an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

My current health condition 3: nerves

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I’ve been to see a physiotherapist/sports medicine specialist, on the advice of a couple of people, and I’m happy with the result. It won’t mean an immediate cure, but the session has provided me with hope and a pathway to recovery.

Today and yesterday, the pain has been fairly minimal, after an excess of pain the day before. It seems to be about managing the medication.
So, to the physio. I described my situation in minute detail, describing as best I could the type of pain I felt, its sudden onset, how it responds to head movements and so forth. He very quickly conjectured that it was a nerve problem, which in fact had been my first intuition before I began researching the problem. He described the ‘queerness’ of nerve injury, or nerve impingement as it’s often termed – how damage in one place can be felt in another seemingly unrelated region. Interestingly, it was my description of how, since this condition has struck me, I’ve had difficulty moving my head back (this causing my shoulder pain to increase), and so not being able to gargle with mouthwash – which I do because of my bronchiectasis – it was this description which made him feel more certain that it was a nerve problem. He could be wrong but I think he’s right.

He did a lot of physical manipulation of the shoulder region and gave me advice. Keep up the medication, maintain activity of the shoulder and arm regions – not too much but not too little – and keep the area warm. He gave me some shoulder exercises to do, and assured me things would come good in time. I’ll revisit him next week.
Now, on this concept of impingement. It’s a term that comes up in the literature, and it was used by the physiotherapist today, so I asked him about it. He obliged by giving an explanation that was complex and difficult to follow, much like the material I’ve been reading online about the subject. So I’ll have a go at explaining it to myself.
Nerve impingement is one term among many (e.g pinched nerve, nerve compression, nerve entrapment), which indicates the trickiness of the condition and its description. In my case the suprascapular nerve is probably involved. As Wikipedia puts it ‘the nerve passes across the posterior triangle of the neck parallel to the inferior belly of the omohyoid muscle and deep to the trapezius muscle.’ I don’t know exactly what this means, but it seems to explain the pain at the back of my neck, left side, when I throw my head back.

The posterior triangle of the neck is a technical term with its own Wikipedia page. Here’s an image of it. As can be seen, it connects the omohyoid muscle and the massive trapezius which goes well down the back.
So nerve impingement/compression/entrapment is what it implies – something is impinging on the nerve, entrapping it, compressing it, pinching it. It could be bones, muscles, tendons, ligaments, cartilege, and that just about exhausts the possibilities. Carpal tunnel syndrome, for example, generally involves a pinched nerve in the wrist. The causes of course, are various. It could be a particular injury – but I can’t trace my own sudden onset to a particular injury (which doesn’t mean that no injury occurred) – or physical stress from repetitive work or sports activity, or some rheumatoid problem (which presumably would’ve shown up as some sign of inflammation, and I’ve never shown any signs of rheumatism) – or obesity.

The possibility that this was caused by lawn bowling remains real, if remote. Fascinatingly, when I told the physiotherapist that the only sports activity I’d taken up in recent times was lawn bowling, he asked me if I played at Walkerville – it turns out that he recognised me as he played in the competitions there too – out team had thrashed his only a few weeks ago! He agreed that bowling as a cause seemed unlikely – but being a bowler himself, he would say that, wouldn’t he?

But whatever the cause – and I won’t be bowling again for a while, if ever – the diagnosis and cure are the things, and it’s amazing what a seemingly effective diagnosis can do to calm the – nerves! I feel I can cope much better now, and I’ve had the humbling experience of knowing what severe pain is like. This is important as I’ve tended to be dismissive of the pain of others, with thoughts of ‘low pain threshold’ and ‘get over it’. So, it’s a lesson.

I’ll be returning to the physiotherapist next week, hopefully for the last time. His feeling was that just one more session would be enough, that if I simply followed the light exercise regime he suggested, things would come good. The pain has risen and fallen since then, but there’s been no relapse into anything agonising. I worked at Eynesbury yesterday, a relief day, but hopefully there won’t be any work for a while. In any case Covid-19 means we probably won’t be getting many, if any, students coming in from overseas over the next few months.

Of course, it’s not all back to normal, though I’ll try to get back to regular reading, writing and the like. Here’s a final quote from the Mayo Clinic on my situation:

If a nerve is pinched for only a short time, there’s usually no permanent damage. Once the pressure is relieved, nerve function returns to normal. However, if the pressure continues, chronic pain and permanent nerve damage can occur.

