Saturday 19 December 2009

Horse in Motion - Again

A small multiple that shows movement in time. The classic "The Horse in Motion" by Eadweard Muybridge. "Sallie Gardner," owned by Leland Stanford; running at a 1:40 gait over the Palo Alto track, 19th June 1878.

The full caption provides a host of interesting technical information;

'The negatives of these photographs were made at intervals of twenty-seven inches of distance, and about the twenty-fifth part of a second in time; they illustrate consecutive positions assumed during a single stride of the mare. The vertical lines were twenty-seven inches apart; the horizontal lines represente elevations of four inches each. The negatives were each exposed during the two-thousandth part of a second and are absolutely "untouched".' 

This is great information - detailed technical data including a calibration standard in each frame. Many modern photos and series are not so well annotated. 

However, what is really intriguing is that if you search on Google for this image you will find a number of 'Horse in Motion' sequences by Muybridge with different horses which is understandable. More interesting are the images that also appear to refer to Sallie Gardner 19th June 1878 but are quite different to the one I attach here with slightly different text and modified calibration grid. For example the image you see on Wikipedia 'The Horse in Motion.jpg' and which I show in an earlier post - is not the same as the one I attach here. Could the real Muybridge stand up please. 

Jan Tschichold- Penguin Composition Rules

I have been reading up on Jan Tschichold ( and in particular his 'Penguin Composition Rules' which was a very short set of rules he articulated for the UK Penguin imprint in about 1947. 

I have had trouble finding them either physically or electronically. There is a set of rules for web pages derived from Tschichold's rules here ( and I have a rather thinly referenced electronic text of them from here ( My intention is to typeset them in LaTeX using the rules themselves as a style guide, thereby showing by example the rules in action. 

2010 Update:

I checked with Penguin who still hold copyright and they have given me permission to set them for my own use but not to distribute further.

Wednesday 16 December 2009

Six Guidelines for Good Typography

A short set of guidelines for Good Typography from the Hand & Eye website - Typeset by Matt in the built in Bookman font using TexNicCenter.

Monday 14 December 2009

Making Books Beautiful Again

Here is a very thoughtful essay by Australian philosopher Adrian Heathcote extolling the virues of LaTeX, especially for small publishers, and some of its clever capabilities;

'There are, however, many other aspects of LaTeX that facilitate high quality typesetting.
For one, the lines are not justified individually, as they are in Pagemaker and Quark, but in
entire paragraph blocks. This simulates the decision making of the master typesetters of old,
who would set a page so as to get the greatest evenness of word spacing. LaTeX—or rather the
underlying TeX hyphenation-justification algorithm—is able to produce that evenness
automatically (see fig. 1). This has been so successful an implementation of this old technique
that it has been borrowed now for Adobe’s InDesign program, where it is called the multi-line
composer. '

Below is his fig 1.

Figure 1: Even text due to hyphenation algorithm. Also note margin kerning and ff
ligatures. (Font: Adobe Garamond)

Thursday 10 December 2009


From the maker of the film Helvetica here is his latest project Objectified

Sunday 6 December 2009

Daniel Danger

One of my favourite print makers is a young artist called Daniel Danger working in New England. His website is here and a 3 x3 collection in the form of a Tuftean 'small multiple' created by Art Lies is shown above. Danger is a very accomplished young print maker working in New England who has been very succesful illustrating gig posters and CD covers for bands. I have a couple of his prints and the density of colour he uses and attention to fine detail make them very special pieces to own.

XKCD's Powers of Ten

Here is a complete order of magnitude comic strip from XKCD: the obserable universe in 2647 pixels (using log scale).

"I think". Charles Darwin July 1837.


Page from Dawins notebooks around July 1837 showing the first-known sketch by Charles Darwin of an evolutionary tree describing the relationships among groups of organisms. This was drawn about a month after he began his first full transmutation notebook. This drawing is the first in which Darwin seeks to explain evolutionary ancestry - above the tree he wrote "I think."

The Horse in motion - 1878

Here is a superb example of what Tufte calls a small multiple.

The Horse in Motion by Eadweard Muybridge. "Sallie Gardner," owned by Leland Stanford; running at a 1:40 gait over the Palo Alto track, 19th June 1878.

Source: Library of Congress Prints and Photographs Division; 

 Here is the set of stills in an animated GIF.

John Ruskin

My last post mentioned John Ruskin (1819 - 1900) - he was a superb draughtsman - here is my favourite example of his work.

John Ruskin's Study of Gneiss Rock, Glenfinlas, 1853. Pen and ink and wash with Chinese ink on paper, Ashmolean Museum, Oxford, England.

Visual Observation and the Camera Lucida

I have been thinking about the link between optical resolution and science. One of the key tools of science remains detailed visual observation. Until the late 1500's the ability of experimental scientists to detect differences visually was limited by the resolving power of the human eye. In addition, their ability to make detailed records of what they observed was limited by the artistic ability of their eye-brain-hand system. Although our image recording technology is now mainly digital, even today some specialised fields of science rely on the ability of humans to visually resolve differences and make hand drawn records.

For microscopic specimens or macro specimens with very fine detail a camera lucida attachment can be added to an ordinary light microscope. This allows you to view the field of view and trace and draw what you see. Having used one I can recommend it. 

I think that we under-appreciate the power of forcing ourselves to draw, it commands us to really see what is going on and to focus on the essentials of the object under scrutiny. In fact it was precisely this aim that motivated the noted English art critic and social thinker John Ruskin (1819 - 1900) to enthusiastically teach workingmen how to draw. He believed that learning to draw would teach people to really see and understand nature and thereby be happier. He told a Royal Commission on Drawing in 1857 that, "My efforts are directed not to making a carpenter an artist, but to making him happier as a carpenter". 

