Biodemography of aging (II)

In my first post about the book I included a few general remarks about the book and what it’s about. In this post I’ll continue my coverage of the book, starting with a few quotes from and observations related to the content in chapter 4 (‘Evidence for Dependence Among Diseases‘).

“To compare the effects of public health policies on a population’s characteristics, researchers commonly estimate potential gains in life expectancy that would result from eradication or reduction of selected causes of death. For example, Keyfitz (1977) estimated that eradication of cancer would result in 2.265 years of increase in male life expectancy at birth (or by 3 % compared to its 1964 level). Lemaire (2005) found that the potential gain in the U.S. life expectancy from cancer eradication would not exceed 3 years for both genders. Conti et al. (1999) calculated that the potential gain in life expectancy from cancer eradication in Italy would be 3.84 years for males and 2.77 years for females. […] All these calculations assumed independence between cancer and other causes of death. […] for today’s populations in developed countries, where deaths from chronic non-communicable diseases are in the lead, this assumption might no longer be valid. An important feature of such chronic diseases is that they often develop in clusters manifesting positive correlations with each other. The conventional view is that, in a case of such dependence, the effect of cancer eradication on life expectancy would be even smaller.”

I think the great majority of people you asked would have assumed that the beneficial effect of hypothetical cancer eradication in humans on human life expectancy would be much larger than this, but that’s just an impression. I’ve seen estimates like these before, so I was not surprised – but I think many people would be if they knew this. A very large number of people die as a result of developing cancer today, but the truth of the matter is that if they hadn’t died from cancer they’d have died anyway, and on average probably not really all that much later. I linked to Richard Alexander’s comments on this topic in my last post about the book, and again his observations apply so I thought I might as well add the relevant quote from the book here:

“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.”

Remove one cause of death and there are plenty of others standing in line behind it. We already knew that; two hundred years ago one out of every four deaths in England was the result of tuberculosis, but developing treatments for tuberculosis and other infectious diseases did not mean that English people stopped dying; these days they just die from cardiovascular disease and cancer instead. Do note in the context of that quote that Alexander is talking about the maximum human lifetime, not average life expectancy; again, we know and have known for a long time that human technology can have a dramatic effect on the latter variable. Of course a shift in one distribution will be likely to have spill-over effects on the other (if more people are alive at the age of 70, the potential group of people also living on to reach e.g. 100 years is higher, even if the mortality rate for the 70-100 year old group did not change) the point is just that these effects are secondary effects and are likely to be marginal at best.

Anyway, some more stuff from the chapter. Just like the previous chapter in the book did, this one also includes analyses of very large data sets:

The Multiple Cause of Death (MCD) data files contain information about underlying and secondary causes of death in the U.S. during 1968–2010. In total, they include more than 65 million individual death certificate records. […] we used data for the period 1979–2004.”

There’s some formal modelling stuff in the chapter which I won’t go into in detail here, this is the chapter in which I encountered the comment about ‘the multivariate lognormal frailty model’ I included in my first post about the book. One of the things the chapter looks at are the joint frequencies of deaths from cancer and other fatal diseases; it turns out that there are multiple diseases that are negatively related with cancer as a cause of death when you look at the population-level data mentioned above. The chapter goes into some of the biological mechanisms which may help explain why these associations look the way they do, and I’ll quote a little from that part of the coverage. A key idea here is (as always..?) that there are tradeoffs at play; some genetic variants may help protect you against e.g. cancer, but at the same time increase the risk of other diseases for the same reason that they protect you against cancer. In the context of the relationship between cancer deaths and deaths from other diseases they note in the conclusion that: “One potential biological mechanism underlying the negative correlation among cancer and other diseases could be related to the differential role of apoptosis in the development of these diseases.” The chapter covers that stuff in significantly more detail, and I decided to add some observations from the chapter on these topics below:

“Studying the role of the p53 gene in the connection between cancer and cellular aging, Campisi (2002, 2003) suggested that longevity may depend on a balance between tumor suppression and tissue renewal mechanisms. […] Although the mechanism by which p53 regulates lifespan remains to be determined, […] findings highlight the possibility that careful manipulation of p53 activity during adult life may result in beneficial effects on healthy lifespan. Other tumor suppressor genes are also involved in regulation of longevity. […] In humans, Dumont et al. (2003) demonstrated that a replacement of arginine (Arg) by proline (Pro) at position 72 of human p53 decreases its ability to initiate apoptosis, suggesting that these variants may differently affect longevity and vulnerability to cancer. Van Heemst et al. (2005) showed that individuals with the Pro/Pro genotype of p53 corresponding to reduced apoptosis in cells had significantly increased overall survival (by 41%) despite a more than twofold increased proportion of cancer deaths at ages 85+, together with a decreased proportion of deaths from senescence related causes such as COPD, fractures, renal failure, dementia, and senility. It was suggested that human p53 may protect against cancer but at a cost of longevity. […] Other biological factors may also play opposing roles in cancer and aging and thus contribute to respective trade-offs […]. E.g., higher levels of IGF-1 [have been] linked to both cancer and attenuation of phenotypes of physical senescence, such as frailty, sarcopenia, muscle atrophy, and heart failure, as well as to better muscle regeneration”.

“The connection between cancer and longevity may potentially be mediated by trade-offs between cancer and other diseases which do not necessarily involve any basic mechanism of aging per se. In humans, it could result, for example, from trade-offs between vulnerabilities to cancer and AD, or to cancer and CVD […] There may be several biological mechanisms underlying the negative correlation among cancer and these diseases. One can be related to the differential role of apoptosis in their development. For instance, in stroke, the number of dying neurons following brain ischemia (and thus probability of paralysis or death) may be less in the case of a downregulated apoptosis. As for cancer, the downregulated apoptosis may, conversely, mean a higher risk of the disease because more cells may survive damage associated with malignant transformation. […] Also, the role of the apoptosis may be different or even opposite in the development of cancer and Alzheimer’s disease (AD). Indeed, suppressed apoptosis is a hallmark of cancer, while increased apoptosis is a typical feature of AD […]. If so, then chronically upregulated apoptosis (e.g., due to a genetic polymorphism) may potentially be protective against cancer, but be deleterious in relation to AD. […] Increased longevity can be associated not only with increased but also with decreased chances of cancer. […] The most popular to-date “anti-aging” intervention, caloric restriction, often results in increased maximal life span along with reduced tumor incidence in laboratory rodents […] Because the rate of apoptosis was significantly and consistently higher in food restricted mice regardless of age, James et al. (1998) suggested that caloric restriction may have a cancer-protective effect primarily due to the upregulated apoptosis in these mice.”

Below I’ll discuss content covered in chapter 5, which deals with ‘Factors That May Increase Vulnerability to Cancer and Longevity in Modern Human Populations’. I’ll start out with a few quotes:

“Currently, the overall cancer incidence rate (age-adjusted) in the less developed world is roughly half that seen in the more developed world […] For countries with similar levels of economic development but different climate and ethnic characteristics […], the cancer rate patterns look much more similar than for the countries that share the same geographic location, climate, and ethnic distribution, but differ in the level of economic development […]. This suggests that different countries may share common factors linked to economic prosperity that could be primarily responsible for the modern increases in overall cancer risk. […] Population aging (increases in the proportion of older people) may […] partly explain the rise in the global cancer burden […]; however, it cannot explain increases in age-specific cancer incidence rates over time […]. Improved diagnostics and elevated exposures to carcinogens may explain increases in rates for selected cancer sites, but they cannot fully explain the increase in the overall cancer risk, nor incidence rate trends for most individual cancers (Jemal et al. 2008, 2013).”

“[W]e propose that the association between the overall cancer risk and the economic progress and spread of the Western lifestyle could in part be explained by the higher proportion of individuals more susceptible to cancer in the populations of developed countries, and discuss several mechanisms of such an increase in the proportion of the vulnerable. […] mechanisms include but are not limited to: (i) Improved survival of frail individuals. […] (ii) Avoiding or reducing traditional exposures. Excessive disinfection and hygiene typical of the developed world can diminish exposure to some factors that were abundant in the past […] Insufficiently or improperly trained immune systems may be less capable of resisting cancer. (iii) Burden of novel exposures. Some new medicines, cleaning agents, foods, etc., that are not carcinogenic themselves may still affect the natural ways of processing carcinogens in the body, and through this increase a person’s susceptibility to established carcinogens. [If this one sounds implausible to you, I’ll remind you that drug metabolism is complicatedUS] […] (iv) Some of the factors linked to economic prosperity and the Western lifestyle (e.g., delayed childbirth and food enriched with growth factors) may antagonistically influence aging and cancer risk.”

They provide detailed coverage of all of these mechanisms in the chapter, below I have included a few select observations from that part of the coverage.

“There was a dramatic decline in infant and childhood mortality in developed countries during the last century. For example, the infant mortality rate in the United States was about 6 % of live births in 1935, 3 % in 1950, 1.3 % in 1980, and 0.6 % in 2010. That is, it declined tenfold over the course of 75 years […] Because almost all children (including those with immunity deficiencies) survive, the proportion of the children who are inherently more vulnerable could be higher in the more developed countries. This is consistent with a typically higher proportion of children with chronic inflammatory immune disorders such as asthma and allergy in the populations of developed countries compared to less developed ones […] Over-reduction of such traditional exposures may result in an insufficiently/improperly trained immune system early in life, which could make it less able to resist diseases, including cancer later in life […] There is accumulating evidence of the important role of these effects in cancer risk. […] A number of studies have connected excessive disinfection and lack of antigenic stimulation (especially in childhood) of the immune system in Westernized communities with increased risks of both chronic inflammatory diseases and cancer […] The IARC data on migrants to Israel […] allow for comparison of the age trajectories of cancer incidence rates between adult Jews who live in Israel but were born in other countries […] [These data] show that Jews born in less developed regions (Africa and Asia) have overall lower cancer risk than those born in the more developed regions (Europe and America).  The discrepancy is unlikely to be due to differences in cancer diagnostics because at the moment of diagnosis all these people were citizens of the same country with the same standard of medical care. These results suggest that surviving childhood and growing up in a less developed country with diverse environmental exposures might help form resistance to cancer that lasts even after moving to a high risk country.”

I won’t go much into the ‘burden of novel exposures’ part, but I should note that exposures that may be relevant include factors like paracetamol use and antibiotics for treatment of H. pylori. Paracetamol is not considered carcinogenic by the IARC, but we know from animal studies that if you give rats paratamol and then expose them to an established carcinogen (with the straightforward name N-nitrosoethyl-N-hydroxyethylamine), the number of rats developing kidney cancer goes up. In the context of H. pylori, we know that these things may cause stomach cancer, but when you treat rats with metronidazol (which is used to treat H. pylori) and expose them to an established carcinogen, they’re more likely to develop colon cancer. The link between colon cancer and antibiotics use has been noted in other contexts as well; decreased microbial diversity after antibiotics use may lead to suppression of the bifidobacteria and promotion of E. coli in the colon, the metabolic products of which may lead to increased cancer risk. Over time an increase in colon cancer risk and a decrease in stomach cancer risk has been observed in developed societies, but aside from changes in diet another factor which may play a role is population-wide exposure to antibiotics. Colon and stomach cancers are incidentally not the only ones of interest in this particular context; it has also been found that exposure to chloramphenicol, a broad-spectrum antibiotic used since the 40es, increases the risk of lymphoma in mice when the mice are exposed to a known carcinogen, despite the drug itself again not being clearly carcinogenic on its own.

Many new exposures aside from antibiotics are of course relevant. Two other drug-related ones that might be worth mentioning are hormone replacement therapy and contraceptives. HRT is not as commonly used today as it was in the past, but to give some idea of the scope here, half of all women in the US aged 50-65 are estimated to have been on HRT at the peak of its use, around the turn of the millennium, and HRT is assumed to be partly responsible for the higher incidence of hormone-related cancers observed in female populations living in developed countries. It’s of some note that the use of HRT dropped dramatically shortly after this peak (from 61 million prescriptions in 2001 to 21 million in 2004), and that the incidence of estrogen-receptor positive cancers subsequently dropped. As for oral contraceptives, these have been in use since the 1960s, and combined hormonal contraceptives are known to increase the risk of liver- and breast cancer, while seemingly also having a protective effect against endometrial cancer and ovarian cancer. The authors speculate that some of the cancer incidence changes observed in the US during the latter half of the last century, with a decline in female endometrial and ovarian cancer combined with an increase in breast- and liver cancer, could in part be related to widespread use of these drugs. An estimated 10% of all women of reproductive age alive in the world, and 16% of those living in the US, are estimated to be using combined hormonal contraceptives. In the context of the protective effect of the drugs, it should perhaps be noted that endometrial cancer in particular is strongly linked to obesity so if you are not overweight you are relatively low-risk.

Many ‘exposures’ in a cancer context are not drug-related. For example women in Western societies tend to go into menopause at a higher age, and higher age of menopause has been associated with hormone-related cancers; but again the picture is not clear in terms of how the variable affects longevity, considering that later menopause has also been linked to increased longevity in several large studies. In the studies the women did have higher mortality from the hormone-related cancers, but on the other hand they were less likely to die from some of the other causes, such as pneumonia, influenza, and falls. Age of childbirth is also a variable where there are significant differences between developed countries and developing countries, and this variable may also be relevant to cancer incidence as it has been linked to breast cancer and melanoma; in one study women who first gave birth after the age of 35 had a 40% increased risk of breast cancer compared to mothers who gave birth before the age of 20 (good luck ‘controlling for everything’ in a context like that, but…), and in a meta-analysis the relative risk for melanoma was 1.47 for women in the oldest age group having given birth, compared to the youngest (again, good luck controlling for everything, but at least it’s not just one study). Lest you think this literature only deals with women, it’s also been found that parental age seems to be linked to cancers in the offspring (higher parental age -> higher cancer risk in the offspring), though the effect sizes are not mentioned in the coverage.

