Neurodegenerative diseases are doubly traumatic. Seemingly healthy people can gradually lose control of their muscles, motor-skills and even their minds. Then, even if the source of the degeneration can be stopped, neurons regenerate extremely slowly, if at all.

The bulk of neurons are formed during pre-natal development from stem cells. These are cells that have the potential to form a wide variety of different types of cells and are undifferentiated. Adults do have stem cells, but these are multipotent or oligopotent, meaning that they can only differentiate into a few types of cells. The adult brain even has a small pool of neural stem cells.

However, the most useful stem cells are those found in embryos, particularly those in the morula phase of foetal development. These stem cells are totipotent and can form any cell at all. It is hoped that research in this area will unlock a way to repair degenerative ailments. 

As far as scientific advancement goes, this is all very encouraging. However, there is one very large problem. The only way that these embryonic stem cells can be harvested is by sacrificing a set of cells that have the potential to become a human being.

The smog of war

Lets start with the bad news: climate change and global warming are already affecting our health and it will get worse. How much worse requires research and assessment and we have not undertaken a comprehensive study. Few middle income countries have but that is no excuse for doing nothing.

Most European have completed what is known as a climate change health impact assessment. Heatstroke related deaths caused by very hot European summers prompted them to take action. As temperatures will rise we must expect more deaths due to heatstroke worldwide.

The raging fires in California, Australia, the Cape (the Cape of Fire Storms!) and elsewhere have tragically highlighted the need to adjust human settlement patterns and prepare better for the devastation they bring.

How does climate change and global warming affect the health of human beings? The 2004 International Comparative Risk Assessment examined health risks and they estimated that 166,000 deaths in 2000. They also estimated that the lives of individuals were shortened by 5,5 million years because of climate change factors.

When one thinks of the 'naturalist' Charles Darwin, it is his contribution to our understanding of how living creatures evolved that casts anything else he might have done into the shadows.

But Darwin's skills were certainly not limited to theorising on the survival of the fittest nor were his eyes fixed only on living creatures as he embarked on his epic voyage on the HMS Beagle in 1831. He was, in fact, a skilled and influential geologist whose work continues to resonate in the field. He was, for instance, the first to make a geological cross-section of the Andes mountains in South America. He also made important observations on both the development of volcanoes and in explaining the occurrence of coral atolls.

The father of evolutionary theory

Charles Darwin was not an atheist. He became an agnostic, which the Oxford English Dictionary defines as ‘a person who believes that nothing is known or can be known of the existence or nature of God.’ Darwin therefore did not deny God, only that knowledge of God was a human impossibility.

A progressive theological view is that Darwin always left open the possibility of divine providence, which is the idea of God creating the laws of, rather than the products of, nature, which human beings can study and comprehend. Today it bears the name of Intelligent Design, a kind of theological evolutionism.

What appeared to move Darwin’s thinking along was the role of pain in nature. He wrote: ‘There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designed the Ichneumonidae (a wasp) with the express intention of their feeding within the bodies of caterpillars, or that a cat should play with mice.’

The death of Darwin’s beloved 10 year old daughter Annie, likely of tuberculosis, traumatized him to the point of disbelief, for why should a innocent child be made to suffer so much? Ill himself, with what we suspect was Chagas disease picked up in South America, Darwin came to terms with the pain of animals only later in his life.

Darwin, writing from the Cape on 3 June, 1836 to his sister Catherine, looked forward expectantly to the next day: "Tomorrow morning I am going to call with Capt. F[itz] R[oy] on the Sir J. Herschel. I have already seen the house which he has purchased; it is six miles from the town & in a most retired charming situation. I have heard so much about his eccentric but very amiable manners, that I have a high curiosity to see the great Man" .

John Herschel and his family had arrived at the Cape of Good Hope in January 1834 with plans for John to sweep the southern sky to catalogue all of objects of interest, just as he and his father, William Herschel, had done for the northern sky . John Herschel was at that time the best known astronomer in Europe and carried the family name of the man who had become famous for his discovery of the planet Uranus in 1781. John was midway through his sojourn at the Cape and had expanded his interests to include the Cape flora, amassing a collection of bulbs that he planted in systematic order in the garden at his estate of Feldhausen.

Have you ever heard of the Darwinian Industry – a group of international scholars who made their academic living from the study of Charles Darwin's manuscript collection at Cambridge University? What follows is the one of the many results of that industry, others being the Correspondence, Charles Darwin's Notebooks and his Natural Selection (the big book he never published in his lifetime). Many years ago David Kohn suggested I should look at Charles Darwin's library which the great Sydney Smith, the inspiration of all Darwin scholars knew was full of margin notes (Marginalia). Sydney thought that the complete transcription of Charles Darwin's marginalia was an impossible task. My valued friend Nick Gill, originally my assistant, now a co-author, thought that at least a catalogue could be made but we decided to attempt the whole thing and in 1990 the first volume of Charles Darwin's Marginalia appeared and last month, almost twenty years later, volume 2 was completed, just on time for the great naturalist's bicentenary. Volume 3 will follow soon (less than twenty years, we think).

The principal locations of Darwin's annotations are the margins around the text of the books, separate sheets or 'slips' of paper, and the front and back inside covers of the book. The 'slips' are now mainly found stuck or pinned the back cover – although we believe that it is where they spent the prime of their working lives. The quality and the colour of the paper used for these slips vary, again probably inplying different bouts of attention. WE have distinguished three broad types: smooth blue paper; rougher yellow-mottles grey-blue paper; and the rest (mainly non descript white or greysh paper). The material found is reported as: notes and/or slips inside the front cover; notes and/or slips inside the back cover; slips attached anywhere else in the body of the book; marginal marks and comments in the body of the book.

