Open Thread

It’s been a long time since I had one of these.

Some random stuff I’ve come across:

i. Reviews of Anything. Some pretty funny stuff there. Examples include:  Our solar system: 1 star. Reviews of this review. The 5 star Rating System: 9/10. Obese Americans, 1 out of 4. Spell Checker: 1 satr.


iii. The Bad Writing Contest. A quote from the link:

“The move from a structuralist account in which capital is understood to structure social relations in relatively homologous ways to a view of hegemony in which power relations are subject to repetition, convergence, and rearticulation brought the question of temporality into the thinking of structure, and marked a shift from a form of Althusserian theory that takes structural totalities as theoretical objects to one in which the insights into the contingent possibility of structure inaugurate a renewed conception of hegemony as bound up with the contingent sites and strategies of the rearticulation of power.”

In contexts where you socialize with people who write that way, dumbpiphanies may happen.


v. I’m not actually sure I liked this lecture very much (I was very much annoyed by the word ‘cristal’ in the slides in the last part of the lecture; he repeatedly misspells the word crystal in the slides. I find that kind of sloppiness irritating, because I tend to use the existence of spelling errors in lecture notes/slides in mathematical lectures as what might be termed a caution heuristic; if the lecturer did not bother to correct spelling errors, I figure he probably also didn’t bother to correct other errors in the slides – and if you start to think along the way that there might be errors in the slides, a lecture to me becomes less enjoyable to watch, especially when the lecture deals with complicated stuff which is hard enough to follow as it is), but I figured I might as well share it anyway:

vi. arXiv vs snarXiv.




September 30, 2014 Posted by | Lectures, Mathematics, Open Thread | 8 Comments

Adolescents and Adults with Autism Spectrum Disorders (1?)

I’ve been reading and I have at this point almost finished Sexual Selection in Primates: New and Comparative Perspectives, an awesome book which I’ll certainly give five stars and most likely add to my goodreads favourites, yet now I find myself covering this borderline-lousy book instead. The reason why I’m doing that is simple: Kappeler & van Schaik’s book (the awesome one) is an oldfashioned paper book, which makes it a lot more work to blog than this one.

I’m not impressed with Volkmar et al.’s coverage, and I’m at the moment considering whether I should even finish it – thus the question mark in the parenthesis; if I don’t read any more of it, I’ll certainly not post another post about the book later. It is a rare thing for me to do, to stop reading a book once I’ve decided that it’s worth reading; I’ll often quite quickly get a sense of whether a book is worth reading or not, and I rarely give up on a book once I’m past the first 100 pages. I did not at any point think this book was awesome and I’ve throughout the book so far been somewhere between one and two stars on goodreads, but it’s one of very few books dealing with the topic covered so it’s not like there are a lot of alternatives out there, and this gave the authors some leeway they would not otherwise have had. The most recent chapter I read, on Pharmacotherapy of Behavioral Symptoms and Psychiatric Comorbidities in Adolescents and Adults with Autism Spectrum Disorders, however was very close to pushing me over the limit. Here are some sample quotes from that chapter:

“A case report described a 25-year-old male with Asperger’s disorder who was diagnosed with bipolar I disorder with psychotic features after exhibiting a period of hyperactive, irritable, and assaultive behavior, reduced need for sleep, and grandiose, persecutory delusions (Arora, Praharaj, Sarkhel, & Sinha, 2011). Symptoms of mania improved on a combination of clozapine 200 mg/day and haloperidol 20 mg/ day”

“Clozapine is an atypical antipsychotic that is limited in use due to an increased risk of agranulocytosis and potential to lower the seizure threshold. A case series in three individuals with autism, aged 15-, 17-, and 27-years-old, highlighted successful treatment with clozapine for the management of recurrent aggression toward self and others (Chen, Bedair, McKay, Bowers, & Mazure, 2001; Gobbi & Pulvirenti, 2001; Lambrey et al., 2010).”

“A case series examined this glutamate antagonist in the treatment of three individuals with autism and MR, aged 15–20 years (Wink, Erickson, Stigler, & McDougle, 2011). Dosages ranged from 100 to 200 mg/day. There were reductions in interfering repetitive behaviors in all three subjects.”

“There is one double-blind, placebo-controlled, crossover study of clonidine involving adolescents and adults in the treatment of “hyperarousal behaviors” associated with autism (Fankhauser, Karumanchi, German, Yates, & Karumanchi, 1992). […] This study examined nine males with autism, aged 5–33 years (mean age, 13 years) […] Transdermal clonidine resulted in significant clinical improvement on the Clinical Global Impression-Improvement (CGI-I) scale.”

“The majority of published research on the pharmacological treatment of comorbid psychiatric disorders is limited to case reports and a few open-label studies. […] Although case reports have found some pharmacologic treatment beneficial for psychiatric comorbidities in individuals with ASDs, double-blind, placebo-controlled studies are needed”

One of the authors of that chapter had multiple conflicts of interest which were disclosed towards the end of the chapter, as he’s apparently received research funds from six different pharmaceutical companies. In the chapter they cover studies involving three individuals and even single case stories like the one above (it’s far from the only one). I’m not sure those two observations are unrelated. I think if all you have is a case series involving 3 individuals it’s probably not necessary to include that stuff in a book like this; that sort of information is close to worthless (single case stories certainly are. That’s what we in other areas call ‘anecdotes’). Once you know that some of the randomized controlled trials in this field involve only 9 subjects, you also start becoming a lot less impressed with those. They make conclusions in that chapter which I would not have made based on the evidence they present. A really serious omission is also that polypharmacy is not even mentioned in the chapter, despite a substantial number of people taking more than one type of drug and despite the fact that we basically have no clue how this affects them (see Lubetsky et al. for more on this). This omission is so much more striking as the polypharmacy issue is actually brought up, or at least mentioned, already in the introductory chapter of the book, where the authors note that “Of those receiving medications [in one study of 480 Canadians from Ontario with ASD], over 80 % received more than one medication.”

One reason why I’ve been reading on is that occasionally there are some interesting data, but another reason is that this book probably provides a good illustration of how people working in this field thinks. They, incidentally much like the authors in Lubetsky et al., seem to think there’s no budget constraint – they worry about it to the extent that they’re not given money to spend, but they seem to have no notion of the existence of questions like: ‘but isn’t it simply insane to be spending that kind of money on this?’ They have  a lot of ideas about how you could improve outcomes, and I’m sure some of those ideas if implemented might improve outcomes – whether it would be ‘worth it’ is however a completely different question, a question they do not ask.

I have added some observations from the first half of the book below.

“adolescence and adulthood in ASD [autism spectrum disorder] remain rather poorly understood. Much of the research and clinical work has centered on young children and those of primary school age […] We now understand that ASD is an early-emerging, usually lifelong neurodevelopmental disorder that significantly impact social, communicative, cognitive, and adaptive skills and has a strong genetic basis […]. There is now an extensive literature of peer-reviewed, scientific papers focused on ASD, and multiple studies on adult outcome have been published (for a review, see Howlin, 2013). As Howlin notes, however, these focus almost exclusively on outcome in young adulthood and information on older individuals is limited […], with almost no research focused on aging […]. Of the studies focused on outcome, most have studied individuals with classic ASD, or “Kanner’s” autism and “outcome” is essentially confined largely to early adulthood. […] heterogeneity in both the disorder itself and in service delivery, render it a complicated landscape for the study of intervention and outcome […]. Changes in nomenclature and diagnostic taxonomy have also complicated interpretation of research over the years and of identification of older individuals on the autism spectrum […] The relationship between severity of early symptoms of autism and ultimate outcome remains unclear, with at least a few studies suggesting that the severity of social skills impairment is the most significant outcome predictor […]. This and many other questions regarding changes in outcome remain to be discovered. Past young adulthood the literature becomes quite sparse. In one review of autism, research studies conducted between 2000 and 2010 only 23 (of an estimated 11,000) were focused on adult services […] Despite the important limitations of the research literature, it does appear that on balance outcome has, and is continuing, to improve.”

“The data available suggest that most individuals as adults live with parents/family and that a minority is employed. […] Even for the most able adults, however, limitations in social interaction, in adaptive/daily life skills, and occupational status [are] striking, with nearly 60 % of cases [in the previously mentioned Canadian study] continuing to live with their families. About one third of [that] sample had had romantic relationships and in a few cases had been married (sometimes with offspring). Most of the sample reported major limitations in social connections (with many having one or fewer social encounters outside their living situation each month). […] Outcome studies have shown a wide range of variation in the number of individuals with autism who have left home to live independently, in a group home, or some supported living arrangement. A number of studies have shown that the majority of young adults continue to live at home with their parents. […] Even when adults with autism live outside the family, their families especially their mothers have extensive contact and involvement in their care. Kraus et al. (2005) reported that 50% of families visited their adult with autism at least weekly and an equal number of adults came weekly to visit at their mother’s home. […] This need for continued parental support crosses the entire spectrum of individuals with autism.”

“Recent reviews of outcomes for individuals with ASD through the National Longitudinal Transition Study-2 (NTLS2) have indicated that, as a group, individuals with ASD have low rates of employment, independent living, and lifelong friendships (Newman, Wagner, Cameto, & Knokey, 2009). This longitudinal study followed 11,000 transition-aged students with disabilities from 2001 to 2009. The age range of youth and young adults included in this study were between 13 and 26. This sample included 922 students with autism spectrum disorders. Outcomes recorded for this sample included the following findings […]: • 32 % of this sample attended post-secondary education of one type or another • Only 6 % achieved competitive employment • 21 % had no job or post-secondary education experiences at all • 80 % continued to live with their parents • 40 % reported having no friends”

“The relationship between typically developing siblings has been extensively studied; however, very few studies have been conducted in order to investigate the interactions and quality of relationship between siblings when one has autism. For a typically developing sibling, the influence of having a brother or sister with autism is associated with higher rates of behavioral and emotional concerns […] and fewer prosocial behaviors towards their sibling with autism in some studies […] Within the literature, higher levels of education of the typically developing sibling as well as living at a distance from their sibling with autism have negative consequences for their perceptions of the sibling bond”

“There is limited research on the spouses of individuals with ASD. With the increasing knowledge and identification of high functioning men and women, there is a growing awareness that a portion of adults with ASD do enter into long-term relationships with others […]. However, there is limited empirical data about the nature of these relationships. […] adolescents and adults with ASD have far fewer sexual experiences than their typically developing peers […] Nichols and Byers (2008) found that participants who were older and had fewer ASD symptoms reported better sexual functioning. Specifically, individuals with fewer ASD symptoms reported greater sexual satisfaction, sexual self-esteem, assertiveness, arousability, and desire. They also reported fewer sexual problems and less anxiety surrounding sexual issues. As such, a sizable population of individuals with ASD is capable of having a satisfying sex life.”

“An impairment in social interaction is a core symptom of ASD […] and can impact social communication, friendship-making, dating, relationship-building, as well as sexuality. These deficiencies can lead to a decrease in social relationships […], an increase in loneliness […], an increase in social isolation, and poor quality friendships […]. Furthermore, co-morbid diagnoses of other mental disorders are common among this population. Individuals with Asperger’s are 5.7 times more likely to develop symptoms of depression in comparison to the typically developing population (McHale, Dariotis, & Kauh, 2003; Stewart et al., 2006). The literature suggests that most individuals with ASDs show a desire for relationships, but experience loneliness because their difficulties with social skills often interfere with friendship formation […] in a study of “high-functioning” individuals with autism, more than 56% had never experienced a sexual relationship and only 25% had dated […] as a whole, studies repeatedly show that although individuals with ASD desire intimate relationships, few actually have them. […] [People] with ASD often lack the social skills knowledge and competence to appropriately pursue and engage in successful romantic relationships […]. For example, individuals with ASD have been known to naively behave in an intrusive manner with potential romantic partners, which may even be perceived as stalking behavior”

“Despite the pervasiveness of social deficits commonly experienced among individuals with ASD, social skills are comparatively much less studied than other aspects of ASD and research examining social skills interventions for adolescents and adults with ASD are especially rare. In a best evidence synthesis of 66 studies of social skills interventions for individuals with ASD published between 2001 and 2008, only three studies contained adolescent or adult participants […] Social deficits are typically a major source of impairment for individuals with ASD, regardless of cognitive or language ability […]. However, the considerable heterogeneity in the level of cognitive functioning and language ability among individuals with ASD may affect the presentation of social deficits. For example, Bauminger, Shulman, and Agam (2003) found that higher-functioning adolescents initiate social interaction with peers more frequently than do their lower-functioning peers; yet, their interactions are often awkward and sometimes even intrusive or offensive. […] high functioning adolescents may be no less affected by social deficits than those with cognitive limitations; rather, their heightened self-awareness and false appearance of being less impaired may actually increase the severity of their social limitations and motivation, perhaps increasing the likelihood of peer rejection and neglect. Consequences of poor social skills often manifest in the form of peer rejection, peer victimization, poor social support, and isolation. Consequently, individuals with ASD generally report higher levels of loneliness and poorer quality of friendships”

“adults with ASD often present with more depression and anxiety than their adolescent counterparts […]. Interestingly, higher-functioning adults with greater intelligence and less autistic symptomatology tend to experience more depression, anxiety, social isolation, withdrawal, and peer victimization […] than lower-functioning individuals. This may be due in part to greater social expectations often placed on higher-functioning adults occurring as a result of placement in less protective and more inclusive settings. With higher-functioning adults with ASD often giving the appearance of seeming more “odd” than disabled by their peers, these individuals may be more susceptible to peer rejection, and consequently greater negative socio-emotional outcomes like depression and anxiety. Furthermore, greater self-awareness about peer rejection and “differentness” more likely found in higher-functioning adults with ASD may also contribute to greater depression and anxiety”

“While social skills training has been utilized for decades and is not a particularly unique or novel treatment for individuals with ASD, the research literature suggests that these approaches have not been tremendously effective in improving the social functioning of individuals on the autism spectrum […] While social skills training has increasingly become a popular method for helping individuals with ASD adapt to their social environment […], a review of the research literature suggests there are very few evidence-based social skills interventions for adolescents and adults with ASD […]. With emphasis on early intervention, most social skills treatment studies have targeted younger children on the autism spectrum, with few clinical research trials focusing on adolescents or adults with ASD. Among the limited number of social skills intervention studies conducted with this population, most have not been formally tested in terms of their efficacy in improving social competence or the development of close friendships, nor do they examine the maintenance of treatment gains months or years after the intervention has ended. […] the literature on social skills training for youth with ASD has been far from encouraging. In a review of the social skills treatment literature, White et al. (2007) identified 14 studies that used group-based social skills training for children and adolescents with ASD. Among these studies, only one used a randomized control group design […] None of these studies examined the maintenance or trajectory of improvement in social competency over time […] Even fewer studies have focused on social skills treatment for adults with ASD. To date, only three published studies appear to have tested the effectiveness of a social skills intervention for adults with ASD […] Only 4 of the 14 studies White et al. (2007) included in their review employed a RCT with a control group. In a similar review of social skills training interventions for children and adolescents with ASD, Rao et al. (2008) found that 9 out of 10 reviewed studies did not use a RCT as their research design. […] Regrettably, most social skills intervention studies are limited in their ability to generalize research findings to other settings and other populations of adolescents and adults with ASD. Two of the biggest offenders to generalization relate to sample size and participant characteristics. Most social skills training intervention studies for adolescents and adults with ASD have small sample sizes […] single-case experimental designs with approximately three or four participants appear to be the most common research design employed within social skills training studies”

