Continue reading »]]> It is customary to write reviews of things when they are fresh and new. This blog post is a little different in the sense that it is a review of 3 years of electronic book usage.

My entry to e-books was with the Kindle: a beautiful, crisp display, fantastic battery life but with a user interface which lagged behind smartphones of the time. More recently I have bought a Nexus 7 tablet on which I use the Kindle app, and very occasionally use my phone to read.

Primarily my reading on the Kindle has been fiction with a little modern politics, and the odd book on technology. I have tried non-fiction a couple of times but have been disappointed (the illustrations come out poorly). Fiction works well because there are just words, you start reading at the beginning of the book and carry on to the end in a linear fashion. The only real issue I’ve had is that sometimes, with multiple devices and careless clicking it’s possible to lose your place; I found this more of a problem than with a physical book. My physical books I bookmark with railtickets, very occasionally they fall out but then I have a rough memory of where they were in the book via the depth axis, and flicking rapidly through a book is easy (i.e. pages per second) – the glimpse of chapter start, the layout of paragraphs is enough to let you know where you are.

There are other times when the lack of a physical presence is galling: my house is full of books, many have migrated to the loft on the arrival of Thomas, my now-toddling son. But many still remain, visible to visitors. Slightly shamefaced I admit to a certain pretention in my retention policy: Ulysses found shelf space for many years whilst science fiction and fantasy made a rapid exit. Nonfiction is generally kept. Books tell you of a persons interests, and form an ad hoc lending library. In the same way as there beaver’s dam is part of its extended phenotype, my books are part of mine. With ebooks we largely lose this display function, I can publish my reading on services like Shelfari but this is not the same a books on shelves. The same applies for train reading, with a physical book readers can see what each other is reading.

Another missing aspect of physicality, I’ve read Reamde by Neal Stephenson a book of a thousand pages, and JavaScript: the Good Parts by Douglas Crockford, only a hundred and fifty or so. The Kindle was the same size for both books! Really it needs some sort of inflatable bladder which inflates to match the number of pages in the book, perhaps deflating as you made your way through the book.

Regular readers of this blog will know I blog what I read, at least for non-fiction. My scheme for this is to read, taking notes in Evernote. This doesn’t work so well on  either the Kindle or Kindle app, too much switching between apps. But the Kindle has a notes and highlighting! I hear you say. Yes, it does but it would appear digital rights management (DRM) has reduced its functionality – I can’t share my notes easily and, if your book is stored as a personal document because it didn’t come from the Kindle store then you can’t even share notes across devices. This is a DRM issue because I suspect functionality is limited because without limits you could simply highlight a whole book, or perhaps copy and paste it. And obviously I can’t lend my ebook in the same way as I lend my physical books, or even donate them to charity when I’m finished with them.

This isn’t to say ebooks aren’t really useful – I can take plenty of books on holiday to read without filling my luggage, and I can get them at the last minute. I have a morbid fear of Running Out of Things To Read, which is assuaged by my ebook. In my experience, technology books at the cheaper / lower volume end of the market are also better electronically (and actually the ones I’ve read are relatively unencumbered by DRM), i.e. they come in colour whilst their physical counterparts do not.

Overall verdict: you can pack a lot of fiction onto an ebook but I’ve been using physical books for 40 years and humans have been using them for thousands of years and it shows!

Continue reading »]]> A rapid change of gear for my book reviewing: having spent several months reading “The Eighth Day of Creation” I have completed “The Dinosaur Hunters” by Deborah Cadbury in only a couple of weeks. Is this a bad thing? Yes, and no – it’s been nice to read a book that rattles along at a good pace, is gripping and doesn’t have me leaping to make notes at every page – the downside is that I feel I have consumed a literary snack rather than a meal.

The Dinosaur Hunters covers the initial elucidation of the nature of large animal fossils, principally of dinosaurs, from around the beginning of the 19th century to just after the publication of Darwin’s “Origin of the Species” in 1859. The book is centred around Gideon Mantell (1790-1852) who first described the Iguanodon and was an expert in the geology of the Weald, at the same time running a thriving medical practice in his home town of Lewes. Playing the part of Mantell’s nemesis is Richard Owen (1804-1892), who formally described the group of species, the Dinosauria, and was to be the driving force in the founding of the Natural History Museum in the later years of the 19th century. Smaller parts are played by Mary Anning (1799-1847), fossil collector based in Lyme Regis; William Buckland (1784-1856) who described Megalosaurus – the first of the dinosaurs and spent much of his life trying to reconcile his Christian faith with new geological findings; George Cuvier (1769-1832) the noted French anatomist who related fossil anatomy to modern animal anatomy and identified the existence of extinctions (although he was a catastrophist who saw this as evidence of different epochs of extinction rather than a side effect of evolution); Charles Lyell (1897-1875) a champion of uniformitarianism (the idea that the modern geology is the result of processes visible today continuing over great amounts of time); Charles Darwin (1809-1882) who really needs no introduction, and Thomas Huxley (1825-1895) a muscular proponent of Darwin’s evolutionary theory.

For me a recurring theme was that of privilege and power in science, often this is portrayed as something which disadvantaged women but in this case Mantell is something of a victim too, as was William Smith as described in “The Map that Changed the World”. Mantell was desperate for recognition but held back by his full-time profession as a doctor in a minor town and his faith that his ability would lead automatically to recognition. Owen, on the other hand, with similar background (and prodigious ability) went first to St Bartholomew’s hospital and then the Royal College of Surgeon’s where he appears to have received better patronage but in addition was also brutal and calculating in his ambition. Ultimately Owen over-reached himself in his scheming, and although he satisfied his desire to create a Natural History Museum, in death he left little personal legacy – his ability trumped by his dishonesty in trying to obliterate his opponents.