Charles Darwin's reading habits

Here we find Charles Darwin instructing himself to pay only cursory attention to the remainder of the book in question(Vaucher's Histoire physiologique de plantes d'europe). What, more generally, has our reading of his marginalia revealed to us about his procedures in reading the scientific books he owned? Given how systematic Charles Darwin seems to have been, it is not difficult to build a general picture.

Charles Darwin acquires a book and begins reading. It does not take him long to make his judgment about the quality and usefulness of the book. If, as was quite frankly the case, the verdict was broadly dismissive, he would usually persist, but less intensively and only in the hope of encountering a handful of useful pieces of data: hence the large skipping ,or comments to the effect "only skimmed". During this basic reading, intensive or otherwise, the margin is scored and peppered with comments. At the end of the reading, he would now list out the locations of his more important comments and margin-scores on an inside cover (usually the back cover), occasionally adding brief mnemonic notes.

The book will now probably lie fallow –maybe even for a number of years- until the lucky moment arrives for it to participate in the process of data-collection for a Charles Darwin publication. At this stage, the list of locations is re-examined, and a new, shorter list made on a separate sheet of a paper of the most important locations, now with details in the form of a long-hand notes about the information to be gleaned at those locations."I will cease extracting", he says at a certain point (668f), reinforcing our growing impression of him as a kind of intellectual dentist. We have the strong feeling that he hardly ever reread the book itself –a feeling underlined by his exceedingly rare self-instruction to "Read Second time " (545c), which would scarcely make sense if he usually did this anyway. However many years later he returned to the book, he was confident that he had already 'extracted' everything of value.

The separate slips containing the vital gems at this point reach the prime of their working lives: we imagine those relevant to the publication in progress now collected in a heap (or in Charles Darwin's systematic case, no doubt a pile) on the writing table, being finally reviewed. It is at this stage, we presume, that the code-letters "Q" or "NQ" are entered on the slips and \ or at the original locations in the text against the items he has decided to use. The set of slips, together with Charles Darwin's own notes and drafts , combine for a while into 'portfolios of working notes' for the writing of the publication in question. Once the publication has been pieced together, "slips all put in proper places" (572h)-i.e. stuck for any future references usually inside the back cover of the now fully harvested-book. A slip may take part in this 'cycle' a number of times-its important underlying content, as we shall see later, being the broad theoretical themes invoked by the data recorded on it.

There are of course exceptions to this general procedure-though not, we feel, all that many; and only two are worth noting specifically. The first concerns books that Charles Darwin read early in his career, where one is likely to encounter inside-cover comments not referred to page numbers in the text of the book, making recovery of the original data extremely tiresome. The other, more significant exception is the occasional set of slips stuck into the text of a book- these were quite possibly part of the initial thorough reading, and are there to facilitate understanding of the text, especially anything requiring calculation. It is for the wider company of Darwinist to embellish this basic picture of Charles Darwin's reading habits, Our brief outline here is but the prelude to analysis of his interaction with his scientific library.

We found one annotation particularly evocative as a metaphor of the contents of the marginalia as a whole:

"I suspect reefs of diff strata in diff parts" (536h)

Apart from reminding us of Charles Darwin's early involvement in geology, this remark suggest a summary of our hypothesis about Charles Darwin's main mode of processing scientific reading matter: the margins, end-notes and the slips of various different paper types constitute physically discrete strata or layers, corresponding more or less closely to different bouts of attention. Insofar as these bouts imply an accumulation across different 'layers' of time, the metaphor of geological disposition seems quite reasonable.

In fact the 'layers' concept begins to unlock the inner nature of Charles Darwin's mode of working with sources: and indeed, we should ideally look upon the whole great corpus of marks and comments not piecemeal, but as a single complex laminate-fused layers not only of time and attention, as we have seen, but also of types of response to the source-material, and also layers of themes reflecting Charles Darwin's lifelong theoretical preoccupations.

Charles Darwin's responses

It is Charles Darwin's extraordinary single-mindedness, already apparent in his hyper-methodical reading habits, which is reflected in our perception of the marginalia as constituting essentially as single structure. Furthermore, Charles Darwin had his theory pretty well framed before all but a handful of books represented in this volume were seriously read. In the main therefore he was not reading to theorise. There are, are rather some half dozen 'layers of response' we detect in the marginalia.

"Many valuable facts referred to proper places" (159c)

Charles Darwin's principal 'layer of response' to a text, constituting the great bulk of the annotations, was in fact data collection, or 'extracting', to revive the Charles Darwin term. At first sight, the sheer detail, quantity and range of these 'extractions' might suggest vicarious activity, but that is not absolutely not the case. On the contrary, the whole process was strongly purposive – namely, to assemble a vast store of sometimes tiny points of information in order to illustrate and support the great theory. This résumé is, as Charles Darwin might himself have remarked:

"good but too hasty" (587f)

We qualify this résumé to some extent in pointing to the existence of several 'layers of response'; nonetheless we believe the reader will see that 'our man in the margins' appear more relentless, dismissive and self-regarding than his modulated public persona would imply. In a sense this is hardly surprising – anyone's personal notes are likely to have a greater curtness to them than their finished texts. Nonetheless two impressions may merit an airing here.

Charles Darwin often judged a book on the sole criterion of its relevance to some aspects of his "Grand Enterprise": "After p. 109 not one word for me" (675d) he pouts; "This only useful for ancient History of Dogs…I doubt whether any use" (843e-g). There are other not infrequent remarks to the effect that books failing to minister to his need for data are eo ipso pointless – his dismissive sign "O/", meaning "nothing for me", being tellingly close to the copy-editor's symbol for "delete" (which his sign can also mean when he waxes subeditorial)."Erase from Memory" might be the early-twenty-first-century translation.

