Monday's Molecule #109

 
Today's molecule is actually two molecules but we only care about the protein. You need to identify this protein, being as specific as possible. A general description of the type of protein won't do because the image clearly show a particular version.

There's are several possible Noble Laureates associated with this molecule. One of them was Michael Smith—last week's Nobel Laureate. The person I'm looking for was never a Professor. That's not necessarily a bad thing, it just helps you narrow down the field of possible prize winners.

The first person to identify the molecule 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 seven ineligible candidates for this week's reward: 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, Nova Syed of the University of Toronto, Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto, and James Fraser of the University of California, Berkeley.

John, David, and Dima have offered to donate their free lunch to a deserving undergraduate so 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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Evolution in The Hamilton Spectator

 
Rama Singh is a Professor in the Department of Biology at McMaster University in Hamilton, Ontario (Canada). He happens to be the supervisor of Carlo Artieri, who writes Musings of the Mad Biologist.

Carlo noted on his blog (Evolution is a fact, not just theory...) that his boss has just published an article on evolution in the local newspaper. Read it at: Evolution is a fact, not just theory.

I'll quote the subheading and a couple of paragraphs and leave it up to my readers to discuss. Is this a good example of how scientists should explain evolutionary biology to the general public?

The only unproven area is Darwin's natural selection

...

Living organisms, on the other hand, evolve by variational evolution that depends on the survival and reproduction of the "fittest" individuals in the population, which is composed of many genotypes.

Unlike evolution, which is taken as a fact, the theory of natural selection, Darwin's mechanism for evolution, has come under criticism as to whether it is sufficient to explain evolution. In particular, early developmental biologists questioned if natural selection was adequate to explain the diversity and complexity of life.

Yet after 150 years of vigorous research (and many Nobel prizes!), no one has come up with a better theory. In fact, the more scientists have explored biology, the more they have become convinced of the facts of evolution.

Natural selection is a fact of everyday life. Resources are limited, individuals differ in their survival and reproduction, and evolution is a common sense conclusion deduced from facts and reasons. The problem with evolutionary change is that it takes place on such a slow place that we do not see it. However, we can imagine how evolution occurs by looking at the spectacular variety of food plants, flowers and domestic animals that we have produced by using the same principles of genetics and selection that nature uses. We may not witness the origin of species, but we have witnessed species becoming extinct in our own life time.

I'll get the conversation going by pointing out that well before the 150 years Professor Singh mentions in his article, random genetic drift was proposed as a pretty good theory about how evolution can occur. It may not be "better" than natural selection but I think it's good enough to have deserved a mention.

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"A" for effort

Anyone involved in teaching has heard the sob story. One student works really, really hard in the course but only gets 65% on the final exam. Another student gets 95% without breaking a sweat.

The "C" student thinks this is very unfair. They should get a much higher mark because they put so much effort into the course.

The issue is addressed in the New York Times a few days ago [Student Expectations Seen as Causing Grade Disputes].

In line with Dean Hogge’s observation are Professor Greenberger’s test results. Nearly two-thirds of the students surveyed said that if they explained to a professor that they were trying hard, that should be taken into account in their grade.

Jason Greenwood, a senior kinesiology major at the University of Maryland echoed that view.

“I think putting in a lot of effort should merit a high grade,” Mr. Greenwood said. “What else is there really than the effort that you put in?”

“If you put in all the effort you have and get a C, what is the point?” he added. “If someone goes to every class and reads every chapter in the book and does everything the teacher asks of them and more, then they should be getting an A like their effort deserves. If your maximum effort can only be average in a teacher’s mind, then something is wrong.”

Michelle Cottle has a comment in The New Republic [An A for Effort? Talk About a Lousy Idea]. Now, this isn't a publication that I routinely look to for views that are similar to my own¹ but her comment below pretty much hits the nail on the head as far as I'm concerned.

No, Jason. What would be wrong is if a university trained its students to believe that they were excellent simply for getting up off their futons and doing what was expected of them. Did the reading? Attended class? Stayed up late working on a paper? Good for you, puppy! Sure, you did a craptastic job on that paper--not to mention the final--suggesting that you have no more than a fourth-grader's grasp of the material. But what the hell!? You worked hard. You showed up--even when you had that reallllly bad hangover. You may not have learned much, but you sure did try. Have a nice fat A. And here's hoping it comes in handy when your first employer fires you for not being able to tell your ass from your elbow when it comes to doing your job.