From a scientific point of view the thread of the book is from the growing understanding of stratigraphy i.e. the consistent sequence of rock deposits through Great Britain and into Europe; the discovery of large fossil animals which had no modern equivalent; the discovery of an increasing range of these prehistoric remnants each with their place in the stratigraphy and the synthesis of these discoveries in Darwin’s theory of evolution. Progress in the intermediate discovery of fossils was slow because in contrast to the the early fossils of marine species such as icthyosaurus and plesiosaurus which were discovered substantially intact later fossils of large land animals were found fragmented in Southern England, which made identifying the overall size of such species and even the numbers of species present in your pile of fossils difficult.

These scientific discoveries collided with a social thread which saw the clergy deeply involved in scientific discovery at the beginning, becoming increasingly discomforted with the account of the genesis of life in Scripture being incompatible with the findings in the stone. This ties in with a scientific community trying to make their discoveries compatible with Scripture and what they perceived to be the will of God with the schism between the two eventually coming to a head by the publication of Darwin’s Origin of Species.

Occasionally the author drops into a bit of first person narration which I must admit to finding a bit grating, perhaps because for people long dead it is largely inference. I’d have been very happy to have chosen this book for a long journey or a holiday, I liked the wider focus on a story rather than an individual.

References

My Evernotes

Continue reading »]]> My reading moves seamlessly from the origins of cosmology (in Koestler’s Sleepwalkers) to the origins of molecular biology in “The Eighth Day of Creation” by Horace Freeland Judson. The book covers the revolution in biology starting with the elucidation of the structure of DNA through to how this leads to the synthesis, by organisms, of proteins – this covers a period from just before the Second World War to the early 1960s although in the Epilogue and Afterwords. Judson comments on the period up to the mid-nineties. Although the book does provide basic information on the core concepts (What is DNA? What is a protein?), I suspect it requires a degree of familiarity with these ideas to make much sense on a casual reading – the same applies to this blog post.

The first third or so of the book covers the elucidation of the structure of DNA. Three groups were working on this problem – that of Linus Pauling in the US, Franklin and Wilkins at Kings College in London and Crick and Watson in Cambridge. Key to the success of Crick and Watson was their collaboration: a willingness to talk to people who knew stuff they needed to know, and piecing the bits together. The structural features of their model were the helix form (this wasn’t news), specific and strong hydrogen bonding between bases, and the presence of two DNA chains (running in opposite directions). On the whole this wasn’t a new story to me, although I wasn’t familiar with the surrounding work which established DNA as the genetic material. Judson returns to the part Rosalind Franklin in the discovery in one of the Afterwords. It has been said that Franklin was greatly wronged over the discovery of DNA, but Judson does not hold this view and I tend to agree with him. The core of the problem is that the Nobel Prize is not awarded posthumously, and with her death at 37 from cancer, Franklin therefore missed out. Watson’s book The Double Helix was a rather personalised view of the characters involved most of whom were alive to carry out damage limitation, whilst Franklin was not – so here she was poorly treated but by Watson rather than a whole community of scientists. Perhaps the thing that said the most to me about the situation is that after she was diagnosed with cancer she stayed with Cricks at their home.

In parallel with the elucidation of the structure of the DNA work had been ongoing with understanding protein synthesis and genetics in viruses and bacteria. This included both how information was coded into DNA, with much effort expended in trying to establish overlapping codes. There are 20 amino acids and four bases in DNA, so three base pairs are required to specify an amino acid if the amino acid sequence is to be unconstrained but it was conceivable that two consecutive amino acids are coded by fewer than 6 base pairs but in this case there is a restriction on the possible amino acid sequences. This area was initiated by the physicist, George Gamow. I struggle a bit to see how it gained so much traction, this type of model was quickly ruled out by consideration of the amino acid sequences that we being established for proteins at the time. It turns out that amino acids are coded by three consecutive base pairs with redundancy (so several different base pair triplets code for the same amino acid). Also covered was the mechanism by which data passed from DNA to the ribosomes where protein synthesis takes place, important here are adaptor molecules which carry the appropriate amino acid to the site of synthesis.

Compared to the structure of DNA this work was a long difficult slog, involving intricate experiments with bacteria, bacteriophage viruses, bacterial sex, ultracentrifugation, chromatography and radiolabelling.

The final part of the book is on the elucidation of the structure of proteins, this was done using x-ray crystallography with the very first clear scattering patterns measured in the 1930s and the first full elucidation made in the late fifties. X-ray crystallography of proteins, containing many thousands of atoms is challenging. Fundamentally there is a issue, the “phase problem”, which means you don’t have quite enough information to determine the structure from the scattering pattern. This issue was resolved by heavy atom labelling, here you try to chemically attach a heavy atom such as mercury to your protein then compare the scattering pattern of this modified protein with that of the unmodified protein, which resolves the phase problem. Nowadays measuring the thousands of spots in an x-ray scattering pattern and carrying out the thousands and thousands of calculations required to resolve the structure is relatively straightforward but in the early days it was a massive manual labour.

As well as resolving structure a key discovery was made regarding the mode of action of proteins: essentially they work as adaptors between chemical distinct systems – when a molecule binds to one site on a protein it effects the ability of another type of molecule to bind to another site on the protein through changes in the protein structure induced by the first molecule’s binding. This feature opens up huge possibilities for cell biology – in the absence of this feature interactions between chemical systems can only occur if the participants in those systems interact with each other chemically.

It isn’t something I’d really appreciated properly but molecular biologists are quite organised in the organisms that they generally agree to work on. The truth is that there are uncountably many viruses and so to aid the progress of science one needs to select which ones to study: E. Coli, the T series bacteriophages, C. Elegans, D. Melanogaster and more recently the zebrafish, they almost play the part of an extra author.

Molecular biology was apparently dominated by physicists, I must admit I found this confusing in the past but Judson highlights the field as defined by its practioners: biochemistry is about energy and matter (and typically small molecules), molecular biology is about information (and typically macromolecules) – a more natural home for physicists.

