases rapidly if the prospect reciprocates one’s interest, peaks when the prospect is deciding whether to copulate, and declines once a long-term relationship is established.”

“People act differently when they’re in love with different people. We tend to match our expressed interests and preferences to those of a desired individual. […] In courtship, we work our way into roles that we think will prove attractive. […] Acting is not the prerogative of a few highly strung professionals, but a human birthright, automatically activated whenever we fall in love. In courtship, all the world became a stage, and all the proto-humans merely players.” (link in case you didn’t get the reference)

September 1, 2013 Posted by | anthropology, biology, books, evolution, Psychology | 14 Comments

The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature

Here’s a link.

I’ve read roughly half the book. It’s interesting, but quite speculative. As with all popular science books it sort of assumes the reader doesn’t know very much about anything, and this of course means that there’s quite a bit of known stuff covered here along the way. The notes/references do quite a bit of the work. So far I’ve enjoyed reading the book, but I’m not that impressed; I’m probably currently at a three-star evaluation, but a little closer to four than two. Compared to a textbook it’s very easy to read.

Some quotes from the first half of the book:

“most experimental psychology views the human mind exclusively as a computer that learns to solve problems, not as an entertainment system that evolved to attract sexual partners.”

“Natural selection [refer] to competition within or between species that affect relative survival ability. Sexual selection [refer] to sexual competition within a species that affects relative rates of reproduction. […] Under natural selection, species adopt to their environments. […] Under sexual selection, species adapt too, but they adapt to themselves. Females adapt to males, males adapt to females. Sexual preferences adapt to the sexual ornaments available, and sexual ornaments adapt to sexual preferences.
This can make things quite confusing. In sexual selection, genes do not code just for the adaptions used in courtship, such as sexual ornaments. They also code for the adaptions used in mate choice, the sexual preferences themselves.”

“brain size within each sex is correlated about 40 percent with general intelligence” (I did not know that!)

“Short-term mating is exciting and sexy, but it is not necessarily where sexual selection has the greatest effect. Human females, much more than other great apes, conceal when they are ovulating. This means that a single act of short-term copulation rarely results in pregnancy. Almost all human pregnancies arise in sexual relationships that have lasted at least several months, if not years. Modern contraception has merely reinforced this effect. […] when it comes to choosing sexual partners for long-term relationships, men and women increase their choosiness to almost identical levels. They also converge in the features they prefer.”

“By suggesting that sexual selection plays a major but neglected role in evolutionary innovation in general and the human mind’s evolution in particular, I am proposing a sort of marketing revolution in biology. Survival is like production, and courtship is like marketing. Organisms are like products, and the sexual preferences of the opposite sex are like consumer preferences. Courtship displays are not a mysterious luxury soaking up excess energy after the business of survival is accomplished. Rather, they are the only way to get one’s genes into the next generation, by fullfilling the sexual preferences of the opposite sex. Survival only matters insofar as it contributes to courtship. If nobody wants to mate with an animal, there’s no evolutionary point in the animal surviving.”

“Our ancestors did not spend all their time worrying about survival problems. They were among the longest-lived species on the planet, which implies that their daily risk of death was miniscule. Like most great apes, they probably spent their time worrying about social and sexual problems.”

“In most primate species, the distribution of food in the environment determines the distribution of females, and the distribution of females determines the distribution of males. When food is so dispersed that females do best by foraging on their own, males disperse to pair up with the lone females. This gives rise to monogamous couples. It is a fairly rare pattern among primates […] When food comes in patches large enough for several females to share, they tend to band together in small groups to find the food, and to protect each other against predators, unwanted males, and competing female groups. As long as the female band is not too large, a single male can exclude other males from sexual access to the band […] This ‘harem’ system of single-male polygyny is fairly common in primates. […] When food comes in still larger patches, female groups can grow too large for any single male to defend them. the males must then form coalitions, resulting in a complex multi-male, multi-female group […] Our hominid ancestors probably lived in such groups, in which sexual selection gets more complicated. […] Most children were probably born to couples who stayed together only a few years. Exclusive lifelong monogamy was practically unknown. The more standard pattern would have been ‘serial monogamy’: a sequence of nearly exclusive sexual partnerships that were socially recognized and jealously defended.” (This last part I consider to be highly speculative, and the notes/references are basically doing all the work here. Given the paucity of the available archaeological evidence – which I’m familar with – and the uncertainties involved when drawing conclusions and inferences based on the behaviours of other great apes, I think there’s a fair amount of uncertainty related to to which extent this account is true. There’s a lot we don’t know and can’t ever know about what was going on back then.)