Sweet Jesus, where did such dizzying nonsense come from? Sure, it's easy to blame today's youth for being whiny, spoiled, and entitled. But the kids had to get these delusional ideas from somewhere. I suspect at least part of the blame lies with all those well-intentioned self-esteem-boosting messages that anxious parents, educators, and coaches feel compelled to spout in this era of making every child feel like a winner all the time. You know, the cheery, you-can-do-it mantras along the lines of, "All that matters is that you tried," "The only way to fail is not to try at all."

Um. No. While I understand the self-defeating doubt that we're trying to short-circuit here, there are, practically speaking, lots of ways to fail--much less fail to get an A. One of those is by not having much of an aptitude for a particular area of study. Not all of us are equipped to be rocket scientists, economists, or playwrights, just as not all of us are equipped to be actors or professional basketball players. If anything, a student who tries really, really, really hard at something and still repeatedly falls short might benefit from realizing that his talents lie elsewhere. (As could the rest of us: Not to state the obvious, but I don't want a brain surgeon who graduated at the top of his class because he had perfect attendance. I want one who is an artist with a scalpel.) Go ahead: Aim for the stars. Don't let anyone tell you you can't do something. But if you actually try that thing and it turns out that you're not so hot at it, don't whine about unfair grading. Acknowledge that you have major room for improvement and decide where to go from there. The sooner kids learn how to deal with failure and move on, the less likely we are to have a bunch of whiny, fragile, self-entitled, poorly qualified adults wandering around wondering why their oh-so-stellar efforts aren't properly appreciated in the real world.

Alternatively, now might be a good time to revisit my dream of becoming a concert pianist. I've never had much of an ear for music, but I bet if I quit my day job and worked at it really, really hard--or at least showed up at all my lessons and did the homework--someone would eventually reward my "excellence."

Hopeful Monster has something to say over on Chance and Necessity [Student effort ≠ high grades].

I want students to recognize that part of what we're testing is innate ability, or intelligence. There's no getting around it. If you are smart and you work hard you are going to get a higher grade than a student who works hard but isn't very smart. It's unfortunate that there are very smart students who don't have to work hard to get an "A," but that's life. What should count in university is how well you understand the material, not how much effort you put in while trying to understand.

By the way, I think that university Professors have to shoulder a great deal of the blame for the current sad state of "higher" education. It's not just the students. We Professors have always had the power to fix the problems but for the most part we have done nothing about it. Many of us have actually contributed to the problems by giving out marks for attendance and allowing "extra" assignments to raise your grade.

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1. By this, I don't mean to imply that The New York Times is any better.

Shopping for Darwin

 
What's a celebration without shopping? Now you can enjoy the Darwin year celebrations by buying hundreds of Darwinian items at the Darwin Year Store. Half of the proceeds go to supporting biodiversity conservation-related charities.



I don't look good in T-shirts but there's plenty of other gifts for me on that site. All those shoppers who might be looking to buy me something for St. Patrick's day should check out the large mugs.

Some of them have even seen the very Darwin notebook where this drawing comes from, do you remember, Ms. Sandwalk? I told you it would be important to see this notebook. Now you know why.

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[Hat Tip: Ryan Gregory]

Nobel Laureate: Michael Smith

 

The Nobel Prize in Chemistry 1993.

"for contributions to the developments of methods within DNA-based chemistry: for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies"


Michael Smith (1932 - 2000) won the Nobel Prize in Chemistry for developing the technique of site-directed mutagenesis. Today this is a common technique in biochemistry labs. It enables researchers to specifically alter a nucleotide in a gene in order to study its effect. It is frequently used in structural biology labs to explore the roles of varous amino acid residues in the function of a protein.

Smith's work was based on the development of DNA sequencing technology in the 1970s and on extensive work on the formation of DNA:DNA double-standed hybrids with oligonucleotides containing mismatches.

Here's the Press Release describing Michael Smith's contribution (there was a co-recipient but we don't mention him unless we have to).