September 27, 2014 Posted by | autism, Books, Medicine, Psychology | Leave a comment


i. “Children are like men, the experience of others does not help them.” (Alphonse Daudet)

ii. “Men grow old, but they do not ripen.” (-ll-)

iii. “Ingratitude calls forth reproaches as gratitude brings renewed kindnesses.” (Marie de Rabutin-Chantal, marquise de Sévigné)

iv. “There is no person who is not dangerous for some one.” (-ll-)

v. “Whatever is worth doing at all, is worth doing well.” (Philip Stanhope, 4th Earl of Chesterfield)

vi. “Idleness is only the refuge of weak minds.” (-ll-)

vii. “Abject flattery and indiscriminate assentation degrade, as much as indiscriminate contradiction and noisy debate disgust. But a modest assertion of one’s own opinion, and a complaisant acquiescence in other people’s, preserve dignity.” (-ll-)

viii. “Knowledge may give weight, but accomplishments give luster, and many more people see than weigh.” (-ll-)

ix. “Let blockheads read what blockheads wrote.” (-ll-)

x. “The moral of the story of the Pilgrims is that if you work hard all your life and behave yourself every minute and take no time out for fun you will break practically even, if you can borrow enough money to pay your taxes.” (Will Cuppy)

xi. “The Bayeux Tapestry is accepted as an authority on many details of life and the fine points of history in the eleventh century. For instance, the horses in those days had green legs, blue bodies, yellow manes, and red heads, while the people were all double-jointed and quite different from what we generally think of as human beings.” (-ll-. Now I’d sort of wish we’d had someone like Cuppy show us around back when I saw the Bayeux Tapestry many years ago…)

xii. “In some respects, Nero was ahead of his time. He boiled his drinking water to remove the impurities and cooled it with unsanitary ice to put them back in. He renamed the month of April after himself, calling it Neroneus, but the idea never caught on because April is not Neroneus and there is no use pretending that it is. During his reign of fourteen years, the outlying provinces are said to have prospered. They were farther away.” (-ll-)

xiii. “[Alexander the Great] was often extremely brutal to his captives, whom he sold into slavery, tortured to death, or forced to learn Greek.” (-ll-)

xiv. “People talk vaguely about the innocence of a little child, but they take mighty good care not to let it out of their sight for twenty minutes.” (Saki)

xv. “It occurred to me that I would like to be a poet. The chief qualification, I understand is that you must be born. Well, I hunted up my birth certificate, and found that I was all right on that score.” (-ll-)

xvi. “The sacrifices of friendship were beautiful in her eyes as long as she was not asked to make them.” (-ll-)

xvii. “Wisdom cannot prevent a fall, but may cushion it.” (Mason Cooley)

xviii. “I am easy-going right up to the borders of my self-interest.” (-ll-)

xix. “Scepticism is always a back road leading to some credo or other.” (-ll-)

xx. “In an aphorism, aptness counts for more than truth.” (-ll-)

September 25, 2014 Posted by | Quotes/aphorisms | Leave a comment

100 Cases in Clinical Pathology

This book is another publication from the 100 Cases … series which I’ve talked about before – I refer to these posts for some general comments about what this series is like and some talk about the other books in the series which I’ve read. The book is much like the others, though of course the specific topics covered are different in the various publications. I liked this book and gave it 3 stars on goodreads. The book has three sections: a section dealing with ‘chemical pathology, immunology and genetics’; a section dealing with ‘histopathology’; and a section dealing with ‘haematology’. As usual I knew a lot more about some of the topics covered than I did about some of the others. Some cases were quite easy, others were not. Some of the stuff covered in Greenstein & Wood’s endocrinology text came in handy along the way and enabled me for example to easily identify a case of Cushing’s syndrome and a case of Graves’ disease. I don’t think I’ll spoil anything by noting that two of the cases in this book involved these disorders, but if you plan on reading it later on you may want to skip the coverage below, as I have included some general comments from the answer sections of the book in this post.

As someone who’s not working in the medical field and who will almost certainly never need to know how to interpret a water deprivation test (also covered in detail in Greenstein and Wood, incidentally), there are some parts of books like this one which are not particularly ‘relevant’ to me; however I’d argue that far from all the stuff included in a book like this one is ‘stuff you don’t need to know’, as there are also for example a lot of neat observations included about how specific symptoms (and symptom complexes) are linked to specific disorders, some related ideas about which other medical conditions might cause similar health problems, and which risk factors are potentially important to have in mind in specific contexts. If you’ve had occasional fevers, night sweats and experienced weight loss over the last few months, you should probably have seen a doctor a while ago – knowledge included in books like this one may make the reader perhaps a bit less likely to overlook an important and potentially treatable health problem, and/or increase awareness of potential modifiable risk factors in specific contexts. A problem is however that the book will be hard to read if you have not read any medical textbooks before, and in that case I would probably advise you against reading it as it’s almost certainly not worth the effort.

I have added a few observations from the book below.

“After a bone marrow transplant (and any associated chemotherapy), the main risks are infection (from low white cell counts and the use of immunosuppressants, such as cyclosporin), bleeding (from low platelet counts) and graft versus host disease (GVHD). […] An erythematous rash that develops on the palms or soles of the feet of a patient 10–30 days after a bone marrow transplant is characteristic of GVHD. […] GVHD is a potentially life-threatening problem that can occur in up to 80% of successful allogeneic bone marrow transplants. […] Clinically, GVHD manifests like an autoimmune disease with a macular-papular rash, jaundice and hepatosplenomegaly and ultimately organ fibrosis. It classically involves the skin, gastrointestinal tract and the liver. […] Depending on severity, treatment of acute GVHD may involve topical and intravenous steroid therapy, immunosuppression (e.g. cyclosporine), or biologic therapies targeting TNF-α […], a key inflammatory cytokine. […] Prognosis is related to response to treatment. The mortality of patients who completely respond can still be around 20%, and the mortality in those who do not respond is as high as 75%.”

“The leading indication for a liver transplant is alcoholic cirrhosis in adults and biliary atresia in children. […] The overall one-year survival of a liver transplant is over 90%, with 10-year survival of around 70%. […] Transplant rejection can be classified by time course, which relates to the underlying immune mechanism: • Hyperacute organ rejection occurs within minutes of the graft perfusion in the operating theatre. […] The treatment for hyperacute rejection is immediate removal of the graft. • Acute organ rejection take place a number of weeks after the transplant […] The treatment for acute rejection includes high dose steroids. • Chronic organ rejection can take place months to years after the transplant. […] As it is irreversible, treatment for chronic rejection is difficult, and may include re-transplantation.”

“Chronic kidney disease (CKD) is characterized by a reduction in GFR over a period of 3 or more months (normal GFR is >90–120 mL/min). It arises from a progressive impairment of renal function with a decrease in the number of functioning nephrons; generally, patients remain asymptomatic until GFR reduces to below 15 mL/min (stage V CKD). Common causes of CKD are (1) diabetes mellitus, (2) hypertension, (3) glomerulonephritis, (4) renovascular disease, (5) chronic obstruction or interstitial nephritis, and (6) hereditary or cystic renal disease”

“The definition of an aneurysm is an abnormal permanent focal dilatation of all the layers of a blood vessel. An AAA [abdominal aortic aneurysm] is defined when the aortic diameter, as measured below the level of the renal arteries, is one and a half times normal. Women have smaller aortas, but for convenience, more than 3 cm qualifies as aneurysmal. The main risk factors for aneurysm formation are male gender, smoking, hypertension, Caucasian/European descent and atherosclerosis. Although atherosclerosis is a risk factor and both diseases share common predisposing factors, there are also differences. Atherosclerosis is primarily a disease of the intima, the innermost layer of the vessel wall, whereas in aneurysms there is degeneration of the media, the middle layer. […] The annual risk of rupture equals and begins to outstrip the risk of dying from surgery when the aneurysm exceeds 5.5 cm. This is the size above which surgical repair is recommended, comorbidities permitting. […] Catastrophic rupture, as in this case, presents with hypovolaemic shock and carries a dismal prognosis.” [The patient in the case history died soon after having arrived at the hospital]

“Stroke refers to an acquired focal neurological deficit caused by an acute vascular event. The neurological deficit persists beyond 24 hours, in contrast to a transient ischaemic attack (TIA) where symptoms resolve within 24 hours, although the distinction is now blurred with the advent of thrombolysis. […] Strokes are broadly categorized into ischaemic and haemorrhagic types, the majority being ischaemic. The pathophysiology in a haemorrhagic stroke is rupture of a blood vessel causing extravasation of blood into the brain substance with tissue damage and disruption of neuronal connections. The resulting haematoma also compresses surrounding normal tissue. In most ischaemic strokes, there is thromboembolic occlusion of vessels due to underlying atherosclerosis of the aortic arch and carotid arteries. In 15–20% of cases, there is atherosclerotic disease of smaller intrinsic blood vessels within the brain[…]. A further 15–20% are due to emboli from the heart. […] The territory and the extent of the infarct influences the prognosis; [for example] expressive dysphasia and right hemiparesis are attributable to infarcts in Broca’s area and the motor cortex, both frontal lobe territories supplied by the left middle cerebral artery.”

“The stereotypical profile of a gallstone patient is summed up by the 4Fs: female, fat, fertile and forty. However, while gallstones are twice as common in females, increasing age is a more important risk factor. Above the age of 60, 10–20% of the Western population have gallstones. […] Most people with cholelithiasis are asymptomatic, but there is a 1–4% annual risk of developing symptoms or complications. […] Complications depend on the size of the stones. Smaller stones may escape into the common bile duct, but may lodge at the narrowing of the hepatopancreatic sphincter (sphincter of Oddi), obstructing the common bile duct and pancreatic duct, leading to obstructive jaundice and pancreatitis respectively. […] In most series, alcohol and gallstones each account for 30–35% of cases [of acute pancreatitis]. […] Once symptomatic, the definitive treatment of gallstone disease is generally surgical via a cholecystectomy.”

“Breast cancer affects 1 in 8 women (lifetime risk) in the UK. […] Between 10 and 40% of women who are found to have a mass by mammography will have breast cancer. […] The presence of lymphovascular invasion indicates the likelihood of spread of tumour cells beyond the breast, thereby conferring a poorer outlook. Without lymph node involvement, the 10-year disease-free survival is close to 70–80% but falls progressively with the number of involved nodes.”

“Melanoma is a cancer of melanocytes, the pigmented cells in the skin, and is caused by injury to lightly pigmented skin by excessive exposure to ultraviolet (UV) radiation […] The change in colour of a pre-existing pigmented lesion with itching and bleeding and irregular margins on examination are indicators of transformation to melanoma. Melanomas progress through a radial growth phase to a vertical growth phase. In the radial growth phase, the lesion expands horizontally within the epidermis and superficial dermis often for a long period of time. Progression to the vertical phase is characterized by downward growth of the lesion into the deeper dermis and with absence of maturation of cells at the advancing front. During this phase, the lesion acquires the potential to metastasize through lymphovascular channels. The probability of this happening increases with increasing depth of invasion (Breslow thickness) by the melanoma cells. […] The ABCDE mnemonic aids in the diagnosis of melanoma: Asymmetry – melanomas are likely to be irregular or asymmetrical. Border – melanomas are more likely to have an irregular border with jagged edges. Colour – melanomas tend to be variegated in colour […]. Diameter – melanomas are usually more than 7 mm in diameter. Evolution – look for changes in the size, shape or colour of a mole.”

“CLL [chronic lymphocytic leukaemia] is the most common leukaemia in the Western world. Typically, it is picked up via an incidental lymphocytosis in an asymptomatic individual. […] The disease is staged according to the Binet classification. Typically, patients with Binet stage A disease require no immediate treatment. Symptomatic stage B and all stage C patients receive chemotherapy. […] cure is rare and the aim is to achieve periods of remission and symptom control. […] The median survival in CLL is between four and six years, though some patients survive a decade or more. […] There is […] a tendency of CLL to transform into a more aggressive leukaemia, typically a prolymphocytic transformation (in 15–30% of patients) or, less commonly (<10% of cases), transformation into a diffuse large B-cell lymphoma (a so-called Richter transformation). Appearance of transformative disease is an ominous sign, with few patients surviving for more than a year with such disease.”

“Pain, swelling, warmth, tenderness and immobility are the five cardinal signs of acute inflammation.”

“Osteomyelitis is an infection of bone that is characterized by progressive inflammatory destruction with the formation of sequestra (dead pieces of bone within living bone), which if not treated leads to new bone formation occurring on top of the dead and infected bone. It can affect any bone, although it occurs most commonly in long bones. […] Bone phagocytes engulf the bacteria and release osteolytic enzymes and toxic oxygen free radicals, which lyse the surrounding bone. Pus raises intraosseus pressure and impairs blood flow, resulting in thrombosis of the blood vessels. Ischaemia results in bone necrosis and devitalized segments of bone (known as sequestra). These sequestra are important in the pathogenesis of non-resolving infection, acting as an ongoing focus of infection if not removed. Osteomyelitis is one of the most difficult infections to treat. Treatment may require surgery in addition to antibiotics, especially in chronic osteomyelitis where sequestra are present. […] Poorly controlled diabetics are at increased risk of infections, and having an infection leads to poor control of diabetes via altered physiology occurring during infection. Diabetics are prone to developing foot ulcers, which in turn are prone to becoming infected, which then act as a source of bacteria for infecting the contiguous bones of the feet. This process is exacerbated in patients with peripheral neuropathy, poor diabetic control and peripheral vascular disease, as these all increase the risk of development of skin breakdown and subsequent osteomyelitis.” [The patient was of course a diabetic…]

“Recent onset fever and back pain suggest an upper UTI [urinary tract infection]. UTIs are classified by anatomy into lower and upper UTIs. Lower UTIs refer to infections at or below the level of the bladder, and include cystitis, urethritis, prostatitis, and epididymitis (the latter three being more often sexually transmitted). Upper UTIs refer to infection above the bladder, and include the ureters and kidneys. Infection of the urinary tract above the bladder is known as pyelonephritis [which] may be life threatening or lead to permanent kidney damage if not promptly treated. UTIs are also classified as complicated or uncomplicated. UTIs in men, the elderly, pregnant women, those who have an indwelling catheter, and anatomic or functional abnormality of the urinary tract are considered to be complicated. A complicated UTI will often receive longer courses of broader spectrum antibiotics. Importantly, the clinical history alone of dysuria and frequency (without vaginal discharge) is associated with more than 90% probability of a UTI in healthy women. […] In women, a UTI develops when urinary pathogens from the bowel or vagina colonize the urethral mucosa, and ascend via the urethra into the bladder. During an uncomplicated symptomatic UTI in women, it is rare for infection to ascend via the ureter into the kidney to cause pyelonephritis. […] Up to 40% of uncomplicated lower UTIs in women will resolve spontaneously without antimicrobial therapy. The use of antibiotics in this cohort is controversial when taking into account the side effects of antibiotics and their effect on normal flora. If prescribed, antibiotics for uncomplicated lower UTIs should be narrow-spectrum […] Most healthcare-associated UTIs are associated with the use of urinary catheters. Each day the catheter remains in situ, the risk of UTI rises by around 5%. Thus inserting catheters only when absolutely needed, and ensuring they are removed as soon as possible, can prevent these.”