We’ll have to wait and see.


Written by stewart henderson

March 18, 2020 at 2:02 pm

My current health condition 2: searching for a diagnosis

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It is easier to find men who will volunteer to die, than to find those who are willing to endure pain with patience.

Julius Caesar (and I’m willing to volunteer)

I haven’t been much in the mood for writing. You could say I’m feeing sorry for myself, or indulging in the pain I’m experiencing, but truth to tell, my current condition doesn’t make it so easy to ‘rise above myself and grasp the world’. I’m hoping at least to rise above my own pain and grasp the world of pain in general! But before I look at the ‘philosophy of pain’ I should update my situation.
The pain – shooting down from the left shoulder – first became acute on February 29. On that Saturday I arrived in an ambulance at Royal Adelaide Hospital, was examined, questioned and released without a diagnosis. Panadol, administered by the paramedic in the ambulance, had relieved the worst of the pain. I bought over the counter medication, ibuprofen and paracetamol, and using them at the upper limit of, and perhaps beyond, what was recommended, I was able to work at Eynesbury College on the following Monday and Tuesday. On Wednesday I visited my GP. I was referred to St Andrews Hospital for an ultrasound and an x-ray. The GP told me that if the pain subsisted or worsened the hospital could give me a corticosteroid injection in the shoulder, which he thought would do the trick, painwise.

Meanwhile I was doing my own research. It seemed that bicipital or biceps tendinitis was the best fit. There was also bursitis and some kind of rotator cuff damage. I couldn’t think of an obvious cause, the only ‘different’ activity I’d been engaging in was lawn bowling, generally associated with geriatrics and hardly recognised as strenuous activity. However, when Sarah, who was also doing some research, noted that one line of enquiry led to ‘dangers and injuries from lawn bowling’, I felt less dismissive.

My appointment at St Andrews was for Friday (March 6), but on Thursday a felt increase in pain had me asking Sarah to ring the GP for stronger medication. I was prescribed ibuprofen plus codeine, which I started taking, again pushing beyond the recommended limits. However, my subjective sense told me that paracetamol was more effective than ibuprofen. Yet ibuprofen was an anti-inflammatory, paracetamol was not. It was all very confusing. Did I have pain without inflammation? How could this be?

I was driven to St Andrews hospital next morning, where I was given, first an X-ray, then an ultrasound test. This was a first for me, and I was able to watch the screen as the young woman administering the test slowly moved the scanner across my shoulder region. From her silent response and my own observation of a kind of softly rolling ocean of muscle disappearing into the distance, I got the strong impression that there was nothing untoward, no sign of damage or dysfunction.

Meanwhile, the pain continued, together with difficulty sleeping, and a general lethargy, which might just be a sort of depression at the sense of restricted movement. I noted that I felt physically at my best when lying still, on the sofa or my bed. Just getting up resulted in shooting pains. Reading, holding a book, was a pain. All of this was on my left side, and I’m very left-handed.

And so it went, until something dramatic happened, I think it was on Sunday (March 8). I experienced severe constipation, certainly unlike anything I’d ever experienced before, and I won’t go into the shitty details, though it did make me think of my mortality (as has this experience of pain in general). How many people have died on the toilet seat? A dirty little secret, no doubt. In any case, I recovered, and, upon further desperate research (and noting that, before this bout, I hadn’t done a ‘number two’ for days – how had I missed that?), I dropped the ibuprofen plus codeine medication and went back to paracetamol.
I work part-time at Eynesbury College, currently two days a week (Monday and Tuesday), barely enough to live on, as a teacher of academic English to foreign students. It’s the most poorly paid job in the teaching profession. I’m paid as a casual, and work from five-week contract to five-week contract. It’s anything but ideal. For example during this current contract, which ends tomorrow (Friday), there were two public holiday Mondays, for which I wasn’t paid. I was offered another five-week contract starting next week, but I’ve made a decision to decline the offer, hoping to get on top of this pain situation once and for all.

I won’t go into my parlous financial situation, but it’s important due to my status vis a vis subsidised health care. More about that anon.

So I worked on Tuesday, and it was something of a struggle. Yesterday (Wednesday March 11) I returned to my GP and received the report from St Andrews Hospital. So I’ll now present the findings together with my comments.

