No more posts this year

My computer broke down yesterday evening. I lost all work I had done on the first 300 pages of The Cambridge Handbook of Personal Relationship (probably something like 15-20 hours, depending on how you measure it – I read 170 pages of the book yesterday, and basically I didn’t do much else besides reading the book during the day, aside from taking shortish breaks along the way), which is, painful*. I take frequent backups, but some data loss is inevitable in such a situation as this. It’s also really painful to know that I won’t have a computer available to me during the Christmas days.

The handbook had some really nice stuff on attachment theory and how those concepts relate to (mostly romantic) relationships. There seems to be a lot of evidence that attachment styles affect how people interact with each other, and that these sorts of patterns play a role in terms of how well people do in romantic relationships; Leary et al. covered that kind of stuff as well, but there was some additional detail included here. People who might be categorized as ‘securely attached’ behave ‘the way you’d like to behave’, whereas anxiously attached individuals display problematic behavioural patterns in some ways and avoidantly attached individuals display other problematic behavioural patterns in the context of interpersonal interactions. The reason I’m mentioning this is that I was thinking about this stuff after the computer broke down, because the thought occurred to me that humans may these days form attachments bonds, or at least have dynamic interaction patterns which in some respects resemble those we have with other humans, with non-humans. This is relevant in part because human attachment patterns are not completely fixed over the lifespan, and may have some domain-specificity, a point they also make in the chapter (‘people may find it easier to trust other people in some contexts than in others’, would be one way to think about this; a related point is that some people are easier to trust than others, leading to the observation that securely attached individuals have better relationships than insecurely attached individuals not only due to selection but also due to positive externalities (and the absence of negative externalities such as those related to mistrust and jealousy associated with an anxious attachment style)). Now, the dynamic interaction patterns to which I refer relate to my ‘interactions’ with things like my computer and my modem. I expect my computer and internet to help me when I feel terrible about what a shitty life I have, and I’ve come to rely on those things to help me when I’m in trouble. Over the last year I’ve repeatedly gotten the message that I can’t rely on these things, because they’re simply unreliable. I had unstable internet for months, and then my computer broke down. I used an old computer, known to be unreliable, for a short while, until it turned out to be completely unreliable. I had to get a new one, and so I did. While all this was happening the internet issues persisted, and they persisted even after I had got a new computer. The internet issue was supposedly fixed multiple times, they kept telling me they’d solved the problem, but each time it turned out that it wasn’t actually fixed and that people had been lying to me. I switched internet service provider because of these issues and of course my new computer then broke down shortly after this. I was seriously asking myself a few months ago if I should have two separate internet service providers simply to avoid getting cut off again – the utility hit associated with just being me, alone in my flat, without access to the outside world, is huge. Suicidal-thoughts huge. Now I’m asking myself if I should always have two computers, because then I’ll have an extra when the other one ‘decides’ to become unreliable (I use this word specifically because that was how I was thinking about it, which is part of what’s interesting), as they all do.

The interesting thing is that when I came up with this idea of always having two computers so that I have an extra when the other one breaks down, the first thought I had was that ‘this won’t help, something else I haven’t thought about is obviously going to go wrong and it doesn’t matter what I do to try to prevent it (‘I can’t rely on things like computers and internet at all, or at least not the people who make these things’) – I keep wanting simply to feel safe, to avoid issues like these which keep fucking up my life, and yet I repeatedly fail at achieving this. Maybe I should just stop trying.’ These thoughts are of course not very constructive, but I find them interesting. This kind of stuff really matters in terms of how we think about and interact with the world. If I’d known less about metacognition, had been less self-aware and/or hadn’t been reading the Cambridge handbook, I might not have been aware of how silly/stupid/unhelpful some of the thoughts which ‘came naturally’ to me yesterday and this morning really are.

*Theoretically it might be the case that no data is actually lost and that this is just a minor issue which is easily resolved, but the default position I take these days is that I lost everything on the harddrive I had not backed up elsewhere, that the computer will never work again, and that the people I bought the obviously worthless piece of junk from will probably refuse to follow their contractual obligations in this context. See above for reasons why I might think that way.

December 22, 2014 Posted by | books, personal | 4 Comments

Evidence-Based Diagnosis

“Evidence-Based Diagnosis is a textbook about diagnostic, screening, and prognostic tests in clinical  medicine. The authors’ approach is based on many years of experience teaching physicians in a  clinical research training program. Although requiring only a minimum of mathematics knowledge, the quantitative discussions in this book are deeper and more rigorous than those in most introductory texts. […] It is aimed primarily at clinicians, particularly those who are academically minded, but it should be helpful and accessible to anyone involved with selection, development, or marketing of diagnostic, screening, or prognostic tests. […] Our perspective is that of skeptical consumers of tests. We want to make proper diagnoses and not miss treatable diseases. Yet, we are aware that vast resources are spent on tests that too frequently provide wrong answers or right answers of little value, and that new tests are being developed, marketed, and sold all the time, sometimes with little or no demonstrable or projected benefit to patients. This book is intended to provide readers with the tools they need to evaluate these tests, to decide if and when they are worth doing, and to interpret the results.”

I simply could not possibly justify not giving this book a shot considering the amazon ratings – it has an insane average rating of five stars, based on nine ratings. I agree with the reviewers: This is a really nice book. It covers a lot of stuff I’ve seen before, e.g. in Fletcher and Fletcher, Petrie and Sabin, Juth and Munthe, Borenstein, Hedges et al., Adam, Baltussen et al. (listing all of these suddenly made me realize how much stuff I’ve actually read about these sorts of topics in the past…), as well as in stats courses I’ve taken, but as the book is focusing specifically on medical testing aspects there is also a lot of new stuff as well. It should be noted that some people will benefit a lot more from reading the book than I did; I’ve spent weeks dealing with related aspects of subtopics they cover in just a few pages, and there were a lot of familiar concepts, distinctions, etc. in the book. Even so, this book is remarkably well-written and these guys really know their stuff. If you want to read a book about the basics of how to make sense of the results of medical tests and stuff like that, this is the book you’ll want to read.

Let’s say you have a test measuring some variable which might be useful in a diagnostic context. How would we know it might be useful? Well, one might come up with some criteria such a test should meet; like that the results of the test doesn’t depend on who’s doing the testing, perhaps it also shouldn’t matter when the test is done. You might also want the test to be somewhat accurate. But what do we even mean by that? There are various approaches to thinking about accuracy, and some may be better than others. So the book covers familiar topics like sensitivity and specificity, likelihood ratios, and receiver operating characteristic (ROC) curves. A test might be accurate, but if the results of a test does not change clinical decision-making it might not be worth it to do the test; so the question of whether a test is accurate or not is different from whether it’s also useful. In terms of usefulness concepts like positive- and negative predictive value and distinctions such as that between absolute and relative risk become important. It might not even be a good idea to use a test even if it distinguishes reasonably well between people who are sick and people who are not, because a very accurate test might be too expensive to be justified undertaking; the book also has a bit of stuff on cost-effectiveness. Of course costs associated with getting tested for a health condition are not limited to monetary costs; a test might be uncomfortable, and it may also for example be the case that a false positive or a false negative result might sometimes have quite severe consequences (e.g. in the context of cancer screening). In such contexts concepts like the number needed to treat might be useful. It might also on the other hand be that a test gives answers which are wrong so often that even if it’s very cheap to do, it still might not be worth doing. There’s stuff in the book about how to think about, and come up with decision-rules about, how to identify things like treatment-thresholds; variables which will be determined by probability of disease and costs associated with testing (/and treatment). A variable like the cost of a treatment might in an analytical framework involve both the costs of treating people with the health condition as well as the costs of treating people who tested positive without being sick and the costs of not treating sick people who tested negative. One might think in one context that it would be twice as bad to miss a diagnosis than it would be to treat someone who does not have the disease, which would lead to one set of decision-rules in terms of when to test and when to treat, whereas in another context it might be a lot worse to miss a diagnosis, so we’d be less worried about treating someone without the disease. There may be more than one relevant threshold in the diagnostic setting; usually there’ll be some range of prior probabilities of disease for which the test will add enough information to change decision-making, but at either end of the range the test might not add enough information to be justified. To be more specific, if you’re almost certain the patient has some specific disease, you’ll want to treat him because the test result will not change anything; and if on the other hand you’re almost certain that he does not have the disease, based e.g. on the prevalence rate and the clinical presentation, then you’ll want to refrain from testing if the test has costs (including time costs, inconvenience, etc.). The book includes formal and reasonably detailed analysis of such topics.

