an autodidact meets a dilettante…

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

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.

References

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

https://www.quora.com/What-is-DNA-unzipping

https://www.yourgenome.org/facts/what-is-dna-replication

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 rotten.com, 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

Epigenetics 8: some terms

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Histone, with DNA wrapping, rendered by the Protein Data Bank (PDB)
Histone, with DNA wrapping, rendered by the Protein Data Bank (PDB)

 

The gene is not more ‘basic’ than the organism, or closer to ‘the essence of life’, whatever that means. Organisms have DNA codes, and they maintain external forms and behaviours. Both are equal and fundamental components of being. DNA does not even build an organism directly, but must work through complex internal environments of embryological development, and external environments of surrounding conditions. We will not know the core and essence of humanity when we complete the human genome project. 

Stephen Jay Gould, ‘Magnolias from Moscow’, in Dinosaur in a Haystack, 1996

I remember ages ago promising that I’d start every blog piece with a quote, then I more or less immediately forgot about it. Anyway the above quote kind of refers to epigenetics, and anticipates, in a way, the disappointment that many have felt about the human genome project and its not-quite-revelatory nature. As we learn more about the complexities of epigenetics, more about the relationships between genotype and phenotype will be revealed, but the process will surely be very gradual, though relentless. But I can’t talk, knowing so little. In this post, I’ll look at a very few key terms to help orient myself in this vast field. Not all will be specifically related to epigenetics, but to the whole field of DNA and genetics. 

nucleosome: described as ‘the basic structural form of DNA packaging in eukaryotes’, it’s a segment of DNA wound round a histone ‘octamer’, a set of eight histones in a cubical structure. All of this is for fitting DNA into nuclei. Nucleosomes are believed to carry epigenetic info which modifies their core histones, and their positions in the genome are not random. Each nucleosome core particle consists of approximately 146 base pairs. 

chromatin: a complex of DNA and protein, which packages DNA protectively, condensing the whole into a tight structure. Histones are essential components of chromatin. Chromatin structure is affected by methylation and acetylation of particular proteins, which in turn affects gene expression. 

nucleotides: the basic building blocks of DNA and RNA, they consist of a nucleoside and a phosphate group. A nucleoside itself is a nitrogenous base (also known as a nucleobase) and a five-carbon sugar ribose (a ribose – these explanations always need more explaining – is a simple sugar, the natural form of which is D-ribose, and which comes in various structural forms). DNA and RNA are nucleic acid polymers made up of nucleotide monomers. 

nucleobase: a nitrogenous base (e.g. adenine, cytosine, thymine, guanine, and uracil which replaces thymine in RNA), the fundamental units of our genetic code. Also simply known as a base. 

base pairs: a base pair, in DNA, is one of the pairings adenine-thymine (A-T) or cytosine-guanine (C-G). They are pyrimidine-purine pairings. Adenine and guanine are purines, the other two pyrimidines. Due to their structure pyrimidines always pair with purines. 

CpG islands: regions of DNA with a high frequency of CpG (C-G) sites, i.e. sites where a cytosine nucleotide is followed by a guanine nucleotide in linear sequence in a particular direction. 

histones: highly alkaline proteins, the chief proteins of chromatin, and the means of ordering DNA into nucleosomes. There are four core histones, H2A, H2B, H3 and H4. These form an octamer structure, around which approximately 146 base pairs are wound. 

Obviously, I’m very much a beginner at comprehending all this stuff, but I note that the number of videos on epigenetics seems to increase almost daily, which is raising my skepticism more than anything. I try to be selective in checking out these videos and other info on the topic, as there’s always this human tendency to claim super-solutions to our problems, as in super-foods and super-fitness regimes and the like. I’m more interested in the how of things, which is always a more complicated matter. Other information sources tend to assume knowledge or to skate over obvious complexities in a facile manner, and then of course there’s the ‘problem’ of being a dilettante, who wants to learn more about areas of scientific and historical knowledge often far removed from each other, and time’s running out, and we keep forgetting…

So anyway, I’ll keep plodding along, because it’s all quite interesting.  

Written by stewart henderson

February 23, 2020 at 12:20 pm

Covid 19, bird flu, etc – why China?

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Covid 19 under the microscope

The recent coronavirus now has an official name, Covid 19, and the death toll at present is a little under 2000, considerably more than that for the SARS coronavirus of 2003. It has spread to at least two dozen countries according to ABC reporting. I note that the WHO are emphasising how co-operative the Chinese authorities have been, I suspect as an attempt to keep those channels of communication and co-operation open, or to open them wider. The infamously over-controlling Beijing government is faced with a dilemma as its economy is taking a major hit – it desperately wants to get over this epidemic, which means downplaying it as much as possible, but its dependence on international trade means having to co-operate with those over whom it has no control. The Middle Kingdom has always been sensitive about this issue of control and dominance, which clashes with the co-operative spirit of modern global trade relations. 

Having said that, Chinese authorities have certainly learned from the reaction to their fairly disastrous early handling of the SARS coronavirus outbreak in 2002. In terms of the really essential stuff, co-operation and information-sharing have rapidly improved – motivated by the apolitical spirit of research, detection and problem-solving that constitutes science’s unique value.  

Of course, one of the questions being asked, with Covid 19, the SARS virus, and other viruses such as H7N9 avian influenza virus (which had a very high mortality rate), is ‘Why China?’ An article from late 2017 in the Smithsonian magazine provides a plausible if shocking answer. 

It seems imprinted in Chinese culture that freshly killed-birds and other animals are tastier and somehow healthier than anything frozen or otherwise processed. The Chinese government has, in the past, been reluctant to interfere with the demand for freshly slaughtered produce, and it’s likely that, even if it enforced a clamp-down, the market would go underground. Melinda Liu, author of the Smithsonian article, described the scene at one of these markets, in the Sichuan city of Chingzhou:

Half a dozen forlorn ducks, legs tied, lay on a tiled and blood-spattered floor, alongside dozens of caged chickens. Stalls overflowed with graphic evidence of the morning’s brisk trade: boiled bird carcasses, bloodied cleavers, clumps of feathers, poultry organs. Open vats bubbled with a dark oleaginous resin used to remove feathers. Poultry cages were draped with the pelts of freshly skinned rabbits. (“Rabbit meat wholesale,” a sign said). These areas – often poorly ventilated, with multiple species jammed together – create ideal conditions for spreading disease through shared water utensils or airborne droplets of blood and other secretions.

Flu viruses can crop up and mutate anywhere – for example, the H5N2 flu strain which broke out in the USA in 2015 led to the slaughter of 48 million poultry – but China’s mixed farming habits, in which poultry and other livestock live in close proximity with their keepers, together with the taste for freshly slaughtered and disturbingly exotic meat, and the conditions in many markets and slaughter-yards, presents a massive cultural problem for China’s huge and increasingly mobile population. The country will have to come to terms with these issues, sooner rather than later, if it wants to recapture and grow beyond the leading economic role it led before the advent of Covid 19.

References

https://www.smithsonianmag.com/science-nature/china-ground-zero-future-pandemic-180965213/

https://www.who.int/emergencies/diseases/novel-coronavirus-2019

https://www.who.int/influenza/human_animal_interface/influenza_h7n9/en/

Written by stewart henderson

February 19, 2020 at 9:15 pm

Posted in China, covid19, health

Tagged with , ,

the wanker in the white palace 3: the impeachment failure

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words words words

It’s not accurate to say that impeachment was bound to fail in getting rid of the wanker, but it became increasingly obvious that it would fail, because too many politicians feel they owe their livelihood to him, or their prestigious position as ‘lawmakers’ and public personae. And of course there are a few who are too stupid to see what a wanker the wanker is, but they’re a small minority.

In this blog I’ve often stated that impeachment is a piece of shite. It would be nice to imagine that this latest débâcle would be enough for it be entirely expunged from the political system, but of course that won’t happen. This is the USA we’re talking about, after all.

It’s an odd term, derived from empêchement, a ‘prevention’ or ‘impediment’ from the verb empêcher. It’s used in many countries but has always struck me as an inadequate substitute for solid L-A-W law, as has been shown in this recent case. Of course, in order for this substitution to be effective, the administration of the law needs to be entirely separate from government. This is proving to be a problem in ‘the world’s greatest democracy’.

Three Presidents have been impeached. None of them have been removed from office. It all seems to be an expense of spirit in a waste of shame. But getting rid of impeachment, unfortunately, is just the beginning. I’ve already pointed out some of the failings of the Presidential system in general. Massive power, massive immunity. Are Americans really this stupid?

Yes, they are, or maybe it can happen to any state that promotes an uncritical, worshipful attitude towards its constitution, which, in the case of the USA, has created a Constitutional Presidency on the basis of the British Constitution Monarchy. And there’s no doubt that, at the outset, it was an improvement on the British system, which had, and still has, a hereditary monarch, rather than an elected President. However, the Westminster system has evolved since then, with the monarch’s power gradually reducing to, essentially, nothing, and all power being held by the duly elected parliament, a team with a team leader, working within the parliament, not in a white palace surrounded by thuggish hand-picked courtiers, who, unless they’re responsible citizens – the last people the wanker would choose – need know or care little about the workings of congress.

The USA regards itself as the first modern democracy. Not true. The very reason the founding fathers looked to the British system as a model was because of its parliamentary system, which, without doubt, the founding fathers improved upon. But, following the British system, with its minuscule franchise, those founding fathers, fearful of the ‘unenlightened’, made sure that the unpropertied and feeble-minded – the natives, the blacks and the women, were excluded from any say in government. And just to emphasise the woman issue, no country on this planet can call itself a modern democracy that doesn’t allow half its adult population to vote. American women weren’t given the vote till the 1920s, almost 30 years after women in my region were given it.

But really, all questions about democracy in the USA are now up for grabs. Things will get worse. It’s preposterous to imagine that the wanker (and this epithet shouldn’t entail under-estimation – he’s been made an extremely dangerous figure by the US political-economic nexus) will give up power peacefully. He’s been taught that he’s an eternal winner, so fasten your seat belts, it’s gonna be a bumpy year.

Written by stewart henderson

February 15, 2020 at 11:54 pm

the wanker in the white palace 2: how did the USA get reduced to this?

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Unfortunately, all votes are equal – and by the way, they spelt Guard wrong

As I write, the wanker is, predictably, expending much energy in exacting revenge against his perceived enemies, and in seeking to manipulate the justice system in support of his long-time associates. I note that, over the last day or so, he has casually stated to the media, obviously not for the first time, that ‘I could do x, I have the absolute power to do x, but I think I’ll do it this way…’ I don’t claim this as a direct quote, because of course I don’t listen carefully to the wanker, and in any case, these remarks are essentially formulaic. This is of the thought-bubble type ‘I can do anything I want nya nya, nobody can tell me what to do, but I won’t do that coz mummy might shout at me.’ It’s nonsense from a reasoning perspective, but it’s absolute sense in the wanker’s little world.

Yet, so far, mummy hasn’t shouted at him enough, or he’s found that her shouts aren’t as prohibitive as he’d feared, so he feels more confident about being naughty. And being naughty and getting away with it is the most fun ever. It’s really quite addictive.

This isn’t a joke, and it’s not an exaggeration, or a simplification – it’s the reality. So how did the USA get reduced to this? 

The USA touts itself, more than any other nation, as the land of the individual. You can achieve anything there, apparently. Total freedom. You can advertise just about anything, you can buy a gun just about anywhere, and if you’re an expert at avoiding tax, you’ll be touted as a hero. The rich, in particular, are objects of veneration. And the wanker has been super-rich – at least from my perspective – since the age of three. 

Democracy has its issues, the most obvious of which was highlighted a couple of centuries ago by some Greek philosophers. They had seen how a super-confident-seeming blowhard, a wanker in short, had swayed the crowd towards disaster for their city-state. You can imagine the slogans – ‘lock up x, y and z, they’re enemies of the state’, ‘drain the swamp’, ‘punish states a, b and c, they’re wrecking our economy’, ‘make our State great again’. ..

In Australia, Britain, and most other democratic countries, we don’t directly elect one person to a position of great power, in a competition against another single person. We elect parties. The leader of the party, in election campaigns, will say ‘we will do, this, or that, for you’, ‘we will offer stable, effective government’, and so forth. This ‘we’ makes a big difference. Think about that, it’s really important. In Australia, in Britain, in every other Westminster-based system, we have a Prime Minister, a first minister, primum inter pares, the captain of the team. Famously, and rightly, if the captain goes rogue, she can be dismissed from her position by a simple vote of no-confidence from her party. The captain is replaced by another captain, and the team plays on. 

There is absolutely no doubt in my mind that this is a vastly superior system than that which the USA has lumbered itself with. And yet, I have never heard an American journalist or historian or pundit admit as much. Why is this?

I think I’ll have to do a lot of exploring to answer that question.

Written by stewart henderson

February 14, 2020 at 2:33 pm

the wanker in the white palace 1: my position

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I hear comments around me and read reports in the media about how and how not to deal with the wanker in the white palace. My position is straightforward, in its apparent foolishness. Responsible people shouldn’t be dealing with him, they should get rid of him. 

By this I don’t mean putting an end to his life, much as I’m in favour of euthanasia. The wanker can’t stop himself from wanking night and day – there is no free will, but that’s another story. The point is that he’s clearly incapable of holding any position of responsibility, in which he’s expected to work for the good of others. No sensible person, I would argue, disagrees with this, and a number of the USA’s top psychologists have spoken out about the wanker’s mental unfitness for the job he holds. They would also agree with one of their rank, speaking on MSNBC, that the damage which makes it impossible for him to behave like a common and garden adult occurred very early in life and is irreversible. The damage he has done to the role of US President won’t be able to be fully assessed until he’s dumped from office – which may, I believe, involve bloodshed. This wanker won’t go quietly.

So why has the wanker managed to inveigle himself into this extraordinary position, and why is he so hard to get rid of? I’ll be exploring this under two ‘headings’, the ‘American psyche’, and the current Presidential system. The two are very obviously linked.

Why ‘wanker’? Well, I’m essentially Australian (though British-born and a dual citizen), and my first reaction to this bloke after witnessing him briefly on TV years ago was the classic ‘what a wanker’ refrain. If I hadn’t heard his name before I would’ve considered this a badly done black comedy, with the lead actor spouting buffoonish imbecilities, and the other performers pretending to fawn over his oafishness, and appearing dazzled by the kitsch furnishings in ‘Trump’ tower – he trumps over everyone, getit, and yet it’s all trumpery, right?

But it’s no joke, even though it is. Even after all this time, it’s hard to take seriously – but then, I’m not a Kurd, or a Central American refugee. 

The USA is an object of mockery and opprobrium worldwide for its production and promotion of the wanker, and it thoroughly deserves to be. The wanker has trumpeted his wankerdom for the whole of his ‘adult’ life – it’s the USA’s fault that he’s been so successful, and yet even his most vociferous critics trumpet the USA as the leader of the free world, the light on the hill, Guard’s own country, the Greatest Nation on Earth, and other enlightened epithets. There is surely no nation more jingoistic, and unself-critical, than the USA, even allowing for the fallacy that all powerful states have fallen for – Egyptian, Roman, British, Soviet, Chinese and so on, – that economic and military power entail moral superiority. 

In future posts I’ll explore the flaw in the American psyche that has allowed the wanker to swank his way into and perhaps permanently corrupt the most powerful position on the planet (currently) and the many related flaws in a presidential system that fortunately has no equivalent in the so-called free world. 

 

Written by stewart henderson

February 13, 2020 at 5:37 pm