THEME:
Nobel Laureates

Background

Chemically, the genetic material of living organisms consists of DNA (deoxyribonucleic acid). DNA molecules consist of two very long strands twisted around each other to form a double helix. Each strand is formed of smaller molecules, nucleotides, that represent the letters of the genetic material. There are only four different letters, designated A, T, C and G. The two DNA strands are complementary, being held together by A - T and G - C bonds. It is only when the genetic code is to be read off e.g. for protein building in the cell that the two strands are separated. The genetic information in DNA exists as a long sentence of code words, each of which consists of 3 letters which can be combined in many different ways (e.g. CAG, ACT, GCC). Each three-letter code word can be translated by special components within the cell into one of the twenty amino acids that build up proteins. It is the proteins that are responsible for the functions of living cells, including their ability to function, among other things, as enzymes maintaining all the chemical reactions required for supporting life. The proteins' three-dimensional structure and hence their function is determined by the order in which the various amino acids are linked together during protein synthesis.

Site-directed mutagenesis

The flow of genetic information goes from DNA via the translator molecule RNA to the proteins. By re-programming the code of a DNA molecule, e.g. changing the word CAC to GAC, it would be possible to obtain a protein in which the amino acid histidine is replaced by the amino acid aspartic acid. In nature, such mix-programming of the genetic material (mutation) occurs randomly, and is nearly always fatal to the organism. However, a dream of biochemical researchers has been to alter a given code word in a DNA molecule so as to be able to study how the properties of the mutated protein differ from the natural. It was through Smith's oligonucleotide-based site-directed mutagenesis that this dream became reality. As early as the 1970s Smith learned to synthesize oligonucleotides, short, single-strand DNA fragments, chemically. He also studied how these synthetic fragments could bind a virus to DNA. Smith then discovered that even if one of the letters of the synthetic DNA fragment was incorrect it could still bind at the correct position in the virus DNA and be used when new DNA was being synthesized. At the beginning of the 1970s Smith was a visiting researcher at Cambridge and the story goes that it was during a coffee-break discussion that the idea arose of getting a reprogrammed synthetic oligonucleotide to bind to a DNA molecule and then having it replicate in a suitable host organism. This would give a mutation which in turn would be able to produce a modified protein. In 1978 Smith and his co-workers made this idea work in practice. They succeeded both in inducing a mutation in a bacteriophagic virus and "curing" a natural mutant of this virus so that it regained its natural properties. Four years later Smith and his colleagues were able for the first time to produce and isolate large quantities of a mutated enzyme in which a pre-determined amino acid had been exchanged for another one.

A protein with a changed (mutated) amino acid can be
produced with site directed mutagenesis. A chemically
synthesized DNA fragment with a changed code word is bound
to a virus DNA which is multiplied in a bacterium. The DNA
molecule with the changed code word is reduplicated and can
be used for producing the changed protein.
Smith's method has created entirely new means of studying in detail how proteins function, what determines their three-dimensional structure and how they interact with other molecules inside the cell. Site-directed mutagenesis has without doubt revolutionised basic research and entirely changed researchers' ways of performing their experiments. The method is also important in biotechnology, where the concept protein design has been introduced, meaning the construction of proteins with desirable properties. It is already possible, for example, to improve the stability of an enzyme which is an active component in detergents so that it can better resist the chemicals and high temperatures of washing water. Attempts are being made to produce biotechnically a mutated haemoglobin which may give us a new means of replacing blood. By mutating proteins in the immune system, researchers have come a long way towards constructing antibodies that can neutralise cancer cells. The future also holds possibilities of gene therapy, curing hereditary diseases by specifically correcting mutated code words in the genetic material. Site-directed mutagenesis of plant proteins is opening up the possibility of producing crops that can make more efficient use of atmospheric carbon dioxide during photosynthesis

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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 on Gradualism

The image on the right was created by Mike Rosulek. You can view the complete set at More Darwin. He's planning to sell T-shirts and poster with all proceeds going to support the National Center for Science Education.

The idea of slow gradual change is an essential component of most people's thinking about evolution.¹ The debate over gradualism began in earnest with the publication of Punctuated Equilibria: an Alternative to Phyletic Gradualism by Eldredge and Gould (1972).

They defined phyletic gradualism as ...

Paleontology's view of speciation has been dominated by the picture of "phyletic gradualism." It holds that new species arise from the slow and steady transformation of the entire population.

They illustrate this point with two "classic" views of gradualism.

In the first view (left) we see speciation by gradual transformation of a single population. This form of speciation is called anagenesis.

