Sunday, 24 November 2013

A pocket Map of the Universe

One of my favourite artefacts is the set of pop-out maps made by PopOut products. They have cleverly identified both a need - high resolution spatial data in a pocket friendly format without the need for connectivity or power (i.e. a map) with a way of packaging it into a pocket sized unit.

The company was founded in 1992 - according to the company history:
1992 - Having spotted a need to cure what he calls 'Map Stress Syndrome' after watching numerous tourists around the City of Bath, England, battling with oversized maps, founder Derek Dacey recalls the invaluable miniature charts he used during his days as a commercial pilot. Aiming to bring this level of usability to the city map market, a small team of designers is recruited to realise what would soon become the PopOut.
Here is an example of the PopOut map of London UK showing the cunning folding mechanism that allows the centre of London to be packed into the pocket sized format. Good old fashioned ingenuity, high quality printing, paper and card put to great use. 

Copyright Compass Maps Ltd.


Pretty cool - but not expansive. 

Below is the Mother of all Pocket Maps. Created in 2005 it shows the whole of the known Universe. Moving out from the centre of the Earth in powers of ten multiples of the radius of the Earth (6371 Kilometres). 





 Further details can be found in the paper HERE.

Saturday, 23 November 2013

The first recorded observation of the moons surface in 1609

On the evening of July 26th 1609 the Englishman Thomas Harriot made a sketch of the surface of the  moon as he had observed it through a telescope. This was four months before Galileo did the same.

Copyright Lord Egremont, Petworth House Archives HMC 241/9 fol 26. West Sussex Record Office, Chichester


More HERE.

The Face of the Moon

John Russell (1745 –  1806) was an English painter and member of the Royal Academy who specialised in oil and pastel portraits. He was also a gifted amateur astronomer who worked to make an accurate record of the lunar surface he was observing through his telescopes. 

One of Russell's masterpieces is a detailed pastel of the moons surface measuring 5ft that he completed in 1795.

More detail HERE.


Below is one of Russell's observational drawings, from July 10th 1787 (from HERE).






Sunday, 17 November 2013

Things exist whole and entire within it...

Thomas Bewick (1753-1828) was an English engraver who used metal-engraving tools on boxwood that was cut across the grain - a major innovation in how illustrations were printed.

Bewick is best known for his illustrated volumes on the History of British Birds. Along with the main subjects of the book, the birds, Bewick also included numerous tiny and beautifully engraved vignettes which helped pad out the visual space of the pages.
"The crucial point about Bewick's vignettes is that they don't have a defined edge. They're not bounded by a formal rectangle or oval... The image's edge is the edge of a rock, a hill, a bush, a tree. Or sometimes, with a stretch of ground or water or sky, the image just fades out at the margin.
Either way, unlike most pictures, these vignettes lack a window frame. The picture is just an extract. The scene continues off-picture. Not so the vignette. In the vignette, the scene does not lead off-picture. You notice how, in Bewick, things like trees and houses are never half-cutoff by the edge of the image, to suggest that the world goes on. Things exist whole and entire within it".
Tom Lubbock The Independent 15th December 2006 (HERE).

Below, one of Bewick's Vignettes, apparently of Bewick himself, as a thirsty traveler drinking from his hat, drawn and engraved by Bewick (1797) from HERE.




One of the remarkable features of these Vignettes is how small they are - in 1971 the Black Cat Press published a limited edition miniature book containing fifteen vignettes printed from original Bewick blocks on Japanese paper. The book was bound in red Moroccan leather and measured just 66mm x 54mm.

Dynamic projections of 3D onto 2D (or a Bird Ballet)


The French film maker Neels Castillon has made a beautiful short film on the movements of thousands of starlings in the evening in the skies around Marseille.

The film is a series of images of a complex and dynamic three dimensional structure - the flock of individually moving starlings - projected onto a two dimensional plane - the CCD chip of the (mainly) stationary video camera.

Below is a set of stills from the video and below that the original film.















All images Copyright N. Castillion.

More background on the animal behaviour studies around this type of flocking (HERE). 

Friday, 15 November 2013

It's that time of year...