I found the first and third parts an enjoyable read, my scientific background is in scattering so the technical material was at least familiar the central section on genetics I found fascinating but a bit of a slog. I’m somewhat in awe of the complexity of the experiments (and their apparent difficulty).

Looking back on my earlier book reviews, I read my comment on R.J. Evan’s book on historiography that history is a literary exercise as well as anything else, as a trained scientist this was something of an alien concept but in common with Koestler’s book the style of this book shines through.

Footnotes

My Evernotes

Continue reading »]]>

I thought I’d mix together a review of my shiny new laptop (a Sony Vaio T13) with one of Windows 8 which came pre-installed on the laptop.

The laptop

Six years after buying my last laptop I have replaced it with another Sony Vaio. At the time I bought the first one I didn’t think I would do this, my old Sony Vaio (VGN-SZ2M) is a nice machine but it was infested with Sony cruftware which added little functionality and what it did try to add didn’t seem to work and  the couriers Sony selected left it with a neighbour without asking whether this was appropriate. It had a weird black plastic finish which was probably described as "carbon fibre". It’s worked fine although I found the 80GB hard disk a little cramped and as the years went by it felt slower and slower when compared to the other machines I use.

After poking around extensively I finally decided on another Sony Vaio, other contenders were the Lenovo Yoga 13 (limited availability and would that hinge really hold out?), the Acer Aspire S7 (more pricey for a poorer config and apparently no option for a big conventional drive) and offerings from Samsung, Toshiba and Dell – the bar for being a contender in this limited set was the touchscreen. I did look at non-touchscreen variants too and particularly liked the look of the Lenovo IdeaPad U410.

Having decided, I bought direct from Sony getting to get a bit more configuration flexibility adding 8GB RAM, an i7 processor and going for the 32GB SSD/500GB conventional hard drive combination, this is an ultrabook class laptop with a 13.3" touchscreen, no optical drive, and Windows 8. I liked the idea of getting a pure SSD system but the price Sony charges for the upgrade is about double the price of the highly regarded Samsung 840 Pro series SSDs so maybe I’ll be opening the thing up soon. It weighs 1.5kg which is light but not the lightest in this class, I decided on a touchscreen since it didn’t seem to add hugely to the cost and it isn’t something you can retrofit should the desire arise.

It is a very beautiful thing: brushed metal with chromed highlights, and in its pristine state it comes out of hibernate very quickly.

Compared to my old laptop it has the same footprint, unsurprising since the screen is the same size. The keyboard is narrower though, losing a column of keys, but the device is about half the thickness  – having lost the optical drive.

I worried a little about the monolithic touchpad with no separate left and right mouse buttons but it has a positive click in these two locations so I’ve not noticed the lack of separate buttons.

The screen resolution may be a little deficient (1366×768) but it is comparable with most of the laptops in its class and I intend using it on an external monitor anyway.

There is a small infestation of cruftware, featuring an update centre which seems to struggle to provide the necessary bandwith and an update-able electronic manual which I can’t seem to get hold of because the instructions for downloading it take you around in a loop.

As if in pique my old desktop PC failed shortly after I got the new Vaio so I’m using it as my sole computer for now, this works fine except it is a pain to install CD based software for various bits of hardware (quite why my video camera shipped with 4 CDs of software I don’t understand).

So overall – the Sony Vaio gets an A, a tick or some number of stars between 5 and 10.

Windows 8

I have a bit of a habit for getting computers with brand new Microsoft operating systems, although fortunately I skipped Windows Vista. Windows 8 takes a bit of getting used to, the best way of thinking about it is as Windows 7 with a mobile phone interface dropped on top of it. This is both good and bad. Personally I rather like Windows 7, and I’m also rather pleased with the Android-based touchscreen interface on my HTC Desire phone but the combination of the two is a bit disturbing.

Actually "a bit disturbing" is wrong "crap" would be better, the new style apps follow very different UI rules from conventional Windows apps and major in form over content – for example the pre-installed twitter app, although pretty and swooshy with the touchscreen is utterly useless as a twitter client. Not only does it have limited functionality but in order to view anything but the briefest of timelines you need to flap your arm about like a deranged semaphorist. The twitter app from twitter is marginally more functional but looks like the portrait aspect ratio phone screen placed in the middle of a wide laptop screen. Comparing my Android phone and tablet it strikes me few people have cracked scaling apps from phone to tablet size screens, let alone all the way to laptop screen sizes.

Live tiles offer interesting possibilities but they are constrained to one of two sizes, and I’ve yet to find one which does anything particularly interesting.

Microsoft is very keen for developers to write the mobile phone style apps, at one point the (free) Express version of Visual Studio was only going to allow developers to target the mobile phone style apps.

The only real redeeming feature of the new Windows 8 additions is that, once you’ve accepted the concept, the Start screen is better than the old Start button.

Not so long ago I would have "struck down upon thee with great vengeance and furious anger those who" touched the screen of any device I owned, these days I’m a little bit more relaxed: I find the touchscreen a nice adjunct to more conventional input but I have a smeary screen now.

It seems to me there are a limited number of things you need to "get" about an operating system in order to use it with a peaceful mind, for Windows 7 a big one was that you didn’t need to go stumbling through a cascade of entries in the Start menu – you just start typing the name of your desired application into the search box and it was revealed fairly promptly. Start typing when you are on the Windows 8 Start screen and you launch just such a search – how the hell you’re supposed to know this is a mystery to me. And this seems like one of the core problems with Windows 8 – there are some nice little interface features but there’s no way you would guess they were there or find them by accident.