The camera lucida is no longer mainstream but research paleontologists such as Simon Conway-Morris (one of key scientists in the re-interpretation of the Burgess Shale fossils) still rely on camera lucida attachments on their light microscope to record the fine details of their fossils. These are great examples of what ET calls Mapped Pictures in Beautiful Evidence. For a recent example see, "New Malacostracan Crustacea from the Carboniferous (Stephanian) Lagerstatte of Montceau-les-mines, France" by Patrick R. Racheboeuf, Frederick R. Schram, and Muriel Vidal in the Journal of Paleontology 83(4):624-629. 2009. This paper includes excellent hand drawn camera lucida images of their newly discovered fossil Crustaceans.

Figure Caption

Palaeocaris secretanaeSchram, 1984, MNHN-SOT 12595, Assise de Montceau, Saint-Louis open cast, bed 0. Camera lucida drawings from latex casts; 1-2, latex cast of the left side of the exoskeleton exhibiting the thoracic and pleomere segments; note the occurrence of possible (?) epibiontic organisms on the thoracic segments (bold arrows); the thin arrows indicate the pereion/pleon limit; 3, latex cast of the right side of the anterior part of the exoskeleton; 4, tentative partial reconstruction of the exoskeleton showing only three pleomeres with posterior spinose margin; compare with Fig. 12 of Perrier et al. (2006). Scale bar = 2 mm

Integrated text, drawings and images

I think readers would very probably appreciate a very famous series of hand drawn walking guides to over 200 individual walks in the "fells" and hills of the English Lake district (Beatrix Potter country). These were made by Alfred Wainwright who lived in the lake district and was a passionate walker. 

They are superb examples of data integration. They include (all hand drawn) text descriptions of the walk, views from the start, views from the summits including angular arrangement of key features visible and distances, topographic information, maps, personal commentary and humour etc. A typical (but by no means the finest) image is shown below from Wikipedia. His book series (A Pictorial Guide to the Lakeland Fells: being an illustrated account of a study and exploration of the mountains in the English Lake District) is still in print and over 2 million copies have been sold. The books were made by him to be used as the walker progressed through the walk and are therefore very nice examples also of "Instructions at the point of Need".

A nice collection of Wainwrights own favourite walks has been published recently (see = including some nice "Look Inside pages").

Brain imaging skewed?

I thought readers would be interested in this paper recently published in Nature Neuroscience that throws some doubt on the analysis used in fMRI studies as published in the World's top Neuroimaging journals.


When I was working on Placenta with a PhD student (Charlie Orton) at the University of Liverpool. We wanted to represent for a cohort of cases all the information relating to a placenta from the mother (age, smoking or not, number of previous pregnancies), via the baby (sex, Apgar score, weight) to the macroscopic condition of the placenta (weight, size, condition) to the microstructure of the various components of the placanta in three layers (e.g. total surface area of terminal villi etc). The resulting display was based on finest Edward Tufte principles and we were very proud of it. I called it the Placentogram. The diagram therefore showed data on over 6 orders of magnitude in length (metres to microns) and allowed clinicians the chance to relate the clinical data they were used to seeing (e.g. Apgar score) with microstructural information that they were unused to.

Here is a real example. This plot shows the data from 14 births each individual birth is a column top to bottom. This was a subset of the Normal Birthweight - Non-smoking group. At the top is the mass of the baby in grams, then gender (I used international symbols for male and female), parity (how many confinements the mother has had at this birth)and the centile for the babys weight. The mass plot shows the max and min to the extreme right with mean and +/- 2 Standard errors. Next down is placental mass in grams, again with with mean and +/- 2 Standard errors, at right. I ordered these in increasing mass as the placenta was the key structure in the study. 

Below this is two boxes of data relating to the microstructure of the fetal capillary bed within the placenta. The terminal villi are anatomically defined and are the finest villi. The volume refers to total volume of terminal villi within the placenta and the three grey boxes indicate how this is distibuted in three equal volume tertiles. The maternal side is uppermost and fetal side lower. The dark grey indicates most volume of terminal villi in that tertile, mid grey the middle rank and white the lowest. The next box refres to the surface area of the terminal villi using same coding as the volume box. 

Comments: I produced this in MS Powerpoint! Which was a drag but the output doesn't look bad I think. The data moves from baby/mother at top to placenta below. Each parameter can be compared across the cohort and each individual up and down. The microstructural data is obtained with rigorous quantitative techniques called stereology (REF: Unbiased Stereology; Three-Dimensional Measurement in Microscopy by C.V. Howard & M.G. Reed Bios 2005). As you might expect there is a higher volume of the terminal villi nearer the maternal side of the placenta and likewise with the surface. The plot is worth looking at closely as one can make connections and comparisons in different ways. I am interested in the microstructural data first but a clinician may well come at it top down. 

Source: All data from an unpublished but excellent PhD thesis by my friend and colleague Dr Charlotte (Charlie) Orton - Stereological analysis of human placental microstructures from pregnancies complicated with intrauterine growth retardation and maternal cigarette smoking: a prospective case-controlled study. University of Liverpool 2002. Charlie looked in detail at about 150 placentas in total. 

Sports Balls

This is a great fun website - I particularly liked the poster below that shows the sizes of different sports balls ( The downside of this one as a piece of analytical design is that it's lacking a scale of measurement. The upside is Craig Robinson's very honest statement about his sources; "Sources: for some stupid reason, I didn't keep a note of where I got this information; I do seem to remember, though, spending a lot of time on the web sites of various sports' ruling bodies." 

Himalayan Panoramas

Here is a link to the Guardian newspaper which is a superb matched pair of Himalayan vistas taken 50 years apart (

The originals were taken by Fritz Muller and Erwin Schneider in the 1950s to map, measure and photograph the glaciers of the Himalayas. The American mountain geographer Alton Byers has returned to the precise locations of the original pictures and replicated 40 of the panoramas from the original 1950's expedition. This article shows a paired vista of the Imja glacier - as the paper says;  "the juxtaposed images are not only visually stunning but also of significant scientific value".

In particular this pair of images shows the transformation of the Imja glacier in the 1950's to the present day Imja lake. 

