Burgess Shale - to Scale

Here is a nice way of showing the scale of some of the signature creatures from the Burgess Shale fauna discovered by Charles Doolittle Walcott (1850-1927 ) and worked on for so many years by Harry Whittington (1916-2010) and his students.

These creatures lived about 505 million years ago.

Image from Wikipedia [Size comparison of selected Burgess Shale fauna and a human. Modified from illustrations by ArthurWeasley, Matt Martyniuk, and Mateus Zica - Dinoguy2 (Corrected Miglewis). This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license. ]

Charles Doolittle Walcott's Field Diary

A page from Charles Doolittle Walcott's field notebook of 1909. The page has contemporaneous sketches of Marrella, Waptia  and Naraoia. The original diary is in the Smithsonian institution.

 

The War on Cancer - the first 40 years.

Here are two recent and thought provoking pieces on cancer.

(1) - A summary of the period 1971-present describing Nixons' 'War on Cancer' http://www.csicop.org/si/show/war_on_cancer_a_progress_report_for_skeptics/

(2)- A discussion of changes in cancer theory that seek to explain multiple paradoxes. In particular the tissue organisation field theory (TOFT) model which proposes that cancer is a tissue-based disease. This theory has been developed and championed over the past 10 years or so by Ana Soto and Carlos Sonnenschein at Tufts medical school.

http://jco.ascopubs.org/cgi/content/full/28/20/3215

One interesting character in this story is the Nobel laureate Peyton Rous. 

" In 1959 Peyton Rous published an essay into which he distilled 50 years of observations and experimentation on cancer. The central conclusion of this essay startles us today. It is the statement that somatic mutation does not play a role in the causation of cancer. It is difficult to understand how such an astute observer, a man who had such a comprehensive knowledge of cancer, could be so far off the mark. " [This is from Peyton Rous: homage and appraisal. PK Vogt - The FASEB Journal, 1996. The paper he refers to is Nature 183, 1357-1361 (16 May 1959) Surmise and Fact on the Nature of Cancer P. Rous ]


His previous cancer discovery in 1911 took 55 years to be acknowledged by the Nobel committee. Perhaps he was always 55 years ahead of his time.

1959 + 55 years = 2014!

So perhaps 2014 is the date to look at.

Some do, some don't...

A genuine Citation Classic

Turn me on Dead Man...

Here is one of my favourite pieces by Michael Shermer from the Scientific American.

"Anecdotal thinking comes naturally; science requires training.

What we have here is a signal-to-noise problem. Humans evolved brains that are pattern-recognition machines, adept at detecting signals that enhance or threaten survival amid a very noisy world. This capability is association learning--associating the causal connections between A and B -- as when our ancestors associated the seasons with the migration of game animals. We are skilled enough at it to have survived and passed on the genes for the capacity of association learning.

Unfortunately, the system has flaws. Superstitions are false associations--A appears to be connected to B, but it is not (the baseball player who doesn't shave and hits a home run). Las Vegas was built on false association learning. 

Consider a few cases of false pattern recognition (Google key words for visuals): the face of the Virgin Mary on a grilled cheese sandwich; the face of Jesus on an oyster shell (resembles Charles Manson, I think); the hit NBC television series Medium, in which Patricia Arquette plays psychic Allison Dubois, whose occasional thoughts and dreams seem connected to real-world crimes; the film White Noise, in which Michael Keaton's character believes he is receiving messages from his dead wife through tape recorders and other electronic devices in what is called EVP, or Electronic Voice Phenomenon. EVP is another version of what I call TMODMP, the Turn Me On, Dead Man Phenomenon--if you scan enough noise, you will eventually find a signal, whether it is there or not."

Here is the famous Virgin Mary on a Piece of Toast that Shermer mentioned;

Membranipora - a confederacy of clones

The Ricketts description set me off looking for information about Membranipora membranacea. It is a fascinating little colonial animal. Here are some notes and a sketch.

From Intertidal invertebrates of California.

 By Robert H. Morris, Robert Hugh Morris, Donald Putnam Abbott, Eugene Clinton Haderlie

Chapter 6 - Bryozoa and Entopracta : The moss animals

John D Soule, Dorothy F Soule and Donald P  abbott

"The bryozoa, or Ectopracta are virtually all colonial forms, with each colony (zoarium) composed of many small attached individuals (zooids). A colony originates from a single, sexually produced individual (the ancestrula) and increases by asexual budding of new individuals. Bryozoans are widely distributed in the sea and many are found on rocky shores that are exposed at only the lowest tides, or on harbor pilings or ships hulls. At first glance some colonies may be mistaken for bushy types of hydroids brancing corals or marine algae.

The individual zooids in a bryozoan colony are usually less than 1mm long and each is encased in a secrteted outer cuticle or exo-skeleton, which stiffens the colony and provides support and protection for the enclosed soft parts. "

Here is a drawing of a couple of zooids - one with tentacles retracted and the other in full action (taken from Bock, P.E., 1982. Bryozoans (Phylum Bryozoa). In: Shepherd, S.A. & Thomas, I.M. (editors), Marine Invertebrates of Southern Australia Part 1: 319-394. South Australian Government, Adelaide).