“David Buss has amassed a lot of evidence that human females across many cultures tend to prefer males who have high social status, good income, ambition, intelligence, and energy – contrary to the views of some cultural anthropologists, who assume that people vary capriciously in their sexual preferences across different cultures. […] [It is a] universal, cross-cultural pattern that men care more about a partner’s age than women do, men generally preferring partners younger than themselves, and women generally preferring partners older than themselves. […] There is strong evidence from evolutionary psychology that men in modern societies generally prefer the physical appearance of women around 20 years old to those who are older (or younger). […] there has been much less research on the age at which women’s minds are most attractive.”

“our ancestors were highly social primates living in groups with children, relatives, and friends. Sexual relationships began and ended within family and tribal contexts.
If mate choice favours good genes, it can be useful to meet a potential mate’s blood relatives, because they share some of the same genes. An individual’s kin give additional information about their heritable fitness. If an intelligent man has foolish brothers or a beautiful woman has ugly sisters, this may lower their attractiveness as potential partners […] Given two sexual prospects who appear to display equal fitness, the one whose relatives appear healthier, brighter, more attractive, more fertile, and more successful probably has higher actual fitness. Since our ancestors tended to live in kin groups, there were plentiful opportunities for mate choice to take into account this sort of kin equality.”

August 21, 2013 Posted by | anthropology, books, evolution | 3 Comments

The Ancestor’s Tale (II)

I finished the book yesterday, after having put it away for almost a month. According to a count I did after finishing the book, this was the 40th book I’ve completed this year so far, meaning that I’ve read roughly five and a half books per month on average, or roughly one book per five and a half days (such an average is deceiving though, as the amount of book reading varies widely throughout the year; more than half the books I’ve read this year I’ve read during the summer, i.e. since the beginning of June…). Let’s just say that getting to 50 (or 52?) before the end of the year should not be an impossible task at this point – I didn’t realize I was that far already.

Back to the book – below is my goodreads review of the Dawkins book:

“Parts of this book is pure awesome, and the best parts are really among the greatest things I’ve read on the subject.

But other parts are not quite so great. The treatment is not as systematic as I’d have liked. At one point an (in my opinion) off-topic political rant in the middle of a book about the evolutionary past of our species made me so angry I simply put the book away for almost a month. I’d pretty much decided not to finish it at that point.

I eventually did pick it up again though, and I’m glad I did. But some parts are much better than others, and it’s a damn shame the variation in the quality of the material is as high as it is.”

I gave it 4 stars, but it was difficult to pick a rating. I really liked the last 100-200 pages. Incidentally I pointed out in my first post that “he talks about different speciation methods/mechanisms throughout the pages, but he doesn’t mention what they are called” – and I should probably add here that he does add the names later on, though the last half of that original comment still applies (“his coverage is non-systematic and spread out over many pages”). I think if you’re the kind of curious mind who’d enjoy reading a book about the history of life on Earth, you have to read this. I think it could have been a bit better, and that’s basically why I didn’t end up with a five star rating – but this account is still probably about as good as it’s going to get, so I think if you’re limiting yourself to one book on the subject, this is probably the book to read. Even if it isn’t, I’m sure you could do a lot worse.

Below I’ve added some quotes from the last few hundred pages; I’ve tried to quote from ‘the good stuff’ only. The book has 600+ pages, so naturally a lot of good stuff didn’t make the cut, and in fact much of the best stuff I decided not to include here because it was too hard to quote out of context, because ‘too much stuff’ had to be included in each quote in order to make sense of it for someone who’d not read the rest of the book – indeed in a few cases basically the rest of the book had been building up to it (the last quote included in the post below is sort of like this, but it can stand on its own as well):

“A mutant animal has a certain probability of being better off as a consequence of its new mutation. ‘Better off’ means better compared to the premutated parental type. […] the smaller the mutation, the more likely it is to be an improvement. […] The essential point, as I have put it before, is that there are many more ways of being dead than of being alive. […] In the multidimensional landscape of all possible animals, living creatures are islands of viability separated from other islands by gigantic oceans of grotesque deformity. Starting from any one island, you can evolve away from it one step at the time, here inching out a leg, there shaving the tip of a horn, or darkening of a feather. Evolution is a trajectory through multidimensional space, in which every step of the way has to represent a body capable of surviving and reproducing as well as the parental type […] Almost inevitably, a megamutation […] will land in the middle of the ocean of inviability …” […]

