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Saturday, 28 May 2016

Sam Weller's microscope

This is an old one that I dredged up from 2006: it never got used then, and I am trying to establish a backlog for while I go travelling, and i imagine it is now somewhat dated, but i may get one reader to run and find out. Please take that into account.

Sam Weller in Pickwick Papers spoke of the problems of seeing. "If they was a pair o' patent double million magnifyin' gas microscopes of hextra power, p'raps I might be able to see through a flight o' stairs and a deal door, but bein' only eyes, you see, my wision's limited", he declared.

As an undergraduate, I often wished we had one of Sam's microscopes, so we could look at genes, and see what the chromosomes did. This was at a time when the genetic code was just beginning to be decoded, long before anybody would think of sequencing a genome for a Ph D — something that can be done in 24 hours, these days.

The advances have been magnificent, but until now, there has been no sign that the equivalent of Sam's dreamt-of unlimited wision has escaped us. Nobody has been too surprised, because a bit of simple physics will tell you that the idea is ridiculous. Impossible, say the older and more experienced scientists.

Somebody, I think it was probably Asimov, once said something along the lines of, "If an old, respected scientist tells you something is possible, he's almost certainly right. But if an old, respected scientist tells you something is impossible, he's very likely wrong." These days, of course, we would have to eschew the gender-specific language that marks this as an old adage — but could this old adage be right?

Quite probably, where Sam's microscope is concerned. In the August 31 (2006!) issue of Nature, there was a story about using multiphoton fluorescence microscopy to watch chromosomes change their form in order to activate their genes to synthesize key proteins in fruit fly cells.

Jie Yao used MPM to make images living salivary gland tissue of Drosophila (fruit flies). Now that takes me back 40 years to crisp autumn and winter mornings in an east-facing lab, where one ripped the heads off fruit fly grubs to drag out the salivary glands, which contain massively multistranded chromosomes. These were then placed on a slide, squashed and marinated in acetic orcein — to this day, the smell of vinegar takes me back to that time.

Proust had his petites madeleines, I have maggot innards in vinegar to switch on my recollections. That is probably the least elegant contrast of the two cultures that I have ever penned before breakfast, but that's how it is, or was.

Unlike other methods, which lack penetrating power and can damage the specimen, MPM delivers crisp, clear images, even in thicker tissue samples like Drosophila salivary glands, and from here, I will rely more heavily in the account I have had from Cornell.

Whenever a cell is stressed it produces proteins that help the cell resist stress. The process is triggered by a molecule called heat shock factor (HSF), which interacts with genes to cue the synthesis of new proteins, but this well-known process had never been seen in living cells.

The polytene cells in the salivary glands, with their giant, multistranded chromosomes, have hundreds of sets of the genome instead of the usual two sets in conventional cells. This enlarges the usual nuclear dimensions by about 10 times, making them large enough to image the detail — which is why we used to squash and stain them four decades back. They are still worth looking at.

The results were stunning. "Within two weeks we had spectacular pictures," says Professor John Lis, Jie Yao's supervisor. The images included pictures of the genes (hsp70 genes) that protect flies from the effects of extreme heat. By cranking up the heat, the researchers could activate these genes, and by using fruit flies specifically bred to carry fluorescent proteins on HSF, they could watch the transcription factors in action.

"This is the first time ever that anyone has been able to see in detail, at native genes in vivo, how a transcription factor is turned on, and how it then is activated," says Watt Webb.

Thursday, 26 May 2016

Curtiosity about Art

More in Seurat than in Ingres.
— P. D. Q. Bach (1729 - 1648), Quoted by Duncan Bain in Against Contrapuntalism, a manifesto, Breek-Anathema Press, 1990.

What a delightful thing this perspective is!
— Paolo Uccello (1397 - 1475

By viewing Nature, Nature's handmaid Art,
Makes mighty things from small beginnings grow
— John Dryden (1631 - 1700

Our sight is the most perfect and delightful of our senses. It fills the mind with the largest variety of ideas, converses with its objects at the greatest distance, and continues the longest in action without being tired or satiated with its proper enjoyments.
— Joseph Addison (1672 - 1719), The Spectator, 411.

If computer art has a future as an art form in its own right, it is to be found in the dynamic, the animated, the interactive. It should look not towards Rembrandt, but towards Verdi's 'Aïda'. Not just the classical 'Aïda', but an 'Aïda' with the audience singing along and scrambling onto the backs of the elephants on stage. Chaos? No. Total theatre.
— Philip J. Davis and Reuben Hersh, Descartes' Dream, Penguin, 1990, p. 53.

