Diversity and Complexity in DNA Recognition by Transcription Factors
Why did anyone think it would be so simple? Let’s first assume complexity and not be surprised when we find it.
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML. Diversity and complexity in DNA recognition by transcription factors. Science. 2009 Jun 26;324(5935):1720-3. [PubMed]
Abstract
Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks.
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The Annie paper in one continuous posting
[I have presented this paper already as ten separate postings, in part to let me do it in dribs and drabs and also to allow people to comment more easily on separate issues. But at a colleague's suggestion here is the whole paper, complete with links, in one continuous posting. Please let me have your comments. Have I convinced you that there is no substance to the "Annie myth"? And if so, what could be done to improve the paper for publication?]
Did the death of his daughter cause Darwin to give up Christianity?
“A long habit of not thinking a thing WRONG, gives it a superficial appearance of being RIGHT” Thomas Paine, Common Sense
“To establish one hypothesis upon another, is building entirely in the air; and the utmost we ever attain, by these conjectures and fictions, is to ascertain the bare possibility of our opinion; but never can we, upon such terms, establish its reality.”
David Hume, Dialogues concerning Natural Religion
Introduction
If you ask the average man or woman what they know about Charles Darwin, one of the dozen or so “facts” that he or she is likely to come up with is that Darwin lost his religious faith as a result of the death of his daughter Annie. Some might also claim that Annie died from tuberculosis and her death influenced Darwin’s later writing on evolution. These claims have wide currency on the Internet, in popular and scholarly publications and even on screen (see Table and list in previous postings).
However, it might surprise you to learn that there is no direct documentary evidence to support these claims in anything written by Darwin or any of his associates—instead, here we argue, they should be classified, along with
Darwin’s finches and
Darwin’s delay, as modern “Darwin myths”, which have arisen only in recent times and were wholly unknown to Darwin, his contemporaries and several subsequent generations of scholars. In fact, scrutiny of Darwin’s own manuscripts, publications and correspondence and other writings of his period suggests that, not only are these claims unsupported by the evidence, they are likely to be wrong.
Thanks to the Darwin Correspondence Project (http://www.darwinproject.ac.uk) and Darwin Online (http://darwin-online.org.uk/), almost all sources of information on Annie’s life and Darwin’s religious beliefs from Darwin and his associates are now available on-line. We have provided a list of links to this original material, so the interested reader can easily verify our assertions and conclusions.
What do we know about the life and death of Annie Darwin?
Let us start by considering what we know of Annie Darwin. The bare facts are that Anne Elizabeth Darwin was born on 2 March 1841 in London and died on 23 April 1851 in Malvern, after an illness that lasted at least several weeks and perhaps as long as nine months. She was Darwin’s second child of ten and one of three to die in childhood. Darwin mentions Annie as a baby briefly in his 1877 paper A Biographical Sketch of an Infant, a publication generally devoted to observations on her elder brother William:
“he [William] held pencils, pens, and other objects far less neatly and efficiently than did his sister [Annie] who was then only 14 months old, and who showed great inherent aptitude in handling anything”
Before her final illness, Annie features in seventeen of Darwin’s letters, usually in statements of affection (e.g. “not so bad a girl”, “I long to kiss Annie’s botty-wotty”), praise (“Annie is something… a second Mozart”) or humour (“Miss Annie is not quite ready to be married yet”). She is also mentioned a dozen or so times in the Notebook of observations on the Darwin children maintained by Charles and Emma, with Emma noting at age three and a half:
“Obstinacy is her chief fault at present.”
Sometime before her tenth birthday, Annie fell ill. A
retrospective note in Emma’s diary for 27 June 1850 records:
‘Annie first failed about this time’
“Her health failed in a slight degree for about nine months before her last illness”.
The series of letters that followed between Charles and Emma Darwin provide a poignant record of the hopes and fears of the parents of dying child. A single entry, chilling in its terseness, in Emma’s diary for April 23rd records the time of Annie’s death: “12 o’clock”.
That Annie’s death caused distress to her parents and family is beyond dispute. A week after her death, Darwin penned
a tender memoir of Annie, which was published in part by his son, Francis in 1887 in The life and letters of Charles Darwin and in full by Colp in 1987 (Colp R Jr. 1987. Charles Darwin’s “insufferable grief”. Free Associations 9: 7-44.). Darwin closes the memoir with the cry from the heart:
“We have lost the joy of the Household, and the solace of our old age:— she must have known how we loved her; oh that she could now know how deeply, how tenderly we do still & shall ever love her dear joyous face. Blessings on her.”
Darwin also mentions Annie’s death in his Autobiography (15):
“We have suffered only one very severe grief in the death of Annie at Malvern on April 24th, 1851, when she was just over ten years old. She was a most sweet and affectionate child, and I feel sure would have grown into a delightful woman. But I need say nothing here of her character, as I wrote a short sketch of it shortly after her death. Tears still sometimes come into my eyes, when I think of her sweet ways.”
