Prepare for a "Boobquake" on Monday, April 26, 2010

 
I don't know what I'm going to do on Monday. On the one hand, I should stay home in case there's a massive earthquake. On the other hand, I may miss all the fun if I stay home [Blogger: Show cleavage to test cleric’s quake theory].

I think I'll take my chances on the university campus.

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Francis Collins on Compatibility

Many of us struggle with the controversy between science and religion. As one who argues that science and religion are not compatible (with minor exceptions), I try hard to understand the views of my opponents. One of the greatest challenges is to understand why Francis Collins sees his position as an argument in favor of compatibility.

Here's a video of a talk he gave last October at The Veritas Forum in California. All of it is really interesting but the punchline comes at 50 minutes when he gives a short summary of his beliefs.

[First Slide] Almighty God, who is not limited in space and time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.

[Second Slide] God's plan included the mechanism of evolution to create the marvelous diversity of living things on our planet. Most especially, that plan included human beings.

[Third Slide] After evolution, in the fullness of time, had prepared a sufficiently advanced neurological "house" (the brain), God gifted humanity with free will and with a soul. Thus humans received a special status, "made in God's image."

[Fourth Slide] We humans used our free will to disobey God, leading to our realization of being in violation of the Moral Law. Thus we were estranged from God. For Christians, Jesus is the solution to that estrangement.

That's it. A very simple but, I think, entirely compatible view that does no violence either to faith or to science. And puts them in a harmonious position ...

Collins goes on to describe this view as "Theistic Evolution." It could also be called the "New Creationism."

I can think of six, perfectly scientific, questions that could be asked.

1. Is there any evidence of purposeful "fine tuning"?
2. Is there any evidence that humans were inevitable?
3. Is there any evidence of a Moral Law?
4. Is there any evidence of a soul?
5. Is there any evidence that humans have something called "free will" that other species lack?
6. Is there any evidence that such a personal God exists?

I think the answer to all six question is "no," therefore, believing those things conflicts with science. They are supposed to part of the natural, observable, universe and they should all be detectable, if they exist.

The Language of God: A Scientist Presents Evidence for Belief from The Veritas Forum on Vimeo.

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Argue Both Sides

 
One of the distinguishing features of a true scientific controversy is that there are good arguments on both sides. In my class on controversies and misconceptions, I teach my students that they have to recognize a real scientific controversy and, when they do, they should be prepared to argue both sides. That's the only way to demonstrate that they understand the issues.

Unfortunately, this simple concept is not widely practiced—even among scientists. Quite often we see a case being made for one side without even acknowledging that there's plenty of evidence for the opposing view. I'm giving a talk on Monday about "Junk DNA" and that's one of the main points. The current literature is full of claims about the demise of junk DNA. The claim is based on some recent findings but nobody ever mentions the older evidence that has to be refuted. When you're advocating a new model you have to do two things: (1) present evidence in favor of our model, and (2) demonstrate that evidence against your model should be rejected.

You can't do one without the other.

This rule only applies to controversies within science. In many cases, the trick is to recognize a "real" scientific controversy from one that only appears to be a scientific controversy. Take Intelligent Design Creationism for example ....

I was thrilled to see a posting by Granville Sewell on one of the IDiot blogs. The title suggested that he was finally recognizing that science had some valid points in this non-scientific controversy [Acknowledging our opponents’ strong points]. My "thrill" rapidly turned to disgust when I read the posting ....

In any debate, it is always good strategy to acknowledge your opponent’s strongest points, thereby taking them off the table. In the debate over ID, our opponents have two very strong points:

1. We have discovered scientific explanations for so many other previously mysterious phenomena, why not evolution as well? The laws God made are very clever and fine-tuned, and probably are sufficient to explain everything in astronomy, geology, chemistry and atmospheric science, for example, so it is hardly surprising that many would insist that they must be able to explain all of biology as well.

2. There are a lot of things about the development of life that give the appearance of natural causes. “This just doesn’t look like the way God would create things,” is an argument frequently used by Darwin, and by modern day evolutionists. There are also things that don’t suggest natural causes–such as the sudden appearance of nearly all the animal phyla at the beginning of the Cambrian era–but much of the history of life admittedly does leave us with a strong impression of natural causes.

All of the “evidence” for evolution falls into one of these two categories, there is no evidence to support the idea that natural selection of random mutations or any other unintelligent process can explain the major steps of evolution. Once you have acknowledged these two strong points, our opponents have nothing.

Oh, dear. He just doesn't get it.

That's why we call them IDiots.

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[Photo Credit: University of Texas El Paso]

Granville Sewell is in the Mathematics Department at the University of Texas El Paso. His major research interest is differential equations.

A vestige of the 18th century

 
I belong to the Committee for the Advancement of Scientific Skepticism (CASS) at the Centre for Inquiry—Canada. Members of that group have published an article about homeopathy on the National Post website: A vestige of the 18th century.

Congratulations to Mitchell Gerskup, Ryan Gray, Michael Kruse, Iain Martel and Justin Trottier for a great contribution to homeopathy awareness. And congratulations to the National Post for publishing it.

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Charles Darwin Died on this Day in 1882

 
Charles Darwin died at Down house during the afternoon of April 19, 1882. Janet Brown describes the moment in her biography (Charles Darwin: The Power of Place p. 495).

He died on the afternoon of 19, April 1882, after sinking very low for two or three days beforehand and suffering what Emma called "fatal attack" at midnight on the 18th. There was no deathbed conversion, no famous last words. "I am not the least afraid to die," he apparently murmured to Emma. "Remember what a good wife you have been." Allfrey signed the death certificate giving "Angina Pectoris Syncope" as the cause of death, the gradual ceasing of the heart. He was seventy-three.

The subtitle of Janet Browne's book (The power of Place) alludes to the remarkable status that Darwin achieved following publication of On the Origin of Species. Darwin was buried in Westminster Abbey at a huge funeral held on Wednesday, April 26, 1882. He was buried next to Sir John Herschel near the tomb of Sir Isaac Newton, "... an honorable place but not as close to [Charles] Lyell as Emma had hoped" (Browne, p. 497).

