Econstudentlog

Random stuff

i. Fire works a little differently than people imagine. A great ask-science comment. See also AugustusFink-nottle’s comment in the same thread.

ii.

iii. I was very conflicted about whether to link to this because I haven’t actually spent any time looking at it myself so I don’t know if it’s any good, but according to somebody (?) who linked to it on SSC the people behind this stuff have academic backgrounds in evolutionary biology, which is something at least (whether you think this is a good thing or not will probably depend greatly on your opinion of evolutionary biologists, but I’ve definitely learned a lot more about human mating patterns, partner interaction patterns, etc. from evolutionary biologists than I have from personal experience, so I’m probably in the ‘they-sometimes-have-interesting-ideas-about-these-topics-and-those-ideas-may-not-be-terrible’-camp). I figure these guys are much more application-oriented than were some of the previous sources I’ve read on related topics, such as e.g. Kappeler et al. I add the link mostly so that if I in five years time have a stroke that obliterates most of my decision-making skills, causing me to decide that entering the dating market might be a good idea, I’ll have some idea where it might make sense to start.

iv. Stereotype (In)Accuracy in Perceptions of Groups and Individuals.

“Are stereotypes accurate or inaccurate? We summarize evidence that stereotype accuracy is one of the largest and most replicable findings in social psychology. We address controversies in this literature, including the long-standing  and continuing but unjustified emphasis on stereotype inaccuracy, how to define and assess stereotype accuracy, and whether stereotypic (vs. individuating) information can be used rationally in person perception. We conclude with suggestions for building theory and for future directions of stereotype (in)accuracy research.”

A few quotes from the paper:

Demographic stereotypes are accurate. Research has consistently shown moderate to high levels of correspondence accuracy for demographic (e.g., race/ethnicity, gender) stereotypes […]. Nearly all accuracy correlations for consensual stereotypes about race/ethnicity and  gender exceed .50 (compared to only 5% of social psychological findings; Richard, Bond, & Stokes-Zoota, 2003).[…] Rather than being based in cultural myths, the shared component of stereotypes is often highly accurate. This pattern cannot be easily explained by motivational or social-constructionist theories of stereotypes and probably reflects a “wisdom of crowds” effect […] personal stereotypes are also quite accurate, with correspondence accuracy for roughly half exceeding r =.50.”

“We found 34 published studies of racial-, ethnic-, and gender-stereotype accuracy. Although not every study examined discrepancy scores, when they did, a plurality or majority of all consensual stereotype judgments were accurate. […] In these 34 studies, when stereotypes were inaccurate, there was more evidence of underestimating than overestimating actual demographic group differences […] Research assessing the accuracy of  miscellaneous other stereotypes (e.g., about occupations, college majors, sororities, etc.) has generally found accuracy levels comparable to those for demographic stereotypes”

“A common claim […] is that even though many stereotypes accurately capture group means, they are still not accurate because group means cannot describe every individual group member. […] If people were rational, they would use stereotypes to judge individual targets when they lack information about targets’ unique personal characteristics (i.e., individuating information), when the stereotype itself is highly diagnostic (i.e., highly informative regarding the judgment), and when available individuating information is ambiguous or incompletely useful. People’s judgments robustly conform to rational predictions. In the rare situations in which a stereotype is highly diagnostic, people rely on it (e.g., Crawford, Jussim, Madon, Cain, & Stevens, 2011). When highly diagnostic individuating information is available, people overwhelmingly rely on it (Kunda & Thagard, 1996; effect size averaging r = .70). Stereotype biases average no higher than r = .10 ( Jussim, 2012) but reach r = .25 in the absence of individuating information (Kunda & Thagard, 1996). The more diagnostic individuating information  people have, the less they stereotype (Crawford et al., 2011; Krueger & Rothbart, 1988). Thus, people do not indiscriminately apply their stereotypes to all individual  members of stereotyped groups.” (Funder incidentally talked about this stuff as well in his book Personality Judgment).

One thing worth mentioning in the context of stereotypes is that if you look at stuff like crime data – which sadly not many people do – and you stratify based on stuff like country of origin, then the sub-group differences you observe tend to be very large. Some of the differences you observe between subgroups are not in the order of something like 10%, which is probably the sort of difference which could easily be ignored without major consequences; some subgroup differences can easily be in the order of one or two orders of magnitude. The differences are in some contexts so large as to basically make it downright idiotic to assume there are no differences – it doesn’t make sense, it’s frankly a stupid thing to do. To give an example, in Germany the probability that a random person, about whom you know nothing, has been a suspect in a thievery case is 22% if that random person happens to be of Algerian extraction, whereas it’s only 0,27% if you’re dealing with an immigrant from China. Roughly one in 13 of those Algerians have also been involved in a case of ‘body (bodily?) harm’, which is the case for less than one in 400 of the Chinese immigrants.

v. Assessing Immigrant Integration in Sweden after the May 2013 Riots. Some data from the article:

“Today, about one-fifth of Sweden’s population has an immigrant background, defined as those who were either born abroad or born in Sweden to two immigrant parents. The foreign born comprised 15.4 percent of the Swedish population in 2012, up from 11.3 percent in 2000 and 9.2 percent in 1990 […] Of the estimated 331,975 asylum applicants registered in EU countries in 2012, 43,865 (or 13 percent) were in Sweden. […] More than half of these applications were from Syrians, Somalis, Afghanis, Serbians, and Eritreans. […] One town of about 80,000 people, Södertälje, since the mid-2000s has taken in more Iraqi refugees than the United States and Canada combined.”

“Coupled with […] macroeconomic changes, the largely humanitarian nature of immigrant arrivals since the 1970s has posed challenges of labor market integration for Sweden, as refugees often arrive with low levels of education and transferable skills […] high unemployment rates have disproportionately affected immigrant communities in Sweden. In 2009-10, Sweden had the highest gap between native and immigrant employment rates among OECD countries. Approximately 63 percent of immigrants were employed compared to 76 percent of the native-born population. This 13 percentage-point gap is significantly greater than the OECD average […] Explanations for the gap include less work experience and domestic formal qualifications such as language skills among immigrants […] Among recent immigrants, defined as those who have been in the country for less than five years, the employment rate differed from that of the native born by more than 27 percentage points. In 2011, the Swedish newspaper Dagens Nyheter reported that 35 percent of the unemployed registered at the Swedish Public Employment Service were foreign born, up from 22 percent in 2005.”

“As immigrant populations have grown, Sweden has experienced a persistent level of segregation — among the highest in Western Europe. In 2008, 60 percent of native Swedes lived in areas where the majority of the population was also Swedish, and 20 percent lived in areas that were virtually 100 percent Swedish. In contrast, 20 percent of Sweden’s foreign born lived in areas where more than 40 percent of the population was also foreign born.”

vi. Book recommendations. Or rather, author recommendations. A while back I asked ‘the people of SSC’ if they knew of any fiction authors I hadn’t read yet which were both funny and easy to read. I got a lot of good suggestions, and the roughly 20 Dick Francis novels I’ve read during the fall I’ve read as a consequence of that thread.

vii. On the genetic structure of Denmark.

viii. Religious Fundamentalism and Hostility against Out-groups: A Comparison of Muslims and Christians in Western Europe.

“On the basis of an original survey among native Christians and Muslims of Turkish and Moroccan origin in Germany, France, the Netherlands, Belgium, Austria and Sweden, this paper investigates four research questions comparing native Christians to Muslim immigrants: (1) the extent of religious fundamentalism; (2) its socio-economic determinants; (3) whether it can be distinguished from other indicators of religiosity; and (4) its relationship to hostility towards out-groups (homosexuals, Jews, the West, and Muslims). The results indicate that religious fundamentalist attitudes are much more widespread among Sunnite Muslims than among native Christians, even after controlling for the different demographic and socio-economic compositions of these groups. […] Fundamentalist believers […] show very high levels of out-group hostility, especially among Muslims.”

ix. Portal: Dinosaurs. It would have been so incredibly awesome to have had access to this kind of stuff back when I was a child. The portal includes links to articles with names like ‘Bone Wars‘ – what’s not to like? Again, awesome!

x. “you can’t determine if something is truly random from observations alone. You can only determine if something is not truly random.” (link) An important insight well expressed.

xi. Chessprogramming. If you’re interested in having a look at how chess programs work, this is a neat resource. The wiki contains lots of links with information on specific sub-topics of interest. Also chess-related: The World Championship match between Carlsen and Karjakin has started. To the extent that I’ll be following the live coverage, I’ll be following Svidler et al.’s coverage on chess24. Robin van Kampen and Eric Hansen – both 2600+ elo GMs – did quite well yesterday, in my opinion.

xii. Justified by More Than Logos Alone (Razib Khan).

“Very few are Roman Catholic because they have read Aquinas’ Five Ways. Rather, they are Roman Catholic, in order of necessity, because God aligns with their deep intuitions, basic cognitive needs in terms of cosmological coherency, and because the church serves as an avenue for socialization and repetitive ritual which binds individuals to the greater whole. People do not believe in Catholicism as often as they are born Catholics, and the Catholic religion is rather well fitted to a range of predispositions to the typical human.”

November 12, 2016 Posted by | books, Chemistry, Chess, data, dating, demographics, genetics, Geography, immigration, Paleontology, papers, Physics, Psychology, random stuff, religion | Leave a comment

Role of Biomarkers in Medicine

“The use of biomarkers in basic and clinical research has become routine in many areas of medicine. They are accepted as molecular signatures that have been well characterized and repeatedly shown to be capable of predicting relevant disease states or clinical outcomes. In Role of Biomarkers in Medicine, expert researchers in their individual field have reviewed many biomarkers or potential biomarkers in various types of diseases. The topics address numerous aspects of medicine, demonstrating the current conceptual status of biomarkers as clinical tools and as surrogate endpoints in clinical research.”

The above quote is from the preface of the book. Here’s my goodreads review. I have read about biomarkers before – for previous posts on this topic, see this link. I added the link in part because the coverage provided in this book is in my opinion generally of a somewhat lower quality than is the coverage that has been provided in some of the other books I’ve read on these topics. However the fact that the book is not amazing should probably not keep me from sharing some observations of interest from the book, which I have done in this post.

we suggest more precise studies to establish the exact role of this hormone […] additional studies are necessary […] there are conflicting results […] require further investigation […] more intervention studies with long-term follow-up are required. […] further studies need to be conducted […] further research is needed (There are a lot of comments like these in the book, I figured I should include a few in my coverage…)

“Cancer biomarkers (CB) are biomolecules produced either by the tumor cells or by other cells of the body in response to the tumor, and CB could be used as screening/early detection tool of cancer, diagnostic, prognostic, or predictor for the overall outcome of a patient. Moreover, cancer biomarkers may identify subpopulations of patients who are most likely to respond to a given therapy […] Unfortunately, […] only very few CB have been approved by the FDA as diagnostic or prognostic cancer markers […] 25 years ago, the clinical usefulness of CB was limited to be an effective tool for patient’s prognosis, surveillance, and therapy monitoring. […] CB have [since] been reported to be used also for screening of general population or risk groups, for differential diagnosis, and for clinical staging or stratification of cancer patients. Additionally, CB are used to estimate tumor burden and to substitute for a clinical endpoint and/or to measure clinical benefit, harm or lack of benefit, or harm [4, 18, 30]. Among commonly utilized biomarkers in clinical practice are PSA, AFP, CA125, and CEA.”

“Bladder cancer (BC) is the second most common malignancy in the urologic field. Preoperative predictive biomarkers of cancer progression and prognosis are imperative for optimizing […] treatment for patients with BC. […] Approximately 75–85% of BC cases are diagnosed as nonmuscle-invasive bladder cancer (NMIBC) […] NMIBC has a tendency to recur (50–70%) and may progress (10–20%) to a higher grade and/or muscle-invasive BC (MIBC) in time, which can lead to high cancer-specific mortality [2]. Histological tumor grade is one of the clinical factors associated with outcomes of patients with NMIBC. High-grade NMIBC generally exhibits more aggressive behavior than low-grade NMIBC, and it increases the risk of a poorer prognosis […] Cystoscopy and urine cytology are commonly used techniques for the diagnosis and surveillance of BC. Cystoscopy can identify […] most papillary and solid lesions, but this is highly invasive […] urine cytology is limited by examiner experience and low sensitivity. For these reasons, some tumor markers have been investigated […], but their sensitivity and specificity are limited [5] and they are unable to predict the clinical outcome of BC patients. […] Numerous efforts have been made to identify tumor markers. […] However, a serum marker that can serve as a reliable detection marker for BC has yet to be identified.”

“Endometrial cancer (EmCa) is the most common type of gynecological cancer. EmCa is the fourth most common cancer in the United States, which has been linked to increased incidence of obesity. […] there are no reliable biomarker tests for early detection of EmCa and treatment effectiveness. […] Approximately 75% of women with EmCa are postmenopausal; the most common symptom is postmenopausal bleeding […] Approximately 15% of women diagnosed with EmCa are younger than 50 years of age, while 5% are diagnosed before the age of 40 [29]. […] Roughly, half of the EmCa cases are linked to obesity. Obese women are four times more likely to develop EmCa when compared to normal weight women […] Obese individuals oftentimes exhibit resistance to leptin and show high levels of the adipokine in blood, which is known as leptin resistance […] prolonged exposure of leptin damages the hypothalamus causing it to become insensitive to the effects of leptin […] Evidence shows that leptin is an important pro-inflammatory, pro-angiogenic, and mitogenic factor for cancer. Leptin produced by cancer cells acts in an autocrine and paracrine manner to promote tumor cell proliferation, migration and invasion, pro-inflammation, and angiogenesis [58, 70]. High levels of leptin […] are associated with metastasis and decreased survival rates in breast cancer patients [58]. […] Metabolic syndrome including obesity, hypertension, insulin resistance, diabetes, and dyslipidemia increase the risk of developing multiple malignancies, particularly EmCa [30]. Younger women diagnosed with EmCa are usually obese, and their carcinomas show a well-differentiated histology [20].

“Normally, tumor suppressor genes act to inhibit or arrest cell proliferation and tumor development [37]. However; when mutated, tumor suppressors become inactive, thus permitting tumor growth. For example, mutations in p53 have been determined in various cancers such as breast, colon, lung, endometrium, leukemias, and carcinomas of many tissues. These p53 mutations are found in approximately 50% of all cancers [38]. Roughly 10–20% of endometrial carcinomas exhibit p53 mutations [37]. […] overexpression of mutated tumor suppressor p53 has been associated with Type II EmCa (poor histologic grade, non-endometrioid histology, advanced stage, and poor survival).”

“Increasing data indicate that oxidative stress is involved in the development of DR [diabetic retinopathy] [16–19]. The retina has a high content of polyunsaturated fatty acids and has the highest oxygen uptake and glucose oxidation relative to any other tissue. This phenomenon renders the retina more susceptible to oxidative stress [20]. […] Since long-term exposure to oxidative stress is strongly implicated in the pathogenesis of diabetic complications, polymorphic genes of detoxifying enzymes may be involved in the development of DR. […] A meta-analysis comprising 17 studies, including type 1 and type 2 diabetic patients from different ethnic origins, implied that the C (Ala) allele of the C47T polymorphism in the MnSOD gene had a significant protective effect against microvascular complications (DR and diabetic nephropathy) […] In the development of DR, superoxide levels are elevated in the retina, antioxidant defense system is compromised, MnSOD is inhibited, and mitochondria are swollen and dysfunctional [77,87–90]. Overexpression of MnSOD protects [against] diabetes-induced mitochondrial damage and the development of DR [19,91].”