September 24, 2014 Posted by | alcohol, Books, Cancer/oncology, Cardiology, Diabetes, Immunology, Medicine, Microbiology, Nephrology, Neurology | Leave a comment

An Introduction to Tropical Rain Forests (III)

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

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

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

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

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

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

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

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

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

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

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

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


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

Four chess games

I’ve started playing active tournament chess again, at least a little bit. The format of the tournament in which I’m participating at the moment is a rapid format, with 45 minutes per player per game, with two games per round – one game with the white pieces and one with the black pieces, against the same opponent. Below I have posted the first four games I’ve played in the tournament so far – this is a short post, but each game lasted a significant amount of time.

Links to the games: 1 (white), 2 (black), 3 (white), 4. (black).

The two first games are actually, I think, quite instructive in that I played against a much lower rated player and managed to win both games in roughly 20 moves. There’s a reason strong chess players do not lose to beginners and games like these will tell you part of the story of why this is.

The last two games were not particularly great and I certainly was not satisfied with my play in either of those, especially not the second one – I had a winning position out of the opening, yet I somehow managed to blunder a piece in the middle game. 17…Rad8 was a blunder (the idea was 18.Bxc6… Rxd2, followed by 19.Qxd2 and …Qxa1+, and after Qd1 (forced) black takes on a2), whereas after 17…e4! the computer gives black an advantage of roughly -4,5 (an advantage corresponding to almost an entire rook, even though the position is materially balanced – I knew the position was winning, but you still have to find the right moves..). I’d of course missed the check on d5 and Rc1, which were played in the game. I considered taking on d5 after the bishop check, and actually my intuition was correct that this was completely winning (the position is at -2 or so after the exchange sac, according to the engine – this is not surprising as white is basically playing without the rook on h1 and also has an exposed king in an open position) – but in the end I decided not to play this as ‘Kh8 is surely winning as well, and an exchange sac is not necessary here’. I was wrong. Actually the position arising shortly after the blunder around move 20 is a good illustration of how important piece activity is; the position after 20…e4, where black is basically a whole piece down, according to the engine is still better for black (-0.3). Black has a lot of activity for the material, despite this ‘sacrifice’ of course being completely unnecessary.

Given that I’ve won all my games so far it’s not possible to calculate a performance rating yet, but I’d say that in terms of results at least I’m doing okay, though perhaps not much better than could have been expected. Anyway the way this tournament works, the more games you win the tougher opponents you get –  I was the rating favourite in both of the matches I’ve played so far, and that’ll change soon enough; I may easily end up playing against a 2200 Elo opponent next round, so I expect to lose and/or draw some games quite soon. If you’re interested in me sharing more of my games here later on, let me know in the comments – I think that if I don’t get any indications that people reading along here would like to see another post like this one again, this will probably be my last post of this kind. I know some of my readers are interested in chess, at least a little bit, but that’s not the same thing as finding posts like this one interesting.

I should note that the internet issue I have had has now, as far as I can tell, been solved. This should make it much easier for me to blog from now on than it has been for the last couple of weeks.

September 23, 2014 Posted by | Chess, Personal | Leave a comment

An Introduction to Tropical Rain Forests (II)

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

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

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

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

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

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

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

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

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

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

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

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

An Introduction to Tropical Rain Forests (I)

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

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

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

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

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

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

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

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

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

Computer trouble

My computer broke down a couple of days ago, and I have had completely unrelated problems with my internet connection as well during the last week. I’m currently relying on an old and highly unreliable laptop with intermittent internet access. I don’t know how long it will take to sort out these problems and/but until the problems have been solved you should expect blogging to be very light.

September 17, 2014 Posted by | Uncategorized | Leave a comment

Aging – Facts and Theories (Interdisciplinary Topics in gerontology, Vol. 39) (II)

(Smbc – click to view full size). The book goes into a bit more detail..

I should probably add a few general remarks related to the previous post before moving on to the coverage of the book. The ‘problem’ is this: I’m getting behind on the book blogging. Earlier this year I had an implicit goal of wanting to cover all non-fiction books I read here. Given that I’ll probably end up reading more than a textbook per week this year and I’ve already gotten significantly behind, I’m no longer sure this goal is achievable in the long run. Currently I’m probably at least something like 6-7 posts behind in terms of stuff I could potentially cover here given what I’ve already read, but I’m not sure how many of those posts I’ll actually ever get to write. You should not make strong assumptions about the quality of the books not covered here based on my decision of whether or not to cover them; sometimes the reason why I’m not blogging a book while reading it (in some sense the preferable approach, because it makes it less likely that I’ll get behind) is simply that it’s a great book which I’d rather be reading than blogging. If a book has a lot of math – like the Ecological Dynamics text, which I’ve still yet to talk about here in part because basically that’s just a math textbook – or is highly technical in other ways, e.g. by dealing with stuff which to a significant extent builds on top of other stuff I’ve read – this book or the endocrinology book are both good examples – then it is really a lot more work to blog the book. The same goes for books which I’ve procured and read offline. Sometimes the relevant decision to make is whether I’d prefer to blog a book or read another book; I spend probably something like 4-5 hours on an Agatha Christie novel, and I can easily end up spending 4 hours on a blog post dealing with a technical book as well.

I think as long as I’m posting something every second day or so on average (I’ve posted 125 posts in 257 days so far this year) I don’t really care too much if I don’t get to cover all the stuff I read, even if I’d prefer to cover it all.

Okay, back to the book. As mentioned in the first post, I gave it one star, but that doesn’t mean there isn’t some interesting stuff in there. There are a lot of these things around: ‘[…]’ in my coverage below, and they’re there for a reason. To be frank, if they weren’t there the quotes from the book would be as unreadable as the book is, and I don’t want that kind of stuff on my blog. The language in many chapters of this book is simply terrible, and I’ve tried to make it less terrible by quoting very selectively and very strategically. If you want to make sure I’m not misrepresenting the views of the authors through the ‘active quoting strategies’ I employ below you’re very welcome to read the book yourself and compare my quotes with the original coverage – I’d consider it likely that you’d prefer my coverage to theirs if you were to do that.

“The cross-linking theory [of aging assumes] that aging is due to the formation of intra- and/or intermolecular covalent cross-links altering the basic structure of the macromolecules to such an extent that even their functions become compromised. […] age-dependent increase in […] cross-linking is fully supported by […] heat denaturation experiments [16–20] […] The main conclusion [from these] was that many of the H-bonds are transformed into covalent cross-links in collagen during aging [and collagen is really important as: “the largest fraction of proteins in the body is the collagen[,] amounting to about 33% of the total protein content”].”

“[T]he free radical theory of aging (FRTA) […] assumes that oxygen free radicals are harmful byproducts of the aerobic life, and as such, are responsible for aging and numerous diseases. Since most of the oxygen free radicals are strong electron acceptors, their main effect is the formation of cross-links, i.e. they may well be the causes of the age-dependent cross-linking of proteins. […] free radical-induced cross-linking is strongly density dependent, i.e. the increased physical density of any biological structure will enhance the cross-linking efficiency of the radical-generating systems. […] this phenomenon has a great significance in the age-dependent alterations of the most compact biological structures, like the cell membranes [25].”

“[A] new […] interpretation of the possible biological role of oxygen free radicals in the living state, cell differentiation and aging […] has been called the membrane hypothesis of aging (MHA) […] The MHA attributes a leading role in differentiation and aging processes to the plasma membrane, undergoing inevitable, continuous alterations during […] life […]. The MHA considers as the main damaging factors of the plasma membrane of cells the following two processes. (a) The continuous production of OH free radicals […] In this sense, MHA follows the concepts of the FRTA. This is justified on the one hand by the widely proven damaging effects of these free radicals on practically [every] class of the biological macromolecules. It is a fact, on the other hand, that the author of MHA has also demonstrated that the oxyradicals cannot be considered only as damaging factors, since their formation is an essential attribute of the living state [39, 40, 45]. Nevertheless, from the point of view of experimental gerontology, the damaging effect of these radicals remains anyway of essential importance. Analyses of the quantitative aspects of the free radical-induced molecular damage have revealed that the cell plasma membrane is the weakest point of the cellular structure […] plasma membranes are really the most critically sensitive structures in […] living cells. (b) In addition to the free radical-induced damage, the cell plasma membrane is exposed to another damaging factor called residual heat production [51], which is negligible or absent in other intracellular membranous components, like the mitochondrial or the endoplasmic reticulum membranes. […] Because the polarity of the cell membranes is discharged very quickly (in about 1–2 ms during each action potential), and also rather frequently (in certain neurons up to 50–100 times per second), the cell membrane is exposed all the time to a considerable local heating. Due to the extremely short time of its development, about 10% of the initial heat cannot be dissipated by the environment, called residual heat remaining in the membrane [51]. As a consequence of this, in spite of the fully recovered membrane potential, one has to assume some persisting alterations of the membrane structure after each action potential. This fact is of great importance; however, most of the experimental gerontologists are not even aware of it. […] This type of membrane alterations can be considered as true ‘wear and tear’ phenomena which certainly contribute to the velocity of the plasma membrane deterioration.”

“[A]ge-dependent water loss starts practically during the embryonic development of mammals, i.e. it is an intrinsic part of the developmental and maturation processes. The whole ontogenesis can be considered as a procedure during which the highly hydrated state of embryos (90–92% water at the beginning), in newborns and young individuals is gradually transformed into a more and more dehydrated one (40–50% water in old body). It is obviously necessary to reach a sufficient increase in the dry mass content in all tissues, organs, etc. in order to achieve a sufficient physical strength of the body to support the load, to perform the requested work, etc. Therefore, this process is useful and absolutely necessary. However, because of the ever ongoing character of this process, it becomes rate limiting first for further growth, and self-destroying during the later phases of life. These considerations imply that the driving ‘force’ of both maturation and aging is the same, i.e. there is no special aging process, just the dehydration of the body beyond the optimum maturation state [causing] a progressive, destructive, inherent and universal rate limitation for […] physiological performance”

“The oncogenes were discovered first in tumor tissues during the early 1980s, and were thought to be of viral origin, but were found very soon in all eukaryotes from yeast to human cells. They have various viral (v-) and cellular (c-) families, the number of which is above 40. The c-oncogenes are also termed proto-oncogenes; they code for proteins being strictly involved in mitotic regulation. Nowadays, they are regarded as playing vital roles in the normal control of mitosis and cell differentiation depending upon cell types and the actual state of maturation. In addition to the oncogenes, so-called antioncogenes (or oncosuppressor genes) have also been identified. These are genes the products of which are important in suppression of cell division and causing differentiation, senescence or apoptosis of cells. […] from the point of view of the MHA, it seems to be extremely important that many of the products of the so far explored oncogenes and antioncogenes are localized in the cell plasma membrane.”

“[The] strong conflict between AMA and A4M [the American Academy of Anti-Aging Medicine] prompted me as the Editor-in-Chief of the journal Archives of Gerontology and Geriatrics to write an Editorial [104] proposing a consensus, according to which aging should generally be considered as a natural AGHD  [Adult Growth Hormone Deficiency] syndrome treatable by hrGH [recombinant human GH].”

I included the quote in the paragraph above for one reason only: To remind people reading along that I don’t always trust the judgment of the authors I read, and that I’m sometimes quite skeptical about what they have to say. Here’s another view on that matter: “There’s little evidence to suggest human growth hormone can help otherwise healthy adults regain youth and vitality. In fact, experts recommend against using HGH to treat aging or age-related conditions.” (link). I don’t take people like ‘the mayo clinic staff’ to be undisputed authorities which I should never question either – people in similar positions have taken medical decisions which I consider to be questionable before, as a specific example I might refer to the comments I made while reading Kolonin et al. about the website of Johns Hopkins University and its coverage of reconstructive breast surgery (see this link). But the situation here is different, as the mayo guys obviously aren’t the ones who have a lot of explaining and justification to do here. I think the author of that chapter would find it very hard to obtain consensus even among the contributors to the publication in question, as more than one of them have in their coverage made clear that they think he’s wrong (not directly, but certainly indirectly).

“Aging is a complex process of progressive decline in overall physiological functions, resulting in a diminished capacity to withstand internal and external damage and an increased susceptibility to diseases and risk of death. The process of aging is controlled by many factors including genetic and environmental influences, and many theories have been proposed to explain the phenomenon of aging. Recent studies have implicated mitochondrial dysfunction and oxidative stress in the aging process and in the pathogenesis of age-associated diseases. It is hypothesized that damage to mitochondria including mitochondrial DNA (mtDNA) caused by the production of reactive oxygen species (ROS) during cellular respiration is one of the drivers of aging. These theories (the free radical theory and the mitochondrial vicious cycle theory of aging) provide an important conceptual framework and have led to interventions aimed at decreasing the level of ROS for health benefits. However, there is an increasing body of evidence challenging these theories, which has led to the emergence of new hypotheses on how age-associated mitochondrial dysfunction may lead to aging”

“ROS are produced as by-products of aerobic metabolism in cells, and mitochondria are the major sites of ROS generation. In humans, more than 90% of oxygen is consumed by mitochondria, and 1–5% of the consumed oxygen is transformed into superoxide because of electron leakage of the electron transport chain (ETC). Superoxide generated in mitochondria is then converted to hydrogen peroxide […] Depending on their types and cellular levels, ROS can act as either crucial biological or deleterious agents. […] under pathophysiological conditions, overproduction of ROS can interact with DNA, RNA, lipids and proteins, leading to destruction or irreversible alteration of the functions of the targeted molecules. Consequently, ROS are identified as major contributors of cellular damage. ROS-induced DNA damage […] can result in alterations in transcription and signal transduction, replication errors, and genomic instability […] Accumulation of ROS and oxidative damage is one of the cellular hallmarks of aging. […] In addition to being a main source of ROS, mitochondria are the prime targets of oxidative damage, which in turn reduces mitochondrial efficiency and leads to the generation of more ROS in a vicious self-destructive cycle. As an extension of the free radical theory, the mitochondrial vicious cycle theory of aging emphasizes and refines the central role of mitochondria in the aging process. […] A wide spectrum of alterations in mtDNA including point mutations, deletions and duplications have been found to accumulate in a variety of tissues during aging [54]. The accumulation of oxidative stress-induced mtDNA mutations has been shown to correlate with a progressive decline in mitochondrial function and contribute to age-related physiological decline [38, 55]. In addition to its proximity to the source of oxidants, mtDNA lacks protection by histones and the DNA repair capacity in mitochondria is relatively low [38]. Moreover, the mitochondrial genome lacks noncoding introns, which increases the likelihood of damage to a coding region and consequently affects the integrity of encoded RNA and proteins. These characteristics make mtDNA more vulnerable to oxidative damage than nuclear DNA in mammalian cells [54]. More importantly, damage to mtDNA can be propagated as mitochondria and cells divide, leading to the amplification of the physiological consequences of the damage.”