Here's a list of the pallbearers from AboutDarwin.com.

George Campbell - The 9th Duke of Argyll
William Cavendish - The 7th Duke of Devonshire
Edward Henry Stanley - The 15th Earl of Derby
James Russell Lowell - The American Ambassador to Britain
William Spottiswoode - Mathematician, physicist, the Queen's Printer, and friend of Darwin
Joseph Dalton Hooker - Darwin's close friend and champion of his Theory of Evolution
Thomas Henry Huxley - Darwin's close friend and champion of his Theory of Evolution
Alfred Russel Wallace - Darwin's friend and the co-founder of Natural Selection
Sir John Lubbock - The 1st Baron of Avebury, Darwin's next door neighbor and close friend

Here's the report of the funeral published in The Times on Thursday, April 27, 1882 [Wikisource].

The Funeral of Mr. Darwin

The mortal remains of Charles Robert Darwin were interred in the Abbey at Westminster yesterday with marks of respect due to one whose name has been for many years familiar as a household word to his countrymen, and whose works have shed so much distinction upon English science. The coffin containing the body was brought to the Abbey late on the previous evening and borne through the cloisters, Mr. Darwin's five sons following, into the Chapel of St. Faith. This is a portion of the Abbey little known to casual visitors. It is a long narrow apartment, with a groined and vaulted roof, situate between the end of the south transept and the vestibule of the Chapter House, and was until a few years ago used as a store room, and for some time was mistakenly called the Chapel of St. Blaize. Sir Gilbert Scott, however, discovered at the east end, where traces of an alter are found, a mural painting of a female figure, evidently a saint, holding in her hands a book and an iron rod — the emblems of St. Faith. The western portion of the room formed of old a revestry. Into this bare chapel, which, to the eyes of of the greatest architect seemed "a picturesque and beautiful room," the coffin was carried on Tuesday night, and, seen by the dim light from two old-fashioned lanterns, the place seemed gloomy and tomb-like in contrast with the lofty, nobly proportioned interior of the Abbey which could be seen through the glass door opening into the south transept. The presence of death was more painfully forced on the mind even than during the solemn ceremonial of yesterday, when the great building was again peopled with the living. Soon after 11 in the morning those who were to follow the body as mourners began to assemble in the Chapter House. The Embassies of France, Germany, Italy, and Spain were represented, and among those invited through Messrs. T, and W. Banting to be present or to send representatives nearly all those who received invitations were present, were:—

The Marquis of Salisbury, K.G., Chancellor of the University of Oxford; Lord Aberdare, President of the Geographical Society; the Speaker of the House of Commons, M.r. Childers, M.P., Sir Stafford Northcote, M.P., Mr. Fawcett, M.P., Mr. Mundella, M.P., Sir T Brassey, M.P., Sir Charles Dilke, M.P., Lord Kensington, M.P., Mr. A. J. Beresford, M.P., and Mr. Spencer Walpole, M.P., the two members of the University of Cambridge; Sir J. R. Mowbray, M.P., and Mr. J. G. Talbot, M.P., the members for the University of Oxford; Mr. J. A. Campbell, M.P. for the Universtiy of Glasgow and Aberdeen; Lord Arthur Russell, M.P., Mr. Plunket, M.P., and Mr. Edward Gibson, Q.C., M.P., the members for the University of Dublin; Dr. Lyon Playfair, M.P., for the Universities for Edinburgh and St. Andrew's; Sir Farrer Herschell, Q.C., M.P., Sir David Wedderburn, M.P., Sir Henry Holland, M.P., Mr Nevil Story Maskelyne, M.P., Mr. H. Broadhurst, M.P., Mr. T,. Burt, M.P., Professor Bryce, M.P.; the vice-Chancellor of the University of Oxford, the Master of Balliol, the Regius Professor of Medicine (Dr. Acland), and the Linacre Professor of Zoology, as representing the University of Oxford; the President of the College of Surgeons, the President of the College of Physicians, the Council of the Royal Society, the Council of the Linnean Society, the Council of the Royal Geographical Society, the council of the Geological Society, the Master of Christ's College, Cambridge, the Head-Master of the Grammar School, Shrewsbury; the Rev. Professor Kennedy, the Rev. Professor Pritchard, F.R.S., Professor Humphry, F.R.S., Professor Max Müller, Professor Henry S. Smith, F.R.S., Professor Prestwick, F.R.S., Professor Hirst, F.R.S., Professor Mosely, F.R.S., Professor Babington, F.R.S., Professor De Chaumont, F.R.S., Sir William Thomson, F.R.S., Sir John Hawkshaw, Dr. W. B. Carpenter, C.B., F.R.S., Mr. Ray Lankester, F.R.S., Sir Henry Maine, Mr. John Simon, C.B., Professor W. Chandler Roberts, F.R.S., Mr. John Murray, Captain Douglas Galton, secretary to the British Association for the Advancement of Science; Mr. W. Onless, R.A., Professor W. B. Richmond, R.A., Mr. George Atherley, Mr. W. Dallas, Mr. H. W. Bates, Mr. Walter White, Mr. J. W. Judd, Mr. G. A. Spottiswoode, Mr. R. C. Hankinson, Mr. John Morley, Mr. R. H. Hutton, Mr. W. C. Leckie, Mr. Frederic Harrison, Captain Abney, R.E., Mr. Frederick Pollock, Mr. W. R. S. Ralston, the Hon. Robert Winthrop, Professor Flower, F.R.S., and Mr. Herbert Spencer, F.R.S.

The Anthropological Institute appointed a deputation to attend, composed of the following members of the Society:— Sir John Lubbock, Mr. John Evans, F.R.S., Mr. E. B. Tylor, F.R.S., Professor Busk, F.R.S., Mr. Hyde Clarke, Professor W. H. Flower, Mr. Francis Galton, F.R.S., Dr. Allen Thomson, F.R.S., Mr. F. W. Rudler, F.G.S., Mr. F. E. W. Brabrook, F.S.A., Mr. J. E. Price, F.S.A., Lieutenant-Colonel H. H. Godwin-Austen, F.R.S., Professor Huxley F.R.S., Mr. R. R. Martin, M.P., Mr. Alfred Tylor, F.G.S., and Mr. George W. Bloxam, M.A., assistant secretary.

