Author's posts
Sep 22 2011
Book review: Ingenious Pursuits by Lisa Jardine
““Ingenious Pursuits” by Lisa Jardine is the second book I have recently recovered from my shelves, first read long ago – the first being “The Lunar Men”. The book covers the late 17th and early 18th century, and is centred around members of the Royal Society in London but branching out from this group. It is divided thematically, with segues between each chapter.
My edition is illustrated with Joseph Wright of Derby’s “An experiment on a bird in the air pump”, painted in 1768. As a developing historical pedant this mismatch in dates has been irritating me!
The book opens with a chapter on Isaac Newton, the first Astronomer Royal John Flamsteed, Edmond Halley and the comet which would eventually take Halley’s name. It’s also an early example of an argument over “open data”, Flamsteed was exceedingly reluctant to give “his” data on the motions of planets to Newton to use in his calculations. Halley is pivotal in this, not so much through the scientific work he did, but through his work as a conduit between the prickly Newton and Flamsteed.
Robert Hooke features strongly in the second chapter alongside Robert Boyle; Hooke had originally been the wealthy Boyle’s pet experimenter – in particular he was operator for the “air pump”, a temperamental device for evacuating a glass vessel. The early Royal Society recognising his skills, persuaded Boyle to allow them to take him on as Curator of Experiments for the Society. Hooke was also involved with Christopher Wren in surveying London after The Great Fire, and designing many of the new buildings. In fact they also designed buildings with one eye to fitting experiments into them, particularly ones requiring a long uninterrupted drop. One sometimes gets the impression of a highly industrious Hooke implementing the vague imaginings of a series of aristocratic Society members. The constant battles with temperamental equipment will ring a bell with many a modern scientist. Robert Hooke is a central character throughout the book, Lisa Jardine has written a biography of him.
Hooke was also responsible for Micrographia a beautiful volume of images observed principally through a microscope, of insects and plants. Antonie Van Leeuwenhoek, a Dutch civil servant and microscopist also supplied his microscopic observations to the Royal Society. It’s interesting that both Leeuwenhoek and later Jan Swammerdam, both based in the Netherlands, were very keen to communicate their results to the Royal Society in London. Interactions with the academiciens in Paris were more formal with another Dutchman, Christian Huygens, a central figure in the French group. Scientific discovery was already a highly international operation.
This was a period in which serious large scale surveying was first undertaken, the French started their great national survey under Cassini. The British, under the direction of Sir Jonas Moore, set up the Royal Observatory at Greenwich, where Flamsteed was employed. Timekeeping was a part of this surveying operation. Finding the latitude, how far you are between equator and pole, is relatively straightforward; finding your longitude – where you are East-West direction is far more difficult. One strategy is to use time: the earth turns at a fixed rate and as it does the sun appears to move through the sky. You can use this behaviour to fix a local noon time: the time at which the sun reaches the highest point in the sky. If, when you measure your local noon, you can also determine what time it is at some reference point Greenwich, for example, then you can find your longitude from the difference between the two times.
To establish the time at your reference point you can either use the heavens as a clock, one method is the timing of the eclipses of the inner moon of Jupiter (Io with a period of 1.8 days), or you can use a mechanical clock. In fact it’s from observations of these eclipses that the first experimental indications of a finite speed of light were identified by Ole Rømer. In the late 17th century the mechanical clock route was starting to become plausible: the requirement is to construct a timepiece which keeps accurate time over long sea journeys, at the equator (the worst case) a degree of longitude is 60 nautical miles and is equivalent to 4 minutes in time. Christian Huygens and Robert Hooke were both producing advances in horology, and would be in (acrimonious) dispute over the invention of the spring driven clock for some time. Huygens’ introduction of the pendulum clock in 1656 produced a huge improvement in accuracy, from around 15 minutes in a day to 15 seconds following further refinement of the original mechanism.
Ultimately the mechanical clock method would win out but only in the second half of the 18th century.This astronomical navigation work was immensely important to nations such as Britain, French and the Netherlands who would even collaborate over measurements in periods when they were pretty much at war. Astronomy wasn’t funded for “wow” it was funded for “where”.