 Copyright M.G. Reed 2010

Saturday, 9 November 2013

"Emma, please insert NMR data here! where are they? and for this compound, just make up an elemental analysis … "




More rather bleak stuff on the state of scientific publishing - Misconduct accounts for the majority of retracted scientific publications. F.C. Fang, R. Grant Steen & A. Casadevall. (2012) PNAS. 109 No 42 17028-17033.

Casadevall and co-authors looked hard at more than 2,000 retracted biomedical research papers since 1977. Of the papers they looked at more than two-thirds were retracted because of fraud, suspected fraud, duplicate publication or plagiarism. Only a fifth of the retractions were the result of error. They estimated that the percentage of scientific papers being retracted due to fraud had increased about 10-fold since the early 1970's.
And some good pieces in the Guardian on the ongoing debates around post-publication peer review - enabled by blogs and sharp eyed readers of scientific journals.

Accusations of fraud spur a revolution in scientific publishing.

Not breaking news: many scientific studies are ultimately proved wrong!
 


Monday, 28 October 2013

Wednesday, 23 October 2013

Ninety Percent of everything is crud

Sturgeon's Law of Quality states that: 'Ninety percent of  everything is crud'. 

The last few posts here have shown that there is compelling evidence that Sturgeons Law of Quality applies to the peer reviewed papers that appear in our finest scientific journals.  

The original statement of this Law is below:

"... they say 'ninety percent of science fiction is crud.' Well, they're right. Ninety percent of science fiction is crud. But then ninety percent of everything is crud, and it's the ten percent that isn't crud that is important. and the ten percent of science fiction that isn't crud is as good as or better than anything being written anywhere."

Theodore Sturgeon 1953

From HERE





Note that the Wikipedia article on Sturgeon's Law refers to this Law as 'Sturgeon's Revelation' with an additional adage being listed as Sturgeon's Law - Nothing is always absolutely so.

See also the OED entry HERE

Thursday, 17 October 2013

Science at-Large on Planet F345, Andromeda Galaxy, Year 3045268

John Ioannidis is on a roll. Ioannidis is a professor at Stanford School of Medicine who does a number of things - one of which is to expose what is wrong with current approaches to publishing science. In particular he enjoys finding methodological weaknesses and flaky statistics. He is the author of the excellent Why Most Published Research Findings Are False (HERE). 

Recently Ioannidis published a paper called Why Science Is Not Necessarily Self-Correcting HERE. The asbtract of this  paper begins "The ability to self-correct is considered a hallmark of science. However, self-correction does not always happen to scientific evidence by default". He goes on to describe a speculative future of science on Planet F345...

"Planet F345 in the Andromeda galaxy is inhabited by a highly intelligent humanoid species very similar to Homo sapiens sapiens. Here is the situation of science in the year 3045268 in that planet. Although there is considerable growth and diversity of scientific fields, the lion’s share of the research enterprise is conducted in a relatively limited number of very popular fields, each one of that attracting the efforts of tens of thousands of investigators and including hundreds of thousands of papers. Based on what we know from other civilizations in other galaxies, the majority of these fields are null fields—that is, fields where empirically it has been shown that there are very few or even no genuine nonnull effects to be discovered, thus whatever claims for discovery are made are mostly just the result of random error, bias, or both. The produced discoveries are just estimating the net bias operating in each of these null fields. Examples of such null fields are nutribogus epidemiology, pompompomics, social psychojunkology, and all the multifarious disciplines of brown cockroach research—brown cockroaches are considered to provide adequate models that can be readily extended to humanoids. Unfortunately, F345 scientists do not know that these are null fields and don’t even suspect that they are wasting their effort and their lives in these scientific bubbles.

Young investigators are taught early on that the only thing that matters is making new discoveries and finding statistically significant results at all cost. In a typical research team at any prestigious university in F345, dozens of pre-docs and post-docs sit day and night in front of their powerful computers in a common hall perpetually data dredging through huge databases. Whoever gets an extraordinary enough omega value (a number derived from some sort of statistical selection process) runs to the office of the senior investigator and proposes to write and submit a manuscript. The senior investigator gets all these glaring results and then allows only the manuscripts with the most extravagant results to move forward. The most prestigious journals do the same. Funding agencies do the same. Universities are practically run by financial officers that know nothing about science (and couldn’t care less about it), but are strong at maximizing financial gains. University presidents, provosts, and deans are mostly puppets good enough only for commencement speeches and other boring ceremonies and for making enthusiastic statements about new discoveries of that sort made at their institutions. Most of the financial officers of research institutions are recruited after successful careers as real estate agents, managers in supermarket chains, or employees in other corporate structures where they have proven that they can cut cost and make more money for their companies. Researchers advance if they make more extreme, extravagant claims and thus publish extravagant results, which get more funding even though almost all of them are wrong.

