Tuesday, July 31, 2012

Carbon Dioxide Fixation in the Dark Ocean

Cells require both a source of energy and a source of building blocks for synthesis of organic (carbon-containing) molecules. Some of the most interesting species are those that only need inorganic molecules to survive. They can make all their carbon compounds from carbon dioxide (CO2) by "fixing" it into more complex molecules like sugars.

These species are called "autotrophs'" The most familiar are the plants. As most of you know, plants can grow quite successfully in a glass of water (with minerals). Animals are the most obvious example of "heterotrophs," species that need to be supplied with complex organic molecules in order to survive. We can't survive on water alone. We need to get sugars and a host of other compounds from eating other (mostly dead) species.

Oscar Miller (1925 - 2012)

Oscar Miller died last January. Steven McKnight, Ann Beyer, and Joseph Gall (2012) wrote up a nice tribute to their former mentor.
Those of us so fortunate as to have worked under his guidance learned how to think freely, yet rigorously, and how to dream big and gamble on new adventures. We learned from Oscar how to free ourselves from convention, yet abide by the principles of science as crafted by its most honorable pillars. We remember two pieces of advice given by Oscar: “Don't believe everything you read in the scientific literature” and “There are a thousand Ph.D. thesis projects in a mound of dung.” The latter brings to mind the famous phrase of Vannevar Bush that science is an “endless frontier.” Oscar Miller was comfortable on the frontier of the unknown; he taught us that it is only on the frontier that discoveries of significance can be made. Our community of science will miss Oscar, as will all his dear friends and family. A good man has passed.
Most of you have never heard of Oscar Miller but you've seen his work. He invented a technique for looking at genes in the electron microscope. The beauty of his technique, called "chromatin spreads" is that it shows genes in action. They are captured in the act of being transcribed and you can see the RNA being produced.

His photographs are in all the textbooks. The example shown here is ribosomal RNA genes being transcribed in the nucleolus. The "Christmas tree" structures are due to multiple transcription complexes transcribing the same gene. (Ribosomal RNA genes are very active.) The newly synthesized RNA is splayed out on either side of the DNA being transcribed. It would look like a cone inside the cell but it appears two dimensional here because it has been spread out on an electron microscope grid.

The initial transcripts are quite short but as the transcription complexes progress along the gene they get longer and longer giving rise to the Christmas tree structure. You can learn a lot from looking at these fantastic pictures. Notice that there are multiple ribosomal RNA genes arranged in tandom along the genome with relatively short spacers between them. These photos were taken before cloning and sequencing were invented so it was our among our first clues about gene organization in eukaryotes.

There's not much actual data from the 1960s that's still shown in modern textbooks. Remember Oscar Miller the next time you see his work.


McKnight, S., Beyer, A., and Gall, J. (2012) Retrospective. Oscar Miller (1925-2012). Science 335:1457. [DOI: 10.1126/science.1220681

Monday, July 30, 2012

Monday's Molecule #179

Last week we discovered two chemically similar reactions that were catalyzed by related enzymes of the same gene family [Monday's Molecule #178]. Today's molecule is a lot more important than any of the four molecules from last week although you won't find it in most biochemistry textbooks. (Surprise! It's in my book.)

What is this molecule (IUBMB name) and why is it important?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is 2-carboxy-3-ketoarabinitol 1,5-bisphosphate, an intermediate in the reaction catalyzed by rubisco (ribulose 1,5-bisphosphate carbozylase-oxygenase). This is the main enzyme responsible for carbon dioxide fixation in plants and one of the most enzymes on the planet.

This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa


Stephen Fry and the Two Cultures Problem (Brits vs Americans)

I can't believe it was almost five years ago that I posted a quotation from Stephen Fry on the differences between dinner conversations in Britain and America [Two Cultures].

Here it is again because it's relevant to our discussion about IDiots. It's from: Getting Overheated (Nov. 19, 2007).
We must begin with a few round truths about myself: when I get into a debate I can get very, very hot under the collar, very impassioned, and I dare say, very maddening, for once the light of battle is in my eye I find it almost impossible to let go and calm down. I like to think I’m never vituperative or too ad hominem but I do know that I fall on ideas as hungry wolves fall on strayed lambs and the result isn’t always pretty. This is especially dangerous in America. I was warned many, many years ago by the great Jonathan Lynn, co-creator of Yes Minister and director of the comic masterpiece My Cousin Vinnie, that Americans are not raised in a tradition of debate and that the adversarial ferocity common around a dinner table in Britain is more or less unheard of in America. When Jonathan first went to live in LA he couldn’t understand the terrible silences that would fall when he trashed an statement he disagreed with and said something like “yes, but that’s just arrant nonsense, isn’t it? It doesn’t make sense. It’s self-contradictory.” To a Briton pointing out that something is nonsense, rubbish, tosh or logically impossible in its own terms is not an attack on the person saying it – it’s often no more than a salvo in what one hopes might become an enjoyable intellectual tussle. Jonathan soon found that most Americans responded with offence, hurt or anger to this order of cut and thrust. Yes, one hesitates ever to make generalizations, but let’s be honest the cultures are different, if they weren’t how much poorer the world would be and Americans really don’t seem to be very good at or very used to the idea of a good no-holds barred verbal scrap. I’m not talking about inter-family ‘discussions’ here, I don’t doubt that within American families and amongst close friends, all kinds of liveliness and hoo-hah is possible, I’m talking about what for good or ill one might as well call dinner-party conversation. Disagreement and energetic debate appears to leave a loud smell in the air.


There Are Many Ways to Improve High School Education: Dumbing It Down Is NOT One of Them

Have you ever been at a social gathering and heard someone proclaim, somewhat proudly, that they just don't "get" math? They dropped it in high school as soon as they could. If so, you probably resisted telling them how sorry you are that they are stupid and you probably avoided getting into a discussion about people who say the same thing about history or literature. You know that those same people would be appalled to hear you say that you don't "get" the arts and dropped them as soon as you could.

If Andrew Hacker has his way, people who can't pass a simple math course will never have to apologize again. He proposes, in the New York Times, no less, to eliminate algebra from high school [Is Algebra Necessary?]. (Andrew Hacker is a former professor of political science.)