Continuous high level of blood glucose in diabetes damages micro and macro blood vessels throughout the body by altering the endothelial cell lining of the blood vessels […] Diabetes threatens vision, and patients with diabetes develop cataracts at an earlier age and are nearly twice as likely to get glaucoma compared to non-diabetic[s] [3]. More than 75% of patients who have had diabetes mellitus for more than 20 years will develop diabetic retinopathy (DR) [4]. […] DR is a slow progressive retinal disease and occurs as a consequence of longstanding accumulated functional and structural impairment of the retina by diabetes. It is a multifactorial condition arising from the complex interplay between biochemical and metabolic abnormalities occurring in all cells of the retina. DR has been classically regarded as a microangiopathy of the retina, involving changes in the vascular wall leading to capillary occlusion and thereby retinal ischemia and leakage. And more recently, the neural defects in the retina are also being appreciated […]. Recently, various clinical investigators [have detected] neuronal dysfunction at very early stages of diabetes and numerous abnormalities in the retina can be identified even before the vascular pathology appears [76, 77], thus suggesting a direct effect of diabetes on the neural retina. […] An emerging issue in DR research is the focus on the mechanistic link between chronic low-grade inflammation and angiogenesis. Recent evidence has revealed that extracellular high-mobility group box-1 (HMGB1) protein acts as a potent proinflammatory cytokine that triggers inflammation and recruits leukocytes to the site of tissue damage, and exhibits angiogenic effects. The expression of HMGB1 is upregulated in epiretinal membranes and vitreous fluid from patients with proliferative DR and in the diabetic retina. […] HMGB1 may be a potential biomarker [for diabetic retinopathy] […] early blockade of HMGB1 may be an effective strategy to prevent the progression of DR.”

“High blood pressure is one of the leading risk factors for global mortality and is estimated to have caused 9.4 million deaths in 2010. A meta‐analysis which includes 1 million individuals has indicated that death from both CHD [coronary heart disease] and stroke increase progressively and linearly from BP levels as low as 115 mmHg systolic and 75 mmHg diastolic upwards [138]. The WHO [has] pointed out that a “reduction in systolic blood pressure of 10 mmHg is associated with a 22% reduction in coronary heart disease, 41% reduction in stroke in randomized trials, and a 41–46% reduction in cardiometabolic mortality in epidemiological studies” [139].”

Several reproducible studies have ascertained that individuals with autism demonstrate an abnormal brain 5-HT system […] peripheral alterations in the 5-HT system may be an important marker of central abnormalities in autism. […] In a recent study, Carminati et al. [129] tested the therapeutic efficacy of venlafaxine, an antidepressant drug that inhibits the reuptake of 5-HT, and [found] that venlafaxine at a low dose [resulted in] a substantial improvement in repetitive behaviors, restricted interests, social impairment, communication, and language. Venlafaxine probably acts via serotonergic mechanisms  […] OT [Oxytocin]-related studies in autism have repeatedly reported lower blood OT level in autistic patients compared to age- and gender-matched control subjects […] autistic patients demonstrate an altered neuroinflammatory response throughout their lives; they also show increased astrocyte and microglia inflammatory response in the cortex and the cerebellum  [47, 48].”

November 3, 2016 Posted by | books, cancer, diabetes, genetics, medicine, Neurology, Pharmacology | Leave a comment

The Biology of Moral Systems (I)

I have quoted from the book before, but I decided that this book deserves to be blogged in more detail. I’m close to finishing the book at this point (it’s definitely taken longer than it should have), and I’ll probably give it 5 stars on goodreads; I might also add it to my list of favourite books on the site. In this post I’ve added some quotes and ideas from the book, and a few comments. Before going any further I should note that it’s frankly impossible to cover anywhere near all the ideas covered in the book here on the blog, so if you’re even remotely interested in these kinds of things you really should pick up a copy of the book and read all of it.

“I believe that something crucial has been missing from all of the great debates of history, among philosophers, politicians, theologians, and thinkers from other and diverse backgrounds, on the issues of morality, ethics, justice, right and wrong. […] those who have tried to analyze morality have failed to treat the human traits that underlie moral behavior as outcomes of evolution […] for many conflicts of interest, compromises and enforceable contracts represent the only real solutions. Appeals to morality, I will argue, are simply the invoking of such compromises and contracts in particular ways. […] the process of natural selection that has given rise to all forms of life, including humans, operates such that success has always been relative. One consequence is that organisms resulting from the long-term cumulative effects of selection are expected to resist efforts to reveal their interests fully to others, and also efforts to place limits on their striving or to decide for them when their interests are being “fully” satisfied. These are all reasons why we should expect no “terminus” – ever – to debates on moral and ethical issues.” (these comments I also included in the quotes post to which I link at the beginning, but I thought it was worth including them in this post as well even so – US).

“I am convinced that biology can never offer […] easy or direct answers to the questions of what is right and wrong. I explicitly reject the attitude that whatever biology tells us is so is also what ought to be (David Hume’s so-called “naturalistic fallacy”) […] there are within biology no magic solutions to moral problems. […] Knowledge of the human background in organic evolution can [however] provide a deeper self-understanding by an increasing proportion of the world’s population; self-understanding that I believe can contribute to answering the serious questions of social living.”

“If there had been no recent discoveries in biology that provided new ways of looking at the concept of moral systems, then I would be optimistic indeed to believe that I could say much that is new. But there have been such discoveries. […] The central point in these writings [Hamilton, Williams, Trivers, Cavalli-Sforza, Feldman, Dawkins, Wilson, etc. – US] […] is that natural selection has apparently been maximizing the survival by reproduction of genes, as they have been defined by evolutionists, and that, with respect to the activities of individuals, this includes effects on copies of their genes, even copies located in other individuals. In other words, we are evidently evolved not only to aid the genetic materials in our own bodies, by creating and assisting descendants, but also to assist, by nepotism, copies of our genes that reside in collateral (nondescendant) relatives. […] ethics, morality, human conduct, and the human psyche are to be understood only if societies are seen as collections of individuals seeking their own self-interests […] In some respects these ideas run contrary to what people have believed and been taught about morality and human values: I suspect that nearly all humans believe it is a normal part of the functioning of every human individual now and then to assist someone else in the realization of that person’s own interests to the actual net expense of those of the altruist. What [the above-mentioned writings] tells us is that, despite our intuitions, there is not a shred of evidence to support this view of beneficence, and a great deal of convincing theory suggests that any such view will eventually be judged false. This implies that we will have to start all over again to describe and understand ourselves, in terms alien to our intuitions […] It is […] a goal of this book to contribute to this redescription and new understanding, and especially to discuss why our intuitions should have misinformed us.”

“Social behavior evolves as a succession of ploys and counterploys, and for humans these ploys are used, not only among individuals within social groups, but between and among small and large groups of up to hundreds of millions of individuals. The value of an evolutionary approach to human sociality is thus not to determine the limits of our actions so that we can abide by them. Rather, it is to examine our life strategies so that we can change them when we wish, as a result of understanding them. […] my use of the word biology in no way implies that moral systems have some kind of explicit genetic background, are genetically determined, or cannot be altered by adjusting the social environment. […] I mean simply to suggest that if we wish to understand those aspects of our behavior commonly regarded as involving morality or ethics, it will help to reconsider our behavior as a product of evolution by natural selection. The principal reason for this suggestion is that natural selection operates according to general principles which make its effects highly predictive, even with respect to traits and circumstances that have not yet been analyzed […] I am interested […] not in determining what is moral and immoral, in the sense of what people ought to be doing, but in elucidating the natural history of ethics and morality – in discovering how and why humans initiated and developed the ideas we have about right and wrong.”

I should perhaps mention here that sort-of-kind-of related stuff is covered in Aureli et al. (see e.g. this link), and that some parts of that book will probably make you understand Alexander’s ideas a lot better even if perhaps he didn’t read those specific authors – mainly because it gets a lot easier to imagine the sort of mechanisms which might be at play here if you’ve read this sort of literature. Here’s one relevant quote from the coverage of that book, which also deals with the question Alexander discusses above, and in a lot more detail throughout his book, namely ‘where our morality comes from?’

“we make two fundamental assertions regarding the evolution of morality: (1) there are specific types of behavior demonstrated by both human and nonhuman primates that hint at a shared evolutionary background to morality; and (2) there are theoretical and actual connections between morality and conflict resolution in both nonhuman primates and human development. […] the transition from nonmoral or premoral to moral is more gradual than commonly assumed. No magic point appears in either evolutionary history or human development at which morality suddenly comes into existence. In both early childhood and in animals closely related to us, we can recognize behaviors (and, in the case of children, judgments) that are essential building blocks of the morality of the human adult. […] the decision making and emotions underlying moral judgments are generated within the individual rather than being simply imposed by society. They are a product of evolution, an integrated part of the human genetic makeup, that makes the child construct a moral perspective through interactions with other members of its species. […] Much research has shown that children acquire morality through a social-cognitive process; children make connections between acts and consequences. Through a gradual process, children develop concepts of justice, fairness, and equality, and they apply these concepts to concrete everyday situations […] we assert that emotions such as empathy and sympathy provide an experiential basis by which children construct moral judgments. Emotional reactions from others, such as distress or crying, provide experiential information that children use to judge whether an act is right or wrong […] when a child hits another child, a crying response provides emotional information about the nature of the act, and this information enables the child, in part, to determine whether and why the transgression is wrong. Therefore, recognizing signs of distress in another person may be a basic requirement of the moral judgment process. The fact that responses to distress in another have been documented both in infancy and in the nonhuman primate literature provides initial support for the idea that these types of moral-like experiences are common to children and nonhuman primates.”

Alexander’s coverage is quite different from that found in Aureli et al.,, but some of the contributors to the latter work deal with similar questions to the ones in which he’s interested, using approaches not employed in Alexander’s book – so this is another place to look if you’re interested in these topics. Margalit’s The Emergence of Norms is also worth mentioning. Part of the reason why I mention these books here is incidentally that they’re not talked about in Alexander’s coverage (for very natural reasons, I should add, in the case of the former book at least; Natural Conflict Resolution was published more than a decade after Alexander wrote his book…).

“In the hierarchy of explanatory principles governing the traits of living organisms, evolutionary reductionism – the development of principles from the evolutionary process – tends to subsume all other kinds. Proximate-cause reductionism (or reduction by dissection) sometimes advances our understanding of the whole phenomena. […] When evolutionary reduction becomes trivial in the study of life it is for a reason different from incompleteness; rather, it is because the breadth of the generalization distances it too significantly from the particular problem that may be at hand. […] the greatest weakness of reduction by generalization is not that it is likely to be trivial but that errors are probable through unjustified leaps from hypothesis to conclusion […] Critics such as Gould and Lewontin […] do not discuss the facts that (a) all students of human behavior (not just those who take evolution into account) run the risk of leaping unwarrantedly from hypothesis to conclusion and (b) just-so stories were no less prevalent and hypothesis-testing no more prevalent in studies of human behavior before evolutionary biologists began to participate. […] I believe that failure by biologists and others to distinguish proximate- or partial-cause and evolutionary- or ultimate-cause reductionism […] is in some part responsible for the current chasm between the social and the biological sciences and the resistance to so-called biological approaches to understanding humans. […] Both approaches are essential to progress in biology and the social sciences, and it would be helpful if their relationship, and that of their respective practitioners, were not seen as adversarial.”

(Relatedly, love is motivationally prior to sugar. This one also seems relevant, though in a different way).

“Humans are not accustomed to dealing with their own strategies of life as if they had been tuned by natural selection. […] People are not generally aware of what their lifetimes have been evolved to accomplish, and, even if they are roughly aware of this, they do not easily accept that their everyday activities are in any sense means to that end. […] The theory of lifetimes most widely accepted among biologists is that individuals have evolved to maximize the likelihood of survival of not themselves, but their genes, and that they do this by reproducing and tending in various ways offspring and other carriers of their own genes […] In this theory, survival of the individual – and its growth, development, and learning – are proximate mechanisms of reproductive success, which is a proximate mechanism of genic survival. Only the genes have evolved to survive. […] To say that we are evolved to serve the interests of our genes in no way suggests that we are obliged to serve them. […] Evolution is surely most deterministic for those still unaware of it. If this argument is correct, it may be the first to carry us from is to ought, i.e., if we desire to be the conscious masters of our own fates, and if conscious effort in that direction is the most likely vehicle of survival and happiness, then we ought to study evolution.”

“People are sometimes comfortable with the notion that certain activities can be labeled as “purely cultural” because they also believe that there are behaviors that can be labeled “purely genetic.” Neither is true: the environment contributes to the expression of all behaviors, and culture is best described as part of the environment.”

“Happiness and its anticipation are […] proximate mechanisms that lead us to perform and repeat acts that in the environments of history, at least, would have led to greater reproductive success.”

“The remarkable difference between the patterns of senescence in semelparous (one-time breeding) and iteroparous (repeat-breeding) organisms is probably one of the best simple demonstrations of the central significance of reproduction in the individual’s lifetime. How, otherwise, could we explain the fact that those who reproduce but once, like salmon and soybeans, tend to die suddenly right afterward, while those like ourselves who have residual reproductive possibilities after the initial reproductive act decline or senesce gradually? […] once an organism has completed all possibilities of reproducing (through both offspring production and assistance, and helping other relatives), then selection can no longer affect its survival: any physiological or other breakdown that destroys it may persist and even spread if it is genetically linked to a trait that is expressed earlier and is reproductively beneficial. […] selection continually works against senescence, but is just never able to defeat it entirely. […] senescence leads to a generalized deterioration rather than one owing to a single effect or a few effects […] In the course of working against senescence, selection will tend to remove, one by one, the most frequent sources of mortality as a result of senescence. Whenever a single cause of mortality, such as a particular malfunction of any vital organ, becomes the predominant cause of mortality, then selection will more effectively reduce the significance of that particular defect (meaning those who lack it will outreproduce) until some other achieves greater relative significance. […] the result will be that all organs and systems will tend to deteriorate together. […] The point is that as we age, and as senescence proceeds, large numbers of potential sources of mortality tend to lurk ever more malevolently just “below the surface,” so that, unfortunately, the odds are very high against any dramatic lengthening of the maximum human lifetime through technology. […] natural selection maximizes the likelihood of genetic survival, which is incompatible with eliminating senescence. […] Senescence, and the finiteness of lifetimes, have evolved as incidental effects […] Organisms compete for genetic survival and the winners (in evolutionary terms) are those who sacrifice their phenotypes (selves) earlier when this results in greater reproduction.”

“altruism appears to diminish with decreasing degree of relatedness in sexual species whenever it is studied – in humans as well as nonhuman species”

October 5, 2016 Posted by | anthropology, biology, books, genetics, philosophy | Leave a comment

Human Drug Metabolism (III)

This is my third post about this book. You can read my previous posts here and here. In this post I have covered material from chapter 7, dealing with ‘factors affecting drug metabolism’.

“Data from animal studies in one country are usually comparable with that of another, provided the animal species and strain are the same. This provides a consistent picture of the basic pharmacological and toxicological actions of a candidate drug in a living organism […] it has been obvious since animal testing began that there would be large differences in the way a drug might perform in man compared with animal species […]. Unfortunately, there is no experimental model yet designed that can not only consider human biochemistry and physiology, but also the effects of age, smoking, legal and illegal drug usage, gender, diet, environment, disease and finally genetic variation. Indeed, many clinical studies have revealed enormous differences in drug clearance and pharmacological effect even in age, sex and ethnically matched individuals. In effect, this means that the first year or so of a drug’s clinical life is a vast, but monitored experiment, involving hundreds of thousands of patients and there is no guarantee of success.”

“Most biotransformational polymorphisms that might potentially cause a problem clinically are due to an inability of those with defective enzymes to remove the drug from the system. Drug failure can occur if the agent is administered as a pro-drug and requires some metabolic conversion to an active metabolite. Drug accumulation can lead to unpleasant side effects and loss of patient tolerance for the agent. […] Overall, there are a large number of factors that can influence drug metabolism, either by increasing clearance to cause drug failure, or by preventing clearance to lead to toxicity. In the real world, it is often impossible to delineate the different conflicting factors which result in net changes in drug clearance which cause a drug to fall out of, or climb above, the therapeutic window. It may only be possible clinically in many cases to try to change what appears to be the major cause to bring about a resolution of the situation to restore curative and non-toxic drug levels.”