“A large body of evidence suggests a link between aging and increased ROS production, accumulated oxidative damages and declined mitochondrial function. Whether and how these changes contribute to aging is an area of interest in aging research. […] considerable progress has been made in our understanding of the role of oxidative stress and mitochondrial dysfunction in aging and age-associated diseases. However, a number of recent studies have challenged the free radical and mitochondrial theories of aging, which postulate a detrimental and toxic role of ROS and dysfunctional mitochondria in aging. Some disconnections exist between oxidative stress and longevity. Long-lived naked mole rats are found to have higher levels of oxidative damage than the short-lived mice [255]. Caloric/glucose restriction extends life span in yeast and Caenorhabditis elegans, but induces mitochondrial respiration and increases oxidative stress [256–259]. Overexpression of major antioxidant enzymes including Cu/ZnSOD, catalase, or combinations of either Cu/ZnSOD and catalase or Cu/ZnSOD and MnSOD does not extend life span in mice [260]. Furthermore, studies have found that mtDNA mutations are generated mainly by replication errors rather than by accumulated oxidative damage [55]. […] 261] . Collectively, these findings suggest that ROS production and mitochondrial dysfunction are not the universal cause of aging in all species. ROS have recently emerged as signaling molecules which facilitate adaptation to stress and maintain cellular homeostasis [262]. The gradual ROS response theory of aging postulates that ROS are not the cause of aging, but rather represent a stress signal in response to age-dependent damage [263]. This theory suggests that ROS can be beneficial by serving as molecular signals to stimulate endogenous defense mechanisms and promote stress resistance and longevity, although high levels of ROS have a deleterious role in aging and late-onset diseases. There is increasing evidence indicating that mitochondrial ROS can induce beneficial responses to cellular stresses during aging.”

“We insisted in the previous sections of this chapter on the crucial role of cell-matrix interactions for correct tissue and organ function. These interactions are mediated by receptors, integrins, the elastin receptor and several others. Messages delivered to cells by these receptors, originating from the ECM [extracellular matrix] are then further transmitted and targeted to intracellular and intranuclear organelles where the message has to be interpreted […] Cells can also send messages to constituents of the surrounding matrix to modify its intermolecular interactions and functions. […] Besides […] direct cell-matrix communication, a number of other messages can and do reach the cells to modulate their behavior. Such messages, as for instance hormones, cytokines, growth factors and many others, communicate with the cells by receptors on the cell membrane, intracellular and intranuclear. […] several receptor-mediated functions decline with age because [of] either […] the loss of receptors or their uncoupling from their specific signalling pathways. […] one of the hallmarks of aging is the decline of a number of physiological functions in response to a variety of stimuli. Among these are the best known and most studied endocrine functions underlying menopause and andropause. Another group of vital physiological functions concern the regulation of cardiovascular functions, intensely studied over decades by a number of investigators […] A third field of intense investigations concerns the nervous system […] Most of these functions are regulated by receptor ligand interactions, followed by the transmission of the message conveyed by the ligand, a hormone for instance, to the interior of the cell where it has to elicit the reaction specified by the nature of the ligand. A complicating factor for such studies is the fact that most receptor-mediated processes proceed by a series of successive steps, all mediated by ‘second messengers’ or other comparable intermediary reactions before reaching the target of the message […] This stepwise transmission of the specific message between the receptor and the corresponding cell machinery complicates the task for the elucidation of the precise mechanism of the age-dependent loss of function.”

September 14, 2014 Posted by | Biology, Books, Medicine, meta | Leave a comment

The Endocrine System at a Glance (I)

3152(Smbc – click to view full size).

Compare with the book:

Adrenal steroid synthesis

(There are other diagrams in the book which look quite a bit more like the SMBC one than does the table above, but none of them deal with 17α-hydroxylase, progesterone, androstenedione and their friends and acquaintances…).

No, I didn’t get all of the stuff covered in this book, but this would probably also be a bit much to expect. There were however more than a few principles presented here which I’d sort of come across elsewhere which I now have a much better understanding of than I used to do. Many of the things covered (but far from all of them) were things I’d read about before, e.g. in McPhee et al. and Sperling et al. But there was also some new stuff in there.

The book has ~118 pages, plus some pages with reading comprehension questions in the back, but the page count is a very deceptive metric if you want to estimate the amount of work required to get through the book; I may be wrong, but I think most people will find it very hard to read even close to 10 pages per hour, certainly ‘in the long run’ (after the first couple of hours) and certainly if they want to understand the stuff and do not have a medical background. You probably need to be willing to look stuff up every now and then to follow what’s going on. I basically read the book two to four pages at a time, with lots of short breaks. Actually I’m not sure this is a good book to read at all if you do not have some medical knowledge – as they state in the introduction: “The book is aimed at undergraduate medical students […] it should also be a useful source of information for clinical medical students and junior doctors”.

The book belongs in the same series as the nutrition text by Barasi I read a while back (another book covering topics which were also looked at in the book, e.g. stuff like energy homeostasis), and it suffers from the same main problem I had with that publication; there’s not a single source provided in the publication. Actually that’s not entirely true as I think one of the graphs were described in the text and so you were told where the numbers came from in that case; but almost all numbers provided are provided without any indication of where they come from, and you have no way to figure out what kind of research they are based on. “Diabetics are three times more likely to have a stroke and 15 times more likely to undergo lower limb amputation than non-diabetic subjects”, they write in the text, yet the latter number is likely to be an underestimate as: “The relative risk of an individual with diabetes undergoing a lower extremity amputation was 20.3 in 2004 and 21.2 in 2008, compared with that of individuals without diabetes.” (link). Given that some of the other numbers included in the book clearly have not been updated since the previous editions – there’s a particularly hilarious forecast of obesity in the UK which provides a linear forecast (using OLS) of what’s likely to happen (?) to the obesity rate from the year 1998 and forward, based on the numbers observed during the previous two decades… (the third edition of the book which I read was published in 2011) – I find it highly unlikely that the mismatch between the relative risk numbers is the result of outcome improvements observed since 2008. The authors are incidentally British, which is why I refer to the specific ~20 RR estimate – I’m assuming they’re relying on UK/British numbers when providing their estimates, even though even that is actually unclear, so relying on such numbers seemed the most fair way to evaluate the accuracy of the estimate. The discrepancy in question is not one of a kind – for example elsewhere they write that: “Macrovascular complications are the major cause of death in people with Type 2 diabetes, accounting for 50% of deaths in this group” – which again seems to be a significant underestimate: “Subjects with both type 1 and type 2 diabetes are at increased risk of developing cardiovascular disease, with approximately three-quarters of patients with diabetes ultimately dying from vascular causes” and: Mortality from CVD accounts for more than 60% of deaths in patients with type 2 diabetes mellitus”. (Quotes from Betteridge and Nicholls’ Managing Cardiovascular Complications in Diabetesblog link here. 50% is way too low).

I assume most of the numbers included in the book are reasonably in line with the evidence, and there aren’t many numbers to begin with as the book deals almost exclusively with key principles etc., but I do find it annoying and slightly troubling that the numbers seem to be a little bit off in areas where I actually know something about those things they talk about, and regardless of whether they’re wrong or not you should provide a damn source anyway. I don’t think it would be that hard to add a few sources without making drastic changes to the format of the book, as one could just add a number in the text and a source in the back. I should make clear that to the extent the estimates provided in the publication are ‘wrong’ I believe them to be wrong on account of being based on old data; I don’t think any inaccuracies in the book are due to the authors ‘not knowing what they’re talking about’.

As might be inferred from the screenshot above the book is very technical, and so it’s a bit difficult to blog. There are many  chapters where most of the coverage consists of complicated diagrams as well as verbal coverage of the same stuff dealt with in those diagrams, and little else. I have tried in my coverage below to mostly cover stuff from the book which I thought might at least be reasonably easy to understand for people reading along here.

“Endocrinology is the study of endocrine hormones and of the organs involved in endocrine hormone release. Classically, hormones have been described as chemical messengers, released and having their actions at distant sites. It is now clear, however, that there is a close relationship between hormones and other factors such as neurotransmitters and growth factors acting in a paracrine or autocrine fashion. Hormones are essential for the maintenance of normal physiological function and hormonal disorders occur at all stages of human life. Clinical endocrinologists thus look after patients of all ages and with a very wide range of disorders”

“Hormones are chemical messengers. They may be classified several ways […]: 1 Autocrine: acting on the cells that synthesized them […] 2 Paracrine: acting on neighbouring cells. An example is insulin, secreted by pancreatic β cells and affecting secretion of glucagon by pancreatic α cells. 3 Endocrine: acting on cells or organs to which they are carried in the bloodstream or through another aqueous ducting system, such as lymph. Examples include insulin, estradiol and cortisol. 4 Neuroendocrine: this is really paracrine or endocrine, except that the hormones are synthesized in a nerve cell (neurone) which releases the hormone adjacent to the target cell (paracrine), or releases it into the bloodstream, which carries it to the target cell […] 5 Neural: this is neurotransmission, when a chemical is released by one neurone and acts on an adjacent neurone […]. These chemicals are termed neurotransmitters. […] 6 Pheromonal transmission is the release of volatile hormones, called pheromones, into the atmosphere, where they are transmitted to another individual and are recognized as an olfactory signal.”

“The movement of chemicals between cells and organs is usually tightly controlled. Diffusion is the movement of molecules in a fluid phase, in random thermal (Brownian) motion […] Facilitated transport is the transport of chemicals across membranes by carrier proteins. The process does not require energy and cannot, therefore, transport chemicals against a concentration gradient. […] Active transport uses energy in the form of adenosine triphosphate (ATP) or other metabolic fuels. Therefore chemicals can be transported across the membrane against a concentration gradient […] Ion channels mediate active transport, and consist of proteins containing charged amino acids that may form activation and inactivation ‘gates’. Ion channels may be activated by receptors, or by voltage changes through the cell membrane. Channels of the ion Ca2+ can be activated by these two methods. Osmosis is the passive movement of water through a semipermeable membrane, from a compartment of low solute concentration to one which has a greater concentration of the solute.”

“Hormones interact with target cells through a primary interaction with receptors which recognize the hormones selectively. There are several different receptor systems, which vary in mechanism and timing […] Receptor antagonism is an important aspect of endocrinology and drug use generally […] antagonists play a large part in the treatment of endocrine disease. The molecule which binds to the receptor and elicits the normal cellular response is termed the agonist. The ligand which binds, but elicits no response, is the antagonist. Antagonists act at the membrane in different ways. For example the β-receptor blocker propranolol competes with epinephrine at its binding site. The anticonvulsant phenytoin blocks ion channels.”

“Living systems possess their own internal environment, which has to survive within an external environment. […] Internal control is achieved through integration of the different systems: neural, biochemical and physical. In all cases, the fundamental components of these systems are: (i) signals; (ii) transducers; (iii) sensors; and (iv) responders. […] Integration of endocrine systems is achieved through a complex interplay of regulatory feedback mechanisms operated through both hormonal and neural communication networks. The most important mechanisms are those commonly called feedback, whereby systems limit each other’s activity around a preset oscillator. […] In endocrinology, the brain–pituitary–target gland axes provide examples of feedback mechanisms in action […]. For virtually every anterior pituitary hormone, a corresponding hypothalamic releasing hormone has been discovered, and in some cases a corresponding inhibitory hypothalamic hormone has been found […]. Feedback systems may involve more than two hormones […] Understanding basic feedback mechanisms is vital in clinical endocrinology where it forms the basis of diagnostic testing. […] Characteristically, endocrine disorders disrupt normal feedback mechanisms and this feature is exploited in the interpretation of a number of endocrine function tests. Furthermore, certain hormones rise in response to stressful stimuli and this too can be utilized for diagnostic purposes. […] Most hormones: • Are subject to diurnal or ultradian rhythms • Are secreted in a pulsatile fashion • Are controlled by feedback from target organs (usually negative) • Develop autonomous secretion in pathological states […] As a general rule: • If the clinical suspicion is of hormone excess then suppression tests are used • If the clinical suspicion is of hormone deficiency then stimulation tests are used”

“Many endocrine conditions have an autoimmune aetiology and patients frequently exhibit antibodies to multiple endocrine organs and have evidence of associated autoimmune disease […] Autoimmunity may be defined as an attack by the host’s immune system on the host’s own tissues. These attacks may be transient immune reactions to infection, for example, which resolve spontaneously. They may, however, become chronic, with pathological consequences. Endocrine autoimmunity often involves an immune attack on specific endocrine glands, for example Addison’s disease, Graves’ disease, Hashimoto’s thyroiditis and insulin-dependent diabetes mellitus, where the gland is damaged or destroyed altogether [‘type 1 diabetes mellitus’ is much better than ‘insulin-dependent diabetes mellitus’ [IDDM] in this context – I dislike the unfortunate naming convention applied, given that many type 2 diabetics, as mentioned before here on this blog, will require insulin-injections over time. I’ve previously seen an estimate which I reported here on the blog which indicated that half of type 2 diabetics will need insulin within 6 years of diagnosis, but the original source for that quote has been taken down and I didn’t write down who the authors were so I can’t find the original estimate. I don’t really trust wikipedia on these things, but the article on insulin includes the (likewise unsourced) observation that: “Over 40% of those with Type 2 diabetes require insulin as part of their diabetes management plan”. As something like ~85% of all diabetics are type 2 diabetics, type 2’s make up a substantial majority of all IDDM cases if that estimate can be trusted. Regardless of precisely how many type 2 diabetics are treated with insulin it’s a very substantial number of patients, and the relevant distinction here, when thinking about autoimmunity-mediated organ damage, is between type 1 and type 2, though that distinction is admittedly also not perfect. This post has more about specific subtypes of diabetes, as does this commentas the remarks included in the latter link in particular illustrates, this stuff is complicated and none of the applied diagnostic conventions really distinguish 100 percent between auto-immune and not-autoimmune, though the type 1/2 distinction comes much closer than does the IDDM/NIDDM distinction, which is one of the reasons why the latter distinction is these years rarely used in lieu of the type 1/2 categorization convention]. These are examples of mainly organ-specific autoimmune diseases […]. In systemic autoimmune disease, on the other hand, the immune system attacks several tissues that may be anatomically distant from each other. Examples of systemic autoimmune disease include rheumatoid arthritis, scleroderma and systemic lupus erythematosus (SLE). There may be both organ-specific and systemic components in most, if not all, autoimmune diseases.”