Darwinists Don't Believe in Junk DNA

The "news" on Uncommon descent continues to amaze me. Today they put up a post with an ironic title: Sometimes, one runs into ID opponents who are just so confused ….

It caught my attention because my name was mentioned. Apparently some "ID opponent" read my take-down of Jonathan Wells' book The Myth of Junk DNA. This prompted the following response from "news" (lawyer, Barry Arrington).
"The Myth of Junk DNA" is actually quite easy to read. We’ve excerpted a number of passages here at UD. The interesting part is that Darwinists thought that the presence of huge amounts of junk DNA was evidence for their position.
If Barry Arrington had bothered to read my review of Wells' book he would know that this is a lie. You can read the entire series of posts at: The Myth of Junk DNA by Jonathan Wells but I want to draw your attention specifically to my comments on the history of the controversy: Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

Sunday, July 29, 2012

Ophelia, Daniel, I Respectfully Disagree

Ophelia Benson has put up several posts recently on the use of insulting terms in blog conversations. She is opposed. Ophelia recently linked to another Freethought blog called Camels with Hammers written by Daniel Fincke. Here's Ophelia's post: A camel with a hammer offers a tap upside the head. And here's Daniel's post: Making My Comments Rules Explicit: “Don’t Bully People With Insulting Names” and “Make Personal Charges Against Others Only In Egregious Cases”. Here's the one rule that I want to discuss; it's from Daniel Fincke's post but Ophelia quotes it approvingly.
No insulting people. This means not calling them abusive names or making insulting insinuations about them which according to my judgment unnecessarily demean them as a person or which I take to be intended to demean them as a person. You may charge that people’s ideas are false, harmful, irrationally derived, etc. You may substantiate charges that someone’s personal behavior deserves moral disrepute where that’s relevant. You may critique an individual’s standards of evidence or question their commitment to reason over faith. But when you do things like this, stick to substantiatable charges. Use words which clearly specify what specific thing makes a person or institution’s ideas, beliefs, behaviors, attitudes, etc. worthy of criticism. Abusive names (like “stupid”, “moron”, “asshole”, “jerk”, “douchebag”, “idiot”, “motherfucker”, “dick”, “cunt”, “nigger”, “Feminazi”, “shitbag”, “mental midget”, “twat”, “fuckwad”, “retard”, “homo”, “fag”, “tranny”, “bitch”, “nutcase”, “crazy”, etc.) are emotional expressions meant solely to hurt other people. They are social equivalents of physical assaults.
I know where they're coming from. They're talking mostly about racist and sexist comments since that's their main concern on Freethought Blogs, for now.

For the record, I do not condone those kind of insults. Nor do I condone accusing someone of racism or sexism without very good evidence.

On the other hand, I frequently use insulting words to describe stupid people. The most obvious example is my use of "IDiot" as a shorthand for Intelligent Design Creationist. A commenter on Daniel Fincke's blog suggested that words like "stupid" were okay since they aren't homophobic, sexist, or racist. Here's how Fincke responded ...
“Stupid” is just not a word that smart people have ruining their self-esteem from the time they’re little kids.

And even yet, it is a false and belittling word that is counterproductive to constructive discourse. Calling someone stupid tempts them to either slink away in shame or to fight back with equal emotional abuse.

There are perfectly good words for telling someone that a specific idea is no good. False, empirically refuted, fallacious, absurd, illogical, unsupported by evidence, irrational, rationally indefensible, superstitious, biased. All these might work and many more. There’s no need to then personalize it by calling the person stupid or the idea stupid, which has the implication of bashing the person for thinking it.
When I use the word "IDiot" I fully intend to bash the IDiots for their stupid ideas. Why? Because their ideas are stupid and they really are idiots.

Here's where Daniel gets it wrong. I don't expect to convince the IDiots of the error of their ways any more than they intend to convince scientists by using insulting terms like "Darwinist," "materialist," and "stupid." There's no such thing as "constructive discourse" with creationists.

My audience is not the creationists I'm debating, it's the readers who might not have made up their minds about Intelligent Design Creationism. They will read the viscous attacks of these creationists on scientists (Darwinists) and wonder whether there's some truth behind them. I could reply with polite phrases like "rationally indefensible" "unsupported by evidence" and "empirically refuted" but that would be like bringing a flyswatter to a gunfight.

The general public needs to hear what passionate scientists really think of these IDiots. The best way to do that is to fight fire with fire. The idea is to plant in the public's mind the notion that these creationists are crazies and kooks, not respectable scientists with a different, but scientifically valid, opinion. We tried treating them politely for several decades and what did it get us? It got us leaders and politicians in many countries who think it's perfectly respectable to believe that evolution is false.

We were up against people like Jerry Falwell, Rush Limbaugh, and Michele Bauchmann but we were fighting with one hand tied behind our back. That's no way to win a fight like this.

The good news for the more polite proponents of rationalism, like Ophelia Benson and Daniel Fincke, is that they can be the "good cops."


What's Wrong with this List?

There are (brief) times when I wonder if it's unfair to label all Intelligent Design Creationists (IDC's) as "IDiots." I see glimmers of hope on the IDC websites where it appears that at least one or two people might actually be exhibiting signs of intelligence.

Those thoughts are short-lived. It never takes the IDiots more than a few hours to disabuse me of any such sympathies.

Yesterday, for example, Sal Cordova (scordova) posted one of the most stupid things I've seen in a long, long, time. He was bragging on Uncommom Descent about a paper by Todd Wood that is about to be published was published last year in the Journal of Evolutionary Biology. This is big news for the IDiots because they don't publish much in the peer-reviewed scientific literature.

But he couldn't leave it at that. Look what he said next [Creationist Paper Published in Peer-Reviewed Biology Journal, UD Author Cited — Origins 2012 Conference] ...
Also congratulations to our very own Uncommon Descent author johnnyb (Jonathan Bartlett) for his work being mentioned in Wood’s paper. To my knowledge, the current tally of Uncommon Descent authors and commenters that have been published or mentioned in scientific journals: William Dembski, Michael Behe, Nick Matzke, Rob Sheldon, Caroline Crocker, Winston Ewert, Paul Nelson, Cornelius Hunter, Granville Sewell, John A. Davison, Allen MacNeill, Andrea Bottaro, Abbie Smith, Peter Olofsson, Albert Voie, Andras Pellionisz, Albert De Roos, Walter ReMine, Paul Giem, Jonathan Sarfati, Arthur Hunt, Steve Matheson, Larry Moran, johnnyb, Eric Anderson, Casey Luskin, and yours truly scordova. [If I missed anyone, please chime in.]
IDiots! There's no other word to describe them.