In terms of how to interpret the results of a test it matters who you’re testing, and as already indicated the authors apply a Bayesian approach to these matters and repeatedly emphasize the importance of priors when evaluating test results (or for that matter findings from the literature). In that context some important notions are included about what you can and can’t use e.g. variables like prevalence and incidence for, how best to use such variables to inform decision-making, and things like how the study design might impact which variables are available to you for analysis (don’t try to estimate prevalence if you’re dealing with a case-control setup, where this variable is determined by the study design).

Of course medical most tests don’t just give two results. Dichotomization adds simplicity compared to more complex scenarios, so that’s where the book starts out, but it doesn’t stop there. If you have a test involving a continuous variable then dichotomizing the results will reduce the value of the test; this is equivalent to using pair-wise comparisons to make sense of continuous data in other contexts. However it’s sometimes useful to do it anyway because you may be in a situation where you need to quickly/easily separate ‘normal’ from ‘abnormal’. Likelihood ratios are really useful in the context of multi-level tests. In the simple dichotomous test, the LR for a test result is the probability of the result in a patient with disease divided by the probability of the result in a patient without disease. If you have lots of possible test results however, you’ll not be limited to two likelihood ratios; you’ll have as many likelihood ratios as there are results of the test. Those likelihood ratios are useful because the LR in the context of a multi-level test is equal to the slope of the ROC curve over the relevant interval. The ROC curve in some sense displays the tradeoff between sensitivity (‘true positive’) and specificity (‘true negative’); each point on the curve represents a different cut-off for calling a test positive. Such curves are quite useful in terms of figuring out if a test adds information or not, how well it distinguishes between patients. If you want to compare different tests and how they perform, Bland-Altman plots also seem to be useful tools.

Sometimes the results of more than one test will be relevant to decision-making, and a key question to ask here is the extent to which tests, and test results, are independent. If tests are not independent, one should be careful about how to update the probability of disease based on a new laboratory finding, and about which conclusions can be drawn regarding the extent to which an additional test might or might not be necessary/useful/required. The book does not go into too much detail, but enough is said on this topic to make it clear that test dependence is a potential issue one should keep in mind when evaluating multiple test results. They do talk a bit about how to come up with decision-rules about which tests to prefer in situations where multiple interdependent tests are available for analysis.

Sometimes blinding is difficult. The book tells us that it’s particularly important to blind when outcomes are subjective (like pain), and when prognostic factors may affect treatment in the study setting.

Medical tests can be used for different things, and not all tests are equal. One important distinction they talk about in the book is the distinction between diagnostic tests, which are done on sick people to figure out why they’re sick, and screening tests, which are mostly done on healthy people with a low prior probability of disease. There are different types of screening tests. One type of test is screening for symptomatic disease, which is sometimes done because people may be sick and have symptoms without being aware of the fact that they’re sick; screening for depression might be an example of this (that may even sometimes be cost-effective). These tests are reasonably similar to traditional diagnostic tests, and so can be evaluated in a similar manner. However most screening tests are of a different kind; they’re aimed at identifying risk factors, rather than ‘actual disease’ (a third kind is screening for presymptomatic disease). This generally tends to make them harder to justify undertaking, for reasons covered in much greater detail in Juth and Munthe (see the link over the word ‘may’ above). There are other differences as well; concepts such as sensitivity and specificity are for example difficult to relate to screening tests aimed at identifying risk factors, as such screening tests have as a goal to estimate incidence, rather than prevalence, which will often make it hard to compare such tests with the established ‘gold standard’ (as is usually the case). I decided to include a few quotes from this part of the coverage:

“the general public tends to be supportive of screening programs. Part of this is wishful thinking. We would like to believe that bad things happen for a reason, and that there are things we can do to prevent them […] .We also tend to be much more swayed by stories of individual patients (either those whose disease was detected early or those in whom it was found “too late”) than by boring statistics about risks, costs, and benefits […]. Because, at least in the U.S., there is no clear connection between money spent on screening tests and money not being available to spend on other things, the public tends not to be swayed by arguments about cost efficacy […]. In fact, in the general public’s view of screening, even wrong answers are not necessarily a bad thing. Schwartz et al. (2004) did a national telephone survey of attitudes about cancer screening in the U.S. They found that 38% of respondents had experienced at least one false-positive screening test. Although more than 40% of these subjects referred to that experience as “very scary” or the “scariest time of my life,” 98% were glad they had the screening test! […] Another disturbing result of the survey by Schwartz et al. was that, even though (as of 2002) the U.S. Preventive Health Services Task Force felt that evidence was insufficient to recommend prostate cancer screening, more than 60% of respondents said that a 55-year-old man who did not have a routine PSA test was “irresponsible,” and more than a third said this for an 80-year old […] Thus, regardless of the efficacy of screening tests, they have become an obligation if one does not wish to be blamed for getting some illnesses.”

There are many reasons why there may be problems with using observational studies to evaluate screening tests, and they talk a bit about those. One is what they call ‘volunteer bias’, which is just basic selection bias. Then there are the familiar problems of lead-time bias and length time bias. It should perhaps be noted here that both of the two latter problems can be handled in the context of a randomized controlled trial; neither lead-time bias nor length time bias are issues if the study is an RCT which compares the entire screened group with the entire unscreened group. Yet another problem is stage-migration bias, which for example can be a problem when more sensitive tests allow for earlier detection which changes how people are staged; this may lead to changes in stage-specific mortality rates, without actually improving overall mortality at all. A final problem they talk about is overdiagnoses related to the problem of pseudodisease, which is disease that would never have affected the patient if it had not been diagnosed by the screening procedure. Again a quote might be in order:

“It is difficult to identify pseudodisease in an individual patient, because it requires completely ignoring the diagnosis. (If you treat pseudodisease, the treatment will always appear to be curative, and you won’t realize the patient had pseudodisease rather than real disease!) In some ways, pseudodisease is an extreme type of stage migration bias. Patients who were not previously diagnosed as having the disease are now counted as having it. Although the incidence of the disease goes up, the prognosis of those who have it improves. […] Lack of understanding of pseudodisease, including the lack of people who know they have had it, is a real problem, because most of us understand the world through stories […]. Patients whose pseudodisease has been “cured” become strong proponents of screening and treatment and can tell a powerful and easily understood story about their experience. On the other hand, there aren’t people who can tell a compelling story of pseudodisease – men who can say, “I had a completely unnecessary prostatectomy,” or women who say, “I had a completely unnecessary mastectomy,” even though we know statistically that many such people exist.
The existence of pseudo–lung cancer was strongly suggested by the results of the Mayo Lung Study, a randomized trial of chest x-rays and sputum cytology to screen for lung cancer among 9,211 male cigarette smokers (Marcus et al. 2000).”

I included the last part also to indicate that this is actually a real problem also in situations where you’d be very likely to imagine it couldn’t possibly be a problem; even a disease as severe as lung cancer is subject to this kind of issue. There are also problems that may make screening tests look worse than they really are; like power issues, unskilled medical personnel doing the testing, and lack of follow-up (if a positive test result does not lead to any change in health care provision, there’s no good reason to assume earlier diagnosis as a result of screening will impact e.g. disease-specific mortality. On a related note there’s some debate about which mortality metric (general vs disease-specific) is to be preferred in the screening context, and they talk a bit about that as well).

I expected to write more about the book in this post than I have so far and perhaps include a few more quotes, but my computer broke down while I was writing this post yesterday so this is what you get. However as already mentioned this is a great book, and if you think you might like it based on the observations included in this post you should definitely read it.