The undercurrent of predation here is notable in itself; but the manner of it – i.e. its near total absorption in pinning the already-formed Weltanschauung down to fact – leads to the first of our impressions: that, from quite early on, Charles Darwin's mind was no longer really 'open' at the level of high theory (however flexible he remained in respect of subservient principles) with one notable exception: by the early 50' he changed his view of adaptation which by then became 'imperfect' from the original 'perfection' he had inherited from Natural Theology.
Our second impression is also connected with fixation. As giants of nineteenth-century creativity, two figures in particular make excellent subjects of comparison as far "fixation" is concerned – Charles Darwin and Richard Wagner.

"What can I have said" (794c), Charles Darwin might have been prompted to wonder… We shall develop this line more fully later. The Darwin-Wagner similarity of relevance immediately is the power of their obsession with their work. Anything that crossed their paths was to be assessed for its usefulness in the construction of their creative monuments. This is reflected in the Wagner's notorious personal exploitation of everyone he encountered. In Darwin's case everything tended eventually to be pressed into the service of the theory. Thus the parts of his correspondents' letters not dealing with science were crossed out so that they will not distract from his reading of the relevant parts. Furthermore, when he wanted to study infant behavior , began by watching the behavior of his own son William, whose development, to cite Janet Browne in Kohn 1985, he followed " as if it were (that of) a barnacle or a promise". He even had ladies who obligingly made their children cry so that he could watch their infants' reactions. These points tend to amplify our view of Darwin's public persona as a certain modulation of the 'inner man'.

"quite opposed to my views"

Connected with the enterprise of data-extraction, and accounting for a large minority of annotations, the second 'layer of response ' we detect is Cd's evaluation of an author and his work. These reactions are usually very forthright, again not infrequently self regarding: "excellent summary of whole; approves of what I had said"(239b); sometimes rather patronizing: "most interesting indeed quite amusing" (393g); or "Good Boy" (242b); and occasionally downright rude: " If I want to show what rubbish has been written a translation of this will do.-" (485d). There is plenty of generous praise – 2all marked wonderful book " (857a)- but a balance negative criticism outweighs the positive variety. "Unread ably dull" (738b) represents a quite noticeable type of reaction. Charles Darwin certainly responded to a degree of entertainment- "2d part funny passage" (217d)- and disliked being bored by an author . Charles Darwin himself is quite entertaining in his reaction to an author and his work; naturally we allow the reader to stumble across these little gems. Our own warped sense of humour detects a tendency towards poisonous wit, especially in putting an author down: "ass prevails-one here", he notes on Lucas' Heredité naturelle (521a), along with another remarks which sound scarcely straight-faced, despite the seriousness with which he took the book as a whole. However, let us en passant charitably suppose that Charles Darwin,s reference to Haeckel as "Hack" (358d) owes more to abbreviation than to denigration.

"Word simple" (541a)

Charles Darwin is evidently more forceful in his marginalia than in his published works, which are the province of what we call we might call 'selection with a human face'. He appears aware of this as deliberate: "I must express things diffuse and with a most wearisome pretence to formulas" (516g), he moans , contemplating the requisites of public style . He as to be so to speak 'the very model of a modern major scientist'- but in his most self he is perhaps convinced that the world is simple, and he is quite impatient of all his deference to 'ifs-and-buts'-ism, disclaimers in face of irritatingly incomplete evidence, and openers to the effect it is therefore by no means inconceivable that'. Charles Darwin himself might have thought this comment.

Too Strong

And it may indeed seem strong in description of someone who after all spent a lifetime reading and writing in meticulous and cautious detail. However , a further example may strengthen the impression; and one basic consideration may help dispel the paradox. The example is the extraordinary tone of Charles Darwin's final dismissal of the thrust of "Bronn's criticism for new edit of origin" (181a-182c)- for example . "As I cannot justify my opinions in any one single case, so I need not in any.- is as true as it is severe- Though I can in no single instance … explain changes yet the structures led me to conclusion.-"(182-c), And that's that. The consideration is that Charles Darwin's ' diffuse and wearisome ' complaint (and indeed is this last quotation) implies that he had seen more fully and more definitively than he felt able to show. Other evidence for this takes us in the first place back to the notebooks, and specifically to that point where Charles Darwin, in some apparent haste perhaps propelled by elation, sets down the finally formulated concepts underlying natural selection. He had held the workings of the living universe in his head with a sense of clarity and comprehensiveness hitherto probably given to no-one. He had struggled with the issues for a long while, but now he knew, and knew that he knew: he had the key. One probable lasting consequence of these hard-won certitudes of insight was that Charles Darwin may never have felt in deed of an elaborated methodology or philosophy of science, confident enough in his seemingly natural instinct for the relationships between solid evidence, creative intuition, the need for ' wearisome formulas' of ever wider explanatory power and physically plausible models of the world. That something like this is the case evident in the marginalia from the near-absence of our third ' layer of response ': comment at the level of high theory. Most of Charles Darwin's comments at this level are really quite perfunctory, even when he is assessing work he took most seriously , or work by earlier evolutionist. It is as if from the security of his vantage point he would see others working (like Candolle?) on areas too specific to enable an appreciation of the grand process: "he has not the key" (145b)- or attempting (like Chambers or Lamarck?) to scale the heights with an insufficient respect for physically feasible mechanisms: "It is doubtful whether Lamarck has done more good by awakening subject, or harm by writing so much with so few facts" (477a). Charles Darwin by contrast had the overview well before he came to the bulk of his reading , in which he was forcing himself by the systematic procedures we outlined before to acquire and retain the detail. He had no great need by this stage to rehearse his case in defence against theories of others. Even his comments on the higher principles relating to his own theories are in the main quite cursory and matter-of-fact. "The natural system", he comments during his reading of Herbert (probably during the 1840's), "seek to know relationship and does not attempt date of separation " (376e), implying that the notion of descent with modification was already to be taken for granted, and that any troublesome grand concepts found upon the lurk had merely to be pushed into line, or reduced to a purely 'operative' status no longer in control of the debate: "It is succession , not resemblance which makes a species'"; and within any one such line of succession "COMES TO WHAT I SAID, AMOUNT OF DIFFERENCE DESERVING A NAME "(630b; cf317f). The conceptual pragmatism here sounds almost off-hand. But we should resist seeing it as a kind of opportunistic abdication of the old problems; it is , rather , they considered solution to them. Furthermore , this attitude is applied consistently , in his understanding of scientific method his whole defense of his theory (see variation , vol.1,p.9), his tiffs with Huxley over experimental proof of natural selection , and so fourth . Further thoughts around these issues are to be found in Di Gregorio (1981); it can now largely unargued philosophical level. Here the marginalia are the crucial bridge between the raw insights of the notebooks and his considered but intensively supported comments on methods and theory made many years later. Such, then, is our third layer of response almost missing . In fact , of course, in a different sense it is there the whole time: it resides, as we shall see, in the thick weave of topics and themes underpinning the whole corpus of annotations', and thus imprinted –"diffuse" indeed, and sometimes even "wearisome"- on every comment. However , the thinness of the layer of explicit 'remarks on high theory ' may come as a disappointment to those who turn to the marginalia of a great thinker expecting them continuously to over flow with great thinks .