“The key to efficient digestion is to expose a large area of absorptive surface to the food. We achieve that by chewing the food into small pieces and passing the fragments through a long coiled gut whose already large area is compounded by a forest of tiny projections, or villi, covering its lining. Each villus in turn has a brush border of hair-like micro-villi, so the total absorptive area of an adult human intestine is millions of square centimeters. A fungus such as the well-named Phallus […] spreads its mycelium over a similar area of soil, secreting digestive enzymes and digesting the soil material where it lies. The fungus doesn’t walk about devouring food and digesting it inside its body as a pig or a rat would. Instead it spreads its ‘intestines’, in the form of thread-like mycelia, right through the food and digests it on the spot. From time to time hyphae come together to form a single solid structure with recognisable form: a mushroom (or toadstool, or bracket). This structure manufactures spores that float high and far on the wind, spreading its genes for making new mycelium and, eventually, new mushrooms.” […]

“By far the largest single organisms that ever lived are plants, and an impressive percentage of the world’s biomass is locked up in plants. This doesn’t just happen to be so. Some such high proportion follows necessarily from the fact that almost* all biomass comes ultimately from the sun via photosynthesis, most of it in green plants, and the transaction at every link of the food chain is only about 10 per cent efficient. The surface of the land is green because of plants, and the surface of the sea would be green too if its floating carpet of photosynthesisers were macroscopic plants instead of microorganisms too small to reflect noticeable quantities of green light. It is as though plants are going out of their way to cover every square centimetre with green, leaving none uncovered. And that is pretty much what they are doing […] From a plant’s point of view, a square centimetre of the Earth’s surface that is anything but green amounts to a negligently wasted opportunity to sweep up photons.” […]

“The really astonishing thing about Kleiber’s Law is that it holds good from the smallest bacterium to the largest whale. That’s about 20 orders of magnitude. You need to multiply by ten 20 times – or add 20 noughts – in order to get from the smallest bacterium to the largest mammal, and Kleiber’s Law holds right across the board. […]
A very small organism has such a large surface area compared to its volume that it can get all the oxygen it needs through its body wall. […] But a large organism has a transport problem because most of its cells are far away from the supplies they need. They need to pipe stuff from place to place. […] if you double the number of cells that need to be supplied, the network volume more than doubles because more pipes are needed to plumb the network into the main system, pipes which themselves occupy space. […] whether you are a mouse or a whale, the most efficient transport system – the one that wastes the least energy in moving stuff around – is one that takes up a fixed percentage of your body. That’s how the mathematics works out […] For example, mammals, whether mice, humans, or whales, have a volume of blood (i.e. the size of the transport system) which occupies between six and seven per cent of their body.
Taking these two points together, it means that if we wish to double the number of cells to be supplied, but still keep the most efficient transport system, we need a more sparsely distributed supply network. And a more sparse network means that less stuff is supplied per cell, meaning that the metabolic rate must go down.” […]

“A nucleus is huge compared to an electron but tiny compared to an electron’s orbit. Your hand, consisting mostly of empty space, meets hard resistance when it strikes a block of iron, also consisting mostly of empty space, because forces associated with the atoms in the two solids interact in such a way as to prevent them passing through each other. Consequently iron and stone seem solid to us because our brains most usefully serve us by constructing an illusion of solidity.” […]

“one of the most momentous events in the history of life was the formation of the eukaryotic cell. Eukaryotic cells are the large and complex cells, with walled nuclei and mitochondria, that make up the bodies of all animals, plants, and indeed […] all living creatures except the true bacteria and the archaea, which used to be called bacteria.” […] […a big exception, it turns out:] “bacteria and archaea are biochemically more versatile than the rest of the living kingdoms put together. Animals and plants perform a fraction of the biochemical mix of tricks available to bacteria. […] At least as a chemist would see it, if you wiped out all life except bacteria, you’d still be left with the greater part of life’s range. […] For the great majority of its career on this planet life has been nothing but prokaryotic life. We animals are a recent afterthought.” […]

“Depriving somebody of oxygen is a swift way to kill them. Yet our own cells, unaided, wouldn’t know what to do with oxygen. It is only mitochondria, and their bacterial cousins, that do.
As with chloroplasts, molecular comparison tells us the particular group of bacteria from which mitochondria are drawn. Mitochondria sprang from the socalled alpha-proteo bacteria and they are therefore related to the rickettsias that cause typhus and other nasty diseases. Mitochondria themselves have lost much of their original genome, and have become completely adapted to life inside the eukaryotic cells. But, like chloroplasts, they still reproduce autonomously by division, making populations within each eukaryotic cell.”