December 22, 2014 Posted by | books, medicine, statistics | Leave a comment

Random stuff

i. I’ve been slightly more busy than usual lately, which has had as a consequence that I’ve been reading slightly less than usual. In a way this stuff has had bigger ‘tertiary effects’ (on blogging) than ‘secondary effects’ (on reading); I’ve not read that much less than usual, but reading and blogging are two different things, and blog-posts don’t write themselves. Sometimes it’s much easier for me to justify reading books than it is for me to justify spending time blogging books I’ve read. I just finished Newman and Kohn’s excellent book Evidence-Based Diagnosis, but despite this being an excellent book and despite me having already written a bit of stuff about the book in a post draft, I just don’t feel like finishing that blog post now. But I also don’t feel like letting any more time pass without an update – thus this post.

ii. On another reading-related matter, I should note that even assuming (a strong assumption here) the people they asked weren’t lying, these numbers seem low:

“Descriptive analysis indicated that the hours students spent weekly (M) on academic reading (AR), extracurricular reading (ER), and the Internet (INT), were 7.72 hours, 4.24 hours, and 8.95 hours, respectively.”

But on the other hand the estimate of 19.4 hours of weekly reading reported here (table 1, page 281) actually seems to match that estimate reasonably well (the sum of the numbers in the quote is ~20.9). Incidentally don’t you also just love when people report easily convertible metrics/units like these – ‘8.95 hours’..? Anyway, if the estimates are true, (some samples of…) college students read roughly 3 hours per day on average over the course of a week, including internet reading (which makes up almost half of the total and may or may not – you can’t really tell from the abstract – include academic stuff like stuff from journals…). I sometimes get curious about these sorts of things, and/but then I usually quickly get annoyed because it’s so difficult to get good data, and no good data seem to exist anywhere on such matters. This is in a way perfectly understandable (but also frustrating); I don’t even have a good idea what would be a good estimate of the ‘average’ number of hours I spend reading on an ‘average’ day, and I’m painfully aware of the fact that you can’t get access to that sort of information just by doing something simple like recording the number of hours/minutes spent reading during the day each day, for obvious reasons; the number would likely cease to be particularly relevant once the data recording process were to stop, even assuming there was no measurement error (’rounding up’). Such schemes might be a way to increase the amount of reading short-term (but if they are, why are they not already used in schools? Or perhaps they are?), but unless the scheme is implemented permanently the data derived from it are not going to be particularly relevant to anything later on. I don’t think unsophisticated self-reports which simply ask people how much they read are particularly useful, but if one assumes such estimates will always tend to overestimate the amount of reading going on, such metrics still do add some value (this is related to a familiar point also made in Newman & Kohn; knowing that an estimate is biased is very different from having to conclude that the estimate is useless. Biased estimates can often add information even if you know they’re biased, and this is especially the case if you know in which direction the estimate is most likely to be biased). Having said this, here are some more numbers from a different source:

“Nearly 52 percent of Americans 18–24 years of age, and just over 50 percent of all American adults, read books for pleasure […] Bibby, et al. (2009) reported that 47 percent of Canadian teenagers 15–19 years of age received a “great deal” or “quite a bit” of pleasure from reading. […] Young Canadian readers were more likely to be female than male: 56 percent of those who reported pleasure reading were female, while only 35 percent were male […] In 2009, the publishing industry reported that men in the United States only accounted for 29 percent of purchases made within the adult fiction market, compared to 40 percent of the U.K. market (Bowker LLC, 2009). The NEA surveys also consistently suggest that more women read than men: about 42 percent of men are voluntary readers of literature (defined as novels, short stories, poems, or plays in print or online), compared to 58 percent of women […] Unfortunately the NEA studies do not include in–depth reading for work or school. If this were included, the overall rates and breakdowns by sex might look very different. […] While these studies suggest that reading is enjoyed by a substantial number of North Americans, on the flip side, about half of the populations surveyed are not readers.”

“In 2008, 98 percent of Canadian high school students aged 15 to 19 were using computers one hour a day or more (Bibby, et al., 2009). About one half of those teenagers were using their computers at least two hours a day, while another 20 percent were on their computers for three to four hours, and 20 percent used their computers five hours or more each day […]. More recently it has been reported that 18–34 year old Canadians are spending an average of 20 hours a week online (Ipsos, 2010). […] A Canadian study using the Statistics Canada 2005 General Social Survey found that both heavy and moderate Internet users spend more time reading books than people who do not use the Internet, although people in all three categories of Internet usage read similar numbers of magazines and newspapers”

It was my impression while reading this that it did not seem to have occurred to the researchers here that one might use a personal computer to read books (instead of an e-reader); that people don’t just use computers to read stuff online (…and play games, and watch movies, etc.), but that you can also use a computer to read books. It may not just be that ‘the sort of people who spend much time online are also the sort of people who’re more likely to read books when they’re not online’; it may also be that some of those ‘computer hours’ are actually ‘book hours’. I much prefer to read books on my computer to reading books on my e-reader if both options are available (of course one point of having an e-reader is that it’s often the case that both options are not available), and I don’t see any good reason to assume that I’m the only person feeling that way.

ii. Here’s a list of words I’ve encountered on recently:


While writing this post I realized that the Merriam-Webster site also has a quiz one can play around with if one likes. I don’t think it’s nearly as useful as’s approach if you want to learn new words, but I’m not sure how fair it is to even compare the two. I scored much higher than average the four times I took the test, but I didn’t like a couple of the questions in the second test because it seemed to me there were multiple correct answers. One of the ways in which is clearly superior to this sort of test is of course that you’re able to provide them with feedback about issues like these, which in the long run should serve to minimize the number of problematic questions in the sample.

If you haven’t read along here very long you’ll probably not be familiar with the site, and in that case you might want to read this previous post on the topic.

iii. A chess kibitzing video:

Just to let you know this is a thing, in case you didn’t know. I enjoy watching strong players play chess; it’s often quite a bit more fun than playing yourself.

iv. “a child came to the hospital with cigarette burns dotting his torso. almost every patch of skin that could be covered with a tee shirt was scarred. some of the marks were old, some were very fresh.

his parents said it was a skin condition.”

Lots of other heartwarming stories in this reddit thread. I’m actually not quite sure why I even read those; some of them are really terrible.

December 19, 2014 Posted by | books, Chess, papers, personal, random stuff | Leave a comment

A few lectures



December 14, 2014 Posted by | astronomy, Lectures, Physics | 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

Origin and Evolution of Planetary Atmospheres – Implications for Habitability

I recently finished this book. I gave the book two stars on goodreads, however I also added this comment to the information about the book on my 2014 book list: “Close to three stars, but the poor language of the publication made it difficult for me to justify giving it that rating.” I liked reading the book, but I do not condone sloppy and/or unclear language and this is something I’ll usually punish.

When I started reading the book I’d assumed there might be some overlap with Gale’s book, which I haven’t covered here, but that actually turned out not really to be the case; the two books focus on different things even if a few of the questions they ask are quite similar, and so the coverage of the two books actually don’t much overlap. Most of this was new stuff, which was nice. The book is in my opinion more technical and harder to read than was Gale’s book, but again, they deal with different stuff so I’m not sure how much sense it makes to compare them. Lammer doesn’t shy away from covering relevant math formulas where they might be helpful to improve understanding, and/but some of these are not easy to understand if you do not have a background in physics; you need to know some stuff about things like electromagnetism, thermodynamics, and plasma physics to understand all of the stuff in this book. I didn’t – I certainly didn’t know ‘enough’ – but his coverage is fortunately such that even if you mentally skip a few formulas without really understanding the details of the dynamics they model, you’ll usually still be able to figure out roughly how they work wrt. the specific issue at hand because he also talks about how they work and which conclusions to draw; though you’ll likely still need to look up some unfamiliar terms along the way in order not to be completely confused.

