Sandwalk

Tuesday, February 10, 2009

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).

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.

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.

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.

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)

Monday, February 09, 2009

Who is this man, and why is he smiling?

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

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.

[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"?

[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.

1. I've been there!.

Monday's Molecule #107

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.

Sunday, February 08, 2009

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.”

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.

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.

Dawkins on Darwin

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

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

[Hat Tip: RichardDawkins.net]

Saturday, February 07, 2009

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.

Darwin's Tree of Life

On reading Origin of Species one can't help but be struck by Darwin's insight and intellect. His description of the tree of life from the summary of Chapter 4: Natural Selection is just one example.

As you read the passage, note how Darwin emphasizes competition between species. This was an important theme in Origin of Species. Modern evolutionary theory tends to describe natural selection as a competition between individuals within a species.

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.

Friday, February 06, 2009

What Causes Speciation?

The latest issue or Science magazine contains a number of articles on speciation.

The one that most interests me is Schluter (2009), a paper that discusses mechanisms of speciation. Schulter begins with ...

It took evolutionary biologists nearly 150 years, but at last we can agree with Darwin that the origin of species, "that mystery of mysteries" (1), really does occur by means of natural selection (2–5). Not all species appear to evolve by selection, but the evidence suggests that most of them do. The effort leading up to this conclusion involved many experimental and conceptual advances, including a revision of the notion of speciation itself, 80 years after publication of On the Origin of the Species, to a definition based on reproductive isolation instead of morphological differences (6, 7).

I've heard this a lot recently but it doesn't make sense to me. How could the evolution of reproductive isolation be selected?

The main question today is how does selection lead to speciation? What are the mechanisms of natural selection, what genes are affected, and how do changes at these genes yield the habitat, behavioral, mechanical, chemical, physiological, and other incompatibilities that are the reproductive barriers between new species? As a start, the many ways by which new species might arise by selection can be grouped into two broad categories: ecological speciation and mutation-order speciation. Ecological speciation refers to the evolution of reproductive isolation between populations or subsets of a single population by adaptation to different environments or ecological niches (2, 8, 9). Natural selection is divergent, acting in contrasting directions between environments, which drives the fixation of different alleles, each advantageous in one environment but not in the other. Following G. S. Mani and B. C. Clarke (10), I define mutation-order speciation as the evolution of reproductive isolation by the chance occurrence and fixation of different alleles between populations adapting to similar selection pressures. Reproductive isolation evolves because populations fix distinct mutations that would nevertheless be advantageous in both of their environments. The relative importance of these two categories of mechanism for the origin of species in nature is unknown.

Is there an expert on speciation out there who can explain this? I understand how two incipient species can adapt to different environments and become morphologically distinct but I don't understand how this kind of adaptation leads to selection for reproductive isolation. This is a problem that we discussed earlier [Testing Natural Selection: Part 2].

The second mechanism is even more difficult for me. I understand how chance mutations can arise and become fixed but to my mind this isn't natural selection. It's speciation by random genetic drift. It's just an accident that the mutations being fixed in the separated populations happen to lead to reproductive isolation.

Schluter tells us that mutation-order speciation is "distinct from genetic drift." He seems to refer to it as "selection" of some sort without explaining why. ("The unidentified component of speciation, if built by selection and not genetic drift, could be the result of either ecological or mutation-order mechanisms.") He says that the mutations that give rise to reproductive isolation are "advantageous" in both populations but they just happened to occur in one of them and not the other. Again, the question is what sort of mutations favoring reproductive isolation would be "advantageous," and therefore selected?

If the mutation arises later on in the other species will it sweep to fixation and remove the reproductive isolation barrier?

