Not Saint Darwin

 
John Wilkins has posted a link to his essay in Resonance. Go to his blog (Evolving Thoughts), click on the link, read, and enjoy.

I can't think of an essay/article that better captures the essential reason why Darwin made such an important contribution to science. It takes a philosopher to make the case.¹

Here's a teaser ... there's much more were this comes from ....

What we remember Darwin for is a synthesis and the empirical support he brought in its defense. He brought together many ideas that were `in the air', so to speak, reading more widely than almost anyone else as well as doing his experimental and anatomical work, and more importantly, managed to filter out most of the bad ideas.

Darwin's achievement was to identify crucial questions and offer a coherent theoretical account that answered them . For instance, in the first half of the nineteenth century, the reasons for the systematic arrangements of plants and animals, why they were arranged 'group with in group' as he put it, was being explored by idealists like William Swainson [12] and William Macleay [13], who offered Pythagorean accounts based on similarities and magic numbers. Darwin offered a general account—which we call common descent—that explained why this was a fact, but also why it was not regular (for example, extinction is not evenly distributed across all groups).

The broader point I want to make here is about the nature of science. Often as not, it is the synthesizers who reorganize how we view things, and as David Hull [14] and others (e.g., Ellegard [15]) have shown, within ten years of the publication of the Origin, nearly all specialists in the sciences concerned had adopted common descent and transmutation (descent with modification). It was the closest any science has ever come to an actual Kuhnian paradigm shift.

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1. Perhaps I should say a "good" philosopher since there are others (Dennett, Ruse) who seem to have missed the point.

Evolution is not "survival of the fittest"

 
By the 6th edition of Origin of Species Darwin had begun to adopt the term "survival of the fittest" and a synonym for "natural selection." His decision was prompted by several colleagues, notably Alfred Russel Wallace. The term "survival of the fittest had recently been coined by Herbert Spencer.

Unfortunately, modern society interprets "survival of the fittest" to mean that only the strong survive. They think of evolution in terms of a winner take all competition between the weak and the strong.

I was reminded of this misconception a few nights ago at our book club meeting. We were discussing Origin of Species and every single member of the group viewed evolution in these terms. Much of the discussion was about the future of human evolution and the book club members were fixated on what kind of mutations would make us stronger and better. What would happen to the poor individuals who couldn't compete?

Michael Shermer has written a nice article in the latest issue of Scientific American: A Skeptic's Take on the Public Misunderstanding of Darwin. His main point deserves to be widely publicized.

Natural selection simply means that those individuals with variations better suited to their environment leave behind more offspring than individuals that are less well adapted. This outcome is known as “differential reproductive success.” It may be, as the second myth holds, that organisms that are bigger, stronger, faster and brutishly competitive will reproduce more successfully, but it is just as likely that organisms that are smaller, weaker, slower and socially cooperative will do so as well.

This second notion in particular makes evolution unpalatable for many people, because it covers the theory with a darkened patina reminiscent of Alfred, Lord Tennyson’s “nature, red in tooth and claw.” Thomas Henry Huxley, Darwin’s “bulldog” defender, promoted this “gladiatorial” view of life in a series of popular essays on nature “whereby the strongest, the swiftest, and the cunningest live to fight another day.” The myth persists. In his recent documentary film Expelled: No Intelligence Allowed, Ben Stein linked Darwinism to Communism, Fascism and the Holocaust.

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Jerry Coyne on Darwinism

Jerry Coyne is an adaptationist. Thus, it comes as no great surprise that he is comfortable with equating evolutionary biology and Darwinism. Here's what he writes in defense of Carl Safina's New York Times article [Darwinism must die????].

Well, how much confusion has really been caused by using the term “Darwinism”? How many people have been made to think that we biologists adhere to an ideology rather than a strongly supported theory?

That's a tough question. I'd estimate it at about 3 billion but I could be off by a factor of two.

Would creationism and its country cousin, intelligent design, suddenly vanish if we started using the terms “modern evolutionary theory” (ugh!) or the insidious-sounding “neoDarwinism”? I don’t think so.

Nope. The problem isn't so much how the IDiots interpret the term "Darwinism," it's how the average evolution supporter interprets it. The average person seems to be completely unaware of the fact that natural selection doesn't explain everything about common descent. They are surprised to learn that many modern scientist are not adaptationists or confirmed traditional Darwinists.

“Darwinism” is a compact, four-syllable term for “modern evolutionary theory,” which is ten syllables long.