Here’s what they conclude at the end of the chapter:

“Some of the factors associated with economic prosperity and a Western lifestyle may influence both aging and vulnerability to cancer, sometimes oppositely. Current evidence supports a possibility of trade-offs between cancer and aging-related phenotypes […], which could be influenced by delayed reproduction and exposures to growth factors […]. The latter may be particularly beneficial at very old age. This is because the higher levels of growth factors may attenuate some phenotypes of physical senescence, such as decline in regenerative and healing ability, sarcopenia, frailty, elderly fractures and heart failure due to muscles athrophy. They may also increase the body’s vulnerability to cancer, e.g., through growth promoting and anti-apoptotic effects […]. The increase in vulnerability to cancer due to growth factors can be compatible with extreme longevity because cancer is a major contributor to mortality mainly before age 85, while senescence-related causes (such as physical frailty) become major contributors to mortality at oldest old ages (85+). In this situation, the impact of growth factors on vulnerability to death could be more deleterious in middle-to-old life (~before 85) and more beneficial at older ages (85+).

The complex relationships between aging, cancer, and longevity are challenging. This complexity warns against simplified approaches to extending longevity without taking into account the possible trade-offs between phenotypes of physical aging and various health disorders, as well as the differential impacts of such tradeoffs on mortality risks at different ages (e.g., Ukraintseva and Yashin 2003a; Yashin et al. 2009; Ukraintseva et al. 2010, 2016).”

March 7, 2017 Posted by | books, cancer, medicine, Pharmacology | Leave a comment


“A recent study estimated that 234 million surgical procedures requiring anaesthesia are performed worldwide annually. Anaesthesia is the largest hospital specialty in the UK, with over 12,000 practising anaesthetists […] In this book, I give a short account of the historical background of anaesthetic practice, a review of anaesthetic equipment, techniques, and medications, and a discussion of how they work. The risks and side effects of anaesthetics will be covered, and some of the subspecialties of anaesthetic practice will be explored.”

I liked the book, and I gave it three stars on goodreads; I was closer to four stars than two. Below I have added a few sample observations from the book, as well as what turned out in the end to be actually a quite considerable number of links (more than 60 it turned out, from a brief count) to topics/people/etc. discussed or mentioned in the text. I decided to spend a bit more time finding relevant links than I’ve previously done when writing link-heavy posts, so in this post I have not limited myself to wikipedia articles and I e.g. also link directly to primary literature discussed in the coverage. The links provided are, as usual, meant to be indicators of which kind of stuff is covered in the book, rather than an alternative to the book; some of the wikipedia articles in particular I assume are not very good (the main point of a link to a wikipedia article of questionable quality should probably be taken to be an indication that I consider ‘awareness of the existence of concept X’ to be of interest/important also to people who have not read this book, even if no great resource on the topic was immediately at hand to me).

Sample observations from the book:

“[G]eneral anaesthesia is not sleep. In physiological terms, the two states are very dissimilar. The term general anaesthesia refers to the state of unconsciousness which is deliberately produced by the action of drugs on the patient. Local anaesthesia (and its related terms) refers to the numbness produced in a part of the body by deliberate interruption of nerve function; this is typically achieved without affecting consciousness. […] The purpose of inhaling ether vapour [in the past] was so that surgery would be painless, not so that unconsciousness would necessarily be produced. However, unconsciousness and immobility soon came to be considered desirable attributes […] For almost a century, lying still was the only reliable sign of adequate anaesthesia.”

“The experience of pain triggers powerful emotional consequences, including fear, anger, and anxiety. A reasonable word for the emotional response to pain is ‘suffering’. Pain also triggers the formation of memories which remind us to avoid potentially painful experiences in the future. The intensity of pain perception and suffering also depends on the mental state of the subject at the time, and the relationship between pain, memory, and emotion is subtle and complex. […] The effects of adrenaline are responsible for the appearance of someone in pain: pale, sweating, trembling, with a rapid heart rate and breathing. Additionally, a hormonal storm is activated, readying the body to respond to damage and fight infection. This is known as the stress response. […] Those responses may be abolished by an analgesic such as morphine, which will counteract all those changes. For this reason, it is routine to use analgesic drugs in addition to anaesthetic ones. […] Typical anaesthetic agents are poor at suppressing the stress response, but analgesics like morphine are very effective. […] The hormonal stress response can be shown to be harmful, especially to those who are already ill. For example, the increase in blood coagulability which evolved to reduce blood loss as a result of injury makes the patient more likely to suffer a deep venous thrombosis in the leg veins.”

“If we monitor the EEG of someone under general anaesthesia, certain identifiable changes to the signal occur. In general, the frequency spectrum of the signal slows. […] Next, the overall power of the signal diminishes. In very deep general anaesthesia, short periods of electrical silence, known as burst suppression, can be observed. Finally, the overall randomness of the signal, its entropy, decreases. In short, the EEG of someone who is anaesthetized looks completely different from someone who is awake. […] Depth of anaesthesia is no longer considered to be a linear concept […] since it is clear that anaesthesia is not a single process. It is now believed that the two most important components of anaesthesia are unconsciousness and suppression of the stress response. These can be represented on a three-dimensional diagram called a response surface. [Here’s incidentally a recent review paper on related topics, US]”

“Before the widespread advent of anaesthesia, there were very few painkilling options available. […] Alcohol was commonly given as a means of enhancing the patient’s courage prior to surgery, but alcohol has almost no effect on pain perception. […] For many centuries, opium was the only effective pain-relieving substance known. […] For general anaesthesia to be discovered, certain prerequisites were required. On the one hand, the idea that surgery without pain was achievable had to be accepted as possible. Despite tantalizing clues from history, this idea took a long time to catch on. The few workers who pursued this idea were often openly ridiculed. On the other, an agent had to be discovered that was potent enough to render a patient suitably unconscious to tolerate surgery, but not so potent that overdose (hence accidental death) was too likely. This agent also needed to be easy to produce, tolerable for the patient, and easy enough for untrained people to administer. The herbal candidates (opium, mandrake) were too unreliable or dangerous. The next reasonable candidate, and every agent since, was provided by the proliferating science of chemistry.”

“Inducing anaesthesia by intravenous injection is substantially quicker than the inhalational method. Inhalational induction may take several minutes, while intravenous induction happens in the time it takes for the blood to travel from the needle to the brain (30 to 60 seconds). The main benefit of this is not convenience or comfort but patient safety. […] It was soon discovered that the ideal balance is to induce anaesthesia intravenously, but switch to an inhalational agent […] to keep the patient anaesthetized during the operation. The template of an intravenous induction followed by maintenance with an inhalational agent is still widely used today. […] Most of the drawbacks of volatile agents disappear when the patient is already anaesthetized [and] volatile agents have several advantages for maintenance. First, they are predictable in their effects. Second, they can be conveniently administered in known quantities. Third, the concentration delivered or exhaled by the patient can be easily and reliably measured. Finally, at steady state, the concentration of volatile agent in the patient’s expired air is a close reflection of its concentration in the patient’s brain. This gives the anaesthetist a reliable way of ensuring that enough anaesthetic is present to ensure the patient remains anaesthetized.”

“All current volatile agents are colourless liquids that evaporate into a vapour which produces general anaesthesia when inhaled. All are chemically stable, which means they are non-flammable, and not likely to break down or be metabolized to poisonous products. What distinguishes them from each other are their specific properties: potency, speed of onset, and smell. Potency of an inhalational agent is expressed as MAC, the minimum alveolar concentration required to keep 50% of adults unmoving in response to a standard surgical skin incision. MAC as a concept was introduced […] in 1963, and has proven to be a very useful way of comparing potencies of different anaesthetic agents. […] MAC correlates with observed depth of anaesthesia. It has been known for over a century that potency correlates very highly with lipid solubility; that is, the more soluble an agent is in lipid […], the more potent an anaesthetic it is. This is known as the Meyer-Overton correlation […] Speed of onset is inversely proportional to water solubility. The less soluble in water, the more rapidly an agent will take effect. […] Where immobility is produced at around 1.0 MAC, amnesia is produced at a much lower dose, typically 0.25 MAC, and unconsciousness at around 0.5 MAC. Therefore, a patient may move in response to a surgical stimulus without either being conscious of the stimulus, or remembering it afterwards.”

“The most useful way to estimate the body’s physiological reserve is to assess the patient’s tolerance for exercise. Exercise is a good model of the surgical stress response. The greater the patient’s tolerance for exercise, the better the perioperative outcome is likely to be […] For a smoker who is unable to quit, stopping for even a couple of days before the operation improves outcome. […] Dying ‘on the table’ during surgery is very unusual. Patients who die following surgery usually do so during convalescence, their weakened state making them susceptible to complications such as wound breakdown, chest infections, deep venous thrombosis, and pressure sores.”

Mechanical ventilation is based on the principle of intermittent positive pressure ventilation (IPPV), gas being ‘blown’ into the patient’s lungs from the machine. […] Inflating a patient’s lungs is a delicate process. Healthy lung tissue is fragile, and can easily be damaged by overdistension (barotrauma). While healthy lung tissue is light and spongy, and easily inflated, diseased lung tissue may be heavy and waterlogged and difficult to inflate, and therefore may collapse, allowing blood to pass through it without exchanging any gases (this is known as shunt). Simply applying higher pressures may not be the answer: this may just overdistend adjacent areas of healthier lung. The ventilator must therefore provide a series of breaths whose volume and pressure are very closely controlled. Every aspect of a mechanical breath may now be adjusted by the anaesthetist: the volume, the pressure, the frequency, and the ratio of inspiratory time to expiratory time are only the basic factors.”

“All anaesthetic drugs are poisons. Remember that in achieving a state of anaesthesia you intend to poison someone, but not kill them – so give as little as possible. [Introductory quote to a chapter, from an Anaesthetics textbook – US] […] Other cells besides neurons use action potentials as the basis of cellular signalling. For example, the synchronized contraction of heart muscle is performed using action potentials, and action potentials are transmitted from nerves to skeletal muscle at the neuromuscular junction to initiate movement. Local anaesthetic drugs are therefore toxic to the heart and brain. In the heart, local anaesthetic drugs interfere with normal contraction, eventually stopping the heart. In the brain, toxicity causes seizures and coma. To avoid toxicity, the total dose is carefully limited”.

Links of interest:

General anaesthesia.
Muscle relaxant.
Arthur Ernest Guedel.
Guedel’s classification.
Beta rhythm.
Frances Burney.
Henry Hill Hickman.
Horace Wells.
William Thomas Green Morton.
Diethyl ether.
James Young Simpson.
Joseph Thomas Clover.
Inhalational anaesthetic.
Pulmonary aspiration.
Principles of Total Intravenous Anaesthesia (TIVA).
Patient-controlled analgesia.
Airway management.
Oropharyngeal airway.
Tracheal intubation.
Laryngeal mask airway.
Anaesthetic machine.
Soda lime.
Sodium thiopental.
Neuromuscular-blocking drug.
Gate control theory of pain.
Multimodal analgesia.
Hartmann’s solution (…what this is called seems to be depending on whom you ask, but it’s called Hartmann’s solution in the book…).
Local anesthetic.
Karl Koller.
Regional anesthesia.
Spinal anaesthesia.
Epidural nerve block.
Intensive care medicine.
Bjørn Aage Ibsen.
Chronic pain.
Pain wind-up.
John Bonica.
Twilight sleep.
Veterinary anesthesia.
Pearse et al. (results of paper briefly discussed in the book).
Awareness under anaesthesia (skip the first page).
Pollard et al. (2007).
Postoperative nausea and vomiting.
Postoperative cognitive dysfunction.
Monk et al. (2008).
Malignant hyperthermia.
Suxamethonium apnoea.

February 13, 2017 Posted by | books, Chemistry, medicine, papers, Pharmacology | 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

Diabetic nephropathies

Bakris et al.‘s text on this topic is the first book I’ve read specifically devoted to the topic of DN. As I pointed out on goodreads, “this is a well-written and interesting work which despite the low page count cover quite a bit of ground. A well-sourced and to-the-point primer on these topics.” Below I have added a few observations from the book.

“Diabetic nephropathy (DN), also known as diabetic kidney disease (DKD), is one of the most important long-term complications of diabetes and the most common cause of endstage renal disease (ESRD) worldwide. DKD […] is defined as structural and functional renal damage manifested as clinically detected albuminuria in the presence of normal or abnormal glomerular filtration rate (GFR). […] Patients with DKD […] account for one-third of patients demanding renal transplantation. […] in the United States, Medicare expenditure on treating ESRD is approximately US $33 billion (as of 2010), which accounts for 8–9 % of the total annual health-care budget […] According to the United States Renal Data System […], the incidence of ESRD requiring RRT [in 2012] was 114,813 patients, with 44 % due to DKD [9]. A registry report from Japan revealed a nearly identical relative incidence, with 44.2 % of the patients with ESRD caused by diabetes”

Be careful not to confuse incidence and prevalence here; the proportion of diabetics diagnosed with ESDR in any given year is almost certainly higher than the proportion of people with ESDR who have diabetes, because diabetics with kidney failure die at a higher rate than do other people with kidney failure. This problem/fact tends to make some questions hard to answer; to give an example, how large a share of the total costs that diabetics contribute to the whole kidney disease component of medical costs seems to me to be far from an easy question to answer, because you in some sense are not really making an apples-to-apples comparison, and a lot might well depend on the chosen discount rate and how to address the excess mortality in the diabetes sample; and even ‘simply’ adding up medical outlays for the diabetes- and non-diabetes samples would require a lot of data (which may not be available) and work. You definitely cannot just combine the estimates provided above, and assume that the 44% incidence translates into 44% of people with ESDR having diabetes; it’s not clear in the text where the ‘one-third of patients’ number above comes from, but if that’s also US data then it should be obvious from the difference between these numbers that there’s a lot of excess mortality here in the diabetes sample (I have included specific data from the publication on these topics below). The book also talks about the fact that the type of dialysis used in a case of kidney failure will to some extent depend on the health status of the patient, and that diabetes is a significant variable in that context; this means that the available/tolerable treatment options for the kidney disease component may not be the same in the case of a diabetic and a case of a patient with, say, lupus nephritis, and it also means that the patient groups most likely are not ‘equally sick’, so basing cost estimates on cost averages might lead to misleading results if severity of disease and (true) treatment costs are related, as they usually are.

“A recent analysis revealed an estimated diabetes prevalence of 12–14 % among adults in the United States […] In the age group ≥65 years, this amounts to more than 20 %”.