"must be a misprint"

Charles Darwin may have found formulae tedious , but he was by no means averse to a bit of genteel pendantry now and then. He not infrequently trips (living) author up on selling or other detail; more significantly on misquotation of himself. Sometimes these minutiae are noted down alongside more substantial comments which look like scraps of drafts of letters to the authors in question: "Allow me to point out that you have unintentionally misrepresented me…"(223g); "I am glad of your somewhat changed views…" (838c) waxing subeditorial, and a scattering of footnote fodder for future volumes of the correspondence…

"what I do not understand" (471f)

Here we find Charles Darwin alluding to a fifth of response', requiring little comment as such – a relatively thick vein consisting of translation and or close paraphrase of the original text, especially prevalent in German books , but not unknown in Italian or even French books either. In the case of German, this may in part have to do with tribulations of the gothic script adding themselves to the trials of the language. But in any event , the consequence for the reader is that the number and density of annotations in a book are no clear guide to the importance either of the book or of the marginalia it contains. Hence our annotation of the title page of part one, taken from Charles Darwin's annotation of Candolle: " upon the whole nothing can be inferred from this list" - a light-hearted motto, but intended as a serious caveat. Indeed , any comparison of the entries for Candolle and Gaertner , the latter taking more space, will quickly show that the former is so of far greater importance.

Mention of Gaertner brings us to Darwin's joke , thus to our sixth layer, general wit and merriment'. It is pleasing to note that Charles Darwin let a few examples of the art of being serious without being solemn- such as the doubles entendres attending the 'cross foxes' of p.705h, the 'high fish' of p,155a, and the 'boring sponge' of p.673d- and that he also shows the tendency of the highly creative mind to put things to itself in a radically offbeat way, as with the comment about the 'man cut in twain'. However we will spoil the readers fun of further discovery only in respect of the aforesaid joke. It is to the effect that Gaertner , despite the name , was probably not much cop as a Gardner. It is actually more important than its flippancy might lead one to suppose: in the first place, it demonstrates that Charles Darwin was good enough at German to invent a bilingual pun, thereby lays to rest the myth of his alleged ineptitude at that language . Furthermore, Charles Darwin liked his joke. This we know because he chose to share it with the future mildew of the margins not just once, but twice (374c, 277a-b). 'It is therefore by no means inconceivable ' (to coin phrase) that this implies a simultaneous reading of the books in question. Charles Darwin was sporadically given to dating his comments ; following through the more, and less serious cross-reference may thus eventually enable the making of a workable historical map of the whole of his interaction with his scientific sources. As Charles Darwin himself remarked , albeit in a rather different context: light will be thrown on the origin… the meaning of this cd hardly be misunderstood , but I can see not the period of going into details.

Nor indeed of going from the marginalia to Charles Darwin private life. Our last layer another almost absent stratum- consist of very rare and insubstantial glimpses (always assuming ,of course, that his rapturous "Flora!" of p.839c does not address a mistress hitherto hidden from history). There are one or two mentions of genuine relations , and the occasional name of a pet or other animal. Most of these references analyse details of behavior – reinforcing our earlier implication that cd was often unable to resist surveying even the domestic scene with the professional eye of a proto-ethologist.