“Most population studies of human polymorphisms list the allelic frequency, that is, how many of an ethnic group contain the alleles in question. […] The actual haplotypes in the population, that is, which individuals express which combinations of alleles, are not the same as the population allelic frequency. […] If an SNP or a combination of SNPs is a fairly mild defect in the enzyme when it is homozygously expressed, then the heterozygotes will show little impairment and the polymorphism may be clinically irrelevant. With other SNPs, the enzyme produced may be completely non-functional.  Homozygotes will be virtually unable to clear the drug and heterozygotes will show impairment also. There are also smaller populations of UMs, or ultra rapid metabolizers which may have a feature of their enzyme which either makes it super efficient or expressed in abnormally high amounts. […] Phenotyping will group patients in very broad EMs [extensive metabolizers], IMs [intermediate metabolizers] or PM [poor metabolizers] categories, but will be unable to distinguish between heterozygous and homozygous EMs. Although genotyping may be very helpful in dosage estimation in the initiation of therapy, there is no substitute for the normal process of therapeutic monitoring, which is effectively phenotyping the individual in the real world in terms of maximizing response and minimizing toxicity.”

“it is clear that there is a vast amount of genetic variation across humanity in terms of biotransformational capability and so the idea that in therapeutics, ‘one size fits all’ is not only outdated, but fabulously naïve. […] Unfortunately, detecting and responding successfully to human biotransformational polymorphisms has proved to be extremely problematic. In terms of polymorphism detection, this area is a classic illustration of how the exploration of the human genome with powerful molecular biological tools may unearth many apparently marked polymorphic defects that may not necessarily translate into a measurable clinical impact in terms of efficacy and toxicity. In reality, many more scientists have the opportunity to discover and publish such polymorphisms in vitro, than there are clinical scientists, resources and indeed cooperative volunteers or patients in sufficient quantity to determine practical clinical relevance.”

the CYP3A group (chromosome 7) metabolize around half of all drugs […] variation in the metabolism of CYP3A substrates […] can be up to ten-fold in terms of drug clearances and up to 90-fold in liver protein expression. […] It is likely that the full extent of the variation in CYP3A4 is still to be discovered […] While it is thought that CYP3A4 is not subject to an obvious major polymorphism, CYP3A5 definitely is. […] *3/*3 individuals form no serviceable CYP3A5. Functional CYP3A5 is found in around 20 per cent of Caucasians, half of Chinese/Japanese, 70 per cent of Hispanics and more than 80 per cent of African Americans.”

“A particularly dangerous polymorphism clinically was identified in the 1980s for one of the methyltransferases. The endogenous role of S-methylating thiopurine S-methyltransferase (TPMT) is not that clear, but […] [t]hese drugs are […] effective in some childhood leukaemias […] TPMT highlights the genotyping/phenotyping issue mentioned earlier in the management of patients with polymorphisms. Genotyping will reveal the level of TPMT expression that should be expected in the otherwise healthy patient. However, there are many factors which impact day-to-day TPMT expression during thiopurine therapy. […] Hence, what might be predicted from a genotype test may bear little resemblance to how the enzyme is performing on a particular day in a treatment cycle. So clinically, it is preferred to test actual TPMT activity.”

“Understanding of sulphonation and its roles in endogenous as well as xenobiotic metabolism is not as advanced compared with that of CYPs; however, the role of SULTs in the activation of carcinogens is becoming more apparent. One of the major influences on SULT activity is their polymorphic nature; in the case of one of the most important toxicologically relevant SULTs, SULT1A1, this isoform exists as three variants, SULT1A1*1 (wild-type), SULT1A1*2 and SULT1A1*3. The *1 variant allele is found in the majority of Caucasians (around 65 per cent), whilst the *2 variant differs only in the exchange of one amino acid for another. This single amino acid change has profound effects on the stability and catalytic activity of the isoform. The *2 variant is found in approximately 32 per cent of Caucasians and catalytically faulty […] About 9 in 10 Chinese people have the *1 allele and about 8 per cent have allele *2. About half of African-Americans have *1 and a third have *2. Interestingly, there is a *3 which is rare in most races but accounts for more than 22 per cent of African Americans. There is also considerable variation in SULT2A1 and SULT2B1, which are the major hydroxysteroid sulphators in the body, which may have implications for sex steroid and cholesterol handling. […] from the cancer-risk viewpoint, a highly active SULT1A1 *1 is usually an advantage in that it usually removes reactive species rapidly as stable sulphates. With some agents it is problematic as certain carcinogens such as acetylfluorene are indirectly activated to reactive species by SULTs. In addition, protective dietary flavonoids […] are also rapidly cleared by SULT1A1 *1, so there is a combination of production of toxins and loss of protective dietary agents. In terms of carcinogenesis risk, SULT1A1*2 could be a liability as potentially damaging substrates such as electrophilic toxins cannot be cleared rapidly. However, in some circumstances the *2 allele can be rather protective as […] it also allows protective agents [to] remain in tissues for longer periods. The combinations are endless and so it is often extremely difficult to predict risks of carcinogenicity for individuals and toxin exposures.”

GSTs are polymorphic and much research has been directed at linking increased predisposition to cytotoxicity and carcinogenicity with defective GST phenotypes. Active wild-type GSTMu-1 is found in around 60 per cent of Caucasians, but a non-functional version of the isoform is found in the remainder. […] GST-M1 null (non-functional alleles) can predispose to risks of prostate abnormalities and GST Pi is subject to several SNPs and many attempts have been made to link these SNPs with the consequences of failure to detoxify reactive species, such as the risk of lung cancer. […] Carcinogenesis may be due to a complex mix of factors, where different enzyme expression and activities may combine with particular reactive species from specific parent xenobiotics that lead to DNA damage only in certain individuals. Resolving specific risk factors may be extremely difficult in such circumstances. […] in cancer chemotherapy, there is evidence that the presence of GST-M1 and GST-T1 null (non-functional) alleles predisposes children to a six-fold higher level of adverse events usually seen with antineoplastic drugs, such as bone marrow damage, nephrotoxicity and neurotoxicity.”

“The effects of age on drug clearance and metabolism have been known since the 1950s, but they have been extensively investigated in the last 20 or so years. It is now generally accepted that at the extremes of life, neonatal and geriatric, drug clearance can be significantly different from the rest of humanity. In general, neonates, i.e. those less than four weeks old, cannot clear certain agents due to immaturity of drug metabolizing systems. Those over retirement age cannot clear the drugs due to loss of efficiency in their metabolizing systems. Either way, the net result can be toxicity due to drug accumulation. […] It seems that the inability of older people to clear drugs is not necessarily related to the efficacy of their CYP-mediated oxidations, which are often not much different from that of younger individuals. Studies with the major CYPs in vitro have revealed that CYP2D6 is unaffected by age, as are most other CYPs, with the exception of CYP1A2, which does decline in activity in the elderly. […] In general, there is little significant change in the inducibility in most CYPs, or in the capability of conjugation systems in vitro. […] there are significant changes in the liver itself, as it decreases in mass and its blood flow is reduced as we age. This occurs at the rate of around 0.5–1.5 per cent per year, so by the time we hit 60–70, we may have up to a 40 per cent decline in liver blood flow compared with a 30-year-old. Other factors include gradual decline in renal function, increased fat deposits and reduction in gut blood flow, which affects absorption. […] The problem arises that the drug’s bioavailability increases due to lack of first-pass clearance; this means that from a standard dose, blood levels can be considerably higher than would be expected in a 40-year-old. This can be a serious problem in drugs with a narrow TI, such as antiarrhythmics. In addition, average doses of warfarin required to provide therapeutic anticoagulation in the elderly are less than half those required for younger people. The person’s lifelong smoking and drinking habits, as well as older individuals ’ sometimes erratic diet also complicate this situation. Among the drugs cleared more slowly in older people are antipsychotics, paracetamol, antidepressants, benzodiazepines, warfarin, beta-blockers and indomethicin.”

“Thousands of polyphenols are found in plants, vegetables, fruit, as well as tea, coffee, wine and fruit juices. […] Flavonoids such as quercetin and fisetin are excellent substrates for COMT, so competitively inhibiting the metabolism of endogenous catecholamine and catechol oestrogens. Quercetin and other polyphenols are found in various foods such as soy (genestein) and they are potent inhibitors of SULT1A1 which sulphate endogenous oestrogens, so potentiating the effects of oestrogens in the body. Many of these flavonoids and isoflavonoids are manufactured and sold as cancer preventative agents; however, it is more likely that their elevation of oestrogen levels may have the opposite effect in the long term. It is also likely that various polyphenols influence other endogenous substrates of sulphotransferases, such as thyroid hormones and various catecholamines. It is gradually becoming apparent that polyphenols can induce UGTs, indeed; it would be surprising if they did not. […] Overall, it is likely that there are a large number of polyphenols that are potent modulators of CYPs and conjugative enzymes. […] It is clear that diet can substantially modulate biotransformation […] As to the effects on prescription drugs, […] abrupt changes in a person’s diet may significantly alter the clearance of drugs and lead to loss of efficacy or toxicity.”

In general, experimental or ‘probe’ drugs […] which are used to study the activities of a number of CYPs, are metabolized more quickly by women than men. This is allowing for differences in weight, fat distribution (body mass index) and volume of distribution […] It appears that CYP expression is linked to growth hormone (GH) and about the same amount is secreted over 24 hours in both sexes. In animals the pattern of release of the hormone is crucial to the effects on the CYPs; in females, GH is secreted in small but more or less continuous pulses, while males secrete large pulses, then periods of no secretion. The system is thought to be similar in humans. […] Little is known of the effects of the menopause and hormone replacement, where steroid metabolism changes dramatically. It is highly likely that these events could have profound effects on female drug clearance. […] females in general are more susceptible to drug adverse reactions than males, especially hepatotoxic effects.”

“For those chronically dependent on ethanol their CYP2E1 levels can be ten-fold higher than non-drinkers and they would clear CYP2E1 substrates extremely quickly if they chose to be sober for a period of time. This may lead to the accumulation of metabolites of the substrates. It is apparent that alcoholics who are sober can suffer paracetamol (acetaminophen)-induced liver toxicity at overdoses of around half that of non-drinkers, which is due to CYP2E1 induction. […]  the vast variation in ADH [alcohol dehydrogenase] catalytic activity across the human race is mainly due to just a few SNPs that profoundly change the efficiency of the isoforms. ADH1B/*1 is the most effective variant and is the ADH wild-type […] Part of a ‘successful’ career as an alcoholic depends possessing the ADH1B/*1 isoform. The other defective isoforms are found in low frequencies in alcoholics and cirrhotics. […] in the vast majority of individuals, whatever their variant of ADH, they are able to process acetaldehyde to acetate and water, as the consequences of failing to do this are severe. With ALDH, the wild-type and gold standard is ALDH2*1/*1, which has the highest activity of all these isoforms and is the second essential component for an alcoholic career. […] the variant ALDH2*1/*2 has less than a quarter of the wild-type’s capacity and is found predominantly in Eastern races. The variant ALDH2*2/*2 is completely useless and renders the individuals very sensitive to acetaldehyde poisoning, although the toxin is removed eventually by ALDH1A1 which does not seem to be affected by polymorphisms. In a survey of 1300 Japanese alcoholics, there was nobody at all with the ALDH2*2/*2 variant. […] Women are much more vulnerable to ethanol damage and on average die in half the time it generally takes for a male alcoholic to drink himself to death. Women drink much less than men also – one study indicated that a group of women consumed about 14,000 drinks to induce cirrhosis, whilst men required more than 44,000 to achieve the same effect. Ethanol distributes in total body water only, so in women their greater fat content means that blood ethanol levels are higher than men of similar weight and age.

September 15, 2016 Posted by | books, genetics, medicine, Pharmacology | Leave a comment

A few lectures

The sound quality of this lecture is not completely optimal – there’s a recurring echo popping up now and then which I found slightly annoying – but this should not keep you from watching the lecture. It’s a quite good lecture, and very accessible – I don’t really think you even need to know anything about genetics to follow most of what he’s talking about here; as far as I can tell it’s a lecture intended for people who don’t really know much about population genetics. He introduces key concepts as they are needed and he does not go much into the technical details which might cause people trouble (this of course also makes the lecture somewhat superficial, but you can’t get everything). If you’re the sort of person who wants details not included in the lecture you’re probably already reading e.g. Razib Khan (who incidentally recently blogged/criticized a not too dissimilar paper from the one discussed in the lecture, dealing with South Asia)…

I must admit that I actually didn’t like this lecture very much, but I figured I might as well include it in this post anyway.

I found some questions included and some aspects of the coverage a bit ‘too basic’ for my taste, but other people interested in chess reading along here may like Anna’s approach better; like Krause’s lecture I think it’s an accessible lecture, despite the fact that it actually covers many lines in quite a bit of detail. It’s a long lecture but I don’t think you necessarily need to watch all of it in one go (…or at all?) – the analysis of the second game, the Kortschnoj-Gheorghiu game, starts around 45 minutes in so that might for example be a good place to include a break, if a break is required.

February 1, 2016 Posted by | anthropology, archaeology, Chess, Computer science, genetics, history, Lectures | Leave a comment

The Origin of Species

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

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

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

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

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

Below I have added some quotes from the book.

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

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

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

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

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

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

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

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

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

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

September 27, 2015 Posted by | biology, books, evolution, genetics, Geology | Leave a comment

An Introduction to Tropical Rain Forests (III)

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

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

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

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

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

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

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

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

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

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

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

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

 

September 23, 2014 Posted by | biology, books, Botany, evolution, genetics, Geography | Leave a comment

Evolution and the Levels of Selection

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

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

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

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

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

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

Open Thread

Some random observations and some links:

i. I’ve written about diabetic hypoglycemia before – I even blogged a book on the topic just a few weeks ago. So I’ll keep this short. Here’s the key observation from the post to which I link: “Hypoglycemia causes functional brain failure that is corrected in the vast majority of instances after the plasma glucose concentration is raised”.

Functional brain failure is pretty much what it sounds like – the brain stops working. The point I want to make here is that hypoglycemia can strike pretty much at any point in time, including when I’m doing stuff like blogging or commenting. I sometimes develop hypoglycemia while deeply engrossed in some intellectual activity, like reading, writing or chess, in part because in those situations I have a tendency to forget to listen to my body’s signals – perhaps I forget to eat because this stuff is really much more interesting than food, perhaps I don’t really care that I should probably take a blood test now because I’d really much rather just finish this book chapter/chess game/blogpost/whatever. That happens. When it happens while I’m blogging, what comes out the other end may look funny. I occasionally write stuff that’s incoherent and stupid. Sometimes the explanation is simple: I’m an idiot. Sometimes other things play a role as well.

This is a variable you cannot observe, but which I have a lot of information about. It’s a variable I’d like readers of this blog to at least be aware of.

ii. Maxwell wrote this post, which you should consider reading. I won’t pretend to have good reasons/justifications for disliking people I conceive of as arrogant, but I do want to note that I do this and always have. Arrogance is a trait I dislike immensely.

iii. Over the last few days I’ve been reading Okasha’s great book Evolution and the Levels of Selection (I’ve almost finished it and I expect to blog it tomorrow) – so of course when Zach Weiner came up with this joke yesterday, I laughed. Loudly:

 

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(Click to view full size. The comic of course has almost nothing to do with the content of the book, but I’ll take any excuse I can get for blogging that comic…)

iv. The Feynman Lectures on Physics. Available to you, online, free of charge. Stuff like this sometimes makes me think we live in a very nice world at this point.

But then I read posts/watch videos like this one and I’m reminded that things are, complicated.

v. A few Khan Academy lectures:

August 8, 2014 Posted by | genetics, history, Khan Academy, Lectures, medicine, personal, Physics | 9 Comments

Autism Spectrum Disorder (I)

Assburger(smbc)

I recently realized that I had actually never read a textbook like this on this topic. I did get some reading materials back when I got diagnosed so it’s not like I’ve never read anything about the stuff (and there was a lot of verbal information back then as well), but as mentioned I haven’t read a text on the topic. It was actually due to the old reading materials in question that I ended up deciding to read this book; I was looking for some other stuff the other day and I ended up perusing some of these materials (which I hadn’t seen in years), and I figured I should probably go read a book on the topic. Now I am.