It should be emphasized in the context of the above numbers that the prevalence of DKD is highly variable across countries/populations – the authors also include in the book the observation that: “Over a period of 20 years, 32 studies from 16 countries revealed a prevalence ranging from 11 to 83 % of patients with diabetes”. Some more prevalence data:

“DKD affects about 30 % of patients with type 1 diabetes and 25–40 % of the patients with type 2 diabetes. […] The global prevalence of micro- and macroalbuminuria is estimated at 39 % and 10 %, respectively […] (NHANES III) […] reported a prevalence of 35 % (microalbuminuria) and 6 % (macroalbuminuria) in patients with T2DM aged ≥40 years [24]. In another study, this was reported to be 43 % and 12 %, respectively, in a Japanese population [23]. According to the European Diabetes (EURODIAB) Prospective Complications Study Group, in patients with T1DM, the incidence of microalbuminuria was 12.6 % (over 7.3 years) [25]. This prevalence was further estimated at 33 % in an 18-year follow-up study in Denmark […] In the United Kingdom Prospective Diabetes Study (UKPDS), proteinuria [had] a peak incidence after around 15–20 years after diabetes diagnosis.”

I won’t cover the pathophysiology parts in too much detail here, but a few new things I learned does need to be mentioned:

“A natural history of DKD was first described in the 1970s by Danish physicians [32]. It was characterized by a long silent period without overt clinical signs and symptoms of nephropathy and progression through various stages, starting from hyperfiltration, microalbuminuria, macroalbuminuria, and overt renal failure to ESRD. Microalbuminuria (30–300 mg/day of albumin in urine) is a sign of early DKD, whereas macroalbuminuria (>300 mg/day) represents DKD progression. [I knew this stuff. The stuff that follows below was however something I did not know:]
However, this ‘classical’ natural evolution of urinary albumin excretion and change in GFR is not present in many patients with diabetes, especially those with type 2 diabetes [34]. These patients can have reduction or disappearance of proteinuria over time or can develop even overt renal disease in the absence of proteinuria [30, 35]. […] In the Wisconsin Epidemiologic Study of Diabetic Retinopathy (WESDR) of patients with T2DM, 45.2 % of participants developed albuminuria, and 29 % developed renal impairment over a 15-year follow-up period [37]. Of those patients who developed renal impairment, 61 % did not have albuminuria beforehand, and 39 % never developed albuminuria during the study. Of the patients that developed albuminuria, only 24 % subsequently developed renal impairment during the study. A significant degree of discordance between development of albuminuria and renal impairment is apparent [37]. These data, thus, do not support the classical paradigm of albuminuria always preceding renal impairment in the progression of DKD. […] renal hyperfiltration and rapid GFR decline are considered stronger predictors of nephropathy progression in type 1 diabetes than presence of albuminuria [67]. The annual eGFR loss in patients with DKD is >3 mL/min/1.73 m2 or 3.3 % per year.”

As for the last part about renal hyperfiltration, they however also note later in the coverage in a different chapter that “recent long-term prospective surveys cast doubt on the validity of glomerular hyperfiltration being predictive of renal outcome in patients with type 1 diabetes”. Various factors mentioned in the coverage – some of which are very hard to avoid and some of which are actually diabetes-specific – contribute to measurement error, which may be part of the explanation for the sub-optimal performance of the prognostic markers employed.

An important observation I think I have mentioned before here on the blog is that diabetic nephropathy is not just bad because people who develop this complication may ultimately develop kidney failure, but is also bad because diabetics may die before they even do that; diabetics with even moderate stages of nephropathy have high mortality from cardiovascular disease, so if you only consider diabetics who actually develop kidney failure you may miss some of the significant adverse health effects of this complication; it might be argued that doing this would be a bit like analyzing the health outcomes of smokers while only tallying the cancer cases, and ignoring e.g. the smoking-associated excess deaths from cardiovascular disease. Some observations from the book on this topic:

“Comorbid DM and DKD are associated with high cardiovascular morbidity and mortality. The risk of cardiovascular disease is disproportionately higher in patients with DKD than patients with DM who do not have kidney disease [76]. The incident dialysis rate might even be higher after adjusting for patients dying from cardiovascular disease before reaching ESRD stage [19]. The United States Renal Data System (USRDS) data shows that elderly patients with a triad of DM, chronic kidney disease (CKD), and heart failure have a fivefold higher chance of death than progression to CKD and ESRD [36]. The 5-year survival rate for diabetic patients with ESRD is estimated at 20 % […] This is higher than the mortality rate for many solid cancers (including prostate, breast, or renal cell cancer). […] CVD accounts for more than half of deaths of patients undergoing dialysis […] the 5-year survival rate is much lower in diabetic versus nondiabetic patients undergoing hemodialysis […] Adler et al. tested whether HbA1c levels were associated with death in adults with diabetes starting HD or peritoneal dialysis [38]. Of 3157 patients observed for a median time of 2.7 years, 1688 died. [this example provided, I thought, a neat indication of what sort of data you end up with when you look at samples with a 20% 5-year survival rate] […] Despite modern therapies […] most patients continue to show progressive renal damage. This outcome suggests that the key pathogenic mechanisms involved in the induction and progression of DN remain, at least in part, active and unmodified by the presently available therapies.” (my emphasis)

The link between blood glucose (Hba1c) and risk of microvascular complications such as DN is strong and well-documented, but Hba1c does not explain everything:

“Only a subset of individuals living with diabetes […] develop DN, and studies have shown that this is not just due to poor blood glucose control [50–54]. DN appears to cluster in families […] Several consortia have investigated genetic risk factors […] Genetic risk factors for DN appear to differ between patients with type 1 and type 2 diabetes […] The pathogenesis of DN is complex and has not yet been completely elucidated […] [It] is multifactorial, including both genetic and environmental factors […]. Hyperglycemia affects patients carrying candidate genes associated with susceptibility to DN and results in metabolic and hemodynamic alterations. Hyperglycemia alters vasoactive regulators of glomerular arteriolar tone and causes glomerular hyperfiltration. Production of AGEs and oxidative stress interacts with various cytokines such as TGF-β and angiotensin II to cause kidney damage. Additionally, oxidative stress can cause endothelial dysfunction and systemic hypertension. Inflammatory pathways are also activated and interact with the other pathways to cause kidney damage.”

“An early clinical sign of DN is moderately increased urinary albumin excretion, referred to as microalbuminuria […] microalbuminuria has been shown to be closely associated with an increased risk of cardiovascular morbidity and mortality [and] is [thus] not only a biomarker for the early diagnosis of DN but also an important therapeutic target […] Moderately increased urinary albumin excretion that progresses to severely increased albuminuria is referred to as macroalbuminuria […] Severely increased albuminuria is defined as an ACR≥300 mg/g Cr; it leads to a decline in renal function, which is defined in terms of the GFR [8] and generally progresses to ESRD 6–8 years after the onset of overt proteinuria […] patients with type 1 diabetes are markedly younger than type 2 patients. The latter usually develop ESRD in their mid-fifties to mid-sixties. According to a small but carefully conducted study, both type 1 and type 2 patients take an average of 77–81 months from the stage of producing macroproteinuria with near-normal renal function to developing ESRD [17].”

“Patients with diabetes and kidney disease are at increased risk of hypoglycemia due to decreased clearance of some of the medications used to treat diabetes such as insulin, as well as impairment of renal gluconeogenesis from having a lower kidney mass. As the kidney is responsible for about 30–80 % of insulin removal, reduced kidney function is associated with a prolonged insulin half-life and a decrease in insulin requirements as estimated glomerular filtration rate (eGFR) decline […] Metformin [a first-line drug for treating type 2 diabetes, US] should be avoided in patients with an eGFR < 30 mL/min /1.73 m2. It is recommended that metformin is stopped in the presence of situations that are associated with hypoxia or an acute decline in kidney function such as sepsis/shock, hypotension, acute myocardial infarction, and use of radiographic contrast or other nephrotoxic agents […] The ideal medication regimen is based on the specific needs of the patient and physician experience and should be individualized, especially as renal function changes. […] Lower HbA1c levels are associated with higher risks of hypoglycemia so the HbA1c target should be individualized […] Whereas patients with mild renal insufficiency can receive most antihyperglycemic treatments without any concern, patients with CKD stage 3a and, in particular, with CKD stages 3b, 4, and 5 often require treatment adjustments according to the degree of renal insufficiency […] Higher HbA1c targets should be considered for those with shortened life expectancies, a known history of severe hypoglycemia or hypoglycemia unawareness, CKD, and children.”

“In cases where avoidance of development of DKD has failed, the second approach is slowing disease progression. The most important therapeutic issues at this stage are control of hypertension and hyperglycemia. […] Hypertension is present in up to 85 % of patients with DN/ DKD, depending on the duration and stage (e.g., higher in more progressive cases). […] In a recent meta-analysis, the efficacy and safety of blood pressure-lowering agents in adults with diabetes and kidney disease was analyzed […] In total, 157 studies comprising 43,256 participants, mostly with type 2 diabetes and CKD, were included in the network meta-analysis. No drug regimen was found to be more effective than placebo for reducing all-cause mortality. […] DKD is accompanied by abnormalities in lipid metabolism related to decline in kidney function. The association between higher low-density lipoprotein cholesterol (LDL-C) and risk of myocardial infarction is weaker for people with lower baseline eGFR, despite higher absolute risk of myocardial infarction [53]. Thus, increased LDL-C seems to be less useful as a marker of coronary risk among people with CKD than in the general population.”

“An analysis of the USRDS data revealed an RR of 0.27 (95 % CI, 0.24–0.30) 18 months after transplantation in patients with diabetes in comparison to patients on dialysis on a transplant waiting list [76]. The gain in projected years of life with transplantation amounted to 11 years in patients with DKD in comparison to patients without transplantation.”

October 27, 2016 Posted by | books, diabetes, medicine, Pharmacology | 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

Diabetes and the Metabolic Syndrome in Mental Health (I)

As I stated in my goodreads review, ‘If you’re a schizophrenic and/or you have a strong interest in e.g. the metabolic effects of various anti-psychotics, the book is a must-read’. If that’s not true, it’s a different matter. One reason why I didn’t give the book a higher rating is that many of the numbers in there are quite dated, which is a bit annoying because it means you might feel somewhat uncertain about how valid the estimates included still are at this point.

As pointed out in my coverage of the human drug metabolism text there are a lot of things that can influence the way that drugs are metabolized, and this text includes some details about a specific topic which may help to illustrate what I meant by stating in that post that people ‘self-experimenting’ may be taking on risks they may not be aware of. Now, diabetics who need insulin injections are taking a drug with a narrow therapeutic index, meaning that even small deviations from the optimal dose may have serious repercussions. A lot of things influence what is actually the optimal dose in a specific setting; food (“food is like a drug to a person with diabetes”, as pointed out in Matthew Neal’s endocrinology text, which is yet another text I, alas, have yet to cover here), sleep patterns, exercise (sometimes there may be an impact even days after you’ve exercised), stress, etc. all play a role, and even well-educated diabetics may not know all the details.

A lot of drugs also affect glucose metabolism and insulin sensitivity, one of the best known drug types of this nature probably being the corticosteroids because of their widespread use in a variety of disorders, including autoimmune disorders which tend to be more common in autoimmune forms of diabetes (mainly type 1). However many other types of drugs can also influence blood glucose, and on the topic of antidepressants and antipsychotics we actually know some stuff about these things and about how various medications influence glucose levels; it’s not a big coincidence that people have looked at this, they’ve done that because it has become clear that “[m]any medications, in particular psychotropics, including antidepressants, antipsychotics, and mood stabilizers, are associated with elevations in blood pressure, weight gain, dyslipidemias, and/or impaired glucose homeostasis.” (p. 49). Which may translate into an increased risk of type 2 diabetes, and impaired glucose control in diabetics. Incidentally the authors of this text observes in the text that: “Our research group was among the first in the field to identify a possible link between the development of obesity, diabetes, and other metabolic derangements (e.g., lipid abnormalities) and the use of newer, second-generation antipsychotic medications.” Did the people who took these drugs before this research was done/completed know that their medications might increase their risk of developing diabetes? No, because the people prescribing it didn’t know, nor did the people who developed the drugs. Some probably still don’t know, including some of the medical people prescribing these medications. But the knowledge is out there now, and the effect size is in the case of some drugs argued to be large enough to be clinically relevant. In the context of a ‘self-experimentation’-angle the example is also interesting because the negative effect in question here is significantly delayed; type 2 diabetes takes time to develop, and this is an undesirable outcome which you’re not going to spot the way you might link a headache the next day to a specific drug you just started out with (another example of a delayed adverse event is incidentally cancer). You’re not going to spot dyslipidemia unless you keep track of your lipid levels on your own or e.g. develop xanthomas as a consequence of it, leading you to consult a physician. It helps a lot if you have proper research protocols and large n studies with sufficient power when you want to discover things like this, and when you want to determine whether an association like this is ‘just an association’ or if the link is actually causal (and then clarifying what we actually mean by that, and whether the causal link is also clinically relevant and/or for whom it might be clinically relevant). Presumably many people taking all kinds of medical drugs these days are taking on risks which might in a similar manner be ‘hidden from view’ as was the risk of diabetes in people taking second-generation antipsychotics in the near-past; over time epidemiological studies may pick up on some of these risks, but many will probably remain hidden from view on account of the amount of complexity involved. Even if a drug ‘works’ as intended in the context of the target variable in question, you can get into a lot of trouble if you only focus on the target variable (“if a drug has no side effects, then it is unlikely to work“). People working in drug development know this.

The book has a lot of blog-worthy stuff so I decided to include some quotes in the coverage below. The quotes are from the first half of the book, and this part of the coverage actually doesn’t talk much about the effects of drugs; it mainly deals with epidemiology and cost estimates. I thus decided to save the ‘drug coverage’ to a later post. It should perhaps be noted that some of the things I’d hoped to learn from Ru-Band Lu et al.’s book (blog coverage here) was actually included in this one, which was nice.

“Those with mental illness are at higher risk and are more likely to suffer the severe consequences of comorbid medical illness. Adherence to treatment is often more difficult, and other factors such as psychoneuroendocrine interactions may complicate already problematic treatments. Additionally, psychiatric medications themselves often have severe side effects and can interact with other medications, rendering treatment of the mental illness more complicated. Diabetes is one example of a comorbid medical illness that is seen at a higher rate in people with mental illness.”