Charles Darwin's themes

We meanwhile must now pass back at surveying the world back at large. Having provided a brief description of the strata visible in the mass of marginalia, we need now to look closely at our first layer, the data-processing' to put it crudely. That forms the bulk of the annotations. It is time to investigate its own internal stratification – the layers of themes and topics – and hopefully in doing so to discover what Charles Darwin might have termed the. "whole key to theory" (164h). The major layers we are considering here are great themes and subthemes that Charles Darwin pursued (or that pursued him) throughout his career. They function like the leitmotive' of a Wagner opera , or to echo Sloan's not dissimilar analogy: a complex keyboard instrument with several keyboards and registers, these registers each able to act sometimes in solo, other times contrapuntually, and times in synchronous harmony. A Wagnerian 'leitmotive' has a comparable flexibility; the leitmotive interwoven are the constitutive matter if the whole composition, and they are repeated and evoked whenever logically necessary. None of them is ever forgotten or allowed to drop out similarly in Darwin's case. Some themes are registers from dominant melody lines at various times… other themes function more as a basso continuo, often submerged but nevertheless present if one looks closely enough. (Sloan again.) This procedure enables continuous integration of detail into the whole, and enables detail constantly to refer to the big serious themes-for example the 'leitmotiv' of the dragon in Wagner, or that of comparing wild and domesticated animals in Darwin. It is this which makes the exceptional range of research of a figure like Darwin mentally manageable . It also explains the many repetitions and (in) direct reference to other parts of their work that both of Wagner and Darwin introduce. We believe we have captured the essence of this continuous state of inter-reference in the structure of the index and conceptual concordance which forms part two of our volumes. The classification headings used in part two reflect the themes and topics we detected in the marginalia . There is a relatively straightforward list of names of animals (under the category 'fauna', 'fa' in our code), plants (under 'flora','fl'), places (under ' geography', 'gr'), populations (under humankind', h'), and geological epochs (under 'time' 'ti'); the document is rounded off with a list of people and works cited. Interwoven however with these names registers is a classified conceptual index ,whose categories were as far as possible inducted cautiously from the annotations themselves, in order to reveal Darwin's 'leitmotiv'. Work on transcribing the annotations in each book was accompanied by nothing down the range of the themes and topics in play. A brief cipher was developed for each topics of these topics , and these are recorded for each annotated book immediately beneath its title in part one. The conceptual index was then prepared by taking each individual annotation and noting down the topics in play there, sub categorizing as necessary within the broad categories previously developed , and adding a few new categories relating to Charles Darwin's other 'layers of response '. The full list of the ciphers denoting these categories and subcategories is recorded on the sheet at the back of the book. The 'concordance '- like aspect came in when we decided to enter each annotation into the index as a string of topic-ciphers, cross referenced under each cipher in the string. Thus a statement involving the four ciphers A,B,C and D appears in the document four times, as a-b-c-d-, b-a-c-d, and d-a-b-c. in this way part two claims to have preserved intact the entire network of Charles Darwin's thought. The resulting document is rather large and very fine-grained . the structure of the entries under each topic-heading is as follows. This arrangement means that those wishing to do battle with the interplay in its full intensity can work from what one could call the 'infra'- structure. Those preferring to take their concepts so to speak lying down and one at a time can work with the same references as collected at the head of each entry. The reader will no doubt be glad that we resisted the temptation to present the whole of part two in the form of an irregularly branching tree. We did however fall for the idea of using coral- and tree like diagrams to punctuate our presentation of the way our analysis of topics-in- play breaks the corpus of annotations down into their elementary strands, the leitmotive of the Darwin's revolutaion. Thus those wishing to study the logical interactions of the leitmotive as it were medium do worse than start from these clustergrams. For our part , let us begin our presentation of these interactions at Charles Darwin's of these interactions at Charles Darwin's own beginning.

"Diversity of organisms first condition of nature" (582a)

Variation ("v" in our code) jut is, basiv, unargued :, "NB when many pistils, then number variable (when many organs apt to be variable; WhY. Hairs and c and c vertebrae of serpents" (253d-e). As we shall further below , this emphasis on the reality of variation is essential to an understanding of the profound change in perspective away from platonic notions that the Darwinian revolution is all about . real variation for Charles Darwin plays something like a role played for Newton by the distribution of matter- the variable density of the universe , to make the analogy sharper. All characteristics of organisms are subject to variation, the behavior of animals and plants ('beh', 'mhp'),not their just their physical structure : "Great diversity of instinct of bees of same genus : variable in species also" (74e); "has been axial twisting vary in same plant" (592c) . Variation , as this last extract implies , distinguished every organism at least minutely from its nearest relatives , and thus the primacy of variation brings the notion of the 'individual' ('in) to the fore: "as individuals differ in some respect…several must be experimented on.-" (267g). if , as Mayr claims Darwin introduced "population thinking", then what matters for him is "variable populations consisting of uniquely different individuals". Variation occurs both in nature and under domestication, as the first two chapters of the origin readily remind us, thus annotations on variation need to be related to those comparing the variations of wild with domesticated animals ('wd'): "tame cows more milk than wild: organs adapt themselves" (84g); or wild with cultivated plants ('wdc'): "old cultivated kinds tend to vary loose the hereditary quality of goodness" (595h). This last extract pushes us onwards to take note of reproduction (fg,for fertilization and generation), and heredity or inheritance (he9. If variation is Darwin's 'matter', then heredity, the passing if characters from parent to offspring which holds the chains of beings together, is perhaps his equivalent of Newton's gravity, the unexplained agency holding the chains of objects together .As we shall see below in mentioning pangenesis , Darwin never quite managed to make variation and heredity cohere conceptually- rather as it was beyond the Newtonian mind to conceive of matter and gravity as co-essential .In remarks which seem to show the shutters partly closing on the fully 'open' mind, he insist: " contrast of adaption and inheritance " (359f); or again: "inheritance cannot be cause of variation has nothing to do with it" (514c)- an annotation which effectively sweeps all before it.

Diagram 1

In this and the following diagrams we attempt to display some fraction of the densely woven threads of themes and topics constituting the bulk of the marginalia. The key to the topic-ciphers is ti be found on the sheet at the back of the book. The diagrams summarise the text immediately preceding them.
"if all species varied equally all wd be in confusion"(432f)

But they don't: variation is itself variable. In the first place, this means that all is not in confusion- groupings of organisms are discernable , which we call varieties, races species and higher groupings ('var', 'Vc', 'sp', 'sph'); and this will refer us eventually to definition and classification, or systematic ('sy'). We have observed Charles Darwin's pragmatism in these matters already; he pauses to praise Lamarck's skepticism: "good remark how arbitrary the distinction race and species is " (477h).