The book is sort of okay. There are various complaints one might make, the most important one of which in the context of me reading the book is perhaps that children with autism-spectrum disorders grow up and become adults, and adults prefer to read chapters about adult stuff, not stuff about e.g. how to teach the preschooler with the diagnosis social skills. I’ve read roughly half the book at this point, and there’s not in my opinion been enough stuff about the adult setting at this point. Another complaint is that I as usual am somewhat mistrustful when guys like these talk about the conclusions to be drawn from some types of empirical evidence; the coverage has in my opinion been of a decidedly mixed quality in terms of the stuff dealing with behavioural interventions, in the sense that they on the one hand at one point reasonably frankly acknowledge that the evidence is sparse and of poor quality, and on the other hand later on seem to become very excited about a longitudinal study and start drawing big conclusions from that single study – which would be sort of fine, I like longitudinal studies, if not for the fact that the study was based on 6 (!) individuals. Similar things happen elsewhere in that part of the coverage – potential power issues are never mentioned in the book, at least they have not been so far – you find yourself reading about a ‘seminal’ study on 19 individuals, and then you move on to their comments about how there have been several other studies supporting those findings, including a study looking closer at 9 of the individuals involved in the original study. Sometimes it’s hard to know what to think, especially in the situations where the only people evaluating the interventions are the people who came up with them in the first place – this doesn’t seem like a particularly smart way to conduct business, though in some parts of psychology it seems to be more or less standard practice.

The stuff on behavioural interventions has in my opinion been some of the weakest stuff in the book so far, which is why I have not talked about this stuff in my coverage below. Some of the proposed interventions are incredibly expensive, and there’s probably a good reason why such things are usually not covered by public health care systems, however the authors do not really seem to consider economic aspects to be all that important, except to the extent that economic factors unfortunately restrict access to all these nice things we could do for these children; they’re aware that parents may not be able to afford the treatment options which are recommended at this point by people who would benefit from these treatment options being more widely used, but they don’t seem to be aware of the existence of things like cost-effectiveness analyses. It’s one thing to argue that there may be developmental gains to be achieved by early childhood interventions (I’ve previously done work in educational economics and I can tell you that it is a common finding in this literature that you can improve outcomes by throwing lots of money and attention after young children – a finding which should perhaps not be super surprising..), it’s quite another thing to argue that the specific interventions comtemplated are cost-effective. To be fair, cost-effectiveness is incredibly hard to evaluate when you’re contemplating evaluating interventions which may have effects lasting basically the rest of the life of the individual and the intervention is supposed to take place during the first years of a child’s life, but in my opinion you sort of need to at least pretend to try to address this aspect somehow; if you don’t, you’re quite likely to end up in a situation where it seems as if you’re acting as if there’s no (societal) budget constraint, and the authors of this book seem to me to move very close to this position at various points in the coverage.

I knew very little (nothing?) about autism-spectrum disorders before I got the diagnosis – I got diagnosed very late, in my adulthood. It’s sort of funny how you can miss important stuff like this without even knowing, and in a way it relates to a point which came up in my recent post on ethics, specifically the point that ‘bad’ people tend to think they are ‘good’ people, or at least no worse than average. How much do you really know about how good other people are at, say, interpreting nonverbal social signals? Would withdrawal from social interaction make the comparison easier or harder? If you don’t really engage in the normal patterns of non-verbal information exchanges, e.g. eye contact exchanges, during social situations, how are you to know that important information is contained in such exchanges? Individuals seem to make assumptions about these things to a large extent based on what they know themselves (about themselves?), and if you have limitations in these areas it may be difficult to figure out that this is the case; another apt analogy might be children who need glasses early on in their lives – we screen for vision impairment in young children in part because young children don’t know, and may never on their own ever realize, that the world is not supposed to be blurry, and that you’re actually supposed to be able to see all the letters written down on the blackboard.

I thought I should make one thing clear before moving on to the main text, a point particularly relevant considering the comic which I decided to start out with; which is that incompetence should not be equated with/interpreted as malicious intent. It seems to me that many people conceive of people with autism-spectrum disorders as inconsiderate jerks who don’t have a clue – I’ve seen quite smart people state relatively similar things in the past. I dislike the ‘jerk’-model because I try to be thoughtful and considerate when interacting with others, and when these people think that way I feel that they’re devaluing the work I put into this stuff. One important problem which is sort of hard to figure out how to deal with is that I’m well aware that the more thoughtful and considerate I am (…or is it: ‘try to be?’) during social encounters, the more taxing the social interactions may become, and taxing social interactions lead to social isolation and withdrawal. Coming up with a good equilibrium level of effort is not an easy task, and I think one needs to address aspects like these before making strong judgments about things like the jerkishness of specific behaviours. In a way people with social anxiety have similar concerns which other people also cannot observe (in this case it would be excessive amounts of thinking during social situations about whether they are doing stuff right now that may mean that they’ll get rejected by others, which then leads to oversensitivity to clues of rejection, leading to social avoidance because of perceived rejection). Of course people with autism-spectrum disorders may be anxious as well, as also mentioned in the coverage below. The level of self-awareness varies a lot in people with autism-spectrum disorders, but people with relatively high levels of self-awareness may certainly face some constraints and tradeoffs which are not immediately obvious to the outsider and which may actually be assumed by neurotypicals to be absent, given the diagnosis.

The textbook answered one question I’d been thinking about a few times without ever worrying enough about it to actually seek out an answer, which is the question of what the recent diagnostic changes might mean, given that I have a diagnosis which by now has been ‘retired’. It turns out that I was diagnosed with what in the textbook are considered to be the ‘gold-standard tools’, which means that this remark related to the recent diagnostic changes that have taken place seems to answer the question: “The DSM 5 noted that “Individuals with a well-established DSM-IV diagnosis of” “Asperger’s disorder” “should be given the diagnosis of autism spectrum disorder””. I’m not going to ‘ask’ for a ‘new’ diagnosis (/a ‘translation’ of my diagnosis) (and quite aside from what other people like to call this stuff, I like the word ‘eccentric’ a lot better than the word ‘autistic’…), but it’s nice to know which recommendations are being made in this area. Some of the quotes below also relate a bit to these aspects.

I’ve added some quotes from the book below.

“Autism is a developmental neurobiological disorder characterized by severe and pervasive impairments in reciprocal social interaction skills and communication skills (verbal and nonverbal), and by restricted, repetitive, and stereotyped behavior, interests, and activities. […] Autism and autistic stem from the Greek word autos, meaning “self.” The term autism originally referred to a basic disturbance, an extreme withdrawal of oneself from social life, or aloneness. […] The critical point in the scientific history of autism was in 1943, when Leo Kanner published Autistic Disturbances of Affective Conduct, a groundbreaking paper that described the symptoms of 11 children presenting similar behaviors that had not been previously recognized. […] Based on Kanner’s terminology, autism was considered for years a psychosis, and child psychiatrists were using “childhood schizophrenia” and “child psychosis” in autism as “interchangeable diagnoses.” […] A parallel line of inquiry to that of Kanner and Eisenberg is represented by the work of Hans Asperger.”

“In Autism and Pervasive Developmental Disorders, Fred Volkmar and Catherine Lord (2004) distinguished important points of differentiation and similarities between Kanner’s and Asperger’s descriptions. […] In concluding their comparison of Kanner’s and Asperger’s descriptions, Volkmar and Lord pondered whether, despite the relevant differences, it was “scientifically and clinically helpful to classify individuals with these traits into separate categories of autism or Asperger’s disorder, or whether it would be better to treat them as parts of a greater continuum.” The utility of the “greater continuum” has led to the category of autism spectrum disorder to be proposed for DSM-5. […] As a result of [various findings] and the lack of reliability in the community in making distinctions among the ASDs [Autism-Spectrum Disorders] [for example: “Variations in clinical severity among ASD cases are not valid indices of differences in pathophysiology or etiology”], the Fifth Edition of the Diagnostic and Statistical Manual (DSM-5) proposes to collapse all of these clinical syndromes into a single diagnosis of “autism spectrum disorder.” Although this revision is appropriate for community diagnosis, and thus the allocation of clinical and support services, research studies will continue to rely on research diagnostic instruments like the Autism Diagnostic Interview (ADI) and the Autism Diagnostic Observation Schedule (ADOS) [these were both part of my work-up, US] to make categorical distinctions between “autism and not autism” and “autism and autism spectrum disorder” (which includes Asperger’s disorder and PDDNOS [Pervasive Developmental Disorder Not Otherwise Specified]). These distinctions have played a vital role in advancing our understanding of the behavioral and neural profile of ASD over the past two decades”

“Recent studies and reports from the Centers for Disease Control […] have shown an increase in the prevalence of children diagnosed with an ASD to one in 110 […] The reported increase is thought to be attributable to several factors. First, there have been changes in diagnostic practices […] Second, there is greater public awareness of ASD and more case-finding […] Finally, there has been a tendency to diagnose many children with intellectual disability as PDD. […] no evidence currently exists to support any association between ASD and a specific environmental exposure. […] Numerous studies have failed to demonstrate a causal relationship between immunizations, particularly thimerosal-containing vaccines, and ASD […] The CDC (2009) reports the median age for a diagnosis of ASD to be between 4.5 and 5.5 years. […] the ASD diagnosis is four times more common for boys than in girls.”

“The essential features of Asperger’s disorder are severe and sustained impairment in social interaction (criterion A); and the development of restricted, repetitive patterns of behavior, interests, and activities (criterion B); which must cause clinically significant impairment in functioning (criterion C). There are no clinically significant delays in language (criterion D) or cognitive development (criterion E).”

“ASD (excluding Asperger’s disorder) has early language and communication impairment. […] almost two thirds of individuals with ASD also have ID [intellectual disability] […] 15%–20 % of cases of ASD are now linked to genetic or
chromosomal abnormalities […] Fragile X Syndrome (FXS) [is] the most common identifiable cause of ASD and the most common inheritable cause of ID. […] Thirty percent of individuals with FXS demonstrate characteristics of ASD.” [In some other conditions penetrance is even higher – examples that could be mentioned are 15q duplication and Timothy Syndrome, but prevalence is lower in these cases and especially in the latter case some might argue that the autism is the least of that child’s problems..]

Challenging behaviors [in individuals with ASD] may reflect pain that is not communicated verbally […] Challenging behaviors may [also] reflect the child’s difficulty with communication, changes, new places, new situations, new experiences, new sounds, new smells, and new people” [I wonder if you can spot a pattern here in terms of what these children (/people) don’t like? I think an important distinction here is to be made between curiosity and the desire to try out new things. I’m often, hesitant, about trying out new things, yet I’m also quite curious about a lot of things. Be careful which categories you apply here and how they may impact your thinking… In a related vein:] “Insistence on sameness and difficulty with change are common symptoms of an ASD. These behaviors should not typically be considered a behavior done to exert control over others.”

“Psychiatric comorbidity is now acknowledged as quite common in ASD [and] psychiatric comorbidity increases the level of impairment […] There is a handful of questionnaires [aiming at spotting psychiatric comorbidities] that have been developed specifically for use in developmentally disordered or ASD populations. […] none of the measures has the level of research support possessed by questionnaires used in other branches of psychiatry. The vast majority of these instruments have just one study behind their development, or have been studied only by the developer of the instrument. […] one of the main challenges in diagnosing psychiatric disorders in individuals with ASD is the possibility of different presenting symptoms and difficulty in differentiating impairment related to the underlying ASD from impairment due to a separate condition. […] While we do not want to miss true comorbid diagnoses, over-diagnosing comorbidity can be equally harmful. […] Mood disorders, such as depression and bipolar disorder, in ASD have recently begun to receive a great deal of attention […] there are many potential psychosocial stressors that could be possible triggers. For example, higher-functioning individuals who are aware of their deficits and badly desire friends, but lack success in this area, are at particular risk. […] Although there is little research on emotion regulation in ASD, there is clear evidence that emotion regulation is highly variable and often problematic in this population, regardless of psychiatric comorbidity […] Therefore, particularly for mood disorders, it is imperative to consider baseline functioning and not over-diagnose mood disorders when the concern may be more temperamental in nature.”

“Anxiety is considered by some to be the most common comorbid psychiatric concern in ASD […]. The DSM-IV-TR notes that individuals with ASD might have unusual fear reactions, and it is also not uncommon for there to be a general tendency toward anxiety for many individuals with ASD. […] There are many aspects of having an ASD that may lead to this increased risk for anxiety, to the degree that some consider anxiety and the social impairment in ASD to have a bidirectional relationship […] An increase in self-awareness is considered a risk factor for higher anxiety; therefore, anxiety is typically thought of as more common among individuals with ASD who have higher intellectual abilities, and older children, adolescents, and adults.”

“autism may be conceptualized as a disorder of complex information processing resulting from disordered development of the connectivity of cortical systems (e.g., failure of cortical systems specialization) […] approximately 15%–20% of infants with an older sibling diagnosed with autism will ultimately be diagnosable with ASD by three to four years of age. […] [Findings from longitudinal sibling studies] do not support the view that autism is primarily a social-communicative disorder and instead suggest that autism disrupts multiple aspects of development rather simultaneously. […] When both elementary and higher-order abilities in many domains are assessed, it becomes evident that deficits exist in several domains not considered to be integral parts of the autism syndrome, including aspects of the sensory-perceptual, motor, and memory domains. Furthermore, there are enhanced skills and impaired abilities within the same domains as deficits (e.g., memory, language, abstraction). […] Causal explanations for ASD must account for the comprehensive pattern of both deficits and intact aspects of the disorder both within and across multiple domains. […] There is no single primary deficit or triad of deficits, brain regions, or neural systems causing autism. […] Rather, autism broadly affects many abilities at the same time and systematically from its earliest presentation and throughout life. […] This pattern [can] be characterized overall as reflecting a disorder of complex or integrative information processing, which results from altered development of cerebral cortical connectivity in ASD. […] Just as the infant sibling studies have clearly demonstrated, studies of children and adults with autism have also demonstrated a broad but selective profile of deficits and intact or enhanced abilities that all reflect a relationship to information-processing demands. […] it is likely that genes affecting signaling pathways that regulate neuronal organization are strongly implicated in the etiology of autism.”

“ASD is now conceptualized as a developmental neurobiological disorder affecting elaboration of the forebrain circuitry that underlies the abilities most unique to human beings. […] Wiring the brain requires that neurons proliferate, acquire the correct identities, migrate to the appropriate locations, extend axons, and make guidance decisions with a high degree of spatial and temporal fidelity. Converging evidence indicates that more than one of these processes may be altered in various combinations to produce the heterogeneous phenotypes observed in ASD. […] Studies examining head circumference (HC) and brain volume (BV) in individuals with ASD have demonstrated altered brain growth trajectories across the lifespan. […]
• Up to 70 % of infants with ASD exhibit abnormally accelerated brain growth in the first year of life. Approximately 20% to 25% of infants in this subset actually meet formal criteria for macrocephaly (i.e., HC of 2.0 standard deviations above the mean) in the first year.
• BV is significantly larger by two to four years of life, and some children meet criteria for megalencephaly (i.e., BV 2.5 S.D. above mean).
• The first two years of life are usually a period of rapid brain growth in infants as neurons undergo significant postnatal growth in cell size and elaboration (actually overproduction) of axons, synapses, and dendrites. It is possible that this process is exaggerated somehow in at least a subset of ASD.
• Whatever the neurobiological basis, abnormal growth rates in ASD tend to decline significantly after the initial acceleration, causing an apparent “normalization” of BV by adolescence or early adulthood. […]
At the time of maximal brain growth in very early childhood, cerebral gray matter (GM) and white matter (WM) are both increased […] The frontal cortical GM and WM show the most enlargement, followed by the temporal lobe GM and WM and the parietal GM.”

“Thus far, [fMRI and fcMRI] studies have identified underconnectivity with the frontal cortex as a specific characteristic of the altered connectivity in autism, and this characteristic is present across the same wide range of domains of complex information processing that are affected in the disorder, including social, language, executive, and motor processes. […] measures of functional connectivity between specific areas have been shown to reliably predict the degree of impairment in specific domains among those diagnosed with autism. For instance, individuals with poorer social functioning measured by the ADI-R show lower functional connectivity between frontal and parietal cortices. These findings gave rise to the underconnectivity theory in autism, which now has sufficient support that it is accepted as a central feature of the pathophysiology of autism […] Results from these studies are consistent with the notion that autism is a disorder of distributed neural systems (e.g., the connections between structures rather than the structures themselves). […] Diffusion-weighted imaging measures the direction and speed of microscopic water movement in the brain, allowing inferences about the microstructure of the tissue that constrains such movement. These studies have consistently found reduced structural integrity of white matter in adults with ASD, indicating reduced anatomical connectivity […] like measures of functional connectivity, measures of anatomical connectivity derived from diffusion imaging have been shown to reliably predict symptom severity among individuals with autism.”