Friday, July 27, 2012

What Do Scientists Know about Ethics?

Rosie Redfield doesn't like the way genetics is taught in most university courses. She thinks we should re-design genetics courses (Redfield, 2012).
As a first step, geneticists need to step back from the current curriculum and decide what 21st century students really need to know about genes and inheritance. These decisions should be based on how students will use what they learn, and not on what we as geneticists value.
She proposes that modern genetics courses should concentrate on subjects that really interest students. Subjects like ...
Is genetic testing a wise thing to do? Is it a sound financial investment? Should I have full access to my genetic information? Should my insurer and my employer? Should athletes be tested for genetic modifications (“gene doping”)? Is it ethical to DNA-fingerprint all convicted criminals? All suspects? Did my genes make me gay? Are genetically modified foods safe? Are cloned animals ethical? How different are human races, and how different are we all from chimpanzees and gorillas?
I explained in an earlier posting why I think this is wrong: Questions for Genetics Students. My main concern was that we might be sacrificing fundamental concepts and principles of genetics (i.e. science) in an attempt to appeal to students.

Rosie's goals sound like noble goals but is it even realistic to address these issues in a genetics course? That's the question that Heather Zeiger asks in her post on Genetics Class 2.0.
Many of these questions are ones bioethicists have been contending with for years. Bioethics is a multi-disciplinary field that is usually occupied by philosophers and healthcare professionals, but in the last twenty years it has seen an influx of lawyers, scientists, and people from many other disciplines.

Redfield suggests that it is the role of the scientist to address ethical questions. However, something that Redfield does not state in her paper, is that scientists are rarely trained in anything that would be helpful in assessing ethical issues, such as moral philosophy or rhetoric, and most programs do not include history and philosophy of science.
Now, I rarely agree with anything posted on The Best Schools but this is a legitimate concern.

My position is that philosophers and healthcare professionals have been spectacularly unsuccessful at clarifying bioethical questions. I cringe just about every time I see a "professional" bioethicist on television. Most of them can't separate science from ethics and most of them are more concerned about appeasing religion than getting to the bottom of a difficult issue.

Scientists often make much more sense but that doesn't mean that all scientists are good at dealing with ethical issues. I teach a course that deals with ethical issues (cloning, reproductive technology, immunization) and I find that it's an excellent way to get students to think critically. However, I've learned a lot from my colleagues about ethics and philosophy over the years and I don't think I would be very effective without this background1.

I doubt very much that the average genetics teacher or TA can really be effective at handling ethical debates in their classrooms. I don't think you should build a course around such issues no matter how much the students want it.


My friend, Rob Allore, taught with me for several years. He's a scientist and a Jesuit priest. This year I'll be teaching with another friend, Chris DiCarlo, a philosopher and author of How to Become a Really Good Pain in the Ass: A Critical Thinker's Guide to Asking the Right Questions.

Redfield, R. (2012) "Why Do We Have to Learn This Stuff?"—A New Genetics for 21st Century Students. PLoS Biol 10(7): e1001356. [doi:10.1371/journal.pbio.1001356]

NASA Confusion About the Origin of Life: Part II

I'm going to keep hammering on this until it sinks in.

We don't know how life began but one of the more fanciful hypotheses is that it began in a primordial soup of organic molecules supplied by meteors, comets, and violent lightening storms. The idea is that the ocean was full of glucose, amino acids, and nucleotides. Glucose and similar carbohydrates supplied the energy for life. Amino acids spontaneously came together to form proteins. Nucleic acids arose by stringing together pre-existing nucleotides or nucleosides.

In the most extreme version, the ocean itself was the primordial soup and concentrations of organic molecules were sufficient to drive the formation of life. A simple back-of-the envelope calculation indicates that the concentration of typical amino acids would have been about 0.1 nM (10-10 M) [Can watery asteroids explain why life is 'left-handed'?]. This is an unlikely scenario [More Prebiotic Soup Nonsense]. You won't get spontaneous formation of polymers in water at that concentration.

High School Students Find LUCA!

What's Wrong with this Picture?

Biology New Net posted a press release today from the American Institute of Physics: Researchers dig through the gene bank to uncover the roots of the evolutionary tree. It advertises the work of William Duax and his colleagues, including some high school students who work in his lab on Fridays.
Ever since Darwin first published The Origin of the Species, scientists have been striving to identify a last universal common ancestor of all living species. Paleontological, biochemical, and genomic studies have produced conflicting versions of the evolutionary tree. Now a team of researchers, led by a professor at the State University of New York at Buffalo and including area high school students, has developed a novel method to search the vast archives of known gene sequences to identify and compare similar proteins across the many kingdoms of life. Using the comparisons to quantify the evolutionary closeness of different species, the researchers have identified Actinobacteria, a group of single membrane bacteria that include common soil and water life forms, as the base of the evolutionary tree. They will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 – Aug. 1 in Boston, Mass.

Thursday, July 26, 2012

The Evolution of Enzymes from Promiscuous Precursors

New enzymes often evolve from old ones via a gene duplication event. This gives rise to gene families encoding evolutionarily related enzymes with similar, but different enzymatic activities.

There are two principle ways to evolve related modern enzymes with specific activities. The first way postulates an ancestral enzyme that catalyzes a specific reaction (e.g. A1 → B1). Following a gene duplication event, one of the copies evolves an enzyme that catalyzes a completely different (but chemically related) reaction: A2 → B2.

Most people think that this is by far the most common pathway. That's because they are used to thinking that enzymes are highly specific—that's what's emphasized in most biochemistry courses. They think that it should be possible to reverse engineer the evolutionary pathway on the right-hand branch and thus transform one enzyme to another.