In the second place, the variability of variation has its own correlates and brings into consideration the size of genera ('nos') and their wide geographical ranges 8'gdw'): "but this is the very point that we are considering that large families are wide rangers and most convertible 8but that is only a few which are wide rangers and most species)…" (115d-e). The whole time , we perceive in the background the fundamental questions of modification and speciation-

"Malthus and Franklin saw the law of increase in animals and plants clearly" (562h)

The other basic condition of nature , again implied by reproduction, is 'increase'- our category 'no' for 'number' includes increase and decrease, and in its subdivision wider concepts such as the 'amount of life'. Increase can discerned directly in special cases like naturalization ('gdn'), where introduced organisms ('gdi') at first increase swiftly: "Europe/U. states 716 in 26 years 600 miles lat. Many other good facts of rapidity/-" (124d); "DR D.Owen says newly introduced plans, first overrun the country and then become scarcer (ask A. Gary)" (545e-f). The finitude of any natural context means that there are checks on increase , principally struggle between organism for relatively scarce relatively such as food and space. the basic process of nature is thus increase checked struggle ('oos'): "ie as far as food and climate (enemies preoccupation by other species) ie conditions allow species and genera to range , so they will range …" (703e); " beasts of prey destroyed others increase immensely, and drive others from haitation2 (703f); every one of such species cover ground if no other species present: if rarity here is step to exclusion,then the greater importance of other organic beings is shown" (109d). The relationships of organism to organism ('oo') are not directly antagonistic; and these complexities constitute perhaps the central focus of Darwin's word-model. Without a clear understanding of the place of the relationships between organisms in the model, one cannot understand either the notion of selection or the Darwinian conception of evolution. Charles Darwin likes Hooker's " good remarks on strife of plants " (404d); and ponders Haeckers good critiscm on my theory of struggle for existence –says ought to be confined to struggle between organisms for same end – all other cases are dependence mistletoe depends on apple" (356b-c).Charles Darwin also painstakingly wrote notes concerning the symbiotic relationships between insects and pollen. In the competition of resources , death and destruction do not only visit themselves upon the old ; indeed , the fate of the variably vigorous young (y) (including eggs 'fge', seeda 'fgs', etc.) is in an evolutionary sense more significant , because dead young do not mature to reproduce , and thus their variations cease to be inherited .<young monkeys and humans> cutting teeth die from fever accompanying" (700A-). Killing by Hawks are white or yellow vars " (430a). External agencies other than that disease ('pat', for pathology) complete the piucture- the direct action of conditions ('cc'), interwoven with direct action of conditions on food.('fd'): "Many wild pigs die in hard winters and in very dry summers " (39b, 40f)-some from harsh weather as such ,but closely allied individuals and /or species (spc9, because these are the most near competitors for the same resources : "closely allied species exterminate each other" (629c).

"selection wd act on a trifle".

The mere trifle of the margins became the trifling characters of chapter 4 of the origin, which are on the contrary of the highest significance , as Charles Darwin was fully aware in his comment , and in his collection of many details concerning variation in the colour, size and reproductive power of animals and plants ('tmp'). Natural selection (sl), the heart of Darwin's vision , invites comparison with the effects and contexts of human selective intervention (br,'ooh'), and thus refers us back to the comparison of wild and domesticated productions: "such selection cd never apply to wild animals , as evey parent must be adapted to same conditions.(509-f)

One especially notable set variations is not-so-trifling physical characters comprises sex difference (sxd) and thence to the topics of breeding ('behb') and other social/ sexual behaviour ('ss'), "Huia with beaks different in 2 sexes and aid each other SS" (99b); sexual s. use of barb of fishes as exciting organs". "it is clear that characters sometimes go with sex- as sometimes polydactylism and c- pouting and wattle , and so it useful to one sex can be selected and returned <does he mean retained ?>" (520-d). This last point, with its passing mention of deformity, reminds us that some naturally occurring sexual characters , developed in the struggle between members of one sex for the attention or possession of members of the other ,invite comparison with artificially produced 'monsters' ('mm'): "a breed of <silkworms of> which females had much finer and not so monstrous wings as in the south" (690g).

"I fancy not in time."

Au contraire, time is of the essence. Selective pressures act an organism all its life –invoking our category of organic time and age (ta): "curious case of quick deterioration by neglect in glamorgan cattle showing some selection always going on" (885f).However as any evolutionary process, selection acts slowly over historical and geological time (ti) as sloe geological change important because domestication shows slowness" (885F-g)- struggle leading in case of the less well adapted parts of population to rarity extinction (ex), especially amongst closely allied forms. "perhaps a decrease or unfavorable conditions might destroy the intermediate vars…" (483c). selection thus leads to divergence (dv); distinction between populations, sharpened by extinction of intermediates –The existence of stations is independently demonstrates by the observation that broadly speaking particular spot can support a greater amount of life (noa) the higher the number of species (nos9 involved . "much life causes much decay makes strata and c and c and c many stations . for different times of year will have species all times of year . good …there wd not be many species without stations ; yes , how many species can be introduced …creations not easy work thus also shown. It worthwhile pointing out that Charles Darwin uses creations here to mean natural formations and does not mean to implicate the almighty . but equally it is worth pointing out that the facts about neutralized introductions often off stripping endemic and indigenous forms (gde)

"It is important to observe no selection cd aid horse in Falkland" Circumstances favoring selection include high numbers of individuals or species in any sizeable area (gr) (because of competition); or isolation 8 is9 because any variation in isolation is subject to changes specific to the location..or horses in Paraguay except strength of constitution and breeding at different time of year; but that cd be effected only if a little earlier or later was more favorable crossing also aids selection; it tends to add vigor and fertility whilst inbreeding tends to reduce it. the converse of the law ill effects of breeding in holds in plants –namely crosses being more fertile (836c-d). The subject of crossing takes us also to those of reproduction and transmission ('het'): "one might fancy that ass crossed with the horse there is a greater potency of race, abd that this potency is transmitted more by male in this case than in others. Niata cow transmits with more force than bull- pouter cook and hen equally" (515-e9 also to the existence of sexes (?sx'), the symbiotic relationships between the habits of plants and animals , and so forth which together account for a very sizable number of annotations. "Nectar is sought eagerly by various insects… The real object is to ensure occasional cross…Think of number of insects which feed on nectar!" (472e-h), part of an extended comment of considerable range and detail)."It may be that lower plants have survived owing to having this advantage of separated sexes." (378h)-sex thus being a topic of capital importance in Charles Darwin's work. it was related by him to variation in his pre-selection theory of evolution (see Kohn 1980). It then remains connected with his life long preoccupation with generation (see hodge in Kohn 19856), and continually surfaces in his mature reflections.

