---
TITLE: We all use notebooks (Module 1 sequence 1)
AUTHOR: Christophe Pouzat
---\n
broken-links:nil c:nil creator:nil

Introduction
============

This sequence discusses a much wider issue than *reproducible research*
(RR). Implementing RR requires thorough note-taking and note-taking
concerns everyone. The purpose of this sequence is therefore to remind
the reader / auditor that he/she already knows: **note-taking concerns
everyone**. Few examples are used to that end.

Annotated manuscripts
=====================

As an introduction to the world of annotated manuscripts, I quote now a
small selection of passages from the first chapter of *LA PAGE. DE
L'ANTIQUITÉ À L'ÈRE DU NUMÉRIQUE* (THE PAGE. FROM ANTIQUITY TO THE
DIGITAL ERA) by Anthony Grafton (Hazan, 2012):

``` example
  By the very movement of his pen on the page, it is clear that
Casaubon masters everything he reads. He constantly underlines the importance of
words and expressions, he notes in the margin key words and summaries
showing that he has read carefully, even when, he states in his
diary that he studied in one day forty to fifty pages
in-folio of Greek with many abbreviations. The most important 
passages give rise to longer comments in the margin.
On the title pages, Casaubon very often carries - a little
as Montaigne - a global judgment on the value of the work.
In addition, he notes his thoughts in notebooks, or takes
notes on texts he can't buy. As they are
gathered in his library, his books represent a whole life of
reading that can be reconstructed over the pages.
```

Pages 32 and 33, about [Isaac
Casaubon](https://en.wikipedia.org/wiki/Isaac_Casaubon) (1559-1614).

``` example
  Yet Harvey left much more than that, including
traces of his readings in the form of more than a hundred books
covered with wonderfully written annotations of his beautiful slanted 
writing - in addition to the notebooks in which he wrote extracts.
Clearly, Harvey considered reading to be his profession,
and he made it an art too. Decade after decade, he lays down his
thoughts on history in an in-folio edition of 1555 of Livy's "History
of Rome". His notes, mostly in Latin, go through
the margins, spread between chapters and fill in
loose sheets, taking on a particularly erudite aspect and
quite daunting.
```

Pages 35 and 36, on [Gabriel
Harvey](https://en.wikipedia.org/wiki/Gabriel_Harvey) (1545-1630).

``` example
... But in the remaining working copy of the
text, the basic edition of 1549, he [Casaubon] introduced so many annotations
that the cataloguers of the Bodleian Library, who were only
not familiar with rhetoric, have classified this printed book as a manuscript.
```

Page 40.

Note cabinets from Placcius and Leibniz
=======================================

I found this example in Ann Blair's work such as [The Rise of
Note-Taking in Early Modern
Europe](https://dash.harvard.edu/bitstream/handle/1/4774908/blair_notetaking.pdf?sequence=1)
and her book *TOO MUCH TO KNOW. Managing Scholarly Information before
the Modern Age*, published by Yale University Press in 2011.

On the preface to *Penguin Island*
==================================

The text can be found *legally* at several places, the [Project
Gutenberg](https://en.wikipedia.org/wiki/Project_Gutenberg) one is
missing the "Preface", so don't use it, go to one of the versions
available on [Internet
Archive](https://archive.org/search.php?query=title%3Apenguin%20island%20AND%20-contributor%3Agutenberg%20AND%20mediatype%3Atexts).
The importance of the preface in illustrated by the following two
quotations:

> One word more if you want your book to be well received, lose no
> opportunity for exalting the virtues on which society is based —
> attachment to wealth, pious senti- ments, and especially resignation
> on the part of the poor, which latter is the very foundation of order.
> Proclaim, sir, that the origins of property — nobility and police —
> are treat- ed in your history with the respect which these
> institutions deserve. Make it known that you admit the supernatural
> when it presents itself. On these conditions you will succeed in good
> society.