No one is interested in replicating anything in F345. Replication is considered a despicable exercise suitable only for idiots capable only of me-too mimicking, and it is definitely not serious science. The members of the royal and national academies of science are those who are most successful and prolific in the process of producing wrong results. Several types of research are conducted by industry, and in some fields such as clinical medicine this is almost always the case. The main motive is again to get extravagant results, so as to license new medical treatments, tests, and other technology and make more money, even though these treatments don’t really work. Studies are designed in a way so as to make sure that they will produce results with good enough omega values or at least allow some manipulation to produce nice-looking omega values.

Simple citizens are bombarded from the mass media on a daily basis with announcements about new discoveries, although no serious discovery has been made in F345 for many years now. Critical thinking and questioning is generally discredited in most countries in F345. At some point, the free markets destroyed the countries with democratic constitutions and freedom of thought, because it was felt that free and critical thinking was a nuisance. As a result, for example, the highest salaries for scientists and the most sophisticated research infrastructure are to be found in totalitarian countries with lack of freedom of speech or huge social inequalities—one of the most common being gender inequalities against men (e.g., men cannot drive a car and when they appear in public their whole body, including their head, must be covered with a heavy pink cloth). Science is flourishing where free thinking and critical questioning are rigorously restricted, since free thinking and critical questioning (including of course efforts for replicating claimed discoveries) are considered anathema for good science in F345."


Of course if science on Earth was performed today like it is on F345 it would be both depressing and very difficult to accurately discern the difference between real-science and psuedo-science.


 Image of Andromeda from HERE


Thursday, 10 October 2013

Current trends in the reliability of science

A nice paper HERE by  Björn Brembs, Katherine Button and Marcus Munafò called "Deep impact: unintended consequences of journal rank".  Go download it.

Their Abstract reads:

Most researchers acknowledge an intrinsic hierarchy in the scholarly journals (“journal rank”) that they submit their work to, and adjust not only their submission but also their reading strategies accordingly. On the other hand, much has been written about the negative effects of institutionalizing journal rank as an impact measure. So far, contributions to the debate concerning the limitations of journal rank as a scientific impact assessment tool have either lacked data, or relied on only a few studies. In this review, we present the most recent and pertinent data on the consequences of our current scholarly communication system with respect to various measures of scientific quality (such as utility/citations, methodological soundness, expert ratings or retractions). These data corroborate previous hypotheses: using journal rank as an assessment tool is bad scientific practice. Moreover, the data lead us to argue that any journal rank (not only the currently-favored Impact Factor) would have this negative impact. Therefore, we suggest that abandoning journals altogether, in favor of a library-based scholarly communication system, will ultimately be necessary. This new system will use modern information technology to vastly improve the filter, sort and discovery functions of the current journal system.

And their Conclusions

While at this point it seems impossible to quantify the relative contributions of the different factors influencing the reliability of scientific publications, the current empirical literature on the effects of journal rank provides evidence supporting the following four conclusions: (1) journal rank is a weak to moderate predictor of utility and perceived importance; (2) journal rank is a moderate to strong predictor of both intentional and unintentional scientific unreliability; (3) journal rank is expensive, delays science and frustrates researchers; and, (4) journal rank as established by IF violates even the most basic scientific standards, but predicts subjective judgments of journal quality.


The following Figure from their paper shows (A) Exponential fit for PubMed retraction notices (data from pmretract.heroku.com) and (D) Linear regression with confidence intervals between Impact Factor and Retraction Index (data provided by Fang and Casadevall, 2011).







Friday, 4 October 2013

Cosmic View (1957)

Long before Charles and Ray Eames made 'Powers of Ten' (1968 & 1977) a Dutch writer called Kees Boeke wrote Cosmic View, it was published in 1957. It also inspired the computer game Spore.