It's not clear to me that we have identified the mechanisms of reproductive isolation in a large number of examples. Schluter seems to agree,

The most obvious shortcoming of our current understanding of speciation is that the threads connecting genes and selection are still few. We have many cases of ecological selection generating reproductive isolation with little knowledge of the genetic changes that allow it. We have strong signatures of positive selection at genes for reproductive isolation without enough knowledge of the mechanisms of selection behind them. But we hardly have time to complain. So many new model systems for speciation are being developed that the filling of major gaps is imminent. By the time we reach the bicentennial of the greatest book ever written, I expect that we will have that much more to celebrate.

Given our lack of knowledge how can biologists be so confident that Darwin was right? How do they know that most speciations are due to natural selection and not random genetic drift—especially since drift and accident seem to be intuitively more likely?

Is this an example of adaptationist bias or is there really lots of evidence to support speciation by natural selection?

Schluter, D. (2009) Evidence for Ecological Speciation and Its Alternative. Science 323: 737 - 741 [DOI: 10.1126/science.1160006]

Evolution Explains Taxonomy

Charles Darwin advanced many different arguments in support of his claim that life has evolved. One of the most potent arguments is that evolution explains the classification scheme proposed by Linnaeus and used by all naturalists in the early part of the nineteenth century.

The following passage is from the summary of Chapter 4: Natural Selection in Origin of Species.

It is a truly wonderful fact the wonder of which we are apt to overlook from familiarity that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold namely, varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. The several subordinate groups in any class cannot be ranked in a single file, but seem rather to be clustered round points, and these round other points, and so on in almost endless cycles. On the view that each species has been independently created, I can see no explanation of this great fact in the classification of all organic beings; but, to the best of my judgment, it is explained through inheritance and the complex action of natural selection, entailing extinction and divergence of character, as we have seen illustrated in the diagram.

Nature tells the world scientific community about Canada's lack of support for science

The latest issue of Nature reports on Prime Minister Stephen Harper's plan to slash the budgets of the major granting agencies [Cash concerns for Canadian scientists].

Billions of dollars in science infrastructure investments have been overshadowed by cuts to major grant-funding programmes in Canada's federal budget....

Although the budget does contain Can$87.5 million for graduate-student scholarships, the research community is perplexed by the government's decision to cut funding to Canada's three federal granting councils. Over three years, the budgets of the Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council and the Social Sciences and Humanities Research Council will be reduced by almost Can$148 million. "It's an unfortunate consequence of getting poor advice or not listening to good advice," says Aled Edwards, a structural biologist at the University of Toronto, Ontario, and director and chief executive of the international Structural Genomics Consortium. He argues that the most efficient way to invest in research is through the funding councils, where peer review determines where the dollars are spent....

But the long-term effect of cutting funds for research may be that Canadian scientists will take their research south of the border, says Edwards. Canada's research funding pales in comparison with that in the United States, and the latest budget threatens to widen the gap between the two countries, he adds. "We're at serious risk of a brain drain."

Thursday, February 05, 2009

Nobel Laureates: John B. Fenn and Koichi Tanaka

The Nobel Prize in Chemistry 2002.

"for their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules"

John B. Fenn (1917 - ) and Koichi Tanaka (1959 - ) were awarded the Nobel Prize for developing techniques using mass spectrometry to determine the molecular mass of proteins and peptides. Here's the Press Release describing their achievements.

THEME:
Nobel Laureates

Mass spectrometry is a very important analytical method used in practically all chemistry laboratories the world over. Previously only fairly small molecules could be identified, but John B. Fenn and Koichi Tanaka have developed methods that make it possible to analyse biological macromolecules as well.

In the method that John B. Fenn published in 1988, electrospray ionisation (ESI), charged droplets of protein solution are produced which shrink as the water evaporates. Eventually freely hovering protein ions remain. Their masses may be determined by setting them in motion and measuring their time of flight over a known distance. At the same time Koichi Tanaka introduced a different technique for causing the proteins to hover freely, soft laser desorption. A laserpulse hits the sample, which is “blasted” into small bits so that the molecules are released.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Darwin Birthday Party in Toronto

Darwin Birthday Party

Starts: Friday, February 13th 2009 at 5:30 pm
Ends: Friday, February 13th 2009 at 7:00 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

Come celebrate Darwin's Birthday! There will be cake, games and a toast to one of the greatest men in science who ever lived. Stick around for the Pre and Post Darwin Science talks that follow.