X-ray and ultrasound left shoulder with subacromial bursal injection

subacromial bursitis has to do with inflammation of the bursa that separates the upper surface of the supraspinatus tendon (one of the rotator cuff set of tendons) from the overlying coraco-acromial ligament, the acromion, and the coracoid. To be explored further. A bursa, or synovial bursa, is a fluid-filled sac which cushions connections between bones, tendons, ligaments etc in joints.

X-ray – no bony injury. Alignment is normal. Subacromial space is preserved. No subacromial calcification.

Nothing to see here.

ultrasound- biceps tendon intact. No fluid in the sheath. The tendon does not sublux during internal/external rotation

Nothing again. Subluxation is a partial or incomplete dislocation of a joint or organ.

supraspinatus and other rotator cuff tendons are intact. No tear or tendinopathy. The subacromial bursa does not appear thickened and no bursal drag with abduction is identified.

So there are four rotator cuff tendons or muscles (not too sure of the difference); supraspinatus, infraspinatus, teres minor and subscapularis. The subacromial bursa is as described above.

The AC joint is normal in appearance and remained stable during forward flexion.

This is the acromioclavicular joint, at the top of the shoulder. It feels to me that the pain comes from ‘inside’ and lower than the shoulder, but it’s actually difficult to locate precisely. It may be a problem with the acromion, however. Or the Glenoid cavity or labrum. It may be a SLAP lesion (symptoms include ‘trouble localising a specific point of pain’. SLAP stands for ‘superior labrum, anterior to posterior’.

I’ll no doubt have to see a specialist, and the worry now is money

Written by stewart henderson

March 12, 2020 at 1:59 pm

My current health condition 1: it’s bizarre

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I can bear any pain as long as it has meaning

Haruki Murakami

stuff to learn about

I haven’t written for a while because I have a new health problem which flared up last Saturday, February 29, 2020. I had been feeling mild pain in my shoulder and I was lying on my bed reading when I tried to get up. Shooting pain from my shoulder down my left arm was so excruciating that I fell back on the bed and and lay down for a while before trying to get up again. Again I couldn’t get up because of the pain. I called for help but even with two of us it was difficult. I may have had a panic attack and exaggerated the pain of rising – I was gasping a lot. To cut a long story short Sarah called an ambulance (and the paramedic got me into a sitting position easily enough). I spent the next few hours in emergency at the Royal Adelaide Hospital.

Due to being given Panadol in the ambulance, and a long wait in reception while the painkiller took effect, by the time the friendly, efficient and strikingly beautiful (oh dear) young intern saw me, the pain, my only symptom, had much reduced. She found that, yes, I could move my arm above my shoulder, flex my elbow and my wrist, and no, I couldn’t precisely describe the nature or location of the pain. She checked my arm for swelling or redness (none), and asked about any recent history of injury to the region (none). I was beginning to feel like a fraud, a malingerer, a milquetoast.

So after some more prodding and questioning and advice from higher authorities, I was released with a report for my local doctor.

I’m very left-handed, so this left arm pain is quite a problem for me. I was due to work on the Monday and I needed some pain relief. It would have to be over the counter at first. The report’s only solid conclusion was ‘skeletal-muscular pain’. Since I needed to work on Monday and Tuesday I could only get to the GP on Wednesday. So on Sunday I started doing what research I could. I’ve never taken regular medication for anything, and I’ve never experienced regular pain like this. The only over-the-counter treatments for pain are ibuprofen and paracetamol as far as I know. Only ibuprofens is an anti-inflammatory. Paracetamol works on pain centres in the brain. Which one would work best? Was it all in my mind? But don’t we always feel pain via the brain? Isn’t that how the nervous system works?

I obtained both medicines. Over the next day or so I experimented with both, singly and in combination, and I got through Monday and Tuesday’s work. The pain never went completely away, though the teaching days, when I had to concentrate on and interact with my students and other teachers, helped to distract me from it, which gave me that guilty ‘it’s all in the mind’ feeling.

Even so, on Wednesday (March 4), the pain came roaring back. My subjective sense told me that the paracetamol was much more effective than the ibuprofen, another surprise. I visited my GP, who smiled at the hospital report, saying, ‘yes, they wanted you out of there as soon as possible – they’re there for acute, intensive care stuff, it’s understandable – a GP can refer you to a specialist, and we can go from there’. So he filled out a referral form for St Andrews Hospital, for an x-ray and an ultrascan. I rang them and organised an appointment, for Friday, March 6 at 11am.