The Introduction was by Arthur H. Compton:

INTRODUCTION

What are we? Where do we live? Who are our neighbors? Children and grown-ups, we all ask these questions.

The answers that Kees Boeke gives are only the beginning of the story, but that beginning is straightforward and clear. The author shows us a series of pictures of a little girl as seen from different distances. Around her are the things that form her world. We see her also as it were from within, showing the parts she is made of. These various views present one school child in an immense range of perspectives. We begin to understand how big things are and how we are related to them.

It is not easy to do what the author has done so well, to tell accurately and in simple language what the world is like. Here is a reliable framework to which further knowledge can be added. In describing this framework, the author has gone as far as the present state of our knowledge permits. Fifty years ago our cosmic view would have been much more limited. Nothing could have been drawn with confidence in pictures 20 to 26 or in pictures -8 to -14. There is reason to question whether we shall ever be able to draw what would be the next pictures, 27 or -14.

So it is that only now, in our day, we can see ourselves so clearly. In this immense and varied universe we find ourselves indeed one with other boys and girls, other men and women. In showing us how we ourselves look in perspective, Kees Boeke as a skillful teacher helps us also to know how and what our neighbors are.

The author deserves our thanks for giving us his answers to our questions in this fascinating and understandable form.

ARTHUR H. COMPTON 


A full set of the images and text are HERE.





Friday, 27 September 2013

Data to Life

I have just published a new book called Data to Life with  a long term collaborator and friend of mine Joss Langford. The back cover blurb:
Digital technologies are becoming ever more integrated into our daily lives. Wearable devices, big data and the Internet of Things are poised to create a myriad of personalised services in health, wellness, commerce and leisure. These will have the potential to deliver huge benefits to society, but there are real and growing concerns they could open the door to Big Brother. Starting with the simplest atoms of behaviour, Data to Life covers a remarkable breadth of topics: the significance of daily rituals, a taxonomy of everyday life and tools for behaviour change. It presents a radical new roadmap for collecting and handling personal data that protects the interests of both individuals and businesses. 





A typical two-page spread below.




Tuesday, 24 September 2013

Swiss Topographic Maps

Edward Tufte argues that the Swiss National mountain maps:  


"... provide a standard of excellence for serious information displays. Specifically:
- all about content
- high-resolution
- vigorous expression of third dimension
- local details always imbedded in larger context
- use of appropriate light colors to avoid optical clutter
- realistic, content-driven colors
- smart, graceful typography done by serious typographers
- size of type proportional to size of object labeled (type is quantified)
- intense quantitative data by means of contour lines (at sparkline resolution)
- contours = sparklines that flow in three dimensions!
- thorough, natural integration of words, numbers, depictions
- shows intense local data information in position without annoying pop-ups
- zero chartjunk, all pixels carrying content
- many exact numbers provided (labels for contour lines, and the height of mountain peaks)
- avoids dequantification found in much datviz stuff
- all about content
- great content (the Swiss Alps!)
- open-source, non-proprietary formats
- driven by content, a spirit of public service, pride in the forever craft of cartography
- not driven by marketplace ethics, not driven by focus groups".
They are available HERE including 1957 vintage topographic maps for purchase.




Thursday, 12 September 2013

ImageQuilts

ImageQuilts is a new site and Google Chrome App for creating 'Quilts' of images obtained from Google image searches. Some examples below.

Josef Albers


Sorting Algorithms



Monday, 2 September 2013

A Quincuncial Projection of the Sphere

The Quincuncial projection of the sphere is a way of projecting what is on the surface of a sphere (like the surface of the Earth) onto a square, or more accurately onto a tessellation of squares. 

It was invented in 1879 by the American polymath and measurement scientists Charles Sanders Peirce. His illustration of the projection is shown below.According to Peirce, his projection has the following properties:

1. The whole sphere is presented on repeating squares.
2. The part where the exaggeration of scale amounts to double that at the centre is only 9% of the area of the sphere, against 13% for Mercator's projection and 50% for the stereographic.
3. The angles are exactly preserved.
4. The curvature of lines representing great circles is, in every case, very slight, over the greater part of their length.

In addition it can be tessellated in all directions.
Image from HERE.