At about 20 minutes to 12 the body was brought out of the Chapel of St. Faith, through the Chapter-house vestibule, into the west cloister, and the procession was formed. The coffin was covered with a black velvet pall edged with white silk, On it were laid many wreaths of beautiful white flowers, one of the wreaths having been sent by members of scientific societies in Liverpool, represented by Mr. Isaac C. Thompson, F.R.M.S., honorary secretary of the Microscopical Society of Liverpool. The pall-bearers were the Duke of Devonshire, the Duke of Argyll, the Earl of Derby, Mr. J. Russell Lowell, the American Minister; Mr. W. Spottiswoode, LL.D., President of the Royal Society; Sir Joseph Hooker, Mr. A. R. Wallace, Professor Huxley, Sir John Lubbock, and the Rev. Canon Farrar. Proceeding slowly along the south cloister those heading the procession were met at the west entrance by members of the family and others, whose names follow:—

Mr. William Erasmus Darwin, chief mourner; Mr. George Darwin, F.R.S., Mrs. William Darwin, Miss Darwin, Mrs. Litchfield, Mr Francis Darwin, Mr. Leonard Darwin, Mr. R. B. Litchfield, Mr. Horace Darwin, Mr. Leonard Darwin, R.E., Mr. Darwin of Elston-hall, Mr. F. Alvey Darwin, Captain Charles Darwin, Mr. Reginald Darwin, of Buxton, Mrs. Vaughan Williams, Miss Wedgwood, the Rev. Charles Parker, Mr. Robert Packer, Mr. H. F. Bristowe, Q.C., Mr. Francis Galton, F.R.S., Mr. Ernest Wedgwood, Mr. Hensleigh Wedgwood, Mr. T. H. Farrer, Secretary of the Board of Trade, Mrs. Farrer, Mr. Godfrey Wedgwood, Miss A. Wedgwood, Mrs. Ruck, the Rev. Arthur Wedgwood, Mr. J. C. Hawkshaw, Mrs. Hawkshaw, Mr. George Allen, Mr. Henry Allen, M.P.; servant, Mr. William Jackson, and Mr. Joseph Parslow.

Within the Abbey a large congregation was assembled, filling the seats on the south side of the nave, the seats in the choir and such as were not reserved for the mourners in the transepts, while a large number admitted without tickets stood on the north side of the nave. Among those present were the Baroness Burdett-Boutts and Mr. Burdett-Coutts, the Lord Mayor, and Lady Mayoress and Miss Ellis, Mr. Sheriff Ogg, the Rev. R. C. Billing, Mr. Mark H. Judge, Mr. L. T. D'Eyncourt, and the Head Constable of Westminster. Masters and Queen's scholars of the Westminster School also attended. At the West Cloister door the mourners were met by the Rev. Canon Prothero, as senior canon in the absence of the Dean, who is abroad. Canon Prothero having read the opening sentence of the Service for the Burial of the Dead, the choir changed the other processional sentences to the music of Croft, as the procession moved down the south aisle to the west end of the church and then up the nave into the choir. Following the choristers came the Rev. J. H. Cheadle and the Rev. J. Troutbeck (minor canons of Westminster), Canon Rowsell, Canon Barry, Canon Duckworth, and the Rev. S. Flood Jones (precentor), and near the senior canon the Chapter Clerk, Mr. C. St. C. Bedford. The body was placed in front of the Communion rails during the first portion of the service. The Psalms were chanted to Purcell's music, and after the Lesson, which was read by Canon Duckworth, an anthem composed for the occasion by Mr. Bridge was sung to the words from the Book of Proverbs, "Happy is the man that findeth wisdom. and getteth understanding. She is more precious than rubies, and all the things thou canst desire are not to be compared unto her. Length of days is in her right hand, and in her left hand riches and honour. Her ways are ways of pleasantness, and all her paths are peace." The soft and subdued ending of the composition, which was sung with much feeling by the choir, prepared the mind for the last sad duty that remained to be performed. The body was not removed to the grave, which is at the north-east corner of the nave next to that of Sir John Herschell, Dr. Bridge playing first Beethoven's Funeral March and then a more plaintive march by Franz Schubert in B minor, while the mourners proceeded to the grave, and the rest of the service was impressively read by Canon Prothero, the choir singing their part to Croft and Purcell's music. Near the grave and just beneath the monument to Sir Isaac Newton stood a remarkable and representative crowd of distinguished men, such as only an occasion of deep and general would bring together. Leaders of men and leaders of thought; political opponents, scientific co-workers; eminent discoverers, and practitioners of the arts. To name only a few as representative, there were Lord Spencer, President of the Council, who represented Her Majesty's Ministers at the funeral; the Marquis of Salisbury, Viscount Sherbrooke, Sir William Jenner, Sir Stafford Northcote, Sir Charles Dilke, Mr. Moncure D. Conway, Dr. Siemens, Sir William Gull, Mr. Childers, Professor Marshall, Sir John Hawkshaw, Mr. Ernest Hart, Mr. W. H. Smith, Mr. Herbert Spencer, Dr. Farquharson, Professor Flower, Mr. Robert Winthrop, and Mr. Ellis. The anthem by Handel, "His body is buried in peace, but his name liveth evermore," was sung, and the senior Canon having pronounced the Benediction, the mourners left, and the public were then allowed to pass round the grave. The inscription on the plate of the white, unpolished oak coffin read, "Charles Robert Darwin. Born February 12, 1809. Died April 19th, 1882."