“In thinking about the genetic basis of autism, it is important to contrast syndromic (or complex) and non-syndromic (or idiopathic/essential) ASD. […] Syndromic ASD includes identifiable autism syndromes with known genetic causes, such as tuberous sclerosis complex, Fragile- X syndrome, Rett syndrome, and Smith-Magenis syndrome.
• Syndromic ASD is associated with a relatively higher propensity for dysmorphic features (including anatomical brain abnormalities), intellectual disability (ID), seizures, and female sex (sex ratios are almost equal).
• Syndromic ASD is also associated with a higher frequency of chromosomal abnormalities in general, many of which have been identified […]. However, it is not yet clear for many of these syndromes which features are typical of autism and which are unique.
Non-syndromic ASD is also called idiopathic autism and consists of cases with and without identifiable micro-deletions or duplications to the DNA. […] individuals with idiopathic ASD are more likely to be male, with sex ratios approximately 1:4 (F:M) but approaching 1:7 in milder cases.”

“Overall, approximately 10 % of children being evaluated for ASD are found to have an identified medical condition with a known genetic lesion such as Fragile X or tuberous sclerosis. An additional 10 % or more have an identifiable chromosomal structural abnormality or copy number variation associated with ASD. […] Recent genome-wide scans using microarray technology have demonstrated a substantial role for small chromosomal deletions or duplications (i.e., copy number variation or CNV) in the etiology of ASD. […] There is [however still] considerable debate concerning the genetic architecture underlying […] the majority of idiopathic autism. Arguments can be made for either the effects of single, but rare Mendelian causes (for which documented CNVs are presumably the tip of the iceberg) or the interaction of numerous common, but low-risk alleles. Genetic linkage and association studies have been traditionally employed to address the latter model, but have failed to consistently identify susceptibility loci.” [An important point I should perhaps make before finishing this post is that if incidence/prevalence of a condition is increasing fast in a population, which seems to be the case here, such an increase is in general considered to be unlikely to only be the result of genetic changes at the population level – that type of pattern is usually indicative of environmental factors playing an important role. It may well be that the ‘average cause’ is different from the ‘marginal cause’, and that it may be a good idea to be careful in terms of which tools to use to explain base rates and growth rates. It might be argued that increased assortative mating among nerds in Silicon Valley has increased incidence locally (I’m sure this might be argued as I’m quite sure I’ve seen this exact argument before…) and I’m not saying this may not be the case, but if close to one percent of the American population get diagnosed, what goes on in Silicon Valley probably isn’t super relevant one way or the other – only roughly 1% of the population live in that area altogether. Even if you were to argue that a similar process is going on everywhere else in the country, it sort of strains belief that ‘something else’ is not going on as well].

July 25, 2014 Posted by | books, genetics, health, medicine, personal, Psychology | Leave a comment

Sexually Transmitted Diseases (4th edition) (IV)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

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

A few lectures

I had trouble following this, but I thought it was an interesting lecture anyway. The sound falls out a couple times for very brief periods of time (a few seconds, but still irritating) and a few other times it’s a bit difficult to tell what he’s saying because he speaks very fast. The guy who controls the camera occasionally forgets to follow him around, which is annoying. But aside from these small problems it’s a good lecture. Here are some links that I found helpful along the way (some were more helpful than others…) while watching the lecture: Duality (projective geometry), Euler characteristic, Big O notation, configuration (geometry), cubic curve, algebraic geometry of projective spaces, Cayley–Bacharach theorem.

I liked most of the lecture, but I agree with Razib Khan’s assessment that: “there may not have been a gene which made humanity, but a subtle complex of numerous genetic and cultural changes which transitioned at a critical point”. Based on his comments towards the end of the lecture, it seems that Pääbo thinks along different lines. It seems to me that the story about the origin and evolution of culture(s) is complex and multidimensional, and to tell the story of how humans got from flint axes to airplanes you need a lot more than to identify a few SNPs. I’d be very surprised if we can ‘narrow it down’ as much as Pääbo seems to assume we might be able to.

This lecture is much less technical than the first two – it’s a rather light and data-poor lecture, but I did find it worth watching.

April 22, 2014 Posted by | genetics, history, Lectures, mathematics | Leave a comment

Random stuff

i. Effects of Academic Acceleration on the Social-Emotional Status of Gifted Students.

I’ve never really thought about myself as ‘gifted’, but during a conversation with a friend not too long ago I was reminded that my parents discussed with my teachers at one point early on if it would be better for me to skip a grade or not. This was probably in the third grade or so. I was asked, and I seem to remember not wanting to – during my conversation with the friend I brought up some reasons I had (…may have had?) for not wanting to, but I’m not sure if I remember the context correctly and so perhaps it’s better to just say that I can’t recall precisely why I was against this idea, but that I was. Neither of my parents were all that keen on the idea anyway. Incidentally the question of grade-skipping was asked in a Mensa survey answered by a sizeable proportion of all Danish members last year; I’m not allowed to cover that data here (or I would have already), but I don’t think I’ll get in trouble by saying that grade-skipping was quite rare even in this group of people – this surprised me a bit.

Anyway, a snippet from the article:

“There are widespread myths about the psychological vulnerability of gifted students and therefore fears that acceleration will lead to an increase in disturbances such as anxiety, depression, delinquent behavior, and lowered self-esteem. In fact, a comprehensive survey of the research on this topic finds no evidence that gifted students are any more psychologically vulnerable than other students, although boredom, underachievement, perfectionism, and succumbing to the effects of peer pressure are predictable when needs for academic advancement and compatible peers are unmet (Neihart, Reis, Robinson, & Moon, 2002). Questions remain, however, as to whether acceleration may place some students more at risk than others.”

Note incidentally that relative age effects (how is the grade/other academic outcomes of individual i impacted by the age difference between individual i and his/her classmates) vary across countries, but are usually not insignificant; most places you look the older students in the classroom do better than their younger classmates, all else equal. It’s worth having both such effects as well as the cross-country heterogeneities (and the mechanisms behind them) in mind when considering the potential impact of acceleration on academic performance – given differences across countries there’s no good reason why ‘acceleration effects’ should be homogenous across countries either. Relative age effects are sizeable in most countries – see e.g. this. I read a very nice study a while back investigating the impact of relative age on tracking options of German students and later life outcomes (the effects were quite large), but I’m too lazy to go look for it now – I may add it to this post later (but I probably won’t).

ii. Publishers withdraw more than 120 gibberish papers. (…still a lot of papers to go – do remember that at this point it’s only a small minority of all published gibberish papers which are computer-generated…)

iii. Parental Binge Alcohol Abuse Alters F1 Generation Hypothalamic Gene Expression in the Absence of Direct Fetal Alcohol Exposure.

Nope, this is not another article about how drinking during pregnancy is bad for the fetus (for stuff on that, see instead e.g. this post – link i.); this one is about how alcohol exposure before conception may harm the child:

“It has been well documented that maternal alcohol exposure during fetal development can have devastating neurological consequences. However, less is known about the consequences of maternal and/or paternal alcohol exposure outside of the gestational time frame. Here, we exposed adolescent male and female rats to a repeated binge EtOH exposure paradigm and then mated them in adulthood. Hypothalamic samples were taken from the offspring of these animals at postnatal day (PND) 7 and subjected to a genome-wide microarray analysis followed by qRT-PCR for selected genes. Importantly, the parents were not intoxicated at the time of mating and were not exposed to EtOH at any time during gestation therefore the offspring were never directly exposed to EtOH. Our results showed that the offspring of alcohol-exposed parents had significant differences compared to offspring from alcohol-naïve parents. Specifically, major differences were observed in the expression of genes that mediate neurogenesis and synaptic plasticity during neurodevelopment, genes important for directing chromatin remodeling, posttranslational modifications or transcription regulation, as well as genes involved in regulation of obesity and reproductive function. These data demonstrate that repeated binge alcohol exposure during pubertal development can potentially have detrimental effects on future offspring even in the absence of direct fetal alcohol exposure.”

I haven’t read all of it but I thought I should post it anyway. It is a study on rats who partied a lot early on in their lives and then mated later on after they’d been sober for a while, so I have no idea about the external validity (…I’m sure some people will say the study design is unrealistic – on account of the rats not also being drunk while having sex…) – but good luck setting up a similar prospective study on humans. I think it’ll be hard to do much more than just gather survey data (with a whole host of potential problems) and perhaps combine this kind of stuff with studies comparing outcomes (which?) across different geographical areas using things like legal drinking age reforms or something like that as early alcohol exposure instruments. I’d say that even if such effects are there they’ll be very hard to measure/identify and they’ll probably get lost in the noise.

iv. The relationship between obesity and type 2 diabetes is complicated. I’ve seen it reported elsewhere that this study ‘proved’ that there’s no link between obesity and diabetes or something like that – apparently you need headlines like that to sell ads. Such headlines make me very, tired.

v. Scientific Freud. On a related note I have been considering reading the Handbook of Cognitive Behavioral Therapy, but I haven’t gotten around to that yet.

vi. If people from the future write an encyclopedic article about your head, does that mean you did well in life? How you answer that question may depend on what they focus on when writing about the head in question. Interestingly this guy didn’t get an article like that.

March 1, 2014 Posted by | alcohol, diabetes, genetics, personal, Psychology, studies, wikipedia | 2 Comments

The Double Helix (II)

I probably didn’t need to write two posts about this book as it’s not very long, but there was a lot of good stuff in there. I’ve given it four stars on goodreads. The main reason why it doesn’t get five stars is that you actually need to know some stuff about these things in order to understand the stuff that’s going on in the book; ideally a book like this would in my view contain detailed enough descriptions of the various problems they encountered along the way not to leave you any more confused than they were, but perhaps that’s too much to ask from a book like this – I occasionally felt that I had to look up stuff in Russell or at wikipedia in order to figure out the details of what he was talking about, and I’m not really sure you should have to do that when reading a book like this. On the other hand some people might rather say that if a book is sufficiently interesting to have you look up stuff in genetics textbooks or online encyclopedias, then that should truly lead to a feeling of ‘mission accomplished’ on part of the author.. As can probably be inferred from these remarks, I’ve not quoted from the most technical parts of the book – I decided to leave such quotes out, as well as potential major ‘spoiler’-quotes.

Aside from some technical stuff a few places which is not quite as clear as I’d have liked it to be, which arguably is just me asking a bit too much from a book like this, it’s a great read. A few quotes from the last half:

“I pilfered Barnal’s and Fankucken’s paper from the Philosophical Library and brought it up to the lab so that Francis could inspect the TMV X-ray picture. When he saw the blank regions that characterize helical patterns, he jumped into action, quickly spilling out several possible helical TMV structrues. From this moment on, I knew I could no longer avoid actually understanding the helical theory. Waiting until Francis had free time to help me would save me from having to master the mathematics, but only at the penalty of my standing still if Francis was out of the room.”

“The chilling prospect of enduring Francis throughout the remaining years of his tenure as the Cavendish Professor was too much to ask of Bragg or anyone with a normal set of nerves.”

“If a student had made a similar mistake, he would be thought unfit to benefit from Cal Tech’s chemistry faculty. Thus, we could not but initially worry whether Linus‘s model followed from a revolutionary re-evaluation of the acid-base properties of very large molecules. The tone of the manuscript, however, argued against any such advance in chemical theory. […] Linus’s chemistry was screwy.”

“Bertrand and Elizabeth looked pleased with themselves. They had just returned from motoring in a friend’s Rolls to a celebrated country house near Bedford. Their host, an antiquarian architect, had never truckled under to modern civilization and kept his house free of gas and electricity. In all ways possible he maintained the life of an eighteenth-century squire, even to providing special walking sticks for his guests as they accompanied him around his grounds.”

“As the clock went past midnight I was becoming more and more pleased. There had been far too many days when Francis and I worried that the DNA structure might turn out to be superficially very dull, suggesting nothing about either its replication or its function in controlling biochemistry. But now, to my delight and amazement, the answer was turning out to be profoundly interesting. For over two hours i happily lay awake with pairs of adenine residues whirling in front of my closed eyes. Only for brief moments did the fear shoot through me that an idea this good could be wrong. […] My scheme was torn to shreds by the following noon.”

“we had lunch, telling each other that a structure this pretty just had to exist.”

“For a while Francis wanted to expand our note to write at length about the biological implications. But finally he saw the point to a short remark and composed the sentence: ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.'”

Watson & Crick’s original 1953 paper, A Structure for Deoxyribose Nucleic Acid, and some related papers are available here. They’re very short (a few pages) and do not take a lot of time to read.

September 18, 2013 Posted by | biology, books, genetics | Leave a comment

The Double Helix (I)

By James Watson. It’s a classic which I’ve long felt that I had to read at some point. I’m roughly half way through – and so far I really enjoy it. The book may be said to be a lot of things, but it is most certainly not boring.

Some quotes:

“One could not be a successful scientist without realizing that, in contrast to the popular conception supported by newspapers and mothers of scientists, a goodly number of scientists are not only narrow-minded and dull, but also just stupid.”

“Clearly Rosy [Rosalind Franklin – US] had to go or be put in her place. The former was obviously preferable […] Unfortunately, Maurice could not see any decent way to give Rosy the boot. […] The thought could not be avoided that the best home for a feminist was in another person’s lab.”

“I was principally interested in birds and managed to avoid taking any chemistry or physics courses which looked of even medium difficulty. Briefly the Indiana biochemists encouraged me to learn organic chemistry, but after I used a bunsen burner to warm up some benzene, I was relieved from further true chemistry. It was safer to turn out an uneducated Ph.D. than to risk another explosion.”

“I was especially interested to hear the talk on nucleic acids to be given by Randall. At that time almost nothing was published about the possible three-dimensional configurations of a nucleic acid molecule. […] The odds, however, were against any real revelation then. Much of the talk about the three-dimensional structure of proteins and nucleic acids was hot air. Though this work had been going on for over fifteen years, most if not all of the facts were soft. Ideas put forward with conviction were likely to be the products of wild crystallographers who delighted in being in a field where their ideas could not be easily disproved.”

“By the time I was back in Copenhagen, the journal containing Linus’s article had arrived from the States. I quickly read it and immediately reread it. Most of the language was above me, and so I could only get a general impression of his argument. I had no way of judging whether it made sense. The only thing I was sure of was that it was written with style.”

“He had lived alone for several years until Odile, some five years his junior, came to Cambridge and hastened his revolt against the stodginess of the middle classes, which delight in unwicked amusements like sailing and tennis, habits particularly unsuited to the conversational life. […] There was no restraint in Francis’s enthusiasms about young women – that is, as long as they showed some vitality and were distinctive in any way that permitted gossip and amusement.”

“it was possible to get a university degree in biology without learning any genetics. That was not to say that the geneticists themselves provided any intellectual help. You would have thougt that with all their talk about genes they should worry about what they were. Yet almost none of them seemed to take seriously the evidence that genes were made of DNA. This fact was unnecessarily chemical.”

“Though Odile could not follow what we were saying, she was obviously cheered by the fact that Francis was about to bring off his second triumph within the month. If this course of events went on, they would soon be rich and could own a car. At no moment did Francis see any point in trying to simplify the matter for Odile’s benefit. Ever since she had told him that gravity went only three miles into the sky, this aspect of their relationship was set. Not only did she not know any science, but any attempt to put some in her head would be a losing fight against the years of her convent upbringing. The most to hope for was an appreciation of the linear way in which money was measured.”

September 17, 2013 Posted by | biology, books, genetics, science | 4 Comments

Wikipedia articles of interest

i. Battle of Passchendaele.