A CFI Members Exclusive Activity!

Pre- and Post-Darwinian Science

Starts: Friday, February 13th 2009 at 7:00 pm
Ends: Friday, February 13th 2009 at 9:30 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

What was science like before Darwin, and how did it change after Darwin?

Larry Moran will be discussion our modern scientific world in light of the impact Darwin and his theory of evolution due to natural selection has had on it.

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto.

$5, $3 for students and FREE for Friends of the Centre

Wednesday, February 04, 2009

Genomics, Proteomics and Mass Spectrometry

The explosion in sequence information as a result of various genome projects has resulted in many unexpected payoffs. One of them has to do with the identification of tiny amounts of unknown protein.

Many experiments in biochemistry and molecular biology lead to the recognition of a novel protein that hasn't been identified. For example, one could go fishing for proteins that bound to other proteins or look at the protein composition of various complexes.

Often the only thing one knows about the protein is its molecular weight on an SDS gel. You can cut out the band containing your protein of interest and extract the protein but that only gives you a tiny amount of denatured protein.

With the development of protein mass spectrometry it becomes possible to determine an accurate molecular weight of the protein [Biochemistry and Mass Spectrometry]. In theory, one could then compare this molecular weight to all the calculated molecular weights of all the proteins encoded in the genome. These calculated molecular weights can be determined from the genome sequence—if you're lucky enough to be working with an organism whose genome has been completely sequenced.

Unfortunately, there are many proteins with similar molecular weights so this straightforward technique doesn't work. However, if you digest the protein with enzymes that cut it several times at specific sites, you create group of peptide fragments. The molecular weights of the peptides can be determined by mass spec and the "fingerprint" of your unknown protein can be compared to calculated fingerprints of every protein in the proteome.

Here's an example of a tryptic digest of an unknown human protein of M_r = 90,000. The sizes of the various fragments can be measured accurately and compared to the predicted fragment sizes based on the known DNA sequence of the gene. If you're lucky, there is only one protein that will give rise to the observed peptides. Thus, the unknown protein can be unambiguously identified from the mass of its peptides.

In this case, the protein is Hsp90. As you might have guessed, the success of this techniques owes almost as much to the development of efficient software and databases as it does to the advances in mass spectroscopy.

The technique is powerful but the equipment is expensive and requires well-trained technicians.

There are many different kinds of mass specs and every lab will have its own customized setup. The one shown here belongs to Joseph Loo of Chemistry & Biochemistry, UCLA (Los Angeles, CA, USA). I "borrowed" it from his website [Joseph Loo].

Modern research facilities will have access to special labs where protein fingerprinting is routinely performed. In some cases, a major facility will serve as a regional center for analyses and charge a fee ($50-150) for each sample.

The image of the tryptic peptides of Hsp90, above, are from the website of such a facility in the Department of Biochemistry at the University of Buffalo (Buffalo, NY, USA) [Proteomic Capabilities]. Now that you know how the technique works, the description on their website will look much less intimidating.

The MALDI-TOF facility housed in the Department of Biochemistry provides access to mass spectrometric fingerprinting of unknown proteins. MALDI-TOF (Matrix-assisted, Laser-Desorption-Ionization/Time of flight) mass spectrometry is presently the method of choice for identification of unknown proteins via mass analysis of proteolytic peptides, and for characterization of post-translational modifications. This technique is rapid, highly sensitive, and applicable to a wide variety of research problems. Applications include direct characterization of mutated proteins, estimating the extent of protein derivatization (e.g., biotinylation), and identification of unknown proteins isolated from polyacrylamide gels. Depending on the specific application and complexity of the system, reliable data can be obtained in the fmol-pmol range.