I was still in pain, though. The OTC medication had reduced the pain to more bearable levels, but I still hadn’t worked out which worked best. Unlike me, Sarah was on many medications, for pain and other problems, including Prodeine (paracetamol plus codeine) and a set of tablets which combined paracetamol and caffeine. I was taking the tabs at the upper level of what was recommended, and beyond. I was trying to monitor the pain, what it felt like. It was always a low-level throbbing, which increased and became a shooting pain if I used the arm too much. It was a strange delayed pain – I would engage in a flurry of physical activity, such as preparing a quick meal, and then lie down, knowing that the pain would rise up as a result of the activity, then slowly subside. I had difficulty sleeping, and I dreaded dressing myself in the morning. Typing this is giving me an ache, and I’m experimenting with dictation – I find the Apple dictation system a pain (mentally speaking). I have to learn more about how to use it effectively.

Stupidly, I hadn’t asked my GP about stronger prescription medication. The day after the consult (Thursday, March 5) I had Sarah ring the surgery – I was experiencing bouts of serious pain, and was finding it hard to track what medication was working, or not. The doctor wrote a prescription, which Sarah collected and had made out at the pharmacy around the corner. It was for ibuprofen (200mg) and codeine phosphate hemihydrate (12.8mg). I was skeptical about the efficacy of ibuprofen, and I had been researching anti-inflammatories, and inflammation generally.

What, exactly, is inflammation? There are, supposedly, five signs of it, remembered under the acronym PRISH – pain, redness, immobility, swelling and heat. My only symptom was pain. There was certainly no redness or swelling. Immobility wasn’t a real problem either. I could move my arm above the shoulder, I could flex my elbow, etc, but some pain would come afterwards. Heat wasn’t something I could measure, but it didn’t seem an issue. Only pain. And I hadn’t pinpointed any cause of all this. I remembered what I’d said, quite often (or at least I thought I did – maybe I was mostly saying it to myself) to the intern at emergency: ‘It’s bizarre!’

Anyway, I’ll wind up this piece, and start on a new one, dealing with my time at St Andrews Hospital, the x-ray and the ultrasound.

Written by stewart henderson

March 8, 2020 at 12:43 pm

the autodidact story 1: family and authority

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When I was young I was somewhat troubled about myself. I was unhappy at home, I hated school, I felt I had no-one to talk to, and my only solace was the ‘rich inner life’ that, much later, I read about in an essay by the philosopher Hilary Putnam. That’s to say, he wrote an essay in which he happened to mention that some outwardly nondescript people might have cultivated a rich inner life, or words to that effect, and this fairly mundane observation was the only thing I took from Putnam’s essay.

I had a difficult time with friendship, and still do. On my birthday – I was probably fourteen – I received a card from another boy I knew well. It read ‘to my best friend ever’. I read it with shock. It made me feel somehow ashamed and miserable. I felt that this friend of mine was deluded, and I’d been the cause of his delusion. Perhaps there was some arrogance in this – I felt that my ‘rich inner life’ was almost completely hidden from him, and everyone else, so how could he think he knew me well enough to consider me his BFF? However, when he left for England with his family a few months later I felt more alone than ever. 

I’ve never felt seriously suicidal, but I do recall a particular moment, when I thought, ‘this is who I am – a loner. I have to learn to live with it’. I cried myself to sleep, and went on. 

Of course, all autobiographies, whether short or long, are mostly lies, beautiful or otherwise, so don’t take any of this too seriously. My parents didn’t get on too well, to put it mildly, and my siblings were – rivals. We lived in one of the most thoroughly working-class regions of Australia, in the newly created town of Elizabeth, built around the manufactory of holden cars, now deceased. My father worked there for a brief time, but he didn’t like working in factories, and I don’t blame him, having worked in quite a few myself. Unfortunately he couldn’t think of anything else to do, so he didn’t do anything much, and my mother was the nagging, harried breadwinner. My relationship with both of them during my teen years could fairly be described as toxic.

We did have books however. Encyclopedias, classics, and surprisingly modern fare, especially in the new feminist line, such as The female eunuch, Patriarchal attitudes, The feminine mystiquue and The second sex. I don’t know where all these books came from, they just always seemed to be there. My mother insisted on getting us to the library regularly, for which I’ll always be grateful, but I rarely saw her reading anything. She had a higher-up job in the nursing profession and when she got home she’d always flip the TV from the ABC to her favourite sit-coms, I love Lucy or The Dick Van Dike show. As for my father, I often wondered if he knew how to read. But these people bestowed upon me their genes, more or less equally, and that was a source of wonder. Was I smart?