Windows 8 is keen for you to login using a Microsoft account, it is possible to just use a local account but I thought “in for a penny, in for a pound” and went ahead and set one up. Interestingly you can see the benefit of this approach when using Google Chrome, when I installed Chrome it automatically installed the plugins I have on other PCs, my autocorrect settings and so forth – instantly I was at home. I guess this is the longer term plan for Windows 8. It also wants me to have an xbox account to buy music and video.

Some hints for new users of Windows 8:

• To shift tiles around on the Start page, hold them and drag then up or down initially (not left-right), to zoom out drag them towards the bottom of the screen;
• If you use Google Chrome as your default browser the title bar icons (minimise, maximise and close) disappear, to fix this don’t use it as your default browser;
• There exist both new style and old style applications, some things are available in both formats, for example Dropbox. The new-style apps resemble phone apps but offer limited functionality;
• New-style apps don’t have an "exit" button, simply navigate away from them as you would a phone app;
• The Start screen replaces the Start menu on the old Windows 7 desktop, to search for anything just start typing!
• Windows 8 style apps cannot play MPEG2 files, this is only available for Windows 8 Pro with added Windows Media Centre. Windows Media Player will play them (suitable codecs installed – I used Shark007) and VLC player works fine.

On the last item: this seems a bit bonkers – the video app on the mobile-style interface can see your video library perhaps containing an unrelenting series of videos of your growing child which will almost inevitably be in MPEG2 format as a default so crippling this functionality seems a bit stupid.

Bottom line: Windows 8 is very pretty and the Start screen is, in my view, better than the old Windows 7 Start menu once you’ve got your head around it. The idea of putting a mobile phone interface, with mobile phone style apps, on top of a desktop interface is stupid – my opinion on this may change if I see some apps that are optimised for laptops. Mobile interfaces such as iOS and Android are optimised for consumption which is fine, but many people will still be getting PC class devices to do “work” and for the main the new mobile interface in Windows 8 gets in the way of that.

And now to install Ubuntu on it… a process so exciting I have made it the subject of a second blog post.

Continue reading »]]> I wanted to dual boot my new Sony Vaio T13 laptop with Windows 8 and Ubuntu 12.10, as it turned out I found it challenging to setup a true dual boot but I have a satisfactory solution.

This process is not straightforward because the T13 uses the Insyde H2O UEFI instead of a old-style BIOS furthermore since  Windows 8 was pre-installed SecureBoot is switched on, these factors mean that only the most recent, 64-bit version of Ubuntu (12.10) has any chance of installing. Also the T13 has no optical drive so I would need to boot from a USB memory stick.

I’ve installed various Linux distributions over the years but they tend not to be my primary OS, I considered three methods for this operation.

Method 1 – install using Wubi

The Wubi installer is a way of installing a Linux distribution effectively as an application in Windows but apparently this doesn’t work because of incompatibilities in with UEFI. I’ve used Wubi in the past – I like it because it reduces the chances of me rendering my Windows install inoperative via a partitioning mistake.

Method 2 – conventional dual boot installation

As of the 64-bit 12.10 version of Ubuntu it should be possible to do a fairly conventional dual boot installation of Ubuntu onto a machine preloaded with Windows 8. The instructions for this are here, essentially they are:

1. Download the appropriate ISO

2. Transfer the ISO to a USB stick using Universal USB Installer

3. Boot from the USB stick (Shift-restart in Windows 8 gives you lots of options for the necessary fiddling to achieve this)  and follow the installation instructions (here).

However when I did this I kept getting this error:

(initramfs) unable to find a medium containing a live file system.

This error persisted through various combinations of enabled/disabled SecureBoot and boot orderings. I don’t know why this doesn’t work, I suspect that the Universal USB Installer is not creating an appropriate boot device perhaps if I flagged the USB drive as legacy rather than UEFI it might work. I was feeling slightly nervous about this because there were some indications (here) that if I had succeeded in producing a new disk partition for Ubuntu then I may have lost my Windows partition! Doing clean installs of both Windows 8 and Ubuntu onto a machine looks like it might be a bit simper (here).

Maybe I should have followed the instructions here, the trick seems to be to create your Ubuntu partition using Windows 8 rather than trying to do it with the Ubuntu installer.

In some ways the problem here is finding an excess of instructions!

Method 3 – install on a virtual machine

Following a suggest on twitter my third method was to try installing Ubuntu onto a virtual machine inside Windows 8, if I’d have splashed out on Windows 8 Pro then I could have used Hyper-V as my virtual machine. However, I’m using VirtualBox. The instructions for installing Ubuntu inside VirtualBox  are here, I switched on hardware virtualization support which was disabled by default.

This worked pretty smoothly, you don’t even need to produce a USB stick from which to boot, simply mount the ISO you downloaded as a virtual optical drive in VirtualBox. After initial installation Ubuntu was rather slow and unresponsive, I think this might have been due to downloading updates but I’m not sure. The only problem was that Ubuntu inside the VirtualBox couldn’t display at full screen resolution. This problem should be fixed by installing “Guest Additions” – this is software that lives on the guest operating system (the one inside the VirtualBox) and helps it interface with the host operating system. You can install the Guest Additions from an ISO image supplied with VirtualBox, the instructions for this are here. I failed to do this by not reading the instructions, in particular I didn’t install Dynamic Kernel Module Support (DKMS) properly. This was a recoverable mistake though, I learnt here that I needed to do this commandline first:

sudo apt-get install build-essential linux-headers-$(uname -r)

and then I re-installed using this commandline:

sudo apt-get install virtualbox-guest-utils

And it worked nicely on rebooting the virtual machine. So now I have Ubuntu 12.10 running in a VirtualBox inside Windows 8 aside from a hint of the VirtualBox menu bar at the bottom of the screen I could just as well be dual booting. Theoretically I might experience reduced performance by not running Ubuntu natively but I have 8GB of RAM in my laptop and an i7 processor so I suspect this won’t be an issue.

Now my eyes have been opened to the magic of virtual machines I want to install more! Sadly Apple’s OS X is not supported for such ventures.

