Quotes (and a brief administrative note)

(Brief admin note: I have been doing a bit of ‘spring cleaning’ on the blog these last few days, as I have been trying to improve upon the category system I currently use. If people have been bothered by old posts of mine showing up in their feeds this is the reason. The changes I have made will make it easier for me to find stuff I might be looking for in the future, but as the changes might also make it easier for other people reading along to find stuff here on the blog in which they might be interested I figured I should mention the fact that these changes have been made to the readers as well. The primary change to the category system which has been made is that I have increased the number of sub-topics used in the context of coverage of topics dealing with biology and medicine. I have also increased the number of topics displayed in the category cloud in the sidebar.)

i. “I do not greatly care whether I have been right or wrong on any point, but I care a good deal about knowing which of the two I have been.” (Samuel Butler)

ii. “Our minds want clothes as much as our bodies.” (-ll-)

iii. “Some like to understand what they believe in. Others like to believe in what they understand” (Stanisław Jerzy Lec)

iv. “The struggle for existence holds as much in the intellectual as in the physical world. A theory is a species of thinking, and its right to exist is coextensive with its power of resisting extinction by its rivals.” (Thomas Henry Huxley)

v. “We should treat our minds, that is, ourselves, as innocent and ingenuous children, whose guardians we are, and be careful what objects and what subjects we thrust on their attention.” (Henry David Thoreau)

vi. “Where there is no bread, there is no philosophy.” (Avram Davidson)

vii. “The price of training is always a certain “trained incapacity”: the more we know how to do something, the harder it is to learn to do it differently.” (Abraham Kaplan)

viii. “We are endowed with genes which code out our reaction to beavers and otters, maybe our reaction to each other as well. We are stamped with stereotyped, unalterable patterns of response, ready to be released. And the behavior released in us, by such confrontations, is, essentially, a surprised affection. It is compulsory behavior and we can avoid it only by straining with the full power of our conscious minds, making up conscious excuses all the way. Left to ourselves, mechanistic and autonomic, we hanker for friends.” (Lewis Thomas)

ix. “I have always had a bad memory, as far back as I can remember.” (-ll-)

x. “It isn’t what people think that’s important, but the reason they think what they think.” (Eugène Ionesco)

xi. “The relationship between commitment and doubt is by no means an antagonistic one. Commitment is healthiest when it is not without doubt but in spite of doubt.” (Rollo May)

xii. “People will resist information unless the price of not knowing it greatly exceeds the price of learning it.” (Calvin Mooers)

xiii. “Beware of averages. The average person has one breast and one testicle.” (Dixy Lee Ray)

xiv. “I saw an advertisement the other day for the secret of life. It said “The secret of life can be yours for twenty-five shillings. Send to Secret of Life Institute, Willesden.” So I wrote away, seemed a good bargain, secret of life, twenty-five shillings. And I got a letter back saying, “If you think you can get the secret of life for twenty-five shillings, you don’t deserve to have it. Send fifty shillings for the secret of life.”” (Peter Cook)

xv. “We believe this to be the work of thieves, and I’ll tell you why. The whole pattern is very reminiscent of past robberies where we have found thieves to be involved. The tell-tale loss of property — that’s one of the signs we look for.” (-ll-)

xvi. “I’ve been reading a very interesting book recently. It’s called The Universe and All That Surrounds It by T J Bleendreeble. It’s an extremely good book about it. It’s about seventy pages long, so it’s fairly comprehensive about the whole thing and it’s fairly interesting. Bleendreeble specialises in the universe. He doesn’t branch out much beyond that. But he’s quite interested in this limited field.” (-ll-)

xvii. “It is the great glory of the quest for human knowledge that, while making some small contribution to that quest, we can also continue to learn and to take pleasure in learning.” (William Alfred Fowler)

xviii. “In science, it is not speed that is the most important. It is the dedication, the commitment, the interest and the will to know something and to understand it — these are the things that come first.” (Eugene Wigner)

xix. “It is not enough to be in the right place at the right time. You should also have an open mind at the right time.” (Paul Erdős)

xx. “If you want to change the way people respond to you, change the way you respond to people.” (Timothy Leary)