Saturday, 31 August 2013

Heaney's Beowolf


Wednesday, 28 August 2013

An Oak Fern printed directly from Nature (1857)

Nature printing is a process whereby a natural object is somehow used directly to create a print (HERE).

Below is a nature printed image of an Oak Fern (Polypodium Dryopteris) from a book by Thomas Moore (1821-1887) - The Ferns of Great Britain and Ireland; Edited by John Lindley. Nature-printed by Henry Bradbury. London: Bradbury and Evans, 1857. 

A digitised copy of the book is available HERE.






Tuesday, 27 August 2013

A Nearly perfect Book

A great piece HERE on the Arion Press in San Francisco - a fine art letterpress printer and publisher. 

In 1970 the Arion Press published an edition of Melville's Moby Dick:
To study the Arion Press edition of Moby-Dick today is to have an almost sacred experience of the power of physical print. Its ink is black, with wide margins and initial letters in a dark, aqueous blue. The paper is a faint blue-gray, like the surface of the ocean on a cloudy day. When the reader lifts a page to turn it, the watermark of a whale shimmers through. Because the letter w is particularly wide, Hoyem made the abutting spaces slightly narrower; every semicolon has a hairsbreadth gap before it, as if signaling the partial stop. The result is something that one would not think possible: a nearly perfect book.
an image from the book [HERE].

Friday, 23 August 2013

A New Candide

From next week the Royal Shakespeare Company are putting on Candide, a new play by Mark Ravenhill inspired by Voltaire's book of the same name.

 Image: Royal Shakespeare Company

Saturday, 17 August 2013

Structure, Substructure, Superstructure

Cyril Stanley Smith (1903-1992) was a historian of science and quantitative metallurgist. 

One of his classic books is Search for Structure: Selected Essays on Science, Art and History (1981, ISBN 0-262-19191-1, MIT Press).

The object stands at the very point where the structures and properties of matter resulting from forces between atoms are in visible interaction with man's ideas and purposes. An artists work preserves a record of both - one in the outer form and decoration, the other in the texture and color and fine contours that result from the interpley of atomic, molecular and crystalline forces.
Below is an image from one of his papers: Structure, Substructure, Superstructure published in the Rev. Mod. Phys. 36, pp 524–532 in 1964. The paper begins as follows:


Anyone who works with the microscope for an intellectual or practical purpose will frequently pause for a moment of sheer enjoyment of the patterns that he sees, for they have much in common with formal art.



CAPTION: Raft of tiny uniform soap bubbles showing 'grain boundaries' where zones of differing orientation meet.

Josef Albers Album Covers

Josef Albers (1888-1976) was, amongst other things, a colour theorist, observer and artist. He also designed album covers. Here is an exhibition of some of his best, four of which are below.


 In an essay on them Joseph Masheck makes the following connection with the work of Cyril Stanley Smith:
Persuasive Percussion (1959; in this case not the Light Brigade but Terry Snyder and the All Stars) shows a tightly packed grid or lattice of small black disks from which a few wander up and out like stray molecules of some light gas; or better still, like the diagrams from a classic essay in which Cyril Stanley Smith would show how natural lattice structures are surprisingly tolerant of irregularities (“Structural Hierarchy in Science, Art, and History,” 1974-75, 1978).




Thursday, 8 August 2013

The Walls of Ireland

A beautiful dry stone wall from Glasdrumman in Ireland.



Image © Copyright Paul McIlroy

Sunday, 4 August 2013

On Nature: Jon McNaught

HERE are the illustrations that Jon McNaught did for On Nature, a collection of essays on getting the most out of the British countryside.

 Image copyright Jon McNaught
 

The Crucian Carp

When I was younger I was a keen fisherman. I fished in the hard fished small farm ponds and canals of the North-West of England. There are two books that I remember helped me get into fishing. The first was first published in 1950 as a Puffin Picture Book - Fish and Fishing by Bernard Venables. This was a basic introduction to the fish, tackle and methods used in coarse fishing. Below is a page from the book - taken from a full set of pages HERE

The image shows several of the different type of Carp. My favourite was the Crucian Carp. Although these do not have the avid following that the other carp do, nor do they attain the same weights, they are a beautiful fish. I always threw the fish back in after catching them.