Wednesday, July 25, 2012

Winners of the Google Science Technology Fair

Anna Kuchment was there [Google Science Fair: Winners tackle breast cancer, hearing loss and water quality]. Just once, I'd like to see a science fair winner who actually did science and discovered something about the natural world that has nothing to do with technology or applications.
An expectant crowd gathered last night inside an airplane hangar at a flight school in Palo Alto, California to hear the winners of the second annual Google Science Fair. The grand prize went to Brittany Wenger, 17, of Sarasota, Florida, who wrote a computer program to help doctors diagnose breast cancer less invasively. Jonah Kohn, 14, of San Diego, Calif. won his age category for creating a device that converts sound into tactile vibration to improve the music-listening experience for the hearing impaired; and a trio from Spain won the 15 to 16 age category for documenting the hazardous and non-hazardous organisms found in water from different parts of their country.
Anna Kuchment works for Scientific American and posts on a blog called Budding Scientist: Everything you always wanted to know about raising science-literate kids.


Gunfights Cause Collateral Damage

I heard on CNN that applications for gun permits are on the rise in Colorado. Apparently there are people who think that arming everyone will cut down on crime. They seriously believe that if more people in the Aurora Theater shooting were packing then there would have been fewer deaths and injuries. The idea is that a gunfight between the psychotic killer and an average citizen would have resulted in the killer's death.

Here's a bit of news from Toronto that might help put this in perspective. On June 2, 2012 a gang member opened fire on another gang member in the food court of the Toronto Eaton Centre. The intended target was killed but so was a nearby shopper. Three others were wounded. On July 15, 2012 two or three rival gang members decided to have a gunfight at a barbecue in a Toronto suburb. One of them was wounded. Two innocent bystanders were killed and 22 others were wounded [Scarborough shootings: What really happened on Danzig?].

Turns out that the average citizen isn't a very good shooter. More often than not, they miss their intended target and hit someone else. Lots of people die in gunfights, not just the bad guys—it's called collateral damage.

Imagine what the death toll in Aurora might have been with more than one person blasting away with an automatic weapon.

All civilized nations have strict gun control laws. Their citizens have this strange notion that killing other people is never a viable option and they can't imagine why anyone would deliberately buy guns with the intention of shooting a fellow citizen, even in self defense or prevention of a presumed crime.

I guess some nations have a long history of solving problem with gun violence and it's difficult to abandon that option.


Image Credits: Charlton Heston (top), Tombstone (bottom)

Do Invasive Mitochondria Spread by Drift or Selection?

Many species are not really "species" according to the biological species concept. They are not reproductively isolated from their closest relatives. A little bit of hybridization occurs in nature leading to the invasion of "foreign" alleles into the main population; a phenomenon known as gene flow.

Sometimes the invading alleles can become fixed (or very prevalent) in the population. This is what is presumed to have happened with Neanderthal or Denisovan alleles in modern humans. Rare matings between modern human ancestors and Neanderthal, for example, led to some gene flow between the populations [How many species of humans were there?].

The spread of invasive mitochondria is an extreme example of the fixation of invasive alleles. The example of polar bear evolution [Speciation in Bears] shows us that mitochondrial DNA can enter a population through a rare mating with an individual from another "species" and then become fixed in the new population over many thousand years.

The question is how does this fixation of "foreign" mitochondria occur? Is it an accident due to random genetic drift or do the foreign mitochondria confer a selective advantage over the original mitochondria? It seems unlikely that the mitochondria in one population (e.g. brown bears) are better than those in a foreign population (e.g. polar bears) that has adapted to a different environment.

John Hawks seems to want to have his cake and eat it too [Polar bear mtDNA replacement] ...
In any single population, the behavior of mtDNA is rarely outside the very wide range of dynamics that happen by genetic drift alone, but that's more a sign of the extremely wide range of possibilities that drift allows. (This is why it took so long to demonstrate a problem with mtDNA in phylogenetic reconstruction). Now we know of many instances like polar bears, where the mtDNA genealogy has a different topology than that typical of nuclear genes. Moreover, we know that across many populations of different species, mtDNA is systematically less variable than the expected ratio from the nuclear genome. So it seems that once it enters a population, mitochondrial DNA sometimes spreads more rapidly and broadly than the typical gene. This dynamic sometimes may reflect extreme population histories, such as population bottlenecks and large-scale migrations. But in many cases it probably reflects selection on the mitochondrial genome.
This is one of those issues where a little bit of evidence would be extremely helpful. Is it true that the fixation of foreign mitochondrial DNA is more common than, say, the fixation of Y chromosomes or the fixation of X-linked genes? What about other genes? Does maternal inheritance of mitochondria influence fixation?

Jerry Coyne suggests that there's something special about mitochondria (and chloroplasts) [A new study of polar bears ...].
The problem is that, for reasons we don’t fully understand, mtDNA also moves between species during hybridization much more readily than does nDNA, and that can screw up species relationships. This is true for both animals and plants, and not just for mtDNA either: in plants, DNA from another organelle, the chloroplasts (site of photosynthesis, this DNA is called “cpDNA”) also moves between species more readily than nDNA.

....

We see this situation over and over again in biology. We don’t really know why mtDNA (and cpDNA) leak so readily between species, but we do know that this leakage makes it dicey to use only organelle’s DNA to make species trees. But the reason for this leakage compared to nDNA (so common to be almost a “rule of biology”) would make a useful paper topic for some enterprising graduate student.
Is it really true that mtDNA is more commonly fixed than nuclear alleles? Is it still true when you take into account maternal inheritance? I hope someone assigns this problem to a graduate student and I hope the graduate student takes care to rule out drift and accident.


Image Credit: Moran, L.A., Horton, H.R., Scrimgeour, K.G., and Perry, M.D. (2012) Principles of Biochemistry 5th ed., © Pearson Education Inc. page 419 [Pearson: Principles of Biochemistry 5/E]

Tuesday, July 24, 2012

Speciation in Bears

I read an interesting article a few months ago. It was a study of the phylogeny of bears with an emphasis of the origin of polar bears. In theory, it should be possible to put a date on the speciation event and to identify the probably ancestor of the modern polar bear.

The first thing you have to know is that polar bears and brown bears are not distinct species as defined by the biological species concept. This definition of "species" requires that there be no interbreeding with other populations, otherwise it's not a true species. (See Jerry Coyne's analysis of the problem with respect to humans.)

Polar bears and brown bears can mate to form hybrids, although this doesn't happen very often in the wild because the two "species" are geographically separated. The interesting question is when did these two populations diverge.