Also during this period there was a growing enthusiasm for collecting things. At the Cape of Good Hope in South Africa, Hendrik Adriaan Van Reede was to start adding more native plants to the local botanic garden on behalf of the Dutch East India Company. The Dutch built their commercial horticulture tradition in this period. In France, botany was only second to astronomy in the money it received from the Academie des Sciences. Again, plants were not collected for fun but for trade. In England Sir Hans Sloane was to start collecting; bringing chocolate back from the West Indies, which he marketed as milk chocolate, popular alongside another exotic botanical product: coffee. He was also to bring back the embalmed body of his employer for the trip, the Duke of Albemarle. Sloane was to continue collecting throughout his life, absorbing the collections of others by purchase or bequest – his collection was to go on to form the foundation of the British Museum collection. In Oxford Elias Ashmole, of Ashmolean Museum fame, was to acquire the collection of the planthunter John Tradescant under rather murky circumstances. The collectors of the time were somewhat indiscriminate and not particularly skilled at organising their rather personally driven collections. In their defence though there was no good taxonomy at the time so raw collecting was a start.
The final thematic chapter is largely about medicine, at the time medicine was in a pretty woeful state. Over the preceding years advances had been made in describing the structure of the human body and William Harvey had identified a function: the circulation of blood. However fixing it when it went wrong was not a strength at that time: surgeons “cutting for the stone” were becoming quite agile but there were few reliable drugs and a wide range of positively unhelpful practices.
The book finishes with an epilogue drawing parallels between the discovery of the structure of DNA, and the intense personal story around it, with the interactions between the people discussed previously at the heart of this book. There is also a “Cast of Characters” which provides a handy overview of the book (should I forget its contents again). Compared to The Lunar Men it is an easier read perhaps because it is more discursive around themes rather than providing great detail.
Footnote
My Evernotes on this book are here
Sep 17 2011
Photographing Chester
I’ve lived in Chester for 7 years but realised recently I have scarcely any photos of the city, so a few weeks ago I went off on a morning of indiscriminate photography using a Canon EF-S 10-22mm f3.5-4.5 on my Canon 400D. You can see the results of my labours on this and an earlier trip here.
The 10-22mm lens is a nice, very wide-angle lens but as you can see below it can produce some odd effects when used close-up to take picture of buildings. This can be seen in the picture of Chester Library shown below:
The library is housed in the old Westminster Coach and Motor Car Works, built around 1913-14 with a rather nice brick and terracotta front (see history here).
Aside from my usual problem of apparently having one leg shorter than the other, the verticals in the building converge. The “short-leg” problem can be fixed using Picasa, the aesthetic problem of converging verticals needs a different approach.
It’s worth pointing out that the image shown above is “correct” in the sense that the vertical lines of the building should converge because the top of the building is further away from the photographer than the bottom of the building. This problem is more severe when using a wide-angle lens. I want something that looks like the image below; what’s sometimes known as an “architectural projection”.
In the old days an architectural projection could be achieved using tilt-shift lenses or rather odd darkroom techniques. By the way, Cambridge in Colour, linked to for tilt-shift above is my first port of call for the mechanics of all manner of photographic things.
These days perspective corrections of this sort can be achieved using software, such as Hugin. Hugin is designed as a photostitching software but as a side-effect of this it needs to have all manner “projective geometry” knowledge. Projective geometry relates the real, 3D world to what will appear in a camera (a 2D projection of that world); it’s important in machine vision applications, computer graphics and in this sort of image processing.
The process of “correcting” converging verticals is described in a very good tutorial on the Hugin website. There is also a related perspective correction tutorial, this stops both horizontal and vertical lines from converging, this can have the effect of shifting you from an oblique view to a square on view (sort of). Applying this to my original image of the library we get this:
Which I find rather pleasing. This is Chester Town Hall, built in 1869, similarly treated:
Finally, the Blue Coat “Hospital” which was never a hospital but actually a school, it’s also a demonstration of the perspective correction pushed a little too far, something odd is going on with the dome tower. This is because the things I am applying a warp to are not all in the same plane.
It’s easy to grow familiar with a place, not realising it is a little bit special. Chester really is architecturally special although it’s at times like this I wish there was a filter for modern signage and vehicles. There are a number of black and white “timber framed” buildings, often these are “mock” dating back to the late 19th century:
Whilst others are genuinely old, such as the Bear and Billet Inn built in 1664:
The Three Old Arches is reputedly the oldest shop front in England:
And there are all manner of interesting little twiddly bits, I keep spotting more of these each time I visit now:
A load more of my photos of Chester here.
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Chester |
Sep 14 2011
Get Organised!
This is a post about how I record my research, I write it in the hope that others will reveal some of themselves and perhaps gain something from the writing. I write it because how exactly people work is something of a mystery.
This seems like something I’ve picked up slowly over many years rather than being taught it all in one big bang as an undergraduate. I suspect there may have been attempts to teach me this, but sometimes it takes getting it horribly wrong for you to learn stuff, like the importance of backing up your files.