I don’t claim to be an expert in this sort of thing so any comments on my understanding and technique are welcome!

Continue reading »]]> It has become a tradition for me to review my posts at the end of each year, OK I’ve done it twice before and now I find myself sounding like a teenage diarist.

Clearly the main event of this year has been The Arrival; Thomas was born on 4th February, as I write he is systematically throwing all his books on the floor whilst muttering to himself, it is 6am. I haven’t written much about Thomas but he fills my real life, looking after a small child is very much like conducting an experiment at a central facility.

I’ve managed to keep reading although at a somewhat reduced rate. I read about geodesy in “The Great Arc” and “Measure of the Earth”, both tales of considerable derring-do conducted in the jungles of India and Ecuador respectively. I read about scientific instruments, in Stargazers, “Decoding the Heavens”, "A computer called Leo" and "The History of Clocks & Watches". The subjects of the last two of these are obvious, the first is on telescopes and the second on the Antikythera mechanism, an astoundingly complex mechanical model of the heavens. I read about Alan Turing, Christiaan Huygens and Benjamin Franklin.

If I was forced to pick a favourite book I think I would go for Arthur Koestler’s "The Sleepwalkers" which traces the development of cosmology from the ancient Greeks to Isaac Newton with its focus on the journey from Copernicus, still obsessed with celestial circles, to Kepler who started to sound like a modern physicist. Keplers’ attempts to identify elliptic orbits takes on a pantomime air at some points… “They’re right in front of you!”. Or perhaps my favourite should be Stargazers since after reading this I bought a telescope – more of which below.

Slightly more miscellaneously I read Tim Harford’s "Adapt" about trial and error as an approach to public policy and management, "The Geek Manifesto" on science and politics and "The Etymologicon" – a casual journey through where words come from. Finally, I also read "Visualize This", capturing the essence of my data twiddling and cluing me into tidying up my plots using Inkscape (or Adobe Illustrator if you have the cash).

Another new thing this year was a telescope, rather than appear some sort of dedicated follower of fashion, rushing out to buy one in the wake of a celebrity astronomonothon, I delayed until May. This turned out to be a bad idea: it doesn’t get properly dark until two hours after sunset and starts to get light two hours before dawn difficult at the best of times, impossible when combined with childcare responsibilities. Consequently I got little star viewing action for quite some time, except for the Sun. My telescope review post (including video) was my most read post of the year. It has been magical though, my first view of Saturn with its rings had me hopping up and down like a small child! More recently I got Jupiter and the four moons discovered by Galileo. I’m still trying for a deep sky object, I don’t count my pictures of the whole Milky Way taken through a normal camera lens.

Not much else in the way of photography this year, obviously I have an enormous collection of photos of Thomas but I won’t bore you with them but I’ll say to expecting parents who are also keen photographers that a 50mm f/1.4 lens is ideal for photographing small children since you are often indoors operating in relatively low light. I also took some pictures of Chester Cathedral, Beeston Castle and in the area of Harlech, where we took our first holiday with Thomas.

I did a little bit of fiddling with data this year, plotting the spending of the Board of Longitude, finding that they did a great deal to support John Harrison through his life, and looking at how quarterly GDP growth figures are revised – basically they’re all over the place!

I also pottered around a little with science policy and politics. “I am Dr Faustus” was an oft-read post, in which I disagreed with Ananyo Bhattacharya’s assertion that basic research in the UK had been corrupted by the idea of showing some application. “GCSE results through the ages” also got a lot of hits, it showed the changes in grades for GCSE and A levels over the years. 

And as the year came to an end I handed in my notice to go to a new job – starting in March. I used some of my blog posts in support of my application!

Continue reading »]]> Another result of my plea for reading suggestions on twitter; this is a review and summary of Arthur Koestler’s book “The Sleepwalkers: A History of Man’s Changing Vision of the Universe”. The book is a history of cosmology running from Pythagoras, in the 6th century BC, to Galileo who spanned the end of the 16th century, just touching lightly on Newton. It traces a revolution from a time when the cosmos, beyond the earth, was considered different, stable and perfect, to a time when it was shown to be subject to earthly physics, be changeable and not perfect by any reasonable definition.

Kuhn’s language of paradigm shifts seems rather overused to me but here is an example of a true paradigm shift. The sleepwalkers in the title refers to the idea that the protagonists didn’t really know where they were headed with their ideas and quite often were lucky with errors which cancelled each other out.

The book starts with a cursory look at Babylonian and early Greek astronomy; despite considerable observational acumen their models of the universe were outright mythical. The Pythagoranean Brotherhood although in many senses still mystical started to think about the physics of the universe. I have a tendency to think of the ancient Greeks as one blob but as the book makes clear there is a huge span of time, and outlook, between Pythagoras, Aristotle and Plato and Ptolemy. Koestler is quite clearly disappointed with the Greeks: they make a promising start with Pythagoras, Aristarchus developed a heliocentric model for the solar system and then with Plato, Aristotle and Ptolemy they regress back to a geocentric model.

Following on from the Greeks the Middle Ages are covered, James Hannam in his book “God’s Philosophers” has covered why this period wasn’t all that bad in terms of intellectual development. Koestler is less sympathetic, his key accusations are that they philosophers of the middle ages were in thrall to the later Greeks and furthermore there were elements of Christian theology that abjured the pleasure of knowledge for knowledge’s sake.

After these preliminaries, Koestler turns to the core of his work: the cosmological developments of Copernicus, Tycho Brahe, Johannes Kepler and Galileo Galilei.