I should make clear that although it may sound from the above as if this is really a rather dull book about mathematical formulas and complicated physics, one thing I find it really hard to term this book is ‘boring’. The book talks about what the Earth was like back when Earth was covered by magma oceans. Freaking magma oceans! It talks about how the Earth was quite likely early on in its ‘lifetime’ (before life on the planet, it should perhaps be noted) covered by a huge hydrogen atmosphere, and how that early atmosphere was blown away by a Sun which was spinning much faster than it does today, bombarding the early proto-atmospheres of the newly formed planets with huge numbers of highly charged particles despite the sun shining ‘less brightly’ back then than it does now. It talks about how a slightly different atmospheric composition back then, with more hydrogen, might have lead to the Earth being unable to get rid of all that hydrogen, most likely leading to the Earth having ended up as a ‘waterworld’ without continents, completely covered by water. It talks about how the Sun slowed down after what was most likely just a few million years, and how it has since then been doing things quite differently from the way it did things in the beginning. Phenomena such as outgassing and impact events are discussed. The book talks about how conditions were different on Mars and Venus from the way they were on Earth, and what role various factors might have played in terms of explaining how the atmospheres got to be the way they are now, and why those planets turned out quite different. The role of gravity, the role of a magnetosphere, which concrete processes lead to loss of (/which) atmospheric components. There’s a lot of stuff in this book, and much of it I found really quite interesting. But it is also hard to read, sometimes hard to understand, and certainly far from always particularly well-written. The topics covered I found quite interesting though.

I was wondering how to cover this book, but I decided early on that given how many things I was looking up along the way it would make a lot of sense to bookmark some relevant links and add them to this post; so below I have added a list of terms and concepts covered in the book. Some of the concepts are much better covered in the book than in the links (the wiki article on atmospheric escape for example has very little stuff on this topic compared to the stuff included in the book about this topic), but in other cases there’s a lot of stuff in the wiki article which was not included in the book (naturally, or it would not have made sense for me to look up stuff there). So the stuff in the links don’t add up to the material covered in the book, but the articles should give you a clue what kind of book this is. Below the list I have added a few quotes from the book. As should be obvious from the number of links, the book has a lot of content despite the relatively low page-count.

Atmosphere of Earth.
Atmospheric escape.
Hydrodynamic escape.
Maxwell–Boltzmann distribution.
Outflow channels.
Scale height.
Larmor radius.
Adiabatic process.
Energetic neutral atom.
Bow shock.
Lyman series.
Roche lobe.
Plasma (physics).
Astrophysical plasma.
Nebular hypothesis.
Stellar evolution.
Protoplanetary disk
Solar wind.
Hydrostatic equilibrium.
Kelvin–Helmholtz instability.
Polar wind.

“As contrasted to meteorology which studies the properties and behavior of the lower atmosphere between the surface and the tropopause where the weather phenomena are generated, aeronomy is a division of atmospheric science that studies physics and chemistry of the upper atmosphere that extends from above the troposphere up to the altitudes where it is modified by the solar wind plasma. […] The central part of [this] monograph presents a detailed discussion of the atmospheric loss mechanisms due to the action of various thermal and non-thermal escape processes for the neutral and ionized particles from a hot, extended atmospheric corona. Scenarios for the formation and evolution of the atmospheres of Earth, Venus, and Mars, that is, the planets orbiting within the habitable zone around the Sun, are considered. A crucial role of the magnetosphere of a planet in protecting its hot, extended, and partially ionized corona from the solar wind erosion is discussed. […] The book presents a brief review of the present state of knowledge of the aeronomy of planetary atmospheres and of their evolution during the lifetime of their host stars by taking into account conventionally accepted concepts, as well as recent observational and theoretical results.”

“the classical concept of the habitable zone and its related questions of what makes a planet habitable is much more complex than having a big rocky body located at the right distance from its host star. […] A careful study of various astrophysical and geophysical aspects indicate that Earth-analogue class I habitats have to be located at the right distance of the habitable zone from their host stars, must lose their protoatmospheres during the right time period, should maintain plate tectonics over the planet’s lifetime, should have nitrogen as the main atmospheric species after the stellar activity decreased to moderate values and finally, the planet’s interior should have developed conditions that an intrinsic strong global magnetic field could evolve.” [I should probably add here that this specific stuff is covered extensively in Gale’s book, but doesn’t make up too much of the coverage of this book].

“The mantle solidification of a magma ocean is a fast process and ends at ∼105 years for Earth-size planets with low volatile contents and at ≤3Myr [million years, US] for planets with higher volatile contents and magma ocean depths of ≤2,000km […] During the magma ocean solidification process, H2O and CO2 molecules can enter the solidifying minerals in relative low quantities [8, 9]. As a result the H2O/CO2 volatiles will degas into dense steam atmospheres […] If the early Earth would have obtained slightly more material from water-rich planetesimals, its CO2 content would have been much higher and Earth’s oceans could have been tens to hundreds of kilometers deep […]. Such environmental conditions would have resulted in a globally covered water world [43, 44] which is surrounded by a Venus-type dense CO2 atmosphere and a hydrogen envelope.” [I tried while reading this to imagine a magma ocean which was something like 2000 kilometers deep, but I failed to do so. Just think about this…]

“There is observational evidence from solar proxies with younger age compared to the present Sun, that during the early history of the Solar System the EUV flux was up to∼100 times larger as it is today […] The evolution of planetary atmospheres can only be understood if one considers that the radiation and particle environment of the Sun or a planet’s host star changed during their life time. The magnetic activity of solar-type stars declines steadily during their evolution on the Zero-Age-Main-Sequence (ZAMS). According to the solar standard model, the Sun’s photospheric luminosity was ∼30 % lower ∼4.5 Gyr ago […] when the Sun arrived on the ZAMS compared to present levels. The observed faster rotation of young stars is responsible for an enhanced magnetic activity and related heating processes in the chromosphere, X-ray emissions are ≥1,000, and EUV, and UV ∼100 and ∼10 times higher compared to today’s solar values. Moreover, the production rate of high-energy particles is orders of magnitude higher at young stars, and from observable stellar mass loss-activity relations one can also expect a much stronger solar/stellar wind during the active stellar phase.”

“The nuclear evolution of the Sun is well known from stellar evolutionary theory and backed by helioseismological observations of the internal solar structure [10]. The results of these evolutionary solar models, indicate that the young Sun was ∼10% cooler and ∼15% smaller compared to the modern Sun ∼4.6Gyr ago. According to the solar standard model, due to accelerating nuclear reactions in the Sun’s core, the Sun is a slowly evolving variable G-type star that has undergone an ∼30% increase in luminosity over the past ∼4.5Gyr. […] the outward flowing plasma carries away angular momentum from the star [which explains] the observed spin-down to slower rotation of young stars after their arrival at the ZAMS [the book mentions elsewhere that it’s been estimated based on observations of other star systems that the young sun was rotating more than 10 times as fast as it does now]. […] the early Earth may have lost during [the first 100 million years] an amount of hydrogen equivalent of ∼20EOs [Earth Oceans] thermally […] after the loss of [a large amount of the original steam atmosphere,] the Earth’s atmosphere environment near the surface reached the critical temperature of ∼650 K. After reaching this temperature the remaining H2O-vapor of ∼1EO could condense and collapsed into the liquid water ocean [84]. Additional amount[s] of water could have been delivered also continuously via impacts, but the bulk of the early Earth’s initial water inventory is most likely a by-product of a condensed fraction of the catastrophically outgassed steam atmosphere. […] One should […] note that in the case of the early Earth due to the Moon forming impact a fraction of ≤30% of atmosphere could have also been lost to space [113].”

“The present average atmospheric mass loss of hydrogen, oxygen, and nitrogen ions from the Earth is ∼ 1.3 × 103 g s-1

“The first protoatmosphere will be captured and accumulated hydrogen- and helium-rich gas envelopes from the nebula. Depending on the planetary formation time, the nebula dissipation time, the numbers of additional planets including gas giants in the system, the protoplanet’s gravity, its orbit location, and the host star’s radiation and plasma environment terrestrial planets may capture tens or even several hundreds of the Earth ocean equivalent amounts of hydrogen around its rocky core.
The second protoatmosphere depends on the initial volatile content of the protoplanet when accretion finished. During the magma ocean solidification […] steam atmospheres with surface pressures ranging from∼100 to several 104 bar can be catastrophically outgassed.
Finally, secondary atmospheres will be produced by tectonic activity such as volcanos and by the delivery of volatiles via large impacts. The origin and initial state of a planet’s protoatmosphere, therefore, determines a planet’s atmospheric evolution and finally if the planet will evolve to an Earth-analog class I habitat or not. […] The efficiency of the solar/stellar forcing is essentially inversely proportional to the square of the distance to the planet’s host star. From that, it follows that the closer a planet orbits around its host star, the more efficient are the atmospheric escape processes. The main effects caused by the stellar radiation and plasma environment on the atmospheres of an effected planet are to ionize, chemically modify, heated, expand, and slowly erode the upper atmosphere throughout the lifetime of a planet. The highest thermal and non-thermal atmospheric escape rates are obtained during the early active phase of the planet’s host star […] Besides the orbital location, a planet’s gravity constitutes an additional major protection mechanism especially for thermal escape of its atmosphere, while the nonthermal escape processes are affected on a weaker scale.”