Membranipora was first described by Linnaeus in 1767 (Linnaeus, C. 1767. Systema naturae, Tom. I. Pars II. Editio duodecima, reformata. Holmiae. (Laurentii Salvii).: 533-1327.). In his system it was originally Flustra membranacea. The page describing the creature is shown.

Of Tide-pools and seeing

Ed ricketts (1897 – 1948) was an American marine biologist, pioneering ecological thinker and polymath. Although he has become more widely appreciated in recent years, particularly amongst scientists, he is still not very widely known in his own right. However, Ricketts not only had his own original view on the world, he also had a significant impact on a number of his friends; most notably the Nobel laureate John Steinbeck and the comparative mythologist Joseph Campbell. Ricketts was a particular inspiration for Steinbeck and he was the model of at least seven of Steinbeck’s lead characters; including the unforgettable Doc of Cannery Row and it’s sequel Sweet Thursday. Ricketts managed to balance his own scientific research programme with the exigencies of making a living for his family from his scientific specimen supply business. He was also a widely read and engaged philosopher of science and he was acutely aware that new scientific insight required an active personal engagement with the world.

Ricketts had a visceral need to see, and this need repeatedly drove him out of his bed and onto the road; to numerous beaches, bays, coves and pools on the Pacific coast of California and Oregon.  He would carefully time his arrival at specific locales to co-incide with the ideal tide conditions required for collecting a particular marine animal. Closer to his home, in Pacific Grove on the Monterey peninsula, he also spent hours observing and collecting in a large rock pool that he christened The Great Tide-Pool. John Steinbeck spent hours with Ricketts in this pool collecting marine invertebrates and he described it as;

. . . a fabulous place: when the tide is in, a wave-churned basin, creamy with foam, whipped by the combers that roll in from the whistling buoy on the reef. But when the tide goes out the little water world becomes quiet and lovely. The sea is very clear and the bottom becomes fantastic with hurrying, fighting, feeding, breeding animals.

Whilst Ed Ricketts was out in the tide-pools and on the shoreline of the Pacific coast, he honed his ability to both see marine animals and collect them. It was here, where he was most in his element, that he showed how an outstanding field naturalist engages with Nature. As Katherine Rodger says in a recently published collection of his writings;

Ricketts was a remarkable collector, with keen eyes and fast, careful hands, often returning from the shore with rare, sometimes unknown, specimens and his major expeditions consistently yielded impressive results.  Regarding the 550 species collected on their Sea of Cortez expedition, for example, he and Steinbeck stated that “almost 10% of these will prove to have been undescribed at the time of capture”.

Given that the Sea of Cortez trip that Rodger refers to in this quotation was only 6 weeks long, this is a new species discovery rate of about 10 per week.

The Pacific littoral

Remarkably, without any University research funds or endowments, Ricketts was able to succesfully use his observational powers and collecting ability to not only pursue his own ambitious research programme in marine biology but also to run a small marine specimen supply company in Monterey called Pacific Biological Labs. During his productive professional life, Ricketts staked out for himself an ambitious agenda - he had in mind an encyclopaedic study of the Pacific littoral 

This was a vast undertaking. Ricketts saw it as reaching from the far south of Chile, via Latin and central america, the continental USA and Canada to the far north-west - Alaska and the Aleutians.
During his life Ed Ricketts co-authored three books that described his explorations and observations across this vast space. Of these, two had been published at the time of his premature death in 1948 and the third was in typescript form. At the time of his death, he had been planning how to use these books as the basic material for a definitive treatise on Pacific coast marine biology. The three books are a fascinating blend of his fundamentally ecological view of nature, holistic philosophical
views, his observations on the littoral ecology of the Pacific coast and a huge volume of very detailed and dedicated collecting notes derived from hours spent in the tidepools and shorelines that he loved so much.


Between Pacific Tides

The 1925 catalogue for Pacific Biological laboratories was Ed Ricketts’ first scientific publication. The catalogue set out the range of species he could supply, based on his access to the varied and abundant marine fauna of the Monterey region. By the mid 1930’s Ricketts had codified his considerable shoreline experience and reading into a book, Between Pacific Tides, co-authored by Jack Galvin. The book was published in 1939 by Stanford University Press and the organising scheme of the book was radical for it’s time. It described the marine invertebrates that could be found in the littoral zone of the Pacific shore organised by ecological niche and habitat, rather than by anatomical or phylogenetic similarity. This organising principle generated considerable opposition from more renowned marine biologists in the US and Ricketts and Galvin had a long battle to get it published. The book was revised and published with a foreword by John Steinbeck in 1948 and new editions appeared regularly between 1952 and 1985. The book is still in print, in a fifth edition, and it is one of Stanford University Press’s biggest ever sellers.