“Depression rates have been studied and are increased in type 1 and type 2 diabetes. In a meta-analysis, Barnard et al. reviewed 14 trials in which patients with type 1 diabetes were surveyed for rates of depression.16 […] subjects with type 1 diabetes had a 12.0% rate of depression compared with a rate of 3.4% in those without diabetes. In noncontrolled trials, they found an even higher rate of depression in patients with type 1 diabetes (13.4%). However, despite these overall findings, in trials that were considered of an adequate design, and with a substantially rigorous depression screening method (i.e., use of structured clinical interview rather than patient reported surveys), the rates were not statistically significantly increased (odds ratio [OR] 2.36, 95% confidence interval [CI] 0.69–5.4) but had such substantial variation that it was not sufficient to draw a conclusion regarding type 1 diabetes. […] When it comes to rates of depression, type 2 diabetes has been studied more extensively than type 1 diabetes. Anderson et al. compiled a large metaanalysis, looking at 42 studies involving more than 21,000 subjects to assess rates of depression among patients with type 1 versus type 2 diabetes mellitus.18 Regardless of how depression was measured, type 1 diabetes was associated with lower rates of depression than type 2 diabetes. […] Depression was significantly increased in both type 1 and type 2 diabetes, with increased ORs for subjects with type 1 (OR = 2.9, 95% CI 1.6 –5.5, […] p=0.0003) and type 2 disease (OR = 2.9, 95% CI 2.3–3.7, […] p = 0.0001) compared with controls. Overall, with multiple factors controlled for, the risk of depression in people with diabetes was approximately twofold. In another large meta-analysis, Ali et al. looked at more than 51,000 subjects in ten different studies to assess rates of depression in type 2 diabetes mellitus. […] the OR for comorbid depression among the diabetic patients studied was higher for men than for women, indicating that although women with diabetes have an overall increased prevalence of depression (23.8 vs. 12.8%, p = 0.0001), men with diabetes have an increased risk of developing depression (men: OR = 1.9, 95% CI = 1.7–2.1 vs. women: OR = 1.3, 95% CI = 1.2–1.4). […] Research has shown that youths 12–17 years of age with type 1 diabetes had double the risk of depression compared with a teenage population without diabetes.21 This amounted to nearly 15% of children meeting the criteria for depression.

As many as two-thirds of patients with diabetes and major depression have been ill with depression for more than 2 years.44 […] Depression has been linked to decreased adherence to self-care regimens (exercise, diet, and cessation of smoking) in patients with diabetes, as well as to the use of diabetes control medications […] Patients with diabetes and depression are twice as likely to have three or more cardiac risk factors such as smoking, obesity, sedentary lifestyle, or A1c > 8.0% compared with patients with diabetes alone.47 […] The costs for individuals with both major depression and diabetes are 4.5 times greater than for those with diabetes alone.53

“A 2004 cross-sectional and longitudinal study of data from the Health and Retirement Study demonstrated that the cumulative risk of incident disability over an 8-year period was 21.3% for individuals with diabetes versus 9.3% for those without diabetes. This study examined a cohort of adults ranging in age from 51 to 61 years from 1992 through 2000.”

Although people with diabetes comprise just slightly more than 4% of the U.S. population,3 19% of every dollar spent on health care (including hospitalizations, outpatient and physician visits, ambulance services, nursing home care, home health care, hospice, and medication/glucose control agents) is incurred by individuals with diabetes” (As I noted in the margin, these are old numbers, and prevalence in particular is definitely higher today than it was when that chapter was written, so diabetics’ proportion of the total cost is likely even higher today than it was when that chapter was written. As observed multiple times previously on this blog, most of these costs are unrelated to the costs of insulin treatment and oral anti-diabetics like metformin, and indirect costs make out a quite substantial proportion of the total costs).

In 1997, only 8% of the population with a medical claim of diabetes was treated for diabetes alone. Other conditions influenced health care spending, with 13.8% of the population with one other condition, 11.2% with two comorbidities, and 67% with three or more related conditions.6 Patients with diabetes who suffer from comorbid conditions related to diabetes have a greater impact on health services compared with those patients who do not have comorbid conditions. […] Overall, comorbid conditions and complications are responsible for 75% of total medical expenditures for diabetes.” (Again, these are old numbers)

“Heart disease and stroke are the largest contributors to mortality for individuals with diabetes; these two conditions are responsible for 65% of deaths. Death rates from heart disease in adults with diabetes are two to four times higher than in adults without diabetes. […] Adults with diabetes are more than twice as likely to have multiple diagnoses related to macrovascular disease compared to patients without diabetes […] Although the prevalence of cardiovascular disease increases with age for both diabetics and nondiabetics, adults with diabetes have a significantly higher rate of disease. […] The management of macrovascular disease, such as heart attacks and strokes, represents the largest factor driving medical service use and related costs, accounting for 52% of costs to treat diabetes over a lifetime. The average costs of treating macrovascular disease are $24,330 of a total of $47,240 per person (in year 2000 dollars) over the course of a lifetime.17 Moreover, macrovascular disease is an important determinant of cost at an earlier time than other complications, accounting for 85% of the cumulative costs during the first 5 years following diagnosis and 77% over the initial decade. [Be careful here: This is completely driven by type 2 diabetics; a 10-year old newly diagnosed type 1 diabetic does not develop heart disease in the first decade of disease – type 1s are also at high risk of cardiovascular disease, but the time profile here is completely different] […] Cardiovascular disease in the presence of diabetes affects not only cost but also the allocation of health care resources. Average annual individual costs attributed to the treatment of diabetes with cardiovascular disease were $10,172. Almost 51% of costs were for inpatient hospitalizations, 28% were for outpatient care, and 21% were for pharmaceuticals and related supplies. In comparison, the average annual costs for adults with diabetes and without cardiovascular disease were $4,402 for management and treatment of diabetes. Only 31.2% of costs were for inpatient hospitalizations, 40.3% were for outpatient care, and 28.6% were for pharmaceuticals.16

Of individuals with diabetes, 2% to 3% develop a foot ulcer during any given year. The lifetime incidence rate of lower extremity ulcers is 15% in the diabetic population.20 […] The rate of amputation in individuals with diabetes is ten times higher than in those without diabetes.5 Diabetic lower-extremity ulcers are responsible for 92,000 amputations each year,21 accounting for more than 60% of all nontraumatic amputations.5 The 10-year cumulative incidence of lower-extremity amputation is 7% in adults older than 30 years of age who are diagnosed with diabetes.22 […] Following amputation, the 5-year survival rate is 27%.23 […] The majority of annual costs associated with treating diabetic peripheral neuropathy are associated with treatment of ulcers […] Overall, inpatient hospitalization is a major driver of cost, accounting for 77% of expenditures associated with individual episodes of lower-extremity ulcers.24

By 2003, diabetes accounted for 37% of individuals being treated for renal disease in the United States. […] Diabetes is the leading cause of kidney failure, accounting for 44% of all newly diagnosed cases. […] The amount of direct medical costs for ESRD attributed to diabetes is substantial. The total adjusted costs in a 24-month period were 76% higher among ESRD patients with diabetes compared with those without diabetes. […] Nearly one half of the costs of ESRD are due to diabetes.27” [How much did these numbers change since the book was written? I’m not sure, but these estimates do provide some sort of a starting point, which is why I decided to include the numbers even though I assume some of them may have changed since the publication of the book]

Every percentage point decrease in A1c levels reduces the risk of microvascular complications such as retinopathy, neuropathy, and nephropathy by 40%.5 However, the trend is for A1c to drift upward at an average of 0.15% per year, increasing the risk of complications and costs.17 […] A1c levels also affect the cost of specific complications associated with diabetes. Increasing levels affect overall cost and escalate more dramatically when comorbidities are present. A1c along with cardiovascular disease, hypertension, and depression are significant independent predictors of health care
costs in adults with diabetes.”

August 10, 2016 Posted by | books, diabetes, economics, medicine, Pharmacology | Leave a comment

Human Drug Metabolism (II)

My first post covering Coleman’s excellent book can be found here, and here you can read my goodreads review of the book; I think it makes sense to read those things before reading this post, if you have not already done that. As I believe I’ve previously mentioned (?) most non-fiction books I read, including those I do not blog, usually get a goodreads review, and actually I’m much more active on goodreads these days than I am on this blog. I have considered cross-posting goodreads reviews here on the blog, but I decided it might be best to just keep these things separate for the time being. I might change my mind about this, though; I don’t like how inactive the blog has become during the last few months, and goodreads reviews I’ve already written take almost no work to cross-post, so this would be an easy way to at least get some ‘activity’ here.

The book includes a lot of information that really pretty much everybody would be likely to benefit from knowing (how many people for example live their entire lives without consuming any alcohol, tobacco, or medical drugs? If you’ve ever consumed any of these things, the book has material of relevance included in the coverage…). I repeat myself here, but  some of the general observations included in the following seem to me to be important takeaways from the book: Drugs work (sometimes very) differently in different people, they interact with different things, including innocuous things like what you eat and drink and whether you exercise or not; drugs may interact with each other, in a very confusing variety of ways; some drugs are metabolized differently in people who have taken the drug for a while (‘induction’), compared to how the drug might be metabolized in someone who’s not taken the drug before (drug-naïve), and sometimes the ability to metabolize the drug faster/more efficiently may be lost (inhibition) because of a third factor, such as e.g. another drug or a dietary factor, which can be very dangerous (an improved ability to metabolize the drug because of habituation may also be lost due to non-consumption of the drug for some time, leading to a ‘reset’ of the metabolic pathway of relevance, an important factor in an abuse context where this can lead to overdose); there are huge racial and genetic differences in terms of how specific drugs are metabolized; the consequences of getting too much of a specific drug (toxicity) tend to be foreseeably different from the consequences of getting not enough of a drug (drug failure); efficient metabolism of a drug may depend upon the body’s ability not just to transform the xenobiotic compound into something useful, but also the ability to get rid of sometimes really quite toxic metabolites which might be created along the way as the body tries to get rid of that thing you just injected/ingested/etc. Many people don’t consider herbal remedies to be ‘real drugs’ and so neglect to tell their medical practitioner that they’re taking them/have recently stopped taking them, despite some of these having the potential to cause quite serious drug interactions (even if nothing is taken but herbal remedies; St. John’s Wort + kava kava = acute hepatitis? As noted in the book, “One point important to emphasize, is that assuming various herbal remedies do contain active and potent substituents, there is virtually nothing known clinically about what effects mixing herbal remedies might have, in terms of pharmacology and toxicity. This area is unfortunately left for patients to discover for themselves”).

This book is not ‘the whole story’ about drug metabolism and related stuff, it just scratches the surface, but the coverage serves to make it clear to you just how much stuff is to be found ‘below the surface’, and this is something I really like about the book. It makes you appreciate how little you know and how complex this stuff is. People write 500+ page textbooks like this one simply about CYP subtypes (I came across a different 1000+ page textbook also about a CYP subtype while reading the book so I know this one is hardly unique, but unfortunately I did not bookmark the book and I didn’t find the book after a brief search for it – but take my word for it, those books are out there…) and alcohol metabolism, they write 700 page textbooks about the side effects of psychiatric drugs (not the intended effects, that is – the side effects!) they write 800 page textbooks about aspirin and related drugs and about how drugs affect the liver… I know that in some circles it’s somewhat common for people to ‘experiment’ with various drugs and substances, illicit or otherwise; I also assume that most people who do this sort of thing have little idea what they’re actually doing and are likely taking a lot of risks the very existence of which they’re likely not aware of. Simply because there’s just so much stuff you need to know to even have a proper concept of what you’re doing when you’re dealing with how the human body works and how it responds to foreign substances we might choose to introduce into it. It might be that they wouldn’t care even if they knew because you’re probably rather low in risk aversion if you engage in that sort of experimentation in the first place (I incidentally am highly risk averse), but I do find it curious.

I have added some observations from the middle of the book below.

“Although there is growing awareness of the clinical problems posed by P-gp [P-glycoprotein] inhibition on drug bioavailability and toxicity, until recently it was very difficult to generalize and predict which classes of drug might be inhibitors of P-gp. […] There are dozens of drugs which are known inhibitors of P-gp […] it is often difficult to establish what contribution cellular transport systems make to bioavailability. Indeed, it is emerging that one of the reasons for the very wide variety of drug bioavailability in modern medicine could be the sheer number of possible inhibitors and substrates that exist for P-gp in the diet, such as a number of natural products like the flavonols, which can be as potent as cyclosporine or verapamil as P-gp inhibitors. Natural dietary inhibitors have advantages in their general lack of toxicity, but the basic problem of a lack of predictability in their effects on P-gp substrates remains. Since no two people’s diets are identical, the impact of P-gp modulation on drug absorption could be simply too complex to unravel.”

“the objectives of metabolizing systems could be summed up thus:
• To terminate the pharmacological effect of the molecule.
• Make the molecule so water-soluble that it cannot escape clearance, preferably by more than one route to absolutely guarantee its removal.
These objectives could be accomplished by:
• Changing the molecular shape so it no longer binds to its receptors.
• Changing the molecular lipophilicity to hydrophilicity to ensure high water solubility.
• Making the molecule larger and heavier, so it can be eliminated in bile as well as urine.
• Efflux pump systems, which ensure that a highly water-soluble metabolite actually leaves the cell to enter the bloodstream, before it is excreted in bile and urine. […]
CYP-mediated metabolism can increase hydrophilicity, but it does not always increase it enough and it certainly does not make the molecule any bigger and heavier, indeed, sometimes the molecule becomes lighter […] CYP-mediated metabolism does not always alter the pharmacological effects of the drug either […] However, CYPs do perform two essential tasks: the initial destabilization of the molecule, creating a ‘handle’ on it. […] CYPs also ‘unmask’ groups that could be more reactive for further metabolism. […] CYP-mediated preparation can make the molecule vulnerable to the attachment of a very water-soluble and plentiful agent to the drug or steroid, which accomplishes the objectives of metabolism. This is achieved through the attachment of a modified glucose molecule (glucuronidation), or a soluble salt such as a sulphate (sulphation) [see also this] to the prepared site. Both adducts usually make the drug into a stable, heavier and water-soluble ex-drug. […] with many drugs, their stability and lipophilicity mean that their clearance must take more than one metabolic operation to make them water-soluble.”