April 27, 2017 Posted by | meta, Quotes/aphorisms | Leave a comment

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

“Peripheral neuropathy is a common medical condition, the diagnosis of which is often protracted or delayed. It is not always easy to relate a neuropathy to a specific cause. Many people do not receive a full diagnosis, their neuropathy often being described as ‘idiopathic’ or ‘cryptogenic’. It is said that in Europe, one of the most common causes is diabetes mellitus but there are also many other known potential causes. The difficulty of diagnosis, the limited number of treatment options, a perceived lack of knowledge of the subject — except in specialised clinics, the number of which are limited — all add to the difficulties which many neuropathy patients have to face. Another additional problem for many patients is that once having received a full, or even a partial diagnosis, they are then often discharged back to their primary healthcare team who, in many instances, know little about this condition and how it may impact upon their patients’ lives. In order to help bridge this gap in medical knowledge and to give healthcare providers a better understanding of this often distressing condition, The Neuropathy Trust has commissioned a new book on this complex topic.

As well as covering the anatomy of the nervous system and the basic pathological processes that may affect the peripheral nerves, the book covers a whole range of neuropathic conditions. These include, for example, Guillain Barre syndrome, chronic inflammatory demyelinating polyneuropathy, vasculitic neuropathies, infectious neuropathies, diabetic and other metabolic neuropathies, hereditary neuropathies and neuropathies in patients with cancer.”

The stuff above is the part of the amazon book description I decided to include when I added the book to goodreads.

The book is dense. There are a lot of terms defined in the book and a lot of topics covered. Despite being a quite shortish book only a couple hundred pages long (compare for example with related books like this one), it’s still the sort of book which many people might consider using as a reference work (I certainly consider doing that). The author really knows his stuff. According to the website of the European Neurological Society, “The ENS has now become the most prominent society of neurologists on the European Continent with a total of 2300 (including all categories) members from 60 countires [sic] worldwide.” I mention this because five years ago Gérard Said, the author, became the President of the ENS. He’s done/accomplished a lot of stuff besides that, the link has more details about him and what’s he’s done but what it boils down to is that this guy as already mentioned really knows his stuff. I disliked the comment on the front cover of the book that it was Written by one of the world’s leading experts and I at first considered it a decent argument against reading the book, but actually it’s probably both a fair and accurate statement; it seems like this guy really is one of the top guys in his field (I have no clue why someone like this does not have a wikipedia page whereas [random celebrity whose name I don’t know] does – well, I do have a clue, but…).

I don’t find the book particularly hard to read, but I’m frequently looking stuff up and I’ve read textbooks dealing with similar topics before (see e.g. here and here) – maybe I’m underestimating how difficult the book might be to read and understand for someone without much medical knowledge, but I think you should be perfectly able to get through the book without already having a detailed understanding of the neurological system; in my opinion the book is potentially useful for patients as well as medical practitioners, at least if the patient is willing to put in some work. An extensive glossary is included at the beginning of the book, defining most of the terms with which people might be unfamiliar. If you were wondering why I looked up so many words and concepts on wikipedia and other online sources (see below) in spite of the glossary, I should note that this is how I generally read books like this one; wiki or google will often provide additional details compared to the information included in standard glossaries, and often it’s even faster to look up such stuff online than it might be to locate the definition in the book. Another big reason for looking up key terms online was that I decided early on that a link collection like the one included below might be the best way to illustrate here on the blog which kind of content is covered in the book. Regardless of how you decide to look up stuff along the way, you should definitely not skip the definitions included in the glossary before reading the book proper – many of the terms you won’t be able to remember just on account of having read the words and definitions once or twice, but it’s definitely a good idea to have a look even so before moving on; this is probably the first book I’ve read in which the glossary was located at the front of the book instead of somewhere in the back, and it’s not a coincidence that the author decided to organize the book this way.

