Hate

What seems like a long time ago - I was a little surprised to find that it was only March - I read a story by Galsworthy called 'The Apple Tree', as noticed at reference 1. I have not got any further with Freud in the interval, at least not as far as the story is concerned, but yesterday, more or less by chance, I happened to put my hand on the book again and read the short story called 'The dog it was that died', written shortly after the end of the First World War.

For some reason it struck a strong chord. Perhaps the misery of all the people caught in the middle of a fight, in this case a German-English family caught in England at the start of that war. The husband being interned and then repatriated. I had not known about this last and I associate to the controversial treatment of Japanese-US families caught in the US at the start of the Second World War. But I never knew anything about what happened to such families caught in Japan - there must have been some, even if the numbers were, I imagine, very much smaller. Or in Germany for that matter.

Perhaps it was the connection to the misery of those caught in the middle in the Kenyan Emergency, noticed yesterday at reference 3. Both involved internment camps, aka concentration camps.

The present story is more about how such fights, such wars, bring to the surface all kinds of unpleasant, perhaps necessary, traits and behaviour. Traits and behaviour which are best put away afterwards - but a putting away which is not always possible. Some people are good for wars, and others are good for peace. I associate to once reading of what used to be called Red Indians, having war chiefs and peace chiefs, knowing full well that the two were not the same.

It all seems a long way from the 'Forsyte Saga' - but further reflection needed.

PS 1: what Galsworthy refers to as an old jingle, comes at the end of a poem by Oliver Goldsmith, turned up by Bing and snapped above. Gemini tells me that 'The poem 'An Elegy on the Death of a Mad Dog' was published in 1766. / It was included in Oliver Goldsmith's novel, The Vicar of Wakefield, which was published in that same year'. I have not checked but I would be very surprised if he had got this wrong. 

I don't think I had ever heard of this poem, but plenty of other people seem to have, including Tom Stoppard who used this very same line as the name of a radio play. While I got no further with Goldsmith than reading the play 'She stoops to conquer' as a child at my secondary school - a play which surfaces from time to time to this day. And about which I can remember nothing at all.

I only managed two of the eleven minutes available at reference 6, snapped above. But it does confirm what Gemini had to say. Perhaps it was his source.

PS 2: Agatha Christie is quite strong on how people who had 'good' wars, often find it difficult to adjust to the peace that eventually follows. It crops up quite often in her stories.

PS 3: after breakfast: two reflections so far, both rather off the point. First, the elegy does not appear in the Opie anthology, with this last to be found, for example, at reference 7. Plenty of other dogs though. Second, in the case of 'She stoops to conquer', I have remembered the catalogue entry for the item in question, but not the item itself. The meta-data rather than the data. I think that this happens quite often, but I dare say the other thing happens too, that an image of some sort comes to mind, but you have not got a clue from where it might have come. I must look out for such a thing.

References

Reference 1: https://psmv5.blogspot.com/2025/03/the-apple-tree.html.

Reference 2: The dog it was that died - John Galsworthy - 1919.

Reference 3: https://psmv5.blogspot.com/2025/08/more-first-impressions.html.

Reference 4: A elegy on the death of a mad dog - Oliver Goldsmith - 1766.

Reference 5: https://en.wikipedia.org/wiki/The_Dog_It_Was_That_Died.

Reference 6: https://youtu.be/aiedppArr7o.

Reference 7: https://psmv5.blogspot.com/2025/04/opie-opie.html.

Trolleys 961, 962, 963 and 964

The first job of the day was to check to see if the special needs trolley from Sainsbury's was still at Stones Road, the one noticed at the end of reference 2, a few days previously. And it was. Furthermore, the caravan which had been on one of its rare excursions, was back again.

While I think the trolley was of a rather heavier construction from the regulars at Sainsbury's.

Checking underneath, no maker's plate from Wanzl of the sort that you get now, but there was a Wanzl sticker, from which I learned that this trolley was more than fifteen years old. Perhaps part of some previous round of procurement which has not yet worked its way out of the system. Now in exile, away from the main stacks, next to Timpsons (of reference 4). Next stop the breaker's yard. Maybe we can still manage trolleys in this country, unlike ships which I believe are sent to Pakistan and Bangladesh, to be beached and broken up there.

Back down East Street to the library, to see whether they had any more Gouge for BH - with her having enjoyed the first two, previously noticed getting on for a couple of months ago at reference 3. 

No luck at the library and no luck at the Oxfam shop across the road, and while I dare say Waterstones could have obliged, I decided to wait. And checking with Surrey Libraries this afternoon, I find that they have plenty. Two more now reserved, including the 'City of Bells' I started with on the train, back in July.