We had come to Australia as ten pound migrants, and I had flickering memories of the boat trip – a camel train on the banks of the Suez, being saved from drowning in the ship’s pool, sitting with a group of kids while my mother, seconded as an educator, taught us spelling or something.  

Education. I became a teenager in 1969. It was a fantastic time for music, and the culture that came with it. I looked out the window at my brother and his friends and they were all wearing levis and it looked so cool. My older siblings were buying records – the Beatles, the Kinks, the Stones, and some now-embarrassing singles like ‘Little Arrows’ by Leapy Lee. Not long afterwards came Dylan and Cohen and I loved all that cool verbiage. Was I smart? I didn’t like school. I couldn’t talk to the teachers like other kids. I didn’t like the inequality, that they might know more than me. I didn’t like being told what to do. I liked to read, to learn stuff in my own way. I didn’t have an imaginary friend exactly, but I was always talking and arguing in my head, and felt the lack of the real thing.  

One day I was somehow invited to some kid’s house whose older sister was visiting from university. Did she live in the university? There was a crowd of kids and I could just see glimpses of the girl-woman through arms and legs. She was sitting on a stool as on a pedestal and she was slim and pretty with neat blonde hair and lipstick and a neat plaid skirt and heels, and I was shocked at this first ever sight of a university student. They were supposed to wear jeans and sandals and tie-dyed t-shirts and be beautifully scruffy and hairy. Disappointing.

Anyway, I left school because I was always in trouble for not doing my homework, inter alia, and I had horrible fights with my mother when she wasn’t having horrible fights with my father, and my father had fist fights with me, which wasn’t much fun as he’d been a boxer in his past and I could see him eyeing me for maximum damage with his dukes up. I would stay at friends’ houses here and there, and I got my first job on an assembly line making Wilkins Servis washing machines. The one shown is of course a much earlier model than the ones I tended to stuff up when I worked there.     

And so my first experience of formal education was botched, and maybe I should blame myself, I don’t know. I continued to read of course, and to argue with myself. A rich inner life.

I read novels, mostly, in those days. I developed an obsession with Thomas Hardy. This was in my fifteenth year, I think. The Return of the Native was my first, and I think I read every single novel except A Laodicean, which critics said was his worst. I wanted to read it, for completeness, like Two Gentlemen of Verona, which I did read. I also wanted to know why it was considered so bad. I loved Thomas Hardy, he was so kind, it seemed to me, and so sad somehow.

(to be continued)

Written by stewart henderson

February 28, 2020 at 7:30 pm

a DNA dialogue 6: Okazaki fragments, as promised

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Canto: Okay, so first off, why are Okazaki fragments so called?

Jacinta: Well as anyone would guess, they’re named after someone Japanese, in this case two, the husband and wife team Reiji and Tsuneko Okazaki, who discovered these short, discontinuously synthesised stretches of DNA nucleotides in the 1960s.

Canto: Yes their story is intriguing – tragic but also inspiring. Reiji, the husband, was born in Hiroshima and died in 1975 from leukaemia, related to the 1945 A-bomb. He was only 44. Tsuneko Okazaki continued their research and went on to make many other contributions to genetics and molecular biology, as a professor, teacher, mentor and director of scientific institutes. Her achievements would surely make her a Nobel candidate, and she’s still alive, so maybe…

Jacinta: Now the key to Okazaki fragments is this lagging strand. Its directionality means that the DNA primase, followed by the DNA polymerase, must work ‘backwards’, away from the replication fork, to add nucleotides. This means that that they have to have periodic breaks – but I’m not sure exactly why – in creating this lagging strand. So the entire replication process is described as semi-discontinuous because of this fundamental difference between the continuously created leading strand and the stop-start ‘fragmentary’ (at least briefly) lagging strand.

Canto: But we need to know why this ‘backward’ movement has to be stop-start, and I’d also like to know more about this primase and polymerase, thank you.  

Jacinta: Well the Okazakis and their team discovered this semi-discontinuous replication process in studying the replication of good old Escherichia coli, the go-to research bacterium, and it was a surprise at the time. Now, I’m looking at the explanation for this necessarily discontinuous process in Wikipedia, and I confess I don’t really understand it, but I’ll give it a go. Apparently the Okazakis ‘suggested that there is no found mechanism that showed continuous replication in the 3′ to 5′ direction, only 5′ to 3′ using DNA polymerase, a replication enzyme’, to quote from Wikipedia. So they were rather cleverly hypothesising that there must be another mechanism for the 3′ to 5′ lagging strand, which must be discontinuous. 