This kind of thinking still dominates today. It's the way most people picture the result of natural selection working on a species over time. The species gradually adapts to a changing environment until its descendants come to look very different from its ancestors. This is the way most people think when they're talking about human evolution over the past several million years. It's the model you probably have in mind when you envisage arms races.

The other form of speciation is called cladogenesis. It's when an ancestral species splits into two parts—often due to geographical separation—and each separate population evolves gradually into distinct species. This is the way most people think about adaptive radiations. The key point, according to Eldredge and Gould, is the slow and steady change in each lineage as they diverge from one another.

Eldredge and Gould (1972) proposed a different way of thinking about evolution and speciation based on their observations of numerous fossil lineages. They suggested that speciation normally takes place via geographic separation of a subset of individuals in a species (allopatric speciation). This isolated group can evolve fairly rapidly so that within a relatively short time (tens of thousand of years) it comes to look very different from its ancestors.

If this geographically isolated population becomes reproductively isolated as well, then it forms a new species, distinct from its parents. The new species may then flow back into the same geographical location as the parent and there won't be any mixing of the gene pools. Meanwhile, the parent species has not changed much, so the effect on the fossil record is the rapid appearance of a new species while the old one continues to exist.²

At that point, both species will persist unchanged for millions of years (stasis) until the process of rapid speciation by cladogenesis repeats in one of both lineages. The pattern observed in the fossil record is called punctuated equilibria. It's a pattern that's very different from classic gradualism.

Here's how they illustrate it in their paper.



The important initial claims of the punctuated equilibria model are: (1) most change takes place rapidly during speciation by cladogenesis, and (2) for most of their existence species do not change very much. Later on, the implications of these two observations became more obvious. If the number of species is constantly increasing by splitting then why aren't we overwhelmed by species? The answer is that not only are species "born", they also "die" (become extinct). The overall pattern of evolution is characterized by the differential birth and death of species and this leads to species sorting as an important mode of evolution.

Lot's of people don't like punctuated equilibria and there are legitimate debates over interpretations of the fossil record. Some people say that the pattern is rarely seen, even when you have a complete record over millions of years. Others say that PE occurs in some lineages but it's not common.

Those who oppose punctuated equilibria are often upset about the claims concerning gradualism. The dispute often boils down to denying that anyone was ever a gradualist. The implication is that there's nothing new about punctuated equilibria so why all the fuss?

Much of the dispute hinges on whether Charles Darwin was a gradualist. It's often based on a misunderstanding of the word "gradualism" as it is used by Eldredge and Gould. Some people interpret it to mean "constant speedism" and they comb Darwin's works to find examples where he wrote about different rates of evolution in a lineage. "Aha!", they say, "see, Darwin wasn't a gradualist at all."

Gould addresses these critics in The Structure of Evolutionary Theory. He points out that there are some trivial examples of gradualism in Darwin's writings but the important definition is ...

Slowness and Smoothness (but not Constancy) of Rate
Darwin also championed the most stringent version of gradualism—not mere continuity of information, and not just insensibility of innumerate transitional steps; but also the additional claim that change must be insensibly gradual even at the broadest temporal scale of geological durations, and that continuous flux (at variable rates to be sure) represents the usual state of nature.

Gould goes on to support his claim based, in part, on Darwin's commitment to Lyell's uniformitarianism. Gould also points out that Huxley was vexed with Darwin for adopting such a gradualist approach to evolution.

You can tell from reading The Structure of Evolutionary Theory that Gould was annoyed at some of his critics. Bear in mind that Gould was a student of the history of biology and a collector of old books on the subject. He wrote numerous essays on the misinterpretation of historical figures (e.g. Goldschmidt). When he makes a claim about what Darwin thought, it shouldn't be dismissed as the deranged delusions of an uniformed scientist.

The same might not be true of other scientists, or philosophers, who write about history ....

Since Darwin prevails as the patron saint of our profession, and since everyone wants such a preeminent authority on his side, a lamentable tradition has arisen for appropriating single Darwinian statements as defenses for particular views that either bear no relation to Darwin's own concern, or that even confute the general tenor of his work....

I raise this point here because abuse of selective quotation has been particularly notable in discussions of Darwin's views on gradualism. Of course Darwin acknowledged great variation in rates of change, and even episodes of rapidity that might be labelled catastrophic (at least on a local scale); for how could such an excellent naturalist deny nature's multifariousness on such a key issue as the character of change itself? But these occasional statements do not make Darwin the godfather of punctuated equilibrium, or a cryptic supporter of saltation....