And more importantly for our present subject:

> The idea occurred to me, in the month of June last year, to go and
> consult on the origins and progress of Penguin art, the lamented M.
> Fulgence Tapir, the learned author of the ‘Universal Annals of
> Painting, Sculpture and Architecture’
>
> Having been shown into his study, I found seated before a roll-top
> desk, beneath a frightful mass of papers, an amaz- ingly short-sighted
> little man whose eyelids blinked behind his gold-mounted spectacles.
>
> To make up for the defect of his eyes his long and mobile nose,
> endowed with an exquisite sense of touch, explored the sensible world.
> By means of this organ Fulgence Tapir put himself in contact with art
> and beauty. It is observed that in France, as a general rule, musical
> critics are deaf and art critics are blind. This allows them the
> collectedness neces- sary for æsthetic ideas. Do you imagine that with
> eyes capable of perceiving the forms and colours with which mysterious
> nature envelops herself, Fulgence Tapir would have raised himself, on
> a mountain of printed and manuscript docu- ments, to the summit of
> doctrinal spiritualism, or that he would have conceived that mighty
> theory which makes the arts of all tunes and countries converge
> towards the Institute of France, their supreme end?
>
> The walls of the study, the floor, and even the ceiling were loaded
> with overflowing bundles, pasteboard boxes swollen beyond measure,
> boxes in which were compressed an in- numerable multitude of small
> cards covered with writing. I beheld in admiration minted with terror
> the cataracts of erudition that threatened to burst forth.
>
> ‘Master,’ said I in feeling tones, ‘I throw myself upon your kindness
> and your knowledge, both of which are inexhaustible. Would you consent
> to guide me in my arduous researches into the origins of Penguin art?’
>
> ‘Sir,’ answered the Master, ‘I possess all art, you under- stand me,
> all art, on cards classed alphabetically and in order of subjects. I
> consider it my duty to place at your dis- posal all that relates to
> the Penguins. Get on that ladder and take out that box you see above.
> You will find in it every- thing you require.’
>
> I tremblingly obeyed. But scarcely had I opened the fatal box than
> some blue cards escaped from it, and slipping through my fingers,
> began to rain down. Almost immediate- ly, acting in sympathy, the
> neighbouring boxes opened, and there flowed streams of pink, green,
> and white cards, and by degrees, from all the boxes, differently
> coloured cards were poured out murmuring like a waterfall on a
> mountain side in April. In a minute they covered the floor with a
> thick layer of paper. Issuing from their inexhaustible reservoirs with
> a roar that continually grew in force, each second in- creased the
> vehemence of their torrential fall. Swamped up to the knees in cards,
> Fulgence Tapir observed the cataclysm with attentive nose. He
> recognised its cause and grew pale with fright
>
> ‘What a mass of art !’ he exclaimed.
>
> I called to him and leaned forward to help him mount the ladder which
> bent under the shower. It was too late. Over- whelmed, desperate,
> pitiable, his velvet smoking-cap and his gold-mounted spectacles
> having fallen from him, he vainly opposed his short arms to the flood
> which had now mounted to his arm-pits. Suddenly a terrible spurt of
> cards arose and enveloped him in a gigantic whirlpool. During the
> space of a second I could see in the gulf the shining skull and little
> fat hands of the scholar, then it closed up and the deluge kept on
> pouring over what was silence and immobility. In dread lest I in my
> turn should be swallowed up ladder and all I maae my escape through
> the topmost pane of the window.

The logbooks
============

I would like to thank Joël Caselli for helping me interpret the content
of Éric Tabarly's logbook.

This example is only superficially anecdotal. Ten years ago, a European
project was aiming at estimating the Atlantic and Indian Oceans climates
during the 18th century using logbooks from ships of the West- and
East-India companies from the Kingdoms of Portugal, Spain, Holland,
Britain and France. See the [Climatological Database for the World's
Oceans 1750-1850](http://webs.ucm.es/info/cliwoc/).

In the same vein, logbooks from slave ships give a lot of quantitative
information about the slave trade between Africa and the "New World"
(see Marcus Rediker frightening book *The Slave Ship: A Human History*,
2007).