September 10, 2014 Posted by | Books, Diabetes, Immunology, Medicine | Leave a comment


i. “Not being known doesn’t stop the truth from being true.” (Richard Bach)

ii. “Argue for your limitations, and sure enough, they’re yours.” (-ll-)

iii. “The best way to pay for a lovely moment is to enjoy it.” (-ll-)

iv. “Science kills credulity and superstition, but to the well-balanced mind it enhances the feeling of wonder, of veneration, and of kinship which we feel in the presence of the miraculous universe.” (John Burroughs)

v. “For certainly it is excellent discipline for an author to feel that he must say all he has to say in the fewest possible words, or his reader is sure to skip them; and in the plainest possible words, or his reader will certainly misunderstand them.” (John Ruskin)

vi. “A little group of wise hearts is better than a wilderness full of fools.” (-ll-)

vii. “One man’s remorse is another man’s reminiscence.” (Ogden Nash)

viii. “I believe that people believe what they believe they believe.” (-ll-)

ix. “That man is not truly brave who is afraid either to seem or to be, when it suits him, a coward.” (Edgar Allan Poe)

x. “A few Cobras in your home will soon clear it of Rats and Mice. Of course, you will still have the Cobras.” (Will Cuppy)

xi. “The Age of Reptiles ended because it had gone on long enough and it was all a mistake in the first place. A better day was dawning at the close of the Mesozoic Era. There were some little warm-blooded animals around which had been stealing and eating the eggs of the Dinosaurs, and they were gradually learning to steal other things, too. Civilization was just around the corner.” (-ll-)

xii. “Aristotle maintains that the neck of the Lion is composed of a single bone. Aristotle knew nothing at all about Lions, a circumstance which did not prevent him from writing a good deal on the subject. […] Aristotle was famous for knowing everything. He taught that the brain exists merely to cool the blood and is not involved in the process of thinking. This is true only of certain persons. […] Pliny the Elder described a Whale called “Balaena or Whirlpool, which is so long and broad as to take up more in length and breadth than two acres of ground.” This brings up again the old question: Are the classics doomed? Our ancestors believed that four years of this sort of information would inevitably produce a President, or at least a Cabinet Member. It didn’t seem to work out that way.” (-ll-)

xiii. “The Egyptians of the First Dynasty were already civilized in most respects. They had hieroglyphics, metal weapons for killing foreigners, numerous government officials, death, and taxes.” (-ll-)

xiv. “Egyptologists say they have no idea what Khufu was doing when he was not building pyramids, since he left no inscriptions describing his daily activities, and they would give a good deal to know. Then they say he had six wives and a harem full of concubines. They do not seem to make the connection, but you get it and I get it. We do not need any hieroglyphics to inform us that Khufu dropped around occasionally to see how things were getting along and to tell the ladies how many cubic yards of limestone he had laid that afternoon.” (-ll-)

xv. “They [the Pilgrim Fathers] believed in freedom of thought for themselves and for all other people who believed exactly as they did.” (-ll-)

xvi. “The best good that you can possibly achieve is not good enough if you have to strain yourself all the time to reach it. A thing is only worth doing, and doing again and again, if you can do it rather easily, and get some joy out of it.” (Don Marquis)

xvii. “The dearest ambition of a slave is not liberty but to have a slave of his own.” (Richard Francis Burton)

xviii. “The more I study religions the more I am convinced that man never worshipped anything but himself.” (-ll-)

xix. “He who sees only what is before his eyes sees the worst part of every view.” (Leslie Stephen)

xx. “History is indeed little more than the register of crimes, follies, and misfortunes of mankind.” (Edward Gibbon)

September 7, 2014 Posted by | Quotes/aphorisms | 2 Comments

Metacognition – Cognitive and Social Dimensions (III)

This will be my last post about the book.

Below I have added some observations from the last chapters of the book and a few comments.

“A critical dimension of social judgment is […] that reality, desired beliefs, and rules of justification [e.g. norms] combine to shape people’s reactions. […] One key feature affecting the normative level of adequacy, however, is that perceivers are notoriously ill-equipped when it comes to scrutinizing their own cognitive processes (for reviews, see Metcalfe & Shimamura, 1994; Nelson, 1992). In other words, although people are expected to call upon their metacognitive abilities to assess the quality of their knowledge about others, they are not very good at identifying the various ingredients comprising their judgment nor, for that matter, are they good at pinpointing the factors which led them to form a specific impression […] all current perspectives on person perception underline the fact that perceivers are extremely quick at categorizing others on the basis of a minimal amount of information. Categories provide people with a host of information about a specific target. Perceivers are thus likely to know quite a bit about any given person simply because of his or her category membership. The critical question then becomes to determine how exactly people are to interpret the resulting impression. Are perceivers in a position to disentangle the individuating from the category-based pieces of information? The answer seems to be that they are not. […] The message of [Nisbett & Wilson’s] provocative review of the literature is that people have little or no direct access to the processes that lead to particular contents of the mind. As a result, naive theories play a major role in people’s accounts of why they think what they think or why they do what they do.”

The idea behind this naive theories view seems to be that we often don’t really know why we think the way we do, and in the absence of actual knowledge about the true factors involved when we’re making judgments about others we make up our own theories for why we think the things we do. One way they’ve researched such aspects of cognitive processing has been to expose people to information about a target which included a bogus judgment mediator (some participants were told that aside from what was obviously supposed to be relevant information about the target, they had also received subliminal information about the target which they would not be able to be consciously aware of…) and asking the judges to make judgments about the target; it turns out that people tend to correct for supposed biases in their thought processes even when these really do not exist. The study they talked about in that chapter found that people exposed to the ‘subliminal information’ were more cautious about making judgments about the target because they thought they might have been manipulated, meaning that they ended up discounting relevant knowledge in order to correct for what really were non-existing inputs to the social judgment. Other approaches have indicated by exposing people to different types of information that people tend to believe they’re more justified in making judgments about others when they have more individuating information about the target. A related finding is this:

“perceivers may […] be very sensitive to the mode of acquisition of the information. Specifically, people may have more confidence in the evidence that they themselves gathered than in information they passively received. […] [Some] findings lend credit to the idea that perceivers who control the acquisition of the information express more confident and polarized ratings. They remain silent, however, as far as the underlying process is concerned.”

Here’s some more stuff about the ‘naive theories’ and related stuff on bias correction mechanisms from a later chapter in the book:

“What metacognitive processes do people use to ensure that their assessments of and feelings toward targets are “accurate” or “legitimate?” In brief, we believe that corrections (i.e. attempts at removing bias from assessments of targets) are often the result of people consulting their naive theories (beliefs) of how potentially biasing factors have influenced (or might yet influence) their views of the target. […] Identification of possible bias is guided, in part, by people’s beliefs or theories about how factors in the judgment setting (factors both internal and external to the perceiver) influence perceptions of targets. Some naive theories are likely to be stored in memory and are then accessed when salient features of the biasing factor are present in the judgment setting. At times, however, naive theories of bias are likely to be generated on-line as biasing factors are encountered in a given situation. Of course, stored theories of bias might also be amended or otherwise changed by experience of the specific biasing factor in the given judgment setting. These perceptions of bias are “naive theories” in that a given perceiver is not likely to have direct access to the effect of the factor(s) on his or her judgments, nor is he or she likely to possess the evidence that would be necessary to know the influence of the factor on the perceptions of others […]. Thus, the person’s naive perception or theory of the effect of the factor is the person’s best estimate of the effect of the factor, regardless of whether that perception is in any way accurate or not (in fact, these theories will often be incorrect in either direction or magnitude).”

“If the perceiver believes that a bias is operating, and if the perceiver is both motivated and able to attempt corrections, then the perceiver engages in a correction guided by the theory of bias. Many different factors could influence motivation or ability to engage in corrections. For instance, some people are more motivated to engage in thoughtful activities in general (e.g. they are high in need for cognition, Cacioppo & Petty, 1982) or are more motivated to avoid “incorrect” judgments in particular (i.e. they are high in fear of invalidity; Thompson, Naccarato, & Parker, 1989). Of course, situational variations in motivation to put effort into a task or to avoid inaccuracy could also influence motivation to engage in corrections. It is also possible for people to identify a bias, but to be unmotivated to correct for it because the bias is viewed as legitimate or even necessary […]. Similarly, either situational or personal factors could distract perceivers or otherwise induce a cognitive load that would decrease ability for theory-based corrections […]. Interestingly, if people are highly motivated to correct and are attempting to do so, but are unable to accomplish this because of the imposition of a cognitive load, bias might even be exaggerated in some circumstances. That is, when people are actively attempting to suppress a thought under cognitive load, this thought can become more accessible than when the thought is not being suppressed […], and this can lead to the thought having a greater contaminating effect on judgment […]. In addition to cognitive load, qualities of the uncorrected perceptions of the target could also influence ability to correct”

“We assume that corrective processes ensue when people become aware of a potential bias (and are motivated and able to engage in corrections).[3] People can become aware of a potential bias before, during, or after judging (or even encountering) the target. Accordingly, corrections for bias need not occur only after reacting to the target, but people might also anticipate a bias and attempt to avoid it by changing how information about the target is gathered or scrutinized. We regard such attempts at avoidance of bias as “preemptive corrections” […]. Especially before people have a great deal of experience with attempts to correct for a given biasing factor, such attempts would likely depend on some level of conscious awareness of the potential bias. However, with more experience of the factor and of the correction process, less conscious awareness of the bias might be sufficient for instigating the correction process (and the correction process itself might become less effortful, that is, to a certain extent, routinized […]). In fact, even in those cases where rather conscious awareness of the biasing factor occurs, we would not generally expect the whole of the correction process to be consciously reportable (consistent with Nisbett & Wilson, 1977). Rather, even if people are able to directly report the content of a given theory of bias, those same people might be unable to report which theory(ies) were used most in a correction, for example (i.e. even if content of a theory of bias is “explicit,” there can still be “implicit” effects of the theory […] corrections are driven by the perceptions of the bias in that judgment setting. That is, corrections are aimed at removing perceived rather than actual bias. Although perceived and actual bias might coincide in certain circumstances, the two elements are conceptually distinct from one another. That is, a person might believe that a particular bias exists (and might attempt to remove that perceived bias) when no bias exists or even when a bias in the opposite direction is objectively present. […] A variety of factors might determine the nature of theories of bias and the likelihood that those theories guide corrective attempts. […] In many settings, the theory of bias that is used is probably some combination of a theory stored in memory along with adjustments to the theory based on the perceiver’s subjective experience of the context and target to be judged.”

“some theory-based corrections are likely to be more cognitively taxing and more thorough than others. In related areas (e.g. attitude change), assessments based on high levels of effortful, integrative elaboration of the qualities of targets lead those assessments of the target to persist over time, resist future attempts at change, and predict behavior better than less elaborated assessments […]. We believe that the same principles apply to corrections as well. If a corrective attempt involves effortful consideration of the qualities of the target and corrections of those considerations, such a correction is more likely to persist over time, resist change, and predict future judgments and behavior than a correction that is not based on a thorough scrutiny of target qualities. A variety of factors might help to determine the extent to which corrections involve elaboration of target-relevant information (e.g. the extent of target-relevant knowledge the person possesses, the importance to the person of arriving at an unbiased assessment of the target, time pressures for judgment, etc.).”

“It is not uncommon to avoid stimuli that we think will elicit negative emotions […] As noted by Wilson and Brekke (1994), people are often at risk of mental contamination, defined as “the process whereby a person has an unwanted judgment, emotion, or behavior because of mental processing that is unconscious or uncontrollable” […]. Wilson and Brekke argued that people’s susceptibility to mental contamination is in part a function of the accuracy of lay theories about how the mind operates. The strategies people use to avoid contamination – such as covering their eyes or changing the [TV] channel – are largely a function of their theories about how their attitudes, emotions, and beliefs change.”

“If people truly want to avoid unwanted belief change, they are better off using earlier mental strategies such as exposure control and mental preparation [rather than later strategies such as resistance and remediation (roughly: belief adjustment/correction which takes place after exposure)]. […] people might be better off if they recognized the limits of resistance, remediation, and behavior control and engaged in some judicious exposure control and mental preparation. […] The belief that other people would be more influenced by mental contaminants than oneself has been found in a variety of other studies […]. One reason for this difference, we suggest, is that people believe that they have a greater ability to resist or remediate the effects of a contaminant than other people do.”

“Obviously, people can make judgments and, obviously, people can provide rationales for their judgments, but what is the relation between the two? […] Do people consciously consider various features of the judgment situation, weigh the positive and negative features of the context and target. develop a conscious understanding of the effects of these features, and then make judgments based upon that understanding? Or do people arrive at judgments for reasons of which they may not be entirely aware, and only later attempt to piece together why they might have made the judgments they did? Each of these positions has its proponents in current social judgment theorizing. […] [We conclude from] our own research on judgmental correction processes [that] people’s conscious theories of social judgment are generally not causal, a priori, or accurate. Rather, these theories are descriptions of what people think they observed themselves doing while forming a judgment, and these theories influence judgments primarily when people are sensitized to (e.g. warned about) a particularly salient bias.”

September 7, 2014 Posted by | Books, Psychology | Leave a comment

Aging – Facts and Theories (Interdisciplinary Topics in gerontology, Vol. 39) (I)

I said some not particularly nice things about this book in my goodreads review. While writing this post I was actually starting to seriously question my rating and asking myself whether I should make some adjustments to the review as well. Given the amount of blogging-worthy stuff included in the first part of the book, in combination with the fact that I’ve still yet to cover a couple of chapters I liked, I thought it might be unfair of me to give this publication one star, all things considered. But I’m not sure if I’ll change my rating. This part of my review stands: “if I don’t give this publication one star it’s really hard for me to imagine when I’d ever do that in the context of an academic publication.” The baseline requirements are set at a high level when you’re dealing with publications like these, and the rating should reflect that.

Below I have added some stuff from the first chapters of the book, and a few comments of my own.