While I was at the library, I could not but notice that quite a large chunk of it had been carved out to make a registration office. I wondered whether this was the thin end of the wedge, the start of the pecking away at our fine library, but I dare say convenient for Epsom residents, who will no longer have to get themselves over to Leatherhead.

Picked up a trolley in Ebbisham Square, possibly something to do with one of the street food sheds there.

Out again in the afternoon, to pick up on this scooter, often parked in the Eclipse Car Park. Nothing on the charging notice about scooters being exempt. Nothing turned up by a quick search on Bing either. But I would not have thought that a learner driver on a scooter would have wanted to be paying several pounds a day to park while he worked in town. Would I get much out of one of those heavily dressed parking enforcement officers they have patrolling the streets?

The third trolley of the day, a medium small trolley from the M&S food hall, was captured outside TK Maxx.

I had thought to take a short route home, down Hook Road, but in the event I fell for the trolley down there, previously noticed and still there a day or so later.

I was reminded that pushing a trolley on the sloping & bumpy western pavement of Hook Road is quite hard work.

Back to a still fairly busy High Street, to find a young man on a bicycle heading for me, on the pavement, at what seemed like a considerable speed. As I had a trolley, I blocked him, something that I would not attempt without, and it did bring him to an abusive halt. He also waved a bandaged arm at me, as if that was some kind of excuse. I suggested that perhaps he should be cycling on the road - it was not a shared use pavement and, even if it had of been, he was not showing much consideration for other pavement users - and maybe my remarks sank in. He was not going to back down in public, but hopefully he would think twice before doing it again.

A bit further down, more water works. That is to say a leak from around a water meter. A big enough leak for movement in the water to be visible.

Thought about Wetherspoon's, but decided against and headed back up West Hill. Just past the Marquis, passing a non-scoring trolley from Waitrose. Scoring trolleys from Waitrose having once been common, now rather a rarity.

A fine rose, captured on Clay Hill Green as I headed towards Meadway. Not the greatest snap from Samsung, the flower having been detached from its surroundings, a UFO, but a lot better than some of his efforts on flowers with strong colours.

References

Reference 1: https://psmv5.blogspot.com/2025/08/trolleys-959-and-960.html.

Reference 2: https://psmv5.blogspot.com/2025/08/trolleys-956-957-and-958.html.

Reference 3: https://psmv5.blogspot.com/2025/07/padded-beef.html.

Reference 4: https://www.timpson.co.uk/.

Group search keys: trolleysk, 20250827.

More first impressions

This morning, I finished my first pass of this novel from the Kenya of around 1960, reference 1, as advertised at reference 2, following in the first impressions steps of reference 3. I have not attempted to put the fragments which follow in a sensible order.

The second part of the author's name is his father's name, so a patronymic after the Russian fashion, rather than a family name after our own. Some people would say that means that the name should be filed under 'N' rather that 'T', but some people does not include Waterstones.

Continuing with the Russians, I found all the foreign names rather hard to get hold of, rather as they are in 19th century novels from Russia. I now suspect that part of the difficulty is that they are from a foreign language as well as a foreign country and one cannot easily say them, in one's head or otherwise, in the way that one can with one's own names. With the result that they fail to lodge in memory. Perhaps next time around, I shall resort to a diagram in Powerpoint, something I do occasionally with novels, for example a Maigret story which I am failing to hold together. A diagram which as well as helping with the names, helps with relationships and with place in story.

I also associated to the novel at reference 4, a novel which I once knew well - initially in Penguin Classics - and which also tells of more or less ordinary people caught up in extraordinary events.

I was impressed by the absence of anger in the novel, anger about what had been done in what was the recent past at the time that the novel was first written. Sadness yes, anger no. Anger which I thought might have been present, given his aggressive stance vis-à-vis his native Kikuyu, my starting point at reference 2. This despite his long service in universities in the US.

By the understanding which he extends to the plight of the civil servants - and their wives - sent out from the UK, many of whom started out with high ideals of doing good. And some of whom ended up on the bottle. And some of whom wrote monographs about the plants and flowers of the countries to which they had been posted, some of which are still to be found in the libraries of places like Wisley - the show garden run by the Royal Horticultural Society.

I was very struck by the point he made about violence. OK, so the British put an end to the endemic, mainly tribal, violence which came before. No doubt they also bore down on what sounds like a high level of community violence, a lot of it drink or women related. But at least the Africans did not go in for world wars which killed many millions of people - although some of them were conscripted to fight in them. I had not known that conscription was involved, a point I ought to check up on.