The Sea of Cortez

In March 1940 Ed Ricketts and John Steinbeck chartered the Western Flyer, a 75-foot purse seiner built in Tacoma in 1937, and sailed from Monterey to the Sea of Cortez, also known as the Gulf of California. This unique marine environment is located between the mainland coast of Mexico and the coast of the Baja peninsula. The Sea of Cortez is one of the most ecologically diverse seas on the planet and is home to more than 5,000 described species. Ricketts and Steinbeck had an ambition   to undertake the first serious scientific study of the Sea of Cortez as an ecological whole. They aimed to emulate the voyaging style of Charles Darwin on their trip and this is reflected in the full title of the book Sea of Cortez: A Leisurely Journal of Travel and Research. The first portion of the book is a log written by Steinbeck, but based closely on the Verbatim Transcript that had been written by Ricketts from the contemporaneous notes he had kept during the voyage.  In addition to the narrative Ricketts had compiled an extensive phylectic catalogue describing the species that they had found, with full cross-references to the known literature on the marine fauna of the region.  The full book is about 600 pages long and was never commercially succesful. In later editions the publishers completely dropped the phylectic catalogue and the log portion was published under the title Log from the Sea of Cortez under Steinbeck’s sole authorship.

The Outer Shores

At the time of Rickett’s death he had completed a number of extended collecting expeditions to Vancouver Island and other coastal regions of British Columbia. His extensive journals were intended to be used as the basis for a book called the The Outer Shores, to be co-authored
with John Steinbeck. After the untimely death of Ricketts in 1948 the project languished and the full transcript of his log has only recently been published in its entirety.


These books are an ongoing testimony to the energy of Ed Ricketts, his ambitious vision and his skill as a field naturalist. His journals are full of the joy of first-hand observation and discovery. For example, here is part of an entry in his Outer Shores transcript dated Tuesday June 12th 1945 in which he describes a days collecting at Echachis Island in British Columbia;

This is one of the finest collecting spots I’ve seen in many a day . . . the fauna is very rich and varied.  Eighty-three species have already been determined; we took certainly more than 100 in this two-hour trip, and I think a reasonably complete census of the naked-eye forms here wouldn’t
stop short of 150 or 175, between tides. 


Ricketts role in marine biology and species discovery is reflected in the fact that about twenty marine organisms have species names of rickettsi or steinbecki, in honor of Ricketts and Steinbeck. For example, these include Eubranchus steinbecki,  a nudibranch named in 1987; Catriona rickettsi a nudibranch named in 1984; Pycnogonum rickettsi a sea spider named in 1934 and Polydora rickettsi a spionid polychaete named in 1961. 

... by its vividness exciting an involuntary movement of imagination and passion

The English essayist and thinker William Hazlitt thought of poetry as `... the language of the imagination and the passions' and went on to define it more carefully as  

...the natural impression of any object or event, by its vividness exciting an involuntary movement of imagination and passion, and producing, by sympathy, a certain modulation of the voice, or sounds, expressing it.

In this lecture, `On Poetry in General', Hazlitt brilliantly pins down some of the essential elements of poetry, and underlines explicitly what poetry is;  textual or verbal and what it is not; visual. This is a crucial distinction to make. Poetry deals explicitly with the translation of sensory and emotional input and creates text, as a means of `modulation of the voice', as output. Nevertheless, great poetry requires a great intensity of observation and reflection and the greatest requires the means to observe and represent nature with an emotional experience that has a higher intensity than `normal'. In the process of such intense observation poets sometimes obtain what William Wordsworth would call a spot of time or James Joyce an epiphany or what Gerard Manley Hopkins called inscape. The visionary scientist Ed Ricketts (1898-1948), making explicit reference to the poem Roan Stallion by Robinson Jeffers called this same quality breaking through.

Writers of poetry, and indeed prose, who achieve epiphany, inscape or breaking through are rare. To achieve this level of excellence requires both the ability to experience intensely and the ability to translate that experience into the linguistic means to represent emotional intensity. Because of the physiological dominance of the visual sense in humans, inevitably much of the input that poets have at their disposal is visual. In fact Marshall McLuhan uses the specific phrase intense seeing to describe the prose style of the artist and writer Wyndham Lewis; `a visionary for whom the most ordinary scenes became the means of intense seeing'. Crucially, although Lewis was an artist, McLuhan is using the expression intense seeing as a synonym for the other non-visual expressions above; epiphany, inscape and breaking through

Regardless of how visual their inspiration and thinking, writers and poets succeed or fail by virtue of their ability to produce a `modulation of the voice'. They do not manipulate visual material nor do they produce visual output; spot of time, epiphany, inscape and breaking through are non-visual expressions.

In contrast to poets and writers, artists and scientists who achieve eminence in their fields have to develop uniquely focused and intense ways of using their visual literacy. This is literally, not figuratively, intense seeing.