Clearly scientific literature (including company internal reports) has always been important to my work. I wrote a little bit about scientific publication a while back (here). Generation 1 of my filing system was Windows 3.1’s Cardfile program which I used at the start of my PhD, for each paper I photocopied I typed the details onto an index card. I wrote a sequence number on the corner of each printed paper along with a couple of keywords which I also enter into whatever indexing system I’m using and filed it away in a filing cabinet, ordered by the sequence number. These days most papers are available as PDF and I file this in a directory with the sequence as the first part of the filename.
After Cardfile I moved on to Endnote, and currently I use Reference Manager which are more specialist pieces of software specifically designed for storing the details of publications and also formatting bibliographies in popular wordprocessing packages. Notes on the contents of a paper still get scribbled onto the paper copy in red ink…
These days Zotero and Mendeley both look like good free options for reference management. I haven’t switched to Zotero because it’s currently tied to the Firefox browser and I haven’t switched to Mendeley because I’m not absolutely certain what it is syncing to the Cloud and what other people can see of it there, exposing even the titles of internal company reports to outsiders is a Very Bad Thing. I also had some minor problems importing my legacy collection into Mendeley. Unlike previous iterations of such software Zotero and Mendeley both make reasonable attempts at extracting paper details from PDF files or webpages.
Stray bits of paper scribbled on at meetings I still haven’t really cracked, I try to write the date and a sequence number on any bit of paper I use, and some link to the project it relates too but this is unsatisfying. For many years I’ve considered scanning in bits of paper; our company photocopiers will e-mail scans of paper to you in PDF format and with harddisk space being so cheap now* it seems odd not to do this. All this means I still have a folder per project where bits of paper end up. And, truth be told, I still find it easier to comment on a bit of work by scribbling on a bit of paper.
I’ve started using OneNote a bit for odd note collecting, the OneNote metaphor is of a collection of notebooks, each notebook is divided into sections by tabs along the top of the page and each section is divided further into pages using tabs down the righthand side of the page. My main problem with OneNote is that it’s not possible to display your notes in date order, I seem to use it mainly for a jumping off point to other things.
My lab books have been the core of my research since I started my PhD., in my loft there’s a sequence of about 20 of them. Some of my colleagues have fantastically neat lab books with diagrams and graphs carefully sellotaped in and orderly paragraphs describing the experiments done, I never really got that well organised but I did a fair job of adding to an index at the front of each one. I still use paper lab books today but at a reduced rate. I’ve switched to a system using Microsoft Word, for each month I have have a document which looks like the one below:
I can type things in, hyperlink to other documents and cut and paste graphs and pictures as well. I use the Document Map view and, by applying appropriate styling, I get quick links to each day with a view of the keywords for the day – in this instance, designing the Death Star in AutoCAD ;-) For each year I get 12 documents which I store in a folder for that year. The thing I haven’t got working in this system is nice keyword searching across multiple years.
I’ve worked on multiple projects throughout my career and I’ve come to the conclusion that trying to separate them for the purposes of lab books and references doesn’t work too well – you end up spending time working out which lab book / file you should be adding stuff to and with decent indexing it just isn’t necessary.
These days you can buy specialised electronic lab book software, it seems it is normally done at a large scale though rather than by individual which I can’t help thinking is not a good thing since we all have individual ways of working which will vary with both the work we do and our own personal ways of doing things.
Looking at my current electronic lab book it strikes me that WordPress could be used for the task. The thing that Word can’t do easily is to give me rapid links by category or date to any part of my labbook but it strikes me that WordPress does this pretty well if you put the appropriate widgets into the sidebar. I suspect any electronic lab book software is essentially a database with a front end, for WordPress the front-end is written in PHP. The benefit of WordPress is that it’s very widely used, with lots of plugins to provide new functionality and extending it is within the reach of most programmers.
Here endeth the world’s dullest blog post, comments on your own “ways of working” are most welcome!
*Except if you’re in a corporate environment, in which case the laws of every decreasing disk space cost seem to work differently.
Sep 10 2011
Don’t call me scum*
Scum. Goodbye NHS. Goodbye Lib Dems. RT
@skynewsbreak: MPs vote in favour of NHS reforms by a majority of 65
This was retweeted on timeline by a number of people on twitter on Wednesday last. As a Liberal Democrat this upsets me, I take it personally. According to Ben Goldacre, Evan Harris is okay, “good scum” presumably – the rest of us have obtained no exemption.
At roughly the same time my twitter feed was full of people decrying Ken Clarke for describing the rioters as a “feral underclass”, not so many were bothered about me being referred to as scum. Clarke had a point but he made it poorly. His point was that what we should be concerned that 75% of the rioters were already known to the police, our justice system had failed to rehabilitate them. It’s a useful example though: if you use language which offends you’ll find people will ignore your argument, assuming you simply don’t have one.