But the above links provide pretty much all we have from Charles and Emma Darwin on their daughter Annie. Let us be clear—nowhere in the millions of words that flowed from his pen does Darwin ever say that Annie’s death had anything to do with his own loss of faith. Indeed, as we shall see, the balance of evidence is that Annie’s death had nothing to do with Darwin’s loss of religious belief.
What do we know about Darwin’s loss of belief in Christianity?
Darwin wrote relatively little about his religious beliefs.
The clearest account occurs in his Autobiography. Immediately following a section headed
From my return to England Oct. 2, 1836 to my marriage Jan. 29, 1839, Darwin opens a section on his religious beliefs that anchors his most intensive reflections on religion to 1837-1838:
“During these two years I was led to think much about religion.”
He affirms his initial orthodox Christian stance:
“Whilst on board the Beagle I was quite orthodox”.
Darwin then elaborates his reasons for abandoning Christianity [Table 2]. Two of his lines of argument are intellectual:
- the Old Testament and Gospels fail as history
- comparative theology highlights the unreliable and inconsistent nature of scripture.
A third, more emotional strand in his argument is grounded in ethics: the immorality of divine retribution and eternal punishment.
Darwin states that although he was reluctant to give up his religious belief:
“disbelief crept over me at a very slow rate, but was at last complete. The rate was so slow that I felt no distress, and have never since doubted even for a single second that my conclusion was correct”.
As we have seen, Annie’s death was probably the most distressing event in Darwin’s life, so Darwin’s reported lack of distress in his progression towards disbelief suggests
Annie’s death had nothing to do with it!
The remainder of Darwin’s discussion of religion in his Autobiography is given over to arguments that address natural theology rather than Christianity [Table 3].
He states that the argument from design fails thanks to the discovery of natural selection and that happiness prevails in the universe, but as a result of natural selection rather than divine intervention. He argues that the problem of suffering cannot be explained away because it supposedly brings moral improvement to humans, as suffering of animals vastly outweighs that of humanity. He dismisses the argument for the existence of God from inner convictions because “all men of all races” have not had “the same inward conviction of the existence of one God” He points out that belief in immortality is a distraction from dealing with the future of this world and lays out arguments for a naturalistic view of morality.
Towards the end of the section, Darwin reveals that one argument for the existence of God holds weight with him:
“I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist.”
However, a few lines later, he argues that finite, evolved minds fail when contemplating the infinite and therefore concludes
“The mystery of the beginning of all things is insoluble by us; and I for one must be content to remain an Agnostic.”
Several other lines of evidence support the idea that the late 1830s were the critical time during which Darwin thought most intensely about religion and, as a result, abandoned conventional Christian belief. He writes in his Journal in 1838,
“All September read a good deal on many subjects: thought much upon religion. Beginning of October ditto.”
His notebooks from the period sketch out arguments similar to those in his Autobiography
“people say I know it, because I was always told so in childhood, hence the belief in the many strange religions.” (link)
“savages (mem York Minster) consider the thunder & lightning the direct will of the God… Those savages who thus argue, make the same mistake, more apparent however to us, as does that philosopher who says the innate knowledge of creator has been implanted in us … by a separate act of God, & not as a necessary integrant part of his most magnificent laws” (link)
He also abandons a Miltonic view of “man’s first disobedience” as the source of evil; instead he looks for an evolutionary explanation:
Our descent, then, is the origin of our evil passions!!—The Devil under form of Baboon is our grandfather! (link)
From 1838 to 1851, in a brown leather-covered notebook, Darwin maintained lists of books-to-be-read and books that he had read. These lists reveal a recurrent interest in the writings of David Hume. In particular, in an entry for September 29th 1839, Darwin includes Hume’s Dialogues Concerning Natural Religion and Natural History of Religion in his list of books read. As Keynes has pointed out in his book Annie’s Box, the topics covered by Hume in his Dialogues (22) correspond well with Darwin’s own discussion of religion in the Autobiography. Darwin also mentions Hume in his M notebook:
Hume has section (IX) on the Reason of Animals, Essays, Vol. 2 ((Sect. XV. Dialogue on Natural Religion.— also on origin of religion or polytheism, at p. 424, Vol. II however he seems to allow it is an instinct.)) I suspect the endless round of doubts & scepticisms might be solved by considering the origin of reason, as gradually developed. See Hume on Sceptical Philosophy. Hume has written “Natural Hist, of Religion” on its origin in Human Mind. (link)
Evidence from his Autobiography and his correspondence also suggest that Darwin was already highly sceptical of Christianity before his marriage to Emma Wedgwood in January 1839. In his Autobiography, he writes
“Before I was engaged to be married, my father advised me to conceal carefully my doubts, for he said that he had known extreme misery thus caused with married persons.”