To see clearly is poetry, prophecy, and religion all in one (John Ruskin)

Drawing makes you look intently, and with purpose. It makes you see differently. 

Richard McDaniel

Magnification & Dilation

The concept of magnification is at the heart of the reducing fraction dilemma. But care is called for as this concept exists as two independent ideas - one in mathematics and the other in optical science. This is confusing and applying a mathematical definition of magnification directly to optical science can be misleading. For clarity magnification in mathematics should be referred to by the technically more correct term dilation and the word magnification reserved for optical science. 

Ed Ricketts Lens - descriptions from Between Pacific Tides (5th Edition)

I have previously explained how Ed Ricketts used a 20X Bausch & Lomb hand magnifier.  However, this claim was based purely on a quote from John Steinbeck. Prompted by a question from Eric Enno Tamm, I have just searched through Between Pacific Tides by Ricketts using Google books and there are 9 specific mentions of using a hand lens to reveal the beauty of what can be seen in the tidepools. Some of these descriptions are poetic - here are some examples.



Page 59. §29 - Tegula brunnea & Crepidula adunca


With a hand lens the embryos of Crepidula can sometimes be seen whirling around in their envelopes in the egg packets.



Page 85. §62 - Transparent shrimp Heptacarpus pictus.


There is such a fairylike beauty to this ephemeral creature that the inexperienced observer will be certain that he is seeing a rare form...


Once captured, the living specimen should be confined in a glass vial not much larger than itself and examined with a hand lens. The beating heart and all the other internal organs can be seen very plainly through the transparent body.


Page116. §88


As would be expected in a haunt so prolific as the lower tidepool zone, the shelter of the hydroid forests attracts a great many smaller animals, both sessile and active. In this work, it is difficult to say at just what point animals become too inconspicuous to be considered, for in the tidelands it is almost literally true that


Great fleas have little fleas
Upon their backs to bite 'em
And little fleas have lesser fleas
And so on ad infinitum.

... Though all of these animals are at least visible to the naked eye, and are abundant, characteristic and certainly not lacking in interest, most of them are too small to be seen in detail without a hand lens or microscope and hence cannot be included in this handbook.


Page 143. §110


On the "leaves" and "stems" of outer-tide-pool kelps, one almost always finds an encrusting white tracery delicate enough to be attributable to our childhood friend Jack Frost. But a hand lens reveals a beauty of design more intricate than any ever etched on frosty window-panes. These encrustations are usually formed by colonies of the bryozoan or ectoproct, Membranipora membranacea (Fig 114), so named in the middle of the eighteenth century by Linnaeus, regarded as the founder of modern classification.


The minute, calcareous cells, visible to the keen naked eye but seen to better advantage with a lens, radiate in irregular rows from the centre of the colony.


...the process of larval settlement has been described for several species. The process can be watched by any careful observer with a good lens.

A membrane-enclosed outgrowth of the brain

"The eye is unique, both as a membrane-enclosed outgrowth of the brain... '' 

Ionic control of ocular growth and refractive change. Sheila G. Crewther, Helena Liang, Barbara M. Junghans and David P. Crewther. PNAS October 17, 2006 vol. 103 no. 42 15663-15668 

From a developmental perspective the eye is an outgrowth of the brain. During fetal development small patches on the outside of the embryo develop into the two eyes.

... an effortlessly natural extension to the eyes and the hand

British naturalist Sir John Lister-Kaye has recently published a fascinating book-long rumination on wildness. The book is based on daily journals kept by Kaye describing the same circular walk from his home in a glen in the scottish highlands up to a small hill loch. One of his essential companions on these walks is a battered pair of Swarovski binoculars, which he descibes as follows;


"Good binoculars are to a field naturalist as a set of spanners is to a mechanic, a stethoscope to a doctor. They must be clear, sharp and an effortlessly natural extension to the eyes and the hand. They are a vital, silent route to where you want to be."

At the Waters Edge; A personal quest for wildness. John Lister-Kaye. Canongate Books. 2010.

John Lister-Kaye comes from a long line of landowners and business leaders. He has an interesting life story, that expains how and why he ended up as a naturalist (Wikipedia has a good entry on him). He has run the Aigas Field Centre in the highlands of Scotland since 1977.

... drawing disciplines the eye and brain, tempers judgement, and makes the hand responsive.

From the Rhode Island School of Design statement of foundation course elements.

In the drawing studio you will work with the development of skills in perceptual drawing, formal visual principles, and abstract thought. Taught by means of the human figure, landscape, still life, or theme, drawing disciplines the eye and brain, tempers judgement, and makes the hand responsive. You will explore form as it pertains to representation and the organization of surface through line, shape, light, texture, and space. At RISD, drawing is considered the basic tool of all art and design disciplines, reflecting the conviction that this skill "the coordination of eye, hand, and brain" is essential to the way the painter, sculptor, architect, or designer creates.

This  is a fabulous statement about the role that drawing plays in Intense Seeing.