PXR [Pregnane X receptor], CAR [constitutive androstane receptor] and FXR [Farnesoid X receptor] are […] part of the process whereby the liver can sense whether its own metabolic capacity and physical size is sufficient to respond to homeostatic demands. Hence, alongside various growth factors, the NRs [nuclear receptors] facilitate the amazing process whereby the liver regenerates itself after areas of the organ are removed or damaged. […] As CYPs, UGTs [Glucuronosyltransferases], other biotransforming systems and efflux transporters are meeting the same xenobiotic or endobiotic stimuli in different tissues and degrees of exposure, it is logical that the […] receptor systems integrate and coordinate their responses. […] These multi-receptor mechanisms enable levels of induction to be customized for individual tissues to deal with different chemical threats. Essentially, according to diet, chemical and drug exposure, each individual will possess a unique expression array of UGTs and CYPs which will be constantly fine-tuned throughout life.”

“Sulphonation is accomplished by a set of enzyme systems known as sulphotransferases (SULTs) and they are found in most tissues to varying degrees of activity. […] The general aim of sulphonation is to make the substrate more water-soluble and usually less active pharmacologically. Sulphonated molecules are more readily eliminated in bile and urine. […] All SULTs are subject to genetic polymorphisms, with a high degree of individual variation in their expression and catalytic activities […] Regarding classification of the superfamily of SULTs, it is assumed that 47 per cent amino acid sequence homology is indicative of same family members and 60 per cent homology for subfamily members. To date, there are 47 mammalian SULT isoforms so far discovered, which are derived from ten human sulphotransferase gene families […] knowledge of the role of NRs and AhR [Aryl hydrocarbon receptor] in human SULT expression has progressed in animals but not really in humans. This is partly due to the fact that rodent SULT profiles are quite different to ours […] Many studies have been carried out in rodents, which have produced rather contradictory results […] It seems that whilst SULTs in general are not as responsive to inducers as CYPs and UGTs, their basal expression is much higher, although interindividual expression does vary considerably and this may have severe toxicological consequences, in terms of xenobiotic toxicity and carcinogenicity. There is also some evidence that diet is a strong influence on individual SULT profiles.”

“One of the main problems with the oxidation of various molecules by CYP enzymes is that they are often destabilized and sometimes form highly reactive products. […] CYPs occasionally form metabolites so reactive that they immediately destroy the enzyme by reacting with it, changing its structure and, therefore, its function. […] The most dangerous forms of reactive species are those that evade UGTs and SULT enzymes, or are inadvertently created by conjugation processes. These species escape into the cytosol and even into the nucleus, where potentially carcinogenic events may result. […] CYPs are not the only source of reactive species generated within cells. Around 75 per cent of our food intake is directed at maintaining our body temperature and a great deal of energy must be liberated from the food to accomplish this. Cells derive the vast majority of their energy through oxidative phosphorylation and this takes place in […] the mitochondria. […] In cells almost all the oxygen we breathe is consumed in oxidative phosphorylation, forming ATP, heat and reactive oxidant species in the mitochondria that could cause severe damage to the structure and function of the cell if they were allowed to escape. So all cells, particularly hepatocytes, have evolved a separate system to accommodate such reactive toxic products and this is based on a three amino acid (cysteine, glycine and glutamate) thiol known as glutathione, or GSH. Thiols in general are extremely effective at reducing and thus ‘quenching’ highly reactive, electrophilic species. […] if cells are depleted of GSH by blocking its synthesis (by using buthionine sulphoxime), cell death follows and the organism itself will die in a few days, due to uncontrolled activity of endogenous radicals. […] If GSH levels are not maintained in the cell over a long period of time, the cell wears out more quickly; for example, diabetic complications and HIV infection are linked with poor GSH maintenance.” [I did not know this…]

“There are several enzymes that promote and catalyze the reaction of GSH with potential toxins to ensure that reactive species are actively dealt with, rather than just passive GSH-mediated reduction. Probably the most important from the standpoint of drug metabolism are the GSH-S-transferases [‘GSTs’, which] are the key cellular defence against electrophilic agents formed from endogenous or xenobiotic oxidative metabolism. […] The GSTs are found in humans in several major classes. […] The classes contain several subfamilies […] These enzymes are polymorphic […] and their individual expression ranges from complete absence in some isoforms to overabundance as a response to anticancer therapy. […] The upregulation of GST is a serious problem within cancer therapeutics and resistance to a range of drugs including melphalan and doxorubicin is linked with GST detoxification. Much research has been directed at inhibitors of GST isoforms to reverse or even prevent the development of resistance to anti-neoplastic agents. Unfortunately this strategy has not been successful”

“once xenobiotics have been converted into low-toxicity, higher-molecular-weight and high-water-solubility metabolites by the combination of CYPs, UGTs, SULTs and GSTs, this appears at first sight to be ‘mission accomplished’. However, these conjugates must be transported against a concentration gradient out of the cell into the interstitial space between cells. Then they will enter the capillary system and thence to the main bloodstream and filtration by the kidneys. The biggest hurdle is the transport out of the cell, which is a tall order, as once a highly water-soluble entity has been created, it will effectively be ‘ion-trapped’ in the cell, as the cell membrane is highly lipophilic and is an effective barrier to the exit as well as entry of most hydrophilic molecules. […] failure to remove the hydrophilic products of conjugation reactions [from the cells] can lead to:
• toxicity of conjugates to various cell components;
• hydrolysis of conjugates back to the original reactive species;
• inhibition of conjugating enzymes.
If the cell can manage to transport them out, then they should be excreted in urine or bile and detoxification can proceed at a maximal rate. […] Consequently, an impressive array of multi-purpose membrane bound transport carrier systems has evolved which can actively remove hydrophilic metabolites and many other low molecular weight drugs and toxins from cells. The relatively recent […] term of Phase III metabolism has been applied to the study of this essential arm of the detoxification process. […] The main thrust of research into efflux transporters has been directed at the ABC-type transporters [this link actually has quite a bit of content, unlike some of the other wiki articles on these topics], of which there are 48 genes that code of a variety of ATP-powered pumps.”

“it is clear that the whole process of detection, metabolism and elimination of endobiotic and xenobiotic agents is minutely coordinated and is responsive to changes in load in individual tissues. The CYPs, UGTs, MRPs [Multidrug Resistance Proteins] and P-gp are all tightly regulated through the NR system of PXR, CAR, FXE, PPAR α, LXR etc, as well as the AhR receptor system [does it even make sense to keep adding links here? I’m not sure it does…]. Some enzyme/pump processes are closely linked, such as CYP3A4 and P-gp, as inducers powerfully increase both systems capacity. The reactive species protection ‘arm’ of biotransformation is also controlled through a separate but almost certainly ‘cross-talking’ Nrf2/Keap1 system which coordinates not only the interception of reactive species by GSTs, but also the supply of their GSH substrate, UGTs and the MRPs. This latter coordination is particularly relevant in resistance to cancer chemotherapy and happens because overexpression of any one entity alone cannot rid the cell of the toxin. […] The MRPs, GSH production and GST/UGT activity must be induced in concert. […] much of the integration and coordination of detoxification processes remains to be uncovered”.

Chapter 7, about ‘factors affecting drug metabolism’, has some very interesting stuff, but I think this post is quite long enough as it is. I might talk about that stuff in detail later on, but I make no promises.

August 9, 2016 Posted by | books, medicine, Pharmacology | Leave a comment

Human Drug Metabolism (I)

“It has been said that if a drug has no side effects, then it is unlikely to work. Drug therapy labours under the fundamental problem that usually every single cell in the body has to be treated just to exert a beneficial effect on a small group of cells, perhaps in one tissue. Although drug-targeting technology is improving rapidly, most of us who take an oral dose are still faced with the problem that the vast majority of our cells are being unnecessarily exposed to an agent that at best will have no effect, but at worst will exert many unwanted effects. Essentially, all drug treatment is really a compromise between positive and negative effects in the patient. […] This book is intended to provide a basic grounding in human drug metabolism, although it is useful if the reader has some knowledge of biochemistry, physiology and pharmacology from other sources. In addition, a qualitative understanding of chemistry can illuminate many facets of drug metabolism and toxicity. Although chemistry can be intimidating, I have tried to make the chemical aspects of drug metabolism as user-friendly as possible.”

I’m currently reading this book. To say that it is ‘useful if the reader has some knowledge’ of the topics mentioned is putting it mildly; I’d say it’s mandatory – my advice would be to stay far away from this book if you know nothing of pharmacology, biochem, and physiology. I know enough to follow most of the coverage, at least in terms of the big picture stuff, but some of the biochemistry details I frankly have been unable to follow; I think I could probably understand all of it if I were willing to look up all the words and concepts with which I’m unfamiliar, but I’m not willing to spend the time to do that. In this context it should also be mentioned that the book is very well written, in the sense that it is perfectly possible to read the book and follow the basic outline of what’s going on without necessarily understanding all details, so I don’t feel that the coverage in any way discourages me from reading the book the way I am – the significance of that hydrogen bond in the diagram will probably become apparent to you later, and even if it doesn’t you’ll probably manage.

In terms of general remarks about the book, a key point to be mentioned early on is also that the book is very dense and has a lot of interesting stuff. I find it hard at the moment to justify devoting time to blogging, but if that were not the case I’d probably feel tempted to cover this book in a lot of detail, with multiple posts delving into specific fascinating aspects of the coverage. Despite this being a book where I don’t really understand everything that’s going on all the time, I’m definitely at a five star rating at the moment, and I’ve read close to two-thirds of it at this point.

A few quotes:

“The process of drug development weeds out agents [or at least tries to weed out agents… – US] that have seriously negative actions and usually releases onto the market drugs that may have a profile of side effects, but these are relatively minor within a set concentration range where the drug’s pharmacological action is most effective. This range, or ‘therapeutic window’ is rather variable, but it will give some indication of the most ‘efficient’ drug concentration. This effectively means the most beneficial pharmacodynamic effects for the minimum side effects.”

If the dose is too low, you have a case of drug failure, where the drug doesn’t work. If the dose is too high, you experience toxicity. Both outcomes are problematic, but they manifest in different ways. Drug failure is usually a gradual process (days – “Therapeutic drug failure is usually a gradual process, where the time frame may be days before the problem is detected”), whereas toxicity may be of very rapid onset (hours).

“To some extent, every patient has a unique therapeutic window for each drug they take, as there is such huge variation in our pharmacodynamic drug sensitivities. This book is concerned with what systems influence how long a drug stays in our bodies. […] [The therapeutic index] has been defined as the ratio between the lethal or toxic dose and the effective dose that shows the normal range of pharmacological effect. In practice, a drug […] is listed as having a narrow TI if there is less than a twofold difference between the lethal and effective doses, or a twofold difference in the minimum toxic and minimum effective concentrations. Back in the 1960s, many drugs in common use had narrow TIs […] that could be toxic at relatively low levels. Over the last 30 years, the drug industry has aimed to replace this type of drug with agents with much higher TIs. […] However, there are many drugs […] which remain in use that have narrow or relatively narrow TIs”.

“metabolites are usually removed from the cell faster than the parent drug”

“The kidneys are mostly responsible for […] removal, known as elimination. The kidneys cannot filter large chemical entities like proteins, but they can remove the majority of smaller chemicals, depending on size, charge and water solubility. […] the kidney is a lipophilic (oil-loving) organ […] So the kidney is not efficient at eliminating lipophilic chemicals. One of the major roles of the liver is to use biotransforming enzymes to ensure that lipophilic agents are made water soluble enough to be cleared by the kidney. So the liver has an essential but indirect role in clearance, in that it must extract the drug from the circulation, biotransform (metabolize) it, then return the water-soluble product to the blood for the kidney to remove. The liver can also actively clear or physically remove its metabolic products from the circulation by excreting them in bile, where they travel through the gut to be eliminated in faeces.”

“Cell structures eventually settled around the format we see now, a largely aqueous cytoplasm bounded by a predominantly lipophilic protective membrane. Although the membrane does prevent entry and exit of many potential toxins, it is no barrier to other lipophilic molecules. If these molecules are highly lipophilic, they will passively diffuse into and become trapped in the membrane. If they are slightly less lipophilic, they will pass through it into the organism. So aside from ‘ housekeeping ’ enzyme systems, some enzymatic protection would have been needed against invading molecules from the immediate environment. […] the majority of living organisms including ourselves now possess some form of effective biotransformational enzyme capability which can detoxify and eliminate most hydrocarbons and related molecules. This capability has been effectively ‘stolen’ from bacteria over millions of years. The main biotransformational protection against aromatic hydrocarbons is a series of enzymes so named as they absorb UV light at 450 nm when reduced and bound to carbon monoxide. These specialized enzymes were termed cytochrome P450 monooxygenases or sometimes oxido-reductases. They are often referred to as ‘CYPs’ or ‘P450s’. […] All the CYPs accomplish their functions using the same basic mechanism, but each enzyme is adapted to dismantle particular groups of chemical structures. It is a testament to millions of years of ‘ research and development ’ in the evolution of CYPs, that perhaps 50,000 or more man-made chemical entities enter the environment for the first time every year and the vast majority can be oxidized by at least one form of CYP. […] To date, nearly 60 human CYPs have been identified […] It is likely that hundreds more CYP-mediated endogenous functions remain to be discovered. […] CYPs belong to a group of enzymes which all have similar core structures and modes of operation. […] Their importance to us is underlined by their key role in more than 75 per cent of all drug biotransformations.”

I would add a note here that a very large proportion of this book is, perhaps unsurprisingly in view of the above, about those CYPs; how they work, what exactly it is that they do, which different kinds there are and what roles they play in the metabolism of specific drugs and chemical compounds, variation in gene expression across individuals and across populations in the context of specific CYPs and how such variation may relate to differences in drug metabolism, etc.