Of course he couldn’t help himself in the end from adding the remarks below in his conclusion (with which I of course agree):

“If it’s amazement you want, the real world has it all. […] although this book […629 pages, US…] has been written from a human point of view, another book could have been written in parallel for any of 10 million starting pilgrims. […] My objection to supernatural beliefs is precisely that they miserably fail to do justice to the sublime grandeur of the real world. They represent a narrowing-down from reality, an impoverishment of what the real world has to offer.”

August 9, 2013 Posted by | biology, books, evolution | Leave a comment

A few Cochrane reviews and links

I’ve spent the last few days at my parents’ place and haven’t had much time for blogging due to social obligations. I read The Murder on the Links the day before yesterday and I’ll finish Lord Edgware Dies later today – I’ll probably blog the books tomorrow. For now I’ll just post a few Cochrane reviews and a couple of links:

i. Abstinence-only programs for preventing HIV infection in high-income countries (as defined by the World Bank). (link to the full paper here)

“Abstinence-only programs are widespread and well-funded, particularly in the United States and countries supported by the US President’s Emergency Plan for AIDS Relief. On the premise that sexual abstinence is the best and only way to prevent HIV, abstinence-only interventions aim to prevent, stop, or decrease sexual activity. These programs differ from abstinence-plus designs: abstinence-plus programs promote safer-sex strategies (e.g., condom use) along with sexual abstinence, but abstinence-only programs do not, and instead often highlight the limitations of condom use. An up-to-date review suggests that abstinence-only programs do not affect HIV risk in low-income countries; this review examined the evidence in high-income countries.

This review included thirteen randomized controlled trials comparing abstinence-only programs to various control groups (e.g., “usual care,” no intervention). Although we conducted an extensive international search for trials, all included studies enrolled youth in the US (total baseline enrollment=15,940 participants). Programs were conducted in schools, community centers, and family homes; all were delivered in family units or groups of young people. We could not conduct a meta-analysis because of missing data and variation in program designs. However, findings from the individual trials were remarkably consistent.

Overall, the trials did not indicate that abstinence-only programs can reduce HIV risk as indicated by behavioral outcomes (e.g., unprotected vaginal sex) or biological outcomes (e.g., sexually transmitted infection). Instead, the programs consistently had no effect on participants’ incidence of unprotected vaginal sex, frequency of vaginal sex, number of sex partners, sexual initiation, or condom use.”

ii. Healthcare financing systems for increasing the use of tobacco dependence treatment.

The short version:

“Apart from providing counselling and drug treatment, strategies that reduce or cover the costs of accessing or providing these treatments could help smokers quit.

We found eleven trials, eight of which involve financial interventions directed at smokers and three of which involve financial interventions directed at healthcare providers.

Covering all the costs of smoking cessation treatment for smokers when compared to providing no financial benefits increased the proportion of smokers attempting to quit, using smoking cessation treatments, and succeeding in quitting. Although the absolute differences in quitting were small, the costs per person successfully quitting were low or moderate. Financial incentives directed at healthcare providers did not have an effect on smoking cessation.”

From the paper:

Summary of main results:

With very high to modest levels of consistency, we detected a statistically significant positive effect of full financial interventions targeting smokers with regard to abstinence from smoking compared to provision of no financial intervention at six months follow-up or more (all abstinence measures: RR 2.45, 95% CI 1.17 to 5.12). The effect of full financial interventions was also extended to favourable outcomes on the use of smoking cessation treatments: the pooled effect of full coverage compared with no financial intervention on the use of smoking cessation treatments was highly significant for each treatment type (NRT, bupropion, and behavioural interventions).Despite the observation of multiple favourable effects of full as compared to no financial intervention, when full coverage was compared to partial coverage, results showed no significant effect on smoking cessation or quit attempts. […]

Five studies presented data on cost effectiveness. When full benefit was compared with partial or no benefit, the costs per quitter ranged from $119 to $6,450. [the $6,450 estimate is an outlier in that group; the other estimates are all much lower, at or below $1500/quitter – US] […]

In this review, covering the full cost to smokers of using smoking cessation treatment increased the number of successful quitters, the number of participants making a quit attempt, and the use of smoking cessation treatment when compared with no financial coverage. As the majority of the studies were rated at high or unclear risk of bias in three or more domains, and there was variation between the settings, interventions and participants of the included studies, the results should be interpreted cautiously. The differences in self-reported abstinence rate, number of participants making a quit attempt and use of smoking cessation treatments were modest.”

iii. Psychosocial and pharmacological treatments for deliberate self harm.

