Wednesday 12 December 2012

Archive of Scientific Illustrations

HERE is a mind boggling archive of thousands of scientific illustrations of many different styles and historical periods. 

The example below is an illustration of a Halichoeres daedalma from The fishes of Samoa. Washington, Government print off.,1906. The image is from HERE.

For further details on the taxonomic status of this species see HERE.

Saturday 8 December 2012

The benefits of tea

The British love their tea. But they don't take it too seriously. Hiroyuki Suzuki does. HERE is his visual book that uses a unique colour coding to describe the benefits of 80 different teas. The combination of benefits creates what the author calls a "Ripple Chart" the more ripple, the more benefits. 

London Blitz Map

This website has mapped the complete census of bombs that landed on London during the Blitz (Oct 1940-June 1941). Users can search for dates and streets to see details of whne bombs landed. 

The image below shows how thoroughly London was bombed. 


Friday 30 November 2012

A potters netsuke collection

The Hare with Amber Eyes is a book by Edmund de Waal - a potter. It describes his inheritance of an incredible collection of 264 antique Japanese Netsuke - tiny carved animals or ornaments. His website is here.

The Hare is shown below.

STYN Pinball Printer

Sam van Doorn has created a modified pinball machine that allows users to create a unique print - the pinball is modified so that a sheet of paper goes in it and the ball is inked. The final images look like colourful bubble chamber plots. His site is HERE.

Tuesday 6 November 2012

Bear Hunt

One of the very best books for children is Michael Rosen & Helen Oxenbury's classic We're Going On a Bear Hunt  (HERE)

The Guardian has a great piece today in which the writer and illustrator describe how they made the book (HERE). 

Illustration: © 1989 Helen Oxenbury.

Sunday 4 November 2012

An Examination into the Structure of the Cells of the Human Lungs

Although best know for botanical art Franz Bauer was also an excellent anatomical artist. 

Below is a figure from "An Examination into the Structure of the Cells of  the Human Lungs; with a View to Ascertain the Office They Perform in Respiration." by Everard Home and F. Bauer published in the Phil. Trans. R. Soc. Lond.  1827 117, 58-64. This paper and others with Bauer illustrations are available as PDF's from the Royal Society (HERE).

The figure caption reads:
Fig 1. represents 1/64th part of an inch of the external surface of the human lung, the cells of which are filled with quicksilver; magnified 20 diameters.

Fig. 2. a transverse section of 1/64th part of an inch of the human ling, in which the arteries are filled with red and the veins with yellow minute injection ; magnified 20 diameters.

Saturday 3 November 2012

On making drawings of microscopic subjects

The Austrian botanical illustrator Franz Bauer came from a family of gifted artists (HERE).  Franz spent nearly 50 years at Kew gardens as a botanical artist (HERE).

Bauer was also one of the most keen eyed observers of his day. He used a range of microscopes and developed his own observation techniques. For example in November 1836 he wrote a letter to Andrew Pritchard describing his method for making accurate microscopic drawings. This letter was published in 1837 as an Appendix to Micrographia by C.R. Goring & Andrew Pritchard (HERE).

The Appendix written by Franz Bauer is entitled "On making drawings of microscopic subjects". Bauer used two ruled glass micrometers (or graticules) both ruled into squares that were 1/40th inch on their sides. One of the graticules was placed in the eyepiece and the other on the stage. The magnification of the microscope was then adjusted until an integral number of the eyepiece divisions fit into a single division of the stage graticule. This meant he could calculate magnification. He could then leave the maicroscope set up and remove the stage graticule. When he now drew what he saw on paper he first drew a sguare grid of one inch squares. Thus he could accurately record on paper the magnification of the object.

One of his figures is shown.

A is 2 1/2 400ths of an inch long and 1/900th inch wide.
B is 2/400ths of an inch long
C is 1/400th of an inch long
D is 1/800th of an inch

The three fossil animacules in E are about 1/1200th inch long

And from Bauers description;
"The globular fungi at F are 1-1600th part of an inch in diameter, and the very minute globules of blood at G are each about 1-2400th or 1-2500th part of an inch in diameter."

Note that 1/2500th of an inch is about 10 microns.

Red blood cells are 6-8 microns in diameter.

Thursday 1 November 2012

Passion fruit pollen

HERE is a beautiful scanning electron microscopy image of three passion fruit pollen grains. Taken by    Louisa Howard - Dartmouth College EM Facility.


Tuesday 30 October 2012

All things are made of atoms

At the heart of modern physics is the atomic hypothesis, the simple notion that the universe is fundamentally granular.

If, in some cataclysm, all scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or atomic fact, or whatever you wish to call it) that all things are made of atoms — little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another. In that one sentence you will see an enormous amount of information about the world, if just a little imagination and thinking are applied.
Feynman, R.P., Leighton, R.B. and Sands, M. (1964). The Feynman Lectures on Physics. Addison Wesley. p1-2.

All things are made of atoms. Tiny particles that humans are unable to directly experience. Although we cannot see, hear, smell or feel individual atoms, there is abundant scientific evidence that they exist. After nearly two hundred years of experimental testing, the atomic hypothesis hasn't been falsified. Informally, many scientists would probably think of the atomic hypothesis as a fact.  Still, the idea remains counter intuitive. Matter does not readily reveal it's fundamental granularity. What we actually see and feel everyday is a continuous world.  

One of the people who took seriously the challenge of experimentally investigating the atomic hypothesis was the French scientist Jean Perrin (1870 – 1942). Perrin studied Brownian motion of minute particles suspended in liquids. His work verified Einstein’s theoretical explanation of this phenomenon.  It confirmed the atomic nature of matter and he won the Nobel Prize for Physics in 1926.

The figure below is a classic experimental image obtained by Perrin. The original text describing his observations is below;
The figure here reproduced shows three drawings obtained by tracing the segments which join the consecutive positions of the same granules of mastic at intervals of 30 seconds. It is the half of the mean square of such segments which verifies the formula of Einstein. One of these drawings shows 50 consecutive positions of the same granule. They only give a very feeble idea of the prodigiously entangled character of the real trajectory. If the positions were indicated second to second, each of these rectilinear segments would be replaced by a polygonal contour of 30 sides, relatively as complicated as the drawing here reproduced, and so on.
 Brownian Movement and Molecular Reality.
By M. Jean Perrin
Translated from the Annales de Chemie et de Physique 8me series
September 1909
F Soddy M.A. F.R.S.

Available HERE.

Friday 26 October 2012

Attenborough's Lear Prints

The Guardian has a really good piece HERE on David Attenboroughs collection of Edwards Lear lithographs of birds.

Culmenated Toucan

Culmenated Toucan (Raphastos culmenatus) from John Gould FRS, A Monograph of the Ramphastidæ, or Family of Toucans (London, 1834)
© The Royal Society

Thursday 25 October 2012

Data Breadcrumbs

One of the most thought provoking pieces I have read about Big Data is by Sandy Pentland HERE on the Edge website. 

The first few paragraphs of this piece;

I  believe  that  the  power  of  Big  Data  is  that  it  is  information  about  people's  behavior  instead  of information about their beliefs. 

It's about the behavior of customers, employees, and prospects for your new business. 

It's not about the things you post on Facebook, and it's not about your searches on Google, which is what most people think about, and it's not data from internal company processes and RFIDs. 

This sort of Big Data comes from things like location data off of your cell phone or credit card, it's the little data breadcrumbs that you leave behind you as you move around in the world.

What those breadcrumbs tell is the story of your life. 

It tells what you've chosen to do. 

That's very different than what you put on Facebook. 

What you put on Facebook is what you would like to tell people, edited according to the standards of the day. 

Who you actually are is determined by where you spend time, and which things you buy. 

Big data is increasingly about real behavior, and by analyzing this sort of data, scientists can tell an enormous amount about you. 

They can tell whether you are the sort of person who will pay back loans. 

They can tell you if you're likely to get diabetes

They can do this because the sort of person you are is largely determined by your social context, so if I can  see  some  of  your  behaviors,  I  can  infer  the  rest,  just  by  comparing  you  to  the  people  in  your crowd.

For more on the Trail of Breadcrumbs see HERE

Tuesday 23 October 2012

Dead Salmon thinking

HERE is a great piece of science. A poster describing an fMRI study of a dead salmon. It serves as a warning for all those scientists who use fMRI that many of the statistical methods they use routinely are fraught with real problems. 

Monday 22 October 2012

Teaching to See

HERE is a great 40 minute video about the lifes work of German born designer Inge Druckery.

Image from the film copyright Graphics Press.

Thursday 4 October 2012

The Unexpected Visitor

Alfred Lukyanovich Yarbus (1914 -1986) was a Russian psychologist who made a number of seminal studies of eye movements. Many of his most interesting results were published in a book, translated into English and published in 1967 as Eye Movements and Vision. [1]  This book is now out of print but you can find PDF copies to download.

I first saw some of Yarbus' data about 13 years ago as scratchy black and white scans from the book.

One of the most compelling of Yarbus' experiments was an eye-tracking study he performed where he asked subjects to look at a reproduction of a Russion oil painting An Unexpected Visitor painted by Ilya Repin in 1884.

Yarbus asked the subjects to look at the same picture in a number of different ways, including; [1] examine the painting freely. [2] estimate the material circumstances of the family. [3] assess the ages of the characters [4] determine the activities of the family prior to the visitor’s arrival. [5] remember the characters’ clothes. And [6] surmise how long the visitor had been away from the family. What is brilliant is that the eye-tracking traces recorded by Yarbus showed that the subjects visually interrogate the picture in a completely different way depending on what they want to get from it.

Cabinet Magazine (Issue 30 The Underground Summer 2008) has a piece by Sasha Archibald called Ways of Seeing that takes the original eye-tracking traces from Yarbus' book and superposes them on a colour reproduction of the painting. This is the first time I have seen this done. The originals in the book by Yarbus are disembodied eye-tracking traces laid out near to, but not overlaying, the reproduction of the Repin painting. 

These new overlays by Archibald are worth comparing. Here is (left) the original image (middle) free examination and (right) what the subject did when asked to estimate the material circumstances of the family.  

[1] A. L. Yarbus, Eye Movements and Vision. New York: Plenum Press, 1967. (Translated from Russian by Basil Haigh. Original Russian edition published in Moscow in 1965.)

Monday 1 October 2012

Instant photography at the push of a button!

The Polaroid SX-70 was a technological breakthrough. It was launched in 1972 and allowed a photographer to take a photo and then instantly see what had been captured. It was famously used by Warhol and Hockney and still has its devotee's today. 

A new book by Christopher Bonanos, Instant: A cultural history of Polaroid, has just been published describing the story of Polaroid's instant cameras HERE.

The blurb from;

"Instant photography at the push of a button!" During the 1960s and '70s, Polaroid was the coolest technology company on earth. Like Apple, it was an innovation machine that cranked out one must-have product after another. Led by its own visionary genius founder, Edwin Land, Polaroid grew from a 1937 garage start-up into a billion-dollar pop-culture phenomenon. Instant tells the remarkable tale of Land's one-of-a-kind invention-from Polaroid's first instant camera to hit the market in 1948, to its meteoric rise in popularity and adoption by artists such as Ansel Adams, Andy Warhol, and Chuck Close, to the company's dramatic decline into bankruptcy in the late '90s and its unlikely resurrection in the digital age. Instant is both an inspiring tale of American ingenuity and a cautionary business tale about the perils of companies that lose their creative edge.
 Although Polaroids later earned a reputation for being low-cost and disposable, as well as instant, Edwin Land had always made a concious effort to get photographers and artists to use his cameras. Below is a picture by the legendary American photographer Ansel Adams of Yosemite Falls & Flowers (1979). And yes that is a classic Polaroid - it is a 3 1/4"  x 3 1/4 " square. 

 WestLicht Collection (HERE)

Thursday 6 September 2012

...a mote of dust suspended in a sunbeam.

The "Pale Blue Dot" is an image taken by the Voyager 1 space craft in 1990 from a distance of about 6 billion kilometres. 

Here it is.

This image prompted Carl Sagan to publish a book in 1994 called Pale Blue Dot. In it he has this passage;

"Look again at that dot. That’s here. That’s home. That’s us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every ‘superstar,’ every ‘supreme leader,’ every saint and sinner in the history of our species lived there — on a mote of dust suspended in a sunbeam.

The Earth is a very small stage in a vast cosmic arena. Think of the endless cruelties visited by the inhabitants of one corner of this pixel on the scarcely distinguishable inhabitants of some other corner, how frequent their misunderstandings, how eager they are to kill one another, how fervent their hatreds. Think of the rivers of blood spilled by all those generals and emperors so that, in glory and triumph, they could become the momentary masters of a fraction of a dot.

Our posturings, our imagined self-importance, the delusion that we have some privileged position in the Universe, are challenged by this point of pale light. Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity, in all this vastness, there is no hint that help will come from elsewhere to save us from ourselves.
The Earth is the only world known so far to harbor life. There is nowhere else, at least in the near future, to which our species could migrate. Visit, yes. Settle, not yet. Like it or not, for the moment the Earth is where we make our stand.
It has been said that astronomy is a humbling and character-building experience. There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we’ve ever known."

Tuesday 21 August 2012

Durers Grid

Durers Grid

The image is from HERE and below is the full page view - from e-rara in Switzerland.

Monday 20 August 2012

Durer's Drawing Frame (Nuremberg 1525)

A drawing frame from Durer's textbook on measurememt (Underweysung der Messung mit dem Zirckel und Richtscheyt). Image from HERE

Friday 17 August 2012

The Art of Limitations

In the early 1980's the English artist David Hockney made a series of very distinctive images using the Polaroid SX-70 instant colour camera. Hockney had hit upon the idea of using the fixed lens of the camera and the white frame of each print to create unique photo montages, or joiners as he called them. Each of the joiners is a single composition that is created from dozens or hundreds of individual Polaroid prints. The separate Polaroid's are stuck together and the frame around each image is left intact. The combination of multiple white frames, when butted up together or overlaid with multiple other Polaroids, creates a grid. This grid is therefore an integral part of the way the joiners are created. 

These images have a unique aspect and perspective. (The New York based band Talking Heads created a cover for their second album More songs about buildings and Food in 1978 using a similar approach. It is not clear whether Hockney had co-incidentally arrived at a similar method or had been influenced by the album cover. )
Why did Hockney, a famous painter, choose to create images that are far from painterly? 

Perhaps the best of the joiners is a piece called Noya and Bill Brandt with self-portrait, Pembroke Studios, London, 8th May 1982.

A combination of the Hockney joiner of Bill & Noya (right) and a stripped down version (left). This version shows just the grid squares that are filled with images of Bill's hands. The grid squares that contain images of either Bill or Noya are shaded dark grey - grid squares without are shaed light grey. The grid squares can be referenced with an alphanumeric code (E3 etc).   Original image copyright Hockney.

How does the grid interact with the scene that Hockney has posed? The grid is completely regular, each Polaroid is laid out so that it butts up to its neighbours, right and left, and it overlaps the Polaroid above it so that there is a completely regular grid of negative space. Within this grid each image is independent. 

The overall composition is simple, Bill and Noya are elderly people sitting down together side on to the viewer. They are looking down at a set of black and white “self portrait” Polaroids on the floor, which is made of bare polished floorboards. There is a large canvas in the background of the image.

The image is composed of a square grid made of 7 x 7 = 49 square frames, each of which is a Polaroid image. By definition the images cannot be captured simultaneously so the image captures time - and not necessarily a linear increment of time between pictures.
Hockney has created within this fixed two dimensional grid elements of 3 dimensions, space and time. Some features of note. Bill's head appears in four of the frames all in a square and all indicating his head has moved during the capturing of the composition but it is staring down at the self-portraits over a period of time. Noyas head appears in just two frames and the overwhelming feeling is that she has been staring steadily in the same direction, quietly and in deep thought, over the course of the capture. This may have been true or not - but it is Hockneys selection of the frames that projects this feeling. 

Bills hands appear in five frames and they show a real dynamic over the time course of the capture. These hands express what Bill thinks of his self portrait. His hands indicate as we read bottom left upwards and rightwards that he is engrossed then relaxed then held in rapture. Because time is not displayed in a linear sequence we cannot infer dynamics - for example consider the 5 images of Bill's hands (E3, D3, C3, C4, C5).  Depending on cultural preference we can "read" this unordered sequence from bottom left up and right or the opposite or the reality may be that the sequence is not as simple as that. 

The images of Bill's hands, laid out as time series. The top series implies that Bill had begun with his hands clasped around his shins and he steadily moves his hands up his body and at the end is sitting back in the chair. The bottom series implies the exact opposite. Neither may be true - and the use of the two dimensional grid of frames leaves completely open this ambiguity. The two dimensional grid has no implied time direction, yet real dynamism.

All we know is that Bills hands had been at some part of the scene capture in these positions, perhaps the bulk of the time Bill's hands were as in E3 and only fleetingly have they been in the other dispositions. These multiple views of Bill's hands, arranged in a dynamic sequence as a subset of the two-dimensional grid, bring enormous life to this scene. This is not a video installation, no pictures are moving. Yet it is not a still life. There is dynamism and movememt in the still image. Hockney has cleverly captured, stretched or compressed and manipulated the time sequence and set of focal lengths into this dynamic image. 

It is also worth noting that Bill and Hoya seem to occupy much more of the area than they would do if it had been a single image (25 of the 49 frames are occupied by Bill or Hoya, they are shaed darker grey below).

David Hockney shows that intense seeing, coupled with an image capture technology of limited resolution and flexibility, and a grid, can be used to create a joiner of immense interest. Hockney knew exactly  what he was doing here - he says that these are "pictures that describe how we see - not all at once, but in discrete, separate glimpses... to synthesize a living impression.' 

…Hockney began making what he referred to as “Joiners.”… “At first I was just going through all this because the result, the depiction of the particular subject, came out looking clearer and more true to life than a single wide-angle version of the same subject… However, fairly early on I noticed that these joiners also had more presence than ordinary photographs. With five photos, for instance, you were forced to look five times. You couldn’t help but look more carefully.”
“My main argument was that a photograph couldn’t be looked at for a long time. Have you noticed that?” Hockney led me back into the studio and picked up a magazine, thumbing through randomly to an ad, a photograph of a happy family picknicking on a hillside green “See? You can’t look at most photos for more than, say, thirty seconds. It has nothing to do with the subject matter. I first noticed this with erotic photographs, trying to find them lively: you can’t. Life is precisely what they don’t have- or rather, time, lived time. All you can do with most ordinary photographs is stare at them- they stare back, blankly- and presently your concentration begins to fade. They stare you down. I mean, photography is all right if you don’t mind looking at the world form the point of view of a paralysed cyclops- for a split second. But that’s not what it’s like to live in the world, or to convey the experience of living in the world.”

Cameraworks. Photographs by David Hockney. Text by Lawrence Weschler. Alfred A. Knopf, New York, 1984.

The negative space in this joiner - the white edges to the Polaroids, that have been preserved in the composite are an integral part of this photo montage technique. If all the white edges had been removed the composition would be completely changed. Although each image in the frames are naturalistic - they are untreated Polaroids after all - the overall image is a dynamic image with pace, rhythm and life.
"... the lens on a Polaroid camera is fixed: you can't add close-up or zoom lenses or anything. So that to get a close-up of the floor, I had to get close up to the floor. In this other one here, of Stephen Spender'' (Hockney pulled out a reproduction of a remarkable composite portrait with the writer seated in the foreground and the living-studio receding into the background), I spent so much time in the back of the room, behind Stephen's chair, that finally he exclaimed, ‘Are you still taking my picture, David?' '' HERE

More on the Bill and Noya piece HERE

Sunday 5 August 2012

The Mentality of Apes

Wolfgang Köhler (1887-1967) was a German psychologist who contributed to the body of knowledge known as Gestalt psychology (though his PhD at the University of Berlin had been in psychophysics during which he had studied with Max Planck and Carl Stumpf). A Wikipedia article on him is HERE.

In 1913, Köhler took up a position in Tenerife as the director of the Prussian Academy of Sciences anthropoid research station. During 1914 Köhler undertook some seminal experiments with chimpanzees, in which he set them difficult but not impossible tasks to understand how the chimps solved problems. Based on these observations he published a book in 1917 on problem solving entitled Intelligenzprn an Anthropoiden  (The Mentality of Apes). A 1921 edition of this is HERE.

One of the key findings of Köhler, described in The Mentality of Apes, was that chimpanzees were capable of problem-solving and that they did not arrive at their methods through trial and error; they exhibit insight and show several of the typical intelligent behaviours that common in humans.

An English translation of the book was published in 1925.

The primate research centre in Leipzig is named after Köhler (HERE) .


Friday 3 August 2012

Strong Inference -- John R. Platt 1964

This paper in Science is well worth reading in full (HERE). It describes how the methods of Francis Bacon, when combined with a method described by  the geologist T.C. Chamberlin from 1897, gives what Platt describes as Strong Inference.

One of the key passages from Chamberlin's paper is below.

An unofficial but full transciption of the Platt paper is HERE.

There is a Wikipedia page describing strong inference and its modifications HERE.

Saturday 14 July 2012


Here is a hand drawn contour map of the inter-atomic distances in Insulin, drawn by Dorothy Hodgin in the 1930's. 

This is on the Wellcome Collection's site, here is the blurb;

This delicate multicoloured drawing dates from the late 1930s when chemist Dorothy Hodgkin (1910-1994), who later won a Nobel Prize, first began to publish her research on insulin. It was selected by Dr Helen Megaw, (1907-2002) who led the Festival Pattern Group at the 1951 Festival of Britain. Diagrams of atomic structure were used as inspiration for wallpaper, curtains, laminates, carpets, dress fabrics, ties and crockery. Hodgkin's drawing inspired a wallpaper design used in the Festival's Regatta Restaurant.

Image from Wellcome Collection / V&A.

Tuesday 10 July 2012

Save our Inboxes!

A Thousand Mile Walk to the Gulf

Ed Ricketts was born in Chicago and he spent most of his childhood there. A flavour of what his life was like in Chicago can be gained from a comment he made later in life after having read Studs Lonigan by James T. Farrell.  He commented that the author had captured what life was like on the streets of Chicago as Ricketts had known them. 

After graduating from high-school Ricketts went to Illinois State Normal University in 1915. After just a year there he left the university and travelled to Texas and New Mexico. In 1917, towards the end of the first world war, he was drafted into the Army Medical Corps to serve at Camp Grant in Illinois. After the war had ended he was discharged from the army and he then attended a wide range of classes at the University of Chicago. Although it was the zooologist Warder Clyde Allee who made the most profound and long-lasting impact on Ricketts, he was not a narrow student and between 1919 and 1922 his classes also included philosophy, English, vertebrate palaeontology and Spanish.  At the end of 1922 Ricketts left the University of Chicago without being awarded a degree and by the end of 1923 he had left his home in Chicago to move to the Monterey peninsula in California. Once in Monterey he set up a marine supplies business, Pacific Biological Laboratories, although this business only provided him with a barely adequate income, it provided  him with a framework for his intellectual life and scientific studies for the rest of his life.

At the end of 1920, during a break in his university studies, Ricketts made a typically pioneering journey, a long solo walk through the southern states of the USA which he describes in an essay, Vagabonding Through Dixie, that was published in 1925. In this essay Ricketts describes his experiences on the road and mentions the book that had inspired his walk, A Thousand-Mile Walk to the Gulf by John Muir. This book by Muir was published in 1916 but describes a walk that Muir had made in 1867.

Below is the map from Muir's book showing the route he took (I have highlighted the route in  light blue). The book can be read online or downloaded HERE.  

The book was republished in 1998 and is available on Amazon HEREThe following blurb is from the inside cover of the 1998 edition;
In 1867, John Muir, age twenty-eight, was blinded in an industrial accident. He lay in bed for two weeks wondering if he would ever see again. When his sight miraculously returned, Muir resolved to devote all his time to the great passion of his life -- studying plants. He quit his job in an Indiana manufacturing plant, said good-bye to his family, and set out alone to walk to the Gulf of Mexico, sketching tropical plants along the way. He kept a journal of this thousand-mile walk and near the end of his life, now famous as a conservation warrior and literary celebrity, sent a typescript of it to his publisher. The result is a wonderful portrait of a young man in search of himself and a particularly vivid portrait of the post-war American South. Here is the young Muir talking with freed slaves and former Confederate soldiers, pondering the uses of electricity, exploring Mammoth Cave, sleeping in a Savannah cemetery, delirious with malarial fever in the home of strangers at Cedar Key, traveling to Havana, Cuba, and sailing to San Francisco Bay. Once in California, Muir promptly set out for Yosemite Valley -- 200 miles away. There Muir found his destiny -- and a mountain range to test his apparently inexhaustible capacity for walking. 


Steinbeck, J. (1961). About Ed Ricketts. 
Ricketts, E.F. (1925). Vagabonding Through Dixie. Travel. Vol. 45 (2). HERE
Muir, J. (1915). A Thousand-Mile Walk to the Gulf . 

Saturday 30 June 2012

In resolution we trust.

In 1609 Galileo made 3 inventions that extended human visual resolution of fine detail. In June or July he made his first three-powered spyglass, by August he had made an eight-powered instrument and by November he had made a twenty-powered instrument.  Galileo then used these instruments to observe the surface details of our Moon, discover the satellites of Jupiter and resolve individual stars from what had previously been fuzzy and indistinct nebular patches. By March 1610 Galileo had published this material including careful observations of the movement of the Moons of Jupiter.  This book Sidereus Nuncius was perhaps the worlds first distinctive scientific data set. In 1610, Galileo then turned his telescope to work at close ranges, by 1623 or 1624 he had perfected a compound microscope.

In Siderius Nuncius he presented the stars that had been visible to the naked eye and those now resolvable using his telescope. The image belows shows the difference.

Voodoo correlations

Ed Vul works at UC San Diego in the department of Psychology, he wrote a nice paper with his colleagues in 2009 called Puzzlingly High Correlations in fMRI Studies of Emotion, Personality, and Social Cognition

Vul had wanted to call the paper Voodoo Correlations in Social Neuroscience, and I for one would have preferred his original title, you can see why when you read the abstract of the published paper;


Functional magnetic resonance imaging (fMRI) studies of emotion, personality, and social cognition have drawn much attention in recent years, with high-profile studies frequently reporting extremely high (e.g., >.8) correlations between brain activation and personality measures. We show that these correlations are higher than should be expected given the (evidently limited) reliability of both fMRI and personality measures. The high correlations are all the more puzzling because method sections rarely contain much detail about how the correlations were obtained. We surveyed authors of 55 articles that reported findings of this kind to determine a few details on how these correlations were computed. More than half acknowledged using a strategy that computes separate correlations for individual voxels and reports means of only those voxels exceeding chosen thresholds. We show how this non-independent analysis inflates correlations while yielding reassuring-looking scattergrams. This analysis technique was used to obtain the vast majority of the implausibly high correlations in our survey sample. In addition, we argue that, in some cases, other analysis problems likely created entirely spurious correlations. We outline how the data from these studies could be reanalyzed with unbiased methods to provide accurate estimates of the correlations in question and urge authors to perform such reanalyses. The underlying problems described here appear to be common in fMRI research of many kinds—not just in studies of emotion, personality, and social cognition.

The full paper is HERE.

Figure 5 from the paper is shown below.

Antediluvian Quantification

It is hard to imagine today how profoundly scarce high quality scientific data was a hundred years ago. For example, in 1910 the American physicist Robert Millikan made a first report of a series of experimental measurements that he had made with his graduate student Harvey Fletcher using their own design of equipment. These measurements involved timing how long it took small drops of watch oil to move up and down in an electric field. The timings were then used to make estimates of the tiny electrical charge of individual electrons. This famous series of ‘oil drop’ experiments of Millikan allowed him to make an estimate of the electron charge that is correct to within about 0.5% of the currently accepted value. This series of experiments and the estimation of electron charge they allowed are celebrated to this day; when Millikan’s value for the electronic charge was inserted into Bohr's formula for the hydrogen spectrum, it accurately gave the Rydberg constant. This confluence of experimentally derived estimation and a new theory was impressive and the experiment is still seen by many scientists as one of the first and most convincing proofs of the quantum theory of the atom proposed by Bohr. 

Millikan’s oil drop data were first reported in 1910, which prompted some controversy particularly with the physicist Felix Ehrenhaft. After improving his experimental setup Millikan then published a full report of his work in 1913 in the Physical Review (Millikan 1913). In this paper Millikan reports the culmination of 4 years of hard experimental effort, designing and mastering a new technique and assessing the sources and magnitudes of the errors in his approach. The conclusions of the paper are based on the detailed analysis of 58 individual oil droplets with measurements on these droplets having been made over a period of 60 consecutive days. On each of these drops about 40 individual timing measurements were made. The data set used for Millikan’s analysis is presented as Table XX in his 1913 paper. If these numbers are entered into a modern spreadsheet file the dataset is about 28 kilobytes.

Notwithstanding the limited number of kilobytes of data reported in this paper of Millikan, this was a fantastic piece of science. The oil-drop experiment showed that an elegant experimental method could not only provide an accurate determination of the fundamental unit of charge, it could also provide evidence that charge is quantized. In 1923 Robert Millikan was awarded the Nobel prize in Physics, “for his work on the elementary charge of electricity and on the photoelectric effect". In his Nobel prize acceptance speech he firstly celebrated how science at that time was a close partnership of theory and experiment;
The fact that Science walks forward on two feet, namely theory and experiment, is nowhere better illustrated than in the two fields for slight contributions  to  which  you  have  done  me  the  great  honour  of  awarding  me  the Nobel Prize in Physics for the year 1923. 
Sometimes it is one foot which is put forward first, sometimes the other, but continuous progress is only made by the use of both - by theorizing and then testing, or by finding new relations in the process of experimenting and then bringing the theoretical foot up and pushing it on beyond, and so on in unending  alternations.

He then describes the importance of the oil drop experiments he had completed a decade earlier ; “..the electron itself, which man has measured…is neither an uncertainty or an hypothesis . It is a new experimental fact…” (Millikan 1924).

The sheer scarcity of high quality data was a major barrier to scientific progress and many of the leading research scientists of the day spent an enormous amount of effort to design and construct physical instruments that were capable of providing high quality, reproducible data. The reason that these scientists spent so much effort on creating physical devices for generating data for their studies was that they simply did not exist. Compared with today, that era of science was antedlivian; literally "before the deluge". Each and every data point had a real value to a practising scientist because they knew exactly how much effort had been expended in obtaining it. 

Those days are long gone. We have never had so much “data”, or so much capacity to store this data, manipulate it and analyse it both mathematically and visually. Yet using data in science has never been more difficult. The problems are not set by the technical limitations of instruments, computers, memory or even mathematical and statistical techniques – though all of these will continue to develop and these developments can help scientists.

The real challenge is in how we can best use the tried and trusted intellectual frameworks that have been the basis of scientific research over the past 400 years in our era of data deluge. Many of our current archetypes of science and our scientific hero’s are products of the data scarce era of science; Galileo, Newton, Kelvin, Einstein, Curie, Feynman, Watson & Crick. These are all antediluvian heroes, they lived, worked and excelled prior to the data deluge. 

How then can it be, that if the core of science is measurement and quantification and both are increasing in capacity at such a great rate, there is a problem? 

The answer is that science is not just the accretion of raw data or even analysed data. It is a fundamentally creative act. It requires a human intelligence to combine what was already known (or thought to be known), with the new data from experiment and observation, into a new level of knowledge. Paradoxically, this process has historically been aided by the fact that it always took time to collect data. A scientist may well have had to design and build the apparatus before he or she could even begin to make the measurements they were interested in. They had to first conquer the experiment before really understanding the object of attention. This is classical science. And it is not so long ago. One of the key weaknesses in today's science is that modern scientists have become personally disconnected from the measurement process - in the sense that Millikan understood it - in that they have never designed, or built a piece of apparatus. This means that they have reduced the connection they have with their data and reduced the amount of down time in their research.

I remember for my own BSc. Chemistry project having to construct an apparatus to image and measure droplets. Gaining a deep understanding of the shortcomings of an experiment by designing and building the kit has aided the development of science over the past three centuries. Today much of this forced downtime has been driven out of modern research labs. A high quality piece of equipment can be purchased and deployed in a matter of weeks. And with modern analytical instruments having high reliability and high data storage capacity they can be set up to run virtually unattended all day every day. 

In previous generations one of the key bottlenecks was the need for experimental quantitation. This in turn led to the need for scientists to be able to develop and deploy scientific instrumentation and the ability to understand what each measured data point meant. This is harked back to by older science teachers who still stress the need for “good lab practice” using paper notebooks, keeping observational records of what is going on etc. Now most scientists do not have a clue about what is going on in their instruments. They have no idea about how much data processing is going on before they get hold of raw data.


Figure 1 from Millikan's 1913 paper.


On the elementary electrical charge and the Avogadro constant. R.A. Millikan.
The Physical Review. Vol II Series II 1913. 

Sunday 24 June 2012

Stepping Dividers (1585)

The western coastline of the British Isles has been eroded for millienia by the power of the Atlantic Ocean and the Irish Sea. To natives of the British isles this coast has a recognisable and familiar irregularity. Yet this familiar coastline is the source of a puzzle that was first uncovered by the British scientist Lewis Fry Richardson (1881 -- 1953) in the 1950's and published posthumously in 1961. This paper was later used by Benoit Mandelbrot in his classic 1967 paper "How long is the Coast of Britain?".

The so-called coastline paradox is that the measured length of a stretch of coastline, such as the west coast of Britain, depends on the scale of measurement. The specific problem noted by Richardson was found when he approximated the length of the coastline by counting the number of steps of a fixed step length required to cover the whole coastline. Richardson notes that as the step length used to make this estimate becomes smaller, the longer the total measured length of the coastline becomes.  

For a general smooth shape this is not the case -- for a circle as the step length decreases so the approximation of the circles circumference gets closer to the real value.  

Measuring the length of a smooth curve is already tricky to do. One approach is to use the maritime method of stepping a set of dividers along the coastline and then multiplying the number of steps by the distance between divider points. This method works exactly for a circle - as the step length decreases so the estimates converges on a stable value. 

A single-handed divider can be used to approximate a distance on a maritime chart or the length of a border between two countries or regions on a map. The divider points are set to a known distance apart and then stepped along the border. One point of the divider is placed on the border and then the dividers is swung around until it crosses the coast again.  

The illustration below shoes a set of dividers in use, it comes from a book published in Antwerp in 1585 by Christoffel Plantijn (image from HERE). This design of divider, usually made from brass and steel, remains virtually unchanged to this day and they are still widely available to purchase.

Image is from Flickr user History of the Book, it is used under the Creative Commons licence BY-NC-SA 2.0 (HERE). 


Richardson, L. (1961), The problem of contiguity: An appendix of statistics of deadly quarrels, General Systems Yearbook. 6, pp. 139-187.