Also by the way that the Mau Mau emergency tainted everything involved. The dreadful behaviour of many of those involved in running the concentration camps spread out to taint ordinary life in the areas concerned. A long legacy of lost, ruined and damaged lives. What this novel has done for me is to offer a peek into this last. A very human - and humane - novel.

A lot of tea was drunk, presumably drunk without milk, as there was little talk of cows. Hot tea was what you offered if someone visited your hut. A hut which was plastered with mud and roofed with grass. I associate to reading a comment about people who comment on the shacks a lot of people lived in in countries like Kenya, to the effect that concrete blocks for the walls and corrugated iron for the roof were much better than the infestations of insects and worse of the olden days. And another about igloos, which might be picturesque, but which were cold in the winter and damp in the spring and autumn. Water dripping off the walls and roof the whole time.

And some of the eating was quite basic, with one wife-free man taking just one meal a day, after work on his smallholding. A meal consisting of a dish of  reheated maize and barley grains, previously boiled up in large batches: a sort of coarse porridge. Fast food of a sort?

I was reminded of the quite unreal expectations of ordinary people caught up in revolutionary change. In this case, how the simple act of removing the British from the top of the heap was going to solve all the problems. Including the Indians who, on this telling, had quite a strong grip on shops and shopping. Everyone would have enough money and enough land, and everyone would have access to education and health.

I have also read the introduction, from which I learn of parallels with Conrad - whom I had thought I knew pretty well, although I have not read him for a while now.

I hope there will be a next time - and the present plan is to try and track the novel in the large map offered by the Times Atlas, snapped above. I note that I had quite forgotten about the snow capped mountains to the south west, quite near Nairobi.

PS 1: I am reminded that blog search - available from the box top left - is not accent blind. 'Ngũgĩ' works, while neither 'ngugi' nor 'Ngugi' do. But at least they all will, as far as the present post is concerned.

PS 2: more news this morning from Microsoft, this time about a senior Labour politician arranging his or her housing affairs to avoid paying tax. There was also talk of the same sort about a senior SNP politician. All perfectly legal, all perfectly reasonable, up to a point. And probably piffling compared with corporate shenanigans elsewhere: just think of the late Lynch and his sale of Autonomy to HP. But it does not play well in the media at a time when our government needs to ask the rest of us to pay a bit more, to help balance our books - presently in rather dire straits.

PS 3: I have now checked up on conscription. It seems that while we avoided the term 'conscription', we did make use of what amounted to press gangs, of the sort used by our navy during the Napoleonic wars. See reference 7 and 8 - with the first of these taking a rather different tone than the second. Without having gone very far into either of them, it occurs to me that there may be some mitigation in that at least some of those caught up in all this would have come from cultures which valued warriors. One gets the odd glimpse of this in the present book.

References

Reference 1: A grain of wheat - Ngũgĩ wa Thiong'o - 1967. Penguin (from Waterstones). Introduction by Abdulrasak Gurnah. Cover snapped above.

Reference 2: https://psmv5.blogspot.com/2025/08/kikuyu-affairs.html.

Reference 3: https://psmv5.blogspot.com/2025/07/first-impressions.html.

Reference 4: And Quiet Flows the Don - Mikhail Sholokhov - c1930.

Reference 5a: https://pumpkinstrokemarrow.blogspot.com/search?q=kenya.

Reference 5b: https://psmv2.blogspot.com/search?q=kenya. Includes notice of one Brain Thompson, who did time in Kenya during the emergency. Who caught my eye today because of one of the central characters of the present book being called John Thompson. Brain Thompson, for an author, is hard to find on the Internet, but I did turn up reference 6.

Reference 5c: https://psmv3.blogspot.com/search?q=kenya. Includes notice of the arrival of our 1968 Times Atlas, still present to my right as I type this, and still used reasonably often, guessing, more than once a month.

Reference 5d: https://psmv4.blogspot.com/search?q=kenya. Includes notice of termination of my Facebook connection with Kenya, a connection I was sorry to lose.

Reference 6: https://www.dailymail.co.uk/home/books/article-490559/I-Idi-Amins-boss.html. 

Reference 7: https://www.newstatesman.com/politics/2019/03/britains-violent-conscription-of-african-soldiers-is-finally-coming-to-light. But see reference 8 below from more than thirty years previously: it had seen light of a sort before.