In practice, the identification of a protein from its predicted fingerprint doesn't always work. The determined molecular weights aren't precise enough to unambiguously identify the protein and some peptides don't "fly." In addition, post-translational modifications of the protein will interfere with the molecular weights calculated from the gene sequence.

In most cases when you send out your sample you get back a list of possibilities that has to be narrowed down by other means (e.g., another protease digest).

This limitation has led to the development of coupled mass specs where the peptides from one are fragmented and fed into another. What this gives you is the sequence of each peptide by a technique called MS/MS. With sequence information you can search all the databases for sequence similarity and identify proteins even if the gene for that particular species hasn't been cloned and sequenced.

Biochemistry and Mass Spectrometry

The following description is from Horton et al.,Principles of Biochemistry 4/e. It explains the use of mass spectrometry in a biochemical context.

Mass spectrometry, as the name implies, is a technique that determines the mass of a molecule. The most basic type of mass spectrometer measures the time that it takes for a charged gas phase molecule to travel from the point of injection to a sensitive detector. This time depends on the charge of a molecule and its mass and the result is reported as the mass/charge ratio. The technique has been used in chemistry for almost one hundred years but its application to proteins was limited because, until recently, it was not possible to disperse charged protein molecules into a gaseous stream of particles.

This problem was solved in the late 1980s with the development of two new types of mass spectromety. In electrospray mass spectrometry the protein solution is pumped through a metal needle at high voltage to create tiny droplets. The liquid rapidly evaporates in a vacuum and the charged proteins are focused on a detector by a magnetic field. The second new technique is called matrix-assisted desorption ionization (MALDI). In this method the protein is mixed with a chemical matrix and the mixture is precipitated on a metal substrate. The matrix is a small organic molecule that absorbs light at a particular wavelength. A laser pulse at the absorption wavelength imparts energy to the protein molecules via the matrix. The proteins are instantly released from the substrate (desorbed) and directed to the detector (see Figure). When time-of-flight (TOF) is measured, the technique is called MALDI–TOF.

The raw data from a mass spectrometry experiment can be quite simple, as shown in the Figure (right). There, a single species with one positive charge is detected so the mass/charge ratio gives the mass directly. In other cases, the spectra can be more complicated, especially in electrospray mass spectrometry. Often there are several different charged species and the correct mass has to be calculated by analyzing a collection of molecules with charges of +1, +2, +3 etc. The spectrum can be daunting when the source is a mixture of different proteins. Fortunately, there are sophisticated computer programs that can analyze the data and calculate the correct masses. The current popularity of mass spectrometry owes as much to the development of this software as it does to the new hardware and new methods of sample preparation.

Mass spectrometry is very sensitive and highly accurate. Often the mass of a protein can be obtained from picomole quantities that are isolated from an SDS–PAGE gel. The correct mass can be determined with an accuracy of less than the mass of a single proton.

©Laurence A. Moran and Pearson/Prentice Hall

Monday's Molecule #106: Winners

UPDATE: The machine is a mass spectrometer and the technique illustrated is matrix-assisted desorption ionization (MALDI) coupled to time-of-flight (TOF) measurement (MADLI-TOF).

The first person to get it right was David Schuller of Cornell University. The first undergraduate from the Toronto area was Nova Syed of the University of Toronto.

This is the second week in a row that Monday's molecule has been on a Tuesday. Sorry for the delay. I promise to get back on schedule next week.

The observant among you might have noticed that this "Monday's" molecule is not a molecule. It's my version of a machine. You have to identify what kind of a machine this is and what it does.

There are two Nobel Laureates who get credit for developing the technique shown here. One of them is responsible for the specific technique and the other for a similar variant. Name the two Nobel Lauretes.

The first person to identify the machine/technique and the Nobel Laureates wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are six 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), and Wesley Butt of the University of Toronto

Bill and John 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.