“Drugs often parallel endogenous molecules in their oil solubility, although many are considerably more lipophilic than these molecules. Generally, drugs, and xenobiotic compounds, have to be fairly oil soluble or they would not be absorbed from the GI tract. Once absorbed these molecules could change both the structure and function of living systems and their oil solubility makes these molecules rather ‘elusive’, in the sense that they can enter and leave cells according to their concentration and are temporarily beyond the control of the living system. This problem is compounded by the difficulty encountered by living systems in the removal of lipophilic molecules. […] even after the kidney removes them from blood by filtering them, the lipophilicity of drugs, toxins and endogenous steroids means that as soon as they enter the collecting tubules, they can immediately return to the tissue of the tubules, as this is more oil-rich than the aqueous urine. So the majority of lipophilic molecules can be filtered dozens of times and only low levels are actually excreted. In addition, very high lipophilicity molecules like some insecticides and fire retardants might never leave adipose tissue at all […] This means that for lipophilic agents:
*the more lipophilic they are, the more these agents are trapped in membranes, affecting fluidity and causing disruption at high levels;
* if they are hormones, they can exert an irreversible effect on tissues that is outside normal physiological control;
*if they are toxic, they can potentially damage endogenous structures;
* if they are drugs, they are also free to cause any pharmacological effect for a considerable period of time.”

“A sculptor was once asked how he would go about sculpting an elephant from a block of stone. His response was ‘knock off all the bits that did not look like an elephant’. Similarly, drug-metabolizing CYPs have one main imperative, to make molecules more water-soluble. Every aspect of their structure and function, their position in the liver, their initial selection of substrate, binding, substrate orientation and catalytic cycling, is intended to accomplish this deceptively simple aim.”

“The use of therapeutic drugs is a constant battle to pharmacologically influence a system that is actively undermining the drugs’ effects by removing them as fast as possible. The processes of oxidative and conjugative metabolism, in concert with efflux pump systems, act to clear a variety of chemicals from the body into the urine or faeces, in the most rapid and efficient manner. The systems that manage these processes also sense and detect increases in certain lipophilic substances and this boosts the metabolic capability to respond to the increased load.”

“The aim of drug therapy is to provide a stable, predictable pharmacological effect that can be adjusted to the needs of the individual patient for as long is deemed clinically necessary. The physician may start drug therapy at a dosage that is decided on the basis of previous clinical experience and standard recommendations. At some point, the dosage might be increased if the desired effects were not forthcoming, or reduced if side effects are intolerable to the patient. This adjustment of dosage can be much easier in drugs that have a directly measurable response, such as a change in clotting time. However, in some drugs, this adjustment process can take longer to achieve than others, as the pharmacological effect, once attained, is gradually lost over a period of days. The dosage must be escalated to regain the original effect, sometimes several times, until the patient is stable on the dosage. In some cases, after some weeks of taking the drug, the initial pharmacological effect seen in the first few days now requires up to eight times the initial dosage to reproduce. It thus takes a significant period of time to create a stable pharmacological effect on a constant dose. In the same patients, if another drug is added to the regimen, it may not have any effect at all. In other patients, sudden withdrawal of perhaps only one drug in a regimen might lead to a gradual but serious intensification of the other drug’s side effects.”

“acceleration of drug metabolism as a response to the presence of certain drugs is known as ‘enzyme induction’ and drugs which cause it are often referred to as ‘inducers’ of drug metabolism. The process can be defined as: ‘An adaptive increase in the metabolizing capacity of a tissue’; this means that a drug or chemical is capable of inducing an increase in the transcription and translation of specific CYP isoforms, which are often (although not always) the most efficient metabolizers of that chemical. […] A new drug is generally regarded as an inducer if it produces a change in drug clearance which is equal to or greater than 40 per cent of an established potent inducer, usually taken as rifampicin. […] inducers are usually (but not always) lipophilic, contain aromatic groups and consequently, if they were not oxidized, they would be very persistent in living systems. CYP enzymes have evolved to oxidize this very type of agent; indeed, an elaborate and very effective system has also evolved to modulate the degree of CYP oxidation of these agents, so it is clear that living systems regard inducers as a particular threat among lipophilic agents in general. The process of induction is dynamic and closely controlled. The adaptive increase is constantly matched to the level of exposure to the drug, from very minor almost undetectable increases in CYP protein synthesis, all the way to a maximum enzyme synthesis that leads to the clearance of grammes of a chemical per day. Once exposure to the drug or toxin ceases, the adaptive increase in metabolizing capacity will subside gradually to the previous low level, usually within a time period of a few days. This varies according to the individual and the drug. […] it is clear there is almost limitless capacity for variation in terms of the basic pre-set responsiveness of the system as well as its susceptibility to different inducers and groups of inducers. Indeed, induction in different patients has been observed to differ by more than 20-fold.”

This one I added mostly because I didn’t know this and I thought it was worth including it here because it would make it easier for me to remember later (i.e., not because I figured other people might find this interesting):

CYP2E1 is very sensitive to diet, even becoming induced by high fat/low carbohydrate intakes. Surprisingly, starvation and diabetes also promote CYP2E1 functionality. Insulin levels fall during diet restriction, starvation and in diabetes and the formation of functional 2E1 is suppressed by insulin, so these conditions promote the increase of 2E1 metabolic capability. One of the consequences of diabetes and starvation is the major shift from glucose to fatty acid/tryglyceride oxidation, of which some of the by-products are small, hydrophilic and potentially toxic ‘ketone bodies’. These agents can cause a CNS intoxicating effect which is seen in diabetics who are very hypoglycaemic, they may appear ‘drunk’ and their breath will smell as if they had been drinking.”

A more general related point which may be of more interest to other people reading along here is that this is far from the only CYP which is sensitive to diet, and that diet-mediated effects may be very significant. I may go into this in more detail in a later post. Note that grapefruit is a major potentially problematic dietary component in many drug contexts:

“Although patients have been heroically consuming grapefruit juice for their health for decades, it took until the late 1980s before its effects on drug clearance were noted and several more years before it was realized that there could be a major problem with drug interactions […] The most noteworthy feature of the effect of grapefruit juice is its potency from a single ‘dose’ which coincides with a typical single breakfast intake of the juice, say around 200–300 ml. Studies with CYP3A substrates such as midazolam have shown that it can take up to three days before the effects wear off, which is consistent with the synthesis of new enzyme. […] there are a number of drugs that are subject to a very high gut wall component to their ‘first-pass’ metabolism […]; these include midazolam, terfenadine, lovastatin, simvastatin and astemizole. Their gut CYP clearance is so high that if the juice inhibits it, the concentration reaching the liver can increase six- or sevenfold. If the liver normally only extracts a relatively minor proportion of the parent agent, then plasma levels of such drugs increase dramatically towards toxicity […] the inhibitor effects of grapefruit juice in high first – pass drugs is particularly clinically relevant as it can occur after one exposure of the juice.”

It may sound funny, but there are two pages in this book about the effects of grapefruit juice, including a list of ‘Drugs that should not be taken with grapefruit juice’. Grapefruit is a well-known so-called mechanism-based inhibitor, and it may impact the metabolism of a lot of different drugs. It is far from the only known dietary component which may cause problems in a drug metabolism context – for example “cranberry juice has been known for some time as an inhibitor of warfarin metabolism”. On a general note the author remarks that: “There are hundreds of fruit preparations available that have been specifically marketed for their […] antioxidant capacities, such as purple grape, pomegranate, blueberry and acai juices. […] As they all contain large numbers of diverse phenolics and are pharmacologically active, they should be consumed with some caution during drug therapy.”

April 7, 2016 Posted by | biology, books, medicine, Pharmacology | Leave a comment

Effects of Antidepressants

I gave the book two stars on goodreads. The contributors to this volume are from Brazil, Spain, Mexico, Japan, Turkey, Denmark, and the Czech Republic; the editor is from Taiwan. In most chapters you can tell that the first language of these authors is not English; the language is occasionally quite bad, although you can usually tell what the authors are trying to say.

The book is open access and you can read it here. I have included some quotes from the book below:

“It is estimated that men and women with depression are 20.9 and 27 times, respectively, more likely to commit suicide than those without depression (Briley & Lépine, 2011).” [Well, that’s one way to communicate risk… See also this comment].

“depression is on average twice as common in women as in men (Bromet et al., 2011). […] sex differences have been observed in the prevalence of mental disorders as well as in responses to treatment […] When this [sexual] dimorphism is present [in rats, a common animal model], the drug effect is generally stronger in males than in females.”

“Several reports indicate that follicular stimulating and luteinizing hormones and estradiol oscillations are correlated with the onset or worsening of depression symptoms during early perimenopause […], when major depressive disorder incidence is 3-5 times higher than the male matched population of the same [age] […]. Several longitudinal studies that followed women across the menopausal transition indicate that the risk for significant depressive symptoms increases during the menopausal transition and then decreases in […] early postmenopause […] the impact of hormone oscillations during perimenopause transition may affect the serotonergic system function and increase vulnerability to develop depression.”

“The use of antidepressant drugs for treating patients with depression began in the late 1950s. Since then, many drugs with potential antidepressants have been made available and significant advances have been made in understanding their possible mechanisms of action […]. Only two classes of antidepressants were known until the 80’s: tricyclic antidepressants and monoamine oxidase inhibitors. Both, although effective, were nonspecific and caused numerous side effects […]. Over the past 20 years, new classes of antidepressants have been discovered: selective serotonin reuptake inhibitors, selective serotonin/norepinephrine reuptake inhibitors, serotonin reuptake inhibitors and alpha-2 antagonists, serotonin reuptake stimulants, selective norepinephrine reuptake inhibitors, selective dopamine reuptake inhibitors and alpha-2 adrenoceptor antagonists […] Neither the biological basis of depression […] nor the precise mechanism of antidepressant efficacy are completely understood […]. Indeed, antidepressants are widely prescribed for anxiety and disorders other than depression.”

“Taken together the TCAs and the MAO-Is can be considered to be non-selective or multidimensional drugs, comparable to a more or less rational polypharmacy at the receptor level. This is even when used as monotherapy in the acute therapy of major depression. The new generation of selective antidepressants (the selective serotonin reuptake inhibitors (SSRIs)), or the selective noradrenaline and serotonin reuptake inhibitors (SNRIs) have a selective mechanism of action, thus avoiding polypharmacy. However, the new generation antidepressants such as the SSRIs or SNRIs are less effective than the TCAs. […] The most selective second generation antidepressants have not proved in monotherapy to be more effective on the core symptoms of depression than the first generation TCAs or MAOIs. It is by their safety profiles, either in overdose or in terms of long term side effects, that the second generation antidepressants have outperformed the first generation.”

“Suicide is a serious global public health problem. Nearly 1 million individuals commit suicide every year. […] Suicide […] ranks among the top 10 causes of death in every country, and is one of the three leading causes of death in 15 to 35-year olds.”

“Considering patients that commit suicide, about half of them, at some point, had contact with psychiatric services, yet only a quarter had current or recent contact (Andersen et al., 2000; Lee et al., 2008). A study conducted by Gunnell & Frankel (1994) revealed that 20-25% of those committing suicide had contact with a health care professional in the week before death and 40% had such contact one month before death” (I’m assuming ‘things have changed’ during the last couple of decades, but it would be interesting to know how much they’ve changed).

“In cases of suicide by drug overdose, TCAs have the highest fatal toxicity, followed by serotonin and noradrenalin reuptake inhibitors (SNRIs), specific serotonergic antidepressants (NaSSA) and SSRIs […] SSRIs are considered to be less toxic than TCAs and MAOIs because they have an extended therapeutic window. The ingestion of up to 30 times its recommended daily dose produces little or no symptoms. The intake of 50 to 70 times the recommended daily dose can cause vomiting, mild depression of the CNS or tremors. Death rarely occurs, even at very high doses […] When we talk about suicide and suicide attempt with antidepressants overdose, we are referring mainly to women in their twenties – thirties who are suicide repeaters.”

“Physical pain is one of the most common somatic symptoms in patients that suffer depression and conversely, patients suffering from chronic pain of diverse origins are often depressed. […] While […] data strongly suggest that depression is linked to altered pain perception, pain management has received little attention to date in the field of psychiatric research […] The monoaminergic system influences both mood and pain […], and since many antidepressants modify properties of monoamines, these compounds may be effective in managing chronic pain of diverse origins in non-depressed patients and to alleviate pain in depressed patients. There are abundant evidences in support of the analgesic properties of tricyclic antidepressants (TCAs), particularly amitriptyline, and another TCA, duloxetine, has been approved as an analgesic for diabetic neuropathic pain. By contrast, there is only limited data regarding the analgesic properties of selective serotonin reuptake inhibitors (SSRIs) […]. In general, compounds with noradrenergic and serotonergic modes of action are more effective analgesics […], although the underlying mechanisms of action remain poorly understood […] While the utility of many antidepressant drugs in pain treatment is well established, it remains unclear whether antidepressants alleviate pain by acting on mood (emotional pain) or nociceptive transmission (sensorial pain). Indeed, in many cases, no correlation exists between the level of pain experienced by the patient and the effect of antidepressants on mood. […] Currently, TCAs (amitriptyline, nortriptiline, imipramine and clomipramine) are the most common antidepressants used in the treatment of neuropathic pain processes associated with diabetes, cancer, viral infections and nerve compression. […] TCAs appear to provide effective pain relief at lower doses than those required for their antidepressant effects, while medium to high doses of SNRIs are necessary to produce analgesia”. Do keep in mind here that in a neuropathy setting one should not expect to get anywhere near complete pain relief with these drugs – see also this post.

“Prevalence of a more or less severe depression is approximately double in patients with diabetes compared to a general population [for more on related topics, see incidentally this previous post of mine]. […] Diabetes as a primary disease is typically superimposed by depression as a reactive state. Depression is usually a result of exposure to psycho-social factors that are related to hardship caused by chronic disease. […] Several studies concerning comorbidity of type 1 diabetes and depression identified risk factors of depression development; chronic somatic comorbidity and polypharmacy, female gender, higher age, solitary life, lower than secondary education, lower financial status, cigarette smoking, obesity, diabetes complications and a higher glycosylated hemoglobin [Engum, 2005; Bell, 2005; Hermanns, 2005; Katon, 2004]”

November 11, 2015 Posted by | books, diabetes, medicine, Pharmacology, Psychology | Leave a comment

Peripheral Neuropathy & Neuropathic Pain: Into the light (II)

Here’s my first post about the book. As I mentioned in that post, I figured I should limit detailed coverage to the parts of the book dealing with stuff related to diabetic/metabolic neuropathies. There’s a chapter specifically about ‘diabetic and uraemic neuropathies’ in the book and most of the coverage below relates to content covered in that chapter, but I have also included some related observations from other parts of the book as they seemed relevant.