“There is now strong evidence that telomere length is reduced during the serial subculture of human fibroblasts [11–13]. At some point before or during the formation of these cells, the enzyme telomerase, which maintains telomere length, is lost. It has therefore been suggested that commitment is in fact the loss of telomerase [14]. From this point, the cells can divide a given number of times, until the loss of DNA from the ends of chromosomes results in the cessation of cell division. The commitment theory proposes that this number of divisions, the parameter M, is constant, or close to constant.”

I believe some aspects of this line of work is well known also by people not working in the field, though I may be mistaken; I assume many people curious about these things have heard about stuff like the Hayflick limit. The book has quite a bit of stuff on research dealing with these things, and below are some critical remarks from the book on this topic:

[Works on human fibroplasts has] led to the concept that the hallmark of cellular aging is the postmitotic cell, the so called senescent cell, which would be one of the causes of the organism’s aging. However, there is no evidence showing that the human organism ages because somatic cells lose the potential to divide. In fact, the assumption goes against all the experiments that have tested the capacity of fibroblasts obtained from old donors to divide. It is obvious that in old age our cells are still capable of proliferating; what takes place is a deregulation in the proliferative response rather than the absence of the capacity to divide [14]. […] Unfortunately, the term cell senescence [has been] generalized and now encompasses anytime a cell enters an irreversible growth arrest due to a variety of causes. Sometimes quite harsh treatments [have been] used to induce growth arrest [in research], which not surprisingly [have induced] DNA damage and arrest of cell division. Since some investigators believe that the terminal postmitotic stage of proliferating cell populations is originated by oxidative stress, hydrogen peroxide is one of those molecules used to induce the ‘senescent phenotype’ […] [A problem is] that in the absence of detailed molecular data on what constitutes normal aging, it is difficult to decide whether the changes [which have been] reported reflect mechanisms underlying normal cellular aging/senescence or rather produce a mimic of cellular aging/senescence by quite different pathways. […] Now that the term cell senescence is well established to designate a postmitotic state, it is difficult to change the usage; however, it should be used only operationally without any connection with aging of the organism.”

“One modification [of DNA methylation during replicative aging] has particularly drawn the attention of gerontologists; it concerned the shortening of chromosome ends, the telomeres. One can still see claims in the literature that this is one of the main causes of aging. […] Since some immortal cell lines express the enzyme telomerase and develop the capacity to reconstitute telomeres after replication, the link between telomere integrity and replication potential seemed established; investigators were quick to equate telomere shortening with proliferation and aging. The reasoning was based on the syllogism: the number of potential divisions decreases with aging, telomeres are shortened during cell proliferation, hence aging is a function of telomere shortening. The syllogism is unjustified because the major and minor propositions have not been ascertained in comparative gerontology studies.
The erosion of telomeres through division is not universal. In humans, the division in vitro of normal keratinocytes [53, 54] , cardiomyocites [55] and astrocytes [56] is independent of telomere size. Results obtained with normal in vivo and in vitro lymphocytes vary with the laboratory and the methodology. […] In humans, telomere lengths [in one study] did not show a clear correlation with tissue renewal times in vivo […]; moreover, the rate of telomere loss slows throughout the human life span [63]. Fibroblasts from patients with Werner’s syndrome, which have a shorter life span than those of normal age-matched control donors, do not have shorter telomeres than control cells [64]. […] There are other caveats concerning the relationship between telomere shortening and proliferation. Human fibroblasts maintained in the presence of 3% oxygen instead of the usual concentration of 20% have an increased proliferation potential but have shorter telomeres [23]. Radiation-induced senescence-like growth arrest is independent of telomere shortening [68]. […] Telomere biology seems to vary with the species in a way unrelated with aging and with the respective cell proliferation life span in vitro. In non-human primates such as rhesus monkey, Japanese monkey, crab-eating monkey, chimpanzee, and orangutan, TRF [Terminal Restriction Fragment] length was more than double that of human somatic tissues [69]. […] Hamster embryonic fibroblasts express telomerase throughout their replicative life span and the average telomere length does not decrease [73]. Long telomeres, fast cell replicative aging in vitro and short longevity are found in either wild or inbred laboratory mice. […] In summary, it seems that the regulation of the length of telomeres has no implications for aging.”

Note that one needs to be careful about which conclusions to draw here. Hayflick’s finding seems to be correct:

“Most scientists who worked according to the guidelines published by Hayflick could reproduce his results. During the 2nd part of the last century, cell and tissue culture methods became standardized, and culture dishes and media became commercially available. This largely contributed to the interlaboratory standardization of culture methodology and settled to a large extent the controversies. Hayflick’s paradigm, stating that normal nontransformed cells cannot duplicate indefinitely in culture unless transformed into malignant cells, is now largely accepted.”

And I think the point is not that Hayflick’s finding was wrong, but rather that the relevance of this finding to how organisms actually age has been called into question. There’s probably a theoretical limit, but the limit is not particularly relevant to the way organisms age because organisms die before such considerations ever become relevant – this was my reading of what some of the authors thought about these things. Whether or not I’ve misunderstood the authors, at least this seems like a sensible solution to me to the problem of how to interpret the many different findings in this field.

Below I have added some coverage from a chapter on ideas about aging derived from evolutionary biology – again I assume some of these ideas may already be familiar to people reading along because such ideas are not exactly unknown, but that perhaps there’s even so perhaps some new stuff included in that part of the coverage as well:

“for any species, there is a compromise between longevity and the other life history traits. Some species, like elephants, need to live long to thrive or simply survive while for other ones, like mice, a high lifespan is superfluous. […] any theory of aging needs to take into account that longevity, like the other life history traits, does not evolve freely, and any hypothesis positing that longevity of human beings could reach astronomic values simply ignores basic concepts in biology.”

“For most of species, life in the wild is rather short because of the threats encountered by animals, with the consequence that many of them die at a younger age than they would in a protected environment. The basic consequence is that all events occurring beyond some age are of no importance to the species and to most of animals […] in animals, deleterious mutations expressed at young age are selected against, because they impair reproduction. […] By contrast, if the mutations are expressed at old age only, they will not be selected against because their bearers have already transmitted their genes to the next generation […] Mutations only expressed at old age will have no real effect on animals because most of them are already dead at this age […]. If the whole process is repeated for many mutations and generations, one can easily understand that deleterious mutations will accumulate at old age, i.e. animals will be loaded with many health problems if they reach old age. This theory [is] called the theory of the accumulation of mutations at old age […] Williams [added to this theory the idea that] some alleles could have favorable effects at young age and deleterious ones at old age […] [the idea being that such] alleles could be selected due to their positive effects at young age, despite the negative effects at old age. […] Williams’ theory is […] called the antagonistic pleiotropy theory of aging. […] for the time being, the evidence in favor of the hypothesis of the antagonistic pleiotropy theory of aging appears to be limited. In addition, because only a very few genes have been found to be associated with aging or longevity, it is difficult to show that mutations accumulate with age, as postulated by the theory of the accumulation of mutations at old age. However, it would be going too far to claim that genes with negative effects at old age (and possibly positive effects at young age) do not exist. For instance, a high growth hormone level is a risk for premature mortality in middle-aged men [50], while a too low level at young age impairs growth. This increased growth hormone level is probably not linked to a severe mutation in a single gene”

“The third classic evolutionary theory of aging, not contradictory with the two previous ones [mentioned in the paragraph above], is the disposable soma theory championed by Kirkwood [23] who argued that the germ line is immortal but soma is disposable, hence the name of the theory. This author emphasized that, because life is short in the wild, it is useless to invest more energy in body maintenance mechanisms (immunity, cellular repair processes, and so on) than needed to provide the expected lifespan in the wild, and thus soma is disposable. Investing more would be a waste and this energy would be better used in reproduction. […] it would be very dogmatic to consider that the whole aging process could be explained by relying on these theories, and the mainstream idea is that some parts of the aging process can be explained by these theories, but that they cannot explain all features of aging.”

“According to the previously described theories, aging is the result of either the accumulation of mutations at old age [21] , negative effects at old age of alleles with positive effects at young age [22], or a compromise between maintenance processes and reproduction [23]. Thus, they have a common theoretical background: genes do not program aging as they program development. Aging occurs because there is an age beyond which the probability to survive in the wild is very low. Beyond this age, no maintenance process can be selected during the course of evolution, simply because most of animals living in the wild are already dead. As no maintenance process has been selected, it is inevitable that the organism will be more and more unable to resist the various threats (e.g. diseases, molecular damage) and to remain as efficient as it was at young age (cognition, physical ability, and so on), and this aging process will be observed if animals live in protected environments. Therefore, it is unneeded to make the hypothesis that genes actively promote aging, simply because aging, contrary to development, can occur without the existence of such genes. If we would nevertheless accept that such genes do exist, it would imply that, as for all the other genes, mutants would also exist: some animals could escape the ‘aging program’ and these ever young animals would be potentially immortal. These mutants would thus only die of external causes, such as accidents, and could reproduce when the other animals are already dead. Due to this selective advantage, these mutants would become very common in a few generations and most of animals would be potentially immortal: such mutants have never been observed […] Aging is not due to genes actively programming aging but […] to the deleterious effects at old age of some genes that have not been selected to display these effects […] If aging is not programmed by genes, the basic consequence is that claims that studies of nematode mutants with extended longevity could allow ‘to think ageing as a disease that can be cured, or at least postponed’ [26] are not warranted. These mutants live longer because for this species increasing longevity is an appropriate strategy when food is scarce […], but it is an illusion to think that a gene governing aging has been discovered […], and there is no reason to be ‘so excited about the prospect of searching for – and finding – the causes of ageing and maybe even the fountain of youth itself’ [26].”

One more observation which although unrelated to the above coverage seemed to me relevant to include in this post as well:

“A remodeling at the cellular level resulting from a different equilibrium between cell compartments, the decline of one leading to overexpression of another, […] contributes to the aging syndrome […] In the skin [for example], the loss of elasticity and increased wrinkling are the result of the rearrangements in the relative proportion of the molecular and cellular constituents. […] There is [also] a causal relationship between changes in vascular compliance and the evolution of the collagen/elastin ratio, and the proportion of endothelial and smooth muscle cells. […] During aging, elastin is degraded and the collagen/elastin ratio increases. As a result, the elastic recoil of the vessel wall decreases […] The results from the investigation of aging of mitotic cells suggest that the evolution of several cell compartments through division constitutes a developmental process where cells are modified with […] consequent repercussions on cell function and cell interactions; this remodeling creates a drift that contributes to aging and senescence of the organism.”

September 6, 2014 Posted by | Biology, Books, Evolutionary biology, Genetics, Medicine | Leave a comment

The True Believer (II)

Here’s my first post about the book, which has a few general remarks and comments – the most important of which is probably that: “It is my opinion that most people would be likely to benefit from reading this book, and it’s a very easy read compared to the books I usually cover on this site.” I’m well aware most people can’t be bothered to start out on books with scary headings like: ‘Mechanisms of hormone action: I Membrane receptors’ (from Greenstein et al.) or ‘Balance equations for spatially explicit models’ (Gurney & Nisbet), and although regular readers of this blog are presumably not ‘most people’ I have no good way of really knowing how different most of you are as you provide very little information about yourselves in the comments. I’ve been asked before here ‘which book(s) I’d recommend’, and such questions are usually difficult for me to answer in part because it’s hard for me to assess how comprehensible many of the books I’m reading really are to people who don’t know what I know. This book is much easier than usual to assess because it doesn’t take any prior knowledge (people do not already have) for granted and can basically be read by anyone who’s not a dyslexic in a few hours – and there are a lot of ideas in there. I’m not in the five-star territory, but if I had been the number of people who might benefit from reading the book would probably have been significantly lower than it is. You can interpret these remarks as a qualified recommendation of the book.

I have added some observations from the second half of the book below, but I think if this stuff seems interesting to you, you should go pick up the book and read all of it.

“A pleasant existence blinds us to the possibilities of drastic change. We cling to what we call our common sense, our practical point of view. Actually, these are but names for an all-absorbing familiarity with things as they are. The tangibility of a pleasant and secure existence is such that it makes other realities, however imminent, seem vague and visionary. Thus it happens that when the times become unhinged, it is the practical people who are caught unaware and are made to look like visionaries who cling to things that do not exist.”

“Those who fail in everyday affairs show a tendency to reach out for the impossible. It is a device to camouflage their shortcomings. For when we fail in attempting the possible, the blame is solely ours; but when we fail in attempting the impossible, we are justified in attributing it to the magnitude of the task. There is less risk in being discredited when trying the impossible than when trying the possible.”

“One of the rules that emerges from a consideration of the factors that promote self-sacrifice is that we are less ready to die for what we have or are than for what we wish to have and to be. It is a perplexing and unpleasant truth that when men already have “something worth fighting for,” they do not feel like fighting. People who live full, worthwhile lives are not usually ready to die for their own interests nor for their country nor for a holy cause.[9] Craving, not having, is the mother of a reckless giving of oneself. […] Dreams, visions and wild hopes are mighty weapons and realistic tools. The practical-mindedness of a true leader consists in recognizing the practical value of these tools.”

“All active mass movements strive […] to interpose a factproof screen between the faithful and the realities of the world. They do this by claiming that the ultimate and absolute truth is already embodied in their doctrine and that there is no truth nor certitude outside it. […] It is startling to realize how much unbelief is necessary to make belief possible. What we know as blind faith is sustained by innumerable unbeliefs. […] It is the true believer’s ability to “shut his eyes and stop his ears” to facts that do not deserve to be either seen or heard which is the source of his unequaled fortitude and constancy. He cannot be frightened by danger nor disheartened by obstacles nor baffled by contradictions because he denies their existence. Strength of faith, as Bergson pointed out, manifests itself not in moving mountains but in not seeing mountains to move.[13] […] Thus the effectiveness of a doctrine should not be judged by its profundity, sublimity or the validity of the truths it embodies, but by how thoroughly it insulates the individual from his self and the world as it is. What Pascal said of an effective religion is true of any effective doctrine: it must be “contrary to nature, to common sense and to pleasure.”[14]”

“The effectiveness of a doctrine does not come from its meaning but from its certitude. No doctrine however profound and sublime will be effective unless it is presented as the embodiment of the one and only truth. It must be the one word from which all things are and all things speak.[15] Crude absurdities, trivial nonsense and sublime truths are equally potent in readying people for self-sacrifice if they are accepted as the sole, eternal truth. It is obvious, therefore, that in order to be effective a doctrine must not be understood, but has rather to be believed in. We can be absolutely certain only about things we do not understand. […] The devout are always urged to seek the absolute truth with their hearts and not their minds. […] If a doctrine is not unintelligible, it has to be vague; and if neither unintelligible nor vague, it has to be unverifiable. One has to get to heaven or the distant future to determine the truth of an effective doctrine. When some part of a doctrine is relatively simple, there is a tendency among the faithful to complicate and obscure it.”