In a letter sent to Darwin in November 1838, Emma writes “our opinions on the most important subject should differ widely” and refers to Darwin’s “honest & conscientious doubts”. A few days before their wedding, in another letter she writes: “our opinions may not agree upon all points of religion”.
Most telling of all is a letter Emma wrote shortly after the wedding (available from both
Darwin Online and the
Darwin Correspondence Project). Here, she highlights Darwin’s apostasy, speaking of Darwin’s elder brother Erasmus “having gone before you” in religious doubts and accusing Darwin of being one-sided in seeing the difficulties of religious belief, rather than also of disbelief:
“you to view chiefly the difficulties on one side, & that you have not had time to consider & study the chain of difficulties on the other, but I believe you do not consider your opinion as formed. May not the habit in scientific pursuits of believing nothing till it is proved, influence your mind too much in other things which cannot be proved in the same way, & which if true are likely to be above our comprehension.”
She also makes it clear that Darwin was by this time questioning belief in revealed religion:
“I should say also that there is a danger in giving up revelation….”
Note again: nowhere in any of Darwin’s writings on his abandonment of religion does he mention Annie’s death!
Annie Darwin’s death in the historiographical record
So how did Annie’s death come to feature so prominently in the historiographical record? Aside from Life and Letters, there was no mention of Annie Darwin’s death by Darwin’s obituary writers or biographers in the nineteenth century. In fact, the first extensive study of Annie’s death and Darwin’s grief—by American psychiatrist Ralph Colp Jr.—was not published until 1987, more than a century after Darwin’s death (Colp R Jr. 1987. Charles Darwin’s “insufferable grief”. Free Associations 9: 7-44).
In his study, Colp catalogues over two dozen references to Annie’s death in the biographical record during the twentieth century, starting with references to Darwin’s memoir of Annie in three accounts of Darwin’s life published in 1927. Subsequently, according to Clop, Annie’s death (and often also Darwin’s memoir of her) is cited in over twenty biographical accounts published from 1937 to 1987, but was omitted from at least half a dozen other biographies.
However, in none of these accounts is there any suggestion of a link between Annie’s death and Darwin’s loss of faith. Similarly, in her
1990 account of Darwin in Malvern, Janet Browne makes no such link.
In his 1987 study, Colp draws on a full-length transcript of Darwin’s sketch of Annie and Darwin’s correspondence to emphasise Darwin’s affection for his daughter and the grief that Darwin suffered at her loss. Colp does not himself provide any evidence to link Annie’s death to Darwin’s loss of faith but does state:
“James Moore has suggested that Annie’s death, together with other factors, caused Darwin finally to give up his diminished belief in Christianity. Dr Moore intends to discuss this, along with the evolution of Darwin’s religious views, in a forthcoming study.”
Colp does, however, link Annie’s death with Darwin’s subsequent writing style:
“His concern about terminal suffering also influenced his imagery of the workings of the war of nature. In the 1844 sketch of his theory of natural selection he had mainly stressed the power of the war to create new species. In his 1859 On the Origin of Species he would then write: ‘we may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt’”
The first links between Annie’s death and Darwin’s loss of faith
So where did the supposed link between Annie’s death and Darwin’s religion originate? This link first appears in the 1978 BBC TV series
The Voyage of Charles Darwin, where writer Robert Reid or producer Christopher Ralling includes a passage on Darwin’s religious beliefs from the Autobiography as a voiceover accompanying a funeral scene [
watch it on YouTube].
However, this appears to be an isolated incident. Instead, the birth of the now-widespread belief that Annie’s death caused Darwin ’s loss of religion—what we might call “the Annie hypothesis”—can be traced to the work of one man:
James Moore.
Moore first makes the link between Darwin’s apostasy and Annie’s death in a throwaway remark in a book chapter published in 1982 (Moore JR, 1982. 1859 and all that: Remaking the Story of Evolution-and-Religion, in Roger G. Chapman and Cleveland T. Duval, eds Charles Darwin 1809-1882: A Centennial Commemorative Wellington, New Zealand: Nova Pacifica Publishing, 1982):
Perhaps it was the “bitter and cruel” death in 1851 of ten-year-old Annie, his favourite child, just a month after he had read the moral challenge to that doctrine in Francis Newman’s “excellent” spiritual Autobiography Faith, that prompted Darwin, as he later said, to give up Christianity once and for all.
However, a full statement of the Annie hypothesis comes a few years later, in 1989, in Moore’s book chapter Of Love and Death: Why Darwin ‘gave up Christianity’ (Moore J R. 1989. In Moore, James R., ed. History, humanity, and evolution: essays for John C. Greene. Only a partial preview of this work is available online).