“Deliberate self-harm is a major health problem associated with considerable risk of subsequent self-harm, including completed suicide. This systematic review evaluated the effectiveness of various treatments for deliberate self-harm patients in terms of prevention of further suicidal behaviour. […]

Main results:

A total of 23 trials were identified in which repetition of deliberate self-harm was reported as an outcome variable. The trials were classified into 11 categories. The summary odds ratio indicated a trend towards reduced repetition of deliberate self-harm for problem-solving therapy compared with standard aftercare (0.70; 0.45 to 1.11) and for provision of an emergency contact card in addition to standard care compared with standard aftercare alone (0.45; 0.19 to 1.07). The summary odds ratio for trials of intensive aftercare plus outreach compared with standard aftercare was 0.83 (0.61 to 1.14), and for antidepressant treatment compared with placebo was 0.83 (0.47 to 1.48). […]

Authors’ conclusions:

There still remains considerable uncertainty about which forms of psychosocial and physical treatments of self-harm patients are most effective, inclusion of insufficient numbers of patients in trials being the main limiting factor. There is a need for larger trials of treatments associated with trends towards reduced rates of repetition of deliberate self-harm. The results of small single trials which have been associated with statistically significant reductions in repetition must be interpreted with caution and it is desirable that such trials are also replicated.”

A few other links which are not from the Cochrane site:

iv. Plausible indeed!

v. Errors in DCP2 cost-effectiveness estimate for deworming.”Over the past few months, GiveWell has undertaken an in-depth investigation of the cost-effectiveness of deworming, a treatment for parasitic worms that are very common in some parts of the developing world. While our investigation is ongoing, we now believe that one of the key cost-effectiveness estimates for deworming is flawed, and contains several errors that overstate the cost-effectiveness of deworming by a factor of about 100. This finding has implications not just for deworming, but for cost-effectiveness analysis in general: we are now rethinking how we use published cost-effectiveness estimates for which the full calculations and methods are not public. […]we see this case as a general argument for expecting transparency, rather than taking recommendations on trust – no matter how pedigreed the people making the recommendations. Note that the DCP2 was published by the Disease Control Priorities Project, a joint enterprise of The World Bank, the National Institutes of Health, the World Health Organization, and the Population Reference Bureau, which was funded primarily by a $3.5 million grant from the Gates Foundation. The DCP2 chapter on helminth infections, which contains the $3.41/DALY estimate, has 18 authors, including many of the world’s foremost experts on soil-transmitted helminths.”

vi. Evolution, Creationism, Intelligent Design – a Gallup poll from last year. According to that poll a majority of Americans (56%) think creationism should be taught in public school science classes. One of the questions asked were: If the public schools in your community taught the theory of evolution, — that is, the idea that human beings evolved from other species of animals — would you be upset, or not?  A third of the people asked (34%) answered yes to this question. Incidentally in related news it should be noted that in a recent poll of South Korean biology teachers, 40% of them “agreed with the statement that “much of the scientific community doubts if evolution occurs”; and half disagreed that “modern humans are the product of evolutionary processes”.”

In slightly related news, according to an older poll conducted shortly before the turn of the century roughly one in five Americans asked back then didn’t know that the Earth revolves around the Sun. Other countries didn’t do any better:

“Gallup also asked the following basic science question, which has been used to indicate the level of public knowledge in two European countries in recent years: “As far as you know, does the earth revolve around the sun or does the sun revolve around the earth?” In the new poll, about four out of five Americans (79%) correctly respond that the earth revolves around the sun, while 18% say it is the other way around. These results are comparable to those found in Germany when a similar question was asked there in 1996; in response to that poll, 74% of Germans gave the correct answer, while 16% thought the sun revolved around the earth, and 10% said they didn’t know. When the question was asked in Great Britain that same year, 67% answered correctly, 19% answered incorrectly, and 14% didn’t know.”

You do have a potential ‘this is a silly question so I want to mess with the people asking it’-effect lurking in the background, but that’s probably mostly related to people giving the wrong answer deliberately. But even if many of the people asked perhaps gave the wrong answer deliberately, there’s still a substantial number of people answering that they ‘don’t know.’ I found the numbers surprising and I would love to see some updated estimates; a brief googling didn’t turn up anything.

July 28, 2013 Posted by | data, demographics, evolution, health, medicine, Psychology, religion, studies | 5 Comments