Canto: And another way of saying that, is that the process must be fragmentary. And they used experiments to test this hypothesis? 

Jacinta: Correct, and I won’t go into the process of testing, as if I could. It involved pulse-labelling. Don’t ask, but it has something to do with radioactivity. Anyway, the test was successful, and was supported by the discovery shortly afterwards of polynucleotide ligase, the enzyme that stitches these fragments together. Now, you want to know more about primase, polymerase, and now ligase no doubt. So here’s a bit of the low-down. DNA primase is, to confuse you, an RNA polymerase, which synthesises RNA from a DNA template. It’s a catalyst in the synthesis of a short RNA segment, known as a primer. It’s extremely important in DNA replication, because no polymerase (and you know how polymerase keeps getting associated with primase) can make anything happen without an RNA (or DNA) primer.

Canto: But why? This is getting so complicated.

Jacinta: I assure you, we’ve barely scratched the surface….

Canto: Well, Socrates was right – there’s an essential wisdom in being aware of how ignorant you are. We’ll battle on in our small way.    





Written by stewart henderson

February 27, 2020 at 5:48 pm

a DNA dialogue 5: a first look at DNA replication

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schematic of ‘replisome’ structures involved in DNA replication


Jacinta: So let’s scratch some more of the surface of the subject of DNA and genetics. A useful datum to remember, the human genome consists of more than 3 billion DNA bases. We were talking last time about pyrimidines and purines, and base pairs. Let’s talk now about how DNA unzips.

Canto: Well the base pairs are connected by hydrogen bonds, and the two DNA strands, the backbones of the molecule, run in opposite, or anti-parallel, directions, from the 5′ (five prime) end to the 3′ (three prime) end. So, while one strand runs from 5′ to 3′ (the sense strand), the other runs 3′ to 5′ (the antisense strand). 

Jacinta: Right, so what we’re talking about here is DNA replication, which involves breaking those hydrogen bonds, among other things. 

Canto: Yes, so that backbone, or double backbone whatever, where the strands run anti-parallel, is a phosphate-sugar construction, and the sugar is deoxyribose, a five-carbon sugar. This sugar is oriented in one strand from 5′ to 3′, that’s to say the 5′ carbon connects to a phosphate group at one end, while the 3′ carbon connects to a phosphate group at the other end, while in the other strand the sugar is oriented in the opposite direction. 

Jacinta: Yes, and this is essential for replication. The protein called DNA polymerase should be introduced here, with thanks to Khan Academy. It adds nucleotides to the 3′ end to grow a DNA strand…

Canto: Yes, but I think that’s part of the zipping process rather than the unzipping… it’s all very complicated but we need to keep working on it…

Jacinta: Yes, according to Khan Academy, the first step in this replication is to unwind the tightly wound double helix, which occurs through the action of an enzyme called topoisomerase. We could probably do a heap of posts on each of these enzymes, and then some. Anyway, to over-simplify, topoisomerase acts on the DNA such that the hydrogen bonds between the nitrogenous bases can be broken by another enzyme called helicase.

Canto: And that’s when we get to add nucleotides. So we have the two split strands, one of which is a 3′ strand, now called the leading strand, the other a 5′ strand, called the lagging strand. Don’t ask.

Jacinta: The leading strand is the one you add nucleotides to, creating another strand going in the 5′ to 3′ direction. This apparently requires an RNA primer. Don’t ask. DNA primase provides this RNA primer, and once this has occurred, DNA polymerase can start adding nucleotides to the 3′ end, following the open zipper, so to speak.

Canto: The lagging strand is a bit more complex though, as you apparently can’t add nucleotides in that other direction, the 5′ direction, not with any polymerase no how. So, according to Khan, ‘biology’ adds primers (don’t ask) made up of several RNA nucleotides.

Jacinta: Again, according to Khan, the DNA primase, which works along the single strand, is responsible for adding these primers to the lagging strand so that the polymerase can work ‘backwards’ along that strand, adding nucleotides in the right, 3′, direction. So it’s called the lagging strand because it has to work through this more long, drawn-out process.