Early in his chapter, Moore provides a summary of the standard position that Darwin lost his faith in the late 1830s. He then discusses family quarrels over the publication of Darwin’s Autobiography and memoir of Annie in an attempt to persuade the reader that something is missing from orthodox accounts of Darwin’s apostasy.
Towards the end of his article Moore attempts to argue that Darwin’s loss of faith occurred much later than usually thought, not in the 1830s, but in the late 1840s and early 1850s, during a period bracketed by the deaths of Darwin’s father and of his daughter Annie.
In rejecting the “prevailing view of Darwin’s loss of faith” wrong, Moore draws on “a pair of reasons that underpin the rest of my analysis”:
1. His own idiosyncratic reinterpretation of the Autobiography:
“First, it takes the Autobiography too seriously as a statement of causality and not seriously enough as an ascription of dynamics.”
2. The Aveling claim:
“The second reason why I dissent from the prevailing view of Darwin’s loss of faith is the uncontroverted testimony of Edward Aveling that Darwin did in fact finally relinquish Christianity at a period approximately ten years later than the one usually assigned.”
Moore’s interpretation of the Aveling claim
Let us consider the Aveling claim. In 1887, five years after Darwin’s death, the English Marxist and atheist
Edward Aveling published a pamphlet entitled
The Religious Views of Charles Darwin. In the pamphlet, Aveling provides an account of a visit by himself and fellow atheist
Ludwig Büchner to Darwin in September 1881. Key to Moore’s arguments is Aveling’s recollection of Darwin stating
“I never gave up Christianity until I was forty years of age.”
Aveling stresses that the utterance proves that Darwin abandoned Christianity before Aveling’s own birth in November 1849:
“I confess that a great joy took possession of me as I heard a statement by its implication so encouraging. I, like the rest of the outside world, was not sure as to his position in regard to religion. Now, from his own lips, I knew that before I was born this, my master, had cast aside the crippling faith. The step taken by so many of us had been taken by him long ago. What a strength and hope are in the thought that the first thinker of our age had abandoned Christianity!”
Next, Aveling states that he asked Darwin why his long delay before giving up Christianity, to which Darwin is said to reply:
“that he had not had time to think about it. His time had been so occupied by his scientific work, that he had none to spare for the careful study of theological questions.”
And then when asked why he gave up his belief, Darwin, according to Aveling, states baldly:
“It is not supported by evidence.”
Note that, as in the
Autobiography, at no point in Aveling’s account does Darwin mention Annie’s death as having anything to do with his own dismissal of Christianity.
Can we believe Aveling? He hardly counts as the most reliable character, despised as he was even by his fellow Marxists for running up debts and for having driven Marx’s daughter Eleanor to suicide. And in an independent, albeit brief, account of the same visit, Büchner fails to mention the “forty years of age” utterance.
But in Aveling’s favour, a late date of Darwin’s break with Christianity goes against what he, as an advocate of atheism, would have preferred and is consistent with his surprise at length of time it took Darwin to give up Christianity. Furthermore, Darwin’s son Francis in
Life and Letters writes, “Dr. Aveling gives quite fairly his impressions of my father’s views” (
link).
However, even if we accept Aveling’s account of what Darwin said, can we believe Darwin himself, particularly when he appears to be contradicting his own account in the Autobiography?
Aveling’s visit occurred less than seven months before Darwin’s death, so was the 72-year-old Darwin liable to confusion? In his
Autobiography, (started when he was 67, but with some later additions) Darwin gets the dates wrong of the deaths of his father (writes 1847 not 1848:
link) and of his daughter (writes 24th not 23rd April:
link). So, when talking to Aveling, perhaps he said “forty” but meant “thirty”?
But if we do take Aveling and Darwin at face value, we are still faced with a fundamental question: what does the phrase “gave up Christianity” mean? Given the abundant evidence of Darwin’s scepticism as early as the late 1830s, the most plausible interpretation is that it means that he gave up the external trappings of religious belief, such as attendance at church, around the age of forty, rather than experiencing any change in his inner convictions at that time.
Whatever the truth of what Darwin said or meant by this statement, a strict interpretation of it would place Darwin’s abandonment of Christianity sometime between his fortieth and forty-first birthdays (12 February 1849-12 February 1850), at least a year and, at most, over two years before Annie’s death. Moore recognizes this but then bends Darwin’s statement to suit his own argument:
Although Darwin turned forty on 12 February 1849, I propose now to treat the age at which, he said, he ‘gave up Christianity’ as a round figure”.
In fact, if one accepts that there is any missing link between Darwin’s supposed break with Christianity and his own life experiences, the death of Darwin’s father is a far more plausible culprit than the death of Annie for several reasons:
- It is much closer in time (13 November 1848) to Darwin’s fortieth birthday (12 February 1849) than Annie’s death (23 April 1851).
