Wednesday, November 25, 2009

Origin of Species at 150: Day Three

Tuesday November 24, 2009

08:00-09:00 Breakfast

09:00-11:00
Symposium V: Taxonomy
Chair: TBA

09:00-09:40
Mary Winsor (University of Toronto)
"Classification is a Census:" Huxley's Private Quarrel
with Darwin and its Public Consequences

09:40-10:20
Kevin Padian (University of California, Berkeley)
What is "Evidence for Evolution" to an Evolutionist?

10:20-11:00
Richard A. Richards (University of Alabama)
Context and Evidence in the History of Science

11:15-12:45
Session 4.i: Ancient Debates, Ancient Roots
Chair: Charissa Varma

11:15-11:45
P. William Hughes (Carleton University)
Aristotle contra Democritus: Anticipation of the Neutralist-Selectionist
Debate and a Haphazard Route Back to Darwin

11:45-12:15
Andreas Avgousti (Columbia University)
Pre-modern, Modern and Natural Understandings of Man:
Plato, Hobbes, and Evolutionary Theory

12:15-12:45
Robin Zebrowski (Beloit College)
The Evolution of Experience and the Experience of Evolution:
Revisiting Dewey's Analysis of the Influence of Darwin on Philosophy

11:15-12:45
Session 4.ii: The Devil’s Chaplain
Chair: David Smillie

11:15-11:45
Peter Sachs Collopy (University of Pennsylvania)
Naturalizing Calvinism: The Darwinism and Anti-Evolutionism
of George Frederick Wright

11:45-12:15
Stephen D. Snobelen (University of King’s College)
Theological Themes in Darwin's Origin of Species (1859)

12:15-12:45
Christopher diCarlo (University of Ontario Institute of Technology)
The Zing of Perceived Control: Memetic Equilibrium
and the Evolution of Religion

11:15-12:45
Session 4.iii: Laws of Evolutionary Economics
Chair: Mike Thicke

11:15-11:45
André Ariew (University of Missouri-Columbia)
Darwin’s Invisible Hand?

11:45-12:15
Eugene Earnshaw-Whyte (University of Toronto)
Breaking the Bonds of Biology: Natural Selection
in Nelson and Winter's Evolutionary Economics

12:15-12:45
Chris Haufe (Virginia Polytechnic Institute and State University)
Darwin’s “Laws”

12:45-13:30 Lunch Break

13:40-15:40
Symposium VI: Evolution and Development
Chair: Jean-Bernard Caron

13:40-14:20
Manfred Laubichler (Arizona State University)
From Boveri to Davidson and Back

14:20-15:00
Jane Maienschein (Arizona State University)
From Epigenesis to Epigenetics and Back

15:00-15:40
Michael Dietrich (Dartmouth College)
From Goldschmidt to Gould and Back

15:50-17:20 Session 5.i: It's All in the Mind
Chair: Eugene Earnshaw-Whyte

15:50-16:20
Byron Kaldis (The Hellenic Open University)
Species-Qua-Individuals and the Modularity of the Mind: The Saving Grace for Humans

16:20-16:50
Alain Ducharme & Sheldon Chow (The University of Western Ontario
Keeping Darwin in Mind

16:50-17:20
Steve DiPaola (Simon Fraser University)
Darwin, Creativity, and Evoluionary Programming

15:50-17:20
Session 5.ii: International Receptions
Chair: Ari Gross

15:50-16:20
Paranbes Nath (Calcutta University)
Darwin and India

16:20-16:50
Alex Levine & Adriana Nova (University of South Florida)
The Fate of Darwinian Analogies in Latin America:
The Reception of Darwinism in 19th Century Argentina

16:50-17:20
Nolan Heie (Queen’s University)
Albert Kalthoff, Entwicklung and the "World View of Modern Man"

15:50-16:50
Session 5.iii: Fitness
Chair: Ellie Louson

15:50-16:20
Marshall Abrams (University of Alabama at Birmingham)
Individuals have no Fitnesses if Fitness Differences Cause Evolution

16:20-16:50
Kent A. Peacock (University of Lethbridge)
The Three Faces of Fitness

15:50-16:50
Session 5.iv: Language and Logic
Chair: S.J. Patterson

15:50-16:20
Alexander G. Yushchenko (Kharkov State Polytechnic University)
Logics & Ethics of Evolution from the Point of View of Evolutionary Theology

16:20-16:50
Justin Humphreys (New School for Social Research)
Darwin on Language

17:20-18:20
Keynote Address: Brian K. Hall (Dalhousie University)
Charles Darwin, Evolutionary Embryology and Evo-Devo


18:20-19:00 Break

19:00-19:45
Keynote Address: Spencer Barrett (University of Toronto)
Charles Darwin and Current Perspectives on the Evolution and Function of Plant Sexual Diversity


Origin of Species at 150: Day Two

Monday November 23, 2009

09:00-11:00Symposium III: Theistic Evolution
Chair: Michael Bourgeois

09:00-09:40
Bernard Lightman (York University)
Christian Evolutionists in the U.S., 1860-1900

09:40-10:20
Michael Ruse (Florida State University)
Are Science and Religion Compatible and If So, Why?

10:20-11:00
Denis O. Lamoureux (University of Alberta)
Darwinian Theological Insights: Toward an Intellectually Fulfilled Theism

11:15-12:45
Session 2.i: Acceptances and Denials
Chair: David Smillie

11:15-11:45
Fermin Fulda (University of Toronto)
Against Fodor Against Darwinism

11:45-12:15
Stefaan Blanke (Ghent University)
"A million guesses strung together:" Creationist Denial of the Science Behind Evolutionary Theory

12:15-12:45
Daniel A. Newman (University of Toronto)
The Rhetoric of Probability: How Darwin Overcame the Argument from Design

11:15-12:45
Session 2.ii: Historical Receptions
Chair: Jaipreet Virdi

11:15-11:45
John Court (University of Toronto)
Darwinian Evolution's First Fifty Years of Impact
on Botany at the University of Toronto. 1859 to 1909

11:45-12:15
David M. Steffes (Arizona State University)
Population Ecology and Evolution: Darwin's Origin and the
Modern Synthesis of the 1940s and 50s

12:15-12:45
Kevin Pent (York University)
Julian Huxley's 'Apogee of Species': Darwin's 'Man' Comes of Age

11:15-12:45
Session 2.iii: A Brave New Darwin
Chair: Chris Belanger

11:15-11:45
Peter Fedor (Comenius University)
Advances in Artificial Intelligence in Species Identification

11:45-12:15
Wybo Houkes (Edinhoven University of Technology)
Hypothesis Testing in Artefact Evolution

12:15-12:45
Laura Landen (Queen's University)
Natural Selection, The Intentional Stance, and Mirror Neuron Research

12:45-13:30 Lunch Break

13:40-15:40
Symposium IV: Species
Chair: Ronald de Sousa

13:40-1420
John Beatty (University of British Columbia)
Darwin on Species

14:20-15:00
Kevin de Queiroz (Natural Museum of National History; Smithsonian)
Charles Darwin and the Evolution of the Species Concept

15:00-15:40
Marc Ereshefsky (University of Calgary)
Mystery of Mysteries: Darwin and the Species Problem

15:45-16:45
Keynote Address: Michael Ruse (Florida State University)
Is Darwinism Past its “Sell-By” Date?