The second book was World Class Match Fishing by Kevin Ashurst. This described in detail Ashurst's methods for winning highly competitive match fishing contests on rivers and canals.  I had no interest in match fishing, but from Ashurst I learnt how to make my own floats from peacock quill, copper wire and balsa wood. I spent hours perfecting my own set of floats, complete with a colour coding scheme for the lead shot that they needed to be perfectly set in the water. Unfortunately, I find I don't call on my float making skills too much these days.

Wednesday, 24 July 2013

Refraction of soldiers through a field of wheat

The Vertebrate eye and Its Adaptive Radiation. G.L. Walls (1942) - HERE 

'This bending of light rays when they pass through boundary surfaces is called 'refraction'. Its basis may be best understood if we use an old favorite analogy for our light beam and our pair of optically different substances. 

Suppose a platoon of soldiers to be marching over bare ground towards the edge of a wheat-field, which is at an angle to their line of march. The ranks of soldiers now represent successive wave-fronts in a light beam, and their files represent the individual light rays in the beam. Obviously the soldiers cannot march as fast through the dense wheat as over open ground, so that the latter may represent air, and the wheat-field a piece of glass of higher optical density.

As the first soldiers in the front rank start into the wheat, they are slowed up, but those at the other end of the front rank are still able to march rapidly since they have not yet reached the wheat (a). Consequently the front rank is swung around as if hinged at one end, and by the time the whole of the rank is in the wheat, it has taken a new direction of march which is of course followed by each rank in the whole platoon (b). 

Upon emerging from the wheat-field on the other side (c), the process is reversed and the platoon's line of march becomes parallel to its original one, displaced laterally a distance which depends upon the width of the wheat-field and the difficulty of marching through it'.


Saturday, 29 June 2013

MIndless Statistics and Feynman's Conjecture

Gerd Gigerenzer is Director at the Max Planck Institute for Human Development and Director of the Harding Center for Risk Literacy in Berlin. His web page is HERE.

He is also the author of an entertaining paper from 2004 called Mindless Statistics (HERE).

The Abstract reads:
Statistical rituals largely eliminate statistical thinking in the social sciences. Rituals are indispensable for identification with social groups, but they should be the subject rather than the procedure of science. What I call the “null ritual” consists of three steps: (1) set up a statistical null hypothesis, but do not specify your own hypothesis nor any alternative hypothesis, (2) use the 5% significance level for rejecting the null and accepting your hypothesis, and (3) always perform this procedure. I report evidence of the resulting collective confusion and fears about sanctions on the part of students and teachers, researchers and editors, as well as textbook writers.
Gigerenzer takes apart what he calls the 'null ritual' that scientists are taught about in statistics lessons. In particular psychologists. 

One of the great pieces of evidence Gigerenzer presents is the result of a test that was set by Haller and Krauss (2002). In this test the researchers posed a question about null hypothesis testing to 30 statistics teachers, including professors of psychology, lecturers, and teaching assistants, 39 professors and lecturers of psychology (not teaching statistics), and 44 psychology students. Teachers and students were from the psychology departments at six German universities. Each statistics teacher taught null hypothesis testing, and each student had successfully passed one or more statistics courses in which it was taught. The question was followed by 6 statements and the people taking the test were asked to mark which of the statements they believed to be true or false.

In fact all 6 of the statements were false. But all 6 of the statements erred "in the same direction of wishful thinking: They make a p-value look more informative than it is".

The results of this study were presented by Gigerenzer:


Gigerenzer also goes on to quote Richard Feynman on hypothesis testing and states Feynman’s conjecture:
To report a significant result and reject the null in favor of an alternative hypothesis is meaningless unless the alternative hypothesis has been stated before the data was obtained.
And quotes Feynman's anecdotal story about his interaction with a psychology researcher at Princeton whilst he was a student.
And it’s a general principle of psychologists that in these tests they arrange so that the odds that the things that happen happen by chance is small, in fact, less than one in twenty. . . . And then he ran to me, and he said, “Calculate the probability for me that they should alternate, so that I can see if it is less than one in twenty.” I said, “It probably is less than one in twenty, but it doesn’t count.” He said, “Why?” I said, “Because it doesn’t make any sense to calculate after the event. You see, you found the peculiarity, and so you selected the peculiar case.” . . . If he wants to test this hypothesis, one in twenty, he cannot do it from the same data that gave him the clue. He must do another experiment all over again and then see if they alternate. He did, and it didn’t work. 