I told a seemingly sane man that I got my artistic education on the Bowery, and he said 'Oh, really? So they have a school of fine arts there?'
— Stephen Crane (1870 - 1900) to James Huneker, quoted in Alfred Kazin, An American Procession, Secker and Warburg, 1985.

'There is a pleasure in painting which none but painters know.' In writing, you have to contend with the world; in painting you have only to carry on a friendly strife with Nature.
— William Hazlitt (1778 - 1830), On the Pleasure of Painting.

TEKEL: Thou art weighed in the balances, and art found wanting.
— Holy Bible, Daniel, 5:27.

Sunday, 15 May 2016

The Speewah dingoes

The dingoes out on the Speewah are smart, as well, but that's probably because they stole away a few of the Speewah dogs, seeing how clever the dingoes are these days.  Anyhow, that's my theory.  I mean, they won't take a bait however hard you try, and they seem to have a special sense that tells them when somebody's tracking them.

If you see one that knows it's being tracked, you can tell straight away, because it walks around backwards.  So all the good trackers know this, and always follow the tracks in the wrong direction.  But like I say, them dingoes are smart, and I reckon any day now, the dingoes will change around, and start going forward when they know they're being tracked.

They're big, the Speewah dingoes, and that's another reason why people think they're carrying some blood from the Speewah dogs, but it might just be the Speewah soil that helps them grow so big and healthy.  But being big, they need a lot to eat, and so while they'd eat a dozen or so sheep at a sitting, and one year, they'd started carrying away cattle, and so it was time to do something about them.

Now while these dingoes are smart, they're not as smart as the Speewah dogs, which can count to about a hundred.  A dingo, if it sees sixteen men go into a hut, and fifteen come out, is usually going to think the hut is empty, so you can get a few that way.  You send a crowd in, leave a few behind, and the rest go away, leaving a tempting little bunch of food behind to bring them in. 

Anyhow, that was the boss said that year, so he got a gang from the shearing shed together, and had us all walk down to a hut that Mick'd put together during his tea break the previous day, and the boss and three of his mates, all crack shots, stayed in the hut while everybody else walked away, all milling around and skylarking to make it harder for the dingoes to count them.  Then Mick came down with half a dozen rams under his arm, and popped them into a pen outside the hut, and walked away again.

It was coming up to a full moon that night, and the Speewah dingoes like to feed at a full moon.  More importantly, even though they would sneak through the shadows, the moonlight lit up their eyes and made them look like small lanterns.  I think they shine their eye light on the sheep and hold them with it.  Anyhow, the boss and his mates were all crack shots.  In fact, it was the same bunch that backed up Crooked Mick when he tackled the drop bears, and they reckoned they'd get a few dingoes by waiting for the glow, and then shooting between the eyes.

There were four of them lying in wait, and they all had repeating rifles, so they got six dingoes the first night, all smack between the eyes, before the rest realised what was happening and took off.  Next morning, Mick hauled them off and burnt the bodies, and the next night, they figured it was worth trying a second time.  Mick told the boss it'd be no good, that the dingoes'd have it all worked out, but the boss still reckoned it was worth a try.

So we all went down to the hut, same as the day before, but there were dingo trails all round the hut, and when we went in, the four rifles were gone, and so were the rams.  There were no two ways about it: the dingoes had taken the four guns when they came back later for a feed.  Well after a bit of discussion, everyone agreed there was no way the dingoes could shoot — or if they could shoot, they wouldn't know how to adjust for wind and range, so the shooters ought to be safe.  So the whole mob of us moved off again, and the shooters got four more rifles, we all went back to the hut again, and left the boss and his mates there again.

It was almost full moon that night, so the shooting ought to be good, they reckoned, but when the dingoes came, they opened fire, and nothing happened.  Then a cloud passed over the moon, there was a quick howl, a few sheepish noises, and when the moon came out again, there were no dingoes and no rams.  They blamed the new rifles, but when they tested them next day, there was no problem with the sights, so they decided they'd all been too nervous about dingoes shooting back, which they now agreed was quite silly.

But the next night, the same thing happened again, so the boss sent Mick out to work out what was going on.  He came back grinning, and took the boss out to look at the tracks, exactly where the boss and his mates had seen the dingoes coming in.  "There's your problem," he said.

The boss looked, and saw just one set of prints, just where his target had been.  "What's the problem then, Mick?" he asked.

