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.

---

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.

---

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 ...

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.

---

[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.

---

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.

---

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."

---

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

---

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