December 11, 2014 Posted by | astronomy, books, Physics | Leave a comment


i. “People are not here to meet your expectations.” (Leo Buscaglia)

ii. “There is no greater challenge than to have someone relying upon you; no greater satisfaction than to vindicate his expectation.” (Kingman Brewster, Jr.)

iii. “Traditionally, psychology has been the study of two populations: university freshmen and white rats.” (Paul Bloom)

iv. “You cannot avoid making judgements but you can become more conscious of the way in which you make them. This is critically important because once we judge someone or something we tend to stop thinking about them or it. Which means, among other things, that we behave in response to our judgements rather than to that to which is being judged.” (Neil Postman)

v. “There is nothing so captivating as new knowledge.” (Peter Mere Latham)

vi. “It takes as much time and trouble to pull down a falsehood as to build up a truth.” (-ll-)

vii. “People in general have no notion of the sort and amount of evidence often needed to prove the simplest matter of fact.” (-ll-)

viii. “What is more important in a library than anything else — is the fact that it exists.” (Archibald MacLeish)

ix. “It is easy to know what you want to say, but not to say it.” (Mario Vargas Llosa)

x. “Like writing, reading is a protest against the insufficiencies of life. When we look in fiction for what is missing in life, we are saying, with no need to say it or even to know it, that life as it is does not satisfy our thirst for the absolute […] and should be better. We invent fictions in order to live somehow the many lives we would like to lead when we barely have one at our disposal.” (-ll-)

xi. “Thank God for the mind. It’s the only place where we have freedom of speech.” (Charles Reis Felix)

xii. “Happiness is the feeling we experience when we are too busy to be miserable.” (Thomas Lansing Masson)

xiii. ““Be yourself” is about the worst advice you can give some people.” (-ll-)

xiv. “The best instruction is that which uses the least words sufficient for the task.” (Maria Montessori)

xv. “Don’t worry that children never listen to you; worry that they are always watching you.” (Robert Fulghum)

xvi. “Human memory, they say, is like a coat closet: The most enduring outcome of a formal education is that it creates rows of coat hooks so that later on, when you come upon a new piece of information, you have a hook to hang it on. Without a hook, the new information falls on the floor.” (Ursula Goodenough)

xvii. “The best of ideas is hurt by uncritical acceptance and thrives on critical examination.” (George Pólya)

xviii. “A teacher who is attempting to teach without inspiring the pupil with a desire to learn is hammering cold iron.” (Horace Mann)

xix. “Doing nothing for others is the undoing of ourselves. We must purposely be kind and generous, or we miss the best part of existence. […] We do ourselves the most good doing something for others.” (-ll-)

xx. “Ignorance breeds monsters to fill up all the vacuities of the soul that are unoccupied by the verities of knowledge.” (-ll-)

December 9, 2014 Posted by | quotes | Leave a comment

Delusion and Self-Deception – Affective and Motivational Influences on Belief Formation (II)

[A brief note before moving on to the book review: I was just notified by wordpress when publishing this post that I have now posted 2001 posts on this blog. It would of course have made more sense to add a remark in the post which came before this one, but I didn’t notice and I had no idea I was that close to the 2000-mark. I don’t know if the number is correct; it somehow seems ‘too high’ to me, but I’m not going to count the posts in order to figure out if the number is correct. Even if I did try to do that I know that I have deleted a lot of posts over the years, so there are a lot fewer posts than that available in the archives, and so I wouldn’t be able to tell anyway from the information which is available to me now. According to the summary information displayed on my dashboard right now, there are 1304 posts in the archives. Anyway, I thought I should mention this here.]

I finished the book.

There were a couple of really nice chapters in the first half, but there was a lot of not-great stuff as well; the average quality and the variance of the quality of the material included in the second half was reasonably similar. Some parts of the second half were quite helpful in terms of making better sense of some of the stuff the poorer chapters in the first part dealt with. I gave the book two stars on goodreads. I must admit that I think the editor might have done a better job; I was very annoyed by the inclusion of multiple articles in the first part of the book which either completely neglected to define terms used in the text, or described them poorly. A couple of times throughout the book I came across an explanation of a term/distinction which had been used in multiple previous chapters where I’d earlier on been sort of semi-guessing what they meant when they talked about this stuff, and suddenly I realized that it was really quite easy to explain, only the previous authors hadn’t done that (/been able to do that?). You could argue that part of the problem is that some of the contributions were not well written and that you can’t blame the editors for that, but to me it seems problematic to include in a book like this some chapters reasonably early in the text which assume you know all about X, and then multiple chapters later you include in the work a chapter written by someone who (more reasonably) assumes that people may perhaps have no clue what X refers to – it might have been smart to include the latter chapter a bit sooner in the coverage..

The book is published by Psychology Press, but some chapters are written by philosophers rather than psychologists. Although not all of the coverage is purely conceptual, there’s a lot of that stuff in this book and the amount of empirical content is not very impressive, at least not if you don’t think much of elaborate descriptions of anecdotes and studies conducted on 6 people or something like that; I recall this having been a big issue for me previously when looking at some related neuroscience (there’s some neuroscience in the book, as also indicated in the previous post), some of which is occasionally mentioned in the work (specifically the research done by Ramachandran & Sacks).

Part of the low rating on my part is surely due to unmet expectations; I’d expected the book to cover in some detail what might be termed ‘common self-deception’ in ordinary people; the type of self-deception normal people engage in all the time. There’s almost none of that in the book, though there are a few comments on that topic here and there. Most book chapters focus mainly on people with specific delusions – especially the Capgras delusion, there are a lot of chapters talking about that one – and then talk about what’s the best way to model this disorder; in the context of the various (conceptual) models proposed, they then occasionally include considerations as to whether such patients are best thought of as self-deceiving or not, and what we might actually mean by this. Although this is interesting enough, I didn’t pick up the book because I thought that was what was inside it. That some expectations were unmet was not the only reason why I mentally subtracted a bit from the overall rating; I have a perhaps irrational tendency to become annoyed when people writing books like these don’t seem to know (relevant) stuff I do, and in this case an author made the ‘mistake’ of talking about Othello syndrome (basically: ‘delusional jealousy’) without seeming to be at all familiar with relevant ethological research such as what’s included in texts like this one. I thought the lack of familiarity with this field meant that the theoretical notions included in that part of the coverage completely overlooked some really big variables and meaningful approaches to how to conceptualize this syndrome. In all fairness it should be noted that another author elsewhere in the book actually does seem familiar with at least some parts of this research and in fact explicitly refers to it in the text.

Although there’s a lot of what might be termed ‘conceptual coverage’ in the book it’s not like there isn’t some empirical stuff as well; to take an example, the book has a chapter called ‘Emotion, Cognition, and Belief – Findings From Cognitive Neuroscience’. To the extent that the coverage is empirical it’s mostly asking questions such as what happens to/in the brains of people with or without specific brain lesions known to be related to specific delusions, and how we can know this/have tested this. This is interesting enough; there’s some work presented suggesting for example that the risk of development of a specific type of quite common stroke-related delusional belief where the patient denies that he’s suffering from paralysis – even if he obviously can’t move his arm or leg – is related to which part of the brain is damaged (see below).

