diff --git a/module1/ressources/module1_supplementary_material.org b/module1/ressources/module1_supplementary_material.org new file mode 100644 index 0000000000000000000000000000000000000000..5eac063d377e0027594e0aac49f920e756847bcf --- /dev/null +++ b/module1/ressources/module1_supplementary_material.org @@ -0,0 +1,274 @@ +# -*- ispell-local-dictionary: "american" -*- +#+OPTIONS: ':nil *:t -:t ::t <:t H:3 \n:nil ^:t arch:headline +#+OPTIONS: author:t broken-links:nil c:nil creator:nil +#+OPTIONS: d:(not "LOGBOOK") date:t e:t email:nil f:t inline:t num:t +#+OPTIONS: p:nil pri:nil prop:nil stat:t tags:t tasks:t tex:t +#+OPTIONS: timestamp:t title:t toc:t todo:t |:t +#+TITLE: Additional Ressources for Module 1 +#+DATE: <2019-02-22 ven.> +#+AUTHOR: Christophe Pouzat +#+EMAIL: christophe.pouzat@parisdescartes.fr +#+LANGUAGE: en +#+SELECT_TAGS: export +#+EXCLUDE_TAGS: noexport +#+CREATOR: Emacs 26.1 (Org mode 9.1.9) +#+STARTUP: indent + +* Sequence 1 + +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): + +#+BEGIN_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. +#+END_EXAMPLE + +Pages 32 and 33, about [[https://en.wikipedia.org/wiki/Isaac_Casaubon][Isaac Casaubon]] (1559-1614). + +#+BEGIN_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. +#+END_EXAMPLE + +Pages 35 and 36, on [[https://en.wikipedia.org/wiki/Gabriel_Harvey][Gabriel Harvey]] (1545-1630). + +#+BEGIN_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. +#+END_EXAMPLE + +Page 40. + +** Note cabinets from Placcius and Leibniz + +I found this example in Ann Blair's work such as [[https://dash.harvard.edu/bitstream/handle/1/4774908/blair_notetaking.pdf?sequence=1][The Rise of Note-Taking in Early Modern Europe]] 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 [[https://en.wikipedia.org/wiki/Project_Gutenberg][Project Gutenberg]] one is missing the "Preface", so don't use it, go to one of the versions available on [[https://archive.org/search.php?query=title%3Apenguin%20island%20AND%20-contributor%3Agutenberg%20AND%20mediatype%3Atexts][Internet Archive]]. The importance of the preface in illustrated by the following two quotations: + +#+BEGIN_QUOTE +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. +#+END_QUOTE + +And more importantly for our present subject: + +#+BEGIN_QUOTE +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. +#+END_QUOTE + +** 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 [[http://webs.ucm.es/info/cliwoc/][Climatological Database for the World's Oceans 1750-1850]]. + +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): + +#+BEGIN_QUOTE +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. +#+END_QUOTE