624px-Chateau_Wood_Ypres_1917

“The Battle of Passchendaele (or Third Battle of Ypres or “Passchendaele”) [Note 2] was a campaign of the First World War, fought by the British and their allies against the German empire. The battle took place on the Western Front, between June and November 1917, for control of the ridges south and east of the Belgian city of Ypres in West Flanders, as part of a strategy decided by the Allies at conferences in November 1916 and May 1917.[3] Passchendaele lay on the last ridge east of Ypres, five miles from a railway junction at Rouselare, which was a vital part of the supply system of the German Fourth Army.[4][Note 3] The next stage of the Allied strategy was an advance to Torhout – Couckelaere, to close the German-controlled railway running through Roeselare and Torhout, which did not take place until 1918. Further operations and a British supporting attack along the Belgian coast from Nieuwpoort, combined with an amphibious landing, were to have reached Bruges and then the Dutch frontier.[6] The resistance of the German Fourth Army, unusually wet weather, the onset of winter and the diversion of British and French resources to Italy, following the Austro-German victory at the Battle of Caporetto (24 October – 19 November) allowed the Germans to avoid a general withdrawal, which had seemed inevitable to them in October.[7] The campaign ended in November when the Canadian Corps captured Passchendaele.[8] In 1918 the Battle of the Lys[9] and the Fifth Battle of Ypres,[10] were fought before the Allies occupied the Belgian coast and reached the Dutch frontier.[11]

A campaign in Flanders was controversial in 1917 and has remained so. […] Matters of dispute by the participants and writers and historians since the war have included: the wisdom of pursuing an offensive strategy in the wake of the failed Nivelle Offensive, rather than waiting for the arrival of the American armies in France; the choice of Flanders over areas further south or the Italian front; the climate and weather in Flanders; Haig’s selection of General Hubert Gough and the Fifth Army to conduct the offensive; debates over the nature of the opening attack between advocates of shallow and deeper objectives; the passage of time between the Battle of Messines and the opening attack of the Battles of Ypres; the extent to which the internal troubles of the French armies motivated British persistence in the offensive; the effect of mud on operations; the decision to continue the offensive in October once the weather had broken, and the human cost of the campaign on the soldiers of the German[15] and British armies.[16] […]

Various casualty figures have been published, sometimes with much acrimony, although the highest estimates for British and German casualties appear to be discredited.[152] In the Official History, (1948) Brigadier-General James E. Edmonds put British wounded and killed at 244,897 and claimed that equivalent German figures were not available, estimating German losses at 400,000. Edmonds considered that 30% needed to be added to German statistcs to make them comparable with British casualty criteria.[153][Note 9] In 2007 Jack Sheldon rejected Edmonds’s calculations, suggesting that although German casualties 1 June – 10 November were 217,194, a figure available in Volume III of the Sanitätsbericht (1934, Medical Report Concerning the German Army 1914 – 1918) Edmonds may not have included them as they did not fit his case. Sheldon noted 182,396 slightly wounded and sick soldiers not struck off unit strength which if included would make German losses 399,590.[163] As yet the British claim to have captured 24,065 prisoners has not been disputed.[164]

ii. n-body problem.

“The n-body problem is the problem of predicting the motion of a group of celestial objects that interact with each other gravitationally. Solving this problem has been motivated by the need to understand the motion of the Sun, planets and the visible stars. Its first complete mathematical formulation appeared in Isaac Newton‘s Principia […]

The 2-body problem has been completely solved. For n = 3, solutions exist for special cases. A general solution in terms of first integrals is known to be impossible. An exact theoretical solution for arbitrary n can be given in terms of Taylor series, but in practice such an infinite series must be truncated, giving an approximate solution. In addition, many solutions by numerical integration exist, but these too are approximate solutions.”

Given the nature of the material covered, this article is of course somewhat technical.

iii. Ming Dynasty (featured).

“The Ming Dynasty, also Empire of the Great Ming, was the ruling dynasty of China for 276 years (1368–1644) following the collapse of the Mongol-led Yuan Dynasty. The Ming, described by some as “one of the greatest eras of orderly government and social stability in human history”,[5] was the last dynasty in China ruled by ethnic Han Chinese. Although the primary capital of Beijing fell in 1644 to a rebellion led by Li Zicheng (who established the Shun Dynasty, soon replaced by the Manchu-led Qing Dynasty), regimes loyal to the Ming throne – collectively called the Southern Ming – survived until 1662.

The Hongwu Emperor (ruled 1368–98) attempted to create a society of self-sufficient rural communities ordered in a rigid, immobile system that would guarantee and support a permanent class of soldiers for his dynasty:[6] the empire’s standing army exceeded one million troops and the navy‘s dockyards in Nanjing were the largest in the world.[7] He also took great care breaking the power of the court eunuchs[8] and unrelated magnates, enfeoffing his many sons throughout China and attempting to guide these princes through published dynastic instructions. This failed spectacularly when his teen-aged successor attempted to curtail his uncles’ power, prompting the uprising that placed the Prince of Yan upon the throne as the Yongle Emperor in 1402. The Yongle Emperor established Yan as a secondary capital and renamed it Beijing, constructed the Forbidden City, and restored the Grand Canal and the primacy of the imperial examinations in official appointments. He rewarded his eunuch supporters and employed them as a counterweight against the Confucian scholar-bureaucrats. One, Zheng He, led seven enormous voyages of exploration into the Indian Ocean as far as Arabia and the coast of Africa.

The rise of new emperors and new factions diminished such extravagances; the capture of the Zhengtong Emperor during the 1449 Tumu Crisis ended them completely. The imperial navy was allowed to fall into disrepair while forced labor constructed the Liaodong palisade and connected and fortified the Great Wall of China into its modern form. Wide-ranging censuses of the entire empire were conducted decennially, but the desire to avoid labor and taxes and the difficulty of storing and reviewing the enormous archives at Nanjing hampered accurate figures.[6] Estimates for the late-Ming population vary from 160 to 200 million,[9] but necessary revenues were squeezed out of smaller and smaller numbers of farmers as more disappeared from the official records or “donated” their lands to tax-exempt eunuchs or temples.[6] Haijin laws intended to protect the coasts from “Japanese” pirates instead turned many into smugglers and pirates themselves.” […]

Ming-Empire2

“The Mongol-led Yuan Dynasty (1271–1368) ruled before the establishment of the Ming Dynasty. Alongside institutionalized ethnic discrimination against Han Chinese that stirred resentment and rebellion, other explanations for the Yuan’s demise included overtaxing areas hard-hit by inflation, and massive flooding of the Yellow River as a result of the abandonment of irrigation projects.[10] Consequently, agriculture and the economy were in shambles and rebellion broke out among the hundreds of thousands of peasants called upon to work on repairing the dykes of the Yellow River.[10] […]

The Ming sporadically sent armed forays into Tibet during the 14th century, which the Tibetans successfully resisted.[34][35] Several scholars point out that unlike preceding Mongols, the Ming Dynasty did not garrison permanent troops in Tibet.[36][37] The Wanli Emperor (r. 1572–1620) attempted to reestablish Sino-Tibetan relations in the wake of a Mongol-Tibetan alliance initiated in 1578, an alliance which affected the foreign policy of the subsequent Manchu Qing Dynasty (1644–1912) in their support for the Dalai Lama of the Yellow Hat sect.[26][38][39][40] By the late 16th century, the Mongols proved to be successful armed protectors of the Yellow Hat Dalai Lama after their increasing presence in the Amdo region, culminating in Güshi Khan‘s (1582–1655) conquest of Tibet in 1642.[26][41][42] […]

The imperial household was staffed almost entirely by eunuchs and ladies with their own bureaus.[90] […] as eunuch power at court increased, so did their administrative offices, with eventual twelve directorates, four offices, and eight bureaus.[90] The dynasty had a vast imperial household, staffed with thousands of eunuchs, who were headed by the Directorate of Palace Attendants. The eunuchs were divided into different directorates in charge of staff surveillance, ceremonial rites, food, utensils, documents, stables, seals, apparel, and so on.[91] The offices were in charge of providing fuel, music, paper, and baths.[91] The bureaus were in charge of weapons, silverwork, laundering, headgear, bronzework, textile manufacture, wineries, and gardens.[91] At times, the most influential eunuch in the Directorate of Ceremonial acted as a de facto dictator over the state.[92] […] Eunuchs during the Ming Dynasty gained unprecedented power over state affairs. […]

After the reign of Hongwu—who from 1373 to 84 staffed his bureaus with officials gathered through recommendations only—the scholar-officials who populated the many ranks of bureaucracy were recruited through a rigorous examination system that was first established by the Sui Dynasty (581–618).[96][97][98] Theoretically the system of exams allowed anyone to join the ranks of imperial officials (although frowned upon for merchants to join); in reality the time and funding needed to support the study in preparation for the exam generally limited participants to those already coming from the landholding class. However, the government did exact provincial quotas while drafting officials.[99] This was an effort to curb monopolization of power by landholding gentry who came from the most prosperous regions, where education was the most advanced.[100] The expansion of the printing industry since Song times enhanced the spread of knowledge and number of potential exam candidates throughout the provinces.[101] For young schoolchildren there were printed multiplication tables and primers for elementary vocabulary; for adult examination candidates there were mass-produced, inexpensive volumes of Confucian classics and successful examination answers.[102] […] The exams increased in difficulty as the student progressed from the local level, and appropriate titles were accordingly awarded successful applicants. Officials were classified in nine hierarchic grades, each grade divided into two degrees, with ranging salaries (nominally paid in piculs of rice) according to their rank. […]

Compared to the flourishing of science and technology in the Song Dynasty, the Ming Dynasty perhaps saw fewer advancements in science and technology compared to the pace of discovery in the Western world. In fact, key advances in Chinese science in the late Ming were spurred by contact with Europe. […]

Sinologist historians still debate the actual population figures for each era in the Ming Dynasty. The historian Timothy Brook notes that the Ming government census figures are dubious since fiscal obligations prompted many families to underreport the number of people in their households and many county officials to underreport the number of households in their jurisdiction.[193] Children were often underreported, especially female children, as shown by skewed population statistics throughout the Ming.[194] Even adult women were underreported;[195] for example, the Daming Prefecture in North Zhili reported a population of 378 167 males and 226 982 females in 1502.[196] The government attempted to revise the census figures using estimates of the expected average number of people in each household, but this did not solve the widespread problem of tax registration.[197] Some part of the gender imbalance may be attributed to the practice of female infanticide. The practice is well documented in China, going back over two thousand years, and it was described as “rampant” and “practiced by almost every family” by contemporary authors.[198] However, the dramatically skewed sex ratios, which many counties reported exceeding 2:1 by 1586, can’t likely be explained by infanticide alone.[195]

iv. Lung cancer (featured).

Lung cancer is a disease characterized by uncontrolled cell growth in tissues of the lung. If left untreated, this growth can spread beyond the lung in a process called metastasis into nearby tissue or other parts of the body. Most cancers that start in lung, known as primary lung cancers, are carcinomas that derive from epithelial cells. The main types of lung cancer are small-cell lung carcinoma (SCLC), also called oat cell cancer, and non-small-cell lung carcinoma (NSCLC). The most common symptoms are coughing (including coughing up blood), weight loss and shortness of breath.[1]

The most common cause of lung cancer is long-term exposure to tobacco smoke,[2] which causes 80–90% of lung cancers.[1] Nonsmokers account for 10–15% of lung cancer cases,[3] and these cases are often attributed to a combination of genetic factors,[4] radon gas,[4] asbestos,[5] and air pollution[4] including second-hand smoke.[6][7] Lung cancer may be seen on chest radiograph and computed tomography (CT scan). The diagnosis is confirmed with a biopsy[8] which is usually performed by bronchoscopy or CT-guidance. Treatment and long-term outcomes depend on the type of cancer, the stage (degree of spread), and the person’s overall health, measured by performance status. […]

Overall, 15% of people in the United States diagnosed with lung cancer survive five years after the diagnosis.[10] Worldwide, lung cancer is the most common cause of cancer-related death in men and women …”

v. Fick’s laws of diffusion.

vi. Hox genes.

August 7, 2013 Posted by | genetics, history, medicine, Physics, wikipedia | Leave a comment

The Ancestor’s Tale

I’ve read approximately half the book by now (320 pages). As I pointed out in the last post, “It’s pop sci and I have been disappointed a few times by some of the remarks he’s made during the first 200 pages”. A few examples of ‘irritating/disappointing remarks’:

“In practice all intermediates between pure hunter-gatherers and pure agriculturalists or pastoralists are found. But, earlier than about 10,000 years ago, all human populations were hunter-gatherers.”

Naturally the last sentence is what I take issue with, not the first part. It’s not that it’s wrong as such, but it will likely give people who don’t know any better the wrong impression – you can’t really leave it at that, without qualifying the statement a bit. As I’ve pointed out before, the development of farming and husbandry took thousands of years and what we still think of mostly as ‘hunter-gatherers’ did a lot of the work that brought about the changes necessary for human groups to switch to something close to the model of farming we know today. Dawkins speaks out against the widespread tendency to adopt an essentialist mindset in the field of taxonomy later on (‘the tyranny of the discontinuous mind’), but by mentioning a cut-off point like this without any qualifiers he’s in my view close to engaging in exactly the same kind of behaviour as are the people he’s criticizing. 10,000 years ago is an arbitrary cut-off point, and the ‘hunter-gatherers’ living before then were some places well on their way to developing farming as we know it – the distinction between ‘farmers’ and ‘hunter-gatherers’ was a lot more fluid in the far past than it is now. How far into the past the process went and how gradual the process from hunter-gathering to farming was surprised me a great deal when I read THP, but unfortunately I don’t have the book at my place at this point (I’ve borrowed it to a friend) – so wikipedia will have to do for now:

“Archaeologists have conducted an exhaustive study of Hut 1 at Ohalo II; this hut yielded over 90,000 seeds. The seeds account for more than 100 species of wild barley and fruits. Such a high concentration of seeds in the hut makes it highly unlikely that they were accidentally deposited into the hut via natural forces such as wind. In addition, statistical analysis demonstrates that the concentration of plant matter was significantly higher around the walls than the center. Had the seeds been deposited by the collapsed roof, they would have evenly scattered on the ground. Furthermore, just 13 species of fruit and cereal make up about half of the total number of seeds found in the area; these include brome grains (Bromus pseudobrachystachys), wild barley (Hordeum spontaneum) and millet grass grains (Piptatherum holciforme), just to name a few. This suggests a marked preference of certain species of edible plants. A seed of particular interest comes from the Rubus fruit, which was fragile, difficult to transport, and preferably eaten immediately after collection. The presence of Rubus seeds at the Ohalo II site could indicate that the seeds were dried in the sun or by the fire for storage: early evidence for advanced planning of plant food consumption. Most importantly, the extremely high concentration of seeds clustering around the grinding stone in the northern wall of Hut 1 led Ehud Weiss, an archeologist, to believe that humans at Ohalo II processed the grain before consumption. The exact spatial distribution of the seed around a grinding stone further indicates extensive preparation.”

This settlement burned to the ground around 19,400 BP. They may not have been ‘farmers’, but people who don’t know about people like these may get the wrong idea when reading Dawkins’ statement quoted above. Later on he mentions that, “Husbandry was not the overnight brainwave of some genius” and talks about the gradual changes required to get from where we were to where we ended up, both when it comes to husbandry and agriculture; but the unqualified 10.000 year mark is still bugging me a bit, and it’d not be hard to read the book and assume that the gradual changes mentioned later on took place only after 10.000 BP.

Here’s another annoying little quote:

“It [Madagascar] is a natural botanical and zoological garden, which houses about five per cent of all the plant and animal land species in the world, more than 80 per cent of them being found nowhere else.” […] [two pages later:] “If you wiped out Madagascar, you would destroy about a thousandth of the world’s total land area, but fully four per cent of all species of animals and plants.”

So which is it – four or five per cent? An editor ought to have caught that one and asked him to clarify or change one of the sentences. The repetition also really isn’t necessary. I’d expect stuff like that in a blog post, not in a published book. [see info’s comment…] Yet another:

[footnote:] “Carrots are rich in beta-carotene from which vitamin A can be made: hence the rumour – rumours can be true – that carrots improve vision.”