One missing: the classic laboratory notebook
============================================

I quote here Sec. 6.2 `Notebooks and Records` of the highly recommended
reading *An Introduction to Scientific Research* by E. Bright Wilson
(reprinted by Dover):

> It is hard to conceive of a perfect laboratory notebook, and it is
> regrettably rare to find one that is even moderately satisfactory; yet
> the keeping of good records of work done is a major key to efficiency.
> There are bound to be dissenters to any set of fixed rules, but these
> will probably be rarer for the ritual of notebook keeping than
> elsewhere. Consequently, a set of rules which is generally regarded as
> satisfactory, or even as essential, will be somewhat dogmatically
> stated.
>
> Some great discoveries have been delayed because of careless record
> keeping. Thus it is related that the astronomer Le Monnier observed
> the planet Uranus on several occasions, before its identification as a
> planet had been announced by Herschel, but decided that it was a fixed
> star. This was probably due in part to the fact that he wrote his
> measurements on scraps of paper, including a paper bag originally
> containing hair powder!
>
> Laboratory notebooks should be permanently and strongly bound and of
> sufficient size, say roughly 8 by 10 inches, with numbered pages.
> Loose-leaf pages or separate sheets are too easily lost to be
> satisfactory, especially since a laboratory notebook gets rather rough
> handling, and perhaps an occasional dousing with acid. An exception is
> the case of routine, repeated measurements, where a printed or
> mimeographed special blank is often useful if a good system is
> established for collecting and binding the separate sheets. Ruled
> pages are generally used, but this is a matter of personal taste, and
> some prefer unruled or cross-sectional pages. A rubber stamp may be
> used to provide headings for routine entries.
>
> Data should be entered directly into the notebook at the time of
> observation. It is intolerable to use memory or scraps of paper for
> primary recording, because of the inevitability of error and loss.
> Therefore, there should be a good place for the notebook at the
> operating position, and the experimenter should never be without his
> book when in action. Data should be recorded in ink, preferably a
> permanent brand, and a blotter should be handy. Otherwise the record
> is too ephemeral. Notebooks get hard usage, and pencil smudges
> rapidly. When the notebook may be used as evidence in a patent case,
> ink is much preferred.
>
> Rough, qualitative graphs can be drawn in directly, but more careful
> ones are usually best prepared on graph paper of the most appropriate
> type These are then carefully pasted in the notebook, a blank page
> being cut out in order to compensate for the bulk of the one added.
>
> Notebooks should carry the name of the user and the dates covered. It
> is convenient in a research group to agree on a standard size, but
> then some sort of external identification is a great timesaver. The
> first eight or ten pages should be reserved for a table of contents.
> This consists of a line added chronologically for each series of
> similar experiments, together with the page reference. The table of
> contents is enormously helpful in finding items later and is very
> simple to keep up. An index in the back of the book is advantageous
> but not indispensable.
>
> Each entry should be dated and, if several individuals use one book
> (not generally recommended), initialed. The material should not be
> crowded on the pages; paper is cheap compared with other research
> expenses. The principal difficulty is in deciding what to put in.
> Obviously, one enters numerical results and those values of the
> independent variables such as temperature, composition, or pressure
> which are directly concerned. It is also necessary to have a system of
> entries or references so that years later it will be possible to tell
> what apparatus was used and under what circumstances. Somewhere there
> should be available a rather complete description of the apparatus.
> Then, when modifications are made, they should be described
> immediately in the notebook. It should also be possible to trace back
> the source of calibration curves, corrections, etc., which were
> appropriate to the data of a given day. It is helpful if the
> requirements for writing a paper, a thesis, or a book are kept in
> mind. Such a task, once carried out, usually leads to solemn resolves
> to keep a more careful notebook in the future. Also extremely salutary
> is the effect of trying to figure out something from another’s book.
> All references to apparatus, places, times, books, papers, graphs, and
> people should be sufficiently explicit to be understandable years
> later. It should be possible to take each scientific paper and show
> just where every figure, description, or statement in it is backed up
> by original observations in the laboratory notebook, and exactly why
> the final and original numbers differ, if they do.
>
> Some statement of the purpose of each experiment and a summary of the
> conclusions reached make the notebook vastly more useful. Sketches,
> drawings, and diagrams are essential. Since so much observation is
> visual, it is important to record what is actually seen, including
> things not fully understood at the time. Bad or unpromising