Many people thought the question had been answered a few years ago when Lindqvist et al. (2010) published the sequence of polar bear mitochondrial DNA ad compared it to that of other bears.

The result is shown here on the left in a figure taken from the recent paper in Science (Hailer et al, 2012). The Lindvist et al. paper showed conclusively that polar bears are relatively young as a "species" (about 150,000 years) and that they clearly arose from within the brown bear clade.

This result was somewhat surprising but not revolutionary. However, there were some experts on speciation who, questioned the conclusion; notably, Jerry Coyne [Do “polar bears” exist?]. They cautioned that using mitochondrial DNA could be misleading.

The latest study in Science shows that their concerns were justified. Hailer et al. (2012) lookd at 14 nuclear genes and constructed the tree shown shown below on the right.

This study indicates that polar bears diverged from brown bears about 800,000 years ago. Furthermore, the two populations of bear (brown and polar) form distinct clades.

What does this mean? It probably means that about 150,000 years ago there was a brief fling between a male polar bear and a female brown bear. The female offspring, carrying brown bear mitochondria, mated with male polar bears and all of their progeny contained brown bear mitochondria with mixtures of brown and polar bear alleles in their nuclei. Over time, the brown bear mitochondria became fixed by random genetic drift in the polar bear population.

This explains why the two trees differ and why you have to be cautious about using mitochondrial DNA in constructing phylogenies.

The story doesn't end there.

Just this week, a new paper appeared in PNAS confirming this result (Miller et al., 2012). Many of the authors are the same ones on the Lindqvist et al. (2012) paper. They are refuting the conclusions of their earlier paper by now showing that the sequence of nuclear genes indicate an earlier divergence of brown bears and polar bears.

I put off blogging about the Science paper because there were more important things to do and because it would have been difficult to explain the problem and the explanation. Fortunately, Jerry Coyne has now taken up the task of explaining the result at: A new study of polar bears underlines the dangers of reconstructing evolution using mitochondrial DNA. Please read his explanation of gene flow in bears based on his extensive knowledge of speciation.

The only issue I have with Coyne's explanation is that I don't think he gives enough emphasis to the idea that fixation of brown bear mitochondria in polar bears could be a genetic accident.

UPDATE: Ed Yong of Not Exactly Rocket Science already wrote about this three months ago [Polar bear origins revised – they’re older and more distinct than we thought]. John Hawks emphasizes Jerry Coyne's warning about using mitochondrial DNA and discuss the implications for hominid evolution [Polar bear mtDNA replacement].


Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnason U, Janke A. (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347. [Abstract] [DOI: 10.1126/science.1216424]

Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A., Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingólfsson, O., Bachmann, L., and Wiig, O. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. (USA) 107:5053-5057. [doi:10.1073/pnas.0914266107]

Millera, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., et al, (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. (USA) Published online before print July 23, 2012. [doi: 10.1073/pnas.1210506109]

How the Heck Did This Happen?

There are two recent events indicating that change is afoot in America. First, there's the recent poll suggesting that a majority of Americans (54%) could now vote for an atheist candidate who was running for President [Niose: Atheists making political inroads].

Then there's another poll showing that 19% of Americans are now nonreligious ("nones") [“Nones” climb to 19%]. The "nones" are not necessarily atheists or agnostics but it's safe to say that many of them are.

Why are these results significant? They're significant because back in 1958 only 18% of American said they could vote for an atheist and that number didn't change much until the 21st century. Also, the "nones" made up only 6% of the populations in 1990 rising to 15% in 2008.

So, what has happened in the past decade to turn people away from religion and make atheism more respectable?

I can think of two possibilities ...
  • The accommodationist approach that has been dominant for several decades has finally started to bear fruit.
  • The rise of "militant atheists" in the past decade has forced large numbers of Americans into realizing that atheism and non-belief are respectable options.
Which explanation do you think is likely?


[Hat Tip: RichardDawkins.net]

Monday, July 23, 2012

Monday's Molecule #178

It's the dog days (dies caniculares) of summer and Sirius is hard at work.

I'm going to let you off easy today. Identify the four molecules whose structures are shown on the right and name the two enzymes that catalyze the reactions. For extra accolades, tell us why those two enzymes are important in evolution and why the blogosphere is currently talking about these kinds of enzymes.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia


Religious Intolerance: United States Is more Tolerant than Europe

I hate it when this happens. I read a book review in yesterday's New York Times Sunday Book Review. If the review is accurate, the book is one of those books that I would probably hurl into the fireplace ... if I had a fireplace.

In order to be fair I have to buy the book (it's not available in Canada) but meanwhile I need to vent about it's probable content.

The book is The New Religious Intolerance by Martha C. Nussbaum and the review is by Damon Linker [Church, Temple, Mosque].

Here's the opening paragraphs of the review...
Mitt Romney’s stump speech during the Republican primaries was filled with appeals to his party’s conservative base, but none consistently inspired more heartfelt cheers than his promise to “stop the days of apologizing for success at home and ­never again apologize for America abroad.” The statement speaks to the widely held suspicion on the right that liberals in general, and Barack Obama in particular, prefer other forms of democracy ­(especially those that prevail in Europe) to the American way of life.

Martha C. Nussbaum’s new book could serve as Exhibit A in liberalism’s defense against this charge. The author of 17 previous books on a wide range of topics — from classical Greek philosophy and tragic drama to modern law, literature and ethics — Nussbaum is one of America’s leading liberal thinkers. In “The New Religious Intolerance,” she turns her attention to the rise of antireligious — and specifically anti-Muslim — zealotry since the terrorist attacks of Sept. 11, 2001. Though she writes in her opening chapter that intolerance disfigures “all Western societies,” it quickly becomes clear that there have been far fewer incidents of bigotry in the United States than in Europe — because of America’s vastly superior approach to guaranteeing the rights of religious minorities. When it comes to freedom to worship, at least, Nussbaum is an unabashed proponent of American exceptionalism.
The essence of her thesis is that: (1) several European countries have laws prohibiting Muslim women from wearing the burqa in public, (2) The Swiss government bans the building of minarets outside mosques, and (3) The Norwegian mass murderer, Anders Behring Breivik, didn't like Muslims. The United States hasn't done any of these things. That's because Americans are much more tolerant of other religious beliefs than Europeans.