As a small aside, I thought this might be a reasonable place to add a ‘meta’ comment related to my book posts more generally. I’ve been considering writing slightly shorter posts about the non-fiction books I’m reading/have read; ‘classical posts’ of the kind I’ve written a lot of in the past can easily end up taking four-five hours for me to write and edit, and this means that if I don’t write short posts about the books I may easily end up not blogging them at all. This is an undesirable outcome for me. What I’ve been doing instead lately is to review more books on goodreads than I used to do; the idea being that if I end up not blogging the book, I’ll at least have reviewed it on goodreads. This incidentally means that if you want to keep track of my reading these days and would like to know what I think about the books I’m reading, the front page of this blog is no longer enough; you may need to also pay attention to my activities on goodreads or keep track of my reading via this link (I update that book list very often, usually every time I’ve finished a book). I don’t like to ‘branch out’ like that, but I also don’t like the idea of cross-posting goodreads reviews on the blog, and recently I’ve found it hard to know how to do these things optimally – this is where I’ve ended up. These days I’ll usually add a goodreads review of a non-fiction book quite shortly after I’ve finished the book, especially if I’m not sure if I’ll blog the book later.

Okay, back to the book: I think I’ll limit semi-detailed discussion of the book’s contents to the stuff included about diabetic/metabolic neuropathies, and although I’ve already encountered some relevant content and useful observations on that topic at this point, I have not yet read the chapter devoted to this topic. So you should expect me to post another post about this book some time in the future. I’ve read roughly half the book at this point and as mentioned in an earlier update on goodreads I’m seriously considering giving this book a five star rating. The book has way too much stuff to talk about all of it in detail, so what I’ll do below is to add some links to topics/terms/etc. discussed in the coverage so far which I looked up along the way, to give you a few more details than did the quote at the beginning:

Peripheral neuropathy.
Spinal nerves.
Anterior grey column.
Motor neuron.
Afferent nerve fiber.
Nodes of Ranvier.
Charcot–Marie–Tooth neuropathy.
Guillain–Barré syndrome.
Acute motor axonal neuropathy.
POEMS syndrome.
Monoclonal gammopathy of undetermined significance.
Vasa nervorum.
Vasculitic neuropathy.
Granulomatosis with polyangiitis.
Churg-Strauss syndrome.
Mononeuritis Multiplex.

October 12, 2015 Posted by | Books, Diabetes, Medicine, meta, Neurology | Leave a comment


Okay, this blog used to be quite active. At the moment it is not.

Last year I noted in September that I’d posted roughly one post every second day on average that year (“I’ve posted 125 posts in 257 days so far this year”, to be specific – here’s a link to the post in question, which however mainly deals with other stuff). Posting frequency has gone down a lot this year, and now I’m finding it difficult to even post once per week. I feel guilty about this, but I also feel silly about feeling guilty about it because I have many much worse and more significant things to feel guilty about (to quote Emil Cioran, “If I were to be totally sincere, I would say that I do not know why I live and why I do not stop living”. My current state of mind is not conducive to blogging).

I recently got the silly idea to leave a link to the blog elsewhere, which has meant that some people have come by and had a look. I’ve noticed that some of them (‘some of you…’) seem to have come by more than once. If you’re one of these people, you should note that the current posting frequency is very much below what has been usual for this blog, which translates into a) there being potentially a lot of stuff in the archives which might be of interest to you, and b) the observation that the current posting frequency is a noisy signal to use for making long-run blog activity-level estimates.