> experiments, even those deemed failures, should be fully recorded.
> They represent an investment of effort which should not be thrown
> away, because often something can be salvaged, even if it is only a
> knowledge of what not to do. Data should always be entered in their
> most primary form, not after recalculation or transformation. If it is
> a ratio of two observations which is of interest but it is the two
> numbers which are actually observed, the two numbers should be
> recorded. If the precise weight of an object is important, the
> individual balance weights used and their identification should be
> included, i.e., the serial number of the box. Otherwise it is not
> possible to apply calibration corrections later or to change the
> corrections if new values appear. Naturally, this detail is not
> necessary if only a rough weight is involved. A tabular form is best
> for numerical data. Units should be noted.
>
> Where patent questions are involved, it may be desirable to witness
> and even to notarize notebook pages at intervals. The witness should
> be someone who understands the material but is not a coinventor.
> Material added to a page at a later date should be in a
> different-colored ink, and any alterations should be initialed,
> witnessed, and dated if they are likely to be important. Industrial
> concerns usually enforce their own rules concerning patent matters.
>
> Identification Numbers. It is foolish to spend time and money making
> records of various kinds such as pen-and-ink recorder sheets,
> photographic records, or spectra if these are then lost or mixed up.
> Every such record should carry indelibly on it complete
> identification. A simple system of doing this which has worked well in
> practice is to write in ink on each record a symbol identifying the
> notebook and then the page number on which the auxiliary data are
> recorded. If more than one record occurs on a page, letters or further
> numerals can be added. Thus EBW II 85c would identify the third record
> discussed on page 85 of the second EBW notebook. This is better than a
> serial number, which doesn’t tell without extra keying where to look
> for the notebook entry. A good filing system is indispensable for all
> films, photographs, charts, graphs, circuit diagrams, drawings,
> blueprints, etc. It is hardest to devise satisfactory filing methods
> for either very small or very large material. The former are easily
> lost and the latter very bulky. Small envelopes are useful for tiny
> films and also protect them from scratching.
>
> It is thoroughly worth while to save drawings and blueprints from
> which apparatus has been built, however rough these may be. These
> should be dated, initialed, and labeled; in fact every piece of paper
> containing useful material should be so marked. When an electronic or
> other similar piece of equipment is built, a careful circuit diagram
> should be prepared, fully labeled with all constants. The apparatus
> should carry a serial number which also appears on the diagram. When
> changes are made, these should be indicated on the diagram and dated
> or a revised, dated diagram made. The old one should not be obscured
> or thrown away because it may be required to explain earlier data,
> later found to be peculiar. It is convenient to draw such diagrams on
> tracing paper with a good black pencil. Cheap ozalid or similarly
> processed copies can then be made. One should be kept in the
> laboratory, where it will usually prove indispensable for trouble
> shooting. Sooner or later, however, it will be used as scratch paper
> by someone with a brilliant idea to demonstrate; so the official copy
> and spares should be filed elsewhere. A great deal of time is
> unnecessarily wasted poking around the insides of an apparatus trying
> to find out where some wire goes. \[…\] Labeling. Related to the
> question of notebooks and records is that of labeling. Naturally
> bottles of chemicals must carry adequate labels, which should include
> not only the chemical name but also the source, or a notebook page
> reference if there has been any special treatment, or initials and
> date. One research worker departed from a certain laboratory to take
> another job and left a good deal of material behind. One bottle of
> clear liquid carried no label. Those assigned to clean up examined it,
> smelled it, finally concluded that it was water, and poured it down
> the drain. It was water, all right—heavy water at $30 an ounce. Some
> supervisors relentlessly throw out unlabeled bottles on sight. It only
> needs to be done once or twice. Labels are also essential on all kinds
> of specimens, pieces of apparatus, gadgets, etc. Controls on apparatus
> should be labeled and the apparatus itself numbered. Every laboratory
> has orphaned pieces of equipment, often electronic, of which no one
> knows the nature and purpose. The notebook page system is good here,
> provided the old notebooks can be found. Labels should be attached so
> that they will stay. Metal tags can be riveted on. Paper labels should
> be covered with some sort of varnish.
>
> The whole purpose of all these recording systems is to preserve
> values. They should be carefully thought out to fit the conditions of
> each laboratory and should be adequate but not overelaborate. If too
> much is demanded of human nature, the system will break down.