I’ve added some observations from a few of the chapters I did not cover in the first post below. Although I may sound critical in my comments above, I should note that there was a reason why I finished the book instead of giving up on it; there were quite a few interesting observations along the way, many of which I found myself unable to include in the coverage of the book here for various reasons.

“Until recently, many delusions were widely regarded as having a motivational psychogenesis. That is, delusions were viewed as being motivated and their formation and maintenance seen as attributable to the psychological benefits they provided to deluded individuals. […] This explicitly motivational formulation, which explains a delusory belief in terms of the psychological benefits it confers, is consistent with a long tradition in psychology, the psychodynamic tradition. […] The key notion in psychoanalytic [/…-dynamic] accounts is that delusions are viewed as having a palliative function; they represent an attempt (however misguided) to relieve pain, tension, and distress. […] Motivational accounts of delusions can be generally distinguished from another major explanatory class — that involving the notion of defect or deficit […] Theories in this second class view delusions as the consequence of fundamental cognitive or perceptual anomalies ranging from complete breakdowns in certain crucial elements of cognitive–perceptual machinery […] to milder dysfunctions involving the distorted operation of particular processes […] There is little doubt that the edifice of psychodynamic thought is replete with theorizing that is at once outrageously presumptive and outlandishly speculative. [I liked this sentence… ] […] For the purposes of this chapter, [however,] the core insight is that motives (conscious or otherwise) are important causal forces doxastically (doxastic = of or relating to belief). Psychoanalysis, of course, contains other conceptual elements and theoretical postulates that we might not want to endorse or consider”

“Self-deception is a notoriously slippery notion that has eluded definitional consensus. Sackeim and Gur (1978) provided what is arguably the most widely accepted characterization in the psychological literature, claiming that self-deception consists in an individual holding two contradictory beliefs simultaneously; the individual, moreover, is aware of only one of these beliefs and is motivated to remain unaware of the other. This kind of conceptualization courts philosophical controversy in that it entails what are known as the “static” and “dynamic” paradoxes of self-deception […]. The static paradox consists in a self-deceived person being simultaneously in two contradictory states: the states of believing and disbelieving a particular proposition. The dynamic paradox arises out of the fact that in order for a person to engage in self-deception, he or she must know what he or she is doing; yet, in order for the project to work, he or she must not know what he or she is doing. Mele (this volume) offers a “deflationary” account of self-deception that skirts these paradoxes. In his account, self-deception occurs when a “desire that p” contributes to a “belief that p.” Mele outlines how this can happen unparadoxically (via such phenomena as negative and positive misinterpretation, selective focusing, and selective evidence-gathering). Regarding self-deception’s relationship to the notion of delusion, the two terms have been variously used as synonyms […], as qualitatively similar concepts that differ quantitatively […], and as quite distinct, if overlapping, concepts […] We argue that it is indeed useful to view delusion and self-deception as distinct concepts that intersect or overlap. […] Essentially, we view delusion as connoting both a dearth of evidential justification and an element of day-to-day dysfunction. A person is deluded when he or she has come to hold a particular belief with a degree of firmness that is utterly unwarranted by the evidence at hand and that jeopardizes their everyday functioning.[13] [Note that at the time they wrote the book, official diagnostic manuals such as the DSM-IV did not include ‘everyday functioning’ as a diagnostic criteria; so the criteria proposed are in some sense more restrictive than the ‘official ones’ applied at that time. I have no idea what the current criteria are, but I also don’t much care – US]. Self-deception, on the other hand, we view (with Mele) as paradigmatically motivated. Self-deceptive beliefs may or may not contradict reality, and they may or may not disrupt daily living. What is important is that they are not formed out of a wholly dispassionate quest for the truth, but rather are somehow influenced or biased by the prevailing motivational state of the individual concerned. […] Theoretically, at least, each may occur in isolation. Thus, some delusions may arise without self-deception via processes that are not remotely motivated. […] Conversely, certain instances of self-deception may not sufficiently disrupt functioning to warrant the label delusion. […] [Common] self-serving tendencies do not ordinarily merit usage of the term delusion.”

“A two-factor account [of delusions] offers distinct answers to […] two questions in terms of two departures from normality. The first factor explains why the false proposition seemed a somewhat salient and credible hypothesis or why it was initially adopted as a belief. The second factor explains why the proposition is not subsequently rejected.”

Another author in the book framed the disctinction as being one between the content of the delusion and the maintenance of the delusion. The second factor has been proposed to relate to belief evaluation mechanisms in some way or other, but most authors aren’t very specific when talking about this stuff and most of that coverage seemed to me very speculative. I won’t talk much more about these accounts/conceptual models here, but I will note that they spend a lot of pages talking about the two-factor accounts in the book. It seems to be difficult to explain the content and the maintenance of delusions, applying the terminology proposed in the other chapter, using only a single factor, which is why such models have been developed:

“The argument for a second factor in the etiology of delusions is that, both normally and normatively, the first factor is not sufficient to explain the delusion. The first factor prompts an apparently salient and somewhat credible hypothesis or candidate belief but the hypothesis or candidate belief normally could be, and normatively should be, rejected. Even if the first factor explains why the hypothesis is initially adopted as a belief, it does not explain the delusion because it does not explain why the belief is tenaciously maintained […] We need a second factor to answer the question of why the patient does not reject the belief.”

It should be noted in the context of the distinction between deficit accounts and motivational accounts above that two-factor accounts do not include motivational factors, being purely deficit accounts, although one author in the book suggests that it might make sense to try to combine the models (a thought that also occurred to me while reading the book). Most accounts of this stuff were as mentioned speculative, but in one context – anosognosia in stroke victims – it seems there’s actually some relevant knowledge and data:

“Patients with anosognosia fail to acknowledge, or even outright deny, their impairment or illness […] In this chapter, we shall be concerned with anosognosia for hemiplegia (paralysis of one side of the body) or, more generally, for motor impairments. A patient whose arm or leg is paralyzed or weak following a stroke may deny the weakness in response to questions like, “Is there anything wrong with your arm or leg? Is it weak, paralyzed or numb?” […], and they may continue to deny the impairment even when it has been demonstrated. For example, the examiner may ask the patient to raise both arms and then demonstrate to the patient that one arm is not raised as high as the other. […] According to the neuropsychological version of the two-factor theory, the second factor, which does its work after the generation of the delusional hypothesis, candidate belief, or initially adopted belief, is a deficit in the cognitive mechanisms responsible for belief evaluation and revision. No very detailed account of this second deficit has yet been provided […] Although the second deficit is poorly specified in terms of cognitive function, there are some suggestions about its neural basis. For example, following a right-hemisphere stroke, patients may deny ownership of their paralyzed left-side limbs […]. The fact that patients with somatoparaphrenia [denial of ownership: The patient may basically for example believe that ‘this is not my arm’, even if it is in fact his arm…US] generally have intact left hemispheres suggests that the second deficit results from right-hemisphere damage, and other evidence supports this suggestion.[4] […] Recent studies of patients in the first 10 days following a stroke suggest a rate of occurrence for anosognosia of 17–21% […] and 21–42% for right-hemisphere patients […] Studies also suggest a rate of occurrence for unilateral neglect [“Patients with unilateral neglect fail to respond to stimuli presented on the side opposite to their lesion”] of 23% […] and 32–42% among right-hemisphere patients [These kinds of delusional beliefs are as illustrated by these numbers not absurd notions which pop up in one in a million patients; they are really common in the stroke contextIt should be mentioned here that in most patients the delusional beliefs seem to resolve over time: “by comparison with anosognosia in the first few days following a stroke, persisting anosognosia is relatively rare.”]