Canto: Yes, and apparently, this means that you have all these fragments of DNA, called Okazaki fragments. I’m not sure how that works…

Jacinta: Let’s devote our next post on this subject entirely to Okazaki fragments. That could clarify a lot. Or not.

Canto: Okay, let’s. Goody goody gumdrops. In any case, these fragments can be kind of sewn together using DNA ligase, presumably another miraculous enzyme. And the RNA becomes DNA. Don’t ask. I’m sure all will be revealed with further research and investigation.


Leading and lagging strands in DNA replication (Khan Academy video)

Written by stewart henderson

February 26, 2020 at 10:59 pm

Trumpdagistan: the new fundamentalism

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The legitimate powers of government extend only to such acts as are injurious to others, but it does me no injury for my neighbour to say there are twenty gods or no god. It neither picks my pocket nor breaks my leg.

Thomas Jefferson

A recent Point of Inquiry podcast has again turned my attention to what I should now call Trumpdagistan, a more or less dictatorial state that borders Canada and Mexico, which for various reasons I shouldn’t really be concerning myself with, as I live very far from the country and have never had any intention of visiting it, even if I had the means. It just seems to be a kind of ghoulishness on my part, my version of addiction to, if that website still exists.

As a completely non-religious person, I’m obviously opposed to any interference of the state by religion, that terribly bad explanation of any and all phenomena. Trumpdagistan, even before it was renamed, was the most religious of all the democratic countries. Their national god is Guard, who guards Trumpdagistan against all evils, including secularism, the world’s primary evil, according to Billy Barr, the dictatorship’s chief toady, who believes that all morality derives from the book of Guard.

Whilst the wanker in the white palace (WWP) is very unlikely to believe in Guard (for his self-obsession is all-consuming but exhausting, as it basically consists of constantly puffing hot air into a balloon full of holes), he recognises the usefulness of a national god in much the same way as every previous dictator has. So he’s happy, indeed delighted, to unleash his toady on secularism and more particularly, secularists. Free-thinkers, in the words of Stephen Dedalus.

The WWP and his toadies have made every effort in their few years of control to create a compliant, Guard-worshipping judiciary, especially at the very top, the Supreme Court. As the Point of Inquiry podcast has pointed out, that court is now stacked with Guard-botherers, more or less bent on overturning the separation between politics and religion, through particular interpretations of the country’s much-worshipped Constitution which somehow bestow a kind of second-class citizenship on secularists. It’s unclear, however, how the Constitution can be so interpreted.

In any case, the WWP’s ‘administration’ has managed to promote two more religious right-wingers to the Supreme Court, for a total of five – just another couple of bricks in the wall, so to speak. The much-worshipped constitution of the former USA actually has very little to say on religion. The first amendment to that constitution, as it pertains to religion, says only this:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof.

That’s it. It’s since been known as the ‘establishment clause’. The rest of that amendment, also quite brief, deals with freedom of speech, without particular reference to religion. The only possible ambiguity in the above clause is ‘respecting’, which could mean ‘having respect for’ or ‘with respect or reference to’. Neither interpretation suggests that the constitution, or the bill of rights, supports any religion; rather it clearly supports keeping out of religion, or maintaining a separation between religion and law-making. And yet, mischief-making religionists, some of them rather powerful, have tried hard to distort the simple meaning. Take the late unlamented Justice Scalia, who in one forgettable judicial opinion came up with this gem:

The establishment clause permits the disregard of polytheists and believers in unconcerned deities, just as it permits the disregard of devout atheists.

Of course the clause has nothing whatever to do with permitting disregard, it simply avoids permission and prohibition equally. Nothing could be clearer. What Scalia seems to be wanting the clause to say is that the law should disregard and so not protect polytheists, atheists and the like. This defies any serious interpretation.

And so we come to the toady. He’s apparently a catholic, and believes that secularism is the principle cause of the ills that Trumpdagistan is suffering from. Those ills don’t, of course, include white collar corruption, which he avidly supports. To their credit, many other catholics are condemning Barr’s evidence-free claims, but in Barr’s Trumpdagistan, a collection of writings penned many centuries ago by scores of individuals of widely varying views and experience, and known today, at least by some, as the bible, is the only source of morality for all humanity, and will no doubt be installed as the basis of all Trumpdagistani law. All of this is making the WWP very popular, if polls are to be believed, so expect much more of it in the future. What would Thomas Jefferson think?

Written by stewart henderson

February 23, 2020 at 5:08 pm