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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Don't Call It "Darwinism"

 
Eugenie C. Scott and Glenn Branch have written an article for the latest issue of Evolution: Education and Outreach in which they urge everyone to talk about evolutionary biology but Don’t Call it “Darwinism”.

Using “Darwinism” as synonymous with “evolutionary biology” is thus a touch unfair to the men and women who have contributed to the scientific edifice to which Darwin provided the cornerstone, including (to name a few) Wallace, Huxley, Weisman, De Vries, Romanes, Morgan, Weidenreich, Teilhard, von Frisch, Vavilov, Wright, Fisher, Muller, Haldane, Dobzhansky, Rensch, Ford, McClintock, Simpson, Hutchinson, Lorenz, Mayr, Delbrück, Jukes, Stebbins, Tinbergen, Luria, Maynard Smith, Price, Kimura, Ostrom, Wilson, Hamilton, and Gould, to say nothing of even more who are still contributing to evolutionary biology. As Olivia Judson (2008) recently commented, terms like “Darwinism” “suggest a false narrowness to the field of modern evolutionary biology, as though it was the brainchild of a single person 150 years ago, rather than a vast, complex and evolving subject to which many other great figures have contributed.”

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Darwin: "I am fully convinced that species are not immutable ..."

 
One of the most famous passages in Origin of Species can be found at the end of the introduction where Darwin makes it very clear that his ideas are meant to challenge special creation.

Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgement of which I am capable, that the view which most naturalists entertain, and which I formerly entertained — namely, that each species has been independently created — is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

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Darwin on Variation

 
Variation, or what we might call mutation, is the raw material on which natural selection acts. Charles Darwin demonstrated that variation was common in many species but he did not know the cause. It wasn't until fifty years after the publication of Origin of Species that geneticists began to understand that mutations were random and spontaneous.

Today we know that most mutations result from errors in replicating DNA and that they arise independently of any effect they might have on the organism.

Here's how Darwin thought of variation in Chapter V: Laws of Variation. He believed that variations arose as a result of the conditions of life and that some variations were due to the use or disuse of organs.

I HAVE hitherto sometimes spoken as if the variations so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation. Some authors believe it to be as much the function of the reproductive system to produce individual differences, or very slight deviations of structure, as to make the child like its parents. But the much greater variability, as well as the greater frequency of monstrosities, under domestication or cultivation, than under nature, leads me to believe that deviations of structure are in some way due to the nature of the conditions of life, to which the parents and their more remote ancestors have been exposed during several generations.

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Dawkins on Darwin

 
Here's a series of videos from the National Geographic Channel. Richard Dawkins explains ...

1. The Importance of Charles Darwin
2. Fossils and Darwin
3. Why Darwin Was Right
4. On Creationism
5. On God and the Universe

Each one is only about 2 minutes long. They are all excellent. Everyone should watch them and learn.

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[Hat Tip: RichardDawkins.net]

National Geographic: What Darwin Didn't Know

 
The main article in the February issue of National Geographic is by science writer Matt Ridley and it's title is Modern Darwins. Here's a quick summary of the article.

Charles Darwin didn't know about DNA so he wasn't aware of the power of molecular evolution and he didn't know that we could trace ancestry by comparing sequences.

Darwin didn't know that we would be able to identify and isolate the genes responsible for natural selection.

Darwin's greatest idea was that natural selection is largely responsible for the variety of traits one sees among related species. Now, in the beak of the finch and the fur of the mouse, we can actually see the hand of natural selection at work, molding and modifying the DNA of genes and their expression to adapt the organism to its particular circumstances.

So Darwin was right about the idea that natural selection is the mechanism that generates most traits among related species.

Darwin thought that evolution was slow but we now know that it can occur very quickly.

Darwin didn't know about the FOXP2 gene.

Darwin was right about sexual selection.

Darwin didn't know that his blue eyes were due to a mutation in the OCA2 gene but he would be happy to know that the trait probably spread by sexual selection.

Darwin didn't know about genetic switches and he didn't know that changes in gene expression could explain the "humiliating surprise" that we have the same number of genes as a mouse.

Darwin didn't know about Tiktaalik, a transitional fossil that show how fish evolved into amphibians.

Darwin's biggest mistake was his messy ideas about genetics. He didn't know about Mendel and particulate inheritance.

That's about it. Apparently Darwin knew about everything else.

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