It is noted in the book’s coverage that diabetes is the commonest cause of neuropathy in industrialized countries. There are many ways in which diabetes can affect the nervous system, and not all diabetes-related neuropathies affect peripheral nerves. Apart from distal symmetric polyneuropathy, which can probably in this context be thought of as ‘classic diabetic neuropathy’, focal or multifocal involvement of the peripheral nervous system is also common, and so is autonomic neuropathy. Diabetics are also at increased risk of inflammatory neuropathies such as CIDP – chronic inflammatory demyelinating polyneuropathy (about which the book also has a chapter). Late stage complications of diabetes usually relate to some extent to vessel wall abnormalities and their effects, and the blood vessels supplying the peripheral nerves can be affected just like all other blood vessels; in that context it is of interest to note that the author mentions elsewhere in the book that “tissue ischaemia is more likely to be symptomatic in nerves than in most other organs”. According to the author there isn’t really a great way to classify all the various manifestations of diabetic neuropathy, but most of them fall into one of three groups – distal symmetrical sensorimotor (length-dependent) polyneuropathy (DSSP); autonomic neuropathy; and focal- and multifocal neuropathy. The first one of these is by far the most common, and it is predominantly a sensory neuropathy (‘can you feel this?’ ‘does this hurt?’ ‘Is this water hot or cold?’ – as opposed to motor neuropathy: ‘can you move your arm?’) with no motor deficit.

Neuropathies in diabetics are common – how common? The author notes that the prevalence in several population-based surveys has been found to be around 30% “in studies using restrictive definitions”. The author does not mention this, but given that diabetic neuropathy usually has an insidious onset and given that diabetes-related sensory neuropathy “can be totally asymptomatic”, survey-based measures are if anything likely to underestimate prevalence. Risk increases with age and duration of diabetes; the prevalence of diabetic peripheral neuropathy is more than 50% in type 1 diabetics above the age of 60.

DSSP may lead to numbness, burning feet, a pins and needles sensation and piercing/stabbing pain in affected limbs. The ‘symmetric’ part of the abbreviation means that it usually affects both sides of the body, instead of e.g. just one foot or hand. The length-dependence mentioned in the parenthesis earlier relates in a way to the pathophysiological process. The axons of the peripheral nervous system lack ribosomes, and this means that essential proteins and enzymes needed in distal regions of the nervous system need to be transported great distances through the axons – which again means that neurons with long axons are particularly vulnerable to toxic or metabolic disturbances (introducing a length-dependence aspect in terms of which nerves are affected) which may lead to so-called dying-back axonal degeneration. The sensory loss can be restricted to the toes, extend over the feet, or it can migrate even further up the limbs – when sensory loss extends above the knee, signs and symptoms of nerve damage will usually also be observed in the fingers/hands/forearms. In generalized neuropathies a distinction can be made in terms of which type of nerve fibres are predominantly involved. When small fibres are most affected, sensory effects relating to pain- and temperature perception predominate, whereas light touch, position and vibratory senses are relatively preserved; on the other hand abnormalities of proprioception and sensitivity to light touch, often accompanied by motor deficits, will predominate if larger myelinated fibres are involved. DSSP is a small fibre neuropathy.

One of the ‘problems’ in diabetic neuropathy is actually that whereas sensation is affected, motor function often is not. This might be considered much better than the alternative, but unimpaired motor function actually relates closely to how damage often occurs. Wounds/ulcers developing on the soles of the feet (plantar ulcers) are very common in conditions in which there is sensation loss but no motor involvement/loss of strength; people with absent pain sensation will not know when their feet get hurt, e.g. because of a stone in the shoe or other forms of micro-trauma, but they’re still able to walk around relatively unimpaired and the absence of protective sensation in the limbs can thus lead to overuse of joints and accidental self-injury. A substantial proportion of diabetics with peripheral neuropathy also have lower limb ischaemia from peripheral artery disease, which further increases risk, but even in the absence of ischaemia things can go very wrong (for more details, see Edmonds, Foster, and Sanders – I should perhaps warn that the picture in that link is not a great appetite-stimulant). Of course one related problem here is that you can’t just stop moving around in order to avoid these problems once you’re aware that you have peripheral sensory neuropathy; inactivity will lead to muscle atrophy and ischaemia, and that’s not good for your feet either. The neuropathy may not ‘just’ lead to ulcers, but may also lead to the foot becoming deformed – the incidence of neuroarthropathy is approximately 2%/year in diabetics with peripheral neuropathy. Foot deformity is sometimes of acute onset and may be completely painless, despite leading to (painless) fractures and disorganization of joints. In the context of ulcers it is important that foot ulcers often take a *very* long time to heal, and so they provide excellent entry points for bacteria which among other things can cause chronic osteomyelitis (infection and inflammation of the bone and bone marrow). Pronounced motor involvement is as mentioned often absent in DSSP, but it does sometimes occur, usually at a late stage.

The author notes repeatedly in the text that peripheral neuropathy is sometimes the presenting symptom in type 2 diabetes, and I thought I should include that observation here as well. The high blood glucose may not be what leads the patient to see a doctor – sometimes the fact that he can no longer feel his toes is. At that point the nerve damage which has already occurred will of course usually be irreversible.

When the autonomic nervous system is affected (this is called Diabetic Autonomic Neuropathy, -DAN), this can lead to a variety of different symptoms. Effects of orthostatic hypotension (-OH) are frequent complaints; blackouts, faintness and dizziness or visual obscuration on standing are not always due to side effects of blood pressure medications. The author notes that OH can be aggravated by tricyclic antidepressants which are often used for treating chronic neuropathic pain (diabetics with autonomous nervous system disorder will often have, sometimes painful, peripheral neuropathy as well). Neurogenic male impotence seems to be “extremely common”; this leads to the absence of an erection at any time under any circumstances. The bladder may also be involved, which can lead to increased intervals between voiding and residual urine in the bladder after voiding, which can lead to UTIs. It is noted that retrograde ejaculation is frequent in people with bladder atony. The gastrointestinal system can be affected; this is often asymptomatic, but may lead to diarrhea and constipation causing weight loss and malnutrition. Associated diarrhea may be accompanied by fecal incontinence. DAN can lead to hypoglycemia unawareness, making glycemic control more difficult to accomplish. Sweating disorders are common in the feet. When a limb is affected by neuropathy the limb may lose its ability to sweat, and this may lead to other parts of the body (e.g. the head or upper trunk) engaging in ‘compensatory sweating’ to maintain temperature control. Abnormal pupil responses, e.g. in the form of reduced light reflexes and constricted pupils (miosis), are common in diabetics.

Focal (one nerve) and occasionally also multi-focal (more than one nerve) neuropathic syndromes also occur in the diabetic setting. The book spends quite a bit of time talking about what different nerves do and what happens when they stop working, so it’s hard to paint a broad picture of how these types of problems may present – it all depends on which nerve(s) is (are) affected. Usually in the setting of these disorders the long-term prognosis is good, or at least better than in the setting of DSSP; nerve damage is often not permanent. It seems that in terms of cranial nerve involvement, oculomotor nerve palsies are the most common, but still quite rare, affecting 1-2% of diabetics. Symptoms are rapid onset pain followed by double vision, and “spontaneous and complete recovery invariably occurs within 2-3 months” – I would like to note that as far as diabetes complications go, this is probably about as good as it gets… In so-called proximal diabetic neuropathy (-PDN), another type of mononeuropathy/focal neuropathy, the thighs are involved, with numbness or pain, often of a burning character which is worse at night, as well as muscle wasting. That syndrome progresses over weeks or months, after which the condition usually stabilizes and the pain improves, though residual muscle weakness seems to be common. Unlike in the case of DSSP, deficits in PDN are usually asymmetric, and both motor involvement and gradual recovery is common – it’s important to note in this context that DSSP virtually never improves spontaneously and often has a progressive course. Multi-focal neuropathies affect only a small proportion of diabetics, and in terms of outcome patterns they might be said to lie somewhere in between mononeuropathies and DSSP; outcomes are better than in the case of DSSP, but long-term sequelae are common.

Diabetics are at increased risk of developing pressure palsies in general. According to the author carpal tunnel syndrome occurs in 12% of diabetic patients, and “the incidence of ulnar neuropathy due to microlesions at the elbow level is high”.

In diabetics with renal failure caused by diabetic nephropathy (or presumably for that matter renal failure caused by other things as well, but most diabetics with kidney failure will have diabetic nephropathy) neuropathy is common and often severe. Renal failure impairs nerve function and is responsible for sometimes severe motor deficits in these patients. “Recovery from motor deficits is usually good after kidney transplant”. Carpal tunnel syndrome is very common in patients on long-term dialysis; 20 to 50 % of patients dialysed for 10 years or more are reported to have carpal tunnel syndrome. The presence of neuropathy in renal patients is closely related to renal function; the lower renal function, the more likely neurological symptoms become.

As you’ll learn from this book, a lot of things can cause peripheral neuropathies – and so the author notes that “In focal neuropathy occurring in diabetic patients, a neuropathy of another origin must always be excluded.” It’s not always diabetes, and sometimes missing the true cause can be a really bad thing; for example cancer-associated paraneoplastic syndromes are often associated with neuropathy (“paraneoplastic syndromes affect the PNS [Peripheral Nervous System] in up to one third of patients with solid tumors”), and so missing ‘the true cause’ in the case of a focal neuropathy may mean missing a growing tumour.

In terms of treatment options, “There is no specific treatment for distal symmetric polyneuropathy.” Complications can be treated/ideally prevented, but we have no drugs the primary effects of which are to specifically stop the nerves from dying. Treatment of autonomic neuropathy mostly relates to treating symptoms, in particular symptomatic OH. Treatment of proximal diabetic neuropathy, which is often very painful, relates only to pain management. Multifocal diabetic neuropathy can be treated with corticosteroids, minimizing inflammation.

Due to how common diabetic neuropathy is, most controlled studies on treatment options for neuropathic pain have involved patients with distal diabetic polyneuropathy. Various treatment options exist in the context of peripheral neuropathies, including antidepressants, antiepileptic drugs and opioids, as well as topical patches. In general pharmacological treatments will not cause anywhere near complete pain relief: “For patients receiving pharmacological treatment, the average pain reduction is about 20-30%, and only 20-35% of patients will achieve at least a 50% pain reduction with available drugs. […] often only partial pain relief from neuropathic pain can be expected, and […] sensory deficits are unlikely to respond to treatment.” Treatment of neuropathic pain is often a trial-and-error process.

October 17, 2015 Posted by | books, diabetes, medicine, Pharmacology | Leave a comment


If you have any alternatives, especially ones which involve not-unpleasant interaction with other people, you should not follow these links or watch this stuff. Go interact with other people instead. Have fun, (try to) enjoy life. If you enjoy this kind of stuff, you’re likely doing things wrong and you’ll probably end up unhappy.

Tet offensive.

Arrest and assassination of Ngo Dinh Diem.

Genetically Modified Crops and Food Security.

War of 1812.

Tichborne case.

Geoguessr. It’s quite fun. My best score so far is 13165 (but who cares?).

June 9, 2013 Posted by | history, Khan Academy, Lectures, medicine, Pharmacology, Physics, random stuff, wikipedia | Leave a comment

From the bookmarks

I won’t talk much about these links or cover them in any detail – but I do encourage you to have a closer look if some of this stuff sounds interesting:

i. Are All Dictator Game Results Artifacts? – “How much would participants in a Dictator Game give to the other person if they did not know they were in a Dictator Game study?”

Given how long people have known about stuff like the Hawthorne effect, I almost can’t believe nobody ever got the idea of doing something like this at some point in the past. I however have no problem believing the results.

ii. Finnish war pics. Fascinating stuff.

iii. The kind of people who apparently receive elite research prizes in Denmark these years – exhibit B: Claudia Welz (Danish link). Unfortunately I couldn’t find a good English webpage describing her activities, in order to illustrate just how mad it is that a person like that receives that kind of money from the Danish taxpayers in order to do the kind of ‘research’ she does, and my life is definitely too short to translate the crap that’s put up at the Danish site.

Exhibit A is of course Milena Penkowa. Naturally more deserving people have received the prize as well this year – at least most of the recipients probably won’t feel any strong need to talk about imaginary entities in their publications.

Here’s a related link (in Danish). It’d be a lot cheaper to just give these people unemployment insurance. I’m sure not all of this research is equally useless, but even so my willingness to pay for this kind of stuff is, well, let’s put it diplomatically – not exactly super high. I don’t really understand why people can not just study that kind of stuff (and less useless stuff…) themselves, during their own time, when they’re not working.

iv. A few more Steven Farmer pharmacology lectures:

There’s a bit of annoying microphone-related noise in parts of the second video and parts of the third one, but aside from that they’re quite good and this should not stop you from watching the videos if you find the topics covered interesting.

v. Twelve Month Prevalence of and Risk Factors for Suicide Attempts in the WHO World Mental Health Surveys.

vi. Does Educational Status Impact Adult Mortality in Denmark? A Twin Approach.

vii. Aspirin, angioplasty, and proton beam therapy: The economics of smarter health care spending.