No it is not. Nobody in their right mind would claim that random genetic drift—the dominant mechanism of evolution—is Darwinian. Nobody in their right mind would suggest that it is just a slight modification of natural selection.

Today we know that new beneficial mutations have only a slight chance of becoming fixed in a population. We know that deleterious mutations can become fixed. And we know that a large percentage of mutations are completely invisible to natural selection but they can, nevertheless, become fixed.

Ryan Gregory made the same point in his posting: Jerry Coyne on Darwinism. So did Eugenie C. Scott and Glenn Branch in Don't Call it "Darwinism".

Jerry Coyne is not stupid. He's well aware of the fact that Darwin didn't know everything. But according to Coyne, the expansion of evolutionary theory hasn't amounted to anything more than simple "refinement" and the term "Darwinism" still encompasses the essence of modern evolutionary theory.

Apparently Coyne has an article about to appear in Current Biology where he says ....

Still, these advances amount to refinements of Darwinism rather than its Kuhnian overthrow. Evolutionary biology hasn’t suffered the equivalent of quantum mechanics. But some biologists, chafing in their Darwinian straitjacket, periodically announce new worldviews that, they claim, will overturn our view of evolution, or at least force its drastic revision. During my career I have heard this said about punctuated equilibrium, molecular drive, the idea of symbiosis as an evolutionary force, evo-devo, and the notion that evolution is driven by the self-organization of molecules. Some of these ideas are worthwhile, others simply silly; but none do more than add a room or two to the Darwinian manse. Often declared dead, Darwinism still refuses to lie down. So by all means let’s retain the term. It is less of a jawbreaker than “modern evolutionary biology,” and has not, as was feared, misled people into thinking that our field has remained static since 1859. What better honorific than “Darwinism” to fête the greatest biologist in history?

This is a remarkable bit of writing. Every modern textbook on evolution has a large section devoted to random genetic drift as a fundamental mechanism of evolution and yet Coyne doesn't even mention it. He also doesn't mention population genetics. Isn't that strange?

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Kill all the science writers?

 
Several bloggers are upset enough at Carl Safina that they have posted detailed critiques of his article in the New York Times: Darwinism Must Die So That Evolution May Live.

I not so upset. In fact I mostly agree with the opening paragraphs of Safina's article ...

Equating evolution with Charles Darwin ignores 150 years of discoveries, including most of what scientists understand about evolution. Such as: Gregor Mendel’s patterns of heredity (which gave Darwin’s idea of natural selection a mechanism — genetics — by which it could work); the discovery of DNA (which gave genetics a mechanism and lets us see evolutionary lineages); developmental biology (which gives DNA a mechanism); studies documenting evolution in nature (which converted the hypothetical to observable fact); evolution’s role in medicine and disease (bringing immediate relevance to the topic); and more.

By propounding “Darwinism,” even scientists and science writers perpetuate an impression that evolution is about one man, one book, one “theory.” The ninth-century Buddhist master Lin Chi said, “If you meet the Buddha on the road, kill him.” The point is that making a master teacher into a sacred fetish misses the essence of his teaching. So let us now kill Darwin.

However, it gets worse from then on and this opens the door for serious criticism. Read P.Z. Myers (Darwin is already dead, and we know it) and John Pieret (Charles Darwin Superstar).

I especially like one of the paragraphs from John's posting¹ ...

Science writers are a different matter altogether, however. But why should Darwin suffer for their sins? Wouldn't the more efficacious solution be to kill all the science writers? It would at least make a refreshing change from lawyers.

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1. John is a lawyer.

Fire the Professors!

 
Colleges and universities in Georgia (USA) have faculty members who are experts on human sexual behavior. Horrors!

Here's what one state legislator thinks they should do about it. Wait 'till Ben Stein hears about this!

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[Hat Tip: Reed Cartwright on De Rerum Natura]

Darwin: Difficulties on Theory

 
Darwin devoted an entire chapter (Chapter VI) to Difficulties on Theory. This is a remarkable chapter since it addresses head-on the most serious objections to his theory of natural selection.

We'd like to think that this behavior—bringing up objections to your ideas—is standard operating procedure for most scientists but, alas, it is a lost art. You would be hard pressed to find a modern science book where an author makes an effort to address criticisms in a fair and rational manner.

Long before having arrived at this part of my work, a crowd of difficulties will have occurred to the reader. Some of them are so grave that to this day I can never reflect on them without being staggered; but, to the best of my judgment, the greater number are only apparent, and those that are real are not, I think, fatal to my theory.