Study of a Peacock Feather, 1873. John Ruskin

The Ecological Fallacy & MAUP

The ecological fallacy occurs when analyses that are based on grouped data lead to conclusions that are different from those based on the analysis of individual data. One of the early examples is given in Robinson (1950). 

From the Wikipedia entry;

`An ecological fallacy (or ecological inference fallacy) is an error in the interpretation of statistical  data in an ecological study, whereby inferences  about the nature of specific individuals are based solely upon aggregate statistics collected for the group to which those individuals belong. This fallacy assumes that individual members of a group have the average characteristics of the group at large...'


(on Robinson 1950) 

`...for each of the 48 states in the US as of the 1930 census, he computed the literacy rate and the proportion of the population born outside the US. He showed that these two figures were associated with a positive correlation of 0.53 — in other words, the greater the proportion of immigrants in a state, the higher its average literacy. However, when individuals are considered, the correlation was ?0.11 — immigrants were on average less literate than native citizens. Robinson showed that the positive correlation at the level of state populations was because immigrants tended to settle in states where the native population was more literate. He cautioned against deducing conclusions about individuals on the basis of population-level, or "ecological" data'

This is closely related to a problem that I have been aware of for a long time under the name of "change of support problem" - which is how it is known in the field of mathematical morphology and integral geometry. I recently found out that within spatial statistics and GIS it has another special name; Modifiable Areal Unit Problem (MAUP). The basic problem is that for spatial data, such as Health outcomes recorded by zip-codes or counties, socio-demographic data from Census tracts, safety or health exposure estimates within a region of suspected source etc etc, statistical inference changes with scale.

A classic early paper is Gehlke and Biehl (1934) who found that the magnitude of the correlation between two variables tended to increase as districts formed from Census tracts increased in size.

Waller & Gotway (2004) describe it as a "geographic manifestation of the ecological fallacy in which conclusions based on data aggregated to a particular set of districts may change if one aggregates the same underlying data to a different set of districts".

The paper by Openshaw and Taylor (1979) described how they had constructed all possible groupings of the 99 Counties in Iowa into larger districts. When considering the correlation between %Republican voters and %elderly voters, they could produce "a million or so" correlation coefficients. A set of 12 districts could be contrived to produce correlations that ranged from -0.97 to +0.99.

More here = http://www.samsi.info/200304/multi/cgcrawford.pdf

From Openshaw (1984);

`the areal units (zonal objects) used in many geographical studies are arbitrary, modifiable, and subject to the whims and fancies of whoever is doing, or did, the aggregating.'

below is an example figure from Openshaw (1984).

References.

Gehlke, C. E. and K. Biehl (1934). Certain effects of grouping upon the size of the correlation coefficient in census tract material. Journal of the American Statistical Association, 29, 169-170.

Openshaw, S. (1984). The Modifiable Areal Unit Problem. CATMOG 38. ISBN 0 86094 134 5

Openshaw, S. and P. Taylor (1979). A million or so correlation coefficients. In N. Wrigley (Ed.), Statistical Methods in the Spatial Sciences, London, pp. 127-144. Pion.

Robinson, W. S. (1950). Ecological correlations and the behavior of individuals. American Sociological
Review, 15, 351–357.

Waller, L.A. and C.A. Gotway. 2004. Applied Spatial Statistics for Public Health Data. Hoboken, NJ: John Wiley & Sons. 

Feynman Page Layout

Richard Feynman is justifiably famous for many things - including a set of Physics textbooks he published in 1964. These are incredibly dense and well written. They also have excellent page layouts. Here is an example.

Daniel Danger Video

A very interesting 45 minute video of Daniel Danger on his website.

“theres nothing out there, I do not hear what you hear”. Ten colour screenprint 2008

Hilbre from the Dunes

Q: What did 1015 Sunsets ever give us? A: Eyes.

This is a profound statement from Prof Ronald Fernald of Stanford.

 

"Light has probably been the most profound selective force to act during biological evolution. The 10¹⁵ sunrises and sunsets that have taken place since life began have led to the evolution of eyes which use light for vision and for other purposes including navigation and timing. Although eyes occur in a variety of shapes, sizes, optical designs and locations on the body, they all provide similar information about wavelength and intensity to their owners."

Fernald, R. D. (2000). "Evolution of eyes." Curr Opin Neurobiol 10(4): 444-50. The file is here = PDF

[NOTE added 25/11/2011. Since posting this I went and re-checked Fernald's estimate and it is wrong by 3 orders of magnitude. I estimate that there have been 10¹²  sunrises and sunsets, not 10¹⁵ .] 