Yeah, well, if you’re going to include a sentence like that you’re gonna have to write a little more than that. Many people today are presumably aware of how the rumour in question came about but it’s likely that far fewer readers are aware of just how severe of a problem vitamin A deficiency still is in many developing countries (“Most common cause of blindness in developing countries […] Approximately 250,000 to 500,000 malnourished children in the developing world go blind each year from a deficiency of vitamin A, approximately half of whom die within a year of becoming blind.”).

I should point out that he talks about different speciation methods/mechanisms throughout the pages, but he doesn’t mention what they are called (see this for an overview) and his coverage is non-systematic and spread out over many pages. This is understandable given that it’s a pop sci book, but stuff like this is part of the reason why I rarely read such books.

Okay, enough with the critical remarks (I could easily include a few more but it’s not worth it) – there’s lots of really good stuff in there as well. I’ll just post a few quotes below with some ‘big picture’ stuff, but do note that most of the book is concerned with the details of how all this stuff happened – it’s a big narrative, going back hundreds of millions of years, a narrative about where we came from; and given that you need to spend some time talking about what the species which came before us were actually like. Did they have the same number of limbs as we do? How big were they? What did they eat? How did they get from A to B? Who else were around back then? And so on…  Anyway, big picture stuff and some other interesting stuff from the book which I couldn’t help including below:

“Biological evolution has no priviliged line of descent and no designated end. Evolution has reached many millions of interim ends (the number of surviving species at the time of observation), and there is no reason other than vanity – human vanity, as it happens, since we are doing the talking – to designate any one as more privileged or climactic than any other. […] A living creature is always in the business of surviving in its own environment. It is never unfinished – or, in another sense, it is always unfinished. So, presumably, are we.”

“for particular genes, you are more closely related to some chimpanzees than to some humans. And I am closer related to some chimpanzees than to you (or to ‘your’ chimpanzees). Humans as a species, as well as humans as individuals, are temporary vessels containing a mix of genes from different sources. Individuals are temporary meeting points on the crisscrossing routes that genes take through history. […]
We normally assume that we can draw a single evolutionary tree for a set of species. But […] different parts of DNA (and thus different parts of an organism) can have different trees. I think this poses an inherent problem with the very idea of species trees. Species are composites of DNA from many different sources. […] each gene, in fact each DNA letter, takes its own path through history. Each piece of DNA, and each aspect of an organism, can have a different evolutionary tree. […] Species trees can be drawn, but they must be considered a simplified summary of a multitude of gene trees.”

“Rodents are one of the great success stories of mammaldom. More than 40 per cent of all mammal species are rodents, and there are said to be more individual rodents in the world than all other mammals combined.”

“Selection drives evolution only to the extent that the alternative types owe their differences to genes: if the differences are not inherited, differential survival has no impact on future generations.”

“Carnivora is an irritating name because, after all, it simply means meat-eater, and meat-eating has been invented literally hundreds of times independently in the animal kingdom. Not all carnivores are Carnivora […] and not all Carnivora are carnivores (think of the gentle giant panda, eating almost nothing but bamboo).”

“Geological time is large not only in comparison to the familiar timescales of human life and human history. It is large on the timescale of evolution itself. This would surprise those, from Darwin’s critics on, who have complained of insufficient time for natural selection to wreak the changes the theory requires of it. We now realise that the problem is, if anything, opposite. There has been too much time! If we measure evolutionary rates over a short time, and then extrapolate, say, to a million years, the potential amount of evolutionary change turns out to be hugely greater than the actual amount. […] Darwinian selection, if we impose it artificially as hard as we’re able, can drive evolutionary change at a rate far faster than we ever see in nature. […]

One million years, which is too short to notice in most parts of the fossil record, is 20,000 times as long as it takes to triple the oil content of maize seeds. […] these experiments serve to warn against looking at apparent trends spread over millions of fossil years, and naively interpreting them as responses to steadily sustained selection pressures.
Darwinian selection pressures are out there, for sure. And they are immensely important […] But selection pressures are not sustained and uniform over the sort of timescales that can normally be resolved by fossils, especially in older parts of the fossil record. The lesson of the maize and the fruit flies is that Darwinian selection could meander hither and yon, back and forth, ten thousand times, all within the shortest time we can measure in the record of the rocks. My bet is that this happens.
Yet there are major trends over long timescales, and we have to be aware of them too. To repeat an analogy I have used before, think of a cork, bobbing about off the Atlantic coast of America. The Gulf Stream imposes an overall eastward drift in the average position of the cork, which will eventually be washed up on some European shore. But if you measure its direction of movement during any one minute, buffeted by waves and eddies and whirlpools, it will seem to move west as often as east. You won’t notice any eastward bias unless you sample its position over much longer periods. Yet the eastward bias is real, it is there, and it too deserves an explanation.”

“Why bother to lose the wings? They took a long time to evolve, why not hang on to them in case one day they might come in useful again? Alas (for the dodo) that is not the way evolution thinks. Evolution doesn’t think at all, and certainly not ahead. […] Evolution, or its driving engine natural selection, has no foresight. In every generation within every species, the individuals best equipped to survive and reproduce contribute more than their fair share of genes to the next generation. The consequence, blind as it is, is the nearest approach to foresight that nature permits. Wings might be useful a million years hence when sailors arrive with clubs. But wings will not help a bird contribute offspring and genes to the next generation […in the specific setting in which the ancestors of the dodos found themselves, US. It seems obvious that in the general case wings do help birds get more offspring or they wouldn’t bother with them…], in the immediate here and now. On the contrary wings, and especially the massive breast muscles needed to power them, are an expensive luxury. Shrink them, and the ressources saved can now be spent on something more immediately useful such as eggs: immediately useful for surviving and reproducing the very genes that programmed the shrinkage.
That’s the kind of thing natural selection does all the time. It is always tinkering: here shrinking a bit, there expanding a bit, constantly adjusting, putting on and taking off, optimising immediate reproductive success. Survival in future centuries doesn’t enter into the calculation, for the good reason that it isn’t really a calculation at all. It all happens automatically, as some genes survive in the gene pool and others don’t. […]

Moas are extreme among flightless birds in that they have no trace of wings at all, not even buried vestiges of wing bones. They thrived in both the North and South Islands of New Zealand until the recent invasion by the Maori people, about 1250 AD. They were easy prey […] and the Maoris slaughtered them all, eating the choicer parts and discarding the rest, belying, not for the first time, the wishful myth of the noble savage living in respectful harmony with its environment. […] Perhaps as many as 200 species [of flightless rail] have gone extinct on tropical Pacific islands since human contact.” […other estimates are even higher]

July 9, 2013 Posted by | archaeology, biology, books, evolution, genetics | 3 Comments

Chromosomal abnormalities..

I finished Peter Jensen’s book, which I also mentioned in the previous post, this morning, and I decided to add a few comments and links to articles covering stuff he also covers in his book. I liked the book and gave it 3 stars on goodreads. It’s old – from 1998 – so a lot of stuff has happened since then in this field (e.g. ‘new’ genetic diseases, such as 17q21.31 microdeletion syndrome, have been ‘discovered’ – though I should caution here that according to Jensen a distinction is to be made between ‘chromosomal abnormalities’ and ‘genetic diseases’; unlike many genetic disorders, chromosomal abnormalities involve mutations which are large enough to be seen using an ordinary light microscope). However my working assumption has been that most of the stuff covered in the book is unlikely to have changed much; how a chromosomal abnormality affects the individuals who have it doesn’t change much from one decade to another, even though improvements in medical technology may have improved outcomes for some specific diseases.

Some links to stuff he talks about in the book, in no specific order: Chromosome abnormality (I should add that pretty much every link in that article is to an article on something which is also covered in the book), Aneuploidy, Robertsonian translocation, Klinefelter syndrome, Turner Syndrome, Williams Syndrome, Down Syndrome, Patau syndrome, Fragile X syndrome, Angelman Syndrome, Prader-Willi syndrome, Barr body, Non-disjunction, Amniocentesis, Trisomy 8, FMR1.

A few general remarks: It should be noted that autosomal chromosomal abnormalities are usually more severe than sex-linked chromosomal abnormalities. More than 95% of chromosomal abnormalities result in spontaneous abortion, and 60% of early spontaneous abortions (within the first trimester) are due to chromosomal abnormalities. Monosomies (including partial ones) tend to have more severe consequences than do trisomies. Even though people tend to think that way about genetic diseases not all chromosomal abnormalities are best thought of as inhabiting a binary event space (either you have it or you don’t); some of them display to a significant extent a dose–response relationship (see e.g. the articles on the FMR1 gene & Fragile X syndrome). As should be obvious from the number of associated abortions, many of the chromosomal abnormalities (particularly the autosomal ones) lead to really horrible outcomes: Among Pataus Syndrome sufferers less than 40% survive past [remember: 1998 numbers] one week after birth, and only 4,5% survive past 6 months [according to wikipedia’s article on the topic, “More than 80% of children with Patau syndrome die within the first year of life” – so mortality is still very high]; when it comes to Edward’s syndrome likewise approximately 60% died within a week, and around 5% were still alive after a year back then – and this is just considering the variable survival, not stuff like blindness, polydactyli, organ malformation (brain, heart, kidneys, …), deafness, etc., etc., which are also very often present in people with these disorders…

Incidentally I read most of Carpe Jugulum today, but I won’t blog that one until tomorrow.

June 7, 2013 Posted by | books, genetics, medicine | Leave a comment

Wikipedia articles of interest

i. History of evolutionary thought (featured).

800px-Huxley_-_Mans_Place_in_Nature

It’s hard to quote from this article but I decided to anyway; it’s an excellent overview article and you should really read it all even though it’s a rather long article. An interesting aspect here is how close to Darwin some people were back in the past, and how reasonably similar ideas have popped up again and again throughout history – to take some examples:

Epicurus (341–270 BC) anticipated the idea of natural selection. Lucretius explicated these ideas in his De rerum natura. In the Epicurean system, it was assumed that many species had been spontaneously generated from “Gaia” in the past, but that only the most functional forms survived to have off-spring. The Epicureans do not seem to have anticipated the full theory of evolution as we now know it and seem to have postulated a separate abiogenetic events for each species rather than postulating a single abiogenetic event coupled with the differentiation of species over time from a single (or small number of) originating parent organism(s).” […]

“the Afro-Arab writer al-Jahiz, wrote in the 9th century. In the Book of Animals, he considered the effects of the environment on an animal’s chances for survival, and described the struggle for existence.[25] Al-Jahiz also wrote descriptions of food chains.[26] Al-Jahiz speculated on the influence of the environment on animals and considered the effects of the environment on the likelihood of an animal to survive. The Book of Animals states,

Animals engage in a struggle for existence; for resources, to avoid being eaten and to breed. Environmental factors influence organisms to develop new characteristics to ensure survival, thus transforming into new species. Animals that survive to breed can pass on their successful characteristics to offspring.”

[…]

“In 1377 Ibn Khaldun wrote the Muqaddimah in which he asserted that humans developed from “the world of the monkeys”, in a process by which “species become more numerous”” […]

The article points out this aspect explicitly and notes that: “It is possible to look through the history of biology from the ancient Greeks onwards and discover anticipations of almost all of Charles Darwin‘s key ideas. […] but such anticipations should not be taken out of the full context of the writings or of cultural values of the time which could make Darwinian ideas of evolution unthinkable.[66]

A little more from the article; here’s a quote on the role of the church in the Middle Ages (and later):

“During the Early Middle Ages, Greek classical learning was all but lost to the West. However, contact with the Islamic world, where Greek manuscripts were preserved and expanded, soon led to a massive spate of Latin translations in the 12th century. Europeans were re-introduced to the works of Plato and Aristotle, as well as to Islamic thought. Christian thinkers of the scholastic school, in particular Abelard and Thomas Aquinas, combined Aristotelian classification with Plato’s ideas of the goodness of God, and of all potential life forms being present in a perfect creation, to organize all inanimate, animate, and spiritual beings into a huge interconnected system: the scala naturæ, or great chain of being.[6][32]

Within this system, everything that existed could be placed in order, from “lowest” to “highest”, with Hell at the bottom and God at the top—below God, an angelic hierarchy marked by the orbits of the planets, mankind in an intermediate position, and worms the lowest of the animals. As the universe was ultimately perfect, the great chain was also perfect. There were no empty links in the chain, and no link was represented by more than one species. Therefore no species could ever move from one position to another. Thus, in this Christianized version of Plato’s perfect universe, species could never change, but remained forever fixed, in accordance with the text of Genesis. For humans to forget their position was seen as sinful, whether they behaved like lower animals or aspired to a higher station than was given them by their Creator.[6]

Creatures on adjacent steps were expected to closely resemble each other, an idea expressed in the saying: natura non facit saltum (“nature does not make leaps”).[6] This basic concept of the great chain of being greatly influenced the thinking of Western civilization for centuries (and still has an influence today). It formed a part of the argument from design presented by natural theology. As a classification system, it became the major organizing principle and foundation of the emerging science of biology in the 17th and 18th centuries.[6]

As I pointed out above it’s hard to choose what to quote because there’s so much good stuff here; if you find this topic interesting you really should read it all. The article is probably easier to read if you’ve heard about people like Hutton, Mendel, Lamarck etc. before and have some familiarity with the concepts mentioned and the (diverse sets of) fields involved; but as the excerpts also illustrate there’s always a link (or several links) if a specific concept is unfamiliar, and I actually believe the article is very readable even if you don’t know a lot about this stuff – though I should note that I may be mistaken, given that I’ve read about most of the concepts and topics covered in the article before.

I should probably point out here that I believe this is really wikipedia at its finest – the featured rating is well-deserved. And note that this part of wikipedia in general contains some really great stuff; the article on evolution, the article about Darwin, and the article about genetics, to take but three other relevant articles about related topics, are also all of them featured. There’s a lot of stuff here. Another place to look is in the archives of Razib Khan’s blog; he’s written some good stuff on related topics.

ii. Triceratops (featured). I doubt there’s a reader of this blog who has not heard the name of these animals or could not tell me roughly how they looked like, but how much do you actually know about those guys? After reading this article you’ll know more..

iii. Gilbert du Motier, Marquis de Lafayette (‘good article’). A lot of interesting lives have been lived by people in the past, and many of the stories of these people never get told. This guy lived a remarkable life:

Marie-Joseph Paul Yves Roch Gilbert du Motier, Marquis de La Fayette (French pronunciation: ​[maʁki də la fajɛt]; 6 September 1757 – 20 May 1834), often known simply as Lafayette, was a French aristocrat and military officer born in Chavaniac, in the province of Auvergne in south central France. Lafayette was a general in the American Revolutionary War and a leader of the Garde nationale during the French Revolution. […]

Lafayette was the most important link between the American and the French Revolutions. As an ardent supporter of the United States’ constitutional principles he called on all nations to follow the American example. […] Under Lafayette’s influence Louis XVI issued the edict of toleration in 1787 (Edict of Versailles), which particularly benefitted the Huguenots.[2] Back in France in 1788, Lafayette was called to the Assembly of Notables to respond to the fiscal crisis. Lafayette proposed a meeting of the French Estates-General, where representatives from the three traditional orders of French society—the clergy, the nobility and the commoners—met. He served as vice president of the resulting body. The Declaration of the Rights of Man and of the Citizen was largely based on his draft.[3] Lafayette was appointed commander-in-chief of the Garde nationale in response to violence. During the French Revolution, Lafayette attempted to maintain order—to the point of ordering the Garde nationale to fire on demonstrators at the Champ de Mars in July 1791—an action for which he ultimately was persecuted by the Jacobins. In August 1792, as the radical factions in the Revolution grew in power, Lafayette tried to flee to the United States through the Dutch Republic. He was captured by Austrians and spent more than five years in prison.