These difficulties and objections may be classed under the following heads:-Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?

Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some animal with wholly different habits? Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?

Thirdly, can instincts be acquired and modified through natural selection? What shall we say to so marvellous an instinct as that which leads the bee to make cells, which have practically anticipated the discoveries of profound mathematicians?

Fourthly, how can we account for species, when crossed, being sterile and producing sterile offspring, whereas, when varieties are crossed, their fertility is unimpaired?

The rest of the chapter is a discussion of possible explanations to account for the first two difficulties. The two others are addressed in separate chapters (Chaper VII: Instinct and Chapter VIII: Hybridism).

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Monday's Molecule #107: Winners

 
The red arrow points to a lysosome and the blue arrows identify peroxisomes. The man who discovered and characterized these organelles is Christian de Duve (1974)

This week's winners are regulars: Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto.

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This Monday's "molecule" looks a lot like an electron micrograph of a cell instead of a molecule. That's because it's hard to connect a specific molecule with some Nobel Laureates. Your task today is to identify the two things identified by the red and blue arrows.

There's one Nobel Laureate who is closely identified with the discovery of these two things. Name this Nobel Laurete.

The first person to identify the images and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are eight ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Maria Altshuler of the University of Toronto, Ramon, address unknown, Jason Oakley of the University of Toronto, John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), Wesley Butt of the University of Toronto, David Schuller of Cornell University, and Nova Syed of the University of Toronto.

Bill, John, and David have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

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Westminster Abbey: Darwin vs Newton

 
Charles Darwin died on April 19, 1882. His friends arranged for him to be buried in Westminster Abbey, an honor befitting the greatest scientist who ever lived.

Here's a excerpt from the Westminster Abbey website [Charles Darwin].

The Dean of Westminster, George Granville Bradley, was away in France when he received a telegram forwarded from the President of the Royal Society in London saying “…it would be acceptable to a very large number of our fellow-countrymen of all classes and opinions that our illustrious countryman, Mr Darwin, should be buried in Westminster Abbey”. The Dean recalled “ I did not hesitate as to my answer and telegraphed direct…that my assent would be cheerfully given”. The body lay overnight in the Abbey, in the small chapel of St Faith, and on the morning of 26 April the coffin was escorted by the family and eminent mourners into the Abbey. The pall-bearers included Sir Joseph Hooker, Alfred Russel Wallace, James Russell Lowell (U.S. Ambassador), and William Spottiswoode (President of the Royal Society).

The burial service was held in the Lantern, conducted by Canon Prothero, with anthems sung by the choir. The chief mourners then followed the coffin into the north aisle of the Nave where Darwin was buried next to the eminent scientist Sir John Herschel, and a few feet away from Sir Isaac Newton. The simple inscription on his grave reads “CHARLES ROBERT DARWIN BORN 12 FEBRUARY 1809. DIED 19 APRIL 1882”. Although an agnostic, Darwin was greatly respected by his contemporaries and the Bishop of Carlisle, Harvey Goodwin, in a memorial sermon preached in the Abbey on the Sunday following the funeral, said “I think that the interment of the remains of Mr Darwin in Westminster Abbey is in accordance with the judgment of the wisest of his countrymen…It would have been unfortunate if anything had occurred to give weight and currency to the foolish notion which some have diligently propagated, but for which Mr Darwin was not responsible, that there is a necessary conflict between a knowledge of Nature and a belief in God…”.

Darwin's grave is simple and very much in keeping with typical British understatement. Everyone knows who Charles Darwin is. It occupies a prime location near many other scientists. Unfortunately, it is not as close to the grave of Charles Lyell as Emma Darwin would have liked.

Isaac Newton is buried nearby. His tomb is a little more gaudy and glittery than Darwin's as if his supporters needed to prove something that wasn't obvious.

Here's another image of Newton's tomb. You can't image anyone writing a book about how Charles Darwin was part of a conspiracy to protect the descendants of Jesus, can you? Somehow this seems perfectly believable for Newton.

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Books by Charles Darwin

 
Most people don't seem to appreciate the depth and breadth of Darwin's work. Someone posted a comment on a recent Sandwalk thread arguing that Darwin was a "one trick pony" compared to Isaac Newton. This is hard to justify when you scan the variety of scientific articles that Darwin published in his lifetime and you consider the record of his scientific correspondance—much of which has been preserved.

But setting all that aside, the list of books that he published gives us a fair impression of the range of subjects that Darwin covered. I'm not even sure that this list is complete.