Aside from the book posts, another resource which might help you navigate older posts I’ve written here more efficiently is the category cloud in the sidebar. If you hover over individual categories you can see how many posts I’ve written about each topic, and if you click the category in question you’ll arrive at a page displaying the posts published on that topic – so for example if you click the ‘anthropology’ link to the right, you’ll get to the 53 posts I’ve written on this topic (other examples: medicine: 163 posts, biology: 159, history: 149, psychology: 137, mathematics: 71 – many of the topics featuring in the cloud have an at least to me reasonably high number of posts). As a side-note I should observe that when going through posts from the archives I’m not sure I would recommend reading posts more than a few years old (but this is again still a substantial number of posts, considering the average length of my posts (/time invested/post) and given the historically relatively high posting frequency). If you’re considering going semi-systematically through the archives – and yes, people sometimes do this – I’d strongly recommend you start out by reading posts published this year and then working your way back in time, rather than you starting out ‘at the beginning’ and working your way forward – the latter approach really cannot be recommended, and if you really want to read posts in the order they were written a much better approach than ‘starting at the beginning’ would be to start out at a random point in time nowhere near the beginning and then working your way forward (that ‘random point in time’ should be January 1st, 2013, or something along those lines – not some date in 2008). I should perhaps also caution that a couple of the categories may cause problems in some contexts; for example if you click the ‘lectures’ category, well, that’s a lot of lectures, and if you’re trying to load, say, 50+ hour-long lectures on one blog page in your browser that may cause problems e.g. with the browser becoming unresponsive (in retrospect this was not a good category to include in the categorization scheme, but I didn’t think of that when I started out). The ‘Khan Academy’ category suffers from the same problem; as I have watched and posted lectures on a wide variety of topics I however think this sort of problem is mostly limited to these two categories. I’m perfectly well aware that the categorization scheme could be improved – e.g. there’s both a ‘health’ category and a ‘medicine’ category, and some reasonably well-covered topics with a substantial number of posts do not feature in the cloud (for example there are 30 posts which deal with archaeology on this blog, despite there being no ‘archaeology’ category in the category cloud) – but the system is better than it used to be and I know from experience that when you have a blog with a very substantial number of posts you can spend a lot of time messing around with tweaking and optimizing this sort of thing, and my time is better spent doing other stuff.

I have no idea how the posting frequency will develop in the future, but in terms of the next weeks/months I’m pessimistic, which is part of why I wrote this post.

July 14, 2015 Posted by | meta | Leave a comment


I’m spending time at my parents’ place at the moment, and that’s actually the only reason why I’m able to write this blog post; the old laptop I’ve been using finally decided to break down earlier this evening. You should expect limited blogging in the week to come – I’m completely cut off at the moment, far away from stuff like computer stores.

I recently realized that the computer- and internet issues have really made blogging a chore, in a way – I’m reading books I can’t easily blog either because my notes keep getting lost or because I’ve lately deliberately been reading books offline (/AFK) to get around these problems. I used to be able to just write a post when I felt like it, but that’s not been the case for the last month; I’ve felt like I had to blog when I had internet, and if I wanted to write when I did not have internet the best I could do was to make a draft using e.g. Word; and I never liked that option. To make it worse, the updating frequency the blog used to have (I don’t know what’ll happen in the weeks to come) was actually quite high, considering the amount of work that’s put into each post; it’s really been far from trivial to just ‘put together a blogpost while internet is up’. Notes and highlights intended among other things to facilitate blogging coverage later on have as mentioned been lost due to hardware issues, and this is actually a much bigger deal than you might think; it’s not that losing the notes put me completely back to square one, but for practical purposes losing my notes have meant that in order for me to provide the same type of coverage I’ve usually provided I’ve had to basically read some of these books twice. Not really, but close enough for it to feel that way. I’ve spent roughly 12 hours or so on Chamberlain’s Symptoms and Signs in Clinical Medicine over the last few days, and now I can basically start over if I want to blog it the way I’d intended to do it – so instead of a post about that book now, you get this post instead (and I may never blog the book in the amount of detail I’d intended to and would have, if not for these issues). I’m not happy about that, but that’s the way it is. Given that I’ve been thinking about stopping blogging completely lately because it just feels like too much work – it does, now, compared to before – I’ll care a lot less about the updating frequency in the time to come than I’ve done in the past. Blogging should be enjoyable, and it used to be very enjoyable, but these issues have been killing my desire to write here.

October 10, 2014 Posted by | meta, Personal | Leave a comment

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


This is just a brief administrative note: I’ll have very limited, if any, access to the internet and this blog during the next week.

I have written a few posts which I have scheduled to be published during my absence, so the blog will still be updated in the week to come – at least if I’ve set it up correctly; I don’t have a lot of experience with scheduling posts.