In an article in to-day's Nature on the late Mr,. Darwin, Professor Huxley writes as follows:— "Not only in these islands, where so many have felt the fascination of personal contact with an intellect which had no superior, and with a character which was even nobler than the intellect, but in all parts of the civilized world it would seem that those who business it is to feel the pulse of the nations and to know what interests the masses of mankind were well aware that thousands of their readers would thin the world poorer for Darwin's death, and would dwell with eager interest upon every incident of his history. In France, in Germany, in Austro-Hungary, in Italy, in the United States, writers of all shades of opinion, for once unanimous, have paid a willing tribute to the worth of our great countryman, ignored in life by the official representatives of the kingdom, but laid in death among his peers in Westminster Abbey by the will of the intelligence of the nation. One could not converse with Darwin without being reminded of Socrates. There was the same desire to find some one wiser than himself; the same belief in sovereignty of reason; the same ready humour; the same sympathetic interest in all the ways and works of men. But instead of turning away from the problems of nature as hopelessly insoluble, our modern philosopher devoted his whole life to attacking them in the spirit of Heraclitus and of Democritus, with results which are as the substance of which their speculations were anticipatory shadows. The due appreciation or even enumeration of these results is neither practicable nor desirable at this moment. There is a time for all things—a time for glorying in our ever extended conquests over the realm of nature, and a time mourning over the heroes who have led us to victory. None have fought better, and none have been more fortunate than Charles Darwin. He found a great truth, trodden under foot, reviled by bigots, and ridiculed by all the world; he lived long enough to see it chiefly by his own efforts, irrefragably established in science, inseparably incorporated with the common thoughts of men, and only hated and feared by those who would revile, but dare not. What shall a man desire more than this? Once more the image of Socrates rises unbidden, and the noble peroration of the 'Apology' rings in our ears as if it were Charles Darwin's farewell:—'The hour of departure has arrived, and we go our ways—I to die and you to live. Which is the better God only knows.'"

We are requested to state that the absence of the Vice-Chancellor and members of the Council of the Senate of the University of Cambridge from the funeral of the late Mr. Darwin was occasioned by the circumstance that it was impossible for them to attend in consequence of the approaching election to the Regius Professorship of Hebrew. By the statute regulating the election it is imperative on the Vice-Chancellor and the members of the Council, who are the electors, to be present during the whole time each of the candidates for the Professorship delivers his exposition on the portions of Hebrew books assigned to him. The times for the delivery of these dissertations had been fixed nearly a month ago, and it was impossible to postpone them and to defer the election. Consequently, much to the regret of the Vice-Chancellor and the members of the Council, none of them could attend as representing the University of Cambridge.

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[Photo Credit: Funeral of Charles Darwin: The Complete Works of Charles Darwin Online, Invitation: English Heritage Prints]

Bill O'Reilly "Discusses" European Paganism

 
I don't watch Bill O'Reilly's show very often so I missed this segment. I find it extremely interesting that a major television network could air such a discussion in the 21st century. To me, it says something about popular views in American culture. It doesn't say that a majority of Americans agree with these idiots but it does say that their point of view is an acceptable part of the cultural mix. That's shocking.

The priest's comments are interesting from the perspective of the accommodationist wars. He claims that Roman Catholicism conflicts with all kinds of things, including socialism. Who knew?

[I haven't been keeping up with financial news. Is it true that Europe is in much worse economic shape that the USA? I didn't notice that during recent visits to Europe and the USA.]

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[Hat Tip: Pharyngula: A priest, a scientist, and a Communist discuss morality]

The "New Creationism"

 
Jerry Coyne has "coyned" a new term to describe people who accept most of science but still want to have their cake [HuffPo screws up evolution again].

I’m coyneing the term “New Creationism” to describe the body of thought that accepts Darwinian evolution but with the additional caveats that 1) it was all started by God, 2) had God-worshipping humans as its goal, and 3) that the evidence for all this is that life is complex, humans evolved, and the the “fine tuning” of physical constants of the universe testify to the great improbability of our being here—ergo God. New Creationism differs from intelligent design because it rejects God’s constant intervention in the process of evolution in favor of a Big, One-Time Intervention, and because these ideas are espoused by real scientists like Kenneth Miller and Simon Conway Morris. (Note that Miller, though, has floated the possibility that God does sometimes intervene in the physical world by manipulating electrons.) New Creationism is bad because, while operating under the deep cover of real science, it tries to gain traction for dubious claims about the supernatural.

This is pretty good but let's not insist that New Creationists have to postulate humans as the only goal of evolution. Some of them do and some of them are content with any kind of sentient being. The common characteristic is that they envisage some kind of purpose to the way the universe has unfolded.

"New Creationism" is a much better term than "Theistic Evolution" and I think I'll use it from now on. It has the advantage of putting the emphasis on "creationism," where it belongs. (Note, this is small-"c" creationism.)

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Theory vs Theory

This is the third in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. In this article we learn about theories.

Please pay attention.

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The Curious Disconnect

Our journey to map out the Curious Disconnect-- the gap between how we think about evolution and how we might think if we were freed from historical baggage-- began last time with part 1 of The Mutationism Myth.

Before continuing with part 2, I would like to take a detour. Issues surrounding "evolutionary theory", and evolutionary theories, are going to be coming up again and again. In fact, I can see these issues emerging already in The Mutationism Myth. So, before we get bogged down in confusion and disagreement, I would like to begin a discussion of "theory" and "theories". We'll return to the Mutationism Myth next time.

An updated version of the post below will be maintained at www.molevol.org/cdblog/theory_vs_theory (Arlin Stoltzfus, ©2010)

Theory1 vs theory2

What does it mean to invoke "evolutionary theory"? Is "neo-Darwinism" (or "Darwinism") a theory, a school of thought, or something else? What gives a theory structure and meaning (e.g., axioms, themes, formulae)? What is the relationship between mathematical formalisms and other statements of "theory" (e.g., what does it mean for a lecturer to show a key equation of quantitative evolutionary genetics and assert "this is neo-Darwinism")? Who decides how a theory is defined, or redefined (e.g., is Ohta's "nearly neutral" theory an alternative to, or a variant of, Kimura's Neutral Theory of Molecular Evolution)?

Confusion regarding "theory" and "theories" is going to be an ongoing topic of attention in The Curious Disconnect. As noted in the Introduction, we're in an enormous muddle. The way to get out of this muddle is to take some time to build common understanding, learn some useful terms, and establish ground rules.