Annotations on crossing and its related concepts are frequently interwoven with those on hybrids.('hy') and the complex subject of relative and fertility and sterility, distinguishing the possible mismatch between fully competent organs and instincts in an attempted cross from the possible inheritance by a hybrid of incompetent organs or instincts , or impaired vigour. "in hybrid crossed with either parent, and thus assuming fertility and the ancestral from, yet fertility variable in such individuals …My point that plants often sterile and yet not unhealthy not touched on-" (275g-h) for instinct migratory and home thrushes can be distinguished –probably do not cross" (45d); "certain that hybrid canaries and goldfinches and siskin's will breed inter se (but first young are weak)" (45c).

"much intermediate variability" (632d)

Many annotations concern intermediate forms and gradations ('ig'). Again , as with variation, we are talking of gradations in behavior as well as in structures – often interwoven: "on the exactly intermediate manner in which apes walk on hands –good it might have been asked how cd there have been transition between hand and foot?" (97).the theory of gradual speciation by descent with modifications subject to selective pressure should in principal be able to show change ('ch') and transition over geological time, grades of affinity ('af') between types of organisms (tma). Embarrassingly it often unable to do so. This refers us back to extinction, and the fact that the record left by geological time is not perfect ('ir for imperfection of record),so that the fossil remains ('fo') will never be able to reveal the whole story: "it is evident thus very few exceptions at whatever stage a genus or Family commences it is continued till it becomes extinct. This being capable of in fact strongest fact I turn against Imperfection of Record. Perhaps only shows no enormously blank intervals" (673g-h). "How isolated would the elephant be without fossils…Mastodon older than Elephas & intermediate in structure of teeth" (649-650e).

An important subtheme here is the 'succession of types' and their distribution ('gd'): "the succession of the genera…would be like showing connection in Geographical range. So in space & time. – [I did not think of this, till beginning Gasteropods: easy to see to it in other orders] In Fish the law had better be tested by Families" (669-670b). Another important subtheme in the study of the record is the relationship between shells ('sh'), deposition during subsidence ('se') (partly explaining the imperfection of the record) and thence to the importance of geology generally ('geo'). It was probably geology that during the Beagle voyage had alerted Charles Darwin to questions of distribution, through which he was able to connect geology with his early training in zoology (see Sloan and Kohn 1985). His own experience here was vital background treading Leopold von Buch and the works of J.D. Hooker.

"This is a case of animal being smaller northwards" (307d).

The topic of geographical distribution, both as a fact ('gd') and a process ('gdd'), accounts for a large and very important set of annotations. The distribution of the representatives of common or widely-ranging forms ('spr', 'gdc', 'gdw') displays networks of affinities and reveals the results of geologically ancient community and subsequent transmutation. "?though we cannot explain same species common to Australia & Fuegoe yet the generic connection is in harmony" (391h); "it has always been my greatest fear that there has been so much modification since Glacial that it would upset view.- some few genera may have been mundane & Tropical & not so.-"(398b-c) Distribution therefore refers us again to geological time and changes in conditions ('cc') and geological features – a striking example is afforded in the comparison of glacial-period distribution and that of present-day mountain tops.
By way of the subtheme of migration ('mg') and its near opposite isolation ('is'), we are led to consider annotations on the manifold means of dispersion of forms ('gdd'): direct or indirect pressure from conditions; the action of wind and weather ('cww') on seeds; the movement of animals and their capacity to carry seeds; sea-currents, icebergs ('ccs'), etc.

"unknown cause prevents man cut in twain from reproducing…" (659h)

Halve a worm, and two may leave the scene of the accident; halve a higher animal, and the result is more likely to be two remnants of a very dead original – what does this imply about the principles governing growth and repair? It used to be said that Darwin did not know enough about physiology ('phy') and morphology ('tms') and was therefore left out of the mainstream of nineteenth-century biology (see E.S. Russell in his otherwise fundamental Form and Function). However, the marginalia do not bear this out. He seems to be especially interested in many aspects of plant physiology ('phyfl), since they bear on problems related to adaptation: "Movements become so firmly associated with certain external influences such as light & gravity that the latter suffices to cause the same process of growth and movement" (242e). A considerable number of annotations on physiology concern Helmholtz's consideration of the imperfection of the eye, directly relevant to Charles Darwin's view of adaptations as non-perfect. Furthermore there are a great number of annotations in Johannes Mueller's Elements of Physiology. "Plants going to sleep without the stimulus of darkness strongly analogous to a voluntary action from a diffused nervous system" (615a); "in playing a tune are the fingers connected with brain? Or cerebellum" (615f-g) Physiology leads back to heredity through the hypothesis of pangenesis and the gemmules ('pan'), whose exsistence Charles Darwin postulated. This ill-fated hypothesis developed from Charles Darwin's interest in the 'gemmmules', stimulated in studying flustra under the guidance of Robert Grant at Edinburgh (see sloan and Hodge in Kohn 1985). He retained this intrest throught his life ; it surfaced particularly in variation, and relates in the marginalia to pathology: "on same part attracting same substances as in tumours (pangenrsis)" (613h-a); embryology and growth (em): pangesis on embroyic limb grafted and developing itself" (225f); cell theory (ct) and physiology generally: "many gemmules may pass into cells – it certainly appeared in intestines and liver that fat passes into and out of cells" (822H) and monstrosity: double monsters pang"(614a)

"intimate parrellism between the embroyic ,zoological and teratoligical series" (313b)

Embroyological resemblance reveals community of descent.. rudiments (rd ) do so also, by impling one time use falling into disuse (ud) through adaptive pressures ."objects there might <be> 100,000 creations as well as one I agree <byut>then these would not have borne of common descent in homologies and embryology and rudimentary organs ." (181-h). morphological resemblecnes ('hom') demonstrates the affinities of organisms within their types. "tissues of all vertebras homologues (6239.