I shall however be unable to read and approve comments during the next week: If a comment happens to get caught by the spamfilter I’ll not know about it, and if you decide to ask me a question I’ll not be able to answer it until I get back. You’re very welcome to comment and ask questions anyway.

August 17, 2014 Posted by | meta | Leave a comment


For some time I’ve wanted to improve upon the ‘category’ system I’ve made use of here on the blog, and yesterday I found out a way to do it as I became aware of the existence of wordpress’ ‘category cloud’-gadget after messing around a bit with the blog settings. So I added the cloud gadget and now you can see a category cloud in the sidebar.

When I implemented the cloud I realized that my categories were really off in terms of what this blog is about – there were terms like ‘comics’ and ‘fun’ in that cloud of most used categories, and although I do consider myself to be a funny guy when it suits me, well, there aren’t actually that many posts of that kind here… Some of the most used categories were basically categories dealing with stuff I hadn’t written about in years. Mostly this was because I’ve not really been very focused on using the categories optimally as they haven’t really been all that relevant to anything – with the implementation of the sidebar cloud the relevance of them certainly increased.

So as a result of this change, I have made some changes to many posts on this blog as I have re-categorized them in order for the cloud to better reflect what’s going on on this site and make it more useful as a blog navigation tool. Before I added the cloud I had a category list but people have basically pretty much never used that at all to navigate the blog, so I’ve removed that tool from the sidebar and replaced it with the cloud; I hope this change will make it easier to navigate the site and allow people to better find the types of posts they’re most interested in. I also hope it may make it easier for newcomers to the site to figure out quickly and painlessly what this blog is about, without them having to spend a great deal of time and effort exploring it.

The re-categorization stuff I’ve done has meant that instead of having wikipedia posts in the archive dealing with historical topics, physics, math and psychology-related topics being categorized under ‘wikipedia’, such posts will now have multiple categories and will now be categorized under: ‘wikipedia’, ‘history’, ‘physics’, ‘mathematics’, and ‘psychology’. A medical textbook will now be categorized under both ‘books’ and ‘medicine’, instead of just being filed under ‘books’. Some new categories have been introduced to the mix, some have been retired, quite a few have become much more common than they used to be. The changes I’ve made probably means that some people using various types of feeds to keep track of the activities that are going on on this blog may have had a lot of old posts pop up again – I recall being told that something similar happened last time I made major adjustments to the blog. I think I’ve made most of the changes I’m going to make at this point, but I’m not really sure if I’ll not be tempted to go through the archives over the next days and perhaps make some more adjustments. If you find another bombardment of old posts from this site to your feed to be annoying you might consider turning it off for a little while, although I think I have made at least most of the changes I’m going to make at this point.

As a little sidenote, I have myself been somewhat happy about my decision to make this change as it’s also made it easier for me to figure out which types of topics I’ve actually blogged on this site – or at least it’s given me some idea. With much more than 1000 posts spread out over some years now, I didn’t really have much of an overview either when I started out the re-categorization process yesterday. You can always argue about the categories being applied and whether or not they’re ‘accurate’ and I’m not sure I’ve given this topic sufficient thought; what I am sure of, however, is that I consider the current state of affairs to be much preferable to the system it has replaced. I hope the readers will share this sentiment.

Lastly I want to thank gwern – whom I hope is reading along here – for linking to me on Hacker News yesterday; quite a few people visited my blog as a consequence of that link, and some of them I could tell (from the stats information) found the topic covered in that post to be interesting.

May 27, 2014 Posted by | meta | 2 Comments

Open Thread

I was recently reminded that I probably ought to revive these things.