This list of Darwin's books is not meant to belittle the contributions of Isaac Newton, that other contender for world's best scientist. After all, we all know that in addition to Principia, Newton also wrote numerous works on the interpretation of the Bible (e.g. Observations on Daniel and The Apocalypse of St. John (1733)) and he spent a lot of time studying alchemy. Newton predicted that the world would end in 2060 and Newton followers will no doubt become very anxious as we approach that date.

Books by Charles Darwin

• The structure and distribution of coral reefs. Being the first part of the geology of the voyage of the Beagle, under the command of Capt. Fitzroy, R.N. during the years 1832 to 1836. (1842)


• Geological observations on the volcanic islands visited during the voyage of H.M.S. Beagle, together with some brief notices of the geology of Australia and the Cape of Good Hope. Being the second part of the geology of the voyage of the Beagle, under the command of Capt. Fitzroy, R.N. during the years 1832 to 1836. (1844)


• Geological observations on South America. Being the third part of the geology of the voyage of the Beagle, under the command of Capt. Fitzroy, R.N. during the years 1832 to 1836. (1846)


• Narrative of the surveying voyages of His Majesty's Ships Adventure and Beagle between the years 1826 and 1836, describing their examination of the southern shores of South America, and the Beagle's circumnavigation of the globe. (1839)


• A monograph of the sub-class Cirripedia, with figures of all the species. The Lepadidae; or, pedunculated cirripedes. [Vol. 1] (1851)


• A monograph of the sub-class Cirripedia, with figures of all the species. The Balanidae, (or sessile cirripedes); the Verrucidae. [Vol. 2] (1854)


• A monograph on the fossil Lepadidae, or, pedunculated cirripedes of Great Britain. [Vol. 1] (1851)


• A monograph on the fossil Balanidae and Verrucidae of Great Britain. [Vol. 2] (1855)


• On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (1st ed.) (1859), 2nd ed (1860). 3rd ed. (1861) , 4th ed. (1866), 5th ed. (1869), 6th ed. (1872)


• On the various contrivances by which British and foreign orchids are fertilised by insects. (1862), 2nd ed. (1877)


• The expression of the emotions in man and animals. (1872)


• Insectivorous plants. (1875), 2nd. ed. (1888)


• The movements and habits of climbing plants. (1875)


• The effects of cross and self fertilisation in the vegetable kingdom. (1876), 2nd ed. (1878)


• The variation of animals and plants under domestication. (1868), 2nd ed. (1875)


• The Descent of Man, and Selection in Relation to Sex (1st ed.) (1871), 2nd ed. (1882)


• The Expression of the Emotions in Man and Animals. (1872)


• The structure and distribution of coral reefs. 2d ed. (1872)


• Geological observations on the volcanic islands and parts of South America visited during the voyage of H.M.S. 'Beagle'. 2d ed. (1876)


• The power of movement in plants. (1880)


• The formation of vegetable mould, through the action of worms. (1881)


• The Autobiography of Charles Darwin 1809–1882. (unpublished until 1958)

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Who is this man, and why is he smiling?

 
Find out in today's Toronto Star [Darwin still spurs tributes, debates].

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Evolution of Pine Genomes

 
There are about 120 species of pine trees (genus Pinus). Their genome sizes range from 18,000 Mbp to 40,000 Mbp, which is about 6x - 13x the size of mammalian genomes.

In some species the increase in genome size among closely related species is due to polyploidization but that's not the case with pine species. All of them have 24 chromosomes and the differences in DNA content are due to increases in the lenghts of the chromosomes.

It's possible that different species of pine could have larger or smaller gene families. This would mean that the species with larger genomes have many more copies of some genes than species with smaller genomes. However, this is unlikely to account for much of the difference since simultaneous duplication events in all parts of the genome.

The most logical explanation is an increase in the amount of junk DNA, specifically the number of retrotransposons. Flowering plants have retrotrapsposons with long terminal repeats (LTRs) just like those found in animal genomes [Junk in your Genome: LINEs].

Morse et al. (2009) have studied the retrotransposons in Pinus taeda and related species. The discovered a new retrotransposon family called Gymny that appears to be confined to Pinus taeda and very closely related members of the same subgenus. Each Gymny element is 6.2 kb in length and the genome contains about 22,000 copies. The total amount of Gymny DNA is equivalent to the size of the Arabidopsis genome (157 Mbp).