- In his Autobiography, Darwin condemns the traditional Christian view that his father as an unbeliever would face eternal damnation; but Annie as an innocent Christian child would face no such fate.
- Darwin’s health suffered greatly in the months after his father’s death (see Letter to Hooker 28 Mar 1849), but far less so after Annie’s death.
However, we have to stress that the existence of any link between the death of Darwin’s father and Darwin’s opinions on religion is purely supposition rather than established fact. The key point is that Aveling’s claim provides scant if any support for Moore’s hypothesis—certainly not enough to erect an entire mythology.
Moore’s interpretations of the Autobiography and Darwin’s reading list
Moore’s analysis of Darwin’s Autobiography includes a prolonged discussion of Darwin family squabbles over which parts of the text should or should be published, which is largely irrelevant to his main thesis that Annie’s death provoked the final phase of Darwin’s apostasy.
Moore also attempts a reconstruction of the state of Darwin’s mind when writing the Autobiography and during the years 1848-51, bracketed by the deaths of Darwin’s father and daughter. Moore’s chief evidence for a link between Darwin’s religious beliefs and Annie’s death comes from their proximity in the text of the
Autobiography:
“he has drawn a line of demarcation in the family memoir, which closely follows the section on religious belief, by recalling poignantly his wife’s ‘beautiful letter’ to him on the subject of his own eternal salvation, and by then remembering the ‘very severe grief’ they suffered and the ’short sketch’ he wrote to commemorate their deceased daughter”.
And rather than accept the obvious explanation (highlighted in a previous posting) that the elderly Darwin was forgetful, Moore (like Colp before him) takes the fact that Darwin gets the dates wrong for his daughter’s (and father’s) death as evidence of their heightened emotional significance for Darwin!
Moore also makes much of Darwin’s reading list, pointing out that Darwin was still reading books on religion in the 1840s and 1850s, even though according to the prevailing view, he was by then a hardened sceptic:
“Since 1840 he had shown an interest in various titles that, on the assumption he was already a confirmed unbeliever, should perhaps not have engaged him.”
Moore builds a lengthy but tenuous reconstruction of the effects of Darwin’s reading on his state of mind before Annie’s final illness. This is built from five brief single-line entries in Darwin’s reading list:
- 1848: April 21 “Norton Genuiness of the Gospels — good” (link)
- 1848: July 20 “Sterlings Memoir of by Hare — moderately good” (link)
- 1849: Sept. 5 “Newman on the Soul” (link)
- 1850: Aug 30 “Hebrew Monarchy,— poor” (link)
- 1851: March 16th “Newman Phases of Faith excellent” (link)
So much speculation here rests on so little—these entries record just five out of the ninety or so books that Darwin recorded reading from 1848 to 1851. And this blogger (and perhaps many readers?) knows from personal experience that rejection of religious belief does not bring an immediate lack of interest in intellectual discussions on the subject.
Speculation hardens into “fact”
So there you have it! The Annie hypothesis and all the derivatives of it in print or on screen rest on two fragile foundations, without any direct unequivocal documentary support at all from anything Darwin ever wrote.
In his 1989 publication, Moore does occasionally acknowledge that he is presenting a hypothesis rather than a series of facts:
“Since Darwin had, I believe, virtually reached this conclusion … in the preceding three years… “.
“If my argument in this essay is accepted…”
“If contemplation of Dr Darwin’s eternal destiny had spiked Christianity…”
However, most of the assertions in his conclusion are presented as declarative statements of fact—taking his hypothesis as proven, even though, as we have seen, his assertions are unsupported by direct documentary evidence:
“Darwin was forty-two years old. Thereafter he would worry about God and pain and immortality, unencumbered by the Christian plan of redemption.”
“Darwin underwent an upheaval that marked him permanently. He began a doubter; he ended a resolute unbeliever… his non-Christian self-identity became established. Emma alone, who had been affected in quite the opposite way by the death of her beloved sister Fanny, understood the significance of the period between 1848 and 1851.”
“Further research will show how far the events surrounding Darwin’s loss of faith subsequently influenced his personal life and his science. Certainly, parts of the Origin of Species and The Expression of the Emotions in Man and Animals will need to be interpreted afresh.”
Moore, like Colp, suggests that Annie’s death influenced Darwin’s writings on evolution (to be covered in a later posting). He concludes the chapter that launched the “Annie industry” with an distorted fusion of Darwin’s evolutionary writings with his memoir of his daughter that culminates in an idiosyncratic vision of Annie “who died at Easter…” (in fact, she died the Wednesday after Easter) becoming “the paschal lamb of Darwin’s post-Christian soteriology”.