Mendel's Garden #28

The 28th edition of Mendel's Garden has just been posted on Quintessence of Dust [Mendel’s Garden 28th Edition].

Hello and welcome to the 28th edition of the genetics blog carnival known as Mendel's Garden, where we celebrate blogging on topics related to anything touching on what Mendel discovered (or thought he discovered). While reading these interesting and informative pieces, please think about work that should be featured in a future edition and/or blogs (like yours) that would serve well as future hosts.

So do tomato seeds get you excited? No? Oh. Well, they should, if you're at all interested in evolutionary genetics.

This is what we're up against.

PZ posted the first video on Pharyngula. I think it's important to watch both of them to see what goes on in church basements. How can we deal with this level of ignorance about science? It's especially frustrating because these young women are obviously intelligent enough that they should know better.

Tuesday, February 03, 2009

Monday's Molecule #106

What Timothy Sandefur says ....

I very much admire Jerry Coyne's article on science vs religion in The New Republic [see: Jerry Coyne on Science vs. Religion]. There's been some discussion on The Edge where participants are asked to address the question Does the empirical nature of science contradict the revelatory nature of faith?.

Timothy Sandefur discusses Coyne's article and the various commnents on his blog Freespace [The future of science teetering on the Edge]. He does such a good job that you should all hop over there as soon as possible and read what he has to say.

Timothy points out that the debate is really about ways of knowing. Can we obtain valid information using the scientific way of knowing? Yes we can. This is rationalism, in my terminology.

Can we obtain valid information using faith as a way of knowing? No we can't. This is superstition and it is the opposite of rationalism.

Is it possible to simultaneously practice both ways of knowing? Here's part of the response by Timothy Sandefur.

Keep the issue in mind: the question is not whether it is possible for someone simultaneously to hold unproven, baseless beliefs about a supernatural dimension and scientific, reasoned conclusions with regard to observed phenomena. It is possible for all sorts of people to believe all sorts of things—just as Humpty Dumpty practiced every day believing six impossible things before breakfast. But it is not possible to do these things and still have intellectual integrity. It requires instead intellectual dis-integration: the skill (if it can be called a skill) of not thinking about the possible connections between the phenomena of the universe. That is, it requires precisely the opposite effort that science requires. It requires one not to think. Alas, as Coyne observes, this effort is officially endorsed by many organizations motivated by political expediency:
It is in [scientists’] personal and professional interest to proclaim that science and religion are perfectly harmonious. After all, we want our grants funded by the government, and our schoolchildren exposed to real science instead of creationism. Liberal religious people have been important allies in our struggle against creationism, and it is not pleasant to alienate them by declaring how we feel. This is why, as a tactical matter, groups such as the National Academy of Sciences claim that religion and science do not conflict. But their main evidence—the existence of religious scientists—is wearing thin as scientists grow ever more vociferous about their lack of faith.
But it’s not just that there aren’t as many religious scientists as some claim. It’s the fact that these two ways of knowing are and always have been, incompatible by their nature, and that those who pledge allegiance to both are either dishonest or simply wrong.

It's nice to see a lawyer making sense.

Gene Genie #43

The 43rd edition of Gene Genie has been posted at Pharmamotion: pharmacology animations and resources [Gene Genie #43: Personal genomics, health and evolution].

Once again, PharmaMotion is hosting a blog carnival. This time is the turn of Gene Genie, a carnival dedicated to cover the buzz around the web about genetics (with some orientation to personalized genetics). I hope that PharmaMotion readers find it interesting.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

Should senior scientists be bloggers?

Eva asks the questions on her Nature Network blog [Bloggers]. I was going to leave a comment there but I can never remember my login name and password.

I hate sites like that.

The answer seems pretty obvious to me. Some small percentage of senior scientists will enjoy blogging but most won't. It's not a big deal. There's no reason to encourage more senior scientists to blog. They'll do it naturally if they feel the need.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

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