First a few ‘meta’ observations regarding content on this blog, then I’ll leave the word to you:

I was recently reminded of the fact that people sometimes read stuff I’ve written a long time ago (usually I try – mostly successfully – to put it out of my mind that this ever happens). So it’s worth pointing out two things here. First, if I wrote something 5 years ago, I’ve probably changed my mind about it at least three times since then. Very occasionally I will by accident realize that I’ve written something awful a long time ago, and if that happens I may decide to delete the post or make corrections to it; but usually that doesn’t happen, so there’s a lot of crud in the archives which I’ve simply neglected to get rid of because it takes a lot of time and effort dealing with that kind of stuff unless you just delete everything indiscriminately, a move I’ve been hesitant to make (perhaps with little justification). Secondly, if I just published a post (people who subscribe to the blog in one way or another will, as far as I’ve been made aware, usually be able to tell when a post was published) here on the blog and you’re reading it right after publication, there’s a high likelihood the post will change later on. I often feel a desire to make corrections and perhaps add stuff to or delete stuff from a post within the first hour or two of a post’s existence. If you only plan on reading a post once then reading it right after I published it might not be the optimal strategy as it’ll likely at that point still be a work in progress. The more words I’ve written on my own, the more likely it is that corrections will be made later on. Sometimes the time-lag between publication and correction can be significant, e.g. it sometimes happens that I post something before I go to bed and then make adjustments to the post the next day. Some people would probably argue that this procedural approach is inefficient and that I ought to finish the post, with corrections, before I publish it, but one reason why I’m not that careful about such things is that I consider most of the stuff published here to be relatively ‘fluid’ anyway; this isn’t a book, I always retain the right and the opportunity to correct errors, delete a paragraph or a post I don’t like, or really whatever strikes my fancy. If a few people happen to come across a few error-ridden and in retrospect only half-finished posts along the way, I don’t really mind that. Usually those errors will get corrected in time and thoughts will be developed in more (or, as the case may be, less) detail. I have considered how to approach major adjustments before – one option I’ve considered is to rename the posts and add a ‘revised’ in a parenthesis to the post title, perhaps with a little note at the beginning as well, in order to inform readers who’ve only read what later turned out to be an early draft that the post has changed – but I haven’t really found a solution I like. So for now it is the way it is. Feedback and ideas are welcome.

Okay, the word is yours. Read anything interesting?

May 4, 2014 Posted by | meta, Open Thread | 3 Comments

A decision

After some conversations with a close friend, I have decided that I’ll not update this blog anymore for the rest of this year.

I’ll reconsider in January whether I should continue blogging, or stop altogether.

December 13, 2013 Posted by | meta | Leave a comment

Blog overhaul

It’s been a gradual process that started out last year, but I think I’m pretty much ‘there’ by now – at least I’ve come a long way. So what has happened?

Well, I’ve removed a lot of posts from the site. I’ve posted 1450 posts by now (this post is number 1450), and I’ve pulled 372 from the site altogether. I didn’t do all of that today or yesterday, this was a gradual process. Even though I’ve taken down a lot of stuff, there are still 1071 posts in the archives available for everyone to read. Most of the stuff I deleted was quite bad and a lot of the posts were posts I wrote during the first year (the blogging learning curve isn’t all that steep). That being said, I should be clear about the fact that ‘low quality’ was but one of three choice parameters under consideration. The other two parameters of interest were ‘political content’ and ‘personal content’. The last couple of days I dealt with the last one in a systematic way, as I also noted on the twitter.

Political stuff doesn’t much interest me anymore, and I used to have strong opinions about that stuff. If I hadn’t blogged in the past and I were about to start up a blog at this point in time, I’m quite certain I’d see no major need to, say, upload tape recordings of political discussions I had with other people 4-5 years ago to the archives of the blog for everybody to listen to at their leisure. The old low-quality political posts have only been in my archives for the last couple of years because I never came around to removing them; now I have. The selection mechanism hasn’t been all that fine-grained, so I’m sure there’s plenty of bad stuff still around and the fact that I’ve not pulled a political post should not be interpreted as ‘current me’ supporting the views expressed in the post – maybe I just never got around to removing it, maybe I overlooked it because I hadn’t categorized it properly, maybe it contained some data that alleviated the problem that the views expressed in the post were stupid, or perhaps I thought it would be weird if there was a gap of several months in the archives even though I’ve posted relatively regularly for most of the period I’ve been blogging, or…

Incidentally, I should probably take the time to note that ‘low quality’ and ‘political content’ were very much correlated post traits – far most of the posts I’ve taken down were political posts. Politics is the Mind-Killer and just because you think of yourself as an independent and reasonable person doesn’t mean that you don’t commit a lot of the same mistakes that all those other unreasonable people make all the time, in part because just like everyone else, you have a strong need to validate and justify the political views you subscribe to. See also this.