The Annie hypothesis gains new impetus
In subsequent writings and on-screen productions (listed in earlier postings), Moore and others treat the “discovery” of the link between Annie’s death and Darwin’s apostasy as established fact rather than as a hypothesis to be tested. In particular, Desmond and Moore’s 1991 biography of Darwin played a major role in propagating the Annie hypothesis, providing an account of Annie’s illness and death drawn from Darwin’s correspondence, interspersed with unsupported interpolations about Darwin’s supposed religious crisis.
In 2001, the Annie hypothesis received fresh impetus from Annie’ Box, a book written by Darwin descendant Randal Keynes. On p. 222 Keynes makes the link:
“After Annie’s death, Charles set the Christian faith firmly behind him. He did not attend church services with the family; he walked with them to the church door, but left them to enter on their own and stood talking with the village constable or walked along the lanes around the parish. He did, though, still firmly believe in a Divine Creator. But while others had faith in God’s infinite goodness, Charles found him a shadowy, inscrutable and ruthless figure.”
Keynes brings no new evidence to bear on the issue of whether Annie’s death led to Darwin’s break with Christianity, but he does weaves several new strands into the Annie hypothesis.
His assertion that Darwin stopped attending church services is based on a passage from the 1889 publication
Darwin and God by
George William Foote (a secularist who was later imprisoned for blasphemy):
“In September 1842 he went to live at Down, where he continued to reside until his death. He helped to found a Friendly Club there, and served as its treasurer for thirty years. He was also treasurer of a Coal Club. The Rev. Brodie Innes says ” His conduct towards me and my family was one of unvarying kindness.” Darwin was a liberal contributor to the local charities, and ” he held that where there was really no important objection, his assistance should be given to the clergyman, who ought to know the circumstances best, and was chiefly responsible.”
He did not, however, go through the mockery of attending church. I was informed by the late head constable of Devonport, who was himself an open Atheist, that he had once been on duty for a considerable time at Down. He had often seen Darwin escort his family to church, and enjoyed many a conversation with the great man, who used to enjoy a walk through the country lanes while the devotions were in progress.”
Here it is worth stressing that in this passage, there is no date associated with the start of Darwin’s non-attendance at church and no link at all to Annie’s death. Darwin’s non-attendance could have started at any time after his move to Down House, whether in the eight and a half years before Annie’s death or in any of the three decades that followed. In a footnote Keynes suggest that the “late head constable of Devonport” may have been “William Soper, who served at Downe between 1858 and the mid-1860s”. No evidence is put forward for this identification, but, if true, it still provides no evidence of a link to Annie’s death, which occurred seven years before 1858.
Keynes also dismisses the cause of Annie’s death recorded by Dr Gully—”bilious fever with typhoid character” and instead suggests that Annie died of tuberculosis. This diagnosis is based on unpublished opinions from four unidentified “experienced physicians and medical historians”. In fact, no definitive diagnosis can ever be made when we have only a scanty record of Annie’s symptoms and no chance to perform modern medical investigations. Yet Keynes’ highly speculative diagnosis is now often repeated as fact in many subsequent publications on Annie.
Bizarrely, attempts at retrospective diagnosis took a new twist in a recent BBC documentary Did Darwin Kill God? where Conor Cunningham (above) claims that Annie died from cholera (highly unlikely given that diarrhea features as a relatively minor symptom in reports of her illness).
Did Annie’s death influence Darwin’s writing?
Colp, Moore and Keynes all suggest that Annie’s death influenced Darwin’s later writings on evolution. All three rather tenuously link the final sentence of Chapter III of The Origin of Species with Annie’s death:
” When we reflect on this struggle, we may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt, and that the vigorous, the healthy, and the happy survive and multiply” (link).
This passage follows a few pages after another that Moore and Keynes have attempted to link with Annie’s death:
“The elder De Candolle and Lyell have largely and philosophically shown that all organic beings are exposed to severe competition… We behold the face of nature bright with gladness, we often see superabundance of food; we do not see, or we forget, that the birds which are idly singing round us mostly live on insects or seeds, and are thus constantly destroying life; or we forget how largely these songsters, or their eggs, or their nestlings, are destroyed by birds and beasts of prey; we do not always bear in mind, that though food may be now superabundant, it is not so at all seasons of each recurring year.” (link)
But a comparison with what Darwin wrote in his 1844 essay shows that there is little or no change in the content or tone of his argument, merely an elaboration in The Origin of what he had written long before Annie’s death:
“De Candolle, in an eloquent passage, has declared that all nature is at war, one organism with another, or with external nature. Seeing the contented face of nature, this may at first be well doubted; but reflection will inevitably prove it is too true. The war, however, is not constant, but only recurrent in a slight degree at short periods and more severely at occasional more distant periods; and hence its effects are easily overlooked.”