For more on this debate, see John Wilkins on Myth 4: Darwin was a gradualist.

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1. The words on the poster are a take-off on one of the campaign slogans of Barack Obama.

2. There are other models that can account for the observations. In other works, Eldredge and Gould have explained how punctuated equilibria is also compatible with sympatric speciation.

Eldredge, N. and Gould, S.J. (1972) Punctuated Equilibria: an Alternative to Phyletic Gradualism. in "Models in Paleobiology" T.J.M. Schopf ed., Freemna, Cooper & Co., San Francisco pp. 82-115. [PDF]

Subway ads and dead stars

 
Today I saw this "advertisement" in the subway on my way to work. I think it's an excellent example of science education and I congratulate the people at the Dunlap Institute for Astronomy and Astrophysics, University of Toronto and CoolCosmos for making the effort. (Click on the ad below to enbiggen and read the fine print. Refresh the page on CoolCosmos to see all five ads.)


Phil Plait will be jealous.

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We Need this Course at the University of Toronto

 
Carl Zimmer ran a Science Writing Workshop at Yale University a few weeks ago.

I want him to give the same workshop here but I don't know if we can afford him.

Carl told us on his blog (The Island of Science Writing) about a short course in science writing that he is teaching this summer at the Shoals Marine Laboratory in Maine (USA). That sounded pretty neat so I thought I'd check it out by following the link [SCIENCE WRITING: BIOSM 3110]. I entertained the hope that I could take this course from Carl ... until I saw the price. The total cost for the week ($2,286) includes room and board but it's still a little steep for me, even considering the quality of the lecturer.

Hey Carl, do you have a discount for senior citizens?

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Blunt Talk from Four Evolutionists

 
Do you remember this cover? It caused a minor uproar a few weeks ago [see Explaining the New Scientist Cover].

Today's issue of New Scientist has a letter signed by four people who criticize the journal for its choice of cover design. It may be just about the only important thing those four have in common. There are; Daniel Dennett, Jerry Coyne, Richard Dawkins, and PZ Myers. What a motley crew! [Darwin Was Right].

What on earth were you thinking when you produced a garish cover proclaiming that "Darwin was wrong" (24 January)?

First, it's false, and second, it's inflammatory. And, as you surely know, many readers will interpret the cover not as being about Darwin, the historical figure, but about evolution.

Nothing in the article showed that the concept of the tree of life is unsound; only that it is more complicated than was realised before the advent of molecular genetics. It is still true that all of life arose from "a few forms or... one", as Darwin concluded in The Origin of Species. It is still true that it diversified by descent with modification via natural selection and other factors.

Of course there's a tree; it's just more of a banyan than an oak at its single-celled-organism base. The problem of horizontal gene-transfer in most non-bacterial species is not serious enough to obscure the branches we find by sequencing their DNA.

Darwin was wrong about a lot of things but the tree of life wasn't one of them. It's still an accurate metaphor for most of the history of life—certainly the parts Darwin wrote about.

That's not to deny the fundamentally accurate part of the inside story. At its base the tree of life looks an awful lot like a web. That's correct. It's just that it has nothing to do with Darwin. The magazine's attempt to connect modern molecular evolution with Charles Darwin was just cheap opportunism.

I can't resist noting an irony in the letter. The authors say that, "It is still true that [life] diversified by descent with modification via natural selection and other factors." The irony is that the article inside the magazine discusses molecular evolution ("molecular genetics" in their terminology). The trees derived from those studies are based almost exclusively on neutral mutations that have become fixed in species by random genetic drift. What these studies show is that life diversified by descent with modification via random genetic drift.

Even when they are writing about changes at the molecular level, some adaptationists just can't bring themselves to utter the words "random genetic drift" in public.

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Welcome to Canada, President Obama

 
President Obama (USA) just arrived in Canada. Here he is being greeted by Governor General Michaelle Jean. You can see the complete video on YAHOO! News.

Gosh, there hasn't been this much excitement over a visit to Canada since the Pope came here in 2002! Obama's visit may even be more exciting that the Queen's last trip in 2005.