As for the last parameter, the personal stuff, there’s no arguing that I’ve written a lot of stuff here over time that I’d not want some random guy on the street to know about me. Maybe not a lot of posts, but if you include parameters like ‘post length’ and ‘size of comment section’ (comment sections which not rarely remained active for perhaps a week after the post was written) in the analysis, it actually turned out to be quite a bit of material. Much of the stuff I’ve taken down was the kind of stuff you’d not want somebody you don’t know very well but might want to get to know better in the future, like a potential future close friend or girlfriend, to have access to all at once right from the get-go – to have that person read stuff like that could easily end up colouring that person’s perception of me, perhaps irrevocably, causing him or her to get the wrong idea and think that I’m someone I’m actually not. “You have to dole out your crazy in little pieces, you can’t do it all at once.”

I’ve had this problem with the blog for some time now; there’d be this person or that (in Real Life) which I’d like to tell about it, but I’ve always felt that given what was currently there to be found in the archives, I really would not feel comfortable telling them about it. Now I’ve changed the equation by removing some of the most personal stuff here. As I also tweeted(?) earlier, if you’ve left a comment that you really liked or you’d like to review a discussion we had here that is no longer available, give me a heads-up and I’ll mail you (/or something like that). Again – I’ve deleted nothing, all of it is still ‘in here’. The obvious alternative to this solution model was a two-tier posting system, where some posts would be password protected and others (most) would be available for all to read. I didn’t like that model, but maybe I’ll change my mind about that later on.

Given that people like to comment on the personal posts, the fact that I’ve taken down quite a few of those also means that the number of comments has probably dropped significantly, and that the blog looks less active than it used to do. A week ago the blog had approximately 2000 comments in the archives – now that number has been reduced significantly. That’s a shame, but I hope you guys will still comment here in the future despite the fact that some of the stuff you’ve written in the past has now been taken down. Anyway – comment sections are discussion fora, not history books.

One last change I’ve made is to drastically reduce the number of categories. There are currently 342 categories in the sidebar to your right which is arguably still way too much, but when I started this process there were more than 700. I hope this will make the blog a little easier to navigate.

January 29, 2012 Posted by | meta, Personal | Leave a comment


First of all, I’ve made a decision to try not to post too often over the next 2 months. Blogging takes time, doing stuff that’s blog-worthy takes time. I have a couple of important exams coming up in January. I should not be spending any of my time on the stuff that I blog about here before those exams are behind me.

Next, a few links.

i. Dying Outside, by Hal Finney. His last update is more than a year old. According to wikipedia, he’s still alive.

ii. What is a gene “for”?

““Scientists discover gene for autism” (or ovarian cancer, or depression, cocaine addiction, obesity, happiness, height, schizophrenia… and whatever you’re having yourself). These are typical newspaper headlines (all from the last year) and all use the popular shorthand of “a gene for” something. In my view, this phrase is both lazy and deeply misleading and has caused widespread confusion about what genes are and do and about their influences on human traits and disease.” […]

“While geneticists may know what they mean by the shorthand of “genes for” various traits, it is too easily taken in different, unintended ways. In particular, if there are genes “for” something, then many people infer that the something in question is also “for” something. For example, if there are “genes for homosexuality”, the inference is that homosexuality must somehow have been selected for, either currently or under some ancestral conditions. Even sophisticated thinkers like Richard Dawkins fall foul of this confusion – the apparent need to explain why a condition like homosexual orientation persists. Similar arguments are often advanced for depression or schizophrenia or autism – that maybe in ancestral environments, these conditions conferred some kind of selective advantage. That is one supposed explanation for why “genes for schizophrenia or autism” persist in the population.