(original MS; transcribed in Darwin, Francis ed. 1909. The foundations of The origin of species. Two essays written in 1842 and 1844. )
Similarly, Moore in the 2009 BBC documentary Darwin’s Struggle has tried to link another “face of nature” passage from Chapter III of Darwin’s Origin of Species with Annie’s death:
“The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force.” (link)
However, this metaphor of wedges and incessant blows appears in the 1844 essay:
“Nature may be compared to a surface, on which rest ten thousand sharp wedges touching each other and driven inwards by incessant blows” (link)
Similar passages also feature in the 1842 pencil sketch and even in one of Darwin’s notebooks from as early as 1838, thirteen years before Annie’s death:
“One may say there is a force like a hundred thousand wedges trying [to] force every kind of adapted structure into the gaps in the oeconomy of nature. or rather forming gaps by thrusting out weaker ones. “
We therefore conclude that there is no evidence to suggest that Darwin’s subsequent scholarly writing was influenced by his feelings over Annie’s death!
Time to bury the Annie hypothesis
We invite the reader to use the references we provide to look at what Darwin himself wrote about his religious beliefs and the life and death of his daughter, without the interpolation of modern commentators. We stress that there is no direct documentary evidence linking the death of his daughter Annie to Darwin’s break with Christianity—any evidence is indirect and any arguments for this view are entirely speculative. A huge burden of conjecture rests on questionable interpretations of so few facts: the one sentence from Aveling, the five lines in Darwin’s list of books read, the proximity of Annie’s death to Darwin’s religious beliefs in his Autobiography. No hypothesis testing has been attempted; instead speculation has hardened into fact, as a mythology has grown up around Annie and her father’s beliefs. We urge a return to the previously orthodox view of Darwin’s loss of faith—a process that began in Darwin’s early thirties and which was driven by intellectual arguments and by his requirement for evidence mixed with a moral rejection of vengeful deity. And we ask for a renewed, respectful consideration of the Darwin family’s grief over the loss of Annie, untainted by religiose mythologising. In Darwin’s bicentenary year, the time has come to reject the Annie hypothesis and to abandon this modern “Darwin myth”.
TABLES
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Argument
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Supporting quotations
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Old Testament fails as history
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“the Old Testament from its manifestly false history of the world, with the Tower of Babel, the rainbow as a sign, etc., etc”.
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Gospels fail as history
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“the Gospels cannot be proved to have been written simultaneously with the events”
“they differ in many important details, far too important as it seemed to me to be admitted as the usual inaccuracies of eye-witnesses”
“morality of the New Testament… depends in part on the interpretation which we now put on metaphors and allegories.”
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Argument from theological relativism
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“[Old Testament] no more to be trusted than the sacred books of the Hindoos, or the beliefs of any barbarian.”
“if God were now to make a revelation to the Hindoos, would he permit it to be connected with the belief in Vishnu, Siva, &c., as Christianity is connected with the Old Testament.”
“many false religions have spread over large portions of the earth like wild-fire “
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Problem of miracles
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“the more we know of the fixed laws of nature the more incredible do miracles become.”
“the men at that time were ignorant and credulous to a degree almost incomprehensible by us”
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Immorality of divine retribution/eternal punishment
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“attributing to God the feelings of a revengeful tyrant”
“the plain language of the text seems to show that the men who do not believe, and this would include my Father, Brother and almost all my best friends, will be everlastingly punished. And this is a damnable doctrine.”
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Table 3 Arguments Darwin gives in his Autobiography on natural theology
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Argument
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Supporting quotations
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Argument from design fails
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“The old argument of design in nature, as given by Paley, which formerly seemed to me so conclusive, fails, now that the law of natural selection has been discovered”
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Happiness prevails, but as a result of natural selection not divine intervention.
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“harmonises well with the effects which we might expect from natural selection. If all the individuals of any species were habitually to suffer to an extreme degree they would neglect to propagate their kind”
“most or all sentient beings have been developed in such a manner through natural selection, that pleasurable sensations serve as their habitual guides “
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Problem of suffering cannot be discounted as bringing moral improvement, but is compatible with natural selection.
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“suffering, is quite compatible with the belief in Natural Selection, which is not perfect in its action, but tends only to render each species as successful as possible in the battle for life “
“A being so powerful and so full of knowledge as a God who could create the universe, is to our finite minds omnipotent and omniscient, and it revolts our understanding to suppose that his benevolence is not unbounded, for what advantage can there be in the sufferings of millions of the lower animals throughout almost endless time? This very old argument from the existence of suffering against the existence of an intelligent first cause seems to me a strong one; whereas, as just remarked, the presence of much suffering agrees well with the view that all organic beings have been developed through variation and natural selection “
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Comparative religion dismisses argument from conviction
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“usual argument for the existence of an intelligent God is drawn from the deep inward conviction and feelings which are experienced by most persons”
“Hindoos, Mahomadans and others might argue in the same manner and with equal force in favour of the existence of one God, or of many Gods, or as with the Buddists of no God. There are also many barbarian tribes who cannot be said with any truth to believe in what we call God: they believe indeed in spirits or ghosts, and it can be explained, as Tyler and Herbert Spencer have shown, how such a belief would be likely to arise.”