Mick pointed to the prints.  "You need to shoot just outside of the pair of eyes, not between them," he said.  Then he explained the tracks, which had left paws on the right, and right paws on the left.  The dogs had come in as pairs, each using the two inside legs on each dog, and with their outside eye closed, so when the boss and his mates put a bullet between the two eyes they could see, the bullet went into empty space.

That night was the last really full moon night, and it didn't come up until late, but the boss and his mates were ready, and they got four pairs of dingoes and a couple of single ones as well, and that either wiped them out or they moved away.  But it's lucky there wasn't more of the Speewah dog intelligence in them, or they'd be taking the Speewah sheep still.

* * * * *

Note: there is a whole book of these stories, which I am currently pitching to publishers, but they will probably appear in an e-book.

There will be quite a number of these on the blog, all with the tags Speewah and Crooked Mick.

Saturday, 7 May 2016

Mystery shrouds

Find the shrouds!
A shroud is a winding sheet for a corpse to most of us, but the shrouds on a ship are part of the standing rigging, heavy, tarred ropes that hold the mast firmly down, and stop it rocking from side to side.

When jolly Jack Tars went aloft in the days of sail, they did so by clambering up light lines strung between the shrouds. Fore and aft, the masts were steadied by other items, the more sensibly-named forestays and backstays, but to port and starboard, there were just shrouds.

All of the standing rigging on a ship was made of rope, and new sailors had to learn the ropes, but in truth, there was just one rope on a ship, the bell rope. All of the other pieces of rope were called by other names: lines, halyards, cables and the sheets used to trim the sails — so there we have another word meaning a flat piece of material, given to one of the pieces of specialised rope on board. There was the rope's end, used by bosuns as a 'starter' on some ships, either because it got the sailors started, or gave them a start, or maybe because it was applied to the start, or tail area.

The word shroud comes from an old Teutonic root meaning to cut, and related to the modern word 'shred', which came from scrud in Old English. Around 1580, there was a term 'shred-pie' used for a mince pie, giving a feel for how the word was used then. It seems that the shroud was cut cloth, and so a garment, but the meaning of a winding sheet or cover for a corpse seemed to take over. By the 17th century, a shroud was a place of shelter or shade, and to shroud was to hide.

In the 18th century, a shroud came to mean other things, like the annular plates on a water wheel that formed the sides of the buckets, but these were just covers to the wheel. Today, we may know the word, but shrouds are rarer — if it doesn't come from Turin, the only shroud you are likely to see will be the casing over an aircraft engine.

In Hamlet, Ophelia sings of a shroud, as white as mountain snow, while in Henry VI, Part 3, the First Keeper suggests to his companion that they shroud themselves under a thick-grown brake, though later in the same play, Queen Margaret speaks of "shrouds and tacklings", clearly referring to standing and running rigging, and in Henry VIII, there is a reference to the noise of wind in the shrouds of a ship at sea. Juliet mentions shrouds several times as she prepares to take Friar Laurence's potion, but in The Tempest, when Trinculo comes ashore after a shipwreck, he declares "I will here shroud till the dregs of the storm be past."

This gets us no closer to the shrouds on board ship, though one doubtful suggestion is that the shrouds were shrouded in leather to stop them rubbing. In fact, the leather was more commonly on the timber yards, and Antonio Pigafetta, one of the survivors of Magellan's world trip, reveals in his account of their discomfort:

We ate biscuit which was no longer biscuit, but powder of biscuits swarming with worms, for they had eaten the good. It stank strongly of the urine of rats. We drank yellow water which had been putrid for many days. We also ate some oxhides which covered the top of the mainyard to prevent the yard from chafing the shrouds, and which had become exceedingly hard because of the sun, rain and wind. We left them in the sea for four or five days, and then placed them for a few moments on top of the embers, and so ate them . . . the gums of both the lower and upper teeth of some of our men swelled, so that they could not eat under any circumstances and therefore died.
The only shroud a sailor got was his hammock, the piece of canvas he had slept in, He was sewn into this, and slipped gently over the side, feet first, with a couple of roundshot at his feet to plummet him down past the sharks — or out of sight fast enough so that the sharks would not be seen feeding on the body.

The hammock, by the way, was a name garnered from the Spaniards, who called it a hamaca, after they adapted the Carib name for the same thing, which was hamac. But why the side stays on a ship are shrouds must remain a mystery, like the purpose of the futtock shrouds. They are the white rods sloping down and in, towards the mast, in the picture above: the rest is left as an exercise for the reader.