It's a Map

An extract from a book about maps - an Ojibwe map from ca. 1820 in Making Maps

A Visual Guide to Map Design for GIS. John Krygier and Denis Wood. ISBN 978-1-59385-200-9

Define Your Space

Traditionally, the recipe for jugged hare begins with the instruction; ‘First catch your

hare’. There is a lot to be said for a recipe like this. Not the least of which is that it

doesn’t miss the obvious. With this example in mind perhaps the first instruction for

Intense Seeing has to be, define your space of exploration. In order to make this instruction

widely useful we should not be limited to thinking about the three-dimensional,

Euclidean, space we are used to navigating around in everday life. In fact it is useful

to learn a few visualisation and conceptual tricks from physicists, who are very used

to manipulating spaces that are different from 3D space. In particular the concept of

a phase space repays consideration, this is an idea that was originally developed by

the brilliant American theoretical physicist Josiah Willard Gibbs (1839-1903), but it’s

general approach is very widely used.

In maths and physics a phase space is the space of all possible states of a physical

system, with each possible state of the system corresponding to one unique point in

the phase space. This mapping of what a physical system is to a single point in a

high-dimensional space is a flexible and powerful concept and by using the word ‘state’

physicists do not simply mean the spatial positions of all of the objects in the system

of interest, these would occupy a physical space or configuration space, but also their

velocities or momenta. These two sets of quantities allow a physicist to understand not

only the initial state of the system but also allow them to follow the evolution of the

system over time. In phase space a changing set of positions and momenta track out a

path over time, to produce a distinctive ’phase portrait’ of the dynamics of the system.

In any scientific or artistic exploration then it pays to have, or develop, a sense of

the shape and scale of the phase space of interest. In order to keep the following free of

mathematics, I will not explain phase space in the strict manner that physicists use the

expression, butt rather try and widen the concept to signify a high-dimensional space

that encompasses the entire range of exploration, taking into account ‘dimensions’ that

are not spatial; cultural, temporal, intellectual.

This is best illustrated with an example inspired by the lifelong work of Ed Ricketts

in the tide-pools of the Pacific coast.

The figure (a) shows a simplified map of the coastline of the Monterey peninsula

on the Pacific coast in California. Using this map we can define any point along

the coastline between Monterey (M) and Carmel-by-the-Sea (C) by giving the linear

distance along the coast line in kilometres. For example, take the point p which is 3.4

kilometres from Monterey. Zooming into this point we show a 200 metre stretch of the

shoreline facing Spanish Bay. The hatched regions shows the extent of the inter-tidal,

or littoral, region of this stretch of beach, which has an area of about ?? m2. Zooming

in again to the line a − b and looking at this line as a cross-section through the beach we see in (c) the topography of the shoreline and the mean sea level. During the

normal ebb and flow of the tides the sea level rises and falls around this mean level

and maps out on the shore an intertidal area that reflects both the range of high and

low tides and the local topography of the shoreline. Now in (d) we show a phase space

representation of the rise and fall of the sea level at the point p. The position of the

point is a one-dimensional distance and this is the x co-ordinate measured in kilometres

and the sea level height is the h co-ordinate measured in metres. This is a new way of

looking at the state of the sea level on the Monterey coast. Each and every point in this

new two-dimensional phase space represents one particular ’state’ of the interaction

between sea level and the coastline of the Monterey peninsula. We can also define

volume of interst within this space – for example, the grey bar shown is the volume of

the phase space represented by the beach at Spanish Bay, over the course of the full

cycle of the tides.

Using this phase space representation we can conceptually interogate the Monterey

peninsula coastline in a number of different ways by describing different ’volumes of

exploration’ within the phase space (they are strictly areas but we soon extend to 3

dimensions and higher in which volume is a better term to use).

The Decision Tree

Street Fighting Mathematics

This has literally just been published by MIT press. 

 

Street-Fighting Mathematics

The Art of Educated Guessing and Opportunistic Problem Solving

Sanjoy Mahajan

Intense Seeing Page Layout

I have been pottering about with the typesetting of my Intense Seeing text. The example below is based on the Tufte class,  I have changed the layout so that it fits onto a Crown Quarto size paper 189 x 246 mm. The font is Palatino. 

The Tex & I

In the summer of 2009 I took on the task of re-typesetting a book I had originally co-authored with my PhD supervisor, colleague and friend Professor Vyvyan Howard. We had originally published Unbiased Stereology in 1998 and it had sold steadily enough that by 2004 another publisher had picked up the rights and we made and published a second edition.

By early 2009 our publishers had sold all the copies of the second edition and had hit on the idea of making a Print On Demand (POD) version that allowed them to keep selling copies of the second edition, but not have to pay upfront for a print run of thousands. This also made sense to us as authors because the book was still current and widely read – by early 2009 it had a total of about 800 citations from other papers and books.

Unfortunately, the overall POD quality was poor. Although the glossy book cover looked good ,the print quality of the figures looked like cheap photocopies and more importantly for us as technical authors the scaling of key images was unpredictable and thus unacceptable in the book. Vyvyan and I decided to pull out of the POD route and walked away from the publisher – prompted by my assertion that I could ‘do it myself’.

I knew that many, many academic scientists active in physics and maths routinely used the TeX and LaTeX systems to prepare papers and books, but I had never learnt how to use these systems myself and previously had been put off teaching myself because of the learning curve and because I thought using MS Word was good enough.