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Stephen Jay Gould Challenged the Modern Synthesis

As most of you know, Gould (1941 - 2002) was a critic of the hardened version of the Modern Synthesis. He thought that evolutionary theory needed to be updated to include some things that the originators of the Modern Synthesis were unaware of—or rejected prematurely.

His paper in Science in 1982 reached a wide audience and most biologists first became aware of his challenge by reading this paper (Gould, 1982) [read it here—if you have a subscription to Science].

But two years earlier, Gould published a more scholarly critique in the journal Paleobiology (Gould 1980). The opening sentence of the abstract throws down the gauntlet.

The modern synthesis, as an exclusive proposition, has broken down on both of its fundamental claims: extrapolationism (gradual allelic substitution as a model for all evolutionary change) and nearly exclusive reliance on selection leading to adaptation.

Ryan Gregory discusses this paper in detail on Genomicron [Gould (1980)]. If you want to be informed in this debate you absolutely must read what he has to say about this key paper in evolutionary theory.

Ryan discusses three important myths about Gould. The false myths are: (1) he rejected natural selection, (2) he wanted to overthrow the Modern Synthesis, (3) saltation and punctuated equilibria are somehow connected.

The last myth is so widespread that people as diverse as Jarry Coyne, Greg Laden, and Daniel Dennett have gotten themselves hopelessly confused about punctuated equilibria by not reading carefully [see Macromutations and Punctuated Equilibria]. They should know better.

They will know better (I hope) once they have read Ryan Gregory's posting.

Today, there are many people who want to change the Modern Synthesis. Advocating some new addition to evolutionary theory has become a minor industry—aided and abetted by science journalist who are more interested in controversy than accuracy. But those failings should not blind us to the very legitimate challenges to the Modern Synthesis raised by Gould over twenty-five years ago.

It's disappointing that most of those challenges are still not understood by biologists. Read Ryan's summary of Gould (1980), and learn.

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[Image Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Gould, S.J. (1980) Is a new and general theory of evolution emerging? Paleobiology 6:119-130.

Gould, S.J. (1982) Darwinism and the expansion of evolutionary theory. Science 216:380-387.

World of Warcraft in France

 
Dear WOW Spammer,

You are spamming my blog with all kinds of links to your websites in France. I don't know what you are trying to achieve because I remove every single one of your comments within a few hours. Please confirm this fact. There's isn't a single link left on Sandwalk.

This is a waste of your time and mine. Please stop.

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The Modern Synthesis

 
Most people do not understand current ideas about evolution. The following is a brief summary of the Modern Synthesis of Genetics and Evolution as put forth by evolutionary biologists in the late 1940s.

The idea that life on Earth has evolved was widely discussed in Europe in the late 1700s and the early part of the 1800s. In 1859 Charles Darwin supplied a mechanism—namely natural selection—that could explain how evolution occurred. Darwin's theory of natural selection helped to convince most people that life has evolved and this point has not been seriously challenged in the past one hundred and fifty years.

It is important to note that Darwin's book The Origin of Species by Means of Natural Selection did two things. It summarized all of the evidence in favor of the idea that organisms have descended with modification from a common ancestor. Darwin built a strong case for evolution. In addition, Darwin advocated natural selection as a mechanism of evolution.

Biologists no longer question whether evolution has occurred or is occurring. That part of Darwin's book is now considered to be so overwhelmingly demonstrated that is is often referred to as the FACT of evolution. However, the MECHANISM of evolution is still debated [Evolution Is a Fact and a Theory].

During the first part of this century the incorporation of genetics and population genetics into studies of evolution led to a Neo-Darwinian theory of evolution that recognized the importance of mutation and variation within a population. Natural selection then became a process that altered the frequency of genes in a population and this came to be the minimal definition evolution [What Is Evolution?].

The earliest version of this essay appears on the TalkOrigins Archive.

A later version is at Evolution by Accident.This point of view held sway for many decades but by the 1940s the classic Neo-Darwinian view was replaced by a new concept that brought together field biology, paleontology, and population genetics. The new version took pains to exclude all mechanisms except natural selection and random genetic drift. This new version was called The Modern Synthesis after the title of a 1942 book by Julian Huxley.

We have learned much since Darwin's time and it is no longer appropriate to claim that natural selection is the only mechanism of evolution. I can understand why this point may not be appreciated by the average non-scientist because natural selection is easy to understand at a superficial level. It has been widely promoted in the popular press and the image of "survival of the fittest" is too powerful and too convenient.