In addition to the full length copies there are many fragments of Gymny retrotransposons and probably many degenerated copies that can no longer be readily detected. The copies are spread out over all chromosomes as shown in the photograph. (Gymny sequences are stained red.)

In addition to Gymny, the authors also found other abundant retrotransposons in the Pinus taeda genome (e.g. Gyspy and Copia) but the Gymny elements appear to be confined to a subset of species in the Pinus genus. They are not found in other flowering plants.

The evolutionary history of these Pinus species suggests that there was a huge expansion of Gymny elements about 50 Myr ago and the expansion of retrotransposons accounts for much of the increase in genome size among these species.

There are now several examples of genome size increase due to expansion in the number of retrotransposons. The authors discuss several of these previously known cases.

It is difficult to imagine how a huge increase in the amount of retrotransposon DNA could be a selective advantage in some species. The most reasonable explanation is that these sequences play no significant role in the life of the organism. It's just junk DNA that's not harmful.

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[Photo Credit: Pinus taeda, loblolly pine]

Morse, A.M., Peterson, D.G., Islam-Faridi ,M.N., Smith, K.E., Magbanua, Z., et al. (2009) Evolution of Genome Size and Complexity in Pinus. PLoS ONE 4(2): e4332. [doi:10.1371/journal.pone.0004332]

The Bishop Is Offended

 
Donate to The Canadian Atheist Bus Campaign and get those atheist signs on Canada's buses and subways.

It's going to happen in Toronto, and Calgary is probably the next city according to the Freethought Association. An article in last week's Calgary Herald highlights some of the opposition to the atheist campaign [Calgary next for atheist bus ads, activist group says].

Calgary Catholic Bishop Fred Henry said the ideal date to launch such a campaign would be April Fool's Day.

"I don't know what the norms Calgary Transit uses to accept advertising, but if the benchmark is that it should be non-offensive, I'm offended," said Henry.

"This is insulting to us. The interfaith dialogue that goes on in this city is characterized by deep respect for all the individual players."

Henry characterized the ad's message as aggressive, inward-looking, self-indulgent and narcissistic.

"Aggressive, inward-looking, self-indulgent and narcissistic," now that's offensive. Is this what Bishop Henry means by "deep respect for all the individual players"?

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[Hat Tip: Jeffrey Shallit at Recursivity.]

Tour Darwin's House

 
Down House, home of Charles Darwin, has been closed for renovations but it reopens this week in time to celebrate Darwin's birthday. You can take a video tour on the BBC website [At home with Darwin... 200 years on].

Of course there's nothing like being there yourself and walking on the Sandwalk. I went with a friend¹ in 2006 and I'd love to go back.

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1. I've been there!.

Monday's Molecule #107

 
This Monday's "molecule" looks a lot like an electron micrograph of a cell instead of a molecule. That's because it's hard to connect a specific molecule with some Nobel Laureates. Your task today is to identify the two things identified by the red and blue arrows.

There's one Nobel Laureate who is closely identified with the discovery of these two things. Name this Nobel Laurete.

The first person to identify the images and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are eight ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Maria Altshuler of the University of Toronto, Ramon, address unknown, Jason Oakley of the University of Toronto, John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), Wesley Butt of the University of Toronto, David Schuller of Cornell University, and Nova Syed of the University of Toronto.

Bill, John, and David have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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Darwin on Uniformitarianism

 
Charles Darwin was a fan of Charles Lyell (1797 - 1875). Lyell's three volume work Principles of Geology did much to convince Darwin that the Earth was very old and that geological change took place slowly over the course of millions of years. This principle of slow, gradual change is called uniformitarianism and it was meant to refute the idea that major geological structures are the result of sudden catastrophic events. Lyell's geology is inconsistent with a great deluge.

Darwin saw his efforts to explain evolution and refute special creation as a way to incorporate uniformitarianism into biology. In Chapter IV: Natural Selection he writes,

I am well aware that this doctrine of natural selection, exemplified in the above imaginary instances, is open to the same objections which were at first urged against Sir Charles Lyell's noble views on 'the modern changes of the earth, as illustrative of geology;' but we now very seldom hear the action, for instance, of the coast-waves, called a trifling and insignificant cause, when applied to the excavation of gigantic valleys or to the formation of the longest lines of inland cliffs. Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications, each profitable to the preserved being; and as modern geology has almost banished such views as the excavation of a great valley by a single diluvial wave, so will natural selection, if it be a true principle, banish the belief of the continued creation of new organic beings, or of any great and sudden modification in their structure.

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