A classic Ed Ricketts List

This is a great list made by John Steinbecks long time collaborator Ed Ricketts. Ricketts was the model for at least 6 of Steinbecks most memorable characters, most notably perhaps "Doc" of Cannery Row. 

Ricketts was not fictional. He was a ground breaking marine biologist, ecologist, traveller and philosopher. I would recommend the interested reader to find the recently published collection of his travelogues "Breaking Through" (edited by K.A. Rodger) which has some of the best lists I have come across.

One of the most interesting pieces of writing in "Breaking Through" is a "Verbatim Transciption" of the trip that Ricketts and Steinbeck took to Baja and subsequently retold in "Log from the Sea of Cortez" by Steinbeck. Ricketts recorded things as the trip progressed and Steinbeck later tidied it up for publication. There are some excellent lists but the one below is one of my favourites and describes the blend of human and biological impressions made on Ricketts whilst in the La Paz area on Friday March 22 1940 (this appears on page 151 of Breaking Through).

"The peso is 5-1/2 or 6 to 1 here. I bought swank-looking huaraches for one dollar and one peso (7 pesos) and a fine iguana belt for 2.50 pesos; Epsom salts at a clothing store, Casa Gomez, one peso per kilo. I liked the blonde daughter. The girl in the pharmacy, I found entirely charming. The people are wonderful here. Ice is cinco centavos per kilo; not very good ice, tho. A quarter liter of Carta Blanca beer is 30 centavos per bottle, about 10 pesos per case, with 2.50 peso bottle return. I got 3 cigars from Sr. Gomez from his personal stock for 60 centavos, twisted - not wonderful, but satisfactory - Vera Cruz tobacco.
Borette is the poisonous puffer fish; its liver is said to be so poisonous that people use it to poison cats and flies.
Cornada is the hammerhead shark.
Barco is the red snapper.
Caracol (also Burrol) is the term for snails in general, particularly for the large conch for blowing like a horn.
Erizo is urchins, both kinds.
Abanico is sea fan, gorgonian.
Broma is barnacle.
Hacha is pinna, large clam."


I would recommend that you also read the Wikipedia entry on Pareidolia, which is defined as "a psychological phenomenon involving a vague and random stimulus being mistakenly perceived as recognizable". Its interest in the psychological literature is as the basis of the famous Rorschach inkblot test. It is also the basis of the "Virgin mary on toasted cheese sandwich" and "Jesus christ on an Oyster shell" type of images you can find via Google image search. It was nicely discussed by Michael Shermer in Scientific American May 2005 ( My belief is that during evolution the cognitive ability that Pareidolia is based on was of high selective value for early humans (its about seeing patterns in a noisy background). 

In my own field of quantitative microscopy this phenomena is particularly pervasive and has to be dealt with rigorously and early in training. Researchers are very adept at seeing a particularly microstructural feature at high magnification and then rationalising what they see as being in favour of or against their pet hypothesis. Beware the pretty pictures! Key evidence that a pretty picture is about to be used in a scientific paper includes the phrase; "A typical micrograph is presented in Figure 1". It is almost never a typical micrograph. Really good analytical reasoning for any inference based on microscopic images must (at least) answer the following issues;
(1) What process was used by design to obtain the sample that was imaged. (2) What precautions has the researcher taken to ensure that representative images were used for measurement. (3) How many measurements were taken and has any consideration been given to the number required to establish good evidence of the conclusion. (4) If the image represents a 2D section through the 3D structure has the researcher given a good explanation of how the 2D measurements she has made relate to the 3D structure of interest. (5) What have the image analysis tricks (PhotoShopping) done to the images and evidence within them.
The scientific discipline of drawing high quality evidence based conclusions from microscopy is known as stereology (pretty good Wikipedia entry on it). And as one famous stereologist Prof Luis Cruz-Orive once put it "Quantifying is a committing task" (Toward a more objective biology. Neurobiology of aging Vol 15 pp 377-378).

Map of the Area surrounding our Holiday Home

A Tom Gauld map of his holiday home. Complete with extensive key.

The extent of Sea Ice at the North Pole

Here is an link to images taken from a high resolution video posted at Bremen University. The data is based on ASMR-E sensors that can be used to compute the extent of sea ice. The videos are quite high resolution and they show the flow patterns of the sea ice. 

I like the unusual way of looking down at the Earth to the North Pole. 

Natural History of Manhattan

This NYT article gives a slideshow about a Natural history of Manhattan over the past 400 years. The new map-based exhibit opened at the Museum of the City of New York. It is called, "Mannahatta/Manhattan: A Natural History of New York City." The exhibit consists of historical accounts, maps and computer models that explore the ecology of Manhattan from the time before it became a city. The project has also its own website HERE and a book. This is a pretty good multi-media site that gives layers of meaning to those who now live in Manhattan. 

Tabula Peutingeriana

Here is a story about  the Tabula Peutingeriana which is a copy of an ancient Roman roadmap of Europe. It is not on display due to its fragility and light sensitivity, however, it was displayed for one day as part of Unesco's Memory of the World Register ( The map is almost a linear East-West mapping of important roads and destinations across Europe and Asia. 

Wikipedia has a good entry ( including a high resolution facsimile that can be downloaded.


This website ( has a great collection of high resolution images of rare books covering arts, history and science. For each book there is a viewer with thumbnails that allow you to browse through two page spreads. You can then zoom in to quite a high resolution. The books are phtographed from start to finish so you can appreciate the bindings, frontispiece, diagrams and text and how thay all interrelate.
This is quite a treasure trove. As an example, you can find a complete set of page view images from Robert Hookes splendid book on microscopy, Micrographia, which was published in London 1664. 

I have seen some of the images from this book before, but never in their proper context, nor at such high resolution. The images below show the spread of pages 114 and 115. The text on page 115 shows some of his explanation of how he obtained these images of cork cells.The figure on page 114 shows Hookes drawings of longituidinal and transverse sections through cork and where he obtained the sample (Hooke found these small separated structures reminded him of the cells of monks and he used that term to describe them - they have been called cells ever since). 

Caslon Letter Founder 1728

Here is a very high resolution scan of a specimen sheet issued by William Caslon, letter founder, from the 1728 edition of Cyclopaedia (
The book itself is here (

Further to my last post here is a picture diary describing exactly how the Old School Press made their first book - "The Bricks of Venice" by John Ruskin =

The image below is one of the first pages of chapter 3, Crenellations. It has some large Bembo italic for the chapter number and title. 

Old School Press

Here is a link to a small British printing press, the Old School Press in Bath, that is using traditional letterpress and binding techniques to make small runs of high quality books - both re-prints of older material and new books. 

This link = is to a book published by them called "The story of the revival of the Fell types in the 125 years from 1864" by Martyn Ould and Martyn Thomas, which describes and uses the type punches and matrices designed by John Fell and used by Oxford University Press - these original punches and types were rediscovered at O.U.P. in the the 1860s and this tells the story of how they were used and shows some of the output.

On Growth and Form

I was browsing my books recently and found my modern reprint copy of 'On Growth and Form' by the great naturalist D'Arcy Wentworth Thompson. Thompson  was a classicist, mathematician and zoologist. The book, originally published in 1917, is a brilliant collection of data graphics, prose and quantified images. 

One of his best know ideas is that simple physical deformations of complex systems can give rise to whole families of apparently unrealted natural forms. The image shown below is page 744 of the first edition (you can find the whole book in electronic form at the Internet Archive = It shows how a complex shape representing the 2D shape of a crabs carapace can after simple geometric transformations give rise to a family of different carapace shapes.

Book typesetting with LATEX

I taught myself LATEX this summer to get some lecture notes in shape. Having originally used the LATEX Book class I have now moved to the memoir class and can thoroughly recomend it. The attached is a two page spread chosen pretty much at random and it shows that you can integrate text, math and figures easily with a pretty professional looking book layout that is the default in memoir. 

The learning curve is reasonable and all the fancy headers, figure numbering, contents etc etc defaults are well chosen. The TEX set up on a PC was easy and free - I use the LED editor and the MikTex 2.7 package.
This is typeset onto B5 paper in PDF format and I have now found a pretty good quality short print run digital printers in the UK (this is not POD which is generally low quality, the shortest print run is 50 copies) to produce final book output. I'll keep you posted how the whole process goes.

The attached JPG is deliberately low resolution - its mainly to show the two page spread.

The elements of typographic style

Here is a nice interview with Robert Bringhurst, author of the book 'Elements of typographic style'( He comes over as a passionate and uncompromising person dedicated to high quality in typesetting and book design more generally. 

An example;

Q: In your opinion, what developments or trends in the design industry look dangerous?
Bringhurst:   The same developments and trends that look dangerous elsewhere: namely, ignorance and greed. The cult of personality and power, and the religion of money. These diseases are as visible in the typographic world as they are in the world of politics.

and a quote;

"The masters of the art, it seems to me, are those who never stop apprenticing".

Scaling images with well known objects

Here is a nice example ( of how to scale an object of interest (a mobile phone) by showing it next to other well known objects; an iPod, a pack of playing cards and a pad of Post-It notes.
This also acts as a link to the blog of Matthew Ericson ( the the deputy graphics director at The New York Times, where he manages a department of journalists, artists and programmers who produce the interactive information graphics for, as well as all the graphics for the print newspaper.
He has some nice maps and interactives graphics - his multi-decade analysis of the #1's of Michael Jackson is also interesting (

Spiral mapped images

Here is an extensively mapped image database of Trajans column ( The site maps the continuous spiral layout of the column's artwork with cartoons that have annotations and links to high resolution images. The navigation allows you to move up and down the column and see either individual panels or a whole spiral piece around the column at a particular height. The image below shows the navigation mechanism. 

Trajans column is much bigger than I had imagined - the human figures are about 2/3 full size and the inside of the column has a spiral staircase.


Sunday 8 November 2009

Unbiased Stereology - Reprint and Sample

I spent the summer teaching myself the LATEX typesetting system, mainly for unpublished lecture notes and case studies. However, I am in the process of re-setting the second edition of my book (on here), a sample chapter is here. The author website for the book is here.

Friday 6 November 2009

Statistics as a Liberal Art

This is a very thought provoking article from David Moore in 1998. His argument is that modern statistics is much less about doing the calculations and more about the 'grand ideas' that for the backbone of statistics as a distinctive discipline.

Some quotes;

" I find it hard to think of policy questions, at least in domestic policy, that have no statistical component. The reason is of course that reasoning about data, variation, and chance is a flexible and broadly applicable mode of thinking. That is just what we most often mean by a liberal art."


"Here is some empirical evidence that statistical reasoning is a distinct intellectual skill. Nisbett et al. (1987) gave a test of everyday, plain-language, reasoning about data and chance to a group of graduate students from several disciplines at the beginning of their studies and again after
two years. Initial differences among the disciplines were small. Two years of psychology, with statistics required, increased scores by almost 70%, while studying chemistry helped not at all. Law students showed an improvement of around 10%, and medical students slightly more than
20%. The study of chemistry or law may train the mind, but does not strengthen its statistical component."

You can get the full paper Here

Saturday 18 July 2009

Quantitative Intuition

To be good at quantification you need to develop an intuition about the relative magnitudes of the quantities you are interested in. This is highlighted nicely by this quote from William Ayrton

"One of the great difficulties experienced by people in mastering the quantitative science of electricity, arises from the fact that we do not number an electrical sense among our other senses, and hence we have no intuitive perception of electrical infant has distinct ideas about hot and cold, although it may not be able to put its ideas into words and yet many a student of electricity of mature years has but the haziest notion of the exact meaning of high and low potential, the electrical analogues of hot and cold."

William E. Ayrton, Practical Electricity, 1887, Preface.
Cited in The morals of measurement. Graeme Gooday. Cambridge University Press. 2004

Carlson Curve

I have written already about Moore's law, and its profound impact on society and science. However, there are other well known geometric progressions in technology, this paper is one example - Carlson, R. (2003). The Pace and Proliferation of Biological Technologies. In Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science Volume 1 No. 3.


The development of powerful laboratory tools is enabling ever more sophisticated measurement of biology at the molecular level. Beyond its own experimental utility, every new measurement technique creates a new mode of interaction with biological systems. Moreover, new measurement techniques can swiftly become means to manipulate biological systems. Estimating the pace of improvement of representative technologies is one way to illustrate the rate at which our ability to interact with and manipulate biological systems is changing."

Here is Figure 1 from the paper.

FIG. 1. On this semi-log plot, DNA synthesis and sequencing productivity are both increasing at least as fast as Moore?s Law (upwards triangles). Each of the remaining points is the amount of DNA that can be processed by one person running multiple machines for one eight hour day, defined by the time required for preprocessing and sample handling on each instrument. Not included in these estimates is the time required for sequence analysis. For comparison, the approximate rate at which a single molecule of E. coli DNA Polymerase III replicates DNA is shown (dashed horizontal line), referenced to an eight-hour day.

Sample processing time and cycle time per run for instruments in production are based on the experience of the scientific staff of the Molecular Sciences Institute and on estimates provided by manufacturers. ABI synthesis and sequencing data and Intel transistor data courtesy of those corporations. Pyrosequencing data courtesy of Mostafa Ronaghi at the Stanford Genome Technology Center. GeneWriter data courtesy of Glen Evans, Egea Biosciences. Projections are based on instruments under development.

McLuhan on TV & Comics asVisual media

"From the three million dots per second on TV, the viewer is able to accept, in an iconic grasp, only a few dozen, seventy or so, from which to shape an image. This image thus made is as crude as that of the comics. It is for this reason that ... the comics provide a useful approach to understanding the TV image, for they offer very little visual information or connected detail."

Understanding Media: The Extensions of Man. New York: McGraw-Hill, 1964 (pg 150).

Wells & Bush on Information

Data Deluge speaks strongly to the dramatic technological changes of the past 20 years or so. But it is of course part of a longer trend over the past 100 years in which the idea that increases in material culture and technology were posing both opportunities and issues associated with a deluge of data and information.

For example, the British science fiction write H.G. Wells imagined in the late 1930’s what a 'World Brain’ would be like and what it would enable (Wells 1938). His idea was that in the future scholars would have access at their desks to the complete catalogue of the Worlds knowledge. Wells imagined that this would be enabled by photographic means - based on the idea of microfilm and microfiche. However, if one replaces talk of micro-fiche with digital data then we can see just how prescient Wells’ vision was;

”our contemporary encyclopedias are still in the coach-and-horse phase of development, rather than in the phase of the automobile and the aeroplane. These observers realize that the modern facilities of transport, radio, photographic reproduction and so forth are rendering practicable a much more fully succinct and accessible assembly of facts and ideas than was ever possible before.”

Wells was not alone, at the end of the second world war the US politician and thinker Vannevar
Bush wrote a piece for Atlantic Magazine in which he reflected on the enormous changes that science and technology had brought in (Bush 1945). He marveled at the fact that;

”There is a growing mountain of research. But there is increased evidence that we are being bogged down today as specialization extends. The investigator is staggered by the findings and conclusions of thousands of other workersconclusions which he cannot find time to grasp, much less to remember, as they appear . . . Professionally our methods of transmitting and reviewing the results of research are generations old and by now are totally inadequate for their purpose.”

These thinkers had enormous foresight. They had begun to observe a significant change in the volume of data and information arising in general, and in scientific and technical work in particular, and realised that there were real issues raised by the deluge of information.

How long is a Petabyte life?

I have been thinking about Petabytes and tryng to get some perspective on how much data that really is.

In digital data terms a petabyte is a lot of data. 1 PB = 1,000,000,000,000,000 B = 1015 byte. Assuming a byte is 8 bits then a petabyte is 8 x 1015 bits.

According to this paper, Google processes more than 20 Petabytes of data per day using its MapReduce program.

According to Kevin Kelly of the New York Times, this reference, "the entire works of humankind, from the beginning of recorded history, in all languages" would amount to 50 petabytes of data.

These are all difficult to understand as they are abstract. So I tried to find a way of understanding what a Petabyte is in human terms. Scientific researchers estimate that the human retina communicates with the brain at a rate of 10 million bits per second (Reference HERE) or 106 bits per second. This sounds pretty impressive. How long does it take a human eye-brain system to move a petabyte of data (assuming that you could keep your eyes permanently open so that you are getting your full 10 million bits per second).

By my calculations a year is 3.15 x 107 seconds. This means a total amount of data per year from retina to brain of 3.15 x 1013 bits. Dividing 8 x 1015 by 3.15 x 1013 we get 254 years. This is a long time to keep your eyes open!

If we take a normal human life to be the biblical standard of Psalms 90: The days of our years are threescore years and ten, then a normal human creates about 0.27 petabytes in their life.

So I will define a new unit, the PetaBlife, with a symbol which is the number of standard human lifetimes required for a human retina to make a PetaByte of data.

If we take Google seriously, then each year they are processing the equivalent of 7.3 x 103 ℘.


Thursday 16 July 2009

No evidence that prayer alleviates ill health

The following is NOT a hoax. It is the summary of a recently published Cochrane review of the evidence for or against the effects of intercessory prayer for the alleviation of ill health.

In fact this is a great example of an objective and balanced analysis of the evidence for the efficacy of a treatment. Full report HERE.

Intercessory prayer for the alleviation of ill health

Leanne Roberts1, Irshad Ahmed2, Steve Hall3, Andrew Davison4

1Hertford College, Oxford, UK. 2Psychiatry, Capital Region Mental Health Center, Hartford, Connecticut, USA. 3The Deanery, Southampton, UK. 4St Stephen's House, Oxford, UK

Contact address: Leanne Roberts, Hertford College, Catte Street, Oxford, OX1 3BW, UK. (Editorial group: Cochrane Schizophrenia Group.)

Cochrane Database of Systematic Reviews, Issue 3, 2009 (Status in this issue: Edited, commented)
Copyright © 2009 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
DOI: 10.1002/14651858.CD000368.pub3
This version first published online: 15 April 2009 in Issue 2, 2009. Re-published online with edits: 8 July 2009 in Issue 3, 2009. Last assessed as up-to-date: 13 November 2008. (Help document - Dates and Statuses explained).

This record should be cited as: Roberts L, Ahmed I, Hall S, Davison A. Intercessory prayer for the alleviation of ill health. Cochrane Database of Systematic Reviews 2009, Issue 2. Art. No.: CD000368. DOI: 10.1002/14651858.CD000368.pub3.


Prayer is amongst the oldest and most widespread interventions used with the intention of alleviating illness and promoting good health. Given the significance of this response to illness for a large proportion of the world's population, there has been considerable interest in recent years in measuring the efficacy of intercessory prayer for the alleviation of ill health in a scientifically rigorous fashion. The question of whether this may contribute towards proving or disproving the existence of God is a philosophical question lying outside the scope of this review of the effects of prayer. This revised version of the review has been prepared in response to feedback and to reflect new methods in the conduct and presentation of Cochrane reviews.

To review the effects of intercessory prayer as an additional intervention for people with health problems already receiving routine health care.

Search strategy
We systematically searched ten relevant databases including MEDLINE and EMBASE (June 2007).

Selection criteria
We included any randomised trial comparing personal, focused, committed and organised intercessory prayer with those interceding holding some belief that they are praying to God or a god versus any other intervention. This prayer could be offered on behalf of anyone with health problems.

Data collection and analysis
We extracted data independently and analysed it on an intention to treat basis, where possible. We calculated, for binary data, the fixed-effect relative risk (RR), their 95% confidence intervals (CI), and the number needed to treat or harm (NNT or NNH).

Main results
Ten studies are included in this updated review (7646 patients). For the comparison of intercessory prayer plus standard care versus standard care alone, overall there was no clear effect of intercessory prayer on death, with the effect not reaching statistical significance and data being heterogeneous (6 RCTs, n=6784, random-effects RR 0.77 CI 0.51 to 1.16, I2 83%). For general clinical state there was also no significant difference between groups (5 RCTs, n=2705, RR intermediate or bad outcome 0.98 CI 0.86 to 1.11). Four studies found no effect for re-admission to Coronary Care Unit (4 RCTs, n=2644, RR 1.00 CI 0.77 to 1.30).Two other trials found intercessory prayer had no effect on re-hospitalisation (2 RCTs, n=1155, RR 0.93 CI 0.71 to 1.22).

Authors' conclusions
These findings are equivocal and, although some of the results of individual studies suggest a positive effect of intercessory prayer,the majority do not and the evidence does not support a recommendation either in favour or against the use of intercessory prayer. We are not convinced that further trials of this intervention should be undertaken and would prefer to see any resources available for such a trial used to investigate other questions in health care.

Plain language summary

Intecessory Prayer for the alleviation of ill health
Intercessory prayer is a very common intervention, used with the intention of alleviating illness and promoting good health. It is practised by many faiths and involves a person or group setting time aside to petition God (or a god) on behalf of another who is in some kind of need, often with the use of traditional devotional practices. Intercessory prayer is organised, regular, and committed. This review looks at the evidence from randomised controlled trials to assess the effects of intercessory prayer. We found 10 studies, in which more than 7000 participants were randomly allocated to either be prayed for, or not. Most of the studies show no significant differences in the health related outcomes of patients who were allocated to be prayed for and those who allocated to the other group.

Wednesday 15 July 2009

Fact Checking

Recently I drew your attention to an article in WIRED in August 2008 that declared the end of science as we know it HERE. It was clearly hubris and I have just found out that this was an understatement. See this interesting article from Peter Norvig who not only explains how he had been misquoted in the WIRED article, but also in passing pays homage to the legendary 'fact checking' of the New Yorker magazine.


Saturday 4 July 2009

R - the de facto Stats standard?

Here is an item on the R language in the The New York Times , highlighting the spread of R as the package of choice for academics and commercial users. And a related NYT blog item is here. One quote is interesting - "Intel Capital has placed the number of R users at 1 million".

Friday 3 July 2009

Data Mining

I have been reading up on using R for graphics and followed up on John Maindonald's book (HERE). He has some great resources on his website describing his view as a statistician on Data Mining (HERE) and I particularly liked this paper Data, science and new computing technology. From the
New Zealand Journal of Science 62 (2005): 126-128.


Monday 29 June 2009

Digitising is NOT measuring

Measurement is an operationally defined process. It requires a well defined protocol that describes what is being measured by what means and with what level of reproducibility and an understanding of the error structure of the problem.

Digitising is the capture of digital data from a sensor. It is a new and low cost way of generating petabytes of data. However, simply taking an analogue input and transforming it to a digital image or signal does not mean it is a measurement.

There are millions and millions of digital images captured every day (perhaps billions). The vast majority of these are NOT measurements they are 'snapshots'. In order to use digital imagery as a measurement modality for science one needs to take care of magnification issues (not always equal in X-Y), linearity of grey scale response and/or colour response, bit depth, illumination set up to highlight features of interest, effect of image compression, frequency response of lenses used etc etc.


Saturday 27 June 2009

Science Studies the Sardine (Ed Ricketts 1947)

The following is the full text of an article published by Ed Ricketts in the Monterey Peninsula Herald in 1947.

Unfortunately for the sardine, and the extended marine food chain that it forms part of, Ricketts was killed in May 1948 and his deep ecological insight and campaigning capability never helped save the sardine. Much later, in 1998, well known fisheries ecologist Dr Daniel Pauly published a seminal paper in Science called 'Fishing Down Marine Food Webs'. This is both a citation classic (with over 1,000 citations) and a highly influential paper. Pauly was not aware of Ricketts work when his paper was published.

Science Studies the Sardine

Mysterious Disappearance Focuses Attention on Woeful Lack of Information Regarding Billion Dollar Fish

By EDWARD F. RICKETTS, Pacific Biological Laboratories

The Herald has undoubtedly reported waterfront opinion correctly in stating that the shortage of sardines is being attributed to a change in the currents. I doubt very much if we can rely on such a simple explanation. I am reminded instead of an old nursery rhyme. Like the "farmer-in-the-Dell" there's a long chain of events involved. And you have to be familiar with all of them in order to know any one very clearly.

This is complicated still further by the fact that scientists haven't yet unravelled it all completely. But already quite a lot of information is available, and from most of the parts we can piece together some sort of picture puzzle. The result may be a labyrinth, but there's no way to avoid it. We just have to be patient and try to follow it through. Because I've done this myself after a fashion, perhaps I can be better than no guide at all.

By means of a very efficient straining apparatus in the gills, sardines are able to feed directly on the most primitive foodstuffs in the ocean. This so-called "plankton," chiefly diatoms (free floating microscopic plants) is the product of oceanic pastures, and like grain and grass and root crops, bears a direct relation to sunlight and fertilizer. Except that in the oceans of course you don't have to depend on the rains for moisture.

Some of these ocean pastures produce more per acre than the others. This is due to variations in the amount of fertilizer brought to the surface by a process called "upwelling."

Only the upper layers of water receive enough light to permit the development of plants. In most places, when the sunlight starts to increase in spring, these plants grow so rapidly that they deplete the fertilizer and die out as a result. In the familiar pattern of dust to dust and ashes to ashes, their bodies disintegrate and relase the chemical elements. These, in the form of a rain of particles, contantly enrich the dark-deeper layers.

On the California coast - one of the few places in the world, incidentally, where this happens - winds from the land blow the surface waters of the shore far out to sea. To replace these waters, vertical currents are formed which bring up cool, fertilizer laden waters from the depths to enrich the surface layers, maintaining a high standard of fertility during the critical summer months. Since the seeds of the minute plants are everywhere ready and waiting to take advantage of favorable conditions, these waters are always blooming. It's a biological rule that where there's food, there's likely to be animals to make use off it. Foremost among such animals is the lowly sardine.

In the long chain, this is the first link. Reproductive peculiarities of the sardine itself provide the second. Above their immediate needs, adult sardines store up food in the form of fat. During the breeding season, ALL this fat is converted into eggs and sperm. The adult sardine is nothing but a factory for sexual products.

The production of plankton is known to vary enormously from year to year. If feeding conditions are good, the sardines will all be fat, and each will produce great quantities of eggs. If the usual small percentage of eggs survive the normal hazards of their enemies, a very large year class will be hatched.

If then feeding conditions are still good at the time and place of hatching (spring in southern California and Northern Mexico), huge quantities of young sardines will be strewn along the Mexican coast by south-flowing currents. Here their enemies are also abundant. Including man - chiefly in the form of bait fishermen from the tuna clippers. Those surviving this hazard move back into California waters, extending each year further and furher up the coast, the oldest finally migrating each summer clear up to Vancouver Island. All return during the winter to the breeding ground. This process builds up until a balance is established. Or until man, concluding that the supply is in fact endless, builds too many reduction plants on that assumption.

On the other had, the small year classes resulting from decreased plankton production, will in themselves deplete the total sardine population. If then the enemies-again chiefly man - try desperately to take the usual amounts, by means for instance of more and larger boats, greater cruising radius, increased fishing skills, etc, sardine resources can be reduced to the danger point.

All this being true, we might be able to forecast the year classes if we could get to know something about the conditions to which the adults are subjected at a given time. Their eggs are produced only from stored fat. The fat comes only from plankton. And there are ways of estimating the amount of plankton produced.

An investigator at the Scripps Institution of Oceanography long ago realized the fundmental importance of plankton. He has been counting the number of cells in daily water samples for more than 20 years. This scientist, now retiring perhaps discouraged because the university recently hasn't seen fit even to publish his not-very-spectacular figures, ought to be better known and more honored. He deals with the information of prime importance to the fisheries. But in order to get this information in sufficient detail, you have to know the man, and get him to write you about it personally.

Figures from only a single point have very limited value. We should have data of this sort for a number of places up and down the coast so as to equalize the variations; and for many years. But we're lucky to have them even for La Jolla. The graph shows 1926, 1931, 1934 to have been poor years, but during those times the total sardine landings were still apparently well within the margin of safety. Years 1941-42 were also poor. But during this time the fishery was bringing in really large quantities. The evidence is that very lean adults resulted from these lean years, producing few eggs. And we would have done well take only a few of them and their progeny. A glance at the chart labelled "California Sardine Landings" will show what actually happened instead.

There's still another index of sardine production. This time the cat of the wife of the farmer-in-the-dell catches herself a fine succulent mouse.

We know that the food of the sardine depends directly on fertility. And that fertility depends on upwelling. Obviously, the water recently brought up from depths is colder than at the surface. When upwelling is active, surface temperatures will be low. Now we can very easily calculate the mean annual sea water temperatures from the readings taken daily at Hopkins Marine Station and elsewhere. The chart which has been prepared to show these figures bears out again the fact that 1941 and'42 must have been unfortunate years for the sardines. Following those years we should have taken fewer so as not to deplete the breeding stock.

Instead, each year the number of canneries increased. Each year we expended more fishing energy pursuing fewer fish. Until in the 1944-46 seasons we reached the peak of effort, but with fewer and fewer results. Each year we've been digging a little further into the breeding stock.

A study of the tonnage chart will show all this, and more. The total figures, including Canada, tell us pretty plainly that the initial damage was done in 1936-37, when the offshore reduction plants were being operated beyond regulation. And the subsequent needs of the war years made it difficult then also for us to heed the warnings of the scientists of the Fish and Game Division.

The answer to the question "Where are the sardines?, becomes quite obvious in this light. They're in the cans! The parents of the sardines we need so badly now were being ground up then into fish meal, were extracted for oil, were being canned; too many of them, far too many.

But the same line of reasoning shows that even the present small breeding stock, given a decent break, will stage a slow comeback. This year's figures from San Pedro, however, indicate no such decent break.

During this time of low population pressure, the migrating few started late, went not far, and came back earlier than usual. Actually we had our winter run during August and September when the fishermen were striking for higher rates. By the time we had put our local house back in order, the fish had gone on south. Many had failed to migrate in the first place, and were milling around their birthplace in the crowded Southern California waters. And the San Pedro fleet, augmented by out-of-work boats from the northern ports, has been making further serious inroads into the already depleted breeding stock.

My own personal belief is nevertheless optimistic. Next fall I expect to see the fish arrive, early again, and in somewhat greater quantity. But a really good year will be an evil thing for the industry. And still worse for Monterey. Because we'll forget our fears of the moment, queer misguided mortals that we are! We'll disregard conservation proposals as we have in the past; we'll sabotage those already enacted. And the next time this happens we'll be really sunk. Monterey will have lost its chief industry. And this time for good!

If on the other hand, next year is moderately bad - not as bad as this year, Heaven forbid, but let's hope it's decently bad! - maybe we'll go along with such conservation measures as will have been suggested by a Fish and Game Commission which in the past has shown itself far, far too deferent to the wishes of the operators - or maybe to their lobby!

We have before us our own depleting forests. We have Sweden's example; now producing more forest products every year than it did a hundred years back when the promise of depletion forced the adoption of conservation measures. We have this year's report on our own halibut landings, like the old days - the result solely of conservation instituted by a United States-Canadian commission which took over in the face of obvious depletion.

If we be hoggish, if we fail to cooperate in working this thing out, Monterey COULD go the way of Nootka, Fort Ross, Notley's Landing, or communities in the Mother Lode, ghost towns that faded when the sea otter or lumber or the gold mining failed. If we'll harvest each year only that year's fair proportion (and it'll take probably an international commission to implement such a plan!) there's no reason why we shouldn't go on indefinitely profiting by this effortless production of sea and sun and fertilizer. The farmer in the dell can go on with his harvesting.

This text from material reprinted for educational purposes by Roy van de Hoek, in its entirety from the newspaper:
MONTEREY PENINSULA HERALD 12th Annual Sardine Edition, p.1,3 March 7, 1947.

Thursday 18 June 2009

"Fact free science"

"I discuss below a particular example of a dynamic system 'Turing's morphogenetic waves' which gives rise to just the kind of structure that, as a biologist, I want to see. But first I must explain why I have a general feeling of unease when contemplating complex systems dynamics. Its devotees are practicing fact-free science. A fact for them is, at best, the output of a computer simulation: it is rarely a fact about the world.

John Maynard Smith, "Life at the Edge of Chaos?," The New York Review of Books, March 2, 1995

Tuesday 16 June 2009

Microscopy Site

The humble light microscope is an icon of research science. It has a practical 'resolution' that on a good day almost achieves the theoretical resolution that was calculated by Abbe in the 1880's. HERE is a great and very large website dedicated to microscopy. Enjoy.

Ancient Geometry, Stereology & Modern Medics

This is a paper HERE that Vyvyan Howard and I had fun writing a few years back and published in Chance magazine. It's a popular science type article on “Ancient Geometry, Stereology & Modern Medics”, that was originally written in 2002 and which I have recently tidied up into a PDF. It links ancient ideas in geometry with random sampling and state-of-the-art scientific imaging.

One of the key characters is a famous mathematician Zu Gengzhi, who had a famous mathematical Father Zu Chongzhi (in the picture).

Zu Gengzhi was the first to describe what we now refer to as Cavalieri's theorem;

"The volumes of two solids of the same height are equal if the areas of the plane sections at equal heights are the same."

The translation by Wagner (HERE) is given as

If blocks are piled up to form volumes,
And corresponding areas are equal,
Then the volumes cannot be unequal.


Inspired by a 2004 paper by Vyvyan Howard et al (HERE) I have been trying to develop a business model whereby high quality quantification of the phenotypic impact of specific gene knock-outs in well defined strains of transgenic mice is provided as a service.

The quantification is achieved with protocolised stereological techniques, and clients get the specific data they need on time and in full. At the same time the parent business builds a proprietary database that can be data-mined to provide new insights and discoveries.

I worked with a Masters Student, James Stone, at the Manchester Science Enterprise Centre in 2007 to develop the concept and try to understand the market positioning for such a business, tentatively called PhenoQuant. James and I did some outline work on a business plan and he explored routes for funding the opportunity. The plan is not mature and it is currently dormant but this is a real opportunity to bring quantification to one key aspect of modern Gene based biomedical research work.

Monday 15 June 2009

The Art of the Soluble

"No scientist is admired for failing in the attempt to solve problems that lie beyond his competence. The most he can hope for is the kindly contempt earned by the Utopian politician. If politics is the art of the possible, research is surely the art of the soluble. Both are immensely practical-minded affairs." P B Medawar, The Art of the Soluble, 1967.

Galileo the quantifier

"The man who undertakes to solve a scientific question without the help of mathematics undertakes the impossible. We must measure what is measurable and make measurable what cannot be measured".

Galileo during his period in Padua before moving to Florence in 1610.

Cited in; The science of measurement: A historical survey. Herbert Arthur Klein. Dover 1988. p509.

The Data Deluge - 1987 Style

The earliest reference I have yet found to a 'Data Deluge' is in the New York Times 22 years ago (30th June 1987).

This article describes how mad baseball fans can get "...the ultimate service for the most avid baseball addict: daily, detailed reports on 16 minor leagues encompassing 154 teams and more than 3,000 players". This data deluge is made possible by facsimile machines installed in more than 150 minor league ball parks.

'Official scorers or a club official are supposed to file the information within an hour after the game and then the phone-line cost to the team is minimal since the fax transmissions take about 40 seconds each.