One of the goals of the Modern Synthesis was to reach consensus on the importance of macroevolution. The founders of the Modern Synthesis insisted that macroevolution could be explained by microevolution and no additional mechanisms—such as the bogeyman of saltation—were required.

Ernst Mayr, one of the original founders of the Modern Synthesis, sums it up this way ...

The term "evolutionary synthesis" was introduced by Julian Huxley in Evolution: The Modern Synthesis (1942) to designate the general acceptance of two conclusions: gradual evolution can be explained in terms of small genetic changes ("mutations") and recombination, and the ordering of the genetic variation by natural selection; and the observed evolutionary phenomena, particularly macroevolutonary processes and speciation, can be explained in a manner that is consistent with the known genetic mechanisms.

Ernst Mayr (1980) "Some Thoughts on the History
of the Evolutionary Synthesis" in The Evolutionary Synthesis,
E. Mayr & W.B. Provine eds. Harvard University Press.

The original version of the Modern Synthesis included mechanisms other than natural selection, especially random genetic drift. Later on, there was a hardening of the synthesis so that natural selection became the predominant mechanism and drift was relegated to a bit part (see Mayr quotation, above). The original version is described by Douglas Futuyma as ....

The major tenets of the evolutionary synthesis, then, were that populations contain genetic variation that arises by random (ie. not adaptively directed) mutation and recombination; that populations evolve by changes in gene frequency brought about by random genetic drift, gene flow, and especially natural selection; that most adaptive genetic variants have individually slight phenotypic effects so that phenotypic changes are gradual (although some alleles with discrete effects may be advantageous, as in certain color polymorphisms); that diversification comes about by speciation, which normally entails the gradual evolution of reproductive isolation among populations; and that these processes, continued for sufficiently long, give rise to changes of such great magnitude as to warrant the designation of higher taxonomic levels (genera, families, and so forth).

Futuyma, D.J. in Evolutionary Biology,
Sinauer Associates, 1986; p.12

This description would be incomprehensible to Darwin since he was unaware of genes and genetic drift. The Modern Synthesis differed from Darwinism in four important ways:

1. It defined evolution as a change in the frequency of alleles in a population; an idea based on population genetics.


2. In addition to natural selection, it recognized random genetic drift as an important mechanism of evolution.


3. It recognized that characteristics are inherited as discrete entities called genes. Variation within a population is due to the presence of multiple alleles of a gene. Variation is caused by mutation.


4. It postulated that speciation is (usually) due to the gradual accumulation of small genetic changes. This is equivalent to saying that macroevolution is simply a lot of microevolution.

The Modern Synthesis was a theory about how evolution worked at the level of genes, phenotypes, and populations whereas Darwinism was concerned mainly with organisms, speciation and individuals. This was a major shift in emphasis and those who fail to appreciate it find themselves out of step with the thinking of evolutionary biologists.

The major controversies among evolutionary biologists today concern the validity of points #2 and #4 (above).

Following the centennial celebrations of the publication of Origin in 1959, there was a gradual hardening of the Modern Synthesis. The 1960s version concentrated almost exclusively on natural selection as a mechanism and random genetic drift was pretty much ignored. Today, there is debate about the relative importance of these two mechanisms and some are calling for an updating of the "hardened" Modern Synthesis.

This update would restore random genetic drift as an important mechanism, recognize neutral theory, and incorporate molecular phylogeny (and the molecular clock).

There are many who believe that the fossil record does not show gradual change but instead long periods of stasis followed by rapid speciation. This model is referred to as Punctuated Equilibrium and it is widely accepted as true, at least in some cases. The debate is over the relative contributions of gradual versus punctuated change, the average size of the punctuations, and the mechanism.

The Modern Synthesis is challenged over the emphasis on gradualism and over the claim that microevolution is sufficient to explain macroevolution. Some evolutionary biologists suggest that evolutionary theory be modified to incorporate mechanisms that occur at levels higher than the population (e.g. species sorting). These scientists advocate an extension called hierarchical theory.

There are other challenges to the Modern Synthesis. Some of them are valid and some of them are silly. But I think it's fair to say that the 50-year old version needs some serious updating to incorporate some of the new concepts.