The model of the universe handed down from the ancient Greeks was one of circles (often referred to in this context as epicycles), they believed that motion in a circle was perfect, that the heavens were a separate, perfect realm and that therefore all motion in the heavens must be based on circular motion. Further, the model dominating at the end of their period, held that the earth lay at the centre of these circular motions. The only problem with this model is that it doesn’t fit well the observed motions of the sun, moon, Mercury, Venus, Mars, Jupiter and Saturn – the observable solar system which lay against an unchanging starry background. Or rather you can get a rough fit at the expense of stacking together a great number of epicycles – something like 50.

Copernicus’ contribution, published on his death in 1543, was to put the sun back at the centre of the universe. Copernicus led a rather uneventful life, was no sort of astronomical observer and only published his thesis at the end of his life at the strong urging of Georg Joachim Rheticus. He’d discussed his model fairly freely during his life, and his reasons for not publishing were more to do with fear of ridicule from his contemporaries rather than theological pressure. After his death his work, with the exception of the astronomical tables, sank into obscurity partly because it was a difficult read and partly because he managed to ostracise his former cheerleader, Rheticus. Copernicus’ model still holds to the epicycles of the Greeks, and only marginally reduces the complexity of the model.

Next up comes Johannes Kepler, interspersed with Tycho Brahe. Brahe was an astronomical observer and nobleman, funded very well by the Danish king; given his own island Hveen where he built his observatory. As a keen astrologer he began his observation programme when he found a conjunction of Jupiter and Saturn was poorly predicted by current astronomical tables – how can you cast an accurate fortune under these circumstances?

Kepler was a theoretician rather than an observer but also a keen astrologer. I emphasise this because these days astrology is not held in high regard but it is the father of observational astronomy. He had started to develop a model of the solar system based on the Platonic solids – something of a mystical exercise but realised he needed better data to support his model. Brahe was the man with the data, Kepler was only just in time though – he travelled to work with Brahe when Brahe moved to Prague less than 2 years later Brahe was dead. Nowadays we know Kepler for his three laws of planetary motion – it’s worth noting that Kepler’s laws are labelled retrospectively.)

He left copious records of his progress which Koestler traces in great detail, Kepler’s struggle to recognise that planetary orbits were ellipses was heroic and has something of a pantomime air to it – “They’re right in front of you!”. His approach was unprecedented in the sense that he sought to accurately model the very best, most recent measurements. Kepler also made some attempts at a physical model to describe the motions but ultimately he is remembered for the detailed description of their motion. Since it is not central to his theme, Koestler makes only passing reference to Kepler’s work on optics.

The penultimate figure in the story is Galileo, despite Kepler’s best efforts Galileo pretty much ignored him. Galileo gets quite short shrift from Koestler who feels that he brought his troubles with the Catholic Church upon himself. Reading this account his position is not unreasonable. Galileo’s two big contributions to the story are his promotion and use of the telescope, and his work on the motion of terrestrial bodies, the generalisation of which and application to the solar system was Newton’s great triumph. Cosmologically he was only later in his life a supporter of the somewhat retro Copernican model which was a cul-de-sac in terms of theoretical developments. At the time the Catholic Church, particularly the Jesuits, were interested in astronomy and not particularly hardline about the interpretation of Scripture to fit observations. Galileo wound them up both by claiming all newly observed celestial phenomena as his own and by putting the words of the Pope in the mouth of an idiot in one of his Dialogues.

This highlights two of the wider themes that Koestler brings to his book. At one point he describes his cast of characters as “moral dwarves”, he states this is relative to their scientific achievements but returns to this theme in the epilogue where he feels that our scientific developments have not been matched by our spiritual development. The second is the schism between science and the Church that began in this period, Koestler seems to put much of the blame for this on Galileo’s head feeling that it is by no means inevitable. In the epilogue he also draws a comparison between biological evolution and scientific developments, highlighting specifically that there are long periods of not that much happening and many diversions from the “true” path.

The book finishes with a brief mention of Newton’s synthesis of Kepler’s laws and Galileo’s dynamics to produce a model of the solar system which is close to that which we hold today.

This really is a rollicking good read! This is a relatively old book, published in 1959 and one might anticipate that it has not fully caught up with modern historiography however a brief look around the internet suggests that he is not criticised in any great sense. Koestler does tend to focus on a limited number of “great” individuals and goes for “firsts” but this perhaps is what makes it a good read.

Footnotes

My Evernotes for the book are here, last page of the book at the top!

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Jupiter (From video acquired on Celestron NexStar 5SE, Baader Hyperion zoom eyepiece at 8mm,Canon 600D, 1/30s at ISO800 stacked in Registax6)

This morning I managed some photos of Jupiter through the telescope, a Celestron NexStar 5SE.

This was helped with my latest purchase: a Baader Hyperion 8mm-24mm zoom eyepiece – this gives me more magnification and allows me to attach to my Canon 600D camera via a couple of mounting rings (here and here). Previously I could only get low magnification on my camera, or high magnification via a 3x Barlow lens.

The Baader-Hyperion is a nice bit of kit, instructions are minimal though so working out how to attach the camera was a case of twisting various bits of the eyepiece to find out what unscrewed – I did this in the light a couple of days ago. The only small problem is that once the camera is attached to the eyepiece it rotates when the zoom level is changed.

I left out the Star Diagonal for these images, this is Celestron’s right angle bending device which gives better naked eye viewing because you can look through the eyepiece from the standing position rather than crawling around on the floor. However, it does seem to introduce some chromatic aberration. The Canon 600D has a rotatable LCD which gives a reasonable viewing position even without the Star Diagonal.

I had a rather disappointing try at Jupiter a few days ago, disappointing because the night started clear but had clouded over almost completely by the time I got my telescope out; then the neighbours started letting off fireworks; then I couldn’t remember how to work my camera in the dark and then it started raining! On top of all that my Baader Hyperion eyepiece hadn’t turned up.

The useful thing I got out of the evening was a fair idea of appropriate ISO number and exposure times to use – Jupiter is surprisingly bright and needs something like ISO800 at 1/50s on my ‘scope, even at high magnification.