“One way to reinterpret delusional subjects is to say that we’ve misidentified the content of the problematic belief. For example, we might say that rather than believing that his wife has been replaced by an impostor, the victim of the Capgras delusion believes that it is, in some respects, as if his wife has been replaced by an impostor. Another is to say that we’ve misidentified the attitude that the delusional subject bears to the content of the delusion. For example, Gregory Currie and coauthors have suggested that rather than believing that his wife has been replaced by an impostor, we should say that the victim of the Capgras delusion merely imagines that his wife has been replaced by an impostor. […] I want to suggest that […] we ought to say that delusional subjects don’t straightforwardly believe the contents of their delusions or straightforwardly imagine them. Instead, they bear some intermediate attitude — we might call it “bimagination” — with some of the distinctive features of believing and some of the distinctive features of imagining. […] People with inconsistent beliefs don’t just infer everything, and it often happens that they find themselves failing to believe some of the consequences of what they believe. […] Closure takes cognitive work, and some of the consequences of our beliefs are easier to spot than others. Here is an explanation of this fact: Not every belief-type representation is equally tied to every other. There are coordination constraints between belief-type representations. These sorts of connections encourage consistency among belief-type representations and the elaboration of belief-type representations or the production of new ones that represent the consequences of things represented in our various beliefs. But these connections are not equally strong everywhere. Some of our beliefs are very closely tied to one another, so the elimination of inconsistency and drawing of inferences comes easily or automatically. However, there are also pairs of belief-type representations that are not so closely tied to one another, where elimination of inconsistency and drawing of inferences is difficult and/or unlikely. […] the belief role isn’t monolithic. Within belief, there’s variation in the sort of behavior-guiding role that’s played by different beliefs, and there’s variation in the sort of inference-generating role that’s played by different beliefs. […]

Here, I think, is the moral: The belief role and the imagination role are a lot more complicated and a lot less unified than we might have thought. It’s not just a matter of a given representation being hooked up like a belief or hooked up like an imagining. A given belief-type representation will have a whole range of different connections to different behavior-planning mechanisms (or to different bits of the one mechanism, or different kinds of connections to the same bit of the same mechanism, or…) and a whole range of different kinds of connections to different representations of various types. There are no necessary connections between these various connections; it’s not the case that anything that’s got one element of a certain package has also got to have all of the rest because we see a variety of mix-and-match patterns even within belief. No belief-type representation plays the whole stereotypical belief role — regulating all behavior all the time and being equally and perfectly coordinated with all of our other beliefs. The different bits of the stereotypical role — for example, regulating this bit of behavior in these circumstances and combining with these sorts of beliefs to generate inference — are separable. Thus, there seems to be no principled reason to think that we can’t get a spectrum of cases, from clear, totally non-belief-like imaginings to clear, full-blooded, paradigmatic beliefs, with intermediate, hard-to-classify states in the middle.”

“If we think that a certain sort of evidence responsiveness is essential to belief, then, in many cases, we’ll be reluctant to say that delusional subjects genuinely believe the contents of their delusions. Thus, we’ll be uncomfortable with characterizing delusions as genuine beliefs. Another respect in which delusions are puzzling, which makes categorizing delusions as beliefs problematic, is that delusions, when compared to other beliefs, seem to have an importantly circumscribed role in subjects’ cognitive economies. […] The first way in which the cognitive role of delusions is circumscribed relative to that of paradigmatic beliefs is inferential. Delusional subjects often do not draw the sorts of inferences that we might expect from someone who believed the content of his or her delusion. A subject with the Capgras delusion, for example, who believes that his wife has been replaced by a duplicate, is likely not to adopt an overall worldview according to which it makes sense that his spouse should have been replaced by an impostor. […] Another respect in which the role of delusional beliefs is circumscribed is behavioral. Delusional subjects fail, in important ways, to act in ways that we would expect from someone who genuinely believed the things that he or she professed to believe. […] Finally, the delusional belief’s role in subjects’ emotional lives seems to be circumscribed as well. Subjects often do not seem to experience the sorts of affective responses that we would expect from someone who believed that, for example, his or her spouse had been replaced by an impostor. […] Imagining displays the right kind of evidence independence. In order to imagine that P, I needn’t have any evidence that P. Further, getting evidence that not-P or noticing that I already had such evidence needn’t interfere at all with my continuing to imagine that P. […] Classifying delusions as straightforward, paradigmatic cases of belief is problematic because it predicts that delusions ought not to display the sorts of circumscription and evidence independence that they in fact display. Classifying them as straightforward, paradigmatic cases of imagination is [however also] problematic because it predicts that they should display more circumscription and evidence independence than they in fact display. What would be nice would be to be able to say that the attitude is something in between paradigmatic belief and paradigmatic imagination — that delusional subjects are in states that play a role in their cognitive economies that is in some respects like that of a standard-issue, stereotypical belief that P and in other respects like that of a standard-issue, stereotypical imagining that P.”

“Some cases of self-deception seem to display the same sort of peculiar circumscription and insensitivity to evidence that’s characteristic of delusions. In these cases, we may have the same sort of reluctance to say that self-deceivers genuinely believe that the relevant proposition is true; however, it also doesn’t seem right to say that they merely desire that it’s true, either. Instead, they seem to be in an intermediate state between belief and desire. […] This would allow for the self-deceiver’s “belief” to be insensitive to evidence for its falsity in the same way as a desire, and yet to play some part of the behavior-guiding role of belief. It would also allow us to account for cases in which the self-deceiver’s “belief” has an impoverished behavior-guiding and inferential role, as seems to be the case sometimes. I don’t want to suggest that this is the right account of self-deception in general. I suspect that self-deception is a many-splendored thing and that there won’t be any single, unified account of self-deception in general to be found. Instead, I want to suggest that this sort of intermediate-state account is the right way to describe what’s going on in some restricted class of cases that might plausibly fall under the heading of “self-deception”—the ones that display the same peculiar sort of evidence independence and circumscription that we see in delusions.
There are, broadly speaking, two sorts of accounts of the origin of intermediate attitudes. […] In the first account, the representations are peculiar from the get-go: Something goes wrong in the original construction of the representation, so it winds up with a nonstandard role in the subject’s cognitive economy. In the second sort of account, the problematic representations start off with a fairly standard functional role and then they drift into some intermediate area. […] The self-deception account […] fits best with this second kind of origin. The most plausible sort of story seems to be one on which some representations start life as desires, but eventually acquire some aspects of the functional role of a belief.”

December 5, 2014 Posted by | books, medicine, Psychology | Leave a comment

Wikipedia articles of interest

i. Trade and use of saffron.

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

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

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

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

ii. Scramble for Africa.

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

Here’s a really neat illustration from the article:


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

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

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

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

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

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

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

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

iii. Cursed soldiers.

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

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

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

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

iv. Affective neuroscience.

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

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

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

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

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

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

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

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

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

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


December 4, 2014 Posted by | biology, Botany, Geography, history, medicine, Psychology, wikipedia | Leave a comment

The Voyage of the Beagle (II)

As earlier mentioned I’ve recently been rereading this book.

I have added some observations and quotes from the book below.

“The river, though it has so little power in transporting even inconsiderable fragments, yet in the lapse of ages might produce by its gradual erosion an effect of which it is difficult to judge the amount. But in this case, independently of the insignificance of such an agency, good reasons can be assigned for believing that this valley was formerly occupied by an arm of the sea. […] If I had space I could prove that South America was formerly here cut off by a strait, joining the Atlantic and Pacific oceans, like that of Magellan. But it may yet be asked, how has the solid basalt been moved? Geologists formerly would have brought into play, the violent action of some overwhelming debacle; but in this case such a supposition would have been quite inadmissible; because, the same step-like plains with existing seashells lying on their surface, which front the long line of the Patagonian coast, sweep up on each side of the valley of Santa Cruz. No possible action of any flood could thus have modelled the land, either within the valley or along the open coast; and by the formation of such step-like plains or terraces the valley itself had been hollowed out. Although we know that there are tides, which run within the Narrows of the Strait of Magellan at the rate of eight knots an hour, yet we must confess that it makes the head almost giddy to reflect on the number of years, century after century, which the tides, unaided by a heavy surf, must have required to have corroded so vast an area and thickness of solid basaltic lava. Nevertheless, we must believe that the strata undermined by the waters of this ancient strait, were broken up into huge fragments, and these lying scattered on the beach, were reduced first to smaller blocks, then to pebbles and lastly to the most impalpable mud, which the tides drifted far into the Eastern or Western Ocean.”