Interestingly Tony Blair was on the radio this morning, a man that lied in order to take us into war in Iraq and stood by as the country disintegrated, unwilling to persuade the US of the critical need for a post-war recovery plan. People on my timeline were upset but no one called him scum.
*It’s a reference to that fine film, Barb Wire.
Sep 10 2011
Medical ultrasound imaging
Alert readers will remember that I am in the process of becoming a father, and that the occasion of this announcement was the "dating scan" (Codename Beetle). In the UK, at least, this is an ultrasound scan targeted to take place at about 12 weeks pregnancy with a view to getting a more precise estimate of birth date from the size of the fetus, measured from “crown” to “rump”. Alongside this a nuchal fold measurement may be made to help test for Down’s Syndrome, it turns out this requires a cooperative fetus willing to assume just the right posture, Beetle wasn’t!
From a scientific point of view this is all really interesting: you can see inside people! In this instance, my wife.
The inside of a human is largely squidgy but different parts have different squidginess, in particular there is a nice contrast between the muscular wall of the womb and the liquid contents and again between the liquid contents of the womb and the fetus. Ultrasound is reflected when there are interfaces between things of different squidginess. There’s a direct analogy between this squidginess and the “impedance” of electrical components in things like hifi equipment, and the transmission of sound waves and the transmission of radio waves.
The scan starts off with the operator squirting generous quantities of lubricant onto the wife’s belly (in a hospital environment this gives me flashbacks to the Unexpected Prostate Examination Incident). The lubricant is to give good “impedance matching” between the ultrasound scanner and the swollen belly of the wife, without it the sound bouncing off the skin surface would be all you heard.
To build up an ultrasound image we listen for echoes. The ultrasound probe lets out a squeak and waits for echoes, the time taken for the echo to arrive tells you how far away the thing that created the echo. This is really obvious in the earliest ultrasound devices which worked in what is know as “A-mode”: sending out a single beam of sound in one direction and recording the sound that came back as a function of time. Typical data* shown below.
The echo marked A represents a structure closer to the surface than the echo marked B.
You can build up a proper image by scanning your beam of sound backwards and forwards to map out a fan, this is known as “B-mode” and is the type of imaging you will be most familiar with, the image at the top of the page is an example. It shows a vertical fan-shaped slice into the body, with features at the bottom of the scan further from the surface than those at the top.
In the old days moving the beam backwards and forwards was a mechanical process but modern scanners do it electronically with no moving parts. This is done with a “phased array” similar to those used in radar systems; a line of transmitters is fed signals with different phases (the sinusoidal sound waves are offset in time by different amounts) the result of this is a sound beam that can be steered backwards and forwards without physically moving any parts.
These days you can even get “4D” scans done. These use a square (2D) array of emitters to scan rapidly over an area, getting the third dimensions from the echo time and a fourth (time) dimension by being able to repeat the process rapidly. These scans are converted to a moving 3D surface (or “baby”) by thresholding the 3D data set and using computer graphics techniques to produce nice graphics. I must admit I find these images a bit creepy (the one on the right is not Beetle). Given my experience of image analysis, extracting a neat surface from the noisy data, in real time, is pretty tricky.
If I’d been paying attention I could probably have read the name of the particular ultrasound scanner used on my wife, but I had other things on my mind. As it was I could identify it because there’s an interesting looking coding on the sonograph (RAB-4-8L/0B) which turns out to be the serial number of a detector for the General Electric Voluson 730 devices. A quick bit of googling reveals a convincing looking image of the scanner, they cost something in the range £20k-£40k.
Ultrasound imaging utilises sound in the frequency range 2-18MHz although for the probe used for Mrs S’s scan the range is 4-8MHz wavelengths for such waves are 0.2-0.3mm which will be the maximum achievable spatial resolution. The lowest of these ultrasound frequencies is 100 times higher than the upper limit of human hearing at 20kHz, and 10 times higher than those used by bats and dolphins.
The velocity of sound waves in water is 1540m/s, for the purposes of this calculation humans are approximately water, the raster rate (speed at which the sound beam goes backwards and forwards) appears to have been 18Hz or once every 1/18th of a second). Given the speed of sound in Mrs S, we could actually image many metres into her – if required. This suggests that the speed sound is not a limiting factor in how fast we can do scans: the noise in the signal is the limiting factor. That’s to say the strength of the echoes we get back is rather weak and looking at the images they are mixed with a lot of noise.
Ultrasound machines are really rather high technology bits of kit, containing lots of interesting physics. I must admit having read up a bit – I want one to play with!
*”Typical data”, in scientific terms means “I’m going to claim this is typical but actually this is the best we collected”.