Jupiter, single image Celestron NexStar 5SE, Baader Hyperion zoom eyepiece at 8mm, Canon 600D, 1/50s at ISO800

Jupiter was one of Galileo’s first targets for his telescope in the early 17th century, importantly he observed the four brightest Jovian moons (Callisto, Io, Europe and Ganymede). Significant because they orbited Jupiter, not the sun or the earth and they changed from night to night – at the time the stars were supposed to be immutable and rotate around the earth, or at least the Sun.

You can see these in two photos I took, on 5th and 10th November – the moons have moved quite obviously.

Jupiter and moons on 5th November at 8pm (Celestron NexStar 5SE, 1/4s at ISO6400)

Jupiter and moons on 10th November at 5am (Celestron NexStar 5SE, Baader Hyperion zoom eyepiece at 16mm?, 1/50s at ISO6400)

Actually, it’s not quite that simple: the photo from the 5th was taken in the early evening with Jupiter in the east whilst that on the 10th was taken in the early morning with Jupiter in the west. Jupiter appears to move between these two locations because of the earth’s rotation and this also means the orientation changes. Not only this, my telescope was configured differently on the two occasions: the Star Diagonal + camera combo flips the image vertically whilst the direct eyepiece view flips both horizontally and vertically. I’ve rectified the images appropriately, and labelled them following Stellarium.

I also took some video on the 600D. You can see it here, the juddering at the beginning and end is the result of me poking buttons on the camera. The rippling of the image is the “seeing”, it’s caused by the atmosphere. The point of taking video is that it can be used to mitigate the effect “seeing” by averaging frames, I did this using Registax 6 but first I had to convert the video from Quicktime to avi format using ffmpeg:

ffmpeg –i filename.mov –sameq filename.avi

ffmpeg can do anything with video, if you give it the right incantation, in this case it recognises that I want to convert an input video from mov (Quicktime) format to avi format, the –sameq flag tells it not to drop the quality of the video as it does so.

I have to admit to not really knowing how to use Registax, I simply let it do its default thing and the result looked okay:

Jupiter (From video acquired on Celestron NexStar 5SE, Baader Hyperion zoom eyepiece at 8mm,Canon 600D, 1/30s at ISO800 stacked in Registax6)

A fun half hour of imaging, I’d have moved on to another target if I’d planned ahead. The earlier, unsuccessful imaging session was helpful in getting me close to the right camera settings and spurring me to learn how to learn how to use the camera in the dark. The Baader Hyperion eyepiece is rather nice!

Continue reading »]]> A brief panic over running out of things to read led me to poll my twitter followers for suggestions, Andrew Hodges’ biography of Alan Turing, Alan Turing: The Enigma  was one result of that poll. Turing is most famous for his cryptanalysis work at Bletchley Park during the Second World War. He was born 23rd June 1912, so this is his 100th anniversary year. He was the child of families in the Indian Civil Service, with a baronetcy in another branch of the family.

The attitude of his public school, Sherbourne, was very much classics first, this attitude seems to have been common and perhaps persists today. Turing was something of an erratic student, outstanding in the things that interested him (although not necessarily at all tidy) and very poor in those things that did not interest him.

After Sherbourne he went to King’s College, Cambridge University on a scholarship for which he had made several attempts (one for my old college, Pembroke). The value of the scholarship, £80 per annum, is quite striking: it is double the value of unemployment benefit and half that of a skilled worker. He started study in 1931, on the mathematics Tripos. His scholarship examination performance was not outstanding. Significant at this time is the death of his close school friend, Christopher Morcom in 1930.

King’s is a notorious hotbed of radicals, and at this time Communism was somewhat in vogue, a likely stimulus for this was the Great Depression: capitalism was seen to be failing and Communism offered, at the time, an attractive alternative. Turing does not appear to have been particularly politically active though.

During his undergraduate degree, in 1933, he provided a proof of the Central Limit Theorem – it turns out a proof had already been made but this was his first significant work. He then went on to answer Hilbert’s Entscheidungsproblem (German for “Decision Problem) in mathematics with his paper, “On computable numbers”¹. This is the work in which he introduced the idea of a universal machine that could read symbols from a tape, adjust its internal state on the basis of those symbols and write symbols on the tape. The revelation for me in this work was that mathematicians of Turing’s era were considering numbers and the operations on numbers to have equivalent status. It opens the floodgates for a digital computer of the modern design: data and instructions that act on data are simply bits in memory there is nothing special about either of them. In the period towards the Second World War a variety of specialised electromechanical computing devices were built, analogue hardware which attacked just one problem. Turing’s universal machine, whilst proving that it could not solve every problem, highlighted the fact that an awful lot of problems could be solved with a general computing machine – to switch to a different problem, simply change the program.

Alonzo Church, at Princeton University, produced an answer for the Entscheidungsproblem  at the same time; Turing went to Princeton to study for his doctorate with Church as his supervisor.

Turing had been involved in a minor way in codebreaking before the outbreak of World War II and he was assigned to Bletchley Park immediately war started. His work on the “Turing machine” provides a clear background for attacking German codes based on the Enigma machine. This is not the place to relate in detail the work at Bletchley: Turing’s part in it was as something of a mathematical guru but also someone interested in producing practical solutions to problems. The triumph of Bletchley was not the breaking of individual messages but the systematic breaking of German systems of communication. Frequently, it was the breaking of a system which was critical in principle the Enigma machine (or variants of it) could offer practically unbreakable codes but in practice the way it was used offered a way in. Towards the end of the war Turing was no longer needed at Bletchley and he moved to a neighbouring establishment, Hanslope Park where he built a speech encrypting system, Delilah with Don Bayley – again a very practical activity.