May 31, 2013 Posted by | economics, history, Lectures, medicine, papers, Pharmacology, Psychology, random stuff | 4 Comments

A few lectures

I only ever covered two of Steven Farmer’s lectures here on the blog, and back when I blogged them I didn’t watch all of the lectures. Recently I went through some old bookmarks and decided to have a go at that stuff again. He’s pretty good:

Completely unrelated but I figured I should mention it: Tomorrow’s the first day of the London Chess Classic tournament. This chess tournament is as good as it gets; The world’s three highest rated players are all playing, as is the World Champion and the world’s strongest female player. Last year the live commentary was provided mainly by IM Lawrence Trent and GM Daniel King. They did a splendid job, but this year the organizers have upped the ante and found some significantly stronger players to do the job; Nigel Short and David Howell. Both of those guys are former contestants in the tournament. As usual the tournament has an unequal number of contestants, and the player with the bye round will join Short and Howell in the commentator box and give his/her views on the games as they proceed. I’ve been really impressed with the way the live commentary has been handled the last few years, and you can learn a lot by watching this stuff (here’s a direct link). The tournament has implemented a 3/1/0-rule (3 points for a win, 1 for a draw, 0 for a loss) so the number of ‘GM-draws’ is likely to be lower than it often is in these kinds of tournaments – the organizers want to incentivize the players to actually play interesting games, and in the past I think they’ve been successful. If you like chess, this is the place to be for the next one and a half weeks.

November 30, 2012 Posted by | Chess, Lectures, medicine, Pharmacology | Leave a comment


i. I started writing this post because I felt that I had to share this (click to view full size):

From abstrusegoose. But I decided that I might as well add a few other links as well.

ii. The Cochrane Foundation has just published a new review article on on ‘Pharmacotherapy for mild hypertension’ – it seems that the benefits of treatment are not as great as they have been made out to be. Via this slate article.

iii. (From Razib Khan’s pinboard feed:) How “god” evolved.

vi. In case you haven’t seen it:

v. Voyage of the James Caird. I may have linked to this before, but I don’t think so.

“The voyage of the James Caird was an open boat journey from Elephant Island in the South Shetland Islands to South Georgia in the southern Atlantic Ocean, a distance of 800 nautical miles (1,500 km; 920 mi). Undertaken by Sir Ernest Shackleton and five companions, its objective was to obtain rescue for the main body of the Imperial Trans-Antarctic Expedition of 1914–17, trapped on Elephant Island after the loss of its ship Endurance. History has come to consider the James Caird’s voyage as one of the greatest small-boat journeys ever accomplished.”

Here’s an image:

1500 kilometres and 16 days in a boat like that. And don’t think the trip was over when they reached the shore; those of them who could still travel had 36 hours of continuous travel across the mountainous and glacier-covered island in front of them before they were able to reach their goal, an inhabited whaling station in Stromness.

iv. I haven’t read this, but I assume that it may be of interest to some of you: Intelligence – A Unifying Construct for the Social Sciences, by Richard Lynn and Tatu Vanhanen.

August 20, 2012 Posted by | comics, history, IQ, medicine, Pharmacology, statistics, studies, wikipedia | 6 Comments

Stuff (updated)

(After Ed Yong published his latest post, I decided to add a couple of links – Monday, 10 a.m.)

i. Introduction to Evolutionary Biology (TalkOrigins)

I read this yesterday, I’m sure some of you will find it to be useful. Some quotes:

“Populations evolve. [evolution: a change in the gene pool] In order to understand evolution, it is necessary to view populations as a collection of individuals, each harboring a different set of traits. A single organism is never typical of an entire population unless there is no variation within that population. Individual organisms do not evolve, they retain the same genes throughout their life. When a population is evolving, the ratio of different genetic types is changing — each individual organism within a population does not change. For example, in the previous example, the frequency of black moths increased; the moths did not turn from light to gray to dark in concert. The process of evolution can be summarized in three sentences: Genes mutate. [gene: a hereditary unit] Individuals are selected. Populations evolve.

Evolution can be divided into microevolution and macroevolution. The kind of evolution documented above is microevolution. Larger changes, such as when a new species is formed, are called macroevolution. Some biologists feel the mechanisms of macroevolution are different from those of microevolutionary change. Others think the distinction between the two is arbitrary — macroevolution is cumulative microevolution.

The word evolution has a variety of meanings. The fact that all organisms are linked via descent to a common ancestor is often called evolution. The theory of how the first living organisms appeared is often called evolution. This should be called abiogenesis. And frequently, people use the word evolution when they really mean natural selection — one of the many mechanisms of evolution. […]

Evolution can occur without morphological change; and morphological change can occur without evolution. Humans are larger now than in the recent past, a result of better diet and medicine. Phenotypic changes, like this, induced solely by changes in environment do not count as evolution because they are not heritable; in other words the change is not passed on to the organism’s offspring. […]

Evolution is not progress. Populations simply adapt to their current surroundings. They do not necessarily become better in any absolute sense over time. A trait or strategy that is successful at one time may be unsuccessful at another.” […]

Organisms are not passive targets of their environment. Each species modifies its own environment. At the least, organisms remove nutrients from and add waste to their surroundings. Often, waste products benefit other species. Animal dung is fertilizer for plants. Conversely, the oxygen we breathe is a waste product of plants. Species do not simply change to fit their environment; they modify their environment to suit them as well. […]

Natural selection may not lead a population to have the optimal set of traits. In any population, there would be a certain combination of possible alleles that would produce the optimal set of traits (the global optimum); but there are other sets of alleles that would yield a population almost as adapted (local optima). Transition from a local optimum to the global optimum may be hindered or forbidden because the population would have to pass through less adaptive states to make the transition. Natural selection only works to bring populations to the nearest optimal point. This idea is Sewall Wright’s adaptive landscape. This is one of the most influential models that shape how evolutionary biologists view evolution. […]

Sexual selection is natural selection operating on factors that contribute to an organism’s mating success. Traits that are a liability to survival can evolve when the sexual attractiveness of a trait outweighs the liability incurred for survival. A male who lives a short time, but produces many offspring is much more successful than a long lived one that produces few. The former’s genes will eventually dominate the gene pool of his species. In many species, especially polygynous species where only a few males monopolize all the females, sexual selection has caused pronounced sexual dimorphism. In these species males compete against other males for mates. The competition can be either direct or mediated by female choice. In species where females choose, males compete by displaying striking phenotypic characteristics and/or performing elaborate courtship behaviors. The females then mate with the males that most interest them, usually the ones with the most outlandish displays. There are many competing theories as to why females are attracted to these displays.” (In humans, females choose so this could be construed as another bit of dating advice to add to this post…) […]

“Most mutations that have any phenotypic effect are deleterious. Mutations that result in amino acid substitutions can change the shape of a protein, potentially changing or eliminating its function. This can lead to inadequacies in biochemical pathways or interfere with the process of development. Organisms are sufficiently integrated that most random changes will not produce a fitness benefit. Only a very small percentage of mutations are beneficial.”

There’s a lot more at the link. Not all of it belongs in the ‘all people who know anything about evolutionary biology would agree on this 100 percent’-category [one example: “Genes are not the unit of selection (because their success depends on the organism’s other genes as well); neither are groups of organisms a unit of selection. There are some exceptions to this “rule,” but it is a good generalization.” – not everybody ‘in the field’ would agree with that], but most of it is relatively incontestable and it covers a lot of ground; a huge number of key concepts are explained and elaborated upon here. Read it, but don’t start reading it before you’re in a situation where you have a decent amount of time to spare. No matter how well-read you are, unless you’ve actually read this piece before odds are you’ll not know everything which is covered here – for instance, you probably didn’t know that “over half of all named species are insects. One third of this number are beetles.” I know I didn’t. The article was written a while ago, so I decided to check up on the data – here’s what wikipedia has to say about the matter today: “Even though the true dimensions of species diversity remain uncertain, estimates are ranging from 1.4 to 1.8 million species. […] About 850,000–1,000,000 of all described species are insects.” I should probably point out that even though it’s written in a manner-of-fact like way all the way through, he incidentally doesn’t exactly beat about the bush at the end:

“Scientific creationism is 100% crap. So-called “scientific” creationists do not base their objections on scientific reasoning or data. Their ideas are based on religious dogma, and their approach is simply to attack evolution. The types of arguments they use fall into several categories: distortions of scientific principles ( the second law of thermodynamics argument), straw man versions of evolution (the “too improbable to evolve by chance” argument), dishonest selective use of data (the declining speed of light argument) appeals to emotion or wishful thinking (“I don’t want to be related to an ape”), appeals to personal incredulity (“I don’t see how this could have evolved”), dishonestly quoting scientists out of context (Darwin’s comments on the evolution of the eye) and simply fabricating data to suit their arguments (Gish’s “bullfrog proteins”).

Most importantly, scientific creationists do not have a testable, scientific theory to replace evolution with. Even if evolution turned out to be wrong, it would simply be replaced by another scientific theory.”

As can also be inferred from the links at the end, this is not the only post of its kind at TalkOrigins. Go have a look if you’re even remotely interested!

ii. Two figures:


iii. How far do Danes commute to go to work? Answer: It varies.

The table includes the Danish municipalities with the ten highest and lowest average commuting distances. The distances given in the table are the distances between the homes of the commuters and their workplaces, not the distances travelled on an average day (which would be twice that number). Local or regional wage differentials and corresponding differences in opportunity cost of time definitely plays a role here. Note that ‘distance travelled’ is not necessarily a good proxy for ‘time spent commuting’, especially not when comparing the commutes of people living in urban areas with those of people living in rural areas (ceteris paribus, d(commuting time)/d(pop-density)>0). The numbers are from this new publication by Statistics Denmark, which also included this map of the gender differences across the country (yellow: the average male commute is less than 6 kilometers longer than the average female commute, etc. The darker, the bigger the difference between the genders..):

The national average commuting distance to work is ~20 km (19.7). The male average is 23.4 km, the female average is 15.9 km.

iv. This should all be known stuff to you guys, but in case it’s not:

v. A number: 27.5% of all inmates in Danish prisons are foreign citizens (article in Danish here). Foreign citizens make up about 7,7% of the population. If you look closer, I’m positive both that you’ll find huge variation across countries, and that you’ll also find that some immigrant groups are significantly less likely to commit crimes than are people with Danish citizenship.

vi. The Long, Fake Life of J.S. Dirr. An internet hoax that survived for 11 years, from the very beginning of social medias almost to the present day. Interesting.

vii. Why You Can’t Kill a Mosquito with a Raindrop. Add this one to the list of questions I had never even thought about asking. Fascinating stuff, a few quotes:

“the consequence of getting hit by a raindrop depends on what part of the mosquito’s body takes the blow. Since the insects are so lanky, 75% of hits happen on the legs or wings. This can throw a mosquito into a brief tumble or even a barrel roll, but it recovers without much trouble.

Direct hits to mosquitos’ bodies are a different kind of carnival ride. The speeding raindrops glom onto the insects and propel them downward. Mosquitos captured on camera sometimes fell as far as 20 body lengths while being pushed by a raindrop. For a human, that would be a 12-story drop and a quick ending to the story. But mosquitos are able to pull away sideways from the raindrops and continue on their way, unharmed.

The only danger seems to come if mosquitos are flying close to the ground when they’re hit, leaving themselves too little time to escape. The authors note that one unlucky bug was driven into a puddle and “ultimately perished.” […]

When the heavy drop hits the airy mosquito, it’s almost like hitting nothing at all. And this, the researchers found, is what keeps the mosquitos alive. By offering barely any resistance, a mosquito minimize the force of the collision. The raindrop doesn’t even splatter when it hits. […]

Humans being hurled downward generally black out around 2 or 3 G’s. But a mosquito suddenly driven toward the ground by a raindrop experiences an acceleration of 100 to 300 G’s. The authors note that “insects struck by rain may achieve the highest survivable accelerations in the animal kingdom.””

viii. TV Tropes tips for writers.

June 10, 2012 Posted by | biology, data, demographics, evolution, genetics, Lectures, medicine, Pharmacology | Leave a comment

Query plus ‘stuff’

i. My birthday is in two months, so I’ll probably be sending out a wish list in a couple of weeks (the kinds of books I usually want have to be sent from other parts of the world and that takes a lot of time…). Which means that now is a good time for you to recommend books and other stuff to me.

After reading this article on ‘The Real War 1939-1945’, (it’s quite long, don’t start reading it if you have but 5 or 10 minutes at your disposal – and thanks for linking to it Gwern!) I decided to add this book to my list. The author died just 6 days ago.

ii. A very good chess ressource. Also, this.

iii. Maybe the ‘good cholesterol’ isn’t all that good after all.

iv. A paper on the effects of alcohol on behaviour which some readers might find interesting.

v. Another one of Steven Farmer’s pharmacology lectures – Antimicrobial Agents 1:

vi. I read two whole chapters in The Human Past today, as well as part of a third. It’s a textbook, so (2,3-2,4?) chapters corresponds to ~10 hours of reading or so (one of the chapters was quite short). I decided to just add some related links from wikipedia below, in no particular order. This is some of the stuff I’ve been reading about:

Domestication of the pig
Terrace (agriculture)
Talheim Death Pit

City formation
Post-glacial rebound
Younger Dryas
Maglemosian culture
Beaker culture
Varna Cemetery
Linearbandkeramik (LBK) / Linear Pottery Culture (LPC)
Hallstatt culture
Lindow Man (featured article)
Ötzi the Iceman (people who read Razib Khan regularly will probably remember his posts on this one)

The climate-related stuff I found fascinating, but there’s only so much of that kind of stuff you can put into a book about ‘the human past’ so naturally the treatment of this subject was not as detailed as I’d perhaps have liked. Did you know that before the end of the last ice age, Japan wasn’t separated from the Asian mainland? Or that Tasmania was part of Australia? That you could walk from Britain to France? Do also read the articles on Sundaland and Doggerland and recall that not that long ago, you could walk from Asia to America… Also, “faunal evidence indicates the presence of domesticated cattle in the central Sahara by at least the 5th millenium BC. Only during the 3rd millenium BC did climate patterns change and the Sahara begin to take on the desert-like character it has today” (p.181) The world isn’t what it was, it’s very different, and you don’t actually need to go very far back in time to get very surprised at what has happened and how much things have changed.

Sorry for the infrequent updates.

May 29, 2012 Posted by | alcohol, anthropology, books, Chess, history, medicine, personal, Pharmacology, wikipedia | Leave a comment

Basic Pharmacology Principles

A very good introductionary lecture on pharmacology:

I decided to post some wikipedia links to a few of the concepts he covers in the lecture below (however I’m pretty sure the lecture is the more efficient way to learn this stuff, at least the basics):

Receptor antagonist.
EC50 (half maximal effective concentration).
Dose-response relationship.

January 30, 2012 Posted by | biology, Lectures, medicine, Pharmacology, wikipedia | Leave a comment