There are important ways in which the United States protects religious minorities ...
The core of the book explores three preconditions of securing religious liberty for minorities — and in all of them the United States does a much better job than Europe. First, a nation must commit itself to protecting the greatest possible freedom of conscience that is compatible with public order and safety — a principle that the United States codifies in the First Amendment’s disestablishment of religion and guarantee of religious free exercise....

The second precondition of religious liberty is an impartial and consistent civic culture. On this measure, Europe fares especially badly, as Nussbaum demonstrates by methodically exposing the double standards and bias at play in the arguments for banning the burqa.

Finally, there is the need for “sympathetic imagination” on the part of citizens. Here the United States has long taken the lead, cultivating respect for religious differences since the 17th century, when Roger Williams founded Rhode Island, the “first colony (anywhere in the world, it seems) in which genuine religious liberty obtained for all.” Nussbaum is particularly impressed with Williams’s respectful treatment of the Narragansett Indians, whose language and culture he struggled to understand at a time when most of the colonists thought of them as beasts or devils.
Wow! It's news to me that the United States is a paragon of religious tolerance but perhaps that's just my anti-American bias. (For the record, Roger Williams was English, not American, and most of the other colonies were somewhat less tolerant.1)

I tend to think of the USA as a place where religious groups want to restrict women's freedom of choice, infringe on the rights of gays and lesbians, oppose non-Christians (and suspected non-Christians) who run for office, rail against euthanasia, and ban the teaching of evolution.

I was under the impression that there are many states where being an non-fundamentalist Christian would be very uncomfortable. Many of these same states insist that the United States is a Christian nation and there are dozens of political leaders who imply that non-Christians are not real Americans. A majority of citizens see nothing wrong with posting the ten commandments in courtrooms, schools, and legislatures. They don't see anything wrong with reciting the Lord's prayer in schools or putting "In God We Trust" on their money (beginning in 1957).

I seem to recall a recent incident where five representatives of the United States House of Representatives expressed points of view that could be interpreted as possibly anti-Muslim [Michele Bachmann finds plenty of friends back home].

These all seem like pretty intolerant viewpoints to me. Am I wrong?

Apparently, Martha C. Nussbaum is a smart woman. Apparently that's why she says,
As Nussbaum notes, the American and European developments differ in important ways. Above all, she writes, nothing in the United States “even remotely approaches the nationwide and regional bans on Islamic dress in Europe, or the nationwide Swiss minaret referendum” — let alone an anti-Islamic massacre.
I guess I'll have to read the book to see if this is what she really thinks. I hate it when that happens.


1. New Amsterdam, the Dutch colony, was noted for religious tolerance. The French colonies in Canada (somewhat tolerant) were on very good terms with many native tribes. The Narragansett Indians were eventually converted to Christianity but not until many of them had been killed or shipped off to slavery in the Caribbean.

Sunday, July 22, 2012

Why All the Fuss About Chromosomes?

I've been following the latest kerfluffle on the fusion of two chromosome into one during human evolution. I understand the superficial dispute involving Carl Zimmer. He had the audacity to ask for evidence to back up a claim being made by the IDiots on their Facebook page and they responded by going nuclear [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Typical.

Let's step back a bit and ask why the IDiots are so upset. Carl Zimmer posted a really nice summary of the evidence that two smallish chimp chromosomes fused to produce human chromosome 2 [The Mystery of the Missing Chromosome]. That evidence is based on an analysis of the chimp, human, and gorilla genomes and it allows scientists to reconstruct the events that led up to the fusion. All of the DNA sequence around the fusion point are consistent with what we might expect, especially the presence of defective telomeres (sequences at the ends of chromosomes).

Why are the IDiots so bothered by this evidence? It's not as if it's new—the essential evidence has been around for decades. There must be something else going on that causes the IDiots to circle the wagons at this time.

It think it's all about their latest book Science & Human Origins by Ann Gauger, Douglas Axe, and Casey Luskin.1 The book is published by the Discovery Institute Press. In that book, two of the authors (Gauger and Luskin), apparently argue that science cannot rule out a recent origin of humans descended from Adam and Eve. The chromosome fusion data threatens that bizarre claim and perhaps that's why they are reacting so strongly.

I think I understand this. The IDiots have made bold claims about some of their recent books (e.g. Signature in the Cell: DNA and the Evidence for Intelligent Design , The Myth of Junk DNA) but those books have been met by yawning indifference from the general public and devastating criticism from real scientists. Two of the authors on this latest book (Gauger and Axe) have substantial scientific credentials so the Discovery Institute must have expected that the book would stand up to criticism by other scientists.

Instead, a "mere" graduate student (Paul McBride) has dimantled the book chapter by chapter [Science & Human Origins: Review] and a "mere" science writer, Carl Zimmer, has challenged the integrity of two "scientists" (and a lawyer). No wonder they're upset. All of their wonderful books are scientific embarrassments.

On what grounds do the IDiots want to deny the chromosomal evidence that humans and chimps share a common ancestor? Carl Zimmer supplies a partial answer when he quotes one of the chief IDiot defenders, David Klinhoffer, who says ...
The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.

But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.

But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.
That's it? The fusion event could have happened relatively recently in human evolution so it's no big deal? And if you don't buy that, then maybe it didn't happen at all because the junction sequence isn't exactly what a typical IDiot might expect if evolution were true?

(Carl asked for the evidence that that the junction sequence isn't what one might expect and that's what caused the latest problem.)

I think that even the most stupid IDiots realize that they are in a very weak position on this one. They have been painted into a corner where the only way out is to admit that chromosome fusions happens&mdashbut only in the past 10,000 years—or that solid scientific evidence is wrong and there was no fusion. Neither option is appealing.

That's why you see people like Cornelius Hunter desperately looking for another way out [Carl Zimmer Doubles Down on Chromosome Two Lies and Misdemeanors] and why the people at Uncommon Descent have picked up on a non-scientific way to defend Intelligent Design Creationism [Why no one can confute Darwinism and, consequently, no one should believe it].

My question for Intelligent Design Creationists is, "why all the fuss?" What is there about the figure at the top of the page that really upsets you? Aren't most of you supporters of common descent in some form or another? Are all of you really going to defend the idea that humans have no evolutionary history with the other apes?