Following the war Turing was seconded to the National Physical Laboratory where it was intended he would help build ACE (a general purpose computer), however this was not to be – in contrast to work during the war building ACE was a slow frustrating process and ultimately he left for Manchester University who were building their own computer. Again Turing shows a high degree of practicality: he worked out that an alcohol water mixture close to the composition of gin would be almost as good as mercury for delay line memory*. Philosophically Turing’s vision for ACE was different from the American vision for electronic computing led by Von Neumann: Turing sought the simplest possible computing machinery, relying on programming to carry out complex tasks – the American vision tended towards more complex hardware. Turing was thinking about software, a frustrating process in the absence of any but the most limited working hardware and also thinking more broadly about machine intelligence.

It was after the war that Turing also became interested in morphogenesis² – how complex forms emerge from undifferentiated blobs in the natural world, based on the kinetics of chemical reactions. He used the early Manchester computer to carry out simulations in this area. This work harks back to some practical calculations on chemical kinetics which he did before going to university.

Turing’s suicide comes rather abruptly towards the end of the book. Turing had been convicted of indecency in 1952, and had undergone hormone therapy as an alternative to prison to “correct” his homosexuality. This treatment had ended a year before his suicide in 1954. By this time the UK government had tacitly moved to a position where no homosexual could work in sensitive government areas such as GCHQ. However, there is no direct evidence that this was putting pressure on Turing personally. Reading the book there is no sick feeling of inevitability as Turing approaches the end you know he has.

Currently there are calls for Turing to be formally pardoned for his 1952 indecency conviction, personally I’m ambivalent about this – a personal pardon for Turing is irrelevant: legal sanctions against homosexual men, in particular, were widespread at the time. An individual pardon for Turing seems to say, “all those other convictions were fine, but Turing did great things so should be pardoned”. Arnold Murray, the man with whom Turing was convicted was nineteen at the time, an age at which their activities were illegal in the UK until 2000.

What struck me most about Turing from this book was his willingness to engage with practical, engineering solutions to the results his mathematical studies produced.

Hodges’ book is excellent: it’s thorough, demonstrates deep knowledge of the areas in which Turing worked and draws on personal interviews with many of the people Turing worked with.

Footnotes

1. “On computable numbers, with an application to the Entscheidungsproblem”, A.M. Turing, Proceedings of the London Mathematical Society 42:230-265 (1936).

2. “The Chemical Basis of Morphogenesis”, A.M. Turing, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 237, No. 641. (Aug. 14, 1952), pp. 37-72.

3. My Evernotes for the book

4. Andrew Hodges’ website to accompany the book (link)

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The Milky Way (Canon 600D, 18mm, ISO6400, 30s, f/4.5)

Regular readers will know I recently bought myself a telescope, a Celestron 5SE Schmidt-Cassegrain reflector but this post covers some astrophotography conducted without the aid of a telescope almost the opposite in fact. I’ve been on holiday recently to somewhere with pretty good dark skies, unfortunately I did not have my telescope with me but I did have a tripod, a Canon 600D SLR and a collection of lenses although in this instance I just used the 18-55mm kit lens at the wide end (18mm). I also had my planisphere and a copy of the free planetarium software, Stellarium.

I’ve used my camera with a standard lens to take photos of the night sky before: to make star trails, so far my experiments in this area have been a bit disappointing. The aim with star trail photographs is to have nice bright trails showing the apparent motion of stars around the pole as the earth rotates, against a dark background. In my experiments I used 30s exposures at f/4, ISO200 on a 10mm lens which I then combined using a simple application called StarTrails.

Back to my holiday snaps – I started my evening taking photos as I had done for my star trails, I have to say this was all a bit disappointing – individual photos do show the stars in the sky and with some effort one can trace out the patterns of the constellations – you might just be able to spot Cassiopeia in the image below.

Cassiopeia (Canon 600D, 18mm, ISO200, 30s, f/4.5)

Getting a bit bored with this, I turned the sensitivity right up so I was imaging at f/4.5 ISO6400 with 30s exposures and suddenly this popped out:

The Milky Way towards Cassiopeia (Canon 600D, 18mm, ISO6400, 30s, f/4.5)

Cassiopeia is in there somewhere but there are just so many more stars (and a few clouds). This opened the flood gates and I indiscriminately fired off shots along the line of the Milky Way, just visible in the image above. At this time of year, in the early evening in the UK the Milky Way goes from horizon to horizon passing almost directly overhead starting a little East of North and finishing a little West of South.

Now this is fun but now I have a bunch of images of parts of the Milky Way. Can I stick them together? It turns out I can, I used Microsoft ICE on the images I had acquired and got this mosaic:

The Milky Way, 5 image mosaic prepared in Microsoft ICE (Canon 600D, 18mm, ISO6400, 30s, f/4.5)

This spans almost horizon to horizon. I was rather pleased with this, however I struggled to work out where I was in the sky, picking out constellations from the huge mess of stars is very tricky. It turns out help is at hand in the form of astrometry.net, this is an online service which takes an image of the night sky and works out which bit of the sky it shows and labels it all nicely. It can’t handle the mosaic image shown above, but can handle the individual images – you can see my images here. One of the formats in which data is provided is Google Earth’s KMZ format, so you can see the images projected onto the celestial sphere in Google Earth – my combined KMZ file is here, it’s 12MB.

There are improvements to be made in the process:

• if I’d had it with me my 10-22mm lens would have been nice – it would give me more sky in one shot;
• better familiarity with my planisphere would mean less indiscriminate firing off of shots;
• ideally I’d have gone for a cloudless night;
• there’s a bit of optimisation on the exposure settings, ISO6400 is at the limit of my camera and if you zoom right in there is some evidence of colour noise, also towards the zenith the stars are motion smeared – as in star trail pictures so shorter exposures would be nice;
• compositionally it would be good to include some of the earthly scenery;
• working out how to turn off the security lights of the holiday cottage we were staying in would have been good.

All in all a rather fun evening!