“On March 1st, 1833, and again on March 16th, 1834, the Beagle anchored in Berkeley Sound, in East Falkland Island. […] After the possession of these miserable islands had been contested by France, Spain, and England, they were left uninhabited. The government of Buenos Ayres then sold them to a private individual, but likewise used them, as old Spain had done before, for a penal settlement. England claimed her right and seized them. The Englishman who was left in charge of the flag was consequently murdered [I’m not sure why, but this sentence incidentally reminded me of this comic]. A British officer was next sent, unsupported by any power. And when we arrived, we found him in charge of a population, of which rather more than half were runaway rebels and murderers.”

“The geological structure of these islands is in most respects simple. The lower country consists of clay-slate and sandstone, containing fossils, very closely related to, but not identical with, those found in the Silurian formations of Europe; the hills are formed of white granular quartz rock. The strata of the latter are frequently arched with perfect symmetry, and the appearance of some of the masses is in consequence most singular. Pernety[8] has devoted several pages to the description of a Hill of Ruins, the successive strata of which he has justly compared to the seats of an amphitheatre. The quartz rock must have been quite pasty when it underwent such remarkable flexures without being shattered into fragments. As the quartz insensibly passes into the sandstone, it seems probable that the former owes its origin to the sandstone having been heated to such a degree that it became viscid, and upon cooling crystallized. While in the soft state it must have been pushed up through the overlying beds.” (This is one neat illustration of the fact that it’s not like people didn’t know anything about geology at this point in time or didn’t have any ideas, even if plate tectonics is still very far away – there’s actually a lot more stuff on this topic later on in the book, for example when Darwin talks about an earthquake (“It is generally thought that this has been the worst earthquake ever recorded in Chile”) which happened in Chile while he was in the area. I may or may not come back to this in my third and presumably last post about the book).

“In the morning the Captain sent a party to communicate with the Fuegians. When we came within hail, one of the four natives who were present advanced to receive us, and began to shout most vehemently, wishing to direct us where to land. When we were on shore the party looked rather alarmed, but continued talking and making gestures with great rapidity. It was without exception the most curious and interesting spectacle I ever beheld: I could not have believed how wide was the difference between savage and civilized man: It is greater than between a wild and domesticated animal, inasmuch as in man there is greater power of improvement. […] Their attitudes were abject, and the expression of their countenance distrustful, surprised, and startled. After we had presented them with some scarlet cloth, which they immediately tied round their necks, they became good friends. […] I have not as yet noticed [meaning in this context: mentioned, US] the Fuegians whom we had on board. During the former voyage of the Adventure and Beagle in 1826 to 1830, Captain Fitz Roy seized on a party of natives, as hostages for the loss of a boat, which had been stolen, to the great jeopardy of a party employed on the survey; and some of these natives, as well as a child whom he bought for a pearl-button, he took with him to England, determining to educate them and instruct them in religion at his own expense. To settle these natives in their own country, was one chief inducement to Captain Fitz Roy to undertake our present voyage; and before the Admiralty had resolved to send out this expedition, Captain Fitz Roy had generously chartered a vessel, and would himself have taken them back.”

“While going one day on shore near Wollaston Island, we pulled alongside a canoe with six Fuegians. These were the most abject and miserable creatures I anywhere beheld. On the east coast the natives, as we have seen, have guanaco cloaks, and on the west they possess seal-skins. Amongst these central tribes the men generally have an otter-skin, or some small scrap about as large as a pocket-handkerchief, which is barely sufficient to cover their backs as low down as their loins. It is laced across the breast by strings, and according as the wind blows, it is shifted from side to side. But these Fuegians in the canoe were quite naked, and even one full-grown woman was absolutely so. It was raining heavily […] Viewing such men, one can hardly make one’s self believe that they are fellow-creatures, and inhabitants of the same world. It is a common subject of conjecture what pleasure in life some of the lower animals can enjoy; how much more reasonably the same question may be asked with respect to these barbarians! At night, five or six human beings, naked and scarcely protected from the win and rain of this tempestuous climate, sleep on the wet ground coiled up like animals. […] They often suffer from famine […] The different tribes when at war are cannibals. From the concurrent, but quite independent evidence of the boy taken by Mr. Low, and of Jemmy Button, it is certainly true, that when pressed in winter by hunger, they kill and devour their old women before they kill their dogs: the boy, being asked by Mr. Low why they did this, answered, “Doggies catch otters, old women no.” This boy described the manner in which they are killed by being held over smoke and thus choked; he imitated their screams as a joke, and described the parts of their bodies which are best to eat. Horrid as such a death by the hands of their friends and relatives must be, the fears of the old women, when hunger begins to press, are more painful to think of; we are told that they often run away into the mountains, but that they are pursued by the men and brought back […] the husband is to the wife a brutal master to a laborious slave.”

“Few if any of these natives [these are incidentally not the same natives as the ones described above, US] could ever have seen a white man […] They were very inoffensive as long as they were few in numbers, but in the morning (21st) being joined by others they showed symptoms of hostility, and we thought that we should have come to a skirmish. An European labours under great disadvantages when treating with savages like these, who have not the least idea of the power of firearms. In the very act of levelling his musket he appears to the savage far inferior to a man armed with a bow and arrow, a spear, or even a sling. Nor is it easy to teach them our superiority except by striking a fatal blow. Like wild beast, they do not appear to compare numbers; for each individual, if attacked, instead of retiring, will endeavour to dash your brains out with a stone, as certainly as a tiger under similar circumstances would tear you.”

“We slept at the gold-mines of Yaquil, which are worked by Mr. Nixon, an American gentleman […] When we arrived at the mine, I was struck by the pale appearance of many of the men, and inquired from Mr. Nixon respecting their condition. The mine is 450 feet deep, and each man brings up about 200 pounds weight of stone. With this load they have to climb up the alternate notches cut in the trunks of trees, placed in a zig-zag line up the shaft. Even beardless young men, eighteen and twenty years old, with little muscular development of their bodies (they are quite naked excepting drawers) ascend with this great load from nearly the same depth. A strong man, who is not accustomed to this labour, perspires most profusely, with merely carrying up his own body. With this very severe labour, they live entirely on boiled beans and bread. They would prefer having bread alone; but their masters, finding that they cannot work so hard upon this, treat them like horses, and make them eat the beans. […] They leave the mine only once in three weeks; when they stay with their families for two days. One of the rules of this mine sounds very harsh, but answers pretty well for the master. The only method of stealing gold is to secrete pieces of the ore, and take them out as occasion may offer. Whenever the major-domo finds a lump thus hidden, its full value is stopped out of the wages of all the men; who thus, without they all combine, are obliged to keep watch over each other. […] Bad as the above treatment of the miners appears, it is gladly accepted of by them; for the condition of the labouring agriculturalists is much worse. Their wages are lower, and they live almost exclusively on beans. […] extreme poverty is very common among the labouring classes in this country.”

“The poverty of the place [Chiloe Island – in Chile, US] may be conceived from the fact, that although containing some hundreds of inhabitants, one of our party was unable anywhere to purchase either a pound of sugar or an ordinary knife. No individual possessed either a watch or a clock; and an old man, who was supposed to have a good idea of time, was employed to strike the church bells by guess. […] There is also a great deficiency of a circulating medium. I have seen a man bringing on his back a bag of charcoal, with which to buy some trifle, and another carrying a plank to exchange for a bottle of wine. Hence every tradesman must also be a merchant, and again sell the goods which he takes in exchange. […] In all parts of Chiloe and Chonos, two very strange birds occur […] One is called by the inhabitants “Cheucau” (Pteroptochos rubecula): it frequents the most gloomy and retired spots within the damp forests. Sometimes, although its cry may be heard close at hand, let a person watch ever so attentively he will not see the cheucau; at other times, let him stand motionless and the red-breasted little bird will approach within a few feet in the most familiar manner. […] The cheucau is held in superstitious fear by the Chilotans, on account of its strange and varied cries. There are three very distinct cries: one is called “chiduco,” and is an omen of good; another, “huitreu,” which is extremely unfavourable; and a third, which I have forgotten. These words are given in imitation of the noises; and the natives are in some things absolutely governed by them. The Chilotans assuredly have chosen a most comical little creature for their prophet.”


December 3, 2014 Posted by | books, Geology, history | Leave a comment