In this post, we'll begin the process of developing a shared framework for productively discussing "theory" and "theories". We will begin by addressing an ambiguity in the use of the word "theory", partly because this particular ambiguity is important, and partly as an exercise in addressing semantics. ⁰

Definitions

Dictionaries provide definitions that can be helpful to clarify the meanings of words and the complications of their usage. Definitions can be descriptive, telling us how a word is used, or prescriptive, telling us how it ought to be used. But, as most of us don't like to be told what we ought to do, I suspect that you share my belief in studying how words are used, in order to determine their denotations (what the word says) and connotations (what the word hints or implies). The English dictionaries used in America typically agree: the definitions that they provide reflect patterns of common usage, not the decrees of authorities.

A difficulty with dictionaries arises given that, within an isolated community, e.g., a scientific discipline, words can take on special meanings. So, dictionaries can be helpful, with the proviso that we need to be sensitive to the special use of terms within a discipline.

The discipline-specific use of a term can be nailed down by looking at examples of usage. For evolutionary biology, the discipline-specific use of a term is to be found in the research literature, and also in the secondary literature of monographs, textbooks, and other disciplinary writings.

Two meanings of "theory"

A good dictionary will distinguish several different senses of the word "theory", including the following two that I believe are the most relevant for our discourse:

1) a major conjecture or systematic hypothesis to account for observed phenomena, as in "prion theory of disease" or "Lamarck's theory of evolution";

2) the body of abstract principles relevant to some discipline, methodology or problem area, as in "music theory" or "population genetics theory"

That is, a theory₁ is a grand hypothesis, a conjecture about the actual world, while a theory₂ is a collection of principles or models or other formalisms that might apply only in an imagined world. Fisher (1930) famously said that "No practical biologist interested in sexual reproduction would be led to work out the detailed consequences experienced by organisms having three or more sexes; yet what else should he do if he wishes to understand why the sexes are, in fact, always two?" Theoreticians aren't necessarily good with facts, so we'll ignore that the sexes (in the sense of mating types) are not, in fact, always two. Fisher clearly encourages us to work out formalisms for imagined or hypothetical cases. The collection of all these models or formalisms about sexes would constitute the theory₂ of sexes. A theory₁ of sexes might propose a causal explanation for the actual historic phenomenon of the origin and maintenance of sexual reproduction in animals, addressing such issues as the heterogametic basis of sex determination. ¹

These two meanings are not just recognized in dictionaries, but are established in scientific usage. Gilbert's "Exon Theory of Genes" (Gilbert 1987) is the conjecture that genes evolved from exons (i.e., large protein-coding genes emerged by joining primordial exon-minigenes). The prion theory₁ of disease clearly revolves around a conjecture that there are actual diseases caused by actual prions. By contrast, population genetics theory₂ is not the conjecture that populations have genetics; likewise, the theory₂ of stochastic processes is not a conjecture that stochastic processes occur, but consists of a body of abstract principles that might be applicable to such stochastic processes as might occur in some actual or imagined universe.

The use of the abstract noun, as in "let's talk about theory" as opposed to "let's talk about { a | the | this } theory", often signals the use of theory₂. For instance, the title of a report by the National Academy of Sciences on "The Role of Theory in Advancing 21st Century Biology" signals a likely emphasis on theory₂, and indeed, the report emphasizes the development of formalisms more than conjectures, and says that "a useful way to define theory in biology is as a collection of models", clearly a reference to theory₂. The report also mixes in some references to theories₁.

Obviously, there is a connection between scientific theories₁ and scientific theory₂. One way of thinking about the connection is that the abstract principles of theory₂, when suitably limited by measurable or observable quantities from the actual world, can provide the basis of a theory₁, and conversely, theories₁ draw on theory₂ for logical structure. Kimura's Neutral Theory (Kimura 1983) provides a clear example because the theory₁ and theory₂ were developed separately: Kimura combined pre-existing theory₂ (of stochastic population genetics) with the concrete assertion that the values of certain quantities (relating to population sizes and mutant effects) were such that, for DNA and protein sequences, neutral evolution by mutation and random fixation would be far more common than anyone had imagined previously. The definition of effectively neutral alleles (perpetually misunderstood by critics) and the probability of fixation under pure drift were known to the canonical founders of population genetics ((Wright 1931); ch. IV of (Fisher 1930); appendix of (Haldane 1932)). Another indication of the distinctness of theory₁ and theory₂ is that opponents of the Neutral Theory₁, who deny the truth of the theory₁, are nonetheless quite happy to make use of its theoretical₂ infrastructure (Kreitman 1996).

Development and application of theory₁ and theory₂

We treat the two kinds of "theory" differently, and rightly so.

A theory₁ contains a major supposition or unproved conjecture about the world. Kimura's Neutral Theory is the conjecture that most changes at the "molecular level" represent the random fixation of effectively neutral alleles. Darwin proposed, but could not prove, that all large-scale evolutionary changes were built from infinitesimal increments of change that emerged by a process of hereditary "fluctuation". A theory₁ takes risks: in Popperian terms, its subject to empirical refutation; in the words of Huxley, a beautiful theory₁ can be "killed by an ugly fact."

The relevant standard of validity for theory₂ is not verisimilitude (trueness to life), but consistency: the principles derived in the theory are consistent with its assumptions. Importantly, new principles added to a body of theory₂ are consistent with previous principles, except in the sense that a body of theory₂ may be subdivided into branches that cover non-overlapping universes. If they are not, a logical error has occurred.

While new theory₂ is consistent with existing theory₂, theories₁ often stimulate interest precisely because they conflict with previous theories₁. Of course theories₁ strive to be internally consistent, but in biology at least, theories₁ are not axiomatic, and often encompass ambiguities that make rigorous analysis difficult. A theory₁ can be brought down by a contradiction that arises internally, e.g., one part can be found to contradict another part.

While a theory₁ is about the actual world, and thus is judged by verisimilitude, principles of theory₂ need not apply to the real world. Indeed, no amount of conflicting data will cause us to discard a principle of theory₂ that is properly derived: a beautiful piece of theory₂ cannot be killed by an ugly fact. Fisher's fundamental theorem either is logically valid or is not logically valid, independent of any facts.