16:45-18:15
Session 3.i: Naturalism
Chair: Curtis Forbes

16:45-17:15
Jason Marsh (University of Western Ontario)
Darwinism and Divine Hiddenness

17:15-17:45
Khaldoun Sweis (Olive-Harvey College)
Philosophical Paradoxs of Darwin Evolutionary Naturalism

17:45-18:15
Maarten Boudry (Ghent University)
Methodological Naturalism as an Intrinsic Property of Science:
A Grist to the Mill of Intelligent Design Theory

16:45-18:15
Session 3.ii: Reconstructing Darwinism
Chair: Erich Weidenhammer

16:45-17:15
Peter Gildenhuys (Lafayette College)
Putting the Struggle for Existence to Work

17:15-17:45
Katharine Browne (University of Toronto)
A Darwinian theory of Games

17:45-18:15
Sarah Winter (University of Connecticut Storrs)
Species as Value: Biosemiotics in Darwin's Origin and Saussurian Linguistics

16:45-18:15
Session 3.iii: Applying Darwinism
Chair: Mike Stuart

16:45-17:15
Marion Blute (University of Toronto at Mississauga)
Darwinism in the Social Sciences Today

17:15-17:45
Howard M. Huynh (Acadia University)
In the Footsteps of Darwin: The Value of Scientific Collecting in
Biodiversity Research and Conservation

17:45-18:15
Joel Velasco (Stanford University)
The Tree of Life: From Darwin to Today

18:15-19:15
Keynote Address: Evelyn Fox Keller
(Massachusetts Institute of Technology)
Darwin as the Newton of a Blade of Grass


Origin of Species at 150: Day One

The conference on Origin of Species at 150 was sponsored by The Institute for the History & Philosophy of Science & Technology, The Department of Ecology and Evolutionary Biology, and The Department of Philosophy at the University of Toronto.

Here's the schedule for the first day.

Sunday November 22, 2009

08:00-09:00 Breakfast

09:00-10:00
Keynote Address: Alison Pearn (Darwin Correspondence Project)
Cast of Thousands: Charles Darwin's Life in Letters

10:00-12:00
Symposium I: Gender, Evolution, and Sexual Selection
Chair: Joan Steigerwald

10:00-10:40
Lisa Lloyd (Indiana University)
Bias in Evolutionary Explanations of the Female Orgasm

10:40-11:20
Marlene Zuk (University of California, Riverside)
Sex and the Scala Naturae

11:20-12:00
Erika Milam (University of Maryland, College Park)
Negotiating Choice: Animal Minds and Human Instincts
in the History of Sexual Selection

12:00-12:30 Lunch Break

12:45-13:45
Session 1.i: Reassessing Themes and Sources
Chair: Michael Cournoyea

12:45-13:15
Scott Sinclair (St. Louis University)
Three American Philosophers’ Response to Darwin

13:15-13:45
Fred Wilson (University of Toronto)
Replacing an Old Paradigm: Intelligent Design and Natural Selection; Hume, Mill, and Darwin

12:45-14:15
Session 1.ii: Social Perceptions
Chair: Jaipreet Virdi

12:45-13:15
Eleanor Louson (University of Toronto)
Nature, Projected: Evolutionary Theory in Wildlife Documentaries

13:15-13:45
David Smillie (University of Toronto)
Evolution and Popular Culture: Darwin on the Box

13:45-14:15
Ian Hesketh (Queen’s University)
Of Apes and Ancestors: Myth and the Cultural Memory of the Oxford Debate of 1860

12:45-14:15
Session 1.iii: Species and Sexuality
Chair: Sebastián Gil-Riaño

12:45-13:15
Masoud Hassanpour Golakani (Macquarie University)
The Spiral Valve Intestine of the Australian Lungfish, a Primitive Characteristic

13:15-13:45
Eugene S. Morton (Hemlock Hill Field Station)
Sexual Conflict and Brood Desertion in Blue-Headed Vireos: How Females Won

13:45-14:15
Jerome Goldsten (San Francisco Clinical Research Center)
The Neurobiology of Sexual Orientation: A Tribute to Charles Darwin

14:30-16:30
Symposium II: Ecology
Chair: Richard Landon
(Coffee/Tea Service Provided)

14:30-15:10
Joan Roughgarden (Stanford University)
Darwin and Ecology

15:10-15:50
Gene Cittadino (New York University)
Reflections on Darwin and Ecology: The History of a Tenuous Relationship

15:50-16:30
Gregory Cooper (Washington and Lee University)
The Darwinian Character of Evolutionary Ecology

16:40-17:40
Keynote Address: James Moore (University of Cambridge)
Darwin’s Progress and the Problem of Slavery

18:00-19:30
Special Presentation
Re: Design: A Dramatisation of the Correspondence between Charles Darwin and Asa Gray (Produced by the Menagerie Theatre Company)


150 Years Ago


On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life was published 150 years ago on November 24, 1859. The publisher, John Murray, had already taken orders for 1,500 copies so the initial printing of 1,250 copies was sold out immediately.
Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists entertain, and which I formerly entertained—namely, that each species is 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 descendants of that species. Furthermore, I am convinced that Natural Selection has been the main but not the exclusive means of modification.



Tuesday, November 17, 2009

Monday's Molecule #144: Winner?

 
The creature is the spirochete, Treponema pallidum. This bacteria causes syphilis. The Nobel Laureate is Julius Wagner-Jauregg who discovered a way to treat the lethal form of dementia that develops in the late stages of the disease.

There were only three people who got the right answer. All of them were ineligible. There is no winner this week!




This is another one of those times when there's no "molecule" that provides a clue to a Nobel Laureate.

Your task is to identify this creature and the reason why it's important. There are three Nobel Laureates who might be associated with the creature but two of them have already been covered. The last name of the this week's Nobel Laureate does not begin with the letters "E" or "D". Who is it?

The first person to identify the "molecule" and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, Bill Chaney of the University of Nebraska, Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong and Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Dima, and Bill have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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



Should Intelligent Design Creationism Be Taught in Schools?

 
PZ Myers and someone named Jerry Bergman debated the question; "Should Intelligent Design be Taught in The Schools?." Bergman said "yes" and PZ said "no."

You can read summaries of the debate on Greg Laden's Blog [Bergman vs. Myers Debate: Should Intelligent Design be Taught in The Schools?] and on Kittywhumpus [I thought it went really well, until he brought up Hitler]. PZ has posted a summary on Pharyngula [That Bergman-Myers debate].

By all accounts it was a rout. PZ won the day for keeping Intelligent Design Creationism out of the classroom. It was like shooting fish in a barrel.

I'd like to debate PZ on this topic. I think Intelligent Design Creationism has to be brought up in the classroom. It's the major misconception that students have and to ignore it is stupid. You have to address the issues that students are confused about or you aren't educating. It's one thing to say that Intelligent Design Creationism isn't science when you are outside of the classroom but unless the students hear it in the classroom you are wasting your time.

We are never going to make progress against scientific illiteracy unless we recognize the elephant in the room and deal with it. Study after study has shown that the misconceptions of students aren't changed when you just present them with facts. They will readily incorporate those facts into their distorted worldview and that's exactly what happens when we teach evolution to creationists.

They need to be shown why their worldview is wrong and this means bringing up in class all the problems with Intelligent Design Creationism. Like it or not, that means teaching Intelligent Design Creationism in the science classroom even if the goal is to refute it.

Astrology is a good analogy. One way to teach critical thinking is to have a lesson on astrology where you explain what's wrong with it and why it doesn't work. You don't ban it from the classroom because it's bad science—you bring it into the classroom because it's bad science and students need to hear why.

If you don't do that, many students will continue to think that astrology is real and before you know it you've created another generation of citizens who don't understand science.

The thing that Intelligent Design Creationists should fear the most is that we actually will confront it in the classroom and expose it for the nonsense it is. They're safe as long as we tip-toe around it. That leaves them free to teach their nonsense in Sunday school without fear of ever being contradicted.

(I'm well aware of the Constitutional arguments in America. If someone like PZ wants to argue that Intelligent Design Creationism should be taught in US schools but the Constitution forbids it, then I'm prepared to agree with him. The debate I want is whether it should be taught in schools that don't have such a silly law. Should it be taught in Canadian schools? I say yes.)


Genetic Load, Neutral Theory, and Junk DNA

The average human newborn has about 130 new mutations that were not found in either parent [Mutation Rates]. These mutations accumulate as a natural result of errors in DNA replication between the time that the zygote is first formed and the time that the sperm and egg cells are produced for the next generation.

A species cannot afford to accumulate deleterious mutations in the genomes of its individuals. Eventually the number of "bad" mutations will reach a level where most genes have multiple "bad" alleles and it becomes impossible to produce offspring.

This phenomenon is referred to as genetic load. It means that species can only survive if the genetic load is below some minimum value. A good rule of thumb is that there can't be more than 0.1 deleterious mutations per individual per generation but in actual populations this value can be a bit higher. [UPDATE: This should be one (1) deleterious mutation per generation.]

How do you reconcile this with the known mutation rate in humans? If there are, on average, 130 mutations per individual per generation, then hardly any of these can be deleterious if the species is to survive.

This is one of the arguments in favor of Neutral Theory. Most mutations are neither deleterious nor beneficial. They are simply neutral with respect to natural selection.

Let's think about a typical protein-encoding gene.1 The coding region is about 2,000 base pairs in length and consist of 666 codons. More than half these codons can be mutated to a new codon encoding a different amino acid without severe effects on the function of the protein.2 These are called amino acid substitutions. Of the "essential" codons, many can tolerate mutations that create synonymous codons. Putting these facts together suggests that only about 20% of mutations to protein encoding regions are detrimental. The rest are effectively neutral.

This partially explains why we can tolerate 130 mutations per individual per generation. If only 20% were detrimental then the genetic load is reduced to about 26 mutations per generation.

That's still unacceptably high. It leads to the idea that a large percentage of our genome must be unaffected by mutations. In other words, genes represent only a small percentage of our genome and mutations can freely accumulate in the rest without detrimental consequences.

In order to bring the genetic load down to acceptable levels, the number of genes has to be less than 40,000 according to the arguments made in the 1960s. We now know that we have only 20,000 genes. Most of them encode proteins and the coding regions of those genes make up about 40,000,000 bp or about 1.3% of our genome [Junk in Your Genome: Protein-Encoding Genes].

Recall that only 20% of mutations in coding regions are likely to be detrimental. That means that the effective target size for detrimental mutations is about 20% x 1.3% = 0.26% of our genome. Out of 130 mutations, only 0.3 per individual per generation will be detrimental.3

Since we are diploid organisms, the 130 mutations in the zygote are spread out over two copies of our genome but almost all of them will be in the chromosomes coming from the father. Every zygote inherits one complete set of chromosomes with hardly any mutations while the other set has less than one detrimental mutation.

Because a large percentage of gene mutations are neutral, and because most of our genome is junk, we can easily tolerate 130 mutations per individual per generation without going extinct.

Creationists will never understand this because: (a) they believe that modern evolutionary theory is all about "Darwinism" and Darwinian evolution doesn't recognize neutral mutations and random genetic drift, and (b) they can't admit to junk DNA because that's the opposite of what intelligent design would look like.


1. Similar arguments apply to genes that make functional RNAs and not proteins.

2. Over the course of several billion years of evolution it is unusual to see more than 30% sequence similarity between homologous genes. I realize that this is a somewhat circular argument but it's still a good one.

3. There are lots of other regions of the genome where mutations can be detrimental. I don't mean to imply that only protein encoding regions can be affected by mutations. Collectively, these other regions don't make up more than a few percent of our genome and they can tolerate many mutations [Genomes & Junk DNA]

Monday, November 16, 2009

Genetic Load

 
If the average rate of deleterious mutations is about 1 per individual per generation then the species can't survive. It means that most offspring will carry a mutation. This is an intolerable genetic load for a species.

In fact it's worse than that. Simple calculations suggest than even a rate of 0.1 deleterious mutations per individual will spell doom for the species. This is a well-known limitation and it was widely used in developing several key components of evolutionary theory and in explaining the size and composition of eukaryotic genomes.

The average total mutation rate in humans is about 130 mutations per genome per generation. Scordova concludes that this proves Intelligent Design Creationism [Nachman’s Paradox Defeats Darwinism and Dawkins’ Weasel]. It does no such thing. It proves once again that a little knowledge is a dangerous thing—especially in the mind of an IDiot.


Monday's Molecule #144

 
This is another one of those times when there's no "molecule" that provides a clue to a Nobel Laureate.

Your task is to identify this creature and the reason why it's important. There are three Nobel Laureates who might be associated with the creature but two of them have already been covered. The last name of the this week's Nobel Laureate does not begin with the letters "E" or "D". Who is it?

The first person to identify the "molecule" and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, Bill Chaney of the University of Nebraska, Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong and Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Dima, and Bill have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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


The Hat Gene

 
Humans have always had a urge to cover their heads with various forms of headgear. There must be a hat gene in our genomes and it probably evolved in the human lineage after it split from chimpanzees. Chimps don't wear hats.

If you believe this then you've probably fallen for the idea that FOXP2 is a gene for language and that there's a gene for God/religion. See The hunt for the Hat Gene for a good discussion of where you're going wrong.


Bill Maher on Vaccination

 
Bill Maher has attempted to clarify his position on vaccination [Vaccination: A Conversation Worth Having]. His blog is a lot like his TV show. It's a confusing, rambling, attempt at justifying an indefensible position using (attempted) humor, sarcasm and anecdote as a substitute for rationalism.

The question is whether vaccinations are good or bad. It's a strictly scientific question with a well-known scientific answer.

As far as I can tell, these are Bill Maher's main reasons for opposing vaccinations.
  1. You wouldn't need to have vaccinations if you had a healthy immune system to begin with. (And I'm sure he has some opinions on what you should eat to ensure a healthy immune system.)

  2. The success of vaccinations has been exaggerated by the medical community but he's not accusing anyone of a conspiracy.

  3. Vaccines have bad things in them and they may be harmful to healthy people.

  4. Vaccinations are supported by drug companies and you need to be skeptical about anything that's supported by large for-profit corporations.
I'm just trying to represent an under-reported medical point of view in this country, I'm not telling a specific pregnant lady what to do. With unlimited air time, I would have, for example, added to my discussion with Dr. Bill Frist on October 2 that, yes, any flu or health challenge can be dangerous when you're pregnant, and if your immune system is already compromised by, for example, eating a typical American diet, then a flu shot can make sense. But someone needs to be representing the point of view that says the preferred way to handle flus is to have a strong immune system to begin with, and getting lots of vaccines might not be the best way to accomplish that over the long haul.

Now, sometimes its OK to fuck with nature -- I believe "intelligent design" is often anything but intelligent; that "God's perfect universe" is actually full of fuck ups and design flaws, like cleft lips and Down Syndrome -- so correcting nature is sometimes the right thing to do. And then, sometimes its not. For me, the flu shot is in the "not" category.

In addition, my audience is bright, they wouldn't refuse a flu shot because they heard me talk about it, but if they looked into the subject a little more, how is that a bad thing? If they went to the CDC Web site and saw what's in the vaccine -- the formaldehyde, the insect repellent, the mercury -- shouldn't they at least get to have the information for themselves?
Instead of setting up this straw man of me not understanding germs or viruses, let's have a real debate about how much we should use vaccines and antibiotics. Of course it's good that we have them in our arsenal, but isn't the real skeptic the one who asks if these powerful but toxic methods do harm to what actually is a a very good defensive system, the one you were born with?

Also, I have never said there was a medical conspiracy. In fact, when Howard Dean asked me that, my response was "I wouldn't call it a conspiracy." Any more than there's a conspiracy for the Pentagon budget to be obscenely bloated and operated largely for the corporate welfare of defense contractors. If these are conspiracies, they're mostly legal ones that happen in plain sight. (Good time here to plug the hostess' book, Pigs At the Trough, it's all in there!) I have, in fact, used the phrase "medical-pharmaceutical-food industry" complex in comparing it to Eisenhower's famous depiction of a "military-industrial complex."
I believe in science and I believe in studies to determine the truth. I also believe Senator Ron Wyden of Oregon was correct when he said recently on MSNBC: "If you've got a checkbook in this town, you can get just about any set of facts you want." So if I remind you of a conspiracy theorist, you sometimes remind me of Britney Spears when she said "we should just do whatever the president says to do, and not ask questions and just support him." The medical community can be brutal on dissent, which would hold more weight if I thought this was a terribly healthy country, which it isn't. Health care is one sixth of our economy, and we spend way more on it than any other nation. The elephant in the room of the health care debate is that we are going to have a high health care bill every year no matter what law they pass because we're sick -- we need a lot of drugs and services.

Am I a conspiracy theorist if I suggest that since the network's nightly news broadcasts are sponsored almost entirely by prescription drug ads, that you might have to hold your breath a long time before you hear the alternative point of view to using pharmaceuticals to cure all our ailments?

Is it conspiracy theory to believe that American medicine too much treats symptoms and not root causes of disease? I always ask my friends when they go to the doctor for something, "Did your doctor ask you what you eat?" The answer is almost always 'no,' and a lot can be cured with diet and a healthier lifestyle. (And a lot can't. I also understand the role of genetics and generations of artificial selection). But Americans don't want to hear that, so doctors don't push it. It's easier and more profitable to write a prescription for Lipitor. They're not bad people, and at the end of the day, you can't make someone eat right. I like and respect all the M.D.s I've had over the years, and for the record, I have a naturopath doctor and I have a Western doctor. I would make an analogy to Republicans and Democrats: in both politics and health, I don't commit to either party because I'm on the side of the truth, whoever has it. In both cases, I'm an Independent.
This last quotation is the most revealing of all. Bill Maher listens to his naturopath doctor and feels competent to distinguish the truth when his quack doctor disagrees with evidence-based medicine (e.g. "Western" medicine).

In addition to falling for quackery, Bill Maher is making an elementary error in logic. Yes, it's true there are problems with modern medicine and the influence of drug companies, especially in the USA. But that's not to be confused with a rational discussion about the value of vaccinations. The scientific judgment about whether vaccinations are good or bad is independent of any opinions you might have about conspiracies, imagined or otherwise. The real question isn't about drug companies, it's whether you accept science or quackery.

The scientific evaluation of vaccination takes place in many countries throughout the world, including those with socialized medicine. They have all concluded that vaccinations are a proven technology that prevents disease.


[Hat Tip and Thank-you to esaul]

Friday, November 13, 2009

timmyme

 
Ms Sandwalk just got an iPhone. She's thrilled by all the things it can do and I'm happy for her. However, most of the things an iPhone does are not important to me. I already have a camera and I'm not interested in iTunes. My Samsung flip phone works just fine, thank-you very much.

Up until last week, getting an iPhone was the last thing on my mind. It was a waste of money as far as I was concerned.

Then I learned about a wonderful app called timmyme [Tim Hortons coffee locator comes to the iPhone]. This little program allows you to find the nearest Tim Hortons no matter where you are in the civilized world.

I have to have an iPhone. To hell with the cost.


Where do we come from? Where are we going?

 
This is the runner-up in Discover magazine's "Evolution in Two Minutes" contest. It was selected by PZ Myers [The Winner: Evolution in Two Minutes].

I seem to be one of the few people who think this is a horrible way to teach the public about evolution. I guess that's why I'm a curmudgeon.

I think we can do much better. I think we should do better.




The Theory of Evolution

 
Here's one of the submissions to Discovery Magazine's "Evolution in Two Minutes" contest. It's the one chosen by viewers [The Winner: Evolution in Two Minutes].

I wish we could stop talking about "The" theory of evolution. There's really no such thing and the term conjurs up thoughts of evolution being only a theory. A better term is evolutionary theory.1 A short description of modern evolutionary theory would include population genetics, the major mechanisms of evolution (natural selection and random genetic drift), and the latest theories of speciation. More sophisticated versions of evolutionary theory might include punctuated equilibria, lateral gene transfer, symbiosis, neutral theory, group selection, kin selection, species sorting and molecular phylogeny.

But before you can talk about any of these things you have to define evolution so that we all know what we're talking about. The consensus scientific definition of evolution—the fact, not the theory—is: "Evolution is a process that results in heritable changes in a population spread over many generations" or some related variation of that statement [What Is Evolution?].

The makers of these videos are free to select a definition that is not the consensus scientific definition but why would they do that? Is it a good idea to use another definition to teach the general public about evolution? What purpose does that serve?




It's OK to talk about The theory of natural selection or The theory of punctuated equilbria.

Thursday, November 12, 2009

Three Options

 
Here's a multiple choice question from Barry Arrington on Uncommon Descent [Is a Modern Myth of the Metals the Answer?].

He's concerned about the "fact" that "Darwinism" leads to immorality.
There are three and only three options.

1. We can continue to fill our children’s heads with standard Darwinian theory (which Dennett rightly calls “universal acid”), understanding that at least some of them are going to put two and two together and realize that the acid has eaten through all ethical principles – and act accordingly.

2. We can try to come up with a secular noble lie. “OK kids. You might have noticed that one of the implications of what I just taught you is that your lives are ultimately meaningless and all morals are arbitrary, but you must never act as if that is true because [fill in the noble lie of your choice, such as “morality is firmly grounded on societal norms or our ability to empathize with others”].

3. We can teach our children the truth – that the universe reveals a wondrous ordered complexity that can only be accounted for by the existence of a super-intelligence acting purposefully. And one of the implications of that conclusion is that God exists, and, reasoning further, He has established an objective system of morality that binds us all, and therefore the moral imperatives you feel so strongly are not just an epiphenomenon of the electro-chemical states of your brain.

Looking around I see that for the last several decades we have tried options one and two, and we have gotten what we have gotten. I vote to give option three a run.
Tough choice. I guess I'll opt for #2 although I don't think that telling children the truth about where morality comes from is a lie.

And correct me if I'm wrong, but haven't we already tried #3? It didn't work out very well, did it?


Wednesday, November 11, 2009

Nobel Laureate: Johannes Fibiger

 

The Nobel Prize in Physiology or Medicine 1926

"for his discovery of the Spiroptera carcinoma"


Johannes Andreas Grib Fibiger (1867 - 1928) won the Nobel Prize for "proving" that gastric tumors could be caused by a nematode, Spiroptera carcinoma (now called Gongylonema neoplasticum). Unfortunately, later work showed that the nematode was not the cause of cancer, although it may contribute to a worsening of the symptoms.

This is one of the worst mistakes that the Nobel Prize committee has ever made in awarding a science prize. How did it happen?

Fiberger is rightly celebrated for his many important contributions to experimental medicine and for pioneering a modern version of clinical trials. When he learned of the work of Katsusaburo Yamagiwa, who induced cancer in rabbits by treating their skin with coal tar, he promoted Yamagiwa's results in Europe. Many people believe that Yamagiwa should have received the Nobel Prize.

Here is the entire Presentation Speech. The work sounds like something that deserves a Nobel Prize, doesn't it?
THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen.

Few diseases have the power of inspiring fear to the same degree as cancer. However, who would be surprised at that? How many times is this affliction not synonymous with a long, painful and grievous illness, how many times is it not equivalent to incurable suffering? It is therefore natural that we should strive to throw light upon its nature; but the road to this discovery is both long and difficult. Cancer always, in fact, presents the investigator with a number of obscure and unsolved problems. Thus the cause of cancer has for a long time baffled the penetrating studies of the most tireless research workers. Fibiger was the first of these to succeed in lifting with a sure hand a corner of the veil which hid from us the etiology of the disease; the first also, to enable us to replace with precise and demonstrable theories the hypotheses with which we had had to content ourselves.

For example, it had been thought for a long time that a causal connection existed between cancer and a prolonged irritation of some sort, mechanical, thermal, chemical, radiant, etc.; this supposition was supported by the incidence, sometimes verified, of cancer as an occupational disease. Cancer occurring in radiologists, chimney sweepers, workers in the manufacture of chemical products, establish so many examples of cancerous infection that one might believe they were provoked by radioactive or chemical irritation. However, each time experiment was resorted to in an attempt to provoke cancer in animals by irritants of this nature, it failed, and the animals refused to contract the disease.

Others, with all the more reason, sought to find in cancer the work of microparasites, for true neoplastic epizootics were thought sometimes to have been established in the animal world. But research into the pathogenic agent, the «cancer bacillus», and the experiments attempting to inoculate the disease had remained fruitless. Cancer has been equally attributed to other parasites, and notably to the worm. But, just as the attempts to provoke cancer, whether by inoculation or by irritation remained unproductive, in the same way it proved impossible to demonstrate experimentally that the disease was attributable to worms. These authorities who continued to support this thesis were, moreover, frequently considered to be fantasts. Because of the failure of attempts to establish, by experiment, the accuracy of any theory, there was no clear idea concerning the cause of cancer, and such in general was the position of this question. Then it was, in 1913, that Fibiger discovered that cancer could be produced experimentally.

It is of the greatest interest to follow Fibiger along the laborious path of his research. The first idea of his discovery, which was to make his name celebrated the world over came to him in 1907: he recorded in three mice in his laboratory (originating from Dorpat), a tumour, unknown until that time in the stomach; in the centre of the neoplasm he noted the presence of a worm belonging to the family of Spiroptera.

Fibiger did not succeed at first in proving a relationship existing between the formation of the neoplasm and the worm. The attempts to provoke a cancer in healthy mice by making them ingest neoplastic tissue from diseased mice, and containing worms or eggs, failed completely. Fibiger then had the idea that perhaps this worm, like many others, underwent part of its evolution from an egg to an adult individual in another animal, which served as an intermediate host. After numerous and vain attempts to find again mice attacked by the tumours seen in 1907 - he unsuccessfully examined more than 1000 animals - Fibiger eventually discovered in a sugar refinery in Copenhagen mice who exhibited in considerable numbers the type of tumour he was seeking; in these tumours he found once again the worm he had observed in 1907. The factory was at this time infested with cockroaches, and Fibiger was then able to establish that the worm in its evolution used these cockroaches as intermediate hosts. The cockroaches ingested the excreta of the mice, and with them the eggs of the worm. These developed in the alimentary tract of the cockroaches into larvae, which, like the trichina, were distributed into the muscles of the insects where they become encapsulated. The cockroaches were in their turn eaten by the mice and in the stomach the larvae transformed into the adult form.

By feeding healthy mice with cockroaches containing the larvae of the spiroptera, Fibiger succeeded in producing cancerous growths in the stomachs of a large number of animals. It was therefore possible, for the first time, to change by experiment normal cells into cells having all the terrible properties of cancer. It was thus shown authoritatively not that cancer is always caused by a worm, but that it can be provoked by an external stimulus. For this reason alone the discovery was of incalculable importance.

But Fibiger's discovery had a still greater significance. The possibility of experimentally producing cancer gave to the particular research into this illness an invaluable and badly needed method, lacking until this time, allowing the elucidation of some of the obscure points in the problem of cancer. Fibiger's discovery also gave remarkable impetus to research. Whereas research had, in many respects, entered upon a period of stagnation, Fibiger's discovery marked the beginning of a new era, of a new epoch in the history of cancer, to which the fruitful research made by him gave fresh vigour. From his discoveries we have continued to march forward and have gained valuable ideas as to the nature of this illness.

It is thus that Fibiger has been and will remain a pioneer in the difficult field of cancer research. «To my mind», says the famous English expert on cancer, Archibald Leitch, to name only one of the numerous critical commentators on Fibiger's research, «Fibiger's work has been the greatest contribution to experimental medicine in our generation. He has built into the growing structure of truth something outstanding, something immortal, quod non imber edax possit diruere.» It is for this immortal research work that Fibiger is today awarded the Nobel Prize for Medicine for 1926.


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.

Was Charles Darwin an Agnostic Atheist?

 
Let me say, right at the start, that I really don't care whether Charles Darwin was a deist, an agnostic, an atheist, or something else entirely. He died on April 19, 1882. That was a very long time ago. And the truth of evolution does not depend on what Darwin may or may not have believed about God.

Still, it's of some historical interest to learn what Darwin thought of religion. My own opinion is that these speculations are never going to be satisfactorily answered because Darwin was not always candid about his beliefs, for Emma's sake.

It may come as a bit of a surprise to find me favorably recommending an article on Uncommon Descent but this article by Flannery deserves your attention: Theist, Agnostic, Atheist: Will the Real Charles Darwin Please Stand Up?.

It's not going to make my agnostic friends happy but I think it's a pretty good analysis of Darwin's beliefs. I especially like the emphasis on the fact that his grandfather wasn't religious and his father (Robert) was an atheist. I'm pretty sure that his brother, Erasmus, was a nonbeliever as well. It strains credibility to imagine that Darwin was ever a religious man.


November 11, 2009

 
Today is Remembrance Day in Canada. It's a day to remember that war is evil and horrible. It's a day to remember that war represents the ultimate failure of a civilization.

War is not glorious. People who kill other people are not heroes. The people they kill are not heroes. We are shamed when we turn average citizens into murderers. We lament their deaths because it means we have failed in our responsibility to maintain peace. They paid the price of our failure.

Soldiers are a necessary evil, like prison guards. The long range goal of a humane society is to eliminate armies (and prisons). Once a year, on this day, we need to think about how far we are from achieving that goal and what we can do to make it a reality.

We need to remember our past—the dirty, ugly, face of death and destruction—and resolve never to repeat it. We need to apologize to those men and women we forced to endure those horrors. We need to promise our children that we won't make them go to war.

No war is necessary. Tanks, bombers, and battleships are not necessary. I dream of an eleventh day of the eleventh month when, at the eleventh hour, no cannons are fired, no soldiers are marching, and no fighter planes are flying overhead. That will be a day to remember.

The greatest generation will be the one that avoids war. Perhaps our children's children will be that generation.


[Photo: Dresden, February 14, 1945]

[Poster by Lorraine Schneider (1925-1972), for the Los Angeles organization Another Mother for Peace, 1967.]

Tuesday, November 10, 2009

The Positive Argument for Intelligent Design Creationism

 
I've often been critical of the arguments made by IDiots Intelligent Design Creationists. They consist mostly of claims that evolution can't happen.

It's only fair that I point you to a rebuttal of this point of view by none other than Casey Luskin [Misrepresenting the Definition of Intelligent Design].
Scott Minnich and Stephen Meyer also explain the positive argument for design:
Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system … in any other context we would immediately recognize such systems as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes. (“Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic Bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (2004).)
Let's see if I've got this right. We know about lots of irreducibly complex systems, such as the Krebs cycle and the bacterial flagella, that could easily have arisen by evolution. Nevertheless, according to the IDiots, we have to conclude that all such systems can only have been created by God.

That's what passes for a positive argument for Intelligent Design Creationism. I assume it's the best they've got.


Monday's Molecule #143: Winner

 
The creature is a nematode, specifically a Soybean cyst nematode. The relevant Nobel Prize was to Johannes Fibiger who got for it "discovering" that the nematode Spiroptera carcinoma causes cancer. This species is now called Gongylonema neoplasticum and it doesn't cause cancer. Oops!

The first person to get it right was Linda Zhang, a former student at the University of Toronto who will soon be on her way to graduate school at the University of Hong Kong. The undergraduate winner is Kirill Zaslavsky, a Neuroscience student at the University of Toronto.

Many others got the right answer. It was easier than I thought it would be.



Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is another one of those times.

This spectacular photograph shows a particular kind of creature and its egg. You need to identify the phylum to which this species belongs and then use that as a clue to come up with an appropriate Nobel Laureate. Your answer should include the particular species that is associated with the Nobel Prize as well as the Nobel Laureate. Be careful, I want the modern name of the species—not the old name that was used when the Nobel Prize was announced.

Here's a clue. The Nobel Prize was awarded in the last century, not the current one. Here's another clue, outside of the Nobel Peace prize and the mini-Nobel Prize in Economics, this award is probably the biggest mistake that the prize committee has ever made.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are six ineligible candidates for this week's reward: Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, and Bill Chaney of the University of Nebraska.

Joshua, Dima, and Bill have all agreed to donate their free lunch to an undergraduate. Consequently, I have three extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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


[Photo Credit: Wikipedia]

PZ Myers Gets It Wrong

 
Discover magazine sponsored a contest where you had to produce a two minute video explaining evolution. The judge was PZ Myers. Here's how PZ explains his choice [see The Winner: Evolution in Two Minutes].



Oh dear. Repeat after me, PZ, evolution is not natural selection!

This is, indeed, the 21st century, and not the Victorian England of Charles Darwin. We now know that evolution is any change in the frequency of alleles in a population. We know that for evolution to occur the change has to be genetic. We know that populations evolve, not individuals. We know that there are two main mechanisms of evolution: natural selection, and random genetic drift. It's a good idea to mention that variation within a species (population) arises from spontaneous mutations that create gene variants called alleles. That's what needs to be explained in two minutes.

Here's the winning video from Scott Hatfield, a high school biology teacher, and, more importantly, a blogger at Monkey Trials. Scott's a cool guy but it's not the video I would have chosen.



2009 AAAS Kavli Science Journalism Awards

 
The American Association for the Advancement of Science has just announced the Kavli Science Journalism Awards for 2009. It's a very interesting group of winners. Among them is Carl Zimmer, who won in the category "Large Newspaper—Circulation of 100,000 or more."

Awards are nice, but the problem with science journalism awards is that they are decided by a panel of science journalists. What this means is that the awards are for good journalism and not necessarily for good science. As most Sandwalk readers know, I'm not happy with the way science is presented to the general public and my main complaint about science writers is that they don't do a very good job of getting the science right. (Many scientists aren't much better, but that's a different issue.)

If we are going to award good science journalism, don't you think that one of the main criteria should be whether the reporting is scientifically accurate? If you accept that premise, then the next question is who should make that call.

Take Carl Zimmer's articles for example. One of them was Now: The Rest of the Genome published in The New York Times in November 2008. This is an article about genes and genomes and the main point is that our concept of a gene is in trouble in light of recent discoveries in genomics.

Carl's article is better than most but it still misrepresents the modern status of a gene and the importance of phenomena like alternative splicing and epigenetics [Genes and Straw Men]. There's no doubt in my mind that Carl is the best of the science writers who could have written about this subject but I'm still troubled by the fact that the prize committee was probably incapable of evaluating the accuracy of the science in his article.

The award is sponsored by AAAS. What would be wrong with having a few scientists as judges?

From the press release ...
"The AAAS awards have long recognized the importance of high-quality science journalism across the board," said Cristine Russell, president of the nonprofit Council for the Advancement of Science Writing. "The Kavli Foundation’s decision to endow the awards is particularly important at a time when accurate, insightful writing about science is threatened by rapid changes in the media marketplace. The future of this program is now assured as a new generation of journalists tackles important science developments and their impact on society.
I don't know Cristine Russel but she's promoting these awards as examples of "accurate, insightful writing about science." I'd love to know who determines whether the reporting is accurate. How does she know they were scientifically accurate?


Boycott Science.org

 
We all get spam in our mail box and usually there's nothing you can do about it. This time there is. I got this message today.
Subject: Award Acknowledgment for sharing great PHYSICS information to the public

Dear Blog Owner,

Our website Science.org is a informational databases and online news publication for anything and everything related to science and technology. We recently ran a poll asking our website users regarding what online informational resources they use to keep up to date or even to simply find great information. It seems many of our users have labeled your blog as an excellent source of Space information. We have reviewed your blog and must say, we absolutely love the information you have made available to the public and would love to make your blog a part of our top science blogs. After browsing your blog, our research team has decided to award you a Top science Blogs award banner.

It is a distinction we offer to the blogs that our team feels is ahead of the curve in terms of content.

Thanks again for the great information and we look forward to the great responses your blog will receive from our site. Your blog presence will be very effective for our users (top science blogs).

We have put great efforts in making this decision to give deserving with award acknowledgment. For listing please reply to request banner.

Sincerely,
--
William Lee
Research team
Science.org
1 international blvd
Mahwah NJ USA - 07430
201 247 8553
editor.science@gmx.com
It turns out that Science.org is an actual website. Mr. Lee apparently believes that by lying to Blog Owners he can enhance the reputation of his website.

That ain't gonna work. Any website that emails such lies does not even deserve a link.



The Wreck of the Edmund Fitzgerald

 
Twenty-nine men died on November 10, 1975 when the S.S. Edmund Fitgerald sank in a storm on Lake Superior.




Monday, November 09, 2009

Amazon's Top Ten Science Books for 2009

 
Check out the Best of 2009 for two lists of the top ten science books. One list was chosen by "editors" and the other list was chosen by "readers."

There are some interesting differences ... and it's not what you expect.


[Hat Tip: Jason Rosenhouse whose book The Monty Hall Problem: The Remarkable Story of Math's Most Contentious Brainteaser made one of the lists.

Monday's Molecule #143

 
Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is another one of those times.

This spectacular photograph shows a particular kind of creature and its egg. You need to identify the phylum to which this species belongs and then use that as a clue to come up with an appropriate Nobel Laureate. Your answer should include the particular species that is associated with the Nobel Prize as well as the Nobel Laureate. Be careful, I want the modern name of the species—not the old name that was used when the Nobel Prize was announced.

Here's a clue. The Nobel Prize was awarded in the last century, not the current one. Here's another clue, outside of the Nobel Peace prize and the mini-Nobel Prize in Economics, this award is probably the biggest mistake that the prize committee has ever made.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are six ineligible candidates for this week's reward: Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Alex Ling of the University of Toronto, and Bill Chaney of the University of Nebraska.

Joshua, Dima, and Bill have all agreed to donate their free lunch to an undergraduate. Consequently, I have three extra free lunches for deserving undergraduates. I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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


[Photo Credit: Wikipedia]

Friday, November 06, 2009

Ginkgo biloba

 
Ginko biloba is the only living species in the division (phylum?) Ginkgophyta. It is a species of deciduous tree that's only distantly related to to the other trees that we see around us. Some taxonomists classify it as a gymnosperm but that's not a universally recognized classification. It's certainly not an angiosperm (flowering plant).

Ginkgo is often called a "living fossil" because it resembles plants that date from 270 million years ago. The term is misleading because, like other "living fossils" Ginko biloba has evolved considerably since the time of its similar-looking ancestors.

The trees are either male or female. I recently visited a beautiful example of a female tree growing in the yard of Frank Lloyd Wright's house in Oak Park in the suburb's of Chicago. The tree was full of "berries" (technically not fruit), which were about to drop. I'm told that the berries are edible but not very pleasant. They smell like human feces. (The pun is obvious ... don't bother. )

I wish I'd been there a bit later 'cause ever since I learned about Ginkgo I've wanted to taste the berries.

All of the trees in North America have been deliberately planted by gardeners. The one in the yard of the Frank Lloyd Wright house was already there when Wright bought the property in 1889. It's estimated to be about 160 years old. They don't grow very well in most parts of Canada.

I was under the impression that the tree is native to some parts of China but recent genotyping of the trees suggests that even those trees may have been deliberately planted there by ancient monks.



Thursday, November 05, 2009

Charles and Camilla Are in Town

 
Charles and Camilla are visiting Toronto but you wouldn't know it if you didn't read the papers. Unless, of course, you just happen to be caught up in one of the mini traffic jams that are associated with such visits.

I witnessed one last night as several motorcycles and police cars with red and blue lights flashing, and sirens wailing, raced up University Avenue and around Queen's Park. They were escorting a convoy of half a dozen limos. I figure they were exceeding the speed limit by quite a bit.

Today, Charles is accompanying Camilla to Dundurn castle in Hamilton. The great house was built by Sir Allan Napier MacNab who happens to be Camilla's great-great-great grandfather. MacNab was Prime Minister of the Province of Ontario and was a member of the ruling elite that William Lyon Mackenzie opposed in the 1837 "rebellion."

This is Camilla's first visit to Canada. Charles has been here too often.

The couple will be opening the Royal Agricultural Winter's Fair before flying back to England.

For those of you interested in genealogy, here's how Camilla is related to MacNab.

Allen Napier MacNab (1798-1862)
m. Mary Stuart (1812-1846)
      Sophia Mary MacNab (1832-1917)
      m. William Coutts Keppel (1832-1894)
            Honourable George Keppel (1865-1947)
            m. Alice Frederica Edmonstone (1869-1947)
                  Sonia Rosemary Keppel (1900-1986)
                  m. Roland Calvert Cubbitt (1899-1962)
                        Honourable Rosalind Maud Cubbitt (1921-1994)
                        m. Bruce Middleton Hope Shand (1917- )
                              Camilla Rosemary Shand (1947- )
                              m. (1) Andrew Henry Parker-Bowles
                                    (2) Charles, Prince of Wales



Nobel Laureate: Lee Hartwell

 

The Nobel Prize in Physiology or Medicine 2001

"for their discoveries of key regulators of the cell cycle"

Leland H. Hartwell (1939 - ) won the Nobel Prize for his contributions to understanding the cell cycle. His discovery of the regulatory molecule CDC28 led to the idea of "checkpoints"—steps in the cell cycle where specific action is needed to progress to the next stage.

Hartwell shared the 2001 Nobel Prize with Paul Nurse and Tim Hunt.

Some of you may think that elucidation of the cell cycle in yeast isn't such a big deal. You would be wrong. No only did this work stimulate a huge field of study in yeast, but the genes and the pathways uncovered in yeast are similar to those in other eukaryotic cells. This is a case where fundamental basic science has lead to a deep understanding of how life works at the molecular level.

THEME:
Nobel Laureates
I already posted the press release under Nobel Laureate: Sir Paul Nurse. It's a very good description of the work that was done by all three Nobel Laureates.

Here's an excerpt from the Presentation Speech.

This year's Nobel Laureates have discovered the key regulators of the cell cycle, cyclin dependent kinase (CDK) and cyclin. Together these two components form an enzyme, in which CDK is comparable to a "molecular engine" that drives the cell through the cell cycle by altering the structure and function of other proteins in the cell. Cyclin is the main switch that turns the "CDK engine" on and off. This cell cycle engine operates in the same way in such widely disparate organisms as yeast cells, plants, animals and humans.

How were the key regulators CDK and cyclin discovered?

Lee Hartwell realized the great potential of genetic methods for cell cycle studies. He chose baker's yeast as a model organism. In the microscope he could identify genetically altered cells - mutated cells - that stopped in the cell cycle when they were cultured at an elevated temperature. Using this method Hartwell discovered, in the early 1970s, dozens of genes specific to the cell division cycle, which he named CDC genes. One of these genes, CDC28, controls the initiation of each cell cycle, the "start" function. Hartwell also formulated the concept of "checkpoints," which ensure that cell cycle events occur in the correct order. Checkpoints are comparable to the program in a washing machine that checks if one step has been properly completed before the next can start. Checkpoint defects are considered to be one of the reasons behind the transformation of normal cells into cancer cells.


[Photo Credit: Susie Fitzhugh and the Fred Hutchinson Cancer Research Center]

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.

"Dr." Charlene Werner on Homeopathy

 
This video illustrates the extreme stupidity of those who believe in homeopathy.

The person who posted the video on YouTube recently received the following letter.
I thought you would like to know that you will be contacted by Dr Werner's Attorney shortly regarding her video. The posting of this video is in violation of copyright laws. We are aware that you have had this video up since March of '08 however I suggest you delete it immediately.

Jayson Patrick
This immediately triggers the Streisand Effect. Won't these people ever learn? No, of course not, that's because they are stupid.

Watch if you dare.





Tuesday, November 03, 2009

Monday's Molecule #142: Winner

 
The diagram should remind you of the cell cycle and the 2001 Nobel Prize in Physiology and Medicine. Since I already covered Tim Hunt and Paul Nurse, this must be about Lee Hartwell. That means the molecule must be "start" or CDC28.

The winner is Bill Chaney of the University of Nebraska. He has agreed to donate his free lunch to an undergraduate. Unfortunately, there weren't any undergraduate who got the right answer this week so I still have three free lunches to give away.




Sometimes it's almost impossible to find an image of a specific molecule that honors a Nobel Laureate. This is one of those times.

The diagram provides all the clues necessary to identify an important process and then to identify a particular molecule associated with this week's Nobel Laureate.

You must name the molecule and the Nobel Laureate. Be careful 'cause it's easy to make a mistake and name someone who has already been the subject of a Monday's Molecule.

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only six ineligible candidates for this week's reward: Frank Schmidt of the University of Missouri, Joshua Johnson of Victoria University in Australia, Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany, Jason Oakley a biochemistry student at the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Alex Ling of the University of Toronto.

Joshua and Dima have agreed to donate their free lunch to an undergraduate. Consequently, I have two extra free lunches for deserving undergraduates so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

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(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes 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.

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