Natural selection is a powerful force but that does not mean every genetic variation we see in humans was selected for, nor does it mean every condition affecting human psychology confers some selective advantage. In fact, mutations like those in the neuroligin genes are rapidly selected against in the population, due to the much lower average number of offspring of people carrying them. The problem is that new ones keep arising – in those genes and in thousands of other required to build the brain. By analogy, it is not beneficial for my car to break down – this fact does not require some teleological explanation. Breaking down occasionally in various ways is not a design feature – it is just that highly complex systems bring an associated higher risk due to possible failure of so many components.

So, just because the conditions persist at some level does not mean that the individual variants causing them do. Most of the mutations causing disease are probably very recent and will be rapidly selected against – they are not “for” anything.”

I have made a similar point in the past, probably more than once.

iii. Stuff you didn’t know about mine fires.

“Whether started by humans or by natural causes, coal seam fires continue to burn for decades or even centuries until either the fuel source is exhausted; a permanent groundwater table is encountered; the depth of the burn becomes greater than the ground’s capacity to subside and vent; or humans intervene. Because they burn underground, coal seam fires are extremely difficult and costly to extinguish, and are unlikely to be suppressed by rainfall.[1] There are strong similarities between coal fires and peat fires. […] Many recent mine fires have started from people burning trash in a landfill that was in proximity to abandoned coal mines, including the much publicized Centralia, Pennsylvania, fire, which has been burning since 1962. Of the hundreds of mine fires in the United States burning today, most are found in the state of Pennsylvania. […] It is estimated that Australia’s Burning Mountain, the oldest known coal fire, has burned for 6,000 years.”

In case you were in doubt, “Extinguishing underground coal fires, which sometimes exceed temperatures of 540°C (1,000°F), is both highly dangerous and very expensive.”

This is probably as good a place as any to once again remind old readers, and to let new ones in on this fact, that this blog is not one of those blogs that’ll just ‘die’ without an explanation. If I decide to close the blog down, I’ll tell you. If I haven’t told you anything and I also don’t update either the blog or my twitter in weeks, the most likely explanation is that I’m dead or something along those lines.

November 15, 2011 Posted by | autism, Genetics, Geology, meta, Personal, Random stuff | Leave a comment

The difference


“StumbleUpon: 1
Google Reader: 1 1
(google images links): 2

Total views referred by links to your blog: 5”


“ 79
Facebook: 2
Google Reader: 1
(another google images link): 1

Total views referred by links to your blog: 83”

Most likely none of those ~80 additional readers will ever revisit the blog. But I’m still surprised at the impact such a link can have. Of course the number keeps growing at the moment as more people click the link.

I should probably thank William for putting up the link – done.

September 29, 2011 Posted by | meta | Leave a comment

God jul / merry christmas

The rest of the family just left for church and everything is pretty much ready already, so I thought I might as well update now that I have the time to do it.

I started reading Austen Wednesday afternoon, finished last night. It’s a wonderful book [tak Ulla!].

December 24, 2010 Posted by | meta | 2 Comments

Post number 1000

I did not expect to ever get close to that when I started this blog. Just as I never expected to get 100.000 hits, a number I’ll likely reach in just a few more months.

So yeah, there are a lot of posts here on this blog by now. If you ever feel like reading some stuff I’ve written about a particular subject, you can use the categories or the search function in the sidebar to navigate. I’ve tried during the lifetime of this blog to make this kind of navigation easier than it used to be, and I do believe I’ve become a lot better at using the categories than I used to be. Quite a few of the categories actually by now have a post volume that I think make them worthwhile using.

Both when it comes to posts I’ve already written and when it comes to posts I have yet to write, I’d like to make it clear that you can’t take it for granted that you’ll always be able to go back to the post on my blog. You should save the post somewhere else if you think it’s worth saving. I don’t write many of those posts anyway, but just in case you stumble upon one or two, keep this in mind.

[Comments in Danish are, as always, welcome]

February 14, 2010 Posted by | blogging, meta | Leave a comment