“It goes without saying that the fanatic is convinced that the cause he holds on to is monolithic and eternal — a rock of ages. Still, his sense of security is derived from his passionate attachment and not from the excellence of his cause. The fanatic is not really a stickler to principle. He embraces a cause not primarily because of its justness and holiness but because of his desperate need for something to hold on to. Often, indeed, it is his need for passionate attachment which turns every cause he embraces into a holy cause. The fanatic cannot be weaned away from his cause by an appeal to his reason or moral sense. He fears compromise and cannot be persuaded to qualify the certitude and righteousness of his holy cause. But he finds no difficulty in swinging suddenly and wildly from one holy cause to another. He cannot be convinced but only converted. His passionate attachment is more vital than the quality of the cause to which he is attached. Though they seem to be at opposite poles, fanatics of all kinds are actually crowded together at one end. It is the fanatic and the moderate who are poles apart and never meet.”

“Mass movements can rise and spread without belief in a God, but never without belief in a devil.”

“The act of self-denial seems to confer on us the right to be harsh and merciless toward others. The impression somehow prevails that the true believer, particularly the religious individual, is a humble person. The truth is that the surrendering and humbling of the self breed pride and arrogance. The true believer is apt to see himself as one of the chosen, the salt of the earth […] There is no telling to what extremes of cruelty and ruthlessness a man will go when he is freed from the fears, hesitations, doubts and the vague stirrings of decency that go with individual judgment. When we lose our individual independence in the corporateness of a mass movement, we find a new freedom — freedom to hate, bully, lie, torture, murder and betray without shame and remorse. Herein undoubtedly lies part of the attractiveness of a mass movement.”

“There is hardly an example of a mass movement achieving vast proportions and a durable organization solely by persuasion. […] It was the temporal sword that made Christianity a world religion. Conquest and conversion went hand in hand, the latter often serving as a justification and a tool for the former. […] It also seems that, where a mass movement can either persuade or coerce, it usually chooses the latter. Persuasion is clumsy and its results uncertain. […] Proselytizing is more a passionate search for something not yet found than a desire to bestow upon the world something we already have. It is a search for a final and irrefutable demonstration that our absolute truth is indeed the one and only truth. The proselytizing fanatic strengthens his own faith by converting others. The creed whose legitimacy is most easily challenged is likely to develop the strongest proselytizing impulse.”

“In order to be assimilated into a collective medium a person has to be stripped of his individual distinctness. He has to be deprived of free choice and independent judgment. Many of his natural bents and impulses have to be suppressed or blunted. […] Faith organizes and equips man’s soul for action. To be in possession of the one and only truth and never doubt one’s righteousness; to feel that one is backed by a mysterious power whether it be God, destiny or the law of history; to be convinced that one’s opponents are the incarnation of evil and must be crushed; to exult in self-denial and devotion to duty — these are admirable qualifications for resolute and ruthless action in any field.”

“Self-contempt, however vague, sharpens our eyes for the imperfections of others. We usually strive to reveal in others the blemishes we hide in ourselves.”

“The fact that mass movements as they arise often manifest less individual freedom[18] than the order they supplant, is usually ascribed to the trickery of a power-hungry clique that kidnaps the movement at a critical stage and cheats the masses of the freedom about to dawn. Actually, the only people cheated in the process are the intellectual precursors. They rise against the established order, deride its irrationality and incompetence, denounce its illegitimacy and oppressiveness, and call for freedom of self-expression and self-realization. They take it for granted that the masses who respond to their call and range themselves behind them crave the same things. However, the freedom the masses crave is not freedom of self-expression and self-realization, but freedom from the intolerable burden of an autonomous existence. […] They do not want freedom of conscience, but faith — blind, authoritarian faith. […] The immediate result of a mass movement usually corresponds to what the people want. They are not cheated in the process.”

“Said Oliver Cromwell: “A man never goes so far as when he does not know whither he is going.”[8] When a mass movement is set in motion to free a nation from tyranny, either domestic or foreign, or to resist an aggressor, or to renovate a backward society, there is a natural point of termination once the struggle with the enemy is over or the process of reorganization is nearing completion. On the other hand, when the objective is an ideal society of perfect unity and selflessness – whether it be the City of God, a Communist heaven on earth, or Hitler’s warrior state – the active phase is without an automatic end. […] Where a mass movement preserves for generations the pattern shaped by its active phase (as in the case of the militant church through the Middle Ages), or where by a successive accession of fanatical proselytes its orthodoxy is continually strengthened (as in the case of Islam[1]), the result is an era of stagnation — a dark age.”

“In the eyes of the true believer, people who have no holy cause are without backbone and character — a pushover for men of faith. On the other hand, the true believers of various hues, though they view each other with mortal hatred and are ready to fly at each other’s throats, recognize and respect each other’s strength.”

September 4, 2014 Posted by | Books, Philosophy, Psychology, Religion | Leave a comment

Metacognition – Cognitive and Social Dimensions (II)

Here’s a link to my first post about the book. I decided that it would be too much work to cover the rest of the book in one post (especially as it’s really bothersome to blog this in the first place, because I as mentioned was unable to highlight while I was reading it), so you can expect a third post about the book at some point in the future.

I know there’s been a lot of psychology-related stuff on the blog lately, but I’m currently finishing a math textbook and I’ll most likely finish a book on biological aspects of aging tomorrow, so you can probably expect me to cover some other topics as well in the near future.

Below I have added some quotes and some comments/observations of my own.

“In accordance with the general notion of Festinger’s social comparison theory (1954), we assume that individuals are particularly susceptible to social influence if they are not confident in their own judgments of the situation. In order to reduce their uncertainty, individuals will rely on information that is, intentionally or unintentionally, subtly or obviously, provided by others. Shifting these considerations from attitudes, beliefs, or behaviors to memory, the belief that an event has occurred can be treated like an attitude that a person may hold. Social influence on memory should then be most likely to occur when individuals lack confidence in their memorial beliefs […] memory is susceptible to social influence if individuals are not confident that the absence of a recollection experience implies the non-occurrence of an event, and if individuals are not confident where the presence of a recollection experience comes from. Thus, it is essential to identify variables that increase or decrease individuals’ confidence in their memory experiences, and to test whether social influence on memory is a function of these variables. […] Whether or not the lack of a recollective experience is sufficient to infer the non-occurrence of an event may often depend on whether the event is perceptually or categorically distinct. […] Specifically, if the item is held to be highly memorable, individuals should be very confident that the absence of a recollective experience implies non-occurrence. In this case, individuals are unlikely to rely on information provided by others, and should therefore be minimally susceptible to social influence. Individuals face a different situation, however, if they cannot remember an event and have no reason to believe that the event in question is particularly memorable. In this case, they remain uncertain whether the absence of a recollective experience is due to the non-occurrence of the event or due to a failure of remembering the event. […] we may speculate on general conditions that increase individuals’ confidence in their own attitudes, beliefs, behaviors, or recollective experiences, and consequently decrease the susceptibility to social influence. In our view, individuals’ self-esteem could constitute a prime candidate for such a general impact. Particularly, we speculate that individuals with chronically or temporarily low self-esteem should be less likely to rely on their own subjective experiences and instead rely on subtle cues in the environment. In contrast, individuals with chronically or temporarily high self-esteem should be more confident in their own subjective experiences. As a consequence, individuals with low self-esteem are expected to be more susceptible to social influence.”

This last part in particular is somewhat speculative and they don’t have any studies to point to, but that’s because research into those topics had not (yet?) been done at the time the book was written which is hardly the fault of the authors. I’m actually somewhat curious if people have looked into this kind of stuff since then. It’s quite plausible that variables such as these play a role in memory formation.

“we all have a powerful intuition that we know our relationship partners. In fact, when it comes to lovers, this feeling of mutual understanding and “knowing” is so powerful that we have invented phrases like “soul mate” and “other half” to describe relationships characterized by it. Despite the pervasive feeling that we come to know one another better as relationships progress from casual to intimate, there is little evidence to suggest that this feeling is based on true gains in accuracy. For example, longitudinal studies have shown that if accuracy increases over time at all, after the initial phases of the relationship such gains are minimal (for a review, see Kenny, 1994). […] The lack of clear evidence that people’s perceptions grow increasingly accurate as relationships progress is so surprising because such gains in accuracy seem self-evident to most of us.”

“We suggest that as people integrate information about their relationship partners into coherent impressions, their representations of those persons become “richer.” One way to increase representational richness is by adding novel information. The longer we are acquainted with people, for example, the more information we gather about them and the richer our representations of them become. Representational richness will also increase as our impressions become better integrated and more coherent. As we become more deeply involved with someone, we may carefully organize and integrate what we know about them even though individual elements may be incongruous with one another […]. Whatever the source of increments in representational richness may be, richness will foster accessibility […] and accessibility will, in turn, promote confidence […]. Although representational richness should make people more confident of their perceptions, it will not necessarily contribute to the accuracy of their perceptions. The reason is that any information may increase representational richness but only information that is truly diagnostic will foster accuracy (Funder, 1995). Moreover, there is ample evidence that people use non-diagnostic information as a basis for forming impressions of others. For example, people are inclined to infer dispositions from behaviors that are, in reality, constrained by situational factors […], attribute characteristics based on dubious “implicit theories” of personality […], and fail to revise their initial opinions of others even when the evidence suggests they should […]. This tendency to make inferences from non-diagnostic information (e.g. category membership, situationally produced behavior, implicit theories of personality), in conjunction with a tendency to use such information as a basis for increasing confidence, could result in people being highly confident of beliefs that are inaccurate and misleading. To test this conceptualization of confidence and accuracy, we have conducted a series of field and laboratory studies.”

“The first study was an investigation of 57 heterosexual couples aged from 17 to 41 (Swann & Gill, 1997). Participants had been dating from three weeks to just over six years, with an average of one and one-half years. […] The task of targets was to rate themselves on a series of four questionnaires, including the Sexual History Questionnaire (SHQ; which includes 10 open-ended questions concerning the respondents’ past sexual behavior), the Self-Liking/Competence Scale (SLC; a measure of global self-esteem), the Self-Attributes Questionnaire (SAQ; a measure of self-perceived intelligence, social competence, artistic/musical ability, athleticism, and physical attractiveness), and the Activity Preferences Questionnaire (APQ; a measure of enjoyment of 37 leisure activities). While targets rated themselves, perceivers guessed how targets would rate themselves and indicated their confidence that their guesses were correct. […] We tapped representational richness in two ways. First, we measured time in the relationship as a proxy for amount of information [this seems like a plausible strategy, but obviously not without problems – US]. Second, we measured involvement in the relationship as a proxy for motivation to integrate information. […] Our major prediction was that representational richness would increase confidence but not necessarily accuracy. Regression analyses confirmed that relationship length and involvement were both associated with confidence but had virtually no relation to the accuracy of perceivers’ knowledge of their partners’ self-ratings. […] confidence ran high while accuracy remained rather modest.”

They did another similar study on 40 university students from Texas. That one dealt with roommates, not romantic partners:

“During the first week of the semester, participants rated themselves and attempted to predict the self-ratings of their roommates. […] [One difference was that] we replaced the SHQ with the SAQ-R, a measure that focused on 10 personality characteristics (sense of humor, extroversion, assertiveness, etc.) […] We collected these ratings during the first week of the semester and again six weeks later. During the second session participants also answered four questions about their level of involvement in the relationship with their roommate (how much time they spent doing things with their roommate, how many conversations they had, how often these conversations dealt with relatively private issues, and how much they liked their roommate). […] For the most part, time was unrelated to accuracy, although there was a slight tendency for accuracy on the SAQ to improve over time. Similarly, there was virtually no relation between involvement and accuracy on the SAQ-R or the SLC and a slight negative relation between involvement and accuracy on the SAQ and the APQ. On the latter two measures, then, involvement was associated with increased confidence but decreased accuracy. […] people [seem to be]
sensitive to the accuracy of their knowledge of their partners’ self-esteem but little else. […] Taken together, the results of our studies of dating couples and roommates provide converging evidence that relationship length and involvement foster confidence. Furthermore, the link between time and confidence does not seem to reflect artifactual processes such as a tendency for people who are unconfident to end their relationships. Finally, the fact that relationship length and involvement were associated with increases in confidence but had little impact on accuracy supports our suggestion that confidence grows out of processes that are unrelated to accuracy.”

I’m not sure how convinced I am at this point that the above findings are ‘true’ (‘how to interpret the findings’), but they are certainly thought-provoking. I’ve long thought of ‘convergence’ as the default consequence of long-term social exposure/bonding, but I can’t really remember where I picked up that idea (maybe Pamela Regan’s book?), and on the other hand it’s also obvious that you need stuff besides convergence to explain things like divorce-statistics and so the process is far from independent of other relevant relationship variables. Funder talked about Kenny’s results as well so this stuff is not completely new to me, but I still find it slightly weird to think about. They note in the text that although there was naturally some variation in the performance, there were no people in their studies who were consistently ‘right’; if people were right on one dimension, they tended to be wrong on another dimension. A thought I remember having while reading the book was that important variation might be overlooked due to the way the variables were applied in their analysis; in particular, I thought it might have been useful to get a measure of how salient the individual variables included in the various constructs were considered to be by the targets (the people who were judged). It seems to me that one should expect there to be important individual-level differences in terms of which variables are considered to be most ‘important’ by the people who get evaluated; not all variables contribute the same to the personality assessment of an individual, as some people will be more or less defined by their high level of extroversion, others by their conscientiousness, etc., and implicitly assuming that all variables included in a composite metric contributes the same to the understanding of how an individual ‘works’, which seems to be what the researchers did here, may be problematic. A weighting procedure of some sort might have been very useful. The confidence estimates relate only to the level of certainty, not the importance/salience of the variable. Obtaining ‘validated’ weightings provided by the target him-/herself, perhaps constructed using target responses from personality inventories, might have been a good idea. There would be some problems associated with interpreting such a variable, as mentioned below, but I think it would have added relevant information.