Digressions

The distinction between theory₁ and theory₂ is hidden in the ambiguous word "theory", but I think it comes out more clearly in specific word-derivatives and grammatical usages that seem to favor one meaning more than the other. I mentioned above that the abstract noun typically signals theory₂. I'm also convinced that when we refer to a "theoretician", we typically do not mean someone like Tom Cavalier-Smith whose scientific output consists of bold conjectures or systematic hypotheses (we might call such people "theorizers"), but instead someone like Joe Felsenstein whose work focuses on mathematical or algorithmic foundations, i.e., theory₂. Its a rare scientist, it seems to me, who is productive both as a theoretician and as a theorizer (e.g., Kimura, Hamilton).

Neither meaning of theory would cause us to relinquish the label "theory" for a proposition that lacks verisimilitude. Clearly the propositions of theory₂ do not have to apply to the real world. And a theory₁ is a conjecture, not necessarily a true conjecture. Thus, even opponents of the Neutral Theory₁, who believe that the theory does not fit the actual world, still refer to it as The Neutral Theory (Kreitman 1996).

I mention this because there is an absurd tendency in the literature of evolution advocacy, e.g., NCSE's screeds, to say that, because scientists reserve the word "theory" only for constructions that have been extensively verified and are accepted as true, the use of "theory of evolution" among scientists means that evolution is well supported.

This argument clearly is false, and the proof does not depend on the theory₁ vs. theory₂ distinction, but only on the fact that scientists habitually choose to refer to Kimura's theory or Lamarck's theory or Gilbert's theory as a "theory", even if its known to be wrong or is considered deeply suspect. This pattern holds, not just in biology, but in other disciplines. In astronomy, the geocentric theory remains a theory though it has been abandoned; in physics, the phlogiston theory, or the aether theory of light propagation (roughly, the theory that space must be substantive in order for waves to propagate in it) remain theories even though they were abandoned. So, write to the NCSE and tell them to stop using this lame argument. Really, we can do better than that.

The NCSE fallacy seems to arise from mixing together the proposed explanation of phenomena aspect of theory₁ and the accepted as valid aspect of theory₂. This is suggested from the way that NCSE's screed cites the NAS report on theory₂ (the same one that I quoted above) as though it provided a definition of theory qua "well substantiated explanation", which definitely is not the same as "collection of models".

Lets try to sort this out in terms of the distinction between theory₁ and theory₂. Evolutionists have recourse to a body of theory₂ (formalisms or models or principles), ranging from purely phenomenological models of branching and character-state change used in phylogenetics, to the breeder's equation used in quantitative genetics, to detailed formulas for population-genetics processes, and so on. We accept the validity of these abstractions in the theory₂ sense of validity, i.e., we accept that they are derived without error, so as to be logically consistent with their assumptions. This body of abstractions, principles, or formalisms (in NAS parlance, this collection of models) is evolutionary theory₂.

But saying that this theory₂ is valid is not at all the same thing as claiming that its true in the sense of verisimilitude; and claiming that it has verisimilitude is not the same as saying that its complete, in the sense of sufficiently accounting for the phenomena of evolution. For instance, the theory₂ of quantitative evolutionary genetics is based on the assumption of infinitesimal variation, but the theory₂ itself does not claim that all traits, nor even any single trait, evolved in this manner-- that would be a theory₁ issue. Kimura's diffusion equations are a part of population genetics theory₂ that provides a way to work out the probability of fixation of alleles under ideal conditions, but it doesn't assert that the results are applicable to any particular case. Got it?

Homework

The wikipedia entry on theory (http://en.wikipedia.org/wiki/Theory) has a "List of Notable Theories" that clearly mixes up theories₁ or grand conjectures (the cell theory, the phlogiston theory) with theories₂ or bodies of abstract principles (music theory, extreme value theory). What are some other clear examples of theory₁ and theory₂ in this list? Which examples are difficult to classify (and what does one learn from those)?

Who, besides Kimura and Hamilton, was productive as both a theoretician and as a theorizer?

Think of a few theories in science, ideally in life sciences. I'm going to assert that they are not axiomatic, i.e., they are not completely encompassed by precisely stated propositions. Given this, how do we really know what defines the theory? If we know a theory from the verbal statements in a body of literature (i.e., "things people say"), what is the relationship of an individual expression (e.g., a paper, a monograph, a quotation) to the theory? Is it the instantiation of a platonic form or essence? How do we get to the essence? Is the distribution of expressions of a theory its "reaction norm", representing environmental noise in the expression of an underly structure (the theory's "genotype")?

The Modern Synthesis as theory₁: into the memory hole

The folks at NCSE and wikipedia are not the only ones blurring the issues. The Modern Synthesis or modern neo-Darwinism ² was put forth originally as a falsifiable theory₁ of evolution, but evolutionists themselves don't treat it that way anymore. For instance, in Maynard Smith's defense of "neo-Darwinism" (Maynard Smith 1969), the only kinds of falsifying observations he can imagine are cases that seem to introduce supernatural forces, e.g., if the spots on a fish always appeared in prime numbers, he says this would contradict neo-Darwinism. He does not imagine variation-induced trends, discontinuous jumps based on individual mutations, or extensive neutral evolution as contradictions of "neo-Darwinism", though these ideas were rejected by the architects of modern neo-Darwinism. Maynard Smith makes the claim in regard to the Neutral Theory that "I have never seen any reason why, as a naive Darwinist, I should reject this theory" (Maynard Smith 1995). It seems that, for Maynard Smith, "neo-Darwinism" is not a theory₁ at all, but merely indicates a commitment to scientific materialism, i.e., seeking natural causes through observation and experiment.