Reference 8: Recruitment and service in the King's African Riles in the Second World War - Jennifer Warner - 1985. A dissertation from the University of Bristol. 220 odd pages of typescript.  https://research-information.bris.ac.uk/ws/portalfiles/portal/34495837/370678.pdf.

Trolleys 959 and 960

For a change, the first trolley of the day was a Sainsbury's trolley captured in East Street, on the Jukes House side of the junction between that house and Defoe Court. Perhaps abandoned by a resident of one of these two establishments.

To find that the patch of bushes just beyond Middle Lane, where I had picked blackberries a few weeks previously had been mown. Will they be back again next year?

And a Lidl trolley by the side of Wickes, before you get to Halfords. A fair step to Lidl's, maybe a half hour with a trolley, so who on earth would have bothered to do that? Despite it being a bit late in the morning, I thought to take it back after I had deposited my Sainsbury's trolley to find that the front wheel was locked. And it was coming on to rain, so that was that. Sheltered for the few minutes that the rain lasted under the Wickes' front wall, by the fried-foodie caravan, and then pushed on back down Middle Lane.

Coming across this bicycle on the town side of the Screwfix underpass, presumably stolen from somewhere, from someone. The saddle looked as if it had been pointlessly scratched with some kind of sharp implement, although this does not show up in zoom today.

Investigating further, I now know that Pendleton is a range of bicycles sold by Halfords and a very successful cyclist who, after cycling, went onto horse racing and jousting. And that the saddle snapped from the Halfords website above is smooth, so something has happened to the one in the passage. See reference 2 and 3.

The rain was more or less over but the whitebeam looks oddly hazy in this snap.

I had bought some more Reeves plums from Gloucestershire from Waitrose, knocked down to £2.20  kilo. But I should have known better as they were well past their best, nothing like as good as the ones that I had bought previously. Probably the same batch, having resided in some cold room in the interval. But the courgettes from Sainsbury's, not very fresh either, visible right, were fine.

Out again later that day to start with a No.49 registration plate on a Ford Transit van, according to Carcheck, a 2020 Leader 300 DCIV. According to Bing, maybe £10,000 - with Transits appearing to lose their value with age rather quickly. Perhaps they tend to do lots of miles. I also clocked a No.28 and a No.44 - but No.39 remains missing. One day.

Followed by a medium small trolley from the M&S food hall, captured outside the T K Maxx front entrance, returned to an empty stack.

Opted for a short circuit via Hook Road, picking up this fine, late convolvulus flower on the way.

Having opted for a short circuit, not in the mood to retrace my steps, so left this one for another day - or another collector. Or perhaps I was already late for Scrabble.

Settled instead for this fine hollyhock.

PS 1: this afternoon, Microsoft News brings me notice of the piece in the Guardian at reference 4. This in the context of opening a new tab in Edge. With further reading at references 5 and 6. As ever, all much more complicated than it might at first appear, but the drift seems to be that it is reasonably likely that the north Atlantic overturning current (AMOC) will collapse before the end of the century and that this is likely to be a very bad thing for the climate here in the UK. Not to mention all kinds of other bad stuff elsewhere.

Previous outings for AMOC at reference 7 and 8 where very similar diagrams to those of today are to be found. Where I notice that an important element of the global thermohaline circulation, of which AMOC is part, is routed right through Indonesia. I have yet to find a more detailed map, but maybe the Indonesians could hold us to ransom by threatening to build some monster dam?

Next stop reference 9. From the horse's mouth.

According to Gemini. This one I will try to check up on later.

PS 2: this evening, I consulted OED (first edition), where there is a long entry for mouth and a very long entry for horse. In the former, there is talk of the mouth of a horse, in connection with a horse getting used to the bit and with a horse being sensitive to the bit, being responsive to the reins. In the latter, I can find nothing at all. In Longmans dictionary of 1984 the phrase is in, but only to be told what it means, not where it comes from. Webster's International of 1971, ditto. So not much further ahead.

Bing does rather better, turning up a website which says:

'The phrase originated around the turn of the 20th century. The earliest printed version I can find of it is from the London newspaper Reynolds Newspaper, June 1896: “As the great British nation takes far more interest in horse racing than in politics, the exchange of rulers would be delightful, because, look you, we’d get all our tips straight from the horse’s mouths, instead of being deluded and swindled every day by their lordly owners.” The colloquial use of the expression above suggests that the paper’s readers were expected to be familiar with it and earlier examples may well be found'.

From which I deduce that the phrase originated in racing circles, and sounded good without there being any very clear origin or meaning. And went on from there. Gemini was content to agree with me.