The concept of descent with the modification there fore provides the ground –rules for that holy grail the 'natural system –although Charles Darwin is too cautious to suppose thet he could put much flesh on that particular skeleton. "I will not specify any genealogies – much too little known at present (164a) Although in the origin Darwin avoided arging directly against what Russell called transcendental morphology (1916 pp.103-12), the archetype " look at Owens Archetypes as more than ideal , as a real representations far as the most consummate skill and loftiest generalizations can represent the present forms of vertebrae.-I follow him that there is a created archtype . the parent of its class- (655c;) This annotation focuses Darwin's philosophical emancipation from the platonic eidos. According to (this there are a number of fixed, unchangeable 'ideas' underlying the concept of variability , with
the eidos (idea) being the only thing that is fixed and real, while the observed variability has no more reality than shadows of an object on a cave wall… any commintment to an unchanging eidos precludes belief in descent with ,modifications, (mayr, 1964,p.xix. for Darwin the type is simply the ancestor of evolving, living forms and the emphasis is on variety, i.e the diversity of life, rather than its unity as with Owen.
How looke my book all this well". we catch Darwin musing quietly. the categories of

The index were as we said before, inducted and subge toiies of the index were , as we
said before inducted from our attempts to classify the annotations themselves. In our
overview here of their logical interconnection. In our overview here of the principal
categories and some of their logical interconnections , we have succeeded, as darnins and
other conversations will have discerned, in recapitulating the ground plan of the origin
(with some of the recapitulating , ie . in recapulating the ground –plan of the big spices .

Influence of particular authors

Darwin's theory was an ecological one: the view of both Wallace and Darwin sprang from the established natural .ecological theory in the manner of Strickland in rays wisdom of god Darwin discerned the ecological approach he made his own in the origin; in ray we find annotations concerning behavior , adaption sex morphology and the relationship of organism to organism. the relationship between instinct and acquisition by habit is the main topic to be found in Kirby and Spence's entomology here Darwin focused on the problem of neuter insects which surfaces in the origin: "one may suppose that originally many queens were ordinarily thus reared and a few workers and the instinct is thus retained" (454g-h)- much is to be found on reason in animals as related to instinct, along with annotation on the struggle for existence , selection, speciation and distribution.

Fleming's Philosophy of Zoology also prompted Charles Darwin to analyses Instinct it is strange according to my theory that habit which results often of intellectual processes.. is related to instinct, which analogy of plants leads one to believe to exist independently of intellect (232b-c) and "The individual who by long intellectual study acquires a habit and can perform action almost directly.

Our emphasis on the Influence of British natural science requires a mention of Darwin's reaction to Natural Theology, and especially its central tenet of perfect adaptation. Charles Darwin read and annotated Brougham's Dissertation on Natural Theology; but here the annotations mainly concern animal behavior and pigeon-breeding. It is in Henslow's Botany that he starts distancing himself definitively from perfect adaptation. "People constantly speak about every organism being perfectly adapted to circumstances, if so how can there be a rare species breeding power being efficient (food not sufficiently abundant is answer". (369d).

It is clear from the quality of annotation that Lyell was of paramount importance to Darwin's development; in fact Lyell is the most heavily annotated author. A lot of British authors had a significant impact on Charles Darwin, who also had a lot of time for books on pigeon-breeding, whether British or continental.
By observing the manner of annotation, we may deduce that Charles Darwin was confident with French, lesso so but still conversant with German, and occasionally read some Italian and Spanish.. He read more Geofroy than Cuvier, while Lamarck is kept in the background, he is there but not as a protagonist.

If he could, Charles Darwin would read an English translation of a German book but if necessary, he would read the original, though quite slowly. His relationship with Ernst Haeckel requires separate and thorough treatment (see Di Gregorio From Here to Eternity. Ernst Haeckel and Scientific Faith, 2005)

CONCLUSION

In conclusion all the process hitherto described has been a continuous amplification of an at first very narrowly defined objective – almost echoing Charles Darwin's request: "clean well the pencil marks-keep book clean. write smallish on one side ,number your pages " (see page277g). we can fairly claim to have done a little better than that, given the latter-day wonders of camera ready copy. Charles Darwin's instructions here were in fact originally issued to one of his amanuenses probably Mr. Norman, a shadowy figure for whom we came to feel considerable sympathy. The ground level of our work has just been about a pedestrian as his, in copying everything out to provide the 'catalogue and transcription' which forms part one of his volume. A least in part two, and more especially here in this introduction, we have the luxury of spreading our wings a little onto the realms of interpretation; such joys were not to be for the hapless amanuensis. "MR. Norman end here" (390c), Charles Darwin instructs whenever the interesting bits seem about to begin.

Our fitful involvement over the years in the production of this material, at computer terminals and in libraries , both in Cambridge and down house , has included many hours spent in the U.L. archives themselves – privilege which facilities our work immensely, despite the curious effects of the changeless book stack weather. The project has also survived a double bomb scare, a fire beneath the computer centre which put the tapes out of action for many a long week ('on a shelf gathereing dust becomes in these latter days on a tape gathereing smoke particles and the near-arrest of the assistant author in a ceratin college library where he was mistaken for the key to a missing case (cf fn12), Charles Darwin's remarks to the intrepid Wallace felt at times pertinent.

"I am astonished you ever returned alive".(842a).