Other authoritative sources suggest that the Modern Synthesis is no longer viewed as a falsifiable conjecture. In Hull's Encyclopedia of Evolution article on the history of evolutionary thought (Hull 2002), the Modern Synthesis is presented as an open-ended "theory" that merely assumes the principle of selection and the rules of genetics, and which has swallowed up the neutral theory along with all other useful ideas:

"Any criticism of the synthetic theory that turned out to have some substance was subsumed in a modified version of this theory. Instead of being a weakness, this ability to change is one of the chief strengths of the synthetic theory of evolution. As in the case of species, scientific theories evolve" (p. E16)

Hull's conception of the Modern Synthesis sounds more like an extensible set of principles, theory₂, than the theory₁ of Mayr, Simpson, Ayala, etc (which is extensible in some ways but closed and falsifiable in others). I'm not necessarily going to say its wrong for scientists to decide that the Modern Synthesis is no longer a theory₁, but can someone please tell me when, and on what basis, did we make this decision? Is there a citation for that? And who decided that we wouldn't tell Richard Dawkins, leaving the poor fellow stuck in a time warp defending the original Modern Synthesis? ³

But I'm getting ahead of myself. I started The Curious Disconnect with the The Mutationism Myth because 1) most evolutionists don't understand how the Modern Synthesis came into existence as a theory₁ that entails risky conjectures, and 2) the mutationist challenge provides the definitive historical proof that the Modern Synthesis is a theory₁ and not just a commitment to selection and the rules of genetics. The historical record will show clearly that the mutationists or "Mendelians" presented a workable synthesis of selection and the rules of genetics, and that their view was rejected by the architects of the Modern Synthesis. Once we find out why, we will understand what makes the Modern Synthesis a theory₁.

Literature cited

Dawkins, R. 2007. Review: The Edge of Evolution. Pp. 2. International Herald Tribune, Paris.

Fisher, R. A. 1930. The Genetical Theory of Natural Selection. Oxford University Press, London.

Gilbert, W. 1987. The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52:901-905.

Haldane, J. B. S. 1932. The Causes of Evolution. Longmans, Green and Co., New York.

Hull, D. L. 2002. History of Evolutionary Thought. Pp. E7-E16 in M. Pagel, ed. Encyclopedia of Evolution. Oxford University Press, New York.

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Kreitman, M. 1996. The neutral theory is dead. Long live the neutral theory. Bioessays 18:678-683.

Maynard Smith, J. 1969. The Status of Neo-Darwinism. Pp. 82-89 in C. H. Waddington, ed. Towards a Theoretical Biology 2. Sketches. Edinburgh Universeity Press, Edinburgh.

Maynard Smith, J. 1995. Life at the Edge of Chaos? Pp. 28-30. New York Review of Books, New York.

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97.

Notes

⁰ I thank Dr. Mike Coulthart for originally drawing my attention to the importance of this distinction.

¹ If we were to propose just that the sexes are always 2 in number, simply because that is what we have seen in the past, I would call this an empirical generalization or "law". Sometimes "theory" is used for such a generalization, but that usage does not correspond to either meaning of "theory" addressed here.

² I'm using "modern neo-Darwinism" as a synonym for "Modern Synthesis". Neo-Darwinism (for our purposes, Darwinism 1.2) is the pre-Mendelian theory of Weissman and Wallace emphasizing the supreme power of selection and infinitesimal variation to build adaptation (and rejecting Darwin's reliance on Lamarckism). The Modern Synthesis (Darwinism 2.0) comes from this tradition and is often called "neo-Darwinism", though "modern neo-Darwinism" is clearer.

³ Kidding aside, its quite useful to have a scholar still defending the actual Modern Synthesis. For instance, in his attempt to rebut Behe (Dawkins 2007), Dawkins claims that mathematical geneticists "have repeatedly shown that evolutionary rates are not limited by mutation" and that Behe's critique based on the idea that evolution depends on specific mutations would mean that "the entire corpus of mathematical genetics, from 1930 to today, is flat wrong". In making this claim, Dawkins is correctly representing the Modern Synthesis view that (due to the buffering effect of the "gene pool") evolution does not depend on the rate of new mutations, a principle that he believes to be an infallible theoretical result.

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Chris Mooney vs Atheists: Part XXXIV

 
Chris Mooney is at it again. His latest posting sounds ominous: Are Top Scientists Really So Atheistic? Look at the Data.

Elaine Howard Ecklund is a sociologist at Rice University; we cited her work on the topic of science and religion in Unscientific America. Now, she is out with a book that is going to seriously undercut some widespread assumptions out there concerning the science religion relationship.

Unfortunately, Chris doesn't present any data because he's not a scientist. Data really isn't his thing.

I don't have a copy of the book so I can't check it myself. Fortunately, Razib Khan, one of Chris Mooney's fellow bloggers on the Discover website, was able to find some of the data [Scientists as “spiritual atheists”].

Let's be clear about one thing. This is not a poll of scientists. It's a poll of American scientists. The title of Ecklund's book, Science vs Religion: What Scientists Really Think, is somewhat misleading.¹ Here's two charts from the book.

Hmmm ... none of my assumptions have been undercut. How about yours?

I guess what Chris Mooney means is that some of his assumptions will have to be re-evaluated. It's about time.

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1. Unless you're an American. Then you probably believe that all scientists live in the USA.

Is Evolution Guided or Unguided?

Michael Ruse has criticized Alvin Plantinga for being critical of evolution. Plantinga defends himself in a letter published in The Chronicle of Higher Eduaction: Evolution, Shibboleths, and Philosophers.

I want to address one particular point that Plantinga makes because it's relevant to the issues that come up in the accommodationist wars.

"Why," asks Ruse, "does Plantinga feel this way?" Because, he says, "In his view, Darwinism implies that there is and can be no direction in life's history." Still another missed distinction. As far as I can see, God certainly could have used Darwinian processes to create the living world and direct it as he wanted to go; hence evolution as such does not imply that there is no direction in the history of life. What does have that implication is not evolutionary theory itself, but unguided evolution, the idea that neither God nor any other person has taken a hand in guiding, directing or orchestrating the course of evolution. But the scientific theory of evolution, sensibly enough, says nothing one way or the other about divine guidance. It doesn't say that evolution is divinely guided; it also doesn't say that it isn't. Like almost any theist, I reject unguided evolution; but the contemporary scientific theory of evolution just as such—apart from philosophical or theological add-ons—doesn't say that evolution is unguided. Like science in general, it makes no pronouncements on the existence or activity of God.

Plantinga is allying himself with Eugenie Scott and other accommodationists who fiercely defend the idea that science can't address issues such as purpose. In fact, Genie fought hard to remove references to "unsupervised, impersonal, unpredictable and natural process" from a statement on evolution by the National Association of Biology Teachers back in 1995 [NCSE v National Association of Biology Teachers].