References 
Feynman, R., 1998. The Meaning of it All: Thoughts of a Citizen-Scientist. Perseus Books, Reading, MA, pp. 80–81.
Haller, H., Krauss, S., 2002. Misinterpretations of significance: a problem students share with their teachers? Methods of Psychological Research—Online [On-line serial], 7, pp 1–20.

Tuesday, 25 June 2013

Its white foot tripped, Then dropped from sight.

The wreck of a small boat on the Caldy shore this morning.



 Copyright M.G. Reed 2013

Thursday, 20 June 2013

Ashmolean Mummy & Penicillin electron density plots

The Ashmolean museum in Oxford is just one of the delights of this brilliant city of learning. 

One of the unexpected exhibits is the gallery of Egyptian mummy's, some of which include elaborate body wrappings and painted portraits (HERE). 

In addition there is a mummy of a 2 year old boy. Next to the mummy and about life size, is a fantastic glass sculpture artwork by Angela Palmer. The 2000 year old mummy was scanned with a CT scanner to create a full 3D data set. Palmer then created a physical representation of this virtual data set by tracing details from the 3D data set onto a set of 111 sheets of glass. The sculpture now sits near to the boy and is a permanent part of the exhibition.

Image copyright Angela Palmer

The technique of drawing contours on parallel sheets of glass that Angela Palmer uses was inspired by her seeing the work of Nobel prize winning crystallographer Dorothy Hodgkin-Crowfoot. Below is an image of her work created in the mid 1940's (from HERE).  An original of this artefact is in the Oxford Museum of the History of Science (HERE).



From the 1949 penicillin monograph published by Princeton University Press. A photograph of electron-density contours drawn on sheets of perspex showing the thiazolidine and beta-lactam of potassium benzylpenicillin. 

Owing to the urgency created by the `extreme importance of penicillin as a military weapon' in WWII, determining the crystal structure of penicillin involved the first crystallographic use in Britain of a Hollerith computer; with Dorothy Hodgkin-Crowfoot as lead crystallographer and with Leslie J. Comrie's Scientific Computing Services Ltd developing the computing methodology. 

As noted in the penicillin monograph: `Under the terms of the contract for the publication of the Chemistry of Penicillin the publisher has agreed to waive its rights under the copyright after five years from the date of publication. Thereafter this volume will be in the public domain and dedicated to the public.' 



Thursday, 13 June 2013

Data Analysis for Politics and Policy

Before Edward Tufte became very well known for his work on data visualisation, he wrote on the application of statistical methods in the social sciences. 

One of his best books is a slim volume published in 1974 by Prentice Hall, Data Analysis for Politics and Policy.  Even if you have no interest in either Politics or Policy, this is a great book for learning about data analysis. 

The book was previously available to download for free from Tufte's site, but is now available there for $2 as an e-book in PDF format (HERE)

Below is one of the figures from the book, which shows a data set on US death rates from motor vehicle accidents that Tufte analyses in some detail through the book. The plot shows the distribution in death rate across each of the states in the US. The graphic doesn't reach the high standards that he set himself later in his career, but it already shows a dedication to showing the data in a clear visual manner. 



Images Copyright E.Tufte.

Sunday, 2 June 2013

On the unreliability of (some) neuroscience

Raymond Tallis has a superb piece in today's Guardian on the ludicrousness of some of the claims that are made by those who use functional brain imaging to try and explain that who we are and what we do is somehow revealed by the particular bits of the brain that 'light up' in big imaging bits of kit. HERE.

In the piece he references a Nature Neuroscience Review paper by Katherine Button and friends. The abstract reads as follows:

A study with low statistical power has a reduced chance of detecting a true effect, but it is less well appreciated that low power also reduces the likelihood that a statistically significant result reflects a true effect. Here, we show that the average statistical power of studies in the neurosciences is very low. The consequences of this include overestimates of effect size and low reproducibility of results. There are also ethical dimensions to this problem, as unreliable research is inefficient and wasteful. Improving reproducibility in neuroscience is a key priority and requires attention to well-established but often ignored methodological principles.
 See  also previous posts HERE and HERE.