Lafayette returned to France after Napoleon Bonaparte secured his release from prison in 1797. He refused to participate in Napoleon’s government, but was elected to the Chamber of Deputies under the Charter of 1815, during the Hundred Days. With the Bourbon Restoration, Lafayette became a liberal member of the Chamber of Deputies in 1815, a position he held until his death. […]

In France, Lafayette worked with Thomas Jefferson to establish trade agreements between the United States and France. These negotiations aimed to reduce U.S. debt to France, and included commitments on tobacco and whale oil.[57] He joined the French abolitionist group Society of the Friends of the Blacks, which advocated the end of the slave trade and equal rights for free blacks. In 1783, in correspondence with Washington, he urged the emancipation of slaves; and to establish them as tenant farmers.[58] […]

King Louis XVI convoked the Assembly of Notables on 29 December 1786, in response to France’s fiscal crisis. The King appointed Lafayette to the body, in the comte d’Artois’ division, which met on 22 February 1787. In an address first read to the assembly, then signed and endorsed by Lafayette, it was proposed to lower unnecessary spending, which included, among other things, purchase of useless estates and gifts to courtiers.[77] He called for a “truly national assembly”, which represented the three classes of French society: clergy, nobility, and commons.[78] On 8 August 1788, the King agreed to hold an Estates General the next year. Lafayette was elected to represent the nobility (Second Estate) from Riom in the Estates General.[79]

The Estates General convened on 5 May 1789; debate began on whether the delegates should vote by head or by Estate. If voting was by Estate then the nobility and clergy would be able to overturn the commons; if by head, then the larger Third Estate could dominate. Before the meeting, he agitated for the voting by head, rather than estate […]

Lafayette was unwilling to cooperate with Napoleon’s government. In 1804, Napoleon was crowned Emperor after a plebiscite in which Lafayette did not participate. He remained relatively quiet, although he spoke publicly on Bastille Day events.[134] After the Louisiana Purchase, Jefferson asked if he would be interested in the governorship. Lafayette declined, citing personal problems and the desire to work for liberty in France.[135] […] As the restored monarchy of Charles X became more conservative, Lafayette re-emerged as a prominent public figure. […] Throughout his legislative career, he continued to endorse causes such as freedom of the press, suffrage for all taxpayers, and the worldwide abolition of slavery.[149] […]

American President Andrew Jackson ordered that Lafayette be accorded the same funeral honors as John Adams and George Washington. Therefore, 24-gun salutes were fired from military posts and ships, each shot representing a U.S. state. Flags flew at half mast for thirty-five days, and “military officers wore crepe for six months”.[157][158] The Congress hung black in chambers and asked the entire country to dress in black for the next thirty days.[159] […] Lafayette reputation in America has always stood very high, and both the popular mind and the scholarship. […] Lafayette reputation among French historians is more problematic. François Furet includes him among the 14 most important actors of the French Revolution, where he played a critical role in 1789-92. He is praised as the embodiment of the liberal ideals of 1789, but he had few eulogies. French historians have said he was too ambitious and yet too mediocre an intellect to play a bigger role. […] To historians on the left, he was a traitor to the glorious cause. To historians on the right, he was too ineffective to be their hero. [168]

Although I’ve blogged some of them before, I guess I should point out that Khan Academy has some quite good videos about the French Revolution and related stuff here.

iv. Klondike Gold Rush (‘good article’).

745px-ChilkootPass_GoldenStairs2

“The Klondike Gold Rush, also called the Yukon Gold Rush, the Alaska Gold Rush, the Alaska-Yukon Gold Rush and the Last Great Gold Rush, was a migration by an estimated 100,000 prospectors to the Klondike region of the Yukon in north-western Canada between 1896 and 1899. Gold was discovered here on August 16, 1896 and, when news reached Seattle and San Francisco the following year, it triggered a “stampede” of would-be prospectors. The journey proved too hard to many and only between 30,000 and 40,000 managed to arrive. Some became wealthy; however, the majority went in vain and only around 4,000 struck gold. The Klondike Gold Rush ended in 1899 after gold was discovered in Nome, prompting an exodus from the Klondike. […] To accommodate the prospectors, boom towns sprang up along the routes and at their end Dawson City was founded at the confluence of the Klondike and the Yukon River. From a population of 500 in 1896, the hastily constructed town came to house around 30,000 people by summer 1898. Poorly built, isolated and unsanitary Dawson suffered from fires, high prices and epidemics. Despite this, the wealthiest prospectors spent extravagantly gambling and drinking in the saloons. The Native Hän people, on the other hand, suffered from the rush. Many of them died after being moved into a reserve to make way for the stampeders.”

An estimated 100.000 people tried to reach the goldfields. The 1900 United States Census put the population of the US at 76.2 million at that time so the estimated number of people leaving their homes in order to dig for gold corresponds to ~0,13% of the total population of the United States at that time; more than one in a thousand of the entire population… (not all prospectors were Americans, but a great majority – ~60-80%, according to the article – were).

“The region was mountainous, the rivers winding and sometimes impassable; the short summers could be hot, while from October to June, during the long winters, temperatures could drop below −50 °C (−58 °F).[60][61][n 10]

Aids for the travelers to carry their supplies varied; some had brought dogs, horses, mules or oxen, whereas others had to rely on carrying their equipment on their backs or on sleds pulled by hand.[64] Shortly after the stampede began in 1897, the Canadian authorities had introduced rules requiring anyone entering Yukon Territory to bring with them a year’s supply of food; typically this weighed around 1,150 pounds (520 kg).[65] By the time camping equipment, tools and other essentials were included, a typical traveler was transporting as much as a ton in weight.[65] […]

Of the estimated 30,000 to 40,000 people who reached Dawson City during the gold rush, only around 15,000 to 20,000 finally became prospectors. Of these, no more than 4,000 struck gold and only a few hundred became rich.[28] By the time that most of the stampeders arrived in 1898, the best creeks had all been claimed, either by the long-term miners in the region, or by the first arrivals of the year before.[131] […]

Skagway rapidly became famous in the international media; the author John Muir described the town as “a nest of ants taken into a strange country and stirred up by a stick”.[181] […] the White Pass leading from Skagway to the Klondike closed in late 1897 and around 5,000 prospectors found themselves stuck in the town, unable to progress or to return home.[182] […] The town was effectively lawless, dominated by drinking, gunfire and prostitution.[184] The visiting NWMP Superintendent Sam Steele noted that it was “little better than a hell on earth … about the roughest place in the world”.[185] Nonetheless, by the summer of 1898, with a population—including migrants—of between 15,000 and 20,000, Skagway was the largest city in Alaska.[186] […]

In late summer 1897 Skagway and Dyea fell under the control of Jefferson Randolph “Soapy” Smith and his men, who arrived from Seattle shortly after Skagway began to expand.[187][188] He was an American confidence man whose gang, 200 to 300 strong, cheated and stole from the prospectors traveling through the region.[189][n 23] He maintained the illusion of being an upstanding member of the community, opening three saloons as well as creating fake businesses to assist in his operations.[191][192] One of his scams was a fake telegraph office where one of his men dressed as a telegraph operator would charge to send messages all over the US and Canada, often pretending to receive a reply.[193] Opposition to Smith steadily grew and, after weeks of vigilante activity, he was killed in Skagway during the shootout on Juneau Wharf on July 8, 1898.[187][194] […]

Prices remained high in Dawson and supply fluctuated according to the season. During the winter of 1897 salt became worth its weight in gold, while nails, vital for construction work, rose in price to $28 ($760) per lb (0.45 kg).[218] Cans of butter sold for $5 ($140) each.[219] The only eight horses in Dawson were slaughtered for dog food as they could not be kept alive over the winter.[218][n 27] The first fresh goods arriving in the spring of 1898 sold for record prices, eggs reaching $3 ($81) each and apples $1 ($27).[222]

Under these conditions scurvy, a potentially fatal illness caused by the lack of vitamin C, proved a major problem in Dawson City, particularly during the winter […] Dysentery and malaria were also common in Dawson, and an epidemic of typhoid broke out in July and ran rampant throughout the summer. […]

Gambling was popular, with the major saloons each running their own rooms; a culture of high stakes evolved, with rich prospectors routinely betting $1,000 ($27,000) at dice or playing for a $5,000 ($140,000) poker pot. […] Wealthy prospectors were expected to drink champagne at $60 ($1,600) a bottle, and the Pavilion dancehall cost its owner, Charlie Kimball, as much as $100,000 ($80 million) to construct and decorate.[234] Elaborate opera houses were built, bringing singers and specialty acts to Dawson.[235] Tales abounded of prospectors spending huge sums of money on entertainment — Jimmy McMahon once spent $28,000 ($760,000) in a single evening, for example.[236] Most payments were made in gold dust and in places like saloons, there was so much spilled gold that a profit could be made just by sweeping the floor.[223]

v. Northrop Grumman B-2 Spirit. A very (advanced? sophisticated? expensive?) aircraft.

800px-B-2_Spirit_original

“The Northrop Grumman B-2 Spirit, also known as the Stealth Bomber, is an American strategic bomber, featuring low observable stealth technology designed for penetrating dense anti-aircraft defenses; it is able to deploy both conventional and nuclear weapons. The bomber has a crew of two and can drop up to eighty 500 lb (230 kg)-class JDAM GPS-guided bombs, or sixteen 2,400 lb (1,100 kg) B83 nuclear bombs. The B-2 is the only aircraft that can carry large air-to-surface standoff weapons in a stealth configuration.

Development originally started under the “Advanced Technology Bomber” (ATB) project during the Carter administration, and its performance was one of the reasons for his cancellation of the B-1 Lancer. ATB continued during the Reagan administration, but worries about delays in its introduction led to the reinstatement of the B-1 program as well. Program costs rose throughout development. Designed and manufactured by Northrop Grumman with assistance from Boeing, the cost of each aircraft averaged US$737 million (in 1997 dollars).[3] Total procurement costs averaged $929 million per aircraft, which includes spare parts, equipment, retrofitting, and software support.[3] The total program cost including development, engineering and testing, averaged $2.1 billion per aircraft in 1997.[3]

Because of its considerable capital and operating costs, the project was controversial in the U.S. Congress and among the Joint Chiefs of Staff. The winding-down of the Cold War in the latter portion of the 1980s dramatically reduced the need for the aircraft, which was designed with the intention of penetrating Soviet airspace and attacking high-value targets. During the late 1980s and 1990s, Congress slashed plans to purchase 132 bombers to 21. In 2008, a B-2 was destroyed in a crash shortly after takeoff, and the crew ejected safely.[4] A total of 20 B-2s remain in service with the United States Air Force.

The B-2 is capable of all-altitude attack missions up to 50,000 ft, with a range of more than 6,000 nautical miles unrefuelled and over 10,000 nautical miles with one refueling. Though originally designed primarily as a nuclear bomber, it was first used in combat to drop conventional bombs on Serbia during the Kosovo War in 1999, and saw continued use during the wars in Iraq and Afghanistan.[5]

May 28, 2013 Posted by | evolution, genetics, history, wikipedia | Leave a comment

Stuff

i. I had a doctor’s appointment today and got the results of my bloodwork back. My Hba1c was 48, or 6.5%. This is the lowest it’s been for as long as I can remember. I have had some trouble with hypoglycemic episodes now and then, but not significantly more than usual and I’ve had no major episodes. I believe the lowered Hba1c is probably mostly a result of lowered nocturnal blood glucose values. These have however at some points been uncomfortably low, so I’m not sure 6,5 is a realistic long-term goal and because of those uncomfortably low values I have made adjustments along the way which probably means that the Hba1c may be a bit higher next time if other things stay pretty much the same (which I know they won’t; for instance I’m planning on significantly increasing my running over the next four months). But even so I was very happy about this result, as I choose to believe that it means I’ll actually be able to obtain <7.0% results in the future without major adverse events if I’m careful and vigilant.

This recent post goes into more detail about the hypoglycemia risk and what it’s about. This Danish post has some data on the distribution of Hba1c results among Danish diabetics – the relevant figure is this one (with 6.5%, I’m in the 10% fractile).

ii. I’m now ‘officially’ a researcher. I have just become a member of Statistics Denmark’s research programme (-forskerordning), which means that I’ve obtained access to a specific data set which I’ll do work on during the next year. Danish registers contain a lot of good information compared to the registers of most other countries, so I may actually be able to look at stuff that a lot of researchers elsewhere are simply not able to analyze due to data issues – which is exciting. Unfortunately I’ll not be comfortable blogging anything about this stuff, as there are a huge number of restrictions on data access/sharing etc. – but I believe it’ll be interesting to work with this stuff and I’m looking forward to it.

iii. A couple of Khan Academy videos:

iv. PlosOne: Sex Differences in Mathematics and Reading Achievement Are Inversely Related: Within- and Across-Nation Assessment of 10 Years of PISA Data.

Abstract: “We analyzed one decade of data collected by the Programme for International Student Assessment (PISA), including the mathematics and reading performance of nearly 1.5 million 15 year olds in 75 countries. Across nations, boys scored higher than girls in mathematics, but lower than girls in reading. The sex difference in reading was three times as large as in mathematics. There was considerable variation in the extent of the sex differences between nations. There are countries without a sex difference in mathematics performance, and in some countries girls scored higher than boys. Boys scored lower in reading in all nations in all four PISA assessments (2000, 2003, 2006, 2009). Contrary to several previous studies, we found no evidence that the sex differences were related to nations’ gender equality indicators. Further, paradoxically, sex differences in mathematics were consistently and strongly inversely correlated with sex differences in reading: Countries with a smaller sex difference in mathematics had a larger sex difference in reading and vice versa. We demonstrate that this was not merely a between-nation, but also a within-nation effect. This effect is related to relative changes in these sex differences across the performance continuum: We did not find a sex difference in mathematics among the lowest performing students, but this is where the sex difference in reading was largest. In contrast, the sex difference in mathematics was largest among the higher performing students, and this is where the sex difference in reading was smallest. The implication is that if policy makers decide that changes in these sex differences are desired, different approaches will be needed to achieve this for reading and mathematics. Interventions that focus on high-achieving girls in mathematics and on low achieving boys in reading are likely to yield the strongest educational benefits.”

v. Genomic responses in mouse models poorly mimic human inflammatory diseases.

Abstract: “A cornerstone of modern biomedical research is the use of mouse models to explore basic pathophysiological mechanisms, evaluate new therapeutic approaches, and make go or no-go decisions to carry new drug candidates forward into clinical trials. Systematic studies evaluating how well murine models mimic human inflammatory diseases are non-existent. Here, we show that, although acute inflammatory stresses from different etiologies result in highly similar genomic responses in humans, the responses in corresponding mouse models correlate poorly with the human conditions and also, one another. Among genes changed significantly in humans, the murine orthologs are close to random in matching their human counterparts (e.g.,R^2 between 0.0 and 0.1). In addition to improvements in the current animal model systems, our study supports higher priority for translational medical research to focus on the more complex human conditions rather than relying on mouse models to study human inflammatory diseases.”

vi. Married men at the age of 40 can expect to live on average 7.1 years longer than unmarried men at the age of 40, and 6.6 years longer than divorced men at the age of 40. For women the life expectancy difference between the married and unmarried group is 4.8 years, and the difference between married women and divorced women is 4.3 years. The excess mortality for unmarried men in their forties (compared with married males) is around 250%, and for men in their fifties it’s still above 200%.

The data reported above is from a new publication by Statistics Denmark which you can read here. Here’s a related publication. Here is a recent publication on the education levels of Danish emigrants. All three publications are unfortunately in Danish.

vii. Nasa – The Tyranny of the Rocket Equation. This part was surprising to me, because I’d never really thought about this:

“If the radius of our planet were larger, there could be a point at which an Earth escaping rocket could not be built. Let us assume that building a rocket at 96% propellant (4% rocket), currently the limit for just the Shuttle External Tank, is the practical limit for launch vehicle engineering. Let us also choose hydrogen-oxygen, the most energetic chemical propellant known and currently capable of use in a human rated rocket engine. By plugging these numbers into the rocket equation, we can transform the calculated escape velocity into its equivalent planetary radius. That radius would be about 9680 kilometers (Earth is 6670 km). If our planet was 50% larger in diameter, we would not be able to venture into space, at least using rockets for transport.”

viii. I’m very surprised they did not already know this.

April 3, 2013 Posted by | data, demographics, diabetes, genetics, Khan Academy, papers, personal | Leave a comment