I disagree with Plantinga, and with the National Center for Science Education. The idea that evolution might be guided by God is a legitimate question for scientists to address. After all, if it's true then parts of evolutionary theory might have to be revised. I do not accept the claim that scientists must avoid this question because it comes from religion.

When you are thinking like a scientist there's only one possible conclusion. There is no scientific evidence to support the hypothesis that the history of life on Earth was guided by God. Everything we know about the history of life is consistent with an entirely natural process—one that's characterized by chance and contingency. It is perfectly reasonable as a scientist to state this position clearly. This is not stepping outside of the boundaries of science.

Let me explain my position by using an analogy. Imagine the claim that aliens visited the Earth 3.5 billion years ago and seeded our planet with cyanobacteria. After much investigation scientists find no support for such a claim. Is it legitimate for them to conclude that aliens are not responsible for life on Earth? Of course it is. All scientists know that you can't prove a negative but that doesn't mean you can't assign probabilities and behave accordingly.

Philosophers aren't likely to get upset if scientists make statements denying that aliens are responsible for life as we know it. That's because belief in alien visitors isn't one of those kooky ideas that demands special status. However, if scientists make the more general claim that life appears to have evolved by purely natural processes then this gets their dander up. All of a sudden science is threatening religion and this is not allowed. It's "philosophical naturalism" and not "methodological naturalism." It's not science according to Plantinga and many accommodationists, including Michael Ruse. Bollocks, I say.

Scientists call it as they see it. If that upsets the theists then they had better learn to deal with it instead of whining about the science being illegitimate.

Science says that evolution is not divinely guided, based on what we know today.

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Teaching the Controversy About Homeopathy

 
I've got a confession to make. I've been posting about homeopathy this week but everything I've said has been negative. You know there must be another side to this "controversy" so in the interest of fairness, here it is. These homeopaths are putting forward the best possible case for taking homeopathic "remedies."¹

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1. If you pay attention, you'll notice that there's no scientific evidence presented. You already know why.

[Hat Tip: Tony Burns]

More Homeopathic Woo: Super-Memory

 
This gets better and better as the week goes on. PZ Myers has discovered a company that markets fragments of DNA to promote good health. You don't actually eat the DNA, instead you drink water that has been exposed to the DNA [More Magic Snake Oil].

The company is called Homeovitality® and one of their products is Super Memory/IQ. I'm showing a picture of the product taken from their website in order to prove to you that it actually exists. This is part of the discussion concerning its scientific/medical efficacy—an important part of science education and social responsibility.

How does it work? Before I explain it to you, you'd better be sitting down. Try and remain calm.

There are two genes in your genome called CRM2 and SNAP-25. CHRM2 encodes a muscarinic receptors and various alleles of this gene have been associated with alcohol dependence and drug dependance, according to the Online Mendelian Inheritance in Man (OMIM) database [CHOLINERGIC RECEPTOR, MUSCARINIC, 2; CHRM2]. SNAP-25 encodes a synaptosomal-associate protein of 25kDa molecular weight. There have been reports that alleles of SNAP-25 are associated with hyperactivity but a separate study did not confirm this association according to OMIN [SYNAPTOSOMAL-ASSOCIATED PROTEIN, 25-KD; SNAP25].

Homeovitality® had some DNA sequences made for each of these genes: a 164 bp fragment in the case of CRM2 and a 144 bp fragment in the case of SNAP-25 [What is Homeovitality®?]. They used these pieces of DNA to make the Super Memory/IQ product.

Homeovitality® products have also been succussed at each dilution stage so they will also help to promote desirable forms of hybrid vigour in a “like promotes like” mode of action involving some of the mechanisms (4) described by Dr. Kratz, (http://kulisz.com/how_does_homeopathy_work.htm).

Homeovitality® products are safe because firstly, they are used at similar dilutions to classical homeopathic disease remedies and secondly, hybrid vigour is a completely natural biological process that has been developed by nature over millions of years to enable all creatures to enjoy “super health” and disease resistance.

"Succussed refers to the practice of forcefully striking the various dilution solutions in order to help "potentize" the effect. "Hybrid vigor" refers to the belief that these DNA sequences—or, more appropriately, the memory of these sequences—will produce heterozygosity in patients and that's a good thing.

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Lance Corporal Robert Alexander Hood (1895 - 1917)

Robert Alexander Hood¹ was born in 1895 in a small village north-west of Waterloo, Ontario, Canada. He went to France in 1916 when he was only 21 years old. Robert fought with the 73rd Battalion and he was killed in action at Vimy Ridge on this day, April 12, in 1917.

Canadians "celebrate" the battle of Vimy Ridge as a great Canadian victory. It was part of the larger Battle of Arras, which in turn was a diversionary attack in support of the larger Nivelle Offensive carried out by the French Army. About 3,600 young Canadian men were killed during the four day battle and 7,000 more were wounded. This is just a small fraction of the casualties on both sides during World War I.

We need to be very careful not to glorify war while remembering all those young mean and women who died in a war that never should have been fought. I will eventually go to Arras and visit the large memorial erected by the Canadian government (see below) but I will do it in order to reinforce my view that war is folly and the deaths of soldiers like Robert Alexander Hood should never have happened.

There is never any glory in war and it's nothing we should ever be proud of.

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1. He was a cousin of Ms. Sandwalk's grandfather.

The "Science" Behind Homeopathy

 
Are all homeopaths and their supporters complete idiots? Do they all think they're practicing some form of black magic? No, they usually don't think that at all. Many of them honestly believe that there's scientific evidence supporting homeopathy. They actually believe that water can retain some magical properties after it has been exposed to certain chemicals. How is this possible? It's because of "nanobubbles."

Here's John Benneth explaining the "science" behind homeopathy. This is woo of the highest order. Read Orac's take-down at Your Friday Dose of Woo: The physics of homeopathy and "nanocrystalloids". There are no reputable scientists who believe what John Benneth claims. If he's implying that there's scientific support for homeopathy, then what he's saying is not true.

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Homeopathy Kills

 
Here's what can happen if a homeopath treats his own daughter. He ends up in jail, she ends up dead.

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