Some scientists continue to refer to modern evolutionary theory as Neo-Darwinian. In some cases these scientists do not understand that the field has changed but in other cases they are referring to what I have called the Modern Synthesis, only they have retained an old name from the early 1900s.

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Monday's Molecule #108: Winner

 
UPDATE: This week's molecule is the genome of ΦX174, a small bacterial virus. It was the first complete genome to be sequenced (Smith et al., 1977, Sanger et al., 1978, Sanger et al., 1978). The sequencing was done in Fred Sanger's lab and Sanger was awarded the Noble Prize a few year later for developing the dideoxy sequencing technology [The Sanger Method of DNA Sequencing].

ΦX174 is interesting because it has overlapping genes—a feature that we now know to be uncommon.

One of the authors on the papers was Michael Smith. He spent a year in Sanger's lab on sabbatical. In 1978 Smith used the ΦX174 sequence in his experiments to develop site-directed mutagenesis (Hutchison et al. 1978). Smith got the Nobel Prize in 1993. He is this week's Nobel Laureate.

This week's winner is James Fraser of the University of California, Berkeley. We will be meeting for lunch in a few months.

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Hutchison, C.A. 3rd, Phillips, S., Edgell, M.H., Gillam, S., Jahnke, P., and Smith, M. (1978) Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 253:6551-6560.

Sanger, F., Air, G.M., Barrell, B.G., Brown, N.L., Coulson, A.R., Fiddes, C.A., Hutchison, C.A., Slocombe, P.M., and Smith, M. (1977) The nucleotide sequence of bacteriophage phiX174. Nature 265:687-695.

Sanger, F., Coulson, A.R., Friedmann, T., Air, G.M., Barrell, B.G., Brown, N.L., Fiddes, J.C., Hutchison, C.A. 3rd, Slocombe, P.M., and Smith, M. (1978) The nucleotide sequence of bacteriophage phiX174. J. Mol. Biol. 125:225-246.

Smith, M., Brown, N.L., Air, G.M., Barrell, B.G., Coulson, A.R., Hutchison, C.A. 3rd, and Sanger, F. (1977) DNA sequence at the C termini of the overlapping genes A and B in bacteriophage phi X174. Nature 265:702-705.

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Today's Monday's Molecule really is a molecule. Your task is to identify the molecule from the cartoon shown here. It won't be sufficient to just find the name of the molecule, you will also have to identify the significance behind determining its chemical structure.

There's one scientist who was involved in that determination who also did some important work based, in part, on knowing the sequence. This scientist was awarded a Nobel Prize for his work but the prize didn't come until 15 years later. Name this Nobel Laureate.

The first person to identify the molecule 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: 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, Nova Syed of the University of Toronto, Dima Klenchin of the University of Wisconsin and undergraduate Alex Ling of the University of Toronto

John, David, and Dima have offered to donate their free lunch to a deserving undergraduate so 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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USA Is Ahead of the World in Science Education

 
This falls into the category of, "Wow, I didn't know that!"¹. According to a press release from Michigan State University: College Science Requirements Keep US Ahead Of World, Researcher Argues ...

Despite frequent warnings of the inadequacy of education in the United States, citizens here are still among the world's most scientifically literate, a Michigan State University researcher said.

You can thank those general education requirements that force English majors to sit through biology classes and budding engineers to read Hemingway, Jon Miller said.

...

Fifty years after English novelist and physicist C.P. Snow warned of a disturbing lack of scientific literacy among the cultural elite and a parallel literary void among Britain's scientists and technologists, little has changed in most of the world, Miller argued. And that's part of what keeps the U.S. at the forefront of scientific endeavor and technological innovation.

"What makes the American market and society different," he said, "is that we have more science- and technology-receptive citizens and consumers, and as a society we're willing to spend money for basic science and have been doing that for years."

Americans as a group tend to be more open-minded about innovations such as genetically modified food, he said. Scientific reasoning also works its way into such disciplines as law, he noted, where facts are routinely marshaled to support or disprove theories.

Who would 'av thunk it? American are better at critical scientific reasoning because there are more science-receptive citizens. And it even extends to the law.

I guess that's why American courts spend so much time trying to keep superstition out of the science classroom.

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1. Personally, I don't think there's all that much difference between science literacy in the USA and other Westeren industrialized nations. However, the idea that the USA is actually superior to other nations does strain belief, somewhat.