“the grandest scenes would not cause any such convictions and feelings to rise in my mind”
“This argument would be a valid one if all men of all races had the same inward conviction of the existence of one God; but we know that this is very far from being the case.”
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Belief in immortality is a distraction from dealing with the future in the real world
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“Believing as I do that man in the distant future will be a far more perfect creature than he now is, it is an intolerable thought that he and all other sentient beings are doomed to complete annihilation after such long-continued slow progress. To those who fully admit the immortality of the human soul, the destruction of our world will not appear so dreadful.”
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Accepts cosmological argument and is therefore a theist
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“impossibility of conceiving this immense and wonderful universe… as the result of blind chance or necessity.”
” I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist.
“
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Argument that finite minds fail when contemplating the infinite, therefore Agnostic
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” can the mind of man, which has, as I fully believe, been developed from a mind as low as that possessed by the lowest animal, be trusted when it draws such grand conclusions “
“constant inculcation in a belief in God on the minds of children producing so strong and perhaps an inherited effect on their brains not yet fully developed, that it would be as difficult for them to throw off their belief in God, as for a monkey to throw off its instinctive fear and hatred of a snake.”
“The mystery of the beginning of all things is insoluble by us; and I for one must be content to remain an Agnostic”
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Non-believers are not immoral; argument for natural morality
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“follow those impulses and instincts which are the strongest or which seem to him the best ones”
“the highest satisfaction is derived from following certain impulses, namely the social instincts “
” approbation of his fellow men and gain the love of those with whom he lives “
“solid satisfaction of knowing that he has followed his innermost guide or conscience.”
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Highlights from Telic Thoughts
Some posts and comments at Telic Thoughts:
Retina Design which links to Is the Backwards Human Retina Evidence of Poor Design? from ICR and Eye Evolution from Viewpoint.
A Materialist Red Herring which has this to say:
The origin of life is a dilemna that has defied attempts at resolution since Darwin. Sure we have a hodgepodge of theories as to how it went down. We also have identified properties of cellular biochemicals thought by OOLers to justify their faith in chemical pathways to cells. Their faith is never so evident as when critiques of their beliefs are branded God in the gaps. The cliche reveals a number of things about those who use it. Lack of originality for one. It is one of the first cliches learned by critics and is subsequently mindlessly tossed about. Ever more so when a telling blow is landed on a theoretical weak spot.
It is also a cliche well suited for those who would presume to know the thoughts of another or simply ignore well known theistic views in the interest of maintaining their own prejudice and the comfort zone that theological ignorance affords them. Most of those who believe in God attribute the origin of all natural laws and natural phenomenon to God. They do not look for gaps thinking that God is detectable in them. That’s the straw man that defines the mindset of critics.
But the most interesting aspect of the cliche is how it is used to hide a sleight of the materialist hand. If materialism is to maintain the fiction that it is sustained by scientific data then it must at least attempt to separate empirically derived assertions from assertions not sustained by empirical data. To assume favorable data exists and has not yet been found is to demonstrate faith in an outcome in lieu of an empirically grounded argument. It also places a philosophical bias into an unknown and asks that discernment be averted in the interest of maintaining an unverified expectation. Don’t mention the inadaquacy of evidence or the fact that the emperor is wearing no clothes.
RNA Polymerase II
Some comments:
This one by Salvador Cordova.
This one from Rock:
I don’t get it. Protein production is ternary, and that’s somehow for our “convenience”?
I also understood that in the nested hierarchy of formal languages, DNA-sequences belong to the class of extended context-free grammars.
For our convenience?
This comment wherein Rock turns the tables:
You know, JW, chemistry bears an “uncanny” resemblance to coding. If I recall correctly (and I’m sure you will correct me—you are a chemist?), modern chemistry really began with the recognition of the existence of a chemical element; that elements are distinguishable by common properties, such as mass, weight, volume, density, etc.; and that elements combine in definite mathematical proportions.
If anyone didn’t know what a “code” is before, I just told you!
A code is a finite set of elements, related by common properties that vary amongst the elements (including mass, weight, volume, density, etc.), and which are combined according to a set of rules (grammar) that are summarized in terms of definite mathematical proportions (such as in the case of the DNA-code, ~3/1).
Let’s say I am a code-designer (not God) and I restrict myself (for the purposes of practical application) to the set of chemical elements. Am I also restricted to use chemistry’s grammatical rules?