One might argue that if people were really great at figuring out what other people are like (‘the long-term partners got all the ‘salient variables’ right, whereas the short-term partners didn’t’), the analysis should not make them out to be systematically overconfident. There are however a few important details to have in mind when thinking about this overconfidence. One thing that’s important to note in this context is the way the criterion problem is handled; in the specific setup these studies apply it’s actually far from trivial to go from ‘disagreement between judge and target about a variable’ to ‘the judge was wrong (and (/thus) overconfident)’. Another interpretation might be that the target was overestimating (or, if you want to put on a more cynical hat, lying about…) e.g. how confident or assertive he/she really is, and that the judge’s evaluation was actually closer to ‘the truth’ than that of the target (for much more on such factors and the role they play in personality judgment, I refer again to Funder), and that the increased confidence on part of the long-term partner was really justified because she really isn’t that assertive, even if she claims to be. You might mix this stuff with some observations related to e.g. how social feedback processes vary over time in relationships (e.g., ‘a new romantic partner will be much less confident because getting an important answer/estimate wrong may end the relationship, whereas the partner in an established relationship risks less and so may be more confident about his/her partner-relevant judgments’); I’m not quite sure where you’ll end up, but there’s a lot of stuff that could potentially be going on here. If such dynamics are driving the results to some extent, the relevant conclusion may perhaps not be that ‘people are bad at figuring out stuff about others’ and that ‘people get overconfident when forming impressions about how good they are at figuring out what another individual is like when they’ve known that individual for a long time’, but rather that ‘people are bad at figuring out stuff about themselves, and hold views about themselves which are inaccurate’. This they surely do, we know that people’s self-perceptions are often at variance with the truth to some extent and that part of that variance is systematic and can be formalized – I’ve talked about such stuff many times before here on the blog, so I don’t see any reason to repeat myself – but the extent to which such aspects may impact the specific results and their interpretation is not perfectly clear to me at this point.

One may well argue that the overconfidence element is not so easy to get rid of, in the sense that regardless of whether the judgments of the judges were ‘actually true’ (‘X isn’t actually that assertive, even though he claims to be’), it’s clear that the judges did not ‘get better over time’ (given the applied identification procedure is valid) at figuring out how the targets would present themselves and answer the questions they were asked, and that couples who’d been together longer were more confident yet did not get enough answers right to justify that increased level of confidence. I’d also not disagree with the notion that it may well be questionable how much a model explaining the increased divergence between confidence and accuracy as a result of accurate beliefs on part of the judge combined with ‘faulty’ self-concepts on part of the target really adds, because self-concepts are a very important part of the identity of an individual; ‘if you really know her that well, you should know that she prefers to think of herself as being assertive’. Regardless of how you want to interpret the combination of an increased confidence ‘over time’ and a stagnant hit rate, something important is clearly going on here – but the underlying dynamics do not to me seem at all well-elucidated. One approach they do not, as far as I can remember, talk about but which sort of seems logical to apply given the context of the book, is perhaps also to think in terms of explanations invoking societal norms and implicit theories to explain the confidence/accuracy gap; one could argue that the people who had known each other longer in the study didn’t actually think they knew the answers to the questions posed much better than the people who had only known each other for a short amount of time, but they did know that other people believe they ought to know the answers (‘when people have known each other for a long time, they’re supposed to know that sort of stuff’) – this would be one approach which to me seems consistent with the ‘confidence and accuracy are independent variables’-view which takes into account potential relationship-length-related shifts in response strategies.

All those things said, it should be noted that the findings don’t just stand on their own as isolated yet interesting observations, and that the observed overconfidence may be ‘real’ and not the result of unaccounted-for methodological problems – as they argue in their conclusion to the chapter:

“Our evidence of dissociations between confidence and accuracy fits nicely into a growing body of literature suggesting that subjective indicators of knowing are often unreliable indicators of objective knowledge or comprehension (see Jacoby, Bjork, & Kelley, 1994, for a review). For example, people misjudge their comprehension of texts […], the correctness of their answers to general knowledge questions […], the correctness of recalled letter strings […], and the correctness of their eyewitness identifications […]. Reder and Ritter (1992) have even shown that familiarity with a question predicts people’s confidence that they know the answer better than does familiarity with the answer. Taken as a whole, this literature suggests that what people think they know is not always what they really know.”

September 1, 2014 Posted by | Books, Psychology | Leave a comment

The True Believer (I)

“Faith in a holy cause is to a considerable extent a substitute for the lost faith in ourselves.”

“However different the holy causes people die for, they perhaps die basically for the same thing.”

“[This] book passes no judgments, and expresses no preferences. It merely tries to explain; and the explanations — all of them theories — are in the nature of suggestions and arguments even when they are stated in what seems a categorical tone. I can do no better than quote Montaigne: “All I say is by way of discourse, and nothing by way of advice. I should not speak so boldly if it were my due to be believed.” […] The reader is expected to quarrel with much that is said in this […] book. He is likely to feel that much has been exaggerated and much ignored. But this is not an authoritative textbook. It is a book of thoughts, and it does not shy away from half-truths so long as they seem to hint at a new approach and help to formulate new questions.”

I’d rather have read an authoritative textbook on these topics, which both the rating I gave the book and the review I wrote on goodreads reflect. That said, this is not a bad book, and it’s very ‘quotable’ – the attentive reader will recall that I’ve quoted Hoffer multiple times before in my quotes posts. In my quotes posts I usually search the blog for all the quotes I intend to add to the new posts before I add them, in order to avoid repeating any quotes I’ve already posted here; it would however be a lot of work to try to avoid repeating anything posted in quotes posts in this post and to limit coverage to stuff I haven’t already blogged. This would also be somewhat counterproductive, as some key points made in the book would likely have to be left out of this post coverage simply on account of having been covered elsewhere on the blog before.

As I pointed out in the goodreads review, “Paraphrasing what I said about Kuhn’s book, ‘it’s a model.’ I don’t think it’s a bad model as such, but there’s a lot of stuff he’s left out of the picture. This, and the speculative nature of the coverage and the over-reliance on anecdotes, makes it difficult for me to give the book a higher rating, despite the fact that I quite liked this book. ” In a way this is a slightly inaccurate way to put it, in the sense that there’s arguably more than one model presented here (there’s a receptiveness model, a model of the evolutionary path of mass movements, a behavioural model, etc.) – this is relevant because some model aspects are more ‘correct’ in hindsight than are others, and this is of course again relevant because it makes it even harder to evaluate the book as a whole. It is my opinion that most people would be likely to benefit from reading this book, and it’s a very easy read compared to the books I usually cover on this site.

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

“This book deals with some peculiarities common to all mass movements, be they religious movements, social revolutions or nationalist movements. It does not maintain that all movements are identical, but that they share certain essential characteristics which give them a family likeness. All mass movements generate in their adherents a readiness to die and a proclivity for united action; all of them, irrespective of the doctrine they preach and the program they project, breed fanaticism, enthusiasm, fervent hope, hatred and intolerance; all of them are capable of releasing a powerful flow of activity in certain departments of life; all of them demand blind faith and singlehearted allegiance. […] This book concerns itself chiefly with the active, revivalist phase of mass movements. This phase is dominated by the true believer — the man of fanatical faith who is ready to sacrifice his life for a holy cause — and an attempt is made to trace his genesis and outline his nature.”

“The powerful can be as timid as the weak. What seems to count more than possession of instruments of power is faith in the future. Where power is not joined with faith in the future, it is used mainly to ward off the new and preserve the status quo. On the other hand, extravagant hope, even when not backed by actual power, is likely to generate a most reckless daring. For the hopeful can draw strength from the most ridiculous sources of power—a slogan, a word, a button. No faith is potent unless it is also faith in the future […] Those who would transform a nation or the world cannot do so by breeding and captaining discontent or by demonstrating the reasonableness and desirability of the intended changes or by coercing people into a new way of life. They must know how to kindle and fan an extravagant hope. It matters not whether it be hope of a heavenly kingdom, of heaven on earth, of plunder and untold riches, of fabulous achievement or world dominion. […] When hopes and dreams are loose in the streets, it is well for the timid to lock doors, shutter windows and lie low until the wrath has passed. For there is often a monstrous incongruity between the hopes, however noble and tender, and the action which follows them.”

“There is a hope that acts as an explosive, and a hope that disciplines and infuses patience. The difference is between the immediate hope and the distant hope. A rising mass movement preaches the immediate hope. It is intent on stirring its followers to action, and it is the around-the-corner brand of hope that prompts people to act. […] Later, as the movement comes into possession of power, the emphasis is shifted to the distant hope — the dream and the vision. For an “arrived” mass movement is preoccupied with the preservation of the present, and it prizes obedience and patience above spontaneous action […] Every established mass movement has its distant hope, its brand of dope to dull the impatience of the masses and reconcile them with their lot in life. Stalinism is as much an opium of the people as are the established religions.”

“The less justified a man is in claiming excellence for his own self, the more ready is he to claim all excellence for his nation, his religion, his race or his holy cause.”

“When people are ripe for a mass movement, they are usually ripe for any effective movement, and not solely for one with a particular doctrine or program. In pre-Hitlerian Germany it was often a toss up whether a restless youth would join the Communists or the Nazis. […] This receptivity to all movements does not always cease even after the potential true believer has become the ardent convert of a specific movement. Where mass movements are in violent competition with each other, there are not infrequent instances of converts — even the most zealous — shifting their allegiance from one to the other.”

“One mass movement readily transforms itself into another. A religious movement may develop into a social revolution or a nationalist movement; a social revolution, into militant nationalism or a religious movement; a nationalist movement into a social revolution or a religious movement. […] It is rare for a mass movement to be wholly of one character. Usually it displays some facets of other types of movement, and sometimes it is two or three movements in one. […] The religious character of the Bolshevik and Nazi revolutions is generally recognized. The hammer and sickle and the swastika are in a class with the cross. The ceremonial of their parades is as the ceremonial of a religious procession. They have articles of faith, saints, martyrs and holy sepulchers. The Bolshevik and Nazi revolutions are also full-blown nationalist movements. The Nazi revolution had been so from the beginning, while the nationalism of the Bolsheviks was a late development.”

“The problem of stopping a mass movement is often a matter of substituting one movement for another. A social revolution can be stopped by promoting a religious or nationalist movement. Thus in countries where Catholicism has recaptured its mass movement spirit, it counteracts the spread of communism. […] In general, any arrangement which either discourages atomistic individualism or facilitates self-forgetting or offers chances for action and new beginnings tends to counteract the rise and spread of mass movements.”

“It is sometimes difficult to tell where a mass migration ends and a mass movement begins—and which came first. […] Every mass movement is in a sense a migration—a movement toward a promised land; and, when feasible and expedient, an actual migration takes place. […] whether in the form of foreign conquest, crusade, pilgrimage or settlement of new land it is practiced by most active mass movements.”

“Misery does not automatically generate discontent, nor is the intensity of discontent directly proportionate to the degree of misery. Discontent is likely to be highest when misery is bearable; when conditions have so improved that an ideal state seems almost within reach. A grievance is most poignant when almost redressed. […] It is not actual suffering but the taste of better things which excites people to revolt. […] The intensity of discontent seems to be in inverse proportion to the distance from the object fervently desired. […] Our frustration is greater when we have much and want more than when we have nothing and want some. We are less dissatisfied when we lack many things than when we seem to lack but one thing.”

“Freedom aggravates at least as much as it alleviates frustration. Freedom of choice places the whole blame of failure on the shoulders of the individual. And as freedom encourages a multiplicity of attempts, it unavoidably multiplies failure and frustration. Freedom alleviates frustration by making available the palliatives of action, movement, change and protest. Unless a man has the talents to make something of himself, freedom is an irksome burden. Of what avail is freedom to choose if the self be ineffectual? We join a mass movement to escape individual responsibility […] They who clamor loudest for freedom are often the ones least likely to be happy in a free society. The frustrated, oppressed by their shortcomings, blame their failure on existing restraints. […] If they clamor for freedom, it is but freedom to establish equality and uniformity.”

“we can never have enough of that which we really do not want, and […] we run fastest and farthest when we run from ourselves.”

“the technique of a mass movement aims to infect people with a malady and then offer the movement as a cure.”

“The vigor of a mass movement stems from the propensity of its followers for united action and self-sacrifice. When we ascribe the success of a movement to its faith, doctrine, propaganda, leadership, ruthlessness and so on, we are but referring to instruments of unification and to means used to inculcate a readiness for self-sacrifice. It is perhaps impossible to understand the nature of mass movements unless it is recognized that their chief preoccupation is to foster, perfect and perpetuate a facility for united action and self-sacrifice. […] With few exceptions,1 any group or organization which tries, for one reason or another, to create and maintain compact unity and a constant readiness for self-sacrifice usually manifests the peculiarities — both noble and base — of a mass movement. On the other hand, a mass movement is bound to lose much which distinguishes it from other types of organization when it relaxes its collective compactness […] The technique of fostering a readiness to fight and to die consists in separating the individual from his flesh-and-blood self—in not allowing him to be his real self. This can be achieved by the thorough assimilation of the individual into a compact collective body […]; by endowing him with an imaginary self (make-believe) […]; by implanting in him a deprecating attitude toward the present and riveting his interest on things that are not yet […]; by interposing a fact-proof screen between him and reality (doctrine) […]; [and] by preventing, through the injection of passions, the establishment of a stable equilibrium between the individual and his self (fanaticism)”.

“To ripen a person for self-sacrifice he must be stripped of his individual identity and distinctness. […] The fully assimilated individual does not see himself and others as human beings. When asked who he is, his automatic response is that he is a German, a Russian, a Japanese, a Christian, a Moslem, a member of a certain tribe or family. He has no purpose, worth and destiny apart from his collective body; and as long as that body lives he cannot really die.”

“Not only does a mass movement depict the present as mean and miserable—it deliberately makes it so. It fashions a pattern of individual existence that is dour, hard, repressive and dull. It decries pleasures and comforts and extols the rigorous life. It views ordinary enjoyment as trivial or even discreditable, and represents the pursuit of personal happiness as immoral. To enjoy oneself is to have truck with the enemy — the present. […] The very impracticability of many of the goals which a mass movement sets itself is part of the campaign against the present. All that is practicable, feasible and possible is part of the present. To offer something practicable would be to increase the promise of the present and reconcile us with it. […] All mass movements deprecate the present by depicting it as a mean preliminary to a glorious future; a mere doormat on the threshold of the millennium. To a religious movement the present is a place of exile, a vale of tears leading to the heavenly kingdom; to a social revolution it is a mean way station on the road to Utopia; to a nationalist movement it is an ignoble episode preceding the final triumph.”

“A glorification of the past can serve as a means to belittle the present. But unless joined with sanguine expectations of the future, an exaggerated view of the past results in an attitude of caution and not in the reckless strivings of a mass movement. On the other hand, there is no more potent dwarfing of the present than by viewing it as a mere link between a glorious past and a glorious future. Thus, though a mass movement at first turns its back on the past, it eventually develops a vivid awareness, often specious, of a distant glorious past. Religious movements go back to the day of creation; social revolutions tell of a golden age when men were free, equal and independent; nationalist movements revive or invent memories of past greatness.”

“It is futile to judge the viability of a new movement by the truth of its doctrine and the feasibility of its promises. What has to be judged is its corporate organization for quick and total absorption of the frustrated. Where new creeds vie with each other for the allegiance of the populace, the one which comes with the most perfected collective framework wins.”

September 1, 2014 Posted by | Books, Philosophy, Psychology, Quotes/aphorisms, Religion | Leave a comment