1. I haven't read the book. It's on order but it still hasn't been released in Canada (see Amazon.ca).

Saturday, July 21, 2012

This Is too Weird

Check out the meowbified version of Sandwalk at http://cat.sandwalk.blogspot.com.meowbify.com/.

The evil deed was performed at Meowbify. Try it on Pharyngula.


[Hat Tip: PZ Myers]

Friday, July 20, 2012

We Called Out IDiot Jonathan Wells, and He Folded

Carl Zimmer had the audacity to post something about the fusion of two ancestral chromosomes in primitive apes. The data is unequivocal. It shows why humans have one less chromosome than modern chimps [The Mystery of the Missing Chromosome (With A Special Guest Appearance from Facebook Creationists)].

Observations like this lend strong support to the idea that humans and chimps share a common ancestor. This doesn't sit well with the IDiots because they are in the midst of hyping their latest book, Science & Human Origins where they try to counter the overwhelming evidence that humans evolved.

So, what did they do? David Klinghoffer challenged Carl Zimmer to pop on over to Evolution News & Views (sic) and debate one of the authors. Carl refused, as would any sane person since that creationist blog is edited by IDiots and no comments are allowed. It would be embarrassing to have one's name on an article at Evolution News & Views [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Here's what Carl said,
I thought the question I asked was pretty simple. I wasn’t asking to hold a Lincoln-Douglas debate. I just asked what the evidence was for one of the claims made by the creationists.

Now it seems that in order to get that answer, I can either buy a book–which apparently is based on no peer-reviewed research of the authors, but just cherry-picked quotes from a ten-year old paper–or I can donate my time to write several thousands words for free for a creationist web site.

Making this offer even richer is Klinghoffer’s ground rules about focusing “strictly on the ideas, not on the personalities.” Klinghoffer himself has used Evolution News & Views to call people pathetic, a worthless bully, cowards, illiterate, and “a tyranny of the unemployed” (referring to Wikipedia editors). In one piece he wrote for Evolution New and Views, Klinhoffer mocked a post by a science blogger as “preening and self-congratulatory.”

That blogger happened to be me.

I will answer Mr. Klinghoffer publicly: no thanks. I never asked for a debate, and your arbitrary decrees, such as a mysterious thousand-word cutoff (my blog post on the chromosomes alone clocked in at over 2,000 words) make it even less appealing. I am particularly opposed to web sites that do not allow readers to comment. That’s how I ended up on Facebook in the first place–because the Discovery Institute’s web sites do not permit commenting. You, on the other hand, are more than welcome to leave a comment on my blog. My comment policy is very lax: I only throw out commenters who curse uncontrollably, hawk their own wares, or can’t stay on topic after repeated warnings. We have a thriving, fascinating discussion here, one from which I regularly learn new things from my readers. You might too.
David Klinghoffer, being David Klinghoffer, responded with a blog posting on Evolution News & Views: We Called Out Darwinist Critic Carl Zimmer, and He Folded.

"Reasoning with a Lynch Mob"

This reminded me of an incident that took place last November. You might remember that I spent a great deal of time and effort reviewing Jonathan Wells' book, The Myth of Junk DNA (see The Myth of Junk DNA by Jonathan Wells). I invited Wells to discuss and debate the issue of junk DNA and my extensive criticism of his book.

Wells declined [Jonathan Wells Sends His Regrets]. Here's what he said ...
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
Sort of makes you wonder, doesn't it? Do you think the IDiots really are interested in debating science or is it only on their own terms, on their own blog, with no comments, and moderated by their own kind?


Better Biochemistry: Good Enough Enzymes

Some enzymes catalyze reactions at extremely fast rates that are only limited by the rate of diffusion of substrate molecules into the active site of the enzyme (diffusion-controlled rate). Some of these enzymes are covered in all the standard biochemistry textbooks; examples are canbonic anhydrase (CAN), triose phosphate ismerase (TIM), and superoxide dismutase (SOD). Superoxide dismutase (right) actually catalyzes reactions at a rate that's faster than the diffusion-controlled limit [Superoxide Dismutase Is a Really Fast Enzyme].

These enzymes are often referred to as "perfect" enzymes but that's a very misleading term because it implies that all other enzyme are less than perfect.

Most enzyme don't need to act any faster than they do. They are quite happy catalyzing reactions at rates that are far below their theoretical optimum [Better Biochemistry: The Perfect Enzyme]. As long as it's good enough there's no selective pressure to get better.

Thursday, July 19, 2012

Do Bacteria Have Sex?

There are three different ways for bacterial to exchange information: conjugation, transduction, and transformation. Do any of these count as sex?

It depends on your definition. Rosie Redfield and I had a discussion about this when we were together in Ottawa. I think some species of bacteria do engage in sex because all three mechanisms can result in gene exchange between different individual bacteria. I think that transformation and conjugation may have arisen, in part, as a way of repairing damaged DNA and escaping the effects of Muller's Rachet.

Rosie thinks that sex, by definition, means mixis—the shuffling of alleles due to sex as in eukaryotes. Here's how she explains it in a recent post on her blog [Claims that Bacteria Do Have Sex].
This work addresses a very important question with big/deep/fundamental importance to the colossal problem of the origin of meiotic sex in eukaryotes. The question is 'Do bacteria have any processes that evolved because of selection for recombination of chromosomal alleles?' We think this selection is the reason for the success of meiotic sexual reproduction in eukaryotes, but compelling evidence for this has been elusive. Bacteria have four well-studied processes that do generate homologous recombination; three that transfer DNA between cells and one that carries out homologous recombination. But almost every aspect of these processes has been shown to cause recombination as an unselected side effect of processes selected for other functions.
I don't think sex evolved in eukaryotes in order to promote mixis so this argument doesn't resonate with me.

Read Rosie's post if only to discover why she thinks transformation evolved. She's thinking of applying for a grant to study this problem so I'm sure she would appreciate your feedback.


[Image Credit: Rosie Redfield]

Where Are the Best University Teachers?

Much to my embarrassment, the University of Toronto is promoting online courses, or MOOCs [Online courses for anyone, anywhere]. These courses seem to be for information only—you can't get a university credit for them.