The following is based on my experience of going from a complete novice at  TeX  to someone with a fully typeset 296 page book finished and printed. In the process I have recently learnt a huge amount about fonts, typography and book design.

The TeX program was created by computer scientist Donald Knuth in 1984 driven by his own inquisitiveness and talents. Within two years Leslie Lamport had created a set of macros called LaTeX that made TeX easier to use and since then a myriad of unnamed Open Source programmers have extended and furthered the vision that Knuth had when he first created TeX. In the process over the past 10 years there has been a quiet, but nevertheless remarkable, revolution in how text is printed onto paper to make physical books.

The latest version of LaTeX is one of the very best things you can get for free, on Mac, Linux or PC. Once downloaded and installed a modern LaTeX  system (depending on the one you choose it will have either a fancy text editor or a a plain one and will have a LaTeX  engine that creates PDF output) will allow you to create a whole book of professionally typeset text, figures and equations.  Virtually all of the defaults help you do something sensible, or better, and hundreds of years of the art and craft of typography, typesetting and page design is opened up.  

The output above is some classic advice on typography from Beatrice Warde. It was created with the raw text file  which has the content text and a small number of TeX commands - to format the text in the same way that a typesetter would have done in the past with physical cast metal text.

The example uses the excellent memoir class which allows you to compose a whole book worth of type. The LaTeX system is pretty complete and comes with a number of useful high quality fonts as standard. I have used both Palatino (for the example here) and a Robert Slimbach designed font called Utopia.

Note that the Crystal Goblet piece has clever hyphenation and justification of the text -  LaTeX uses a hyphenation algorithm based on work by Donald Knuth and Michael F. Plass and further enhanced by Frank Liang. This method considers a paragraph as a whole to decide where to add line breaks and language specific patterns to decide hyphenation patterns. More recent developments enable LaTeX to move characters slightly into the margin to generate optically straight margins. These are cleverly NOT geometrically straight but when read they look straight. These computer algorithms are able to simulate the decision making of master typesetters of the past.

Equipped with LaTeX an amateur typesetter can begin to learn about typesetting by  practicing on eitiher their own text or using some existing electronic files (Project Gutenberg has hundreds of classic books in flat text files you can be Charles Darwins typesetter if you wish). If you have Robert Bringhurst's, Elements of typographic Style available and a couple of Edward Tufte books for inspiration you can really get going on more sophisticated things.

The LaTeX  memoir class was developed by Peter Wilson, it is a professional strength typesetting package that is capable of managing all aspects of a complete book project. As well as page by page typesetting it does chapter headings, layout on the paper size of choice, and gives incredible flexibility. Just by using default settings in memoir you can easily give you great page design and typesetting. For example, the command \medievalpage will use the paper size you have selected and produce a medieval page layout based on classic proportions such as those of the 13th century French architect Villard de Honnecourt who devised an ingenious method of setting out optimum proportions for margins and text block on a book page. Other simple commands deliver Robert Bringhurst layouts. If necessary you can set up your own or use a whole class that implements the iconic book layout of Edward Tufte’s books on information design.

And there is a worldwide community of like minded souls. For example, in a thoughtful essay by an Australian philosopher called Adrian Heathcote on how using free, robust and clever LaTeX typesetting programs can help small printers in the UK and Australia make better, more beautiful, books, you can find the following:

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. 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.

So not only is LaTeX free, but it is also remarkably sophisticated. Donald Knuth knew something when he created TeX – that although computers are a modern science, in the end placing marks on paper is an old art and all art requires craft.

The Anatomy of Texture

“…the anatomy of texture, is that which shews the composition of the organs: it is a kind of analysis, reducing these into their constituent elements.”

William Lawrence FRS 1829. On the Nature and Classification of Diseases. Lecture III October 5th 1829. Printed in the London Medical Gazette.

William Lawrence was an outstanding surgeon and famous in his time for two volumes of lectures he published when he was in his mid thirties - these contained pre-Darwinian and essentially evolutionary ideas on man's nature. Wikipedia has a good article on him. 

The Majoor skeleton

Here is a figure showing some of the excellent work of Dutch typographer Martin Majoor and his large family of fonts Scala, that include very closely matched serif and sans-serif faces.

His website explains that "In my opinion, mixing serif with sans only makes sense when the serif and the sans typefaces are both derived from the same foundation, or even from the same skeleton."

This figure shows how he made that come to life for Scala.

Top Left. How Majoor cretaed Scala Sans from his face Scala. "Scala Sans was literally derived from Scala. Using a black marker and some correction fluid, I changed the serif characters into sans."

Bottom Left. The lowercase letters a-g for serif (upper) and sans-serif (lower) show that the final published forms of the fonts retain the closeness of origin.

Top Right. Majoor shows that both serif and sans-serif sit on the same skeleton; "When I was designing Scala and Scala Sans my motto became: ‘two typefaces, one form principle’. This can be demonstrated by isolating the common skeleton of the roman and the italic in both Scala and in Scala Sans."

Bottom Right: Exactly overlain examples of a-b-c lower case are shown. Although both serif and sans-serif give markedley different texture and colour to a block of text set in the two different typefaces they differ less than about 10% in shape between the two faces.

Robert Bringhurst has a very complimentary write up on Majoors Scala faces in his book Elements of Typographic Style.

Anatomy of Utopia

Here is a figure that I have just knocked up to illustrate some aspects of typography for an article I'm writing. It uses the Utopia font that Robert Slimbach designed for Adobe and which found its way (via some controversy between 1992 and 2006) into a free software font that is packaged with LaTeX distributions.

Left panel;

Top - examples of the font including full alphabets of capitals, lowercase, and italics. The Utopia font as parcelled with LaTeX doesn't have a proper set of small caps or old style numerals (the full price version from Adobe does).

Bottom - An illustration of terminals, serifs aperture and axis. Utopia is a transitional font (transitional between old style and modern faces).

Right panel;

Top - the fi and fl ligatures that come as standard in the font.

Middle - In a proper typesetting software, such as LaTeX, the letter spacing should be modified so that certain pairs of letters are moved slightly closer together, this is called kerning. Each pair has a yellow box added to indicate the overlap.

Bottom - An example of LaTeX hyphenation and justification engine on a fragment of text from the Voyage of the Beagle by Charles Darwin. The algorithm not only very cleverly breaks the words in the most appropriate manner it also adjusts the right hand edge so that it is optically straight (even though as you can see if you look carefull it is not geometrically straight).

Many Dimensions of a Book mapped out

I am working on a journal piece on Text and have tried to get my head around the idea of a book being a multidimensional mapping of black ink into a structured 3D space.

As part of this I wanted to try and show that if you break open a book and consider it as a 2D object then there is an extended dynamic range of lengthscales that have to be right for the book to work. It has to have a coherence and structure in the use of black ink in white space over a set of objects: Book - Page - TextBlock - Paragraph - Line - Word - Glyph.

[Robert Bringhurst makes the point in ETS 3.1 - when describing the Digital typeface Requiem by Jonathon Hoefler that, "...Requiem, unlike Bembo, Centaur and Dante, was born in the digital medium, where two dimensions have to do the work of three" p244.

In an interview with Jonathon Hoeffler he returns the compliment and says; "Robert Bringhurst put it best when he said that typography is an art where the microscopic and macroscopic constantly converge."].

I have chosen to measure the area of each of these 'objects' in millimetres squared and plotted these areas as a measure of the length scale of coherence of the text. The example is based on some pages of text from an article I wrote a few years ago about Ancient Geometry, Stereology and Modern Medics.

The typesetting has been done with the memoir class in LaTeX and the free font Utopia that was designed by Robert Slimbach and released for 'free' use by Adobe.

LEFT PANEL:

Book [Here represented by an eight page spread - but a 296 page book is this multiplied by 32 times]

Page [Here shown as a grey on white diagram.]

Textblock [Here is the actual textblock, individual words can now be seen and the structure of the paragraphs and headings etc. If you zoom in you can read it.]

RIGHT PANEL:

Paragraph [Words and their spacing, leading between lines, justification.]

Line [How words interact and word and letter white space, punctuation]

Word [how glyphs and whitespace interacts]

Glyph [the fi glyph looks close up]

In each case I have measured the area of the object (page or line or glyph etc) in squared millimetres and plotted these estimates in the graph lower right on a logarithmic axis.

 

Reducing Fraction (2)

Reed's Razor

Reeds Razor*;

For Intense Seeing, magnify just enough to gain new insight; but no more

Matt Reed 2010.

*This is a nod to two other Razor aphorisms. 

One great one, Ockhams Razor; Entities must not be multiplied beyond necessity,

and one facetious one, Hanlons Razor; Never attribute to malice that which can be adequately explained by stupidity.

The Reducing Fraction problem

I arrived at Intense Seeing via a particular and contingent route; from quantitative microscopy. This routing both colours my view and provides me with a chance to describe an analytical insight into the whole area. In quantitative microscopy there are a number of issues that have to be tackled to make progress, one of which is the `reducing fraction' problem. It's a really obvious problem; the higher the magnification you are using to resolve the details you are looking at, the lower the fraction of the whole object you can see in any one `field of view' (Unbiased Stereology. Howard & Reed First Edition 1998).

It can be illustrated in a number of ways but the figure shown is a very simple two dimensional example.

Note that however attractive the Eames Powers of Ten film and book it is quite disorienting. Even increasing the linear magnification by factors of 2, after a small number of iterations, leads to a vanishing fraction of the original area. The 8x gives a 1/64 th; keep going another two powers of two and you get to 32x magnification, which is a /1024 th of the original area.

Clearly in three dimensions things are even worse.