Unfortunately, while I could very probably find the piece in question at reference 10 to give the short quote above a bit of context, it might take a while and I may have to pay. Maybe tomorrow.

References

Reference 1: https://psmv5.blogspot.com/2025/08/trolleys-956-957-and-958.html.

Reference 2: https://www.halfords.com/cycling/bikes/pendleton/. 

Reference 3: https://en.wikipedia.org/wiki/Victoria_Pendleton.

Reference 4: Collapse of critical Atlantic current is no longer low-likelihood, study finds: Scientists say ‘shocking’ discovery shows rapid cuts in carbon emissions are needed to avoid catastrophic fallout - Damian Carrington, Guardian - 2025.

Reference 5: ‘We don’t know where the tipping point is’: climate expert on potential collapse of Atlantic circulation - Jonathan Watts, Guardian - 2025.

Reference 6: https://en.wikipedia.org/wiki/Atlantic_meridional_overturning_circulation.

Reference 7: https://psmv5.blogspot.com/2023/12/lisiecki-and-raymo-2005-used.html.

Reference 8: https://psmv5.blogspot.com/2021/12/tricky-business.html. Just 500 trolleys ago.

Reference 9: https://www.realclimate.org/.

Reference 10: https://www.britishnewspaperarchive.co.uk/.

Group search keys: trolleysk, 20250826.

Trolleys 956, 957 and 958

The first trolley of the day was a medium trolley from the M&S food hall, captured by the bus stop outside Enterprise, at the town end of West Hill. Distinguished from the medium small by having an extra bar around the bottom of the basket.

As can be seen from this second trolley, captured outside T K Maxx, with just the one bar. A medium small.

Various runners to be seen in town and this marker in the Kokoro Passage. The sort of running which used to be called orienteering. Perhaps it still is. There was another such marker at the bottom of the steps leading down underneath Hudson House.

Further along the High Street, a tractor with a front-loader out front and a large, hay filled trailer behind. Presumably on its way to one of the stables up on the Downs.

At the start of East Street, the repairs to the clap-board house had nearly finished. Just the roof of the  porch to attend to. Repairs which must have cost in cash terms a lot more than the house cost when it was built. The builder told me very little brick was involved in its construction, not much more than the chimneys.

Late morning by now and quite hot, so I went to the length of crossing the road and walking up the shady southside of East Street to Kiln Lane. No sunshade on this occasion.

It being a Sunday, no builders out on the flats going up at the top of Kiln Lane, but I was reminded that they are to be called Thistle Court.

Who would think that there is a Tier 1 Sainsbury's right behind? And a busy road in front? Snap lifted from reference 2.

Discover this prestigious collection of 16 meticulously designed apartments in the heart of Epsom, crafted Mac Group Ltd. These homes are a testament to high-end living, featuring contemporary interiors by Cheeca, and finished with superior specifications and attention to detail ... Ideally located, this development offers seamless connectivity with Epsom’s mainline station just 0.5 miles away and major arterial routes into London.

Neither Bing nor Google seem to know much about 'Cheeca', but Google does turn up reference 3. Misprint by the waffle generator? But probably a bit too fancy for flats in a not particularly good part of Epsom.

Down through the Screwfix passage to inspect the whitebeam. In vicinity of which I was able to pick a small number of late blackberries. Big enough and some of them were a little overripe to my taste.

Some eye-catching flowering bushes outside a house opposite the Hook Road end of Blenheim Road. Presumably fakes, but I did not get close enough to be absolutely sure.

Zoom today more or less confirms first impressions.

Picked up some neighbourly apples on the way in, some green, some red blushed. I have eaten several of these last raw and very good they were too. Fresh, crisp and sharp, quite like the James Grieve I used to like as a child and have had occasionally since, quite unlike the sort of apples presently available in the big store.

While BH had picked up a 1917 penny, an old penny that is to say, just surfaced in the flower bed outside our front wall. It must have been there quite a long time - and I can only suppose that interesting forces in our clayey soil gradually pushed it back up to the surface.

Later in the day, a second circuit produced this M&S trolley from Station Approach.

Which found a friend at the top of the Kokoro Passage. Plus a young person sitting in a shady spot, back right, above the trolley handle. I did not like to inquire.

Proceedings closed by recording the presence of this Sainsbury's special needs trolley in Stones Road. Not captured on this occasion, but marked down for another. Will it still be there? Will some passing member of the Sainsbury's team pick it up on his or her way in in the morning? I dare a decent number come across from the Longmead Estate.

PS: the white, Autumn cyclamen are coming out at the top of the garden. That is to say, at the back, near the brick compost heap. Have to stop myself saying 'down the garden' which was always where my father was when he was gardening in his back garden when I was a child, even though, in his case, the garden was quite flat, with neither up nor down.

References

Reference 1: https://psmv5.blogspot.com/2025/08/trolley-955.html.

Reference 2: https://macgroupltd.co.uk/.

Reference 3: https://checawoid.com/. 'Designing extraordinary experiences in hospitality and residential interiors is Checa Woid’s passion ... A female driven studio, designing tailor made unique spaces full of charm and identity – for hospitality spaces people will talk about tomorrow'.

Group search keys: trolleysk, 20250824.

Tuberculosis

At reference 1, I took a look at some whizzy graphics that I had come across in my travels. Today I start with a much simpler graphic, snapped above.

To give this graphic some context, tuberculosis has been around since at least the time of the cave men; was the scourge of France in Simenon’s day; carried off Molière, D. H. Lawrence, Muhammad Ali Jinnah, George Orwell and Vivien Leigh amongst many others; and, lingered on here in the UK until my own childhood in the 1950s. Still a major problem in the world at large, particularly in south Asia. It is also a major problem with cattle. One result of all of which is the huge amount of effort being put into bringing it under control.

The modern tuberculosis lineages L2-L4 account for most of the continuing & considerable disease burden, especially L4. The older L1 is mainly confined to South Asia; L7 to East Africa, possibly the original seat of the disease. Lineages L5-L9 more generally are confined to Africa, where they are important. Mycobacterium Bovis infects a range of mammals, including both humans and cattle, for which last tuberculosis is an economically important disease. Studying these lineages is an important tool in trying to deal with the tuberculosis we have now.

All this arises from trying to read reference 2, part of trying to make a bit more sense of genome sequencing – not so much why one does it but how one does it. Where Figure 1 above was all very well, but where did it come from? What did the colours mean? The size of the triangles, the lengths of the horizontal or vertical bars?

The first stop was reference 10, the paper referenced at the bottom of the snap above. But before I get into that, a bacterial digression.

M. tuberculosis

It seems that the bacteria which cause tuberculosis have been very thoroughly studied, with the central cluster being called the Mycobacterium tuberculosis complex (MTBC). Some of them specialise in humans, others in various other animals and still others can infect a variety of hosts.

Mycobacterium is a genus of over 190 species of bacteria in the group Actinobacteria, with the ‘myco’ prefix referring to their tendency to form mold like colonies. So not necessarily unicellular.

Turning to reference 4, I find that the Actinobacteria are one of fourteen groups into which the Eubacteria are divided, with the Eubacteria being one of the legs of the tripod of life, with the other two legs being the Archaea and the Eukaryotes. Viruses don’t count as being properly alive. Active or inactive, but not alive or dead.

Moving from the general to the particular, lots of things are easier in the world of genome sequencing if one has a good quality reference genome to tie one’s new sequences into. It seems that in this case the reference genome is something called H37Rv, to be found at reference 5.

Then moving forward from 1905 to just a few years ago, we have reference 6, where the abstract tells us that:

… three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100%  identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4kb additional base pairs…

So a good deal more accurate than I had thought, first in replication, organic or otherwise, These cultured bacteria much more stable than I would have thought. Second, in sequencing: perhaps clever statistics have neutralised, have tamed the messy chemistry. But I have not worked out how an assembly differs from a genome.

I have tried analysing a tuberculosis genome taken from reference 7, expressed as 5,647 genes specified in terms of start position and end position, expressed as base pair number, running from 1 to something over 4 million – leaving out of account all the non-coding data. Which is all very straightforward, much more straightforward than I would expect the much larger human genome to be. With one catch being that there is a lot of overlap, with the total length of the genes exceeding the total number of base pairs by something more than 50,000 base pairs. All this illustrated by the figure snapped above. Something appears to be wrong – quite possibly something to do with the many repeats I understand to be present.

There is a superficially simpler presentation of a similar genome at reference 8, snapped above, from more than twenty years ago. Despite which, the count agrees pretty well with that given above, if you allow for the newly added 6,500 or so base pairs. We have clearly known quite a lot about the tuberculosis genome for quite a long time.

Superficially simpler, but it would take me a good while to work out what it was all about. Not attempted and, oddly, not even tempted.

In any event, all rather different to the purple figure of the human chromosome set to be found at reference 9.

From a sequencing point of view, bacteria have the advantages that one can store them for long periods and that they are easily cultured, that is to say they replicate themselves. One does not need to go in for chemical trickery. And they are not very big, with a genome of the order of one thousandth the size of the human genome: a much more accessible object of study. On the other hand, some of them are dangerous and may only be handled in a secure laboratory.

Varieties of tuberculosis

People have been interested in the various varieties of tuberculosis bacteria for a long time. Also in the evolution of those varieties in time and their distribution in space across the world. The current story seems to be that, to some extent at least, tuberculosis bacteria evolve to work with the human genome available. To that extent, the geographic spread of the bacteria matches that of the human genome. Figure 1 from reference 2, at the top of the present post is evidence of that interest.

A figure which is primarily about lineage, about the tree structure, which, in itself, is scale free. Notwithstanding which, one supposes the vertical and horizontal scales are significant too.

[Taken from reference 10]

This figure is said to have been adapted from reference 10, so that was clearly the place to go to find out how it was put together. To find that my Figure 1 was probably some version of Figure 2 there. Where ‘L’ is for lineage.

A figure which admits more or less indefinite zoom, from which I deduced that the vertical scale is the number of samples in, for example, lineage L2. Which might, depending on the data used by the study at hand, reflect its prevalence in the population at large.

[Figure taken into Powerpoint from reference 3]

Then there is Figure 1 in reference 3, very much the same sort of thing. Furthermore, I was able to download the table of the 851 genomes involved into an Excel worksheet, where I was able to count up the various lineages.

This is snapped above. BCG is the live but feeble version of the bacillus which is the active ingredient in the widely used BCG inoculation. The ‘M’ lines in the lower half of the table are for various animal related strains of the Tuberculosis bacillus, with some of these strains having a strong preference for some particular host, for example Mycobacterium mungi for the mongoose, 

And the ratio of human to animal genomes there very roughly agreed with the corresponding vertical distances in the figure.

However, the numbers of the individual lineages in the upper half of the table did not correspond to the size of the triangles on the figure (Figure 1) that I started with.

I then found my way to the downloadable Table 1 of reference 11, possibly a more population orientated sample of genomes, resulting in the pivot table snapped above. But this did not agree very well with my starting figure either.

At this point I gave up on the vertical scale. I neglect the possibility that the vertical scale is all about geographical spread, a thought arising from the correlation of strain with geography.

The horizontal scale is about the difference between the various strains, measured by the number of single nucleotide polymorphisms – which I take to mean the number of differences between corresponding nucleotides – expressed as a ratio of the number of differences per so many base pairs: differences at the level of base pairs. Sometimes used as a proxy for time, given a steady rate of mutation.

A lot of these differences in base pairs make no appreciable difference to the bacillus. No need to invent new species or varieties.

[A zoom of the figure taken from reference 3]

We have a scale bar, no doubt meaningful to workers in the field. And maybe the long grey bar reflects the amount of change in that lineage, since it split off from the pink lineage at the left, before it split again at the right, before the amount of change or the sort of change warranted splitting the lineage. But what all the 100s are I have not been able to fathom.

The colouring of the triangles in my figure, the one I started with, has largely been lifted from the version at reference 10. Here they just for decoration, to brighten up the graphic, there they serve to better identify the clusters of interest in a busy graphic.

The left hand vertices look to be very roughly indicative of when the lineage started to branch out. 

But, leaving aside most of the animal lineages and leaving aside order down the page, we seem, at least, to have broad agreement about the tree structure of the human lineages across the three sources – just about visible in the snap above – very possibly generated by the same sort of algorithm as generated the trees decorating the graphic at the top of reference 1. The weasel words ‘simplified’ and ‘adapted’ in the caption to the left hand figure cover it.

Other odds and ends arising along the way

Deaths

Along the way I stumbled across reference 12, which, as it turned out, it was not relevant to the present inquiry. But I was struck by the figure snapped below.

Perhaps 50 million deaths here out of a total deaths for the year of 70 million, for a world population of near 8 billion. Which does not seem very many. I have not checked, but I can only suppose that most of the world’s population is very young – with only the rich countries growing old.

Google’s Gemini seems to have a very reasonable grasp of the matter, adding the idea that infant mortality continues to decline in countries with high birth rates into the mix. But without coming up with anything specific.

Note 1: ischemic heart disease is about problems arising from a narrowing or blocking of coronary arteries, in particular poor blood supply to the heart. Hypertensive heart disease is about problems arising from high blood pressure.

Note 2: you can get a very different picture if you look at individual countries. See, for example, Afghanistan at reference 13.

Data

Reference 10  explains that: ‘… Supporting external data includes sequences from studies PRJEB3334, PRJNA52007, PRJEB3223, PRJEB23179, PRJEB5162, PRJEB9680, PRJEB2138, PRJEB7727, PRJNA211633, PRJNA211637…’. 

I tried searching in Bing for ‘PRJNA211663’ and all this turned up was reference 10 itself – but at least it was able to turn the paper up on the basis of what amounted to an obscure identifier – a test of search capability used when searching large datasets was relatively new and I was involved in a procurement to buy some. I then tried ‘PRJNA211663 tuberculosis archived bacteria sample’ and that was not much better – but I did get to an interesting paper in ResearchGate, another candidate digression. On the same search term, Google offers just two results, neither of them containing the string of interest. But Gemini cracked the problem in short order, with the start of my interchange with him snapped above. He also puts me in my place: a serious person would have known without having to ask!

Bovine TB

According to Gemini, ‘if left untreated, bovine tuberculosis (bTB) in cattle is a chronic, progressive, and ultimately fatal disease’. Infected cattle can be a hazard to humans, primarily though infected milk, and the value of the carcase is much reduced. It is well worth spending serious money to keep TB in cattle down and here in the UK, as in most developed countries, infected cattle are identified and culled, usually before there are visible symptoms.

I note that it is getting very easy just to ask Gemini and to make use of what he says without checking. He is a very convenient source of convincing information and I do not catch him out in a significant way very often these days.

Famous victims

Asking the Internet for famous victims of tuberculosis proved to be a bit hit and miss, with some of those listed not checking out. Or at least only checking out to the extent of possible or probable. A reminder that one needs to be careful.

Conclusions

[copy of the figure we started with]

I conclude that the Figure 1 I started with, copied above, is intended to show a simple family tree of the human portion of the tuberculosis bacillus. M. canettii is an outgroup of the sort featured at reference 14. See also reference 15.

The vertical scale is vaguely indicative of prevalence in humans and the horizontal scale is vaguely indicative of difference between the lineages. But vague: don’t get picky about it.

Which to my data analyst turn of mind, is not really good enough. One ought to be more careful about such things. But then again, it is all too likely that my reading of reference 2 has been careless too.

I might say in passing that the standard of the Excel worksheets that I come across in this context is not high. They are there and the data is available – which is good – but the authors could have taken a bit more care with their design. Maybe thought about the likely needs of the intended user.

[BP514-14. Turned up by Google. FIG. 1. Colony morphology of the “Mycobacterium canettii” isolate on Middlebrook 7H10 agar (4 weeks old). “Mycobacterium canettii” Isolated from a Human Immunodeficiency Virus-Positive Patient: First Case Recognized in the United States - Akos Somoskovi and others - 2009]

References

Reference 1: https://psmv5.blogspot.com/2025/08/another-whizzy-graphic.html. 

Reference 2: The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions - Benjamin N. Koleske, William R. Jacobs Jr., William R. Bishai – 2023. 

Reference 3: A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex - Brites, D. et al. – 2018. 

Reference 4: The tree of life: a phylogenetic classification – Lecointre and Le Guyader – 2006.

Reference 5: https://en.wikipedia.org/wiki/H37Rv. 

Reference 6: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome – Poonam Chitale, Alexander D. Lemenze, Emily C. Fogarty, Avi Shah, Courtney Grady, Aubrey R. Odom-Mabey, W. Evan Johnson, Jason H. Yang, , A. Murat Eren, Roland Brosch, Pradeep Kumar, David Alland – 2022. 

Reference 7: https://mycobacterium.biocyc.org/. 

Reference 8: Mycobacterium tuberculosis Pathogenesis and Molecular Determinants of Virulence – Issar Smith – 2003. 

Reference 9: https://psmv5.blogspot.com/2025/06/a-cell.html. 

Reference 10: Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history – Coscolla M, et al. – 2021. Reference 60 in reference 3 above. 

Reference 11: Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies – Gary Napier, Susana Campino, Yared Merid, Markos Abebe, Yimtubezinash Woldeamanuel, Abraham Aseffa, Martin L. Hibberd, Jody Phelan, Taane G. Clark – 2020. The source of the 92 row table of lineages.

Reference 12: Global tuberculosis report – WHO – 2024. 

Reference 13: https://www.who.int/data/gho/data/themes/mortality-and-global-health-estimates/ghe-leading-causes-of-death. 

Reference 14: https://psmv5.blogspot.com/2024/05/outgroups.html. 

Reference 15: https://en.wikipedia.org/wiki/Mycobacterium_canettii.