I'm not opposed to offering free "courses" for people who don't have easy access to a university campus. In fact, I think it's a good thing. But let's make sure we distinguish between public lectures and serious education. In my opinion, if the quality of an online course is equal to the quality of a course given on campus then all that says is that the campus-based course is lousy. We should not refer to these online examples as "university courses." They should be labelled as "public lectures."

I'll have more to say about this later but today I want to return to an issue I raised before. Is it true that the "best" universities also do the best teaching? I have suggested that the answer to this question is probabyy "no" [On the Quality of Online Courses] [Is Canada Lagging Behind in Online Education?].

University Tuitions in Canada and the United States

The University of Toronto is the largest university in North America (70,000 students) and one of the top 20 universities in the world1 [The World University Rankings 2011-2012]. It ranks near the top among the group of very large public universities [World University Rankings].

The University of Toronto is a public university. A large percentage of its operating budget comes directly from the provincial government. In that sense, it is comparable to many of the large state schools in the United States. When we're judging ourselves,2 we use a list of nine American state schools of comparable size and quality.

Tuition costs have been in the news in Canada recently since there have been vocal student protests in Quebec over government plans to raise tuition costs in Quebec schools. The combination of tuition and fees will increase from $2,890 per year to $4,700 per year over a five year phase-in period.

What is the average cost of tuition plus fees at the University of Toronto and how does this compare with similar American schools? President David Naylor gives us the answer on his website where he discusses the problem of student debt in Canada and the United States [Student Debt Redux].


If you're an American, consider sending your children to a Canadian university. You'll save a lot of money and there's an added bonus—we get to show them what a real "socialist" country looks like.


Note: One of the signs in the protest says, "Marx is dead, God is dead, and I don't feel so good."

1. There are many problems with these ranking but the bottom line is that the University of Toronto is a pretty good university as judged by outsiders.

2. Which we do obsessively every few months.

Wednesday, July 18, 2012

Stress and Telomere Length—Do You Believe this Study?

Healthy skepticism is an important part of science. One of the biggest differences between scientists and intelligent design creationists, for example, is that the creationists are rarely skeptical of anything they read in the scientific literature. If it appears to support their agenda, then it goes right onto the blogs without any discussion of whether it might be true or not.

Scientists, on the other hand, are often very skeptical of work that appears in the scientific literature. They treat most papers as tentative results that need to be confirmed. The most obvious flawed papers will be refuted by further work, as in the recent arsenic in DNA paper or earlier work on cold fusion. Usually, flawed papers will just be ignored and they will die a quiet death.

Questions for Genetics Students

Rosie Redfield has published a (deliberately) provocative article on teaching genetics in the 21st century (Redfield, 2012). I disagree strongly with her premises and her conclusions but the issues are complex—too complex for a single posting.

Let's start by looking at one aspect of her proposal.

Rosie thinks that a 21st century course on genetics should focus on information that students can use later on. Here's how she would begin her new course ...
Box 4 gives a suggested syllabus for a 21st century genetics course. It begins with a human focus, introducing personal genomics and our natural genetic variation. Students then learn about the underlying molecular explanations—how differences in DNA sequences arise and evolve, and how they cause differences in phenotype—followed by how genetic differences are inherited and recombined.

Tuesday, July 17, 2012

Evolution Is Purposeless and Unguided—Deal with It!

Many prominent scientists get it right when they say that evolution is purposeless and unguided. The same is true for plate tectonics, supernovas, radioactive decay, and the weather.

If you have a problem with this, read Jerry Coyne at What’s the problem with unguided evolution? and take it up with him. I'm tired of trying to convince theists and accommodationists of something that's as plain as the nose on your face.
Not to beat a dead horse (I think it’s still alive), but I vehemently oppose those evolutionists and accommodationists who won’t affirm that evolution is unguided and purposeless (in the sense of not being directed by a higher intelligence or teleological force). For to the best of our knowledge evolution, like all natural processes, is purposeless and unguided. After all, scientists have no problem saying that the melting of glaciers, the movement of tectonic plates, or the decay of atoms are processes that are unguided and purposeless.
Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.

Emile Zucherkandl and Linus Pauling (1965)

Eschaton 2012

Most of you missed the exciting Evolution Ottawa 2012 meeting earlier this month but, cheer up, you have another chance to visit Ottawa form Novermber 30 to December 2, 2012.

The meeting is called Eschaton 2012 where "eschaton" refers to the end of the world. That's because, as you all know by now, the world is going to end on December 21, 2012. The Mayans said so and so do a lot of modern kooks.

Here's an outline of the meeting.
The conference opens with a Friday night plenary session on the historical relationship between humans and our apocalypses. Saturday morning and afternoon, we have parallel tracks: 1) Talks and panels on skepticism/science/science communication (including a live recording of Ottawa Skeptics' podcast, The Reality Check) and 2) "The Immaculate Convention" - talks and panels on religion from an academic and sociological perspective. Saturday evening there will be a reception with food and drink in the early evening at the Canadian Museum of Nature (around the corner from the hotel), after which there will be a talk by PZ Myers, followed by a meet-and-greet social, with snacks, cash bar, and access to some of the galleries and exhibits. On Sunday the parallel tracks include panels and workshops on ethics, gender identity, parenting, and other exciting topics to be announced.
Here's the latest list of speakers. (I changed the order somewhat from the one on the website.)
I'm planning to talk about the accommodationist wars and why science and religion are incompatible. Hopefully, Genie Scott will represent the accommodationist position as promoted by NCSE.

Chris DiCarlo and I are teaching a course at the University of Toronto next Fall on scientific controversies and misconceptions (including evolution vs creationism). Maybe we can have a workshop on Sunday to discuss science literacy?


Vote for Jesus for President (of the United States)

PZ Myers approves of this plan to cast a vote for Jesus [An excellent suggestion for the Bible-believing Christians].

Isn't there a problem? Who's going to produce a valid birth certificate?



Monday, July 16, 2012

Monday's Molecule #177

This is a very important molecule. It's found in (almost?) all living species where it serves a very important function. What is the common name of this molecule and what role does it play in metabolism?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch with a very famous person, or me.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is S adenosylmethionine (SAM). It is the major methyl donor in biochemical reactions